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= 007614
(596 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HUK|A Chain A, Mate Transporter Norm-ng In Complex With Tpp And Monobody
pdb|4HUL|A Chain A, Mate Transporter Norm-ng In Complex With Cs+ And Monobody
pdb|4HUM|A Chain A, Mate Transporter Norm-ng In Complex With Ethidium And
Monobody
pdb|4HUN|A Chain A, Mate Transporter Norm-ng In Complex With R6g And Monobody
Length = 459
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 88/392 (22%), Positives = 155/392 (39%), Gaps = 57/392 (14%)
Query: 144 LIVLTLPAIAGQVIDPLAQLMETAYVGRLGSVELASAGVSISIFNIVSKLFNIPLLSVAT 203
L L LP + QV ++T G G +LA+ + S F +V
Sbjct: 16 LTALALPMLLAQVAQVGIGFVDTVMAGGAGKEDLAAVALGSSAFA-----------TVYI 64
Query: 204 SFVAEDIAKNLTKDLAAGLEGNGKPPNGTTERKQXXXXXXXXXXXXGIGIFEAAALSLAS 263
+F+ A N + A L G GK +Q +GIF + A
Sbjct: 65 TFMGIMAALN---PMIAQLYGAGKTGEAGETGRQGIWFGLI------LGIFGMILMWAAI 115
Query: 264 GPFLNLMGVPSASAMHGPAKKFLMLRALGSPAFVVSLALQGIFRGFKDTKTPVLCLGIGN 323
PF N + + + + G ++++ +L PA +V AL + +L
Sbjct: 116 TPFRNWLTL--SDYVEGTMAQYMLFTSLAMPAAMVHRALHAYASSLNRPRLIMLVSFAAF 173
Query: 324 LLAVFLFPILIYFCQLGMP-----GAAISTVVSQYIVAVTMIWFLNKKVVLMPPKMGALQ 378
+L V L I +Y + GMP G ++T+ + A+ + ++ K+ P + A +
Sbjct: 174 VLNVPLNYIFVY-GKFGMPALGGAGCGVATMAVFWFSALALWIYIAKEKFFRPFGLTA-K 231
Query: 379 FG--DYV------KSGG------FLLGRTLAVLITMTLGTSMAARQGSDAMAAHQICMQV 424
FG D+ K G FL + ++ + A G D +AA Q+ + +
Sbjct: 232 FGKPDWAVFKQIWKIGAPIGLSYFLEASAFSFIVFLI------APFGEDYVAAQQVGISL 285
Query: 425 WLAVSLLTDALAASGQALIASYVSKGDFKTVREITNFVLKIGVLTGVSLATILGLSF--- 481
+ ++ ++ ++G I + + +F R I+ + +++G LA I LS
Sbjct: 286 SGILYMIPQSVGSAGTVRIGFSLGRREFSRARYISG----VSLVSGWVLAVITVLSLVLF 341
Query: 482 -GSLAPLFTKDPKVLGIVGTGVLFVSASQPIN 512
LA ++ DP VL I T +LF QP +
Sbjct: 342 RSPLASMYNDDPAVLSIASTVLLFAGLFQPAD 373
>pdb|2PW0|A Chain A, Crystal Structure Of Trans-Aconitate Bound To
Methylaconitate Isomerase Prpf From Shewanella
Oneidensis
pdb|2PW0|B Chain B, Crystal Structure Of Trans-Aconitate Bound To
Methylaconitate Isomerase Prpf From Shewanella
Oneidensis
Length = 397
Score = 33.1 bits (74), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 262 ASGPFLNLMGVPSASAMHGPAKKFLMLRALGSP 294
+ G F L +P A+ + GPA+ L+LR +GSP
Sbjct: 22 SKGVFFRLQDLPEAAQVPGPARDALLLRVIGSP 54
>pdb|2PVZ|A Chain A, Crystal Structure Of Methylaconitate Isomerase Prpf From
Shewanella Oneidensis
pdb|2PVZ|B Chain B, Crystal Structure Of Methylaconitate Isomerase Prpf From
Shewanella Oneidensis
Length = 397
Score = 33.1 bits (74), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 262 ASGPFLNLMGVPSASAMHGPAKKFLMLRALGSP 294
+ G F L +P A+ + GPA+ L+LR +GSP
Sbjct: 22 SKGVFFRLQDLPEAAQVPGPARDALLLRVIGSP 54
>pdb|3TJ4|A Chain A, Crystal Structure Of An Enolase From Agrobacterium
Tumefaciens (Efi Target Efi-502087) No Mg
pdb|3TJ4|B Chain B, Crystal Structure Of An Enolase From Agrobacterium
Tumefaciens (Efi Target Efi-502087) No Mg
pdb|4H19|A Chain A, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|B Chain B, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|C Chain C, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|D Chain D, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|E Chain E, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|F Chain F, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|G Chain G, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|H Chain H, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|I Chain I, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|K Chain K, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|L Chain L, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|M Chain M, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|N Chain N, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|P Chain P, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|J Chain J, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
