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= 007913
(585 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3L1L|A Chain A, Structure Of Arg-Bound Escherichia Coli Adic
Length = 445
Score = 55.8 bits (133), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 59/220 (26%), Positives = 93/220 (42%), Gaps = 14/220 (6%)
Query: 269 GTEGVFEAAA-VVYWSYTGFDMVATMAEETKKPSRDIPIGLVGSMCMITAVYCLMALALT 327
GT G ++ V WS+ G + + A K P R++PI +G + + Y L A+
Sbjct: 188 GTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIM 247
Query: 328 MMVKYTEIDMNAA-YSIAFRQIGMNWAKYLVSVCALKGMTTSLLVGSLGQARYTTQIARA 386
M+ + ++A+ + A R + A +VS CA G SL +L + A
Sbjct: 248 GMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADD 307
Query: 387 HMIPPWFALVHPKTQTPINATLLVTTLSAIIALFS-------SLNILSSVFSFSTLSIFM 439
+ PP FA V+ K TP+ ++V L I L S ++SSV TL ++
Sbjct: 308 GLFPPIFARVN-KAGTPVAGLIIVGILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYL 366
Query: 440 LMAIALLVRRYYEKDVTPKNNL----VKFLVCLTVVVASS 475
ALL+ + L + FL C+ VV S
Sbjct: 367 YTCAALLLLGHGHFGKARPAYLAVTTIAFLYCIWAVVGSG 406
>pdb|3LRB|A Chain A, Structure Of E. Coli Adic
pdb|3LRB|B Chain B, Structure Of E. Coli Adic
pdb|3LRC|A Chain A, Structure Of E. Coli Adic (P1)
pdb|3LRC|B Chain B, Structure Of E. Coli Adic (P1)
pdb|3LRC|C Chain C, Structure Of E. Coli Adic (P1)
pdb|3LRC|D Chain D, Structure Of E. Coli Adic (P1)
Length = 445
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 59/220 (26%), Positives = 93/220 (42%), Gaps = 14/220 (6%)
Query: 269 GTEGVFEAA-AVVYWSYTGFDMVATMAEETKKPSRDIPIGLVGSMCMITAVYCLMALALT 327
GT G ++ V WS+ G + + A K P R++PI +G + + Y L A+
Sbjct: 188 GTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIM 247
Query: 328 MMVKYTEIDMNAA-YSIAFRQIGMNWAKYLVSVCALKGMTTSLLVGSLGQARYTTQIARA 386
M+ + ++A+ + A R + A +VS CA G SL +L + A
Sbjct: 248 GMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADD 307
Query: 387 HMIPPWFALVHPKTQTPINATLLVTTLSAIIALFS-------SLNILSSVFSFSTLSIFM 439
+ PP FA V+ K TP+ ++V L I L S ++SSV TL ++
Sbjct: 308 GLFPPIFARVN-KAGTPVAGLIIVGILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYL 366
Query: 440 LMAIALLVRRYYEKDVTPKNNL----VKFLVCLTVVVASS 475
ALL+ + L + FL C+ VV S
Sbjct: 367 YTCAALLLLGHGHFGKARPAYLAVTTIAFLYCIWAVVGSG 406
>pdb|3OB6|A Chain A, Structure Of Adic(N101a) In The Open-To-Out Arg+ Bound
Conformation
pdb|3OB6|B Chain B, Structure Of Adic(N101a) In The Open-To-Out Arg+ Bound
Conformation
Length = 445
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 59/220 (26%), Positives = 93/220 (42%), Gaps = 14/220 (6%)
Query: 269 GTEGVFEAAA-VVYWSYTGFDMVATMAEETKKPSRDIPIGLVGSMCMITAVYCLMALALT 327
GT G ++ V WS+ G + + A K P R++PI +G + + Y L A+
