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= 008725
(556 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DN7|A Chain A, Crystal Structure Of Putative Abc Transporter, Atp-Binding
Protein From Methanosarcina Mazei Go1
pdb|4DN7|B Chain B, Crystal Structure Of Putative Abc Transporter, Atp-Binding
Protein From Methanosarcina Mazei Go1
Length = 429
Score = 126 bits (316), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 97/405 (23%), Positives = 181/405 (44%), Gaps = 38/405 (9%)
Query: 154 NFQDMCYYSAPKKKPTLNSLDEADPELIRYFDKLGVPLNEQNRLANVAVDAVLDSVSIAT 213
+F+ Y K + L D E + ++GV +E+ R + V LD+ A
Sbjct: 47 DFELEKYEEGSKVSKPIEDLQSLDEESKKTLLQVGVIPSEEGRSGSFLV---LDN---AV 100
Query: 214 THRKTLEEAGVIFCSISEAIREHPDLVRKYLGRVVPSEDNYYAALNAAVFSDGSFCYIPK 273
+H TL++ V S +A ++ + ++ Y ++V + + Y A +DG F +P
Sbjct: 101 SH-STLKDKNVELXSTHKAXEKY-EWLKDYSWKLVQVDADKYTAKTYLEDADGYFIRVPA 158
Query: 274 NTKCPMPISTYFRINAMETGQFERTLIVADEGSFVEYLEGCTAPSYDRNQLHAAVVELYC 333
K P+ T + + + Q +I+ +EG+ ++ + GCT LH + E Y
Sbjct: 159 GKKTSXPVQTCLXLGSKKAAQTVHNIIIVEEGATLDIITGCTTKKGVEEGLHLGISEXYI 218
Query: 334 AEGAEIKYSTVQNW----------YAGDEEGNGGIYNFVTKRGLCAGDRSKISWTQVETG 383
+G + ++ + NW EEG + N++ + + RS V+T
Sbjct: 219 KKGGTLNFTXIHNWAEQIGVRPRTVVSVEEGGTYVSNYICLKPV----RS------VQT- 267
Query: 384 SAITWKYPSVVLEGDDTVGEFYSVALTNNYQQADTGTKMIHKGKNTRSRIISKGISVGNS 443
YP+V LEG+ V ++A+ + + D G+K I TR+ +IS+ I++G
Sbjct: 268 ------YPTVRLEGEGAVTRLNTIAIAHPGSELDLGSKAIFNAPGTRAELISRTITIGG- 320
Query: 444 RNCYRGLVQVQSKAENARNSSQCDSMLLGDTAAANTYPYIQVKNPTARVEHEASTSKIGE 503
R RG + A+ A+ +C ++L D + P ++ + HEA+ KI +
Sbjct: 321 RLIARG--EXIGNAKGAKGHLECKGLVLTDKGSQLAIPILEANVDDIELTHEAAVGKIAK 378
Query: 504 DQLFYFQQRGIDYEKAMAAMISGFCRDVFNELPDEFGAEVNQLMS 548
DQ+ Y RG+ ++A+ +I GF +P+E E+ ++
Sbjct: 379 DQVEYLXARGLTEDEAVGXIIRGFLDVGIRGIPEELKEEIENTIA 423
>pdb|2ZU0|A Chain A, Crystal Structure Of Sufc-Sufd Complex Involved In The
Iron- Sulfur Cluster Biosynthesis
pdb|2ZU0|B Chain B, Crystal Structure Of Sufc-Sufd Complex Involved In The
Iron- Sulfur Cluster Biosynthesis
Length = 423
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 81/180 (45%), Gaps = 1/180 (0%)
Query: 359 YNFVTKRGLCAGDRSKISWTQVETGSAITWKYPSVVLEGDDTVGEFYSVALTNNYQQADT 418
++F L A D + S + + G A+ S L G+++ S+A+ + DT
Sbjct: 226 HHFAHNDLLLAEDATAFSHSFL-LGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDT 284
Query: 419 GTKMIHKGKNTRSRIISKGISVGNSRNCYRGLVQVQSKAENARNSSQCDSMLLGDTAAAN 478
T + H SR + K I R + GL+ V A +++L+G A +
Sbjct: 285 RTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVD 344
Query: 479 TYPYIQVKNPTARVEHEASTSKIGEDQLFYFQQRGIDYEKAMAAMISGFCRDVFNELPDE 538
T P +++ + H A+ +I ++Q+FY + RGI+ + A +I F ++ L DE
Sbjct: 345 TKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDE 404
>pdb|1VH4|A Chain A, Crystal Structure Of A Stabilizer Of Iron Transporter
