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= 002814
(877 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 42/141 (29%), Positives = 69/141 (48%), Gaps = 22/141 (15%)
Query: 270 IDACGKGGVDFKHVVEIFDDMLRNGVQPDRITFNSLLAVCSRGGLWEAA-RNLFNEMVHR 328
+D C K G D + ++D+ RNGVQ + +N LL VCS L EAA + N + R
Sbjct: 33 LDMCSKKG-DVLEALRLYDEARRNGVQLSQYHYNVLLYVCS---LAEAATESSPNPGLSR 88
Query: 329 GIDQDIFTYNTLLDAIC-------KGAQM-------DLAFEIMAEMPAKNISPNVVTYST 374
G DIF ++D + GA++ ++AF+++ +M A I P + +Y
Sbjct: 89 GF--DIFK-QMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145
Query: 375 MIDGYAKAGRLDDALNMFSEM 395
+ G+ + G D A + + M
Sbjct: 146 ALFGFCRKGDADKAYEVDAHM 166
Score = 36.2 bits (82), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 30/132 (22%), Positives = 54/132 (40%), Gaps = 12/132 (9%)
Query: 239 GRSGYCQEAISVFNSMKRYNLKPNLVTYNAVIDACG--------KGGVDFKHVVEIFDDM 290
+ G EA+ +++ +R ++ + YN ++ C +IF M
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 291 LRNGVQPDRITFN--SLLAVCSRGGLWEAARNLFNEMVHRGIDQDIFTYNTLLDAICKGA 348
+ + V P+ TF + LAV E A ++ +M GI + +Y L C+
Sbjct: 97 IVDKVVPNEATFTNGARLAVAKDDP--EMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154
Query: 349 QMDLAFEIMAEM 360
D A+E+ A M
Sbjct: 155 DADKAYEVDAHM 166
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 22/137 (16%)
Query: 270 IDACGKGGVDFKHVVEIFDDMLRNGVQPDRITFNSLLAVCSRGGLWEAA-RNLFNEMVHR 328
+D C K G D + ++D+ RNGVQ + +N LL VCS L EAA + N + R
Sbjct: 33 LDXCSKKG-DVLEALRLYDEARRNGVQLSQYHYNVLLYVCS---LAEAATESSPNPGLSR 88
Query: 329 GIDQDIFTYNTLLDAI-------CKGAQM-------DLAFEIMAEMPAKNISPNVVTYST 374
G DIF ++D + GA++ + AF+ + + A I P + +Y
Sbjct: 89 GF--DIFK-QXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGP 145
Query: 375 MIDGYAKAGRLDDALNM 391
+ G+ + G D A +
Sbjct: 146 ALFGFCRKGDADKAYEV 162
>pdb|3NF1|A Chain A, Crystal Structure Of The Tpr Domain Of Kinesin Light Chain
1
Length = 311
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 47/179 (26%), Positives = 79/179 (44%), Gaps = 28/179 (15%)
Query: 344 ICKGAQMDLAFEIMAEMPAKNISPNVVTYSTMID-GYAKAGRLDDALNMFSE---MKFLG 399
+CK A DL E + + P+V T ++ Y + DA N+ ++ ++
Sbjct: 49 LCKQALEDL------EKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKT 102
Query: 400 IGLDR----VSYNTVLSIYAKLGRFEEALLVCK---EMESSGIRKD----AVTYNALLGG 448
+G D + N + +Y K G+++EA +CK E+ + KD A N L
Sbjct: 103 LGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALL 162
Query: 449 YGKQGKYDEVRRMFE------QMKADCVSPNLL-TYSTLIDVYSKGGLYKEAMQIFREF 500
QGKY+EV ++ Q K PN+ T + L Y K G +K+A +++E
Sbjct: 163 CQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEI 221
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 36.6 bits (83), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 53/121 (43%), Gaps = 2/121 (1%)
Query: 407 YNTVLSIYAKLGRFEEALLVCKEMESSGIRKDAVTYNALLGGYGKQGK-YDEVRRMFEQM 465
YN V+ +A+ G F+E + V ++ +G+ D ++Y A L G+Q + + R EQM
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 466 KADCVSPNLLTYSTLIDVYSKGGLYKEAMQIFREFK-QAGLKADVVLYSALIDALCKNGL 524
+ + L + L+ + + K ++ F L V L D K+G
Sbjct: 228 SQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGR 287
Query: 525 V 525
V
Sbjct: 288 V 288
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 34/159 (21%), Positives = 63/159 (39%), Gaps = 34/159 (21%)
Query: 227 TVYAFSALISAYGRSGYCQEAISVFNSMKRYNLKPNLVTYNAVIDACGKGGVDFKHVVEI 286
T+ ++A++ + R G +E + V +K L P+L++Y A + G+ D +
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC 223
Query: 287 FDDMLRNGVQPDRITFNSLLAVCSRGGLWEAARNLFNEMVHRGIDQDIFTYNTLLDAICK 346
+ M + G++ + LL+ R T+L A+ K
Sbjct: 224 LEQMSQEGLKLQALFTAVLLSEEDRA--------------------------TVLKAVHK 257
Query: 347 GAQMDLAFEIMAEMPAKNISPNVVTYSTMIDGYAKAGRL 385
+ F + ++P P V T + D YAK GR+
Sbjct: 258 ---VKPTFSLPPQLP-----PPVNTSKLLRDVYAKDGRV 288
>pdb|3IBD|A Chain A, Crystal Structure Of A Cytochrome P450 2b6 Genetic Variant
In Complex With The Inhibitor
4-(4-Chlorophenyl)imidazole
pdb|3QOA|A Chain A, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-Benzylpyridine.
