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= 009536
(532 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 161 bits (407), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 137/476 (28%), Positives = 220/476 (46%), Gaps = 52/476 (10%)
Query: 86 FPHVLIASMSNFLFGYHIGVMNGPIVSI------AKELGFEGNPILEGLVVSIFIAGAFV 139
F L+A++ LFGY V++G + S+ + L L G V+ + G +
Sbjct: 11 FSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCII 70
Query: 140 GSISSGSLADKLGCRRTFQIDTIPLILGAIISAQ------------------AHSLDEML 181
G G +++ G R + +I + + + SA A + E +
Sbjct: 71 GGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFV 130
Query: 182 WGRFLVGLGIGVNTVLVPIYISEVAPTKYRGSLGTLCQVGTCLG--IITSLFLGIPAEDD 239
R + G+G+G+ ++L P+YI+E+AP RG L + Q G ++ + I D
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGD 190
Query: 240 PHW-----WRTMLYIASLPGFILALGMQFTVESPRWLCKGGMLNDAKAVIANLWGESEIN 294
W WR M +P + + + ESPRWL G A+ ++ + G +
Sbjct: 191 ASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLAT 250
Query: 295 KAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIGGALFLLQQFAGINGVLYFSSLTFQ 354
+A++E K D + L V IG L + QQF GIN VLY++ F+
Sbjct: 251 QAVQEI-----KHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFK 305
Query: 355 DVGI-TDGAL-ASLLVGVTNFAGALCASYLMDKEGRQKLLIGSYLGMAISMLLVVGA--T 410
+G TD AL +++VGV N + A +DK GR+ L I LGMAI M + A T
Sbjct: 306 TLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYT 365
Query: 411 SLPLDEDFSHNLSILGTLFYIFTFAIGAGPVTGLVIPELSSNRTRGKIMGFSFSVHWVCN 470
P +++L LFY+ FA+ GPV +++ E+ N RGK + + + W+ N
Sbjct: 366 QAP------GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419
Query: 471 FLVGLFF--LD----LVETFGVAPVYAGFGGVSLLSALFAYYFIVETKGRSLEEIE 520
+ V F +D LV F Y +G + +L+ALF + F+ ETKG++LEE+E
Sbjct: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELE 475
>pdb|4DEY|A Chain A, Crystal Structure Of The Voltage Dependent Calcium Channel
Beta-2 Subunit In Complex With The Cav1.2 I-Ii Linker
Length = 337
Score = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 22 FTPSPAKMKTLRFSFSHRSTKFKVLAAKKQLP 53
F PSP K++ +R R+ +FK+ + +K++P
Sbjct: 94 FIPSPVKLENMRLQHEQRAKEFKLHSKEKRMP 125
>pdb|4DEX|A Chain A, Crystal Structure Of The Voltage Dependent Calcium Channel
Beta-2 Subunit In Complex With The Cav2.2 I-Ii Linker
Length = 339
Score = 33.1 bits (74), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 22 FTPSPAKMKTLRFSFSHRSTKFKVLAAKKQLP 53
F PSP K++ +R R+ +FK+ + +K++P
Sbjct: 96 FIPSPVKLENMRLQHEQRAKEFKLHSKEKRMP 127
>pdb|2VHV|A Chain A, Crystal Structure Of The D270a Mutant Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis In Complex
With Nadh.
pdb|2VHV|B Chain B, Crystal Structure Of The D270a Mutant Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis In Complex
With Nadh
Length = 377
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 88/188 (46%), Gaps = 20/188 (10%)
Query: 230 LFLGIPAEDDPHWWRTMLYIASLPGFILALGMQFTVESPRWLCKGGMLNDA--KAVIANL 287
+ +GIP E + +R + A + + G + +++ +G + DA KA A L
Sbjct: 1 MRVGIPTETKNNEFRVAITPAGV-AELTRRGHEVLIQA--GAGEGSAITDADFKAAGAQL 57
Query: 288 WGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIGGALFLLQQFAGINGVLY 347
G ++ A + L +K+ + +++ L H ++ F L L A + +L
Sbjct: 58 VGTADQVWADADLLLKVKEP---IAAEYGRLR---HGQILFT--FLHLAASRACTDALLD 109
Query: 348 --FSSLTFQDVGITDGALASLLVGVTNFAGALCAS----YLMDKEGRQKLLIGSYLGMAI 401
+S+ ++ V DGAL LL ++ AG L A +LM +G + +L+G G+
Sbjct: 110 SGTTSIAYETVQTADGAL-PLLAPMSEVAGRLAAQVGAYHLMRTQGGRGVLMGGVPGVEP 168
Query: 402 SMLLVVGA 409
+ ++V+GA
Sbjct: 169 ADVVVIGA 176
>pdb|2VHW|A Chain A, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Open And Closed
Conformation
pdb|2VHW|B Chain B, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Open And Closed
Conformation
pdb|2VHW|C Chain C, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Open And Closed
Conformation
pdb|2VHW|D Chain D, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Open And Closed
Conformation
pdb|2VHW|E Chain E, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Open And Closed
Conformation
pdb|2VHW|F Chain F, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Open And Closed
Conformation
pdb|2VHX|A Chain A, Crystal Structure Of The Ternary Complex Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis With Nad+
And Pyruvate
pdb|2VHX|B Chain B, Crystal Structure Of The Ternary Complex Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis With Nad+
And Pyruvate