Sbjct: 188 GTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIM 247
Query: 328 MMVKYTEIDMNAA-YSIAFRQIGMNWAKYLVSVCALKGMTTSLLVGSLGQARYTTQIARA 386
M+ + ++A+ + A R + A +VS CA G SL +L + A
Sbjct: 248 GMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADD 307
Query: 387 HMIPPWFALVHPKTQTPINATLLVTTLSAIIALFS-------SLNILSSVFSFSTLSIFM 439
+ PP FA V+ K TP+ ++V L I L S ++SSV TL ++
Sbjct: 308 GLFPPIFARVN-KAGTPVAGLIIVGILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYL 366
Query: 440 LMAIALLVRRYYEKDVTPKNNL----VKFLVCLTVVVASS 475
ALL+ + L + FL C+ VV S
Sbjct: 367 YTCAALLLLGHGHFGKARPAYLAVTTIAFLYCIWAVVGSG 406
>pdb|3NCY|A Chain A, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|B Chain B, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|C Chain C, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|D Chain D, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
Length = 445
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 56/210 (26%), Positives = 92/210 (43%), Gaps = 15/210 (7%)
Query: 279 VVYWSYTGFDMVATMAEETKKPSRDIPIGLVGSMCMITAVYCLMALALTMMVKYTEIDMN 338
V WS+ G + + A K P R++PI +G + + Y L A+ M+ + ++
Sbjct: 199 VTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVS 258
Query: 339 AA-YSIAFRQIGMNWAKYLVSVCALKGMTTSLLVGSLGQARYTTQIARAHMIPPWFALVH 397
A+ + A R + A +VS CA G SL +L + A + PP FA V+
Sbjct: 259 ASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVN 318
Query: 398 PKTQTPINATLLVTTLSAIIALFSSLN--------ILSSVFSFSTLSIFMLMAIALLVRR 449
K TP+ L+V L I FSS++ ++SSV TL ++ ALL+
Sbjct: 319 -KAGTPVAGLLIVGVLMTIFQ-FSSMSPNAAKEFGLVSSVSVIFTLVPYLYTCAALLLLG 376
Query: 450 YYE----KDVTPKNNLVKFLVCLTVVVASS 475
+ + + V F+ C+ V+ S
Sbjct: 377 HGHFGKARPLYLLITFVAFVYCIWAVIGSG 406
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 84/411 (20%), Positives = 161/411 (39%), Gaps = 59/411 (14%)
Query: 76 QKCLTWWDLTWLCFGSVVGSGIFVITGQEAKKHAGPAIVXXXXXXXXXXXXXXFCYTEFA 135
K L+ W+ + G ++G+ IF I G AK AG + + YT+
Sbjct: 5 NKKLSLWEAVSMAVGVMIGASIFSIFGVGAKI-AGRNLPETFILSGIYALLVAYSYTKLG 63
Query: 136 VEIPVAGGSFSFLRVELGDFVAYIAAGNIXXXXXXXXXXXXRSWSSYLASMIDSNNSDLL 195
+I G +F+ +GD NI W SY+ S
Sbjct: 64 AKIVSNAGPIAFIHKAIGD--------NIITGALSILL-----WMSYVIS---------- 100
Query: 196 RFKVDCFADGF------------NLLDPVAVLILLVCNGIAMS--GTRRSSWLNWXXXXX 241
+ FA GF N + I +V A++ G++ +
Sbjct: 101 ---IALFAKGFAGYFLPLINAPINTFNIAITEIGIVAFFTALNFFGSKAVGRAEFFIVLV 157
Query: 242 XXXXXXXXXXXGFVHGKTTNLDPFL-PYGTEGVFEAAAVVYWSYTGFDMVATMAEETKKP 300
G + + + P L P G+ A+A+ + SY GF ++ +E + P
Sbjct: 158 ALLILGLFIFAGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENP 217
Query: 301 SRDIPIGLVGSMCMITAVYCLMALA------LTMMVKYTEIDMNAAYSIAFRQIGMNWAK 354
