From: Martin Goldberg 4 Jun 94 17:24
To : ALL
Subj: Next post
The next post is to Jesse Hornbacher. He has asked me for
references that in many species Hemoglobin is very similar and
that, in particular, the similarity rate between humans and
chimps is 98%. What I have done, instead, is to run a
similarity search using human hemoglobin as a match criterion
and searched the entire Genbank data base. What is in the post
is the reply to my inquiry. I will commnet on it as I post it.
Technically, those that understand computers will likely
understand it more than others as it relies on some algorithms
to do these matchings. John P. is now posting in here and at
one point told me that he had written some of these types of
programs.
--- msgedsq 2.1
* Origin: Welcome to the lab. Now roll up your sleeve. (1:124/4115.221)
From: Martin Goldberg 4 Jun 94 17:27
To : Jesse Hornbach
Subj: Hemoglobin
You asked for this data, and here it is.
I will explain as we go along....
This is a representation of the best matches. I asked for 80 of
the best ones or we would have gotten too much background. The
scores show how many matches of how many are perfect matches.
Remember that a semi conservative substitution is not counted
as a miss or a hit, although it is almost the same thing as an
exact match.
Score Init1 Initn
< 2 33 33:=================
4 5 5:===
6 18 18:=========
8 60 60:==============================
10 307 307:==================================================
12 534 534:==================================================
14 691 691:==================================================
16 2298 2298:==================================================
18 3161 3161:==================================================
20 5391 5391:==================================================
22 6375 6375:==================================================
24 4620 4620:==================================================
26 3732 3732:==================================================
28 2927 2874:==================================================
30 2047 1929:==================================================
32 1251 1133:==================================================
34 776 700:==================================================
36 456 458:==================================================
38 288 333:==================================================
40 189 252:==================================================
42 133 187:==================================================
44 68 106:==================================++++++++++++++++
46 36 76:==================++++++++++++++++++++
48 31 53:================+++++++++++
50 25 54:=============++++++++++++++
52 11 21:======+++++
54 8 29:====+++++++++++
56 2 20:=+++++++++
58 2 8:=+++
60 0 3:++
62 1 4:=+
64 4 6:==+
66 0 5:+++
68 0 2:+
70 4 2:=-
72 0 0:
74 1 0:-
76 1 0:-
78 1 1:=
80 0 0:
80 513 519:==================================================
mean initn score: 20.9 (3.94)
mean init1 score: 20.9 (3.94)
The "="'s are exact matches ofr the lineup....the "+"'s are
semi conservative subs and the "-"'s are misses.
The best scores are: init1 initn opt..
Sw:Hba_Human P01922 HEMOGLOBIN ALPHA CHAIN. 2/94 655 655 655
Sw:Hba_Gorgo P01923 HEMOGLOBIN ALPHA CHAIN. 7/86 654 654 654
Sw:Hba_Preen P01924 HEMOGLOBIN ALPHA CHAIN. 7/86 653 653 653
Sw:Hba_Ponpy P06635 HEMOGLOBIN ALPHA CHAIN. 2/91 649 649 649
Sw:Hba_Macas P21766 HEMOGLOBIN ALPHA-1, ALPHA-2, AND ALP... 648 648 648
Sw:Hba_Macfa P21767 HEMOGLOBIN ALPHA-A, ALPHA-Q, ALPHA-R... 647 647 647
Sw:Hba_Macmu P01925 HEMOGLOBIN ALPHA CHAIN. 5/91 646 646 646
Sw:Hba_Cerae P01926 HEMOGLOBIN ALPHA CHAIN. 7/86 646 646 646
Sw:Hba_Sagfu P01929 HEMOGLOBIN ALPHA CHAIN. 7/86 646 646 646
Sw:Hba_Macne P19002 HEMOGLOBIN ALPHA-1, ALPHA-2, AND ALP... 645 645 645
