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= 005459
(696 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NR0|A Chain A, Two Seven-Bladed Beta-Propeller Domains Revealed By The
Structure Of A C. Elegans Homologue Of Yeast Actin
Interacting Protein 1 (Aip1).
pdb|1PEV|A Chain A, Crystal Structure Of The Actin Interacting Protein From
Caenorhabditis Elegans
Length = 611
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 79/387 (20%), Positives = 147/387 (37%), Gaps = 112/387 (28%)
Query: 52 VRLGKYKRDS-ESVQREGENLQAVWSPDTKLIAVVTSSLYLHIFKVQI--TEKSIQIGGK 108
+ G ++ DS ++V G WSPD IA ++ + I+ V EK+I +G +
Sbjct: 223 TKTGVFEDDSLKNVAHSGSVFGLTWSPDGTKIASASADKTIKIWNVATLKVEKTIPVGTR 282
Query: 109 ---QPSGLFFIK---ISLVLNEQLPFAEKGL-SVSNIVSDNKHMLLGLS---DG-SLYSI 157
Q G+ + K +S+ N + F L S+ + + + LS DG +L+S
Sbjct: 283 IEDQQLGIIWTKQALVSISANGFINFVNPELGSIDQVRYGHNKAITALSSSADGKTLFSA 342
Query: 158 SWKGEFYG----------AFELVHSSNDSSVAALSH----------HF---PSNGLASVD 194
+G F VH++ + + S H P+ G + VD
Sbjct: 343 DAEGHINSWDISTGISNRVFPDVHATMITGIKTTSKGDLFTVSWDDHLKVVPAGG-SGVD 401
Query: 195 TSGAFVSD-HKFPISSAI-----IWLELCLPMRLLFVLYSNGQLMSCSVSKKGLKLAEFI 248
+S A + P+ A+ I + C +YS+G+L +S
Sbjct: 402 SSKAVANKLSSQPLGLAVSADGDIAVAACYKH---IAIYSHGKLTEVPISY--------- 449
Query: 249 KIDKELGSGDAVCASIAPEQQILAVGTRRGVVELYDLAESA----------SLIRTVSLY 298
++ C +++ ++Q +AVG + V +Y L+ ++ + I +V+
Sbjct: 450 ---------NSSCVALSNDKQFVAVGGQDSKVHVYKLSGASVSEVKTIVHPAEITSVAFS 500
Query: 299 DWG--------------YSMDD-------------TGPVSCIAWTPDNSAFAVGWKSRGL 331
+ G YS+ + T V+C++W+PDN A G +
Sbjct: 501 NNGAFLVATDQSRKVIPYSVANNFELAHTNSWTFHTAKVACVSWSPDNVRLATGSLDNSV 560
Query: 332 TVWS----------VSGCRLMSTIRQI 348
VW+ + G MS++ +
Sbjct: 561 IVWNMNKPSDHPIIIKGAHAMSSVNSV 587
>pdb|3DM0|A Chain A, Maltose Binding Protein Fusion With Rack1 From A. Thaliana
Length = 694
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 61/126 (48%), Gaps = 16/126 (12%)
Query: 288 SASLIRTVSLYDW----GYSMDDTGP-----VSCIAWTPDN---SAFAVGWKSRGLTVWS 335
SAS RT+ L++ Y++ + G VSC+ ++P+ + + W + + VW+
Sbjct: 489 SASRDRTIKLWNTLGECKYTISEGGEGHRDWVSCVRFSPNTLQPTIVSASW-DKTVKVWN 547
Query: 336 VSGCRLMSTIRQISLSSISSPIVKPNQDCKYEPLMSGTSMMQWD-EYGYRLYAIEEGSSE 394
+S C+L ST+ + +S+ V P+ G ++ WD G +LY++E S
Sbjct: 548 LSNCKLRSTLAGHT-GYVSTVAVSPDGSLCASGGKDGVVLL-WDLAEGKKLYSLEANSVI 605
Query: 395 RVLIFS 400
L FS
Sbjct: 606 HALCFS 611
Score = 29.6 bits (65), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 11/84 (13%)
Query: 263 SIAPEQQILAVGTRRGVVELYDLAESASLIRTVSLYDWGYSMDDTGPVSCIAWTPDNSAF 322
+++P+ + A G + GVV L+DLAE L YS++ + + ++P N +
Sbjct: 568 AVSPDGSLCASGGKDGVVLLWDLAEGKKL----------YSLEANSVIHALCFSP-NRYW 616
Query: 323 AVGWKSRGLTVWSVSGCRLMSTIR 346
G+ +W + ++ ++
Sbjct: 617 LCAATEHGIKIWDLESKSIVEDLK 640
>pdb|1R5M|A Chain A, Crystal Structure Of The C-Terminal Wd40 Domain Of Sif2
Length = 425
Score = 33.1 bits (74), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 17/113 (15%)
Query: 244 LAEFIKIDKELGSGDAVCASI-AP-EQQILAVGTRRGVVELYDLAES------------- 288
L F+KI KE+ D + +S P ++ ILA G + V L + E+
