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= 004976
(721 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 = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 50/122 (40%), Gaps = 9/122 (7%)
Query: 149 RKGEVNKAIELFGEIKSNGVSPDNCSYNTI--VNGLCKAKR-------FKEALDILPDME 199
+KG+V +A+ L+ E + NGV YN + V L +A DI M
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 200 AVGCCPNLITYSTLMDGLCKDGRVDEAMGLLEEMKAKGLDADVVVYSALISGFCSNGSFD 259
PN T++ + A ++++MKA G+ + Y + GFC G D
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 260 KG 261
K
Sbjct: 158 KA 159
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 67/161 (41%), Gaps = 18/161 (11%)
Query: 4 KAAFNPCRSFPERILRLPVKCFSSVPQSDVETQLRLLFEKPN-----SQYAEAVSLFQRA 58
KA + PE +L+ + S + DV LRL E SQY V L+
Sbjct: 15 KAKKKAIQQSPEALLKQKLDMCSK--KGDVLEALRLYDEARRNGVQLSQYHYNVLLY--- 69
Query: 59 ICSDRLPSGSVCNSLMEALVRSKNYEYAFSVYSKMTCVHIFPSFLSLSGLIEVFVQTQKP 118
+CS L + +S L R F ++ +M + P+ + + + V P
Sbjct: 70 VCS--LAEAATESSPNPGLSR------GFDIFKQMIVDKVVPNEATFTNGARLAVAKDDP 121
Query: 119 KFALGVIGLILKRGFVVNIYAFNLILKGFCRKGEVNKAIEL 159
+ A ++ + G + ++ L GFCRKG+ +KA E+
Sbjct: 122 EMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 36/166 (21%), Positives = 59/166 (35%), Gaps = 46/166 (27%)
Query: 214 MDGLCKDGRVDEAMGLLEEMKAKGLDADVVVYSALISGFCS----------NGSFDKGKK 263
+D K G V EA+ L +E + G+ Y+ L+ CS N +G
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFD 91
Query: 264 LFDDMLEKGISPNVVTYNSLMHCLCKIGQWKEAIAMLDAMMERGIRPDVVTYTCLIEGLC 323
+F M+ + PN T+ + A+A D M
Sbjct: 92 IFKQMIVDKVVPNEATFTNGARL---------AVAKDDPEM------------------- 123
Query: 324 KGGRATKAIDLLNWMVKKGEKLSVITYNVLIKGLCQKGLVGEAYEI 369
A D++ M G + + +Y + G C+KG +AYE+
Sbjct: 124 -------AFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>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 = 37.0 bits (84), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 47/122 (38%), Gaps = 9/122 (7%)
Query: 149 RKGEVNKAIELFGEIKSNGVSPDNCSYNTI--VNGLCKAKR-------FKEALDILPDME 199
+KG+V +A+ L+ E + NGV YN + V L +A DI
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 200 AVGCCPNLITYSTLMDGLCKDGRVDEAMGLLEEMKAKGLDADVVVYSALISGFCSNGSFD 259
PN T++ + A +++ KA G+ + Y + GFC G D
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 260 KG 261
K
Sbjct: 158 KA 159
Score = 35.8 bits (81), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 11/131 (8%)
Query: 214 MDGLCKDGRVDEAMGLLEEMKAKGLDADVVVYSALISGFCS----------NGSFDKGKK 263
+D K G V EA+ L +E + G+ Y+ L+ CS N +G
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFD 91
Query: 264 LFDDMLEKGISPNVVTYNSLMHCLCKIGQWKEAIAMLDAMMERGIRPDVVTYTCLIEGLC 323
+F + + PN T+ + + A + GI+P + +Y + G C
Sbjct: 92 IFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFC 151
Query: 324 KGGRATKAIDL 334
+ G A KA ++
Sbjct: 152 RKGDADKAYEV 162
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 4/94 (4%)
Query: 69 VCNSLMEALVRSK---NYEYAFSVYSKMTCVHIFPSFLSLSGLIEVFVQTQKPKFALGVI 125
VC SL EA S F ++ + + P+ + + + V P+ A +
Sbjct: 70 VC-SLAEAATESSPNPGLSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXV 128
Query: 126 GLILKRGFVVNIYAFNLILKGFCRKGEVNKAIEL 159
G + ++ L GFCRKG+ +KA E+
Sbjct: 129 KQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|2O20|A Chain A, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|C Chain C, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|D Chain D, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|B Chain B, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|E Chain E, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|F Chain F, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|G Chain G, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
pdb|2O20|H Chain H, Crystal Structure Of Transcription Regulator Ccpa Of
