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= 009250
(539 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 = 154 bits (390), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 137/483 (28%), Positives = 220/483 (45%), Gaps = 59/483 (12%)
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-ASLLVGVTNFAGLRSEKYCALCASYLMDKEGRQKLLIGSYLGMAISMLL 412
+G TD AL +++VGV N + A +DK GR+ L I LGMAI M
Sbjct: 306 TLGASTDIALLQTIIVGVINLT-------FTVLAIMTVDKFGRKPLQIIGALGMAIGMFS 358
Query: 413 VVGA--TSLPLDEDFSHNLSILGTLFYIFTFAIGAGPVTGLVIPELSSNRTRGKIMGFSF 470
+ A T P +++L LFY+ FA+ GPV +++ E+ N RGK + +
Sbjct: 359 LGTAFYTQAP------GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAV 412
Query: 471 SVHWVCNFLVGLFF--LD----LVETFGVAPVYAGFGGVSLLSALFAYYFIVETKGRSLE 524
+ W+ N+ V F +D LV F Y +G + +L+ALF + F+ ETKG++LE
Sbjct: 413 AAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLE 472
Query: 525 EIE 527
E+E
Sbjct: 473 ELE 475
>pdb|4G4S|P Chain P, Structure Of Proteasome-Pba1-Pba2 Complex
Length = 269
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 333 LFLLQQFAGINGVLYFSSLTFQDVGITDGALASLLVGVTNFA----GLRSEKYCALCASY 388
L L Q + +N L+F+ +FQD D + +L + N + LRS KYC+ A+
Sbjct: 157 LHLNDQESMVNNWLHFTPTSFQDKISVDQPIFKILFQILNASQRPKALRSIKYCSCLAN- 215
Query: 389 LMDKEGRQKLLIGSYLGMAISMLLVVGA 416
EG L +L IS ++ A
Sbjct: 216 ----EGDNSLDSQQFLQWIISQKVIKNA 239
>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 = 0.45, 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|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 = 0.45, 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|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 = 5.9, 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 = 6.2, 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|3QD5|A Chain A, Crystal Structure Of A Putative Ribose-5-Phosphate
Isomerase From Coccidioides Immitis Solved By Combined
Iodide Ion Sad And Mr
pdb|3QD5|B Chain B, Crystal Structure Of A Putative Ribose-5-Phosphate
Isomerase From Coccidioides Immitis Solved By Combined
Iodide Ion Sad And Mr
Length = 167
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 7/102 (6%)
Query: 344 GVLYFSSLTFQDVGITDGALASLL--VGVTNFAGLRSEKYCALCASYLMD--KEGRQKLL 399
GV Y +L ++D L S + VGVT+ + + A+ A+ L+ K R ++
Sbjct: 23 GVSYKEALKAH---LSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMI 79
Query: 400 IGSYLGMAISMLLVVGATSLPLDEDFSHNLSILGTLFYIFTF 441
G+ LG+AIS V G ++ + FS +IL + F
Sbjct: 80 XGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCF 121
>pdb|3SDW|A Chain A, Crystal Structure Of A Ribose-5-Phosphate Isomerase B Rpib
From Coccidioides Immitis Bound To Phosphate
pdb|3SGW|A Chain A, Crystal Structure Of Ribose-5-Phosphate Isomerase B Rpib
From Coccidioides Immitis Semi-Covalently Bound To
Malonic Acid
Length = 184
Score = 28.5 bits (62), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 7/102 (6%)
Query: 344 GVLYFSSLTFQDVGITDGALASLL--VGVTNFAGLRSEKYCALCASYLMD--KEGRQKLL 399
GV Y +L ++D L S + VGVT+ + + A+ A+ L+ K R ++
Sbjct: 40 GVSYKEALKAH---LSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMI 96
Query: 400 IGSYLGMAISMLLVVGATSLPLDEDFSHNLSILGTLFYIFTF 441
G+ LG+AIS V G ++ + FS +IL + F
Sbjct: 97 CGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCF 138
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: 15,488,083
Number of Sequences: 62578
Number of extensions: 638986
Number of successful extensions: 1281
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: 1272
Number of HSP's gapped (non-prelim): 14
length of query: 539
length of database: 14,973,337
effective HSP length: 104
effective length of query: 435
effective length of database: 8,465,225
effective search space: 3682372875
effective search space used: 3682372875
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)