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= 038994
(471 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 = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 63/282 (22%), Positives = 108/282 (38%), Gaps = 7/282 (2%)
Query: 83 ALITAELSTAFPGDGGFVIWADRAFGPFFGSLMGSWKFLSGVINIAAFPVLCIDYLKKVI 142
+++ A++S P GG +A R FGPF G +L+ I A V+ + YL
Sbjct: 57 SMVYAKMSFLDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF 116
Query: 143 HPLESGWPRSLAIMVSTCILSFLNFTGLTIVGYAAVLLGLVSLSPFIIMSLAA----IPK 198
L+ W ++ +V I LN G ++ + +++L P + +++ +
Sbjct: 117 PILKDPWVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGE 176
Query: 199 IKPHRWFSSGQKGLKKDXXXXXXXXXXXXXXXDNVSTLAGEVDRPQKTFPVALLVAVIFT 258
W SG G ++ S AG V P++ P+A + V+
Sbjct: 177 TYMAAWNVSGL-GTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIA 235
Query: 259 CVAYLIPLFAVIGAVNVDQSQWDSGFHATAAEMIAGKWLKIWLEVGAVLSAIGLFEAQLS 318
V Y++ A++G + + + AA M G + A +G
Sbjct: 236 AVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTL 295
Query: 319 SSAYQILGMADLGFLPKFFGLRSKKFNTPWVG-ILVSTLITL 359
+ AD G P F R K TP G I+V L+T+
Sbjct: 296 LAGQTAKAAADDGLFPPIFA-RVNKAGTPVAGLIIVGILMTI 336
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 69/307 (22%), Positives = 119/307 (38%), Gaps = 19/307 (6%)
Query: 57 PAVKAAGPLYALLGFMIFPFIWSIPEALITAELSTAFPGDGGFVIWADRAFGPFFGSLMG 116
PA AA A+ G+++ I ++ +++ A++S+ P GG +A R FGPF G
Sbjct: 32 PANLAATGGIAIYGWLV-TIIGALALSMVYAKMSSLDPSPGGSYAYARRCFGPFLGYQTN 90
Query: 117 SWKFLSGVINIAAFPVLCIDYLKKVIHPLESGWPRSLAIMVSTCILSFLNFTGLTIVGYA 176
+L+ I A V+ + YL L+ +L + I LN G ++
Sbjct: 91 VLYWLACWIGNIAMVVIGVGYLSYFFPILKDPLVLTLTCVAVLWIFVLLNIVGPKMITRV 150
Query: 177 AVLLGLVSLSPFIIMSLAAIPKIKPHR----WFSSGQKGLKKDXXXXXXXXXXXXXXXDN 232
+ +++L P + +++ K W SG ++
Sbjct: 151 QAVATVLALVPIVGIAVFGWFWFKGETYMAAWNVSGMNTFGA-IQSTLNVTLWSFIGVES 209
Query: 233 VSTLAGEVDRPQKTFPVALLVAVIFTCVAYLIPLFAVIGAVNVDQSQWDSGFHATAAEMI 292
S AG V P++ P+A + V+ V Y++ A++G + + + AA M
Sbjct: 210 ASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLSTTAIMGMIPNAALRVSASPFGDAARMA 269
Query: 293 AGKWLKIWLEVGAVLSAIG------LFEAQLSSSAYQILGMADLGFLPKFFGLRSKKFNT 346
G + A +G L Q + +A AD G P F R K T
Sbjct: 270 LGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAA------ADDGLFPPIFA-RVNKAGT 322
Query: 347 PWVGILV 353
P G+L+
Sbjct: 323 PVAGLLI 329
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 62/282 (21%), Positives = 107/282 (37%), Gaps = 7/282 (2%)
Query: 83 ALITAELSTAFPGDGGFVIWADRAFGPFFGSLMGSWKFLSGVINIAAFPVLCIDYLKKVI 142
+++ A++S P GG +A R FGPF G +L+ I A V+ + YL
Sbjct: 57 SMVYAKMSFLDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGAIAMVVIGVGYLSYFF 116
Query: 143 HPLESGWPRSLAIMVSTCILSFLNFTGLTIVGYAAVLLGLVSLSPFIIMSLAA----IPK 198
L+ ++ +V I LN G ++ + +++L P + +++ +