+++P + S+ ++ VY +A++ + ++K +E A ++A + N
Sbjct: 218 KKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASE----NALAVAAKPFLGNLGF 273
Query: 355 YLVSVCALKGMTTSLLVGSLGQARYTTQIARAHMIPPWFALVHPKTQTPINATLLVTTLS 414
L+S+ AL +++++ G A +A+ +P +F K L +T S
Sbjct: 274 LLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF---ERKVWFKSTEGLYIT--S 328
Query: 415 AIIALFSSLNILSSVFSFSTLSIFMLMAIALLVRRYYEKD-VTPKNNLVKF 464
A+ LF+ L + V S ++ ++FM++ + +++ Y D V + +V F
Sbjct: 329 ALGVLFALLFNMEGVASITS-AVFMVIYLFVILSHYILIDEVGGRKEIVIF 378
>pdb|3GI9|C Chain C, Crystal Structure Of Apct Transporter Bound To 7f11
Monoclonal Fab Fragment
pdb|3GIA|A Chain A, Crystal Structure Of Apct Transporter
Length = 444
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 84/411 (20%), Positives = 161/411 (39%), Gaps = 59/411 (14%)
Query: 76 QKCLTWWDLTWLCFGSVVGSGIFVITGQEAKKHAGPAIVXXXXXXXXXXXXXXFCYTEFA 135
K L+ W+ + G ++G+ IF I G AK AG + + YT+
Sbjct: 5 NKKLSLWEAVSMAVGVMIGASIFSIFGVGAKI-AGRNLPETFILSGIYALLVAYSYTKLG 63
Query: 136 VEIPVAGGSFSFLRVELGDFVAYIAAGNIXXXXXXXXXXXXRSWSSYLASMIDSNNSDLL 195
+I G +F+ +GD NI W SY+ S
Sbjct: 64 AKIVSNAGPIAFIHKAIGD--------NIITGALSILL-----WMSYVIS---------- 100
Query: 196 RFKVDCFADGF------------NLLDPVAVLILLVCNGIAMS--GTRRSSWLNWXXXXX 241
+ FA GF N + I +V A++ G++ +
Sbjct: 101 ---IALFAKGFAGYFLPLINAPINTFNIAITEIGIVAFFTALNFFGSKAVGRAEFFIVLV 157
Query: 242 XXXXXXXXXXXGFVHGKTTNLDPFL-PYGTEGVFEAAAVVYWSYTGFDMVATMAEETKKP 300
G + + + P L P G+ A+A+ + SY GF ++ +E + P
Sbjct: 158 KLLILGLFIFAGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENP 217
Query: 301 SRDIPIGLVGSMCMITAVYCLMALA------LTMMVKYTEIDMNAAYSIAFRQIGMNWAK 354
+++P + S+ ++ VY +A++ + ++K +E A ++A + N
Sbjct: 218 KKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASE----NALAVAAKPFLGNLGF 273
Query: 355 YLVSVCALKGMTTSLLVGSLGQARYTTQIARAHMIPPWFALVHPKTQTPINATLLVTTLS 414
L+S+ AL +++++ G A +A+ +P +F K L +T S
Sbjct: 274 LLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF---ERKVWFKSTEGLYIT--S 328
Query: 415 AIIALFSSLNILSSVFSFSTLSIFMLMAIALLVRRYYEKD-VTPKNNLVKF 464
A+ LF+ L + V S ++ ++FM++ + +++ Y D V + +V F
Sbjct: 329 ALGVLFALLFNMEGVASITS-AVFMVIYLFVILSHYILIDEVGGRKEIVIF 378
>pdb|4DJI|A Chain A, Structure Of Glutamate-Gaba Antiporter Gadc
pdb|4DJI|B Chain B, Structure Of Glutamate-Gaba Antiporter Gadc
pdb|4DJK|A Chain A, Structure Of Glutamate-Gaba Antiporter Gadc
pdb|4DJK|B Chain B, Structure Of Glutamate-Gaba Antiporter Gadc
Length = 511
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/144 (22%), Positives = 69/144 (47%), Gaps = 10/144 (6%)
Query: 283 SYTGFDMVATMAEETKKPSRDIPIGLVGSMCMITAVYCLMALALTMMVKYTEIDMNAA-- 340
SY G + AT E P RD P+ ++ M + + L++ M++ EI+++A
