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= 042218
(655 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F9L|A Chain A, 3d Structure Of Inactive Human Rab11b Gtpase
pdb|2F9M|A Chain A, 3d Structure Of Active Human Rab11b Gtpase
Length = 199
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW A Q+ +R + S++ G A +
Sbjct: 38 IGVEFATRSIQVDGKTIKAQIW-------DTAGQE-----RYRRITSAYYRGAVGALLVY 85
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 86 DIAKHLTY 93
>pdb|3RDK|A Chain A, Protein Crystal Structure Of Xylanase A1 Of Paenibacillus
Sp. Jdr-2
pdb|3RDK|B Chain B, Protein Crystal Structure Of Xylanase A1 Of Paenibacillus
Sp. Jdr-2
pdb|4E4P|A Chain A, Second Native Structure Of Xylanase A1 From Paenibacillus
Sp. Jdr-2
pdb|4E4P|B Chain B, Second Native Structure Of Xylanase A1 From Paenibacillus
Sp. Jdr-2
pdb|3RO8|A Chain A, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|B Chain B, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|C Chain C, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|D Chain D, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|E Chain E, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|F Chain F, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|G Chain G, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
pdb|3RO8|H Chain H, Crystal Structure Of The Catalytic Domain Of Xyna1 From
Paenibacillus Sp. Jdr-2
Length = 341
Score = 33.1 bits (74), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 270 SFASEYIEQMVLNMQAKDEISPT--LRTIVNQYDEDNR-RSSDTFSSIQKLVDQVEAVHN 326
+ S+Y+EQ L + + +P+ ++ N Y+EDN+ +++ ++ ++ + D+ A HN
Sbjct: 162 AIGSDYVEQAFLAAREVLDENPSWNIKLYYNDYNEDNQNKATAIYNMVKDINDRYAAAHN 221
Query: 327 NEAESDGVAF 336
+ DGV
Sbjct: 222 GKLLIDGVGM 231
>pdb|1YZK|A Chain A, Gppnhp Bound Rab11 Gtpase
Length = 184
Score = 32.7 bits (73), Expect = 0.72, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW A Q+ +R++ S++ G A +
Sbjct: 53 IGVEFATRSIQVDGKTIKAQIW-------DTAGQE-----RYRAITSAYYRGAVGALLVY 100
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 101 DIAKHLTY 108
>pdb|1OIV|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex
With Gdp
pdb|1OIV|B Chain B, X-Ray Structure Of The Small G Protein Rab11a In Complex
With Gdp
Length = 191
Score = 32.3 bits (72), Expect = 0.94, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW A Q+ +R++ S++ G A +
Sbjct: 62 IGVEFATRSIQVDGKTIKAQIW-------DTAGQE-----RYRAITSAYYRGAVGALLVY 109
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 110 DIAKHLTY 117
>pdb|1OIW|A Chain A, X-ray Structure Of The Small G Protein Rab11a In Complex
With Gtpgammas
pdb|1OIX|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex
With Gdp And Pi
Length = 191
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW D +R++ S++ G A +
Sbjct: 62 IGVEFATRSIQVDGKTIKAQIW------------DTAGLERYRAITSAYYRGAVGALLVY 109
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 110 DIAKHLTY 117
>pdb|2HV8|A Chain A, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3
pdb|2HV8|B Chain B, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3
pdb|2HV8|C Chain C, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3
Length = 172
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW D +R++ S++ G A +
Sbjct: 41 IGVEFATRSIQVDGKTIKAQIW------------DTAGLERYRAITSAYYRGAVGALLVY 88
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 89 DIAKHLTY 96
>pdb|2D7C|A Chain A, Crystal Structure Of Human Rab11 In Complex With Fip3 Rab-
Binding Domain
pdb|2D7C|B Chain B, Crystal Structure Of Human Rab11 In Complex With Fip3 Rab-
Binding Domain
Length = 167
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW D +R++ S++ G A +
Sbjct: 38 IGVEFATRSIQVDGKTIKAQIW------------DTAGLERYRAITSAYYRGAVGALLVY 85
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 86 DIAKHLTY 93
>pdb|2GZD|A Chain A, Crystal Structure Of Rab11 In Complex With Rab11-Fip2
pdb|2GZD|B Chain B, Crystal Structure Of Rab11 In Complex With Rab11-Fip2
pdb|2GZH|A Chain A, Crystal Structure Of Rab11 In Complex With Rab11-Family
Interacting Protein 2
Length = 173
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 560 VEVEYDKTSKQVDVQTLKETIWVHIQESPQMAAQDPEKTVSFRSLLSSFPSGCRAAATIK 619
+ VE+ S QVD +T+K IW D +R++ S++ G A +
