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Blast Lab


Using the New QBLAST Reformatting Feature
to Detect Conserved Amino Acids


One of the strengths of the recently implemented QBLAST system is its ability to generate output quickly in any of several formats after a search has been completed. Choosing one of the Master-Slave alignment formats, rather than the default Pairwise format, allows one to easily visualize patterns of residue conservation in sequence families.

As an example, consider the CxC family of small cytokines. This protein family is characterized by a conservation of four cysteine residues involved in disulfide bond formation. One can compare the human sequence of Interleukin-8 (P10145), a member of this group, with the sequences of related cytokines from the sheep, pig, and cow by running a blastp search of the nr database using a 49-amino acid stretch from P10145 containing all four cysteines as the query. It is possible to exclude other very closely related human sequences and focus on the sheep, pig, and cow by entering “Cetartiodactyla” into the organism filter box on the BLAST search page.

The search shown here was run using an Expect value of “.01,” and the Flat-Master Slave with Identities alignment format. This alignment format uses periods in place of residues in the “slave” sequences (database hits) that are identical to the aligned residues in the “master” sequence (the query sequence). The output here clearly shows the four conserved cysteine residues as uninterrupted columns of periods (highlighted).

DW

.
.
.

Sequences producing significant alignments:
.
Score
(bits)
.
E
Value

  .
  .
sp|P36925|IL8_SHEEP INTERLEUKIN-8 PRECURSOR (IL-8) >gi|5431...
sp|P79255|IL8_BOVIN INTERLEUKIN-8 PRECURSOR (IL-8) >gi|1699...
emb|CAA43461| (X61151) interleukin-8 [Sus scrofa]
pir||A44253 alveolar macrophage chemotactic factor-I (AMCF-...
sp|P26894|IL8_PIG INTERLEUKIN-8 PRECURSOR (IL-8) (ALVEOLAR ...
gb|AAD02808| (AF061521) interleukin-8 [Bos taurus]
sp|P22952|AMC2_PIG ALVEOLAR MACROPHAGE CHEMOTACTIC FACTOR I...
sp|P80221|GCP2_BOVIN GRANULOCYTE CHEMOTACTIC PROTEIN 2 (GCP...
sp|P30034|PLF4_PIG PLATELET FACTOR 4 (PF-4)
sp|O46677|GROB_BOVIN GROWTH REGULATED PROTEIN HOMOLOG BETA ...
sp|O46676|GROA_BOVIN GROWTH REGULATED PROTEIN HOMOLOG ALPHA...
sp|O46675|GROG_BOVIN GROWTH REGULATED PROTEIN HOMOLOG GAMMA...
sp|P43030|PF4L_PIG PLATELET BASIC PROTEIN PRECURSOR (PBP) >...
gi|2735499 (U95814) GRO [Ovis aries]
bbs|140204 neutrophil-activating peptide 2, pNAP-2-S {short...
bbs|140202 neutrophil-activating peptide 2, pNAP-2-L {long...
sp|P30035|PLF4_SHEEP PLATELET FACTOR 4 (PF-4)
pdb|1PLF|A Bos taurus >gi|494447|pdb|1PLF|B Bos taurus >gi|...
sp|P02777|PLF4_BOVIN PLATELET FACTOR 4 (PF-4) >gi|72110|pir...
bbs|161256 epithelial-derived neutrophil-activating peptide...

.
96
93
92
92
92
65
58
57
53
53
53
52
52
52
51
51
49
46
44
43

.
7e-22
4e-21
6e-21
6e-21
6e-21
1e-12
2e-10
3e-10
4e-09
5e-09
5e-09
7e-09
7e-09
9e-09
2e-08
2e-08
8e-08
5e-07
3e-06
6e-06


tmpseq_1
463254
1699354
516197
346456
1235612
4106336
399030
462169
585702
3913773
3913772
3913771
457754
2735499
452976
739009
266800
494448
225004
861479
1
32
32
32
32
32
32
1
50
10
23
38
38
37
52
6
13
23
10
23
5
LR
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.Q
.Q
.Q
..
C
.
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.
.
.
.
.
.
Q
.
.
.
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.
M
V
V
.
.
.
L
.
L
L
V
V
V
.
C
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
V
IKTYSKPFHPKFIKELRVIESGPH
...H.T..................
...H.T..................
.N.H.T..................
.N.H.T..................
.N.H.T..................
...............
LT.-TPGI...M.SD.Q..PA..Q
LT.-TPGI...TVSD.Q..AA..Q
V..I.G-VS..H.SS.E..GA...
LQ.L-QGI.L.N.QSVK.TTP...
LQ.L-QGI.L.N.QSVK.TTP...
LQ.L-QGI.L.N.QSVK.TTP...
LN.V.G-I..SN.QS.E..RA.A.
LQ.V-QGI.L.NMQSVK.TPP...
LN.V.G-I..SN.QS.E..RA.A.
LN.V.G-I..SN.QS.E..RA.A.
L..T.G-I..RH.SS.E..GA.L.
L..T.G-IN.RH.SS.E..GA.L.
L..T.G-IN.RH.SS.E..GA.T.
.LT.-TPGI...TVSD.Q..AA..
C
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
Q
ANTEIIVKLSDGREL
E.S......TN.K.V
E.S......TN.N.V
E.S......VN.K.V
E.S......VN.K.V
E.S......VN.K.V
E.S......TN.N.V.
SKA.V.AT.KN.K.V
SKV.V.AT.KN...V
PSPQL.AT.KK.HKI
DQ..V.AS.KT.Q.V
DQ..V.AS.KT.Q.V
DQ..V.AT.KT.Q.V
.KV.V.AT.KNDKKI
GQ..V.AT.KT.Q.V
.KV.V.AT.KNDDKI
.KV.V.AT.KNDDKI
PSPQL.AT.KT..KI
PSPQL.AT.KT..KI
PSPQLLATKKT..KI
.SKV.V.AT.KN.
C
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.
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.
.
.
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.
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.
.
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.
.
.
.
LDP
...
.N.
...
...
...
.N.
...
...
...
.N.
.N.
.N.
...
.N.
...
...
..
..
..

49
80
80
80
80
80
35
97
57
70
85
85
84
99
84
53
60
69
56
69
45
.
. . .

The BLAST Lab feature is intended to provide detailed technical information on some of the more specialized uses of the BLAST family of programs. Topics are selected from the range of questions received by the BLAST Help Group.



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NCBI News | Fall 99