Sw:Hba_Macsi P21768 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 645 645 645
Sw:Hba_Macsp P07402 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 644 644 644
Sw:Hba_Calar P18972 HEMOGLOBIN ALPHA CHAIN. 11/90 643 643 643
Sw:Hba_Atege P01927 HEMOGLOBIN ALPHA CHAIN. 4/90 642 642 642
Sw:Hba_Cebap P01928 HEMOGLOBIN ALPHA CHAIN. 7/86 641 641 641
Sw:Hba_Cebca P07421 HEMOGLOBIN ALPHA CHAIN. 4/88 641 641 641
Sw:Hba_Certo P01933 HEMOGLOBIN ALPHA CHAIN. 11/90 635 635 635
Sw:Hba_Colba P01930 HEMOGLOBIN ALPHA CHAIN. 7/86 634 634 634
Sw:Hba_Mansp P08258 HEMOGLOBIN ALPHA-I AND ALPHA-II CHAI... 633 633 633
Sw:Hba_Nycco P01937 HEMOGLOBIN ALPHA CHAIN. 7/86 629 629 629
Sw:Hba_Cynsp P11753 HEMOGLOBIN ALPHA CHAIN. 10/89 628 628 628
Sw:Hba_Lorta P01938 HEMOGLOBIN ALPHA CHAIN. 5/92 627 627 627
Sw:Hba3_Gorgo P01934 HEMOGLOBIN ALPHA-3 CHAIN. 7/86 627 627 627
Sw:Hba_Myove P11757 HEMOGLOBIN ALPHA CHAIN. 10/89 626 626 626
Sw:Hba_Tarba P01940 HEMOGLOBIN ALPHA CHAIN. 7/86 626 626 626
Sw:Hba_Papcy P01931 HEMOGLOBIN ALPHA CHAIN. 11/88 625 625 625
Sw:Hba_Thege P01932 HEMOGLOBIN ALPHA CHAIN. 7/86 625 625 625
Sw:Hba3_Pantr P01935 HEMOGLOBIN ALPHA-3 CHAIN. 5/91 625 625 625
Sw:Hba2_Galcr P01939 HEMOGLOBIN ALPHA-B CHAIN (ALPHA-II)... 624 624 624
Sw:Hba_Rouae P01956 HEMOGLOBIN ALPHA CHAIN. 7/86 623 623 623
Sw:Hba1_Galcr P14259 HEMOGLOBIN ALPHA-A CHAIN (ALPHA-I).... 621 621 621
Sw:Hba_Pteal P14389 HEMOGLOBIN ALPHA CHAIN. 5/91 619 619 619
Sw:Hba_Marma P08852 HEMOGLOBIN ALPHA CHAIN. 11/88 619 619 619
Sw:Hba_Spepa P11750 HEMOGLOBIN ALPHA CHAIN. 11/90 617 617 617
Sw:Hba_Tapge P28780 HEMOGLOBIN ALPHA CHAIN. 12/92 616 616 616
Sw:Hba_Antpa P14387 HEMOGLOBIN ALPHA CHAIN. 1/90 616 616 616
Sw:Hba_Turtr P18978 HEMOGLOBIN ALPHA CHAIN. 11/90 615 615 615
Sw:Hba_Horse P01958 HEMOGLOBIN ALPHA CHAINS (SLOW AND FA... 614 614 614
Sw:Hba_Speci P09420 HEMOGLOBIN ALPHA CHAIN. 3/89 613 613 613
Sw:Hba_Macca P09839 HEMOGLOBIN ALPHA CHAIN. 1/90 612 612 612
Sw:Hba_Speto P07403 HEMOGLOBIN ALPHA CHAIN. 4/90 612 612 612
Sw:Hba_Ctegu P20854 HEMOGLOBIN ALPHA CHAIN. 11/91 611 611 611
Sw:Hba_Ptepo P14390 HEMOGLOBIN ALPHA CHAIN. 5/91 611 611 611
Sw:Hba_Phyca P09904 HEMOGLOBIN ALPHA CHAIN. 11/90 610 610 610
Sw:Hba_Cersi P01963 HEMOGLOBIN ALPHA CHAIN. 7/86 609 609 609
Sw:Hba_Tapte P01962 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 608 608 608
Sw:Hba_Hipam P19015 HEMOGLOBIN ALPHA CHAIN. 11/90 608 608 608
Sw:Hba_Rabit P01948 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 608 608 608
Sw:Hba1_Tadbr P11755 HEMOGLOBIN ALPHA-1 CHAIN. 10/89 608 608 608
Sw:Hba_Rhiun P09906 HEMOGLOBIN ALPHA CHAIN. 3/89 607 607 607
Notice that all the hits that were made were for hemoglobin. As
you can see, the human matched the human for a perfect score.
As we go down the list you can see that they line up less and
less. the top of the list are the simians and the apes. At the
bottom are things like rabbits and the like. I will show the
actual matches...
Hemo
Sw:Hba_Human
DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)
DT 01-FEB-1994 (REL. 28, LAST ANNOTATION UPDATE)
DE HEMOGLOBIN ALPHA CHAIN. . . .
SCORES Init1: 655 Initn: 655 Opt: 655
100.0% identity in 141 aa overlap
^^^^^^
10 20 30 40 50 60
Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Hba_Hu VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
10 20 30 40 50 60
70 80 90 100 110 120
Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Hba_Hu KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
70 80 90 100 110 120
130 140
Hemo VHASLDKFLASVSTVLTSKYR
|||||||||||||||||||||
Hba_Hu VHASLDKFLASVSTVLTSKYR
130 140
Top line labeled "HEMO" is my sequence of Hemoglobin submitted.
Bottom is the target sequence. Obviously it matches 100%. No
one could argue, but this is how the computer works.
Hemo
Sw:Hba_Gorgo
ID HBA_GORGO STANDARD; PRT; 141 AA.
