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= 004744
(732 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 = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 59/129 (45%), Gaps = 9/129 (6%)
Query: 427 RNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEAD---------DLFNEML 477
+ G VLEAL++ DE G + YN +L A+ TE+ D+F +M+
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 478 ERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME 537
V P+ TFT + A ++ M I+P + +Y + GFC+ G+ +
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 538 KANKLWADM 546
KA ++ A M
Sbjct: 158 KAYEVDAHM 166
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/167 (24%), Positives = 73/167 (43%), Gaps = 11/167 (6%)
Query: 497 KDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE----------MEKANKLWADM 546
K G++ +AL L+D + ++ YN L+ C + E + + ++ M
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 547 ISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA 606
I K+ PN ++ + AF + +M GI+P L S + G+CR GDA
Sbjct: 97 IVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDA 156
Query: 607 SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN 653
KA E + MV V P+ L+ + +N DK + + ++ +
Sbjct: 157 DKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRD 203
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 54/122 (44%), Gaps = 9/122 (7%)
Query: 224 AREVYAEVVRSGIELNVYTLNIM--VNALCKDHKIDSAKMFLC-------EMEQKGVYPD 274
A +Y E R+G++L+ Y N++ V +L + S L +M V P+
Sbjct: 45 ALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPN 104
Query: 275 TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEVLD 334
T+ + E AF ++ M G++P + +Y + G C+KG D+A EV
Sbjct: 105 EATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDA 164
Query: 335 EM 336
M
Sbjct: 165 HM 166
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 566 CSM-GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA----------SKADEFLS 614
CS G V EA RL+ E G++ + N ++ C +A S+ +
Sbjct: 36 CSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFK 94
Query: 615 KMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG 674
+M+ + V P+ ++ V +++ + AF +V +M+ G+ P + +Y L GFCR+G
Sbjct: 95 QMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154
Score = 35.8 bits (81), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 52/129 (40%), Gaps = 9/129 (6%)
Query: 322 KKGRCDRAKEVLDEMLQMGLSPDTATYNTLL---------VESCRKENMSEAEEIFCEMS 372
KKG A + DE + G+ YN LL ES +S +IF +M
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 373 RRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNGFVL 432
V P+ +F+ + + A ++MK+ G+ P Y + G+CR G
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 433 EALKMRDEM 441
+A ++ M
Sbjct: 158 KAYEVDAHM 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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 52/122 (42%), Gaps = 9/122 (7%)
Query: 427 RNGFVLEALKMRDEMLEKGCVMDVVTYNTILNGLCRAKMLTEAD---------DLFNEML 477
+ G VLEAL++ DE G + YN +L A+ TE+ D+F + +
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 478 ERGVFPDFYTFTTLIHGHCKDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEME 537
V P+ TFT + A + I+P + +Y + GFC+ G+ +
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 538 KA 539
KA
Sbjct: 158 KA 159
Score = 37.4 bits (85), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 30/118 (25%), Positives = 51/118 (43%), Gaps = 9/118 (7%)
Query: 224 AREVYAEVVRSGIELNVYTLNIM--VNALCKDHKIDSAKMFLCE----MEQK---GVYPD 274
A +Y E R+G++L+ Y N++ V +L + S L +Q V P+
Sbjct: 45 ALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXIVDKVVPN 104
Query: 275 TVTYNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDRAKEV 332
T+ + E AF + G++P + +Y + G C+KG D+A EV
Sbjct: 105 EATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
Score = 36.2 bits (82), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 68/167 (40%), Gaps = 11/167 (6%)
Query: 497 KDGNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGE----------MEKANKLWADM 546
K G++ +AL L+D + ++ YN L+ C + E + + ++
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQX 96
Query: 547 ISRKISPNYISYGILINGYCSMGHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA 606
I K+ PN ++ + AF + GI+P L S + G+CR GDA
Sbjct: 97 IVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDA 156
Query: 607 SKADEFLSKMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMEN 653
KA E + V V P+ L+ +N DK + + ++ +
Sbjct: 157 DKAYEVDAHXVESEVVPEEPELAALLKVSXDTKNADKVYKTLQRLRD 203
