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= psy4738
(1188 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O7P|A Chain A, Crystal Structure Of The E.Coli Fucose:proton Symporter,
Fucp (N162a)
Length = 438
Score = 39.3 bits (90), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 46/105 (43%), Gaps = 3/105 (2%)
Query: 564 LLPEESQQYEFDWDETTQGLILGSFYWGYVIMHIPGGLLAQKFGGKHTLGFGILSTAIFT 623
LLP+ Q F GLI +FY+GY I+ IP G+L +K K + G+ A+
Sbjct: 48 LLPQFQQ--AFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGA 105
Query: 624 ILT-PMAAYMGPVWLIVWRFFEGLGEGTTFPAANQLLAAWIPKTE 667
L P A M +V F G G AAN + P++
Sbjct: 106 ALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPESS 150
Score = 34.7 bits (78), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%)
Query: 66 DNEFDWDEKTQGLILSAFYWGYVIMHIPGGLLAQKFGGK 104
F GLI SAFY+GY I+ IP G+L +K K
Sbjct: 53 QQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYK 91
>pdb|3O7Q|A Chain A, Crystal Structure Of A Major Facilitator Superfamily (Mfs)
Transporter, Fucp, In The Outward Conformation
Length = 438
Score = 39.3 bits (90), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 46/105 (43%), Gaps = 3/105 (2%)
Query: 564 LLPEESQQYEFDWDETTQGLILGSFYWGYVIMHIPGGLLAQKFGGKHTLGFGILSTAIFT 623
LLP+ Q F GLI +FY+GY I+ IP G+L +K K + G+ A+
Sbjct: 48 LLPQFQQ--AFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGA 105
Query: 624 ILT-PMAAYMGPVWLIVWRFFEGLGEGTTFPAANQLLAAWIPKTE 667
L P A M +V F G G AAN + P++
Sbjct: 106 ALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPESS 150
Score = 34.7 bits (78), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%)
Query: 66 DNEFDWDEKTQGLILSAFYWGYVIMHIPGGLLAQKFGGK 104
F GLI SAFY+GY I+ IP G+L +K K
Sbjct: 53 QQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYK 91
>pdb|1F3D|H Chain H, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten.
pdb|1F3D|K Chain K, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten
Length = 217
Score = 33.9 bits (76), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 66 DNEFDWDEKTQGLILSAFYWGYVIMHIPGGLLAQKFGGKHTLGFGILSTAIFTLLTPFAA 125
D W +++ G L + GY++ + G QKF GK TL S+ F L
Sbjct: 31 DYNIHWVKQSHGKSLE--WIGYIVPYSGGTTFNQKFKGKATLTVDKSSSTAFMHLNSLTF 88
Query: 126 RQSANWLIALRFFEGL--GEGTTFPALNTLLAQWVPPT 161
SA + A ++G+ G+GTT L A+ PP+
Sbjct: 89 EDSAVYYCA-NDYDGVYWGQGTT---LTVSSAKTTPPS 122
>pdb|3K6U|A Chain A, M. Acetivorans Molybdate-binding Protein (moda) In
Unliganded Open Form
pdb|3K6V|A Chain A, M. Acetivorans Molybdate-Binding Protein (Moda) In
Citrate-Bound Open Form
pdb|3K6W|A Chain A, Apo And Ligand Bound Structures Of Moda From The Archaeon
Methanosarcina Acetivorans
pdb|3K6X|A Chain A, M. Acetivorans Molybdate-Binding Protein (Moda) In
Molybdate-Bound Close Form With 2 Molecules In
Asymmetric Unit Forming Beta Barrel
pdb|3K6X|B Chain B, M. Acetivorans Molybdate-Binding Protein (Moda) In
Molybdate-Bound Close Form With 2 Molecules In
Asymmetric Unit Forming Beta Barrel
Length = 354
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 7/58 (12%)
Query: 353 GFFY----PSLKVNALDLSPNYAGTLMAIVNGIGAISGIISPYLIGILVPNNGVLSSL 406
GF Y P++ +++L+ + NY+ + +VNG ++G SP + G+ +PNN S L