Sbjct: 213 SYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVM 272
Query: 341 --YSIAFRQIG--MNWAKYLVSVCALKGMTTSLLVGSLGQARYTTQIARAHMIPPWFALV 396
+++ + + W ++S L G+ + +G +R A+ +++P FA +
Sbjct: 273 QTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKM 332
Query: 397 HPKTQTPIN---ATLLVTTLSAII 417
+ K P+ + L++T+++ II
Sbjct: 333 N-KNGVPVTLVISQLVITSIALII 355
>pdb|3SYL|A Chain A, Crystal Structure Of The Aaa+ Protein Cbbx, Native
Structure
pdb|3SYL|B Chain B, Crystal Structure Of The Aaa+ Protein Cbbx, Native
Structure
Length = 309
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 30 EPSFENTTSYKSALKQTYPRLKNRLFSRST---DATELITLQQES 71
+P F N S ++AL + R NRLF+ S+ DA L T+ +E
Sbjct: 242 QPHFANARSIRNALDRARLRQANRLFTASSGPLDARALSTIAEED 286
>pdb|3ZUH|A Chain A, Negative Stain Em Map Of The Aaa Protein Cbbx, A Red-Type
Rubisco Activase From R. Sphaeroides
pdb|3ZUH|B Chain B, Negative Stain Em Map Of The Aaa Protein Cbbx, A Red-Type
Rubisco Activase From R. Sphaeroides
pdb|3ZUH|C Chain C, Negative Stain Em Map Of The Aaa Protein Cbbx, A Red-Type
Rubisco Activase From R. Sphaeroides
pdb|3ZUH|D Chain D, Negative Stain Em Map Of The Aaa Protein Cbbx, A Red-Type
Rubisco Activase From R. Sphaeroides
pdb|3ZUH|E Chain E, Negative Stain Em Map Of The Aaa Protein Cbbx, A Red-Type
Rubisco Activase From R. Sphaeroides
pdb|3ZUH|F Chain F, Negative Stain Em Map Of The Aaa Protein Cbbx, A Red-Type
Rubisco Activase From R. Sphaeroides
Length = 289
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 30 EPSFENTTSYKSALKQTYPRLKNRLFSRST---DATELITLQQES 71
+P F N S ++AL + R NRLF+ S+ DA L T+ +E
Sbjct: 235 QPHFANARSIRNALDRARLRQANRLFTASSGPLDARALSTIAEED 279
>pdb|3SYK|A Chain A, Crystal Structure Of The Aaa+ Protein Cbbx,
Selenomethionine Structure
pdb|3SYK|B Chain B, Crystal Structure Of The Aaa+ Protein Cbbx,
Selenomethionine Structure
Length = 309
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 30 EPSFENTTSYKSALKQTYPRLKNRLFSRST---DATELITLQQES 71
+P F N S ++AL + R NRLF+ S+ DA L T+ +E
Sbjct: 242 QPHFANARSIRNALDRARLRQANRLFTASSGPLDARALSTIAEED 286
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
0.324 0.136 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,358,176
Number of Sequences: 62578
Number of extensions: 559665
Number of successful extensions: 1187
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1169
Number of HSP's gapped (non-prelim): 26
length of query: 585
length of database: 14,973,337
effective HSP length: 104
effective length of query: 481
effective length of database: 8,465,225
effective search space: 4071773225
effective search space used: 4071773225
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: 54 (25.4 bits)