pdb|3QU8|A Chain A, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-(4-Nitrobenzyl)pyridine.
pdb|3QU8|B Chain B, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-(4-Nitrobenzyl)pyridine.
pdb|3QU8|C Chain C, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-(4-Nitrobenzyl)pyridine.
pdb|3QU8|D Chain D, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-(4-Nitrobenzyl)pyridine.
pdb|3QU8|E Chain E, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-(4-Nitrobenzyl)pyridine.
pdb|3QU8|F Chain F, Crystal Structure Of A Human Cytochrome P450 2b6
(Y226hK262R) IN Complex With The Inhibitor
4-(4-Nitrobenzyl)pyridine.
pdb|3UA5|A Chain A, Crystal Structure Of P450 2b6 (Y226hK262R) IN COMPLEX WITH
TWO Molecules Of Amlodipine
pdb|3UA5|B Chain B, Crystal Structure Of P450 2b6 (Y226hK262R) IN COMPLEX WITH
TWO Molecules Of Amlodipine
Length = 476
Score = 32.7 bits (73), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 31/136 (22%), Positives = 54/136 (39%), Gaps = 33/136 (24%)
Query: 662 EDASMLLEELR-----------LFD----NQVYGVAHGLLMGYRDNIWVQALSLFDEVKL 706
E+A L+EELR LF N + + G Y+D +++ L+LF +
Sbjct: 129 EEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFS 188
Query: 707 MDSSTASAFYNALTDMLWHFGQKRGAQLVVLEGKRRQVWENVWSESCLDLH-------LM 759
+ SS + + L HF G RQV++N+ + H +
Sbjct: 189 LISSVFGQLFELFSGFLKHF-----------PGAHRQVYKNLQEINAYIGHSVEKHRETL 237
Query: 760 SSGAARAMVHAWLLNI 775
A R ++ +LL++
Sbjct: 238 DPSAPRDLIDTYLLHM 253
>pdb|1QH9|A Chain A, Enzyme-Product Complex Of L-2-Haloacid Dehalogenase
pdb|1JUD|A Chain A, L-2-haloacid Dehalogenase
Length = 232
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 31/117 (26%), Positives = 51/117 (43%), Gaps = 10/117 (8%)
Query: 399 GIGLDRVSYNTVLSIYAKLGRFEEALLVCKEMESSGIRKDAVTYN---ALLGGY--GKQG 453
GI D Y T+ +++ +GR +EA S+ R+ + Y +L+ Y +Q
Sbjct: 6 GIAFD--LYGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQA 63
Query: 454 KYDEVRRMFEQMKADCVSPNLLTYSTLIDVYSKGGLYKEAMQIFREFKQAGLKADVV 510
D +R + D + T STL D Y + + E RE K+ GLK ++
Sbjct: 64 TEDALRFTCRHLGLDL---DARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAIL 117
>pdb|1ZRM|A Chain A, Crystal Structure Of The Reaction Intermediate Of
L-2-Haloacid Dehalogenase With 2-Chloro-N-Butyrate
pdb|1ZRN|A Chain A, Intermediate Structure Of L-2-haloacid Dehalogenase With
Monochloroacetate
Length = 232
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 31/117 (26%), Positives = 51/117 (43%), Gaps = 10/117 (8%)
Query: 399 GIGLDRVSYNTVLSIYAKLGRFEEALLVCKEMESSGIRKDAVTYN---ALLGGY--GKQG 453
GI D Y T+ +++ +GR +EA S+ R+ + Y +L+ Y +Q
Sbjct: 6 GIAFD--LYGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQA 63
Query: 454 KYDEVRRMFEQMKADCVSPNLLTYSTLIDVYSKGGLYKEAMQIFREFKQAGLKADVV 510
D +R + D + T STL D Y + + E RE K+ GLK ++
Sbjct: 64 TEDALRFTCRHLGLDL---DARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAIL 117
>pdb|1E4F|T Chain T, Ftsa (Apo Form) From Thermotoga Maritima
pdb|4A2A|A Chain A, Thermotoga Maritima Ftsa:ftsz(336-351)
pdb|4A2A|B Chain B, Thermotoga Maritima Ftsa:ftsz(336-351)
pdb|4A2B|A Chain A, Thermotoga Maritima Ftsa With Atp Gamma S
Length = 419
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 46/85 (54%), Gaps = 12/85 (14%)
Query: 517 DALCKNGLVESAVSLLDEMTKEGIRPN-VVTYNSIIDAFGRSATTECTVDDVERDLGKQK 575