Sbjct: 32 LDGFVKILKEIVKLDNIVSSTWNPLDESILAYGEKNSVARLARIVETDQEGKKYWKLTII 91
Query: 289 ASLIRTVSLYDWGYSMDDTGPVSCIAWTPDNSAFAVGWKSRGLTVWSVSGCRL 341
A L +L S T V+C+AW+ D ++ G ++ L +W+ +G L
Sbjct: 92 AELRHPFALS--ASSGKTTNQVTCLAWSHDGNSIVTGVENGELRLWNKTGALL 142
>pdb|1XQK|A Chain A, Effect Of A Y265f Mutant On The Transamination Based
Cycloserine Inactivation Of Alanine Racemase
pdb|1XQK|B Chain B, Effect Of A Y265f Mutant On The Transamination Based
Cycloserine Inactivation Of Alanine Racemase
pdb|1XQL|A Chain A, Effect Of A Y265f Mutant On The Transamination Based
Cycloserine Inactivation Of Alanine Racemase
pdb|1XQL|B Chain B, Effect Of A Y265f Mutant On The Transamination Based
Cycloserine Inactivation Of Alanine Racemase
Length = 388
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 60 DSESVQREGENLQAVWSPDTKLIAVVTSSLYLHIFKVQITEKSIQIGGKQPSGLFFIKIS 119
D +++ ENL+ + DT ++AVV ++ Y H VQ+ +++ G + + F
Sbjct: 13 DLDAIYDNVENLRRLLPDDTHIMAVVKANAYGH-GDVQVARTALEAGASRLAVAF----- 66
Query: 120 LVLNEQLPFAEKGLSVSNIV 139
L+E L EKG+ +V
Sbjct: 67 --LDEALALREKGIEAPILV 84
>pdb|2SFP|A Chain A, Alanine Racemase With Bound Propionate Inhibitor
pdb|2SFP|B Chain B, Alanine Racemase With Bound Propionate Inhibitor
pdb|1L6F|A Chain A, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-L-
Alanine
pdb|1L6F|B Chain B, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-L-
Alanine
pdb|1L6G|A Chain A, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-D-
Alanine
pdb|1L6G|B Chain B, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-D-
Alanine
pdb|1NIU|A Chain A, Alanine Racemase With Bound Inhibitor Derived From L-
Cycloserine
pdb|1NIU|B Chain B, Alanine Racemase With Bound Inhibitor Derived From L-
Cycloserine
Length = 388
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 60 DSESVQREGENLQAVWSPDTKLIAVVTSSLYLHIFKVQITEKSIQIGGKQPSGLFFIKIS 119
D +++ ENL+ + DT ++AVV ++ Y H VQ+ +++ G + + F
Sbjct: 13 DLDAIYDNVENLRRLLPDDTHIMAVVKANAYGH-GDVQVARTALEAGASRLAVAF----- 66
Query: 120 LVLNEQLPFAEKGLSVSNIV 139
L+E L EKG+ +V
Sbjct: 67 --LDEALALREKGIEAPILV 84
>pdb|1EPV|A Chain A, Alanine Racemase With Bound Inhibitor Derived From D-
Cycloserine
pdb|1EPV|B Chain B, Alanine Racemase With Bound Inhibitor Derived From D-
Cycloserine
pdb|1FTX|A Chain A, Crystal Stucture Of Alanine Racemase In Complex With D-
Alanine Phosphonate
pdb|1FTX|B Chain B, Crystal Stucture Of Alanine Racemase In Complex With D-
Alanine Phosphonate
Length = 387
Score = 33.1 bits (74), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 60 DSESVQREGENLQAVWSPDTKLIAVVTSSLYLHIFKVQITEKSIQIGGKQPSGLFFIKIS 119
D +++ ENL+ + DT ++AVV ++ Y H VQ+ +++ G + + F
Sbjct: 12 DLDAIYDNVENLRRLLPDDTHIMAVVKANAYGH-GDVQVARTALEAGASRLAVAF----- 65
Query: 120 LVLNEQLPFAEKGLSVSNIV 139
L+E L EKG+ +V
Sbjct: 66 --LDEALALREKGIEAPILV 83
>pdb|1SFT|A Chain A, Alanine Racemase
pdb|1SFT|B Chain B, Alanine Racemase
pdb|1BD0|A Chain A, Alanine Racemase Complexed With Alanine Phosphonate
pdb|1BD0|B Chain B, Alanine Racemase Complexed With Alanine Phosphonate
Length = 388
