BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy4720
(95 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AQS|A Chain A, Laminin Beta1 Ln-Le1-4 Structure
Length = 525
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 34/81 (41%), Gaps = 20/81 (24%)
Query: 11 PCQCDIDGSKS---------FECEQFGGQCQCKPNVIGRRCEMCATGYYGFPDCHPCNC- 60
PC CD GS++ F GQC+CK +V G RC++C G+Y P C
Sbjct: 380 PCTCDPAGSENGGICDGYTDFSVGLIAGQCRCKLHVEGERCDVCKEGFYDLSAEDPYGCK 439
Query: 61 ----------PFTAVCDSYTG 71
P CDS TG
Sbjct: 440 SCACNPLGTIPGGNPCDSETG 460
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 11 PCQCDIDGSKSFECEQFGGQCQCKPNVIGRRC 42
PC CD+ G+ + C + GQC C P++IGR+C
Sbjct: 492 PCDCDLGGALNNSCSEDSGQCSCLPHMIGRQC 523
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 24 CEQFGGQCQCKPNVIGRRCEMCATGYYGFPD----CHPCNCPFTAVCDS 68
C+ G C CK V G+RC+ C ++G + C PC+C ++
Sbjct: 455 CDSETGYCYCKRLVTGQRCDQCLPQHWGLSNDLDGCRPCDCDLGGALNN 503
Score = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 14/57 (24%)
Query: 28 GGQC-QCKPNVIGRRCEMCATGYYGFPD--------CHPCNC-----PFTAVCDSYT 70
GG C C+ N +GR CE C Y+ P+ C PC C +CD YT
Sbjct: 342 GGVCDNCQHNTMGRNCEQCKPFYFQHPERDIRDPNLCEPCTCDPAGSENGGICDGYT 398
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 16/38 (42%)
Query: 16 IDGSKSFECEQFGGQCQCKPNVIGRRCEMCATGYYGFP 53
+DG G C C+ N G CE+C Y+ P
Sbjct: 266 VDGVNEEVEGMVHGHCMCRHNTKGLNCELCMDFYHDLP 303
>pdb|1NPE|B Chain B, Crystal Structure Of Nidogen/laminin Complex
Length = 164
Score = 32.3 bits (72), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 20 KSFECEQFGGQCQCKPNVIGRRCEMCATGYYGF 52
+ C GQCQC P+V GR C C GYY
Sbjct: 124 QQSSCNPVTGQCQCLPHVSGRDCGTCDPGYYNL 156
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 14/66 (21%)
Query: 32 QCKPNVIGRRCEMCATGYYGFP--------DCHPCNC------PFTAVCDSYTGKLAQVL 77
C G+RCE+C GY+G P C PC C C+ TG+ + +
Sbjct: 24 HCPTGTAGKRCELCDDGYFGDPLGSNGPVRLCRPCQCNDNIDPNAVGNCNRLTGECLKCI 83
Query: 78 IQVVTF 83
F
Sbjct: 84 YNTAGF 89
>pdb|1KLO|A Chain A, Crystal Structure Of Three Consecutive Laminin-Type
Epidermal Growth Factor-Like (Le) Modules Of Laminin
Gamma1 Chain Harboring The Nidogen Binding Site
Length = 162
Score = 32.3 bits (72), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 20 KSFECEQFGGQCQCKPNVIGRRCEMCATGYYGF 52
+ C GQCQC P+V GR C C GYY
Sbjct: 122 QQSSCNPVTGQCQCLPHVSGRDCGTCDPGYYNL 154
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 14/66 (21%)
Query: 32 QCKPNVIGRRCEMCATGYYGFP--------DCHPCNC------PFTAVCDSYTGKLAQVL 77
C G+RCE+C GY+G P C PC C C+ TG+ + +
Sbjct: 22 HCPTGTAGKRCELCDDGYFGDPLGSNGPVRLCRPCQCNDNIDPNAVGNCNRLTGECLKCI 81
Query: 78 IQVVTF 83
F
Sbjct: 82 YNTAGF 87
>pdb|1E3J|A Chain A, Ketose Reductase (Sorbitol Dehydrogenase) From Silverleaf
Whitefly
Length = 352
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 28 GGQCQCKPNVIGRRCEMCATGYYGF-PDCHPCNCP 61
G + +P V RRC+ C G Y PD C P
Sbjct: 85 GDRVAVEPGVPCRRCQFCKEGKYNLCPDLTFCATP 119
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 57 PCNCPFTAVCDS 68
PCNC + VCDS
Sbjct: 316 PCNCSYPLVCDS 327
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 57 PCNCPFTAVCDS 68
PCNC + VCDS
Sbjct: 316 PCNCSYPLVCDS 327
>pdb|4AQT|A Chain A, Laminin Gamma1 Ln-Le1-2 Structure
Length = 375
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 2 TISFLHEALPCQCDIDGSKSFEC---------EQFGGQC-QCKPNVIGRRCEMCATGYYG 51
T E LPC C+ +S EC GG C C+ N G +CE C ++
Sbjct: 301 TAESASECLPCDCN---GRSQECYFDPELYRSTGHGGHCTNCRDNTDGAKCERCRENFFR 357
Query: 52 FPDCHPCN 59
+ C+
Sbjct: 358 LGNTEACS 365
>pdb|3V4P|B Chain B, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1
pdb|3V4P|D Chain D, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1
pdb|3V4V|B Chain B, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1 And Ro0505376
pdb|3V4V|D Chain D, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1 And Ro0505376
Length = 503
Score = 25.0 bits (53), Expect = 9.5, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 13/47 (27%)
Query: 6 LHEALPCQCD---------IDGSKSFECEQFGGQCQCKPNVIGRRCE 43
LH C C DG +C G C C P +GR CE
Sbjct: 451 LHTLCDCNCSDTQPQAPHCSDGQGHLQC----GVCSCAPGRLGRLCE 493
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.328 0.142 0.524
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,145,072
Number of Sequences: 62578
Number of extensions: 113509
Number of successful extensions: 240
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 224
Number of HSP's gapped (non-prelim): 28
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)