Score = 35.8 bits (81), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 12/120 (10%)
Query: 566 CSM-GHVTEAFRLWYEMVGKGIKPTLVSCNTIIKGYCRSGDA----------SKADEFLS 614
CS G V EA RL+ E G++ + N ++ C +A S+ +
Sbjct: 36 CSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFK 94
Query: 615 KMVSEGVDPDSISYNTLINGFVREENMDKAFALVSKMENQGLVPDVITYNVILTGFCRQG 674
+ + + V P+ ++ V +++ + AF V + + G+ P + +Y L GFCR+G
Sbjct: 95 QXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 9/117 (7%)
Query: 322 KKGRCDRAKEVLDEMLQMGLSPDTATYNTLL---------VESCRKENMSEAEEIFCEMS 372
KKG A + DE + G+ YN LL ES +S +IF +
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 373 RRGVAPDIVSFSTLIGIFSRNGQLDRALMYFREMKSAGLVPDNVLYTIIINGYCRNG 429
V P+ +F+ + + A ++ K+ G+ P Y + G+CR G
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 27/131 (20%), Positives = 58/131 (44%), Gaps = 8/131 (6%)
Query: 278 YNTLINAYCREGFLEEAFQLMNSMSGKGLKPGVFTYNSLINGLCKKGRCDR----AKEVL 333
YN ++ + R+G +E ++ + GL P + +Y + + + GR D+ + L
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCM---GRQDQDAGTIERCL 224
Query: 334 DEMLQMGLSPDTATYNTLLVESCRKENMSEAEEIFCEMSRRGVAPDIVSFSTLI-GIFSR 392
++M Q GL LL E R + ++ S P V+ S L+ ++++
Sbjct: 225 EQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAK 284
Query: 393 NGQLDRALMYF 403
+G++ ++
Sbjct: 285 DGRVSYPKLHL 295
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 663 YNVILTGFCRQGRMHDSELILWRMIEKGLNPDRSTYTTLIN 703
YN ++ G+ RQG + +L+ + + GL PD +Y +
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ 208
>pdb|3N6O|A Chain A, Crystal Structure Of The Gef And P4m Domain Of DrraSIDM
FROM Legionella Pneumophila
pdb|3N6O|B Chain B, Crystal Structure Of The Gef And P4m Domain Of DrraSIDM
FROM Legionella Pneumophila
Length = 311
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 21/114 (18%)
Query: 441 MLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGN 500
MLEKG + + L+ + K L E DDL E+ ++ + P Y + G D +
Sbjct: 23 MLEKGNISGYLKAANELHKFMKEKNLKE-DDLRPELSDKTISPKGYAILQSLWGAASDYS 81
Query: 501 MNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN 554
A +T+ +++P +V+ NK+ A + K+SPN
Sbjct: 82 RAAA-----TLTESTVEPGLVSA---------------VNKMSAFFMDCKLSPN 115
>pdb|2WWX|B Chain B, Crystal Structure Of The SidmDRRA(GEFGDF DOMAIN)-Rab1
(Gtpase Domain) Complex
Length = 217
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 21/114 (18%)
Query: 441 MLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKDGN 500
MLEKG + + L+ + K L E DDL E+ ++ + P Y + G D +
Sbjct: 43 MLEKGNISGYLKAANELHKFMKEKNLKE-DDLRPELSDKTISPKGYAILQSLWGAASDYS 101
Query: 501 MNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN 554
A +T+ +++P +V+ NK+ A + K+SPN
Sbjct: 102 RAAA-----TLTESTVEPGLVSA---------------VNKMSAFFMDCKLSPN 135
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 29.6 bits (65), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 312 TYNSLINGLCKKGRCDRAKEVLDEMLQMGLSPDTA-TYNTLLVESCRKENMSEAEEIFCE 370
Y +L N L +KG A++ + L+ L P A + N L + N+ EA ++
Sbjct: 273 AYCNLANALKEKGSVAEAEDCYNTALR--LCPTHADSLNNLANIKREQGNIEEAVRLY-- 328
Query: 371 MSRRG--VAPDIVS-FSTLIGIFSRNGQLDRALMYFRE 405
R+ V P+ + S L + + G+L ALM+++E
Sbjct: 329 --RKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKE 364
>pdb|3JZA|B Chain B, Crystal Structure Of Human Rab1b In Complex With The Gef
Domain Of DrraSIDM FROM LEGIONELLA PNEUMOPHILA
Length = 197
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 49/116 (42%), Gaps = 21/116 (18%)
Query: 439 DEMLEKGCVMDVVTYNTILNGLCRAKMLTEADDLFNEMLERGVFPDFYTFTTLIHGHCKD 498
+ MLEKG + + L+ + K L E DDL E+ ++ + P Y + G D
Sbjct: 21 NSMLEKGNISGYLKAANELHKFMKEKNLKE-DDLRPELSDKTISPKGYAILQSLWGAASD 79
Query: 499 GNMNKALNLFDIMTQKSIKPDIVTYNTLIDGFCKVGEMEKANKLWADMISRKISPN 554
+ A +T+ +++P +V+ NK+ A + K+SPN
Sbjct: 80 YSRAAA-----TLTESTVEPGLVSA---------------VNKMSAFFMDCKLSPN 115
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
0.323 0.138 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,871,391
Number of Sequences: 62578
Number of extensions: 789242
Number of successful extensions: 1713
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1679
Number of HSP's gapped (non-prelim): 23
length of query: 732
length of database: 14,973,337
effective HSP length: 106
effective length of query: 626
effective length of database: 8,340,069
effective search space: 5220883194
effective search space used: 5220883194
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)