Score = 33.1 bits (74), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 60 DSESVQREGENLQAVWSPDTKLIAVVTSSLYLHIFKVQITEKSIQIGGKQPSGLFFIKIS 119
D +++ ENL+ + DT ++AVV ++ Y H VQ+ +++ G + + F
Sbjct: 13 DLDAIYDNVENLRRLLPDDTHIMAVVKANAYGH-GDVQVARTALEAGASRLAVAF----- 66
Query: 120 LVLNEQLPFAEKGLSVSNIV 139
L+E L EKG+ +V
Sbjct: 67 --LDEALALREKGIEAPILV 84
>pdb|3GRE|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Vps15 Wd
Repeat Domain
Length = 437
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 51/100 (51%), Gaps = 14/100 (14%)
Query: 240 KGLKLAEFIKIDKELGSGDAVCASIAPEQQILAVGTRRGVVELYDLAESASLIRTVSLYD 299
+ L+ + I+ G+ ++C I E +L +GT RG+++++D+ + LIR+
Sbjct: 200 RTLERLQIIENSPRHGAVSSIC--IDEECCVLILGTTRGIIDIWDIRFNV-LIRS----- 251
Query: 300 WGYSMDDTGPVSCIA---WTPDNSAFAVGWKSRG-LTVWS 335
+S D P++ + + NS VG S+ LT+W+
Sbjct: 252 --WSFGDHAPITHVEVCQFYGKNSVIVVGGSSKTFLTIWN 289
>pdb|2WD0|A Chain A, Crystal Structure Of Nonsyndromic Deafness (Dfnb12)
Associated Mutant D124g Of Mouse Cadherin-23 Ec1-2
pdb|2WD0|C Chain C, Crystal Structure Of Nonsyndromic Deafness (Dfnb12)
Associated Mutant D124g Of Mouse Cadherin-23 Ec1-2
pdb|4AQA|A Chain A, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2d124g And Protocadherin-15 Ec1-2 Form I
Length = 214
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 11/69 (15%)
Query: 251 DKELGSGDAVCASIAPEQQILAVGTRRGVVEL-----YDLAESASLIRTVSLYDWGYSMD 305
D +LG+G +V S P A+ + RG+V + Y++ ++ L TV+ D D
Sbjct: 136 DPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQL--TVNATD----QD 189
Query: 306 DTGPVSCIA 314
T P+S +A
Sbjct: 190 KTRPLSTLA 198
>pdb|2WCP|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2
pdb|2WHV|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 (all Cation
Binding Sites Occupied By Calcium)
pdb|4APX|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form I
pdb|4AQ8|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AQ8|B Chain B, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2 Form Ii
pdb|4AXW|A Chain A, Crystal Structure Of Mouse Cadherin-23 Ec1-2 And
Protocadherin-15 Ec1-2, Form I 2.2a
Length = 214
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 11/69 (15%)
Query: 251 DKELGSGDAVCASIAPEQQILAVGTRRGVVEL-----YDLAESASLIRTVSLYDWGYSMD 305
D +LG+G +V S P A+ + RG+V + Y++ ++ L TV+ D D
Sbjct: 136 DPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQL--TVNATD----QD 189
Query: 306 DTGPVSCIA 314
T P+S +A
Sbjct: 190 KTRPLSTLA 198
>pdb|4AQE|A Chain A, Crystal Structure Of Deafness Associated Mutant Mouse
Cadherin-23 Ec1-2s70p And Protocadherin-15 Ec1-2 Form I
Length = 214
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 11/69 (15%)
Query: 251 DKELGSGDAVCASIAPEQQILAVGTRRGVVEL-----YDLAESASLIRTVSLYDWGYSMD 305
D +LG+G +V S P A+ + RG+V + Y++ ++ L TV+ D D
Sbjct: 136 DPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQL--TVNATD----QD 189
Query: 306 DTGPVSCIA 314
T P+S +A
Sbjct: 190 KTRPLSTLA 198
>pdb|3MVS|A Chain A, Structure Of The N-Terminus Of Cadherin 23
Length = 210
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 11/69 (15%)
Query: 251 DKELGSGDAVCASIAPEQQILAVGTRRGVVEL-----YDLAESASLIRTVSLYDWGYSMD 305