pdb|1VH4|B Chain B, Crystal Structure Of A Stabilizer Of Iron Transporter
Length = 435
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 81/180 (45%), Gaps = 1/180 (0%)
Query: 359 YNFVTKRGLCAGDRSKISWTQVETGSAITWKYPSVVLEGDDTVGEFYSVALTNNYQQADT 418
++F L A D + S + + G A+ S L G+++ S+A+ + DT
Sbjct: 228 HHFAHNDLLLAEDATAFSHSFL-LGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDT 286
Query: 419 GTKMIHKGKNTRSRIISKGISVGNSRNCYRGLVQVQSKAENARNSSQCDSMLLGDTAAAN 478
T + H SR + K I R + GL+ V A +++L+G A +
Sbjct: 287 RTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVD 346
Query: 479 TYPYIQVKNPTARVEHEASTSKIGEDQLFYFQQRGIDYEKAMAAMISGFCRDVFNELPDE 538
T P +++ + H A+ +I ++Q+FY + RGI+ + A +I F ++ L DE
Sbjct: 347 TKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDE 406
>pdb|3O6F|C Chain C, Crystal Structure Of A Human Autoimmune Tcr Ms2-3c8 Bound
To Mhc Class Ii Self-Ligand MbpHLA-Dr4
pdb|3O6F|G Chain G, Crystal Structure Of A Human Autoimmune Tcr Ms2-3c8 Bound
To Mhc Class Ii Self-Ligand MbpHLA-Dr4
pdb|3T0E|C Chain C, Crystal Structure Of A Complete Ternary Complex Of T Cell
Receptor, Peptide-Mhc And Cd4
Length = 206
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 25/93 (26%)
Query: 188 GVPLNEQNRLANVAVDAVLDSVSIATTHRKTLEEAGVIFCSISEAIREHPDLVRKYLGRV 247
G+ N NR+A++A+ S S HR TL +A V +C++
Sbjct: 51 GLTSNVNNRMASLAIAEDRKS-STLILHRATLRDAAVYYCTV------------------ 91
Query: 248 VPSEDNYYAALNAAVFSDGSFCYIPKNTKCPMP 280
Y A N +F G+ + N + P P
Sbjct: 92 ------YGGATNKLIFGTGTLLAVQPNIQNPDP 118
>pdb|3KN3|A Chain A, Crystal Structure Of Lysr Substrate Binding Domain
(25-263) Of Putative Periplasmic Protein From Wolinella
Succinogenes
pdb|3KN3|B Chain B, Crystal Structure Of Lysr Substrate Binding Domain
(25-263) Of Putative Periplasmic Protein From Wolinella
Succinogenes
pdb|3KN3|C Chain C, Crystal Structure Of Lysr Substrate Binding Domain
(25-263) Of Putative Periplasmic Protein From Wolinella
Succinogenes
Length = 242
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 345 QNWYAGDEEGNGGIYNFVT-KRGLCAGDRSKISWTQVETGSAITWKYPSV-VLEGDDTVG 402
++WY +G N ++GL DR T ++ S K P V VLEGD+T+
Sbjct: 145 ESWYIEAGQGXLATINIAEEQKGLTLTDRG----TFIKYESNHKGKPPXVIVLEGDNTLK 200
Query: 403 EFYSVALTN 411
FYS+ N
Sbjct: 201 NFYSIXAVN 209
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
0.316 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: 16,171,314
Number of Sequences: 62578
Number of extensions: 673872
Number of successful extensions: 1613
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1608
Number of HSP's gapped (non-prelim): 6
length of query: 556
length of database: 14,973,337
effective HSP length: 104
effective length of query: 452
effective length of database: 8,465,225
effective search space: 3826281700
effective search space used: 3826281700
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)