pdb|4H19|O Chain O, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup, Target Efi-502087) From Agrobacterium
Tumefaciens, With Bound Mg And D- Ribonohydroxamate,
Ordered Loop
Length = 372
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 160 LAQLMETAYVGRLGSVELASAGVSISIFNIVSKLFNIPL 198
LA+ +VGR G LA A V +++++I +K +PL
Sbjct: 88 LARYPSLQWVGRAGITHLALAAVDVALWDIKAKKAGVPL 126
>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
Length = 460
Score = 29.6 bits (65), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 88/414 (21%), Positives = 166/414 (40%), Gaps = 45/414 (10%)
Query: 130 EVASKSHTQDAKNELIVLTLPAIAGQVIDPLAQLMETAYVGRLGSVELASAGVSISIFNI 189
E + + ++A N LI L P + V ++T G + ++++A+ ++ SI+ +
Sbjct: 1 ENSVHRYKKEASN-LIKLATPVLIASVAQTGMGFVDTIMAGGVSAIDMAAVSIAASIW-L 58
Query: 190 VSKLFNIPLLSVATSFVAEDIAKNLTKDLAAGLEGNGKPPNGTTERKQXXXXXXXXXXXX 249
S LF + LL VA+ L G G+ E Q
Sbjct: 59 PSILFGVGLLMALVPVVAQ-------------LNGAGRQHKIPFEVHQGLILALLVSVPI 105
Query: 250 GIGIFEAAALSLASGPFLNLMGVPSASAMHGPAKKFLMLRALGSPAFVVSLALQGIFRGF 309
+F+ + + M V A A ++ A+ PA+++ AL+ G
Sbjct: 106 IAVLFQTQFI-------IRFMDVEEAMATKTVGYMHAVIFAV--PAYLLFQALRSFTDGM 156
Query: 310 KDTKTPVLCLG-IGNLLAVFLFPILIY----FCQLGMPGAAISTVVSQYIVAVTMIWFLN 364
TK P + +G IG LL + L I +Y +LG G ++T + +I+ + +++++
Sbjct: 157 SLTK-PAMVIGFIGLLLNIPLNWIFVYGKFGAPELGGVGCGVATAIVYWIMLLLLLFYIV 215
Query: 365 KKVVLMPPKMGALQFGDYVKSG----------GFLLGRTLAVLITM-TLGTSMAARQGSD 413
L K+ F + K GF + L +T+ + + A GS
Sbjct: 216 TSKRLAHVKV----FETFHKPQPKELIRLFRLGFPVAAALFFEVTLFAVVALLVAPLGST 271
Query: 414 AMAAHQICMQVWLAVSLLTDALAASGQALIASYVSKGDFKTVREITNFVLKIGVLTGVSL 473
+AAHQ+ + V + ++ A+ + + + D K N L G+ T
Sbjct: 272 VVAAHQVALNFSSLVFMFPMSIGAAVSIRVGHKLGEQDTKGAAIAANVGLMTGLATACIT 331
Query: 474 ATILGLSFGSLAPLFTKDPKVLGIVGTGVLFVSASQPINALAFIFDGLHYGVSD 527
A + L +A L+T++ V+ + +LF + Q ++A+ + G G D
Sbjct: 332 ALLTVLFREQIALLYTENQVVVALAMQLLLFAAIYQCMDAVQVVAAGSLRGYKD 385
>pdb|1GMM|A Chain A, Carbohydrate Binding Module Cbm6 From Xylanase U
Clostridium Thermocellum
pdb|1UXX|X Chain X, Cbm6ct From Clostridium Thermocellum In Complex With
Xylopentaose
Length = 133
Score = 28.9 bits (63), Expect = 8.6, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 27/61 (44%)
Query: 459 TNFVLKIGVLTGVSLATILGLSFGSLAPLFTKDPKVLGIVGTGVLFVSASQPINALAFIF 518
TN L++G TG + T+ S G K + G L++ S P+N FIF
Sbjct: 67 TNIQLRLGSPTGTLIGTLTVASTGGWNNYEEKSCSITNTTGQHDLYLVFSGPVNIDYFIF 126
Query: 519 D 519
D
Sbjct: 127 D 127
>pdb|1VL4|A Chain A, Crystal Structure Of A Putative Modulator Of A Dna Gyrase
(Tm0727) From Thermotoga Maritima Msb8 At 1.95 A
Resolution
pdb|1VL4|B Chain B, Crystal Structure Of A Putative Modulator Of A Dna Gyrase
(Tm0727) From Thermotoga Maritima Msb8 At 1.95 A
Resolution
Length = 447
Score = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 100 EENGFTNSNKEHSEMRG-VTVSESHTLVEKIEVASKSHTQDAKNELIVL 147
E+ F KE+ EM V E ++ EK+++A K+H AK+E +V+
Sbjct: 102 EKEYFFEGGKEYREMETYVGRFEKLSVKEKMDMAKKAHESAAKDERVVM 150
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
0.322 0.136 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,417,902
Number of Sequences: 62578
Number of extensions: 578904
Number of successful extensions: 1366
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1358
Number of HSP's gapped (non-prelim): 8
length of query: 596
length of database: 14,973,337
effective HSP length: 104
effective length of query: 492
effective length of database: 8,465,225
effective search space: 4164890700
effective search space used: 4164890700
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)