Sbjct: 117 PILKDPLVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGE 176
Query: 199 IKPHRWFSSGQKGLKKDXXXXXXXXXXXXXXXDNVSTLAGEVDRPQKTFPVALLVAVIFT 258
W SG G ++ S AG V P++ P+A + V+
Sbjct: 177 TYMAAWNVSGL-GTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIA 235
Query: 259 CVAYLIPLFAVIGAVNVDQSQWDSGFHATAAEMIAGKWLKIWLEVGAVLSAIGLFEAQLS 318
V Y++ A++G + + + AA M G + A +G
Sbjct: 236 AVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTL 295
Query: 319 SSAYQILGMADLGFLPKFFGLRSKKFNTPWVG-ILVSTLITL 359
+ AD G P F R K TP G I+V L+T+
Sbjct: 296 LAGQTAKAAADDGLFPPIFA-RVNKAGTPVAGLIIVGILMTI 336
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 62/282 (21%), Positives = 107/282 (37%), Gaps = 7/282 (2%)
Query: 83 ALITAELSTAFPGDGGFVIWADRAFGPFFGSLMGSWKFLSGVINIAAFPVLCIDYLKKVI 142
+++ A++S P GG +A R FGPF G +L+ I A V+ + YL
Sbjct: 57 SMVYAKMSFLDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF 116
Query: 143 HPLESGWPRSLAIMVSTCILSFLNFTGLTIVGYAAVLLGLVSLSPFIIMSLAA----IPK 198
L+ ++ +V I LN G ++ + +++L P + +++ +
Sbjct: 117 PILKDPLVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGE 176
Query: 199 IKPHRWFSSGQKGLKKDXXXXXXXXXXXXXXXDNVSTLAGEVDRPQKTFPVALLVAVIFT 258
W SG G ++ S AG V P++ P+A + V+
Sbjct: 177 TYMAAWNVSGL-GTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIA 235
Query: 259 CVAYLIPLFAVIGAVNVDQSQWDSGFHATAAEMIAGKWLKIWLEVGAVLSAIGLFEAQLS 318
V Y++ A++G + + + AA M G + A +G
Sbjct: 236 AVCYVLSTTAIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTL 295
Query: 319 SSAYQILGMADLGFLPKFFGLRSKKFNTPWVG-ILVSTLITL 359
+ AD G P F R K TP G I+V L+T+
Sbjct: 296 LAGQTAKAAADDGLFPPIFA-RVNKAGTPVAGLIIVGILMTI 336
>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 = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 85/385 (22%), Positives = 151/385 (39%), Gaps = 54/385 (14%)
Query: 64 PLYALLGFMIFPFI------WSIPEALITAELSTAFP-GDGGFVIWADRAFGPFFGSLMG 116
P +A GF + F+ W IP L AE++T +GG W GP +G
Sbjct: 33 PTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAI 92
Query: 117 SWKFLS---GVINIAAFPVLCIDYLKKVIHPLESGWPRSLAIMVSTCILSFLNFTG---- 169
S+ +L G I + F + + Y+ K E +++A ++ L+ F G
Sbjct: 93 SFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYT 152
Query: 170 --LTIVGYAAVLLGLVSLSPFIIMSLAAI---------PKIKPHRWFSSGQKGLKKDXXX 218
+ VG+ A +L L FI+++LAAI ++ +F K
Sbjct: 153 ARIAKVGFFAGIL----LPAFILIALAAIYLHSGAPVAIEMDSKTFFPDFS---KVGTLV 205
Query: 219 XXXXXXXXXXXXDNVSTLAGEVDRPQKTFPVALLVAVIFTCVAYLIPLFAVIGAVNVDQS 278
+ +T E+ P + +P+A+L+ ++ + ++ + ++
Sbjct: 206 VFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEI 265
Query: 279 QWDSGFHATAAEMIAGKWLKIWLEVGAVLSAIGLFEAQLSSSAYQILG-------MADLG 331
+G T +++ +I V V+SA+ L L+ A I+G A
Sbjct: 266 NLSAGVMQTFTVLMSHVAPEIEWTV-RVISAL-LLLGVLAEIASWIVGPSRGMYVTAQKN 323