AC P01923;
DT 21-JUL-1986 (REL. 01, CREATED)
DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)
DT 21-JUL-1986 (REL. 01, LAST ANNOTATION UPDATE)
DE HEMOGLOBIN ALPHA CHAIN. . . .
SCORES Init1: 654 Initn: 654 Opt: 654
99.3% identity in 141 aa overlap
^^^^^
Gorilla.
10 20 30 40 50 60
Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
||||||||||||||||||||||:|||||||||||||||||||||||||||||||||||||
Hba_Go VLSPADKTNVKAAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
10 20 30 40 50 60
70 80 90 100 110 120
Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Hba_Go KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
70 80 90 100 110 120
130 140
Hemo VHASLDKFLASVSTVLTSKYR
|||||||||||||||||||||
Hba_Go VHASLDKFLASVSTVLTSKYR
130 140
SCORES Init1: 653 Initn: 653 Opt: 653
97.9% identity in 141 aa overlap
^^^^^
One of the simians...
10 20 30 40 50 60
Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
||||||||||||||||||:|:|||||||||||||||||||||||||||||||||||||||
Hba_Pr VLSPADKTNVKAAWGKVGGHGGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
10 20 30 40 50 60
70 80 90 100 110 120
Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
|||||||||||||||||:||||||||||||||||||||||||||||||||||||||||||
Hba_Pr KVADALTNAVAHVDDMPHALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
70 80 90 100 110 120
130 140
Hemo VHASLDKFLASVSTVLTSKYR
|||||||||||||||||||||
Hba_Pr VHASLDKFLASVSTVLTSKYR
130 140
If you look carefully at the last two comparisons, you can see
where the differences occur.
There is no more reason to list all the matches here. I will
list the similarities
97.9% identity in 141 aa overlap
97.2% identity in 141 aa overlap
97.2% identity in 141 aa overlap
96.5% identity in 141 aa overlap
96.5% identity in 141 aa overlap
96.5% identity in 141 aa overlap
96.5% identity in 141 aa overlap
96.5% identity in 141 aa overlap
96.5% identity in 141 aa overlap
95.7% identity in 141 aa overlap
95.7% identity in 141 aa overlap
92.9% identity in 141 aa overlap
93.6% identity in 141 aa overlap
93.6% identity in 141 aa overlap
90.1% identity in 141 aa overlap
92.9% identity in 141 aa overlap
89.4% identity in 141 aa overlap
90.8% identity in 141 aa overlap
91.5% identity in 141 aa overlap
92.2% identity in 141 aa overlap
91.5% identity in 141 aa overlap
88.7% identity in 141 aa overlap
92.2% identity in 141 aa overlap
90.1% identity in 141 aa overlap
92.2% identity in 141 aa overlap
87.2% identity in 141 aa overlap
90.8% identity in 141 aa overlap
90.8% identity in 141 aa overlap
90.1% identity in 141 aa overlap
90.1% identity in 141 aa overlap
83.7% identity in 141 aa overlap
87.9% identity in 141 aa overlap
90.1% identity in 141 aa overlap
89.4% identity in 141 aa overlap
ID HBA_MACCA STANDARD; PRT; 141 AA.
AC P09839;
DT 01-MAR-1989 (REL. 10, CREATED)
DT 01-MAR-1989 (REL. 10, LAST SEQUENCE UPDATE)
DT 01-JAN-1990 (REL. 13, LAST ANNOTATION UPDATE)
DE HEMOGLOBIN ALPHA CHAIN. . . .
SCORES Init1: 612 Initn: 612 Opt: 612
10 20 30 40 50 60
Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
|||:|||:||||||:|||::||||||||||||||||||||||||||||:|||||||||||
Hba_Ma VLSAADKGNVKAAWDKVGGQAGEYGAEALERMFLSFPTTKTYFPHFDLAHGSAQVKGHGK
10 20 30 40 50 60
70 80 90 100 110 120
Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
||||||||||:|:||:|:||||||||||:|||||||||||||||||||||:| |||||||
Hba_Ma KVADALTNAVGHMDDLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLASHHPAEFTPA
70 80 90 100 110 120
130 140
Hemo VHASLDKFLASVSTVLTSKYR
:|||||||:||||||||||||
Hba_Ma IHASLDKFFASVSTVLTSKYR
130 140
This is the last one. You can see that there are more
differences in it fromt he first one, but then rabbits are
somewhat more removed from humans than chimps.
The point of all of this is to whow you that relatedness occurs
on a molecular level. I can look at the DNA of any animal and
tell how far removed it is from another by getting the sequence
of the DNA and showing base pair differences. A single pair
difference is enough. This makes much more logical sense to me
thatn believing in a fairy story that sounds as if some kid
made it up.
--- msgedsq 2.1
* Origin: Welcome to the lab. Now roll up your sleeve. (1:124/4115.221)
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