pdb|2VHX|C Chain C, Crystal Structure Of The Ternary Complex Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis With Nad+
And Pyruvate
pdb|2VHX|D Chain D, Crystal Structure Of The Ternary Complex Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis With Nad+
And Pyruvate
pdb|2VHX|E Chain E, Crystal Structure Of The Ternary Complex Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis With Nad+
And Pyruvate
pdb|2VHX|F Chain F, Crystal Structure Of The Ternary Complex Of L-Alanine
Dehydrogenase From Mycobacterium Tuberculosis With Nad+
And Pyruvate
pdb|2VHY|A Chain A, Crystal Structure Of Apo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis
pdb|2VHY|B Chain B, Crystal Structure Of Apo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis
pdb|2VHZ|A Chain A, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Closed Conformation
pdb|2VHZ|B Chain B, Crystal Structure Of Holo L-Alanine Dehydrogenase From
Mycobacterium Tuberculosis In The Closed Conformation
Length = 377
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 88/188 (46%), Gaps = 20/188 (10%)
Query: 230 LFLGIPAEDDPHWWRTMLYIASLPGFILALGMQFTVESPRWLCKGGMLNDA--KAVIANL 287
+ +GIP E + +R + A + + G + +++ +G + DA KA A L
Sbjct: 1 MRVGIPTETKNNEFRVAITPAGV-AELTRRGHEVLIQA--GAGEGSAITDADFKAAGAQL 57
Query: 288 WGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIGGALFLLQQFAGINGVLY 347
G ++ A + L +K+ + +++ L H ++ F L L A + +L
Sbjct: 58 VGTADQVWADADLLLKVKEP---IAAEYGRLR---HGQILFT--FLHLAASRACTDALLD 109
Query: 348 --FSSLTFQDVGITDGALASLLVGVTNFAGALCAS----YLMDKEGRQKLLIGSYLGMAI 401
+S+ ++ V DGAL LL ++ AG L A +LM +G + +L+G G+
Sbjct: 110 SGTTSIAYETVQTADGAL-PLLAPMSEVAGRLAAQVGAYHLMRTQGGRGVLMGGVPGVEP 168
Query: 402 SMLLVVGA 409
+ ++V+GA
Sbjct: 169 ADVVVIGA 176
>pdb|2VOE|A Chain A, Crystal Structure Of Rv2780 From M. Tuberculosis H37rv
pdb|2VOE|B Chain B, Crystal Structure Of Rv2780 From M. Tuberculosis H37rv
pdb|2VOE|C Chain C, Crystal Structure Of Rv2780 From M. Tuberculosis H37rv
pdb|2VOE|D Chain D, Crystal Structure Of Rv2780 From M. Tuberculosis H37rv
pdb|2VOE|E Chain E, Crystal Structure Of Rv2780 From M. Tuberculosis H37rv
pdb|2VOE|F Chain F, Crystal Structure Of Rv2780 From M. Tuberculosis H37rv
pdb|2VOJ|A Chain A, Ternary Complex Of M. Tuberculosis Rv2780 With Nad And
Pyruvate
pdb|2VOJ|C Chain C, Ternary Complex Of M. Tuberculosis Rv2780 With Nad And
Pyruvate
pdb|2VOJ|E Chain E, Ternary Complex Of M. Tuberculosis Rv2780 With Nad And
Pyruvate
Length = 371
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 88/188 (46%), Gaps = 20/188 (10%)
Query: 230 LFLGIPAEDDPHWWRTMLYIASLPGFILALGMQFTVESPRWLCKGGMLNDA--KAVIANL 287
+ +GIP E + +R + A + + G + +++ +G + DA KA A L
Sbjct: 1 MRVGIPTETKNNEFRVAITPAGV-AELTRRGHEVLIQA--GAGEGSAITDADFKAAGAQL 57
Query: 288 WGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIGGALFLLQQFAGINGVLY 347
G ++ A + L +K+ + +++ L H ++ F L L A + +L
Sbjct: 58 VGTADQVWADADLLLKVKEP---IAAEYGRLR---HGQILFT--FLHLAASRACTDALLD 109
Query: 348 --FSSLTFQDVGITDGALASLLVGVTNFAGALCAS----YLMDKEGRQKLLIGSYLGMAI 401
+S+ ++ V DGAL LL ++ AG L A +LM +G + +L+G G+
Sbjct: 110 SGTTSIAYETVQTADGAL-PLLAPMSEVAGRLAAQVGAYHLMRTQGGRGVLMGGVPGVEP 168
Query: 402 SMLLVVGA 409
+ ++V+GA
Sbjct: 169 ADVVVIGA 176
>pdb|4IXN|A Chain A, Crystal Structure Of Zn(ii)-bound E37a,c66a,c67a Triple
Mutant Yjia Gtpase
pdb|4IXN|B Chain B, Crystal Structure Of Zn(ii)-bound E37a,c66a,c67a Triple
Mutant Yjia Gtpase
Length = 318
Score = 29.3 bits (64), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 287 LWGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIG 330
LW + E N+ + FQ V + +D D W + E+PHS + FIG
Sbjct: 262 LWIDGEPNRLL--FQGVQRLYSADWDRPWGD--EKPHSTMVFIG 301
>pdb|1NIJ|A Chain A, Yjia Protein
pdb|4IXM|A Chain A, Crystal Structure Of Zn(ii)-bound Yjia Gtpase From E. Coli
pdb|4IXM|B Chain B, Crystal Structure Of Zn(ii)-bound Yjia Gtpase From E. Coli
Length = 318
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 287 LWGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIG 330
LW + E N+ + FQ V + +D D W + E+PHS + FIG
Sbjct: 262 LWIDGEPNRLL--FQGVQRLYSADWDRPWGD--EKPHSTMVFIG 301
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
0.323 0.140 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,283,780
Number of Sequences: 62578
Number of extensions: 631819
Number of successful extensions: 1276
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1267
Number of HSP's gapped (non-prelim): 14
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)