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= 043011
(133 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 52/104 (50%), Gaps = 8/104 (7%)
Query: 1 MGAPSNSRFRRP---KAGEDERSPN-LFVANCGPAVGVSYEAIGSVFSAFGDVKGIYAAD 56
+G PSN +P + E+ R+ N ++VA+ +S + I SVF AFG +K A
Sbjct: 87 VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQ--DLSDDDIKSVFEAFGKIKSCTLAR 144
Query: 57 D--SGARVIVSYFDEGSAQAAFNSLHSRPCPDLANRFLHISYSV 98
D +G + + AQ++ +++ S DL ++L + +V
Sbjct: 145 DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 53/109 (48%), Gaps = 8/109 (7%)
Query: 1 MGAPSNSRFRRP---KAGEDERSPN-LFVANCGPAVGVSYEAIGSVFSAFGDVKGIYAAD 56
+G PSN +P + E+ R+ N ++VA+ +S + I SVF AFG +K A
Sbjct: 86 VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQ--DLSDDDIKSVFEAFGKIKSCTLAR 143
Query: 57 D--SGARVIVSYFDEGSAQAAFNSLHSRPCPDLANRFLHISYSVLEDSP 103
D +G + + AQ++ +++ S DL ++L + +V P
Sbjct: 144 DPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXP 192
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 52/104 (50%), Gaps = 8/104 (7%)
Query: 1 MGAPSNSRFRRP---KAGEDERSPN-LFVANCGPAVGVSYEAIGSVFSAFGDVKGIYAAD 56
+G PSN +P + E+ R+ N ++VA+ +S + I SVF AFG +K A
Sbjct: 102 VGRPSNIGQAQPIIDQLAEEARAFNRIYVASV--HQDLSDDDIKSVFEAFGKIKSATLAR 159
Query: 57 D--SGARVIVSYFDEGSAQAAFNSLHSRPCPDLANRFLHISYSV 98
D +G + + AQ++ +++ S DL ++L + +V
Sbjct: 160 DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
>pdb|3CU7|A Chain A, Human Complement Component 5
pdb|3CU7|B Chain B, Human Complement Component 5
pdb|3KLS|A Chain A, Structure Of Complement C5 In Complex With Ssl7
pdb|3KLS|B Chain B, Structure Of Complement C5 In Complex With Ssl7
pdb|3KM9|A Chain A, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|3KM9|B Chain B, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|4E0S|A Chain A, Crystal Structure Of C5b-6
Length = 1676
Score = 28.9 bits (63), Expect = 0.78, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 16/73 (21%)
Query: 70 GSAQAAFNS------LHSRPCPDLANRFLHISYSVLEDS---------PATRHITSSVPV 114
G AQ F+S L DL N++L+I+ +V+E + P +++ S +
Sbjct: 295 GIAQVTFDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKL 354
Query: 115 SLVASELNI-PGL 126
+LVA+ L + PG+
Sbjct: 355 NLVATPLFLKPGI 367
>pdb|3PRX|A Chain A, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PRX|C Chain C, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PVM|A Chain A, Structure Of Complement C5 In Complex With Cvf
pdb|3PVM|C Chain C, Structure Of Complement C5 In Complex With Cvf
Length = 1676
Score = 28.9 bits (63), Expect = 0.79, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 16/73 (21%)
Query: 70 GSAQAAFNS------LHSRPCPDLANRFLHISYSVLEDS---------PATRHITSSVPV 114
G AQ F+S L DL N++L+I+ +V+E + P +++ S +
Sbjct: 295 GIAQVTFDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKL 354
Query: 115 SLVASELNI-PGL 126
+LVA+ L + PG+
Sbjct: 355 NLVATPLFLKPGI 367
>pdb|4A5W|A Chain A, Crystal Structure Of C5b6
Length = 1580
Score = 28.9 bits (63), Expect = 0.84, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 16/73 (21%)
Query: 70 GSAQAAFNS------LHSRPCPDLANRFLHISYSVLEDS---------PATRHITSSVPV 114
G AQ F+S L DL N++L+I+ +V+E + P +++ S +
Sbjct: 277 GIAQVTFDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKL 336
Query: 115 SLVASELNI-PGL 126
+LVA+ L + PG+
Sbjct: 337 NLVATPLFLKPGI 349
>pdb|2X9Q|A Chain A, Structure Of The Mycobacterium Tuberculosis Protein,
Rv2275, Demonstrates That Cyclodipeptide Synthetases
Are Related To Type I Trna-Synthetases.