D +LG+G +V S P A+ + RG+V + Y++ ++ L TV+ D D
Sbjct: 135 DPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQL--TVNATD----QD 188
Query: 306 DTGPVSCIA 314
T P+S +A
Sbjct: 189 KTRPLSTLA 197
>pdb|1XMC|A Chain A, C323m Mutant Structure Of Mouse Carnitine
Octanoyltransferase
pdb|1XMC|B Chain B, C323m Mutant Structure Of Mouse Carnitine
Octanoyltransferase
Length = 612
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 354 SSPIVKPNQDCK-YEPLMSGTSMMQWDEYGYRLYAIEEGSSERVLIFSFGKCCLNRGVSG 412
SSP P + + +E L+ G ++W + Y L + G FG CC +
Sbjct: 281 SSPHATPEEYSQVFEMLLGGDPSVRWGDKSYNLISFANGI--------FGMCCDHAPYDA 332
Query: 413 MTYARQVIYGEDRLLVVQSEDTDELKILHLNLP 445
M Y ++R+L + K+ + LP
Sbjct: 333 MVMVNIAHYVDERVLETEGRWKGSEKVRDIPLP 365
>pdb|1XMD|A Chain A, M335v Mutant Structure Of Mouse Carnitine
Octanoyltransferase
pdb|1XMD|B Chain B, M335v Mutant Structure Of Mouse Carnitine
Octanoyltransferase
Length = 612
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 354 SSPIVKPNQDCK-YEPLMSGTSMMQWDEYGYRLYAIEEGSSERVLIFSFGKCCLNRGVSG 412
SSP P + + +E L+ G ++W + Y L + G FG CC +
Sbjct: 281 SSPHATPEEYSQVFEMLLGGDPSVRWGDKSYNLISFANG--------IFGCCCDHAPYDA 332
Query: 413 MTYARQVIYGEDRLLVVQSEDTDELKILHLNLP 445
M Y ++R+L + K+ + LP
Sbjct: 333 MVVVNIAHYVDERVLETEGRWKGSEKVRDIPLP 365
>pdb|3UW6|A Chain A, Crystal Structure Of Engineered Protein, Northeast
Structural Genomics Consortium Target Or120
pdb|3UW6|B Chain B, Crystal Structure Of Engineered Protein, Northeast
Structural Genomics Consortium Target Or120
pdb|3UW6|C Chain C, Crystal Structure Of Engineered Protein, Northeast
Structural Genomics Consortium Target Or120
Length = 390
Score = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 60 DSESVQREGENLQAVWSPDTKLIAVVTSSLYLHIFKVQITEKSIQIGGKQPSGLFFIKIS 119
D +++ ENL+ + DT + A V + Y H VQ+ +++ G + + F
Sbjct: 13 DLDAIYDNVENLRRLLPDDTHIXASVCGNAYGH-GDVQVARTALEAGASRLAVAF----- 66
Query: 120 LVLNEQLPFAEKGLSVSNIVS 140
L+E L EKG+ +V+
Sbjct: 67 --LDEALALREKGIEAPILVT 85
>pdb|1PGU|A Chain A, Yeast Actin Interacting Protein 1 (aip1), Se-met Protein,
Monoclinic Crystal Form
pdb|1PGU|B Chain B, Yeast Actin Interacting Protein 1 (aip1), Se-met Protein,
Monoclinic Crystal Form
Length = 615
Score = 28.9 bits (63), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 263 SIAPEQQILAVGTRRGVVELYDLAESASLIRTVSLYDWGYSMDDTGPVSCIAWTP 317
SI+P + +A G G + LYDL R V W + T ++ I+W P
Sbjct: 495 SISPSETYIAAGDVXGKILLYDLQS-----REVKTSRWAFR---TSKINAISWKP 541
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
0.320 0.135 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,891,067
Number of Sequences: 62578
Number of extensions: 784294
Number of successful extensions: 1584
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1569
Number of HSP's gapped (non-prelim): 40
length of query: 696
length of database: 14,973,337
effective HSP length: 106
effective length of query: 590
effective length of database: 8,340,069
effective search space: 4920640710
effective search space used: 4920640710
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)