Sbjct: 44 IGVEFATRSIQVDGKTIKAQIW------------DTAGLERYRAITSAYYRGAVGALLVY 91
Query: 620 DISPHLCF 627
DI+ HL +
Sbjct: 92 DIAKHLTY 99
>pdb|1CLX|A Chain A, Catalytic Core Of Xylanase A
pdb|1CLX|B Chain B, Catalytic Core Of Xylanase A
pdb|1CLX|C Chain C, Catalytic Core Of Xylanase A
pdb|1CLX|D Chain D, Catalytic Core Of Xylanase A
Length = 347
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 127 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 182
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 183 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 220
>pdb|1W2V|A Chain A, The 3-Dimensional Structure Of A Thermostable Mutant Of A
Xylanase (Xyn10a) From Cellvibrio Japonicus
pdb|1W2V|B Chain B, The 3-Dimensional Structure Of A Thermostable Mutant Of A
Xylanase (Xyn10a) From Cellvibrio Japonicus
Length = 348
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 128 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 183
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 184 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 221
>pdb|1W32|A Chain A, The 3-Dimensional Structure Of A Thermostable Mutant Of A
Xylanase (Xyn10a) From Cellvibrio Japonicus
pdb|1W32|B Chain B, The 3-Dimensional Structure Of A Thermostable Mutant Of A
Xylanase (Xyn10a) From Cellvibrio Japonicus
Length = 348
Score = 29.6 bits (65), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 128 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 183
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 184 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 221
>pdb|1W3H|A Chain A, The 3-Dimensional Structure Of A Thermostable Mutant Of A
Xylanase (Xyn10a) From Cellvibrio Japonicus
pdb|1W3H|B Chain B, The 3-Dimensional Structure Of A Thermostable Mutant Of A
Xylanase (Xyn10a) From Cellvibrio Japonicus
Length = 359
Score = 29.6 bits (65), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 139 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 194
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 195 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 232
>pdb|1XYS|A Chain A, Catalytic Core Of Xylanase A E246c Mutant
pdb|1XYS|B Chain B, Catalytic Core Of Xylanase A E246c Mutant
Length = 347
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 127 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 182
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 183 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 220
>pdb|1E5N|A Chain A, E246c Mutant Of P Fluorescens Subsp. Cellulosa Xylanase A
In Complex With Xylopentaose
pdb|1E5N|B Chain B, E246c Mutant Of P Fluorescens Subsp. Cellulosa Xylanase A
In Complex With Xylopentaose
Length = 348
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 128 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 183
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 184 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 221
>pdb|1W2P|A Chain A, The 3-Dimensional Structure Of A Xylanase (Xyn10a) From
Cellvibrio Japonicus
pdb|1W2P|B Chain B, The 3-Dimensional Structure Of A Xylanase (Xyn10a) From
Cellvibrio Japonicus
Length = 348
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 9/103 (8%)
Query: 242 QVLFDSQEVPGKGMSCASQHSMSDTIDLSFASEYIEQMVLNMQAKDEISPTLRTIVNQYD 301
+ LFDS + P G A+ + S EYI++ +A D PT N ++
Sbjct: 128 EALFDSADDP-DGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAAD---PTAELYYNDFN 183
Query: 302 EDNRRSSDTFSSIQKLVDQVEAVHNNEAESDGVAFDDCGTNDF 344
+ + T LV+ V+ + NN DGV F ND+
Sbjct: 184 TEENGAKTT-----ALVNLVQRLLNNGVPIDGVGFQMHVMNDY 221
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
0.314 0.132 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,402,464
Number of Sequences: 62578
Number of extensions: 825363
Number of successful extensions: 1361
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1353
Number of HSP's gapped (non-prelim): 16
length of query: 655
length of database: 14,973,337
effective HSP length: 105
effective length of query: 550
effective length of database: 8,402,647
effective search space: 4621455850
effective search space used: 4621455850
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)