pdb|2X9Q|B Chain B, Structure Of The Mycobacterium Tuberculosis Protein,
Rv2275, Demonstrates That Cyclodipeptide Synthetases
Are Related To Type I Trna-Synthetases
Length = 289
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/132 (24%), Positives = 53/132 (40%), Gaps = 33/132 (25%)
Query: 32 VGVSYEAIG-----SVFSAFGDVKGIYAA--------DDSGARVIVSYFDEGSAQAAFNS 78
V SYEA+G + A +++G+ A D +GAR+ V E + A+
Sbjct: 122 VAESYEALGDSAIEARRKAVKNIRGVRAKITTTVNELDPAGARLCVRPXSEFQSNEAYRE 181
Query: 79 LHSR-------------PCPDLANRFLHISYSVLEDSPATR------HITSSVPVSL-VA 118
LH+ C DL RFL + + AT+ +I + P+ L
Sbjct: 182 LHADLLTRLKDDEDXRAVCQDLVRRFLSTKVGPRQGATATQEQVCXDYICAEAPLFLDTP 241
Query: 119 SELNIPGLHSCF 130
+ L +P +C+
Sbjct: 242 AILGVPSSLNCY 253
>pdb|2XBT|A Chain A, Structure Of A Scaffoldin Carbohydrate-Binding Module
Family 3b From The Cellulosome Of Bacteroides
Cellulosolvens: Structural Diversity And Implications
For Carbohydrate Binding
Length = 160
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 49 VKGIYAADDSGARVIVS-YFDEGSAQAAFNSLHSRPCPDLANRFLHI 94
++ Y +DD A S Y GSA A FN+L P AN+++ I
Sbjct: 47 IRYFYTSDDDKALTYYSDYVSIGSASATFNNL--SPVHAKANKYIEI 91
>pdb|1SGV|A Chain A, Structure Of Trna Psi55 Pseudouridine Synthase (Trub)
pdb|1SGV|B Chain B, Structure Of Trna Psi55 Pseudouridine Synthase (Trub)
Length = 316
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 40 GSVFSAFGDVKGIYAADDSGARVIVSYFDEGS 71
G A G + G+YAA D+ RVI DEGS
Sbjct: 252 GRSLPAVG-IDGVYAACDADGRVIALLRDEGS 282
>pdb|3U3Y|B Chain B, Mouse Trex1 D200h Mutant
pdb|3U3Y|A Chain A, Mouse Trex1 D200h Mutant
Length = 314
Score = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 2 GAPSNSRFRRPKAGEDERSPN 22
G+PSN R RRPK+ E+ P
Sbjct: 260 GSPSNGRSRRPKSPPPEKVPE 280
>pdb|3U6F|B Chain B, Mouse Trex1 D200n Mutant
pdb|3U6F|A Chain A, Mouse Trex1 D200n Mutant
Length = 314
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 2 GAPSNSRFRRPKAGEDERSPN 22
G+PSN R RRPK+ E+ P
Sbjct: 260 GSPSNGRSRRPKSPPPEKVPE 280
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
0.318 0.133 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,888,711
Number of Sequences: 62578
Number of extensions: 146923
Number of successful extensions: 378
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 365
Number of HSP's gapped (non-prelim): 38
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)