Query: 332 FLPKFFGLRSKKFNTPWVGILVSTLI-----------TLGVSYMDFESIVASANFLYSLG 380
LP F +K N V +++S L+ T G + M F +A +Y
Sbjct: 324 LLPAAFAKMNK--NGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCA 381
Query: 381 MLLEFAAFIWLRMKKPQLKRPYRVP 405
+ F +I L +K P LKR + +P
Sbjct: 382 YFMLFIGYIVLVLKHPDLKRTFNIP 406
>pdb|3GI8|C Chain C, Crystal Structure Of Apct K158a Transporter Bound To 7f11
Monoclonal Fab Fragment
Length = 444
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 1/106 (0%)
Query: 233 VSTLAGEVDRPQKTFPVALLVAVIFTCVAYLIPLFAVIGAVNVDQ-SQWDSGFHATAAEM 291
++ + ++ P+K P A+ ++++ Y+ + IG + +D+ + A AA+
Sbjct: 207 ITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKP 266
Query: 292 IAGKWLKIWLEVGAVLSAIGLFEAQLSSSAYQILGMADLGFLPKFF 337
G + + +GA+ S A + A +A G LP+FF
Sbjct: 267 FLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF 312
>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 = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 1/106 (0%)
Query: 233 VSTLAGEVDRPQKTFPVALLVAVIFTCVAYLIPLFAVIGAVNVDQ-SQWDSGFHATAAEM 291
++ + ++ P+K P A+ ++++ Y+ + IG + +D+ + A AA+
Sbjct: 207 ITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKP 266
Query: 292 IAGKWLKIWLEVGAVLSAIGLFEAQLSSSAYQILGMADLGFLPKFF 337
G + + +GA+ S A + A +A G LP+FF
Sbjct: 267 FLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFF 312
>pdb|4HKQ|A Chain A, Protein Dna Complex
Length = 681
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 135 IDYLKKVIHPLESGWPRSLAIMVSTCILSFLNFTGLTIVGYAAVLLGLVSLSPFIIMSLA 194
+ YL K + P+ +GWP L ++ + +L+ G +G LV L+P + +L
Sbjct: 402 VAYLSKKLDPVAAGWPPCLRMVAAIAVLT--KDAGKLTMGQP-----LVILAPHAVEALV 454
Query: 195 AIPKIKPHRWFSSGQ 209
P P RW S+ +
Sbjct: 455 KQP---PDRWLSNAR 466
>pdb|1RW3|A Chain A, The Crystal Structure Of The Monomeric Reverse
Transcriptase From Moloney Murine Leukemia Virus
Length = 455
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 135 IDYLKKVIHPLESGWPRSLAIMVSTCILSFLNFTGLTIVGYAAVLLGLVSLSPFIIMSLA 194
+ YL K + P+ +GWP L ++ + +L+ G +G LV +P + +L
Sbjct: 373 VAYLSKKLDPVAAGWPPCLRMVAAIAVLT--KDAGKLTMGQP-----LVIKAPHAVEALV 425
Query: 195 AIPKIKPHRWFSSGQ 209
P P RW S+ +
Sbjct: 426 KQP---PDRWLSNAR 437
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
0.327 0.142 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,284,023
Number of Sequences: 62578
Number of extensions: 472250
Number of successful extensions: 1020
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1003
Number of HSP's gapped (non-prelim): 20
length of query: 471
length of database: 14,973,337
effective HSP length: 102
effective length of query: 369
effective length of database: 8,590,381
effective search space: 3169850589
effective search space used: 3169850589
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)