DA+ V + + L+E ++ +R + V++++S+ +F R T +ERD G++K
Sbjct: 52 DAIAFKESVNTLLKELEEQLQKSLRSDFVISFSSV--SFEREDTV------IERDFGEEK 103
Query: 576 ESANLD---AMCSQDDKDVQEAGRT 597
S LD M S+ + ++E G+T
Sbjct: 104 RSITLDILSEMQSEALEKLKENGKT 128
>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Trigonal Crystal Form)
pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Orthorombic Crystal Form)
Length = 136
Score = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 29/96 (30%), Positives = 44/96 (45%), Gaps = 8/96 (8%)
Query: 414 YAKLGRFEEALLVCKEMESSGIRKDAVTYNALLGGYGKQGKYDEVRRMFEQ-MKADCVSP 472
Y K G ++EA+ ++ R YN L Y KQG YDE +++ ++ D S
Sbjct: 11 YYKQGDYDEAIEYYQKALELDPRSAEAWYN-LGNAYYKQGDYDEAIEYYQKALELDPRSA 69
Query: 473 NLLTYSTLIDVYSKGGLYKEAMQIFREFKQAGLKAD 508
+ L + Y K G Y EA+ E+ Q L+ D
Sbjct: 70 E--AWYNLGNAYYKQGDYDEAI----EYYQKALELD 99
>pdb|1E4G|T Chain T, Ftsa (Atp-Bound Form) From Thermotoga Maritima
Length = 419
Score = 30.4 bits (67), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 12/85 (14%)
Query: 517 DALCKNGLVESAVSLLDEMTKEGIRPN-VVTYNSIIDAFGRSATTECTVDDVERDLGKQK 575
DA+ V + + L+E ++ +R + V++++S+ +F R T +ERD G++K
Sbjct: 52 DAIAFKESVNTLLKELEEQLQKSLRSDFVISFSSV--SFEREDTV------IERDFGEEK 103
Query: 576 ESANLDAMC---SQDDKDVQEAGRT 597
S LD + S+ + ++E G+T
Sbjct: 104 RSITLDILSEXQSEALEKLKENGKT 128
>pdb|1Z15|A Chain A, Crystal Structure Analysis Of Periplasmic
Leu/ile/val-binding Protein In Superopen Form
pdb|1Z16|A Chain A, Crystal Structure Analysis Of Periplasmic
Leu/ile/val-binding Protein With Bound Leucine
pdb|1Z17|A Chain A, Crystal Structure Analysis Of Periplasmic
LeuILEVAL-Binding Protein With Bound Ligand Isoleucine
pdb|1Z18|A Chain A, Crystal Structure Analysis Of Periplasmic
LeuILEVAL-Binding Protein With Bound Valine
Length = 344
Score = 29.3 bits (64), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 481 IDVYSKGGLYKEAMQIFREFKQAGLKADVVLYSALIDALCKNGLVESAVSLLDEMTKEGI 540
ID GG + E QI R+ + AGLK + + + N ESA LL +TK
Sbjct: 194 IDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLL--VTKPKN 251
Query: 541 RPNVVTYNSIIDAF 554
V I+DA
Sbjct: 252 YDQVPANKPIVDAI 265
>pdb|2LIV|A Chain A, Periplasmic Binding Protein Structure And Function.
Refined X-Ray Structures Of The
LeucineISOLEUCINEVALINE-Binding Protein And Its Complex
With Leucine
Length = 344
Score = 29.3 bits (64), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 481 IDVYSKGGLYKEAMQIFREFKQAGLKADVVLYSALIDALCKNGLVESAVSLLDEMTKEGI 540
ID GG + E QI R+ + AGLK + + + N ESA LL +TK
Sbjct: 194 IDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLL--VTKPKN 251
Query: 541 RPNVVTYNSIIDAF 554
V I+DA
Sbjct: 252 YDQVPANKPIVDAI 265
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 0.134 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,826,206
Number of Sequences: 62578
Number of extensions: 998043
Number of successful extensions: 2420
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 2389
Number of HSP's gapped (non-prelim): 43
length of query: 877
length of database: 14,973,337
effective HSP length: 107
effective length of query: 770
effective length of database: 8,277,491
effective search space: 6373668070
effective search space used: 6373668070
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: 56 (26.2 bits)