Sbjct: 255 GFEYVALPPAIDLSSLEYADNYSKVQVEMVNG-EVVTG--SPIVYGVTIPNNAENSEL 309
>pdb|3CFX|A Chain A, Crystal Structure Of M. Acetivorans Periplasmic Binding
Protein Moda/wtpa With Bound Tungstate
pdb|3CFX|B Chain B, Crystal Structure Of M. Acetivorans Periplasmic Binding
Protein Moda/wtpa With Bound Tungstate
Length = 296
Score = 32.0 bits (71), Expect = 2.0, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 7/58 (12%)
Query: 353 GFFY----PSLKVNALDLSPNYAGTLMAIVNGIGAISGIISPYLIGILVPNNGVLSSL 406
GF Y P++ +++L+ + NY+ + +VNG ++G SP + G+ +PNN S L
Sbjct: 217 GFEYVALPPAIDLSSLEYADNYSKVQVEMVNG-EVVTG--SPIVYGVTIPNNAENSEL 271
>pdb|1UWG|H Chain H, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
pdb|1UWG|Y Chain Y, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
Length = 225
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 71 WDEKTQGLILSAFYWGYVIMHIPGGLLAQKFGGKHTLGFGILSTAIFTLLTPFAARQSAN 130
W +++ G L + G + H G + QKF GK TL S+ F L + SA
Sbjct: 36 WVKQSHGKNLE--WIGGIDPHNGGPVYNQKFNGKATLTVDKSSSTAFMHLNSLTSEDSAV 93
Query: 131 WLIAL---RFFEGLGEGTT 146
+ A+ FF+ G GTT
Sbjct: 94 YYCAIFYGNFFDYWGPGTT 112
>pdb|3G5U|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G5U|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
Length = 1284
Score = 31.2 bits (69), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 47/191 (24%), Positives = 80/191 (41%), Gaps = 26/191 (13%)
Query: 150 LNTLLAQWVPPTERGKIGSFVFAGNQIGTVF---SSFLSGFLLKYTDGDWPEIFYLFGIL 206
LNT L V G G++IG F ++F GF++ +T G W + I
Sbjct: 167 LNTRLTDDVSKINEG-------IGDKIGMFFQAMATFFGGFIIGFTRG-WKLTLVILAIS 218
Query: 207 GVLWFVA--WCFL--CYNDPASHPYISQREKEYLADTIGCLARNKI---GHDWGLFMISA 259
VL A W + + D H Y + +A+ + R I G L +
Sbjct: 219 PVLGLSAGIWAKILSSFTDKELHAYA---KAGAVAEEVLAAIRTVIAFGGQKKELERYNN 275
Query: 260 DLPKYMKSVMKFSIAKNGVLSSLPFLLMWLTAIVAGWFSDYLVSKDIFSVTVIRKIFTTI 319
+L + + +K +I N + + FLL++ + +A W+ LV +S+ + +F ++
Sbjct: 276 NLEEAKRLGIKKAITANISMGA-AFLLIYASYALAFWYGTSLVISKEYSIGQVLTVFFSV 334
Query: 320 A----SVGPAS 326
SVG AS
Sbjct: 335 LIGAFSVGQAS 345
>pdb|3G60|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G60|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G61|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G61|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
Length = 1284
Score = 31.2 bits (69), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 47/191 (24%), Positives = 80/191 (41%), Gaps = 26/191 (13%)
Query: 150 LNTLLAQWVPPTERGKIGSFVFAGNQIGTVF---SSFLSGFLLKYTDGDWPEIFYLFGIL 206
LNT L V G G++IG F ++F GF++ +T G W + I
Sbjct: 167 LNTRLTDDVSKINEG-------IGDKIGMFFQAMATFFGGFIIGFTRG-WKLTLVILAIS 218
Query: 207 GVLWFVA--WCFL--CYNDPASHPYISQREKEYLADTIGCLARNKI---GHDWGLFMISA 259
VL A W + + D H Y + +A+ + R I G L +
Sbjct: 219 PVLGLSAGIWAKILSSFTDKELHAYA---KAGAVAEEVLAAIRTVIAFGGQKKELERYNN 275
Query: 260 DLPKYMKSVMKFSIAKNGVLSSLPFLLMWLTAIVAGWFSDYLVSKDIFSVTVIRKIFTTI 319
+L + + +K +I N + + FLL++ + +A W+ LV +S+ + +F ++
Sbjct: 276 NLEEAKRLGIKKAITANISMGA-AFLLIYASYALAFWYGTSLVISKEYSIGQVLTVFFSV 334
Query: 320 A----SVGPAS 326
SVG AS
Sbjct: 335 LIGAFSVGQAS 345
>pdb|1B6R|A Chain A, N5-Carboxyaminoimidazole Ribonucleotide Synthetase From E.