Lactococcus Lactis
Length = 332
Score = 36.2 bits (82), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 35/58 (60%), Gaps = 12/58 (20%)
Query: 252 FCSNGSFDKGKKLFDDMLEKGISPNVVTYNSLMHCLCKIGQWKEAIAMLDAMMERGIR 309
F N S+++GK L + +LE+G + VV+++++ A+ +L AMM++G++
Sbjct: 219 FEGNYSYEQGKALAERLLERGATSAVVSHDTV------------AVGLLSAMMDKGVK 264
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 175 YNTIVNGLCKAKRFKEALDILPDMEAVGCCPNLITYSTLMDGLCKDGRVDEAMGL----L 230
YN ++ G + FKE + +L ++ G P+L++Y+ + + GR D+ G L
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCM---GRQDQDAGTIERCL 224
Query: 231 EEMKAKGLDADVVVYSALIS 250
E+M +GL + + L+S
Sbjct: 225 EQMSQEGLKLQALFTAVLLS 244
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 340 KKGEKLSVITYNVLIKGLCQKGLVGEAYEILNMMIEKGMMPDVVSYNTLLMGIGK----F 395
+K + L++ YN ++ G ++G E +L M+ + G+ PD++SY L +G+
Sbjct: 158 QKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDA 217
Query: 396 GKVDEALE 403
G ++ LE
Sbjct: 218 GTIERCLE 225
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 26/121 (21%), Positives = 59/121 (48%), Gaps = 2/121 (1%)
Query: 280 YNSLMHCLCKIGQWKEAIAMLDAMMERGIRPDVVTYTCLIEGLCKGGRATKAIDL-LNWM 338
YN++M + G +KE + +L + + G+ PD+++Y ++ + + + I+ L M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 339 VKKGEKLSVITYNVLIKGLCQKGLVGEAYEILNMMIEKGMMPDVVSYNTLLMGI-GKFGK 397
++G KL + VL+ + ++ +++ +P V+ + LL + K G+
Sbjct: 228 SQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGR 287
Query: 398 V 398
V
Sbjct: 288 V 288
>pdb|1X87|A Chain A, 2.4a X-Ray Structure Of Urocanase Protein Complexed With
Nad
pdb|1X87|B Chain B, 2.4a X-Ray Structure Of Urocanase Protein Complexed With
Nad
Length = 551
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 361 GLVGEAYEILNMMIEKGMMPDVVSYNT 387
GLVG A E+L ++E G +PDV++ T
Sbjct: 234 GLVGNAAEVLPRLVETGFVPDVLTDQT 260
>pdb|2JFE|X Chain X, The Crystal Structure Of Human Cytosolic Beta-Glucosidase
Length = 469
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 250 SGFCSNGSFDKGKKLFDDMLEKGISPNVVTYN-SLMHCLCKIGQW-KEAI 297
+GF + D K+ DD+L+ G++P V Y+ L L G W EAI
Sbjct: 89 TGFINQKGIDYYNKIIDDLLKNGVTPIVTLYHFDLPQTLEDQGGWLSEAI 138
>pdb|2E9L|A Chain A, Crystal Structure Of Human Cytosolic Neutral
Beta-Glycosylceramidase (Klotho-Related Prote:klrp)
Complex With Glucose And Fatty Acids
pdb|2E9M|A Chain A, Crystal Structure Of Human Cytosolic Neutral Beta-
Glycosylceramidase (Klotho-Related Prote:klrp) Complex
With Galactose And Fatty Acids
Length = 469
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 250 SGFCSNGSFDKGKKLFDDMLEKGISPNVVTYN-SLMHCLCKIGQW-KEAI 297
+GF + D K+ DD+L+ G++P V Y+ L L G W EAI
Sbjct: 89 TGFINQKGIDYYNKIIDDLLKNGVTPIVTLYHFDLPQTLEDQGGWLSEAI 138
>pdb|2ZOX|A Chain A, Crystal Structure Of The Covalent Intermediate Of Human
Cytosolic Beta-Glucosidase
pdb|3VKK|A Chain A, Crystal Structure Of The Covalent Intermediate Of Human
Cytosolic Beta-Glucosidase-Mannose Complex
Length = 469
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 250 SGFCSNGSFDKGKKLFDDMLEKGISPNVVTYN-SLMHCLCKIGQW-KEAI 297
+GF + D K+ DD+L+ G++P V Y+ L L G W EAI
Sbjct: 89 TGFINQKGIDYYNKIIDDLLKNGVTPIVTLYHFDLPQTLEDQGGWLSEAI 138
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
0.322 0.138 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,786,170
Number of Sequences: 62578
Number of extensions: 868771
Number of successful extensions: 2283
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2252
Number of HSP's gapped (non-prelim): 28
length of query: 721
length of database: 14,973,337
effective HSP length: 106
effective length of query: 615
effective length of database: 8,340,069
effective search space: 5129142435
effective search space used: 5129142435
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)