Coli
pdb|3ETH|A Chain A, Crystal Structure Of E. Coli Purk In Complex With Mgatp
pdb|3ETH|B Chain B, Crystal Structure Of E. Coli Purk In Complex With Mgatp
pdb|3ETJ|A Chain A, Crystal Structure E. Coli Purk In Complex With Mg, Adp,
And Pi
pdb|3ETJ|B Chain B, Crystal Structure E. Coli Purk In Complex With Mg, Adp,
And Pi
Length = 355
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 23/105 (21%)
Query: 714 LWFVVWLFIGYSEPGSNPF---ISQKEMDYLEETIGSLTRRKYVLRKHADKYNRFQDLPP 770
L VW +EP + PF + E++ ET +LTR+ L +H NR
Sbjct: 23 LGIAVWPVGLDAEPAAVPFQQSVITAEIERWPET--ALTRQ---LARHPAFVNR------ 71
Query: 771 TPWKEMATSWPVIALVITQVVLISLFYLPPTPWKEMA--TSWPVI 813
+P+IA +TQ L +LP PW+ +A + WP +
Sbjct: 72 -------DVFPIIADRLTQKQLFDKLHLPTAPWQLLAERSEWPAV 109
>pdb|1B6S|A Chain A, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
pdb|1B6S|B Chain B, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
pdb|1B6S|C Chain C, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
pdb|1B6S|D Chain D, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
Length = 355
Score = 30.4 bits (67), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 45/105 (42%), Gaps = 23/105 (21%)
Query: 714 LWFVVWLFIGYSEPGSNPF---ISQKEMDYLEETIGSLTRRKYVLRKHADKYNRFQDLPP 770
L VW +EP + PF + E++ ET +LTR L +H NR
Sbjct: 23 LGIAVWPVGLDAEPAAVPFQQSVITAEIERWPET--ALTRE---LARHPAFVNR------ 71
Query: 771 TPWKEMATSWPVIALVITQVVLISLFYLPPTPWKEMA--TSWPVI 813
+P+IA +TQ L +LP PW+ +A + WP +
Sbjct: 72 -------DVFPIIADRLTQKQLFDKLHLPTAPWQLLAERSEWPAV 109
>pdb|1UWE|H Chain H, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
pdb|1UWE|V Chain V, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
pdb|1UWE|Y Chain Y, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
Length = 218
Score = 30.4 bits (67), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 71 WDEKTQGLILSAFYWGYVIMHIPGGLLAQKFGGKHTLGFGILSTAIFTLLTPFAARQSAN 130
W +++ G L + G + H GG QKF K TL S+ + L + SA
Sbjct: 34 WVKQSHGDSLE--WIGGIDPHNGGGAYNQKFRVKATLTVDTSSSTAYIHLNSLTSEDSAV 91
Query: 131 WLIAL---RFFEGLGEGTT 146
+ A+ FF+ G+GTT
Sbjct: 92 YYCAIFYGNFFDYWGQGTT 110
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
0.326 0.141 0.454
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,065,492
Number of Sequences: 62578
Number of extensions: 1471404
Number of successful extensions: 3536
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 3524
Number of HSP's gapped (non-prelim): 29
length of query: 1188
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1078
effective length of database: 8,089,757
effective search space: 8720758046
effective search space used: 8720758046
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (26.6 bits)