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= 039029
(319 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 = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 62/133 (46%), Gaps = 12/133 (9%)
Query: 20 MC-KEGRLEEASRMLEQMKENGLVPTAVTYNTLI----------DGYCNKGNLEMAFSFR 68
MC K+G + EA R+ ++ + NG+ + YN L+ + N G L F
Sbjct: 35 MCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPG-LSRGFDIF 93
Query: 69 DEMVKQGIMPTASTYNLLIHELLMERKMVEADDMLKEMGEKGIVPDSITYNILINGYCRC 128
+M+ ++P +T+ + + A DM+K+M GI P +Y + G+CR
Sbjct: 94 KQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRK 153
Query: 129 GNAKKAFSLHDEM 141
G+A KA+ + M
Sbjct: 154 GDADKAYEVDAHM 166
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/120 (22%), Positives = 51/120 (42%), Gaps = 9/120 (7%)
Query: 129 GNAKKAFSLHDEMIHKGIQPTMLTYTSLIFVLSKQNRMIEAD---------QLFENFLAK 179
G+ +A L+DE G+Q + Y L++V S E+ +F+ +
Sbjct: 40 GDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVD 99
Query: 180 GMLPDIVMFNALIDGHCTNGNIERAFSLLKEMDRMKVHPDEVTYNTLMHGRCRQGKVEEA 239
++P+ F + E AF ++K+M + P +Y + G CR+G ++A
Sbjct: 100 KVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/136 (25%), Positives = 60/136 (44%), Gaps = 20/136 (14%)
Query: 52 IDGYCNKGNLEMAFSFRDEMVKQGIMPTASTYNLLIHELLMERKMVEAD---------DM 102
+D KG++ A DE + G+ + YN+L++ + E+ D+
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 103 LKEMGEKGIVPDSITYNILINGYCRCGNAKK----AFSLHDEMIHKGIQPTMLTYTSLIF 158
K+M +VP+ T+ NG R AK AF + +M GIQP + +Y +F
Sbjct: 93 FKQMIVDKVVPNEATFT---NG-ARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALF 148
Query: 159 VLSKQNRMIEADQLFE 174
++ +AD+ +E
Sbjct: 149 GFCRKG---DADKAYE 161
Score = 32.0 bits (71), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 6 VQPDSYTYGSFVSGMCKEGRLEEASRMLEQMKENGLVPTAVTYNTLIDGYCNKGNLEMAF 65
V P+ T+ + + E A M++QMK G+ P +Y + G+C KG+ + A+
Sbjct: 101 VVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAY 160
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 1 MKSRGVQPDSYTYGSFVSGMCKEGRLEEA 29
MK+ G+QP +YG + G C++G ++A
Sbjct: 131 MKAFGIQPRLRSYGPALFGFCRKGDADKA 159
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 9/120 (7%)
Query: 129 GNAKKAFSLHDEMIHKGIQPTMLTYTSLIFVLSKQNRMIEAD---------QLFENFLAK 179
G+ +A L+DE G+Q + Y L++V S E+ +F+ +
Sbjct: 40 GDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXIVD 99
Query: 180 GMLPDIVMFNALIDGHCTNGNIERAFSLLKEMDRMKVHPDEVTYNTLMHGRCRQGKVEEA 239
++P+ F + E AF +K+ + P +Y + G CR+G ++A
Sbjct: 100 KVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/126 (23%), Positives = 56/126 (44%), Gaps = 11/126 (8%)
Query: 22 KEGRLEEASRMLEQMKENGLVPTAVTYNTLI----------DGYCNKGNLEMAFSFRDEM 71
K+G + EA R+ ++ + NG+ + YN L+ + N G L F +
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPG-LSRGFDIFKQX 96
Query: 72 VKQGIMPTASTYNLLIHELLMERKMVEADDMLKEMGEKGIVPDSITYNILINGYCRCGNA 131
+ ++P +T+ + + A D +K+ GI P +Y + G+CR G+A
Sbjct: 97 IVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDA 156
Query: 132 KKAFSL 137
KA+ +
Sbjct: 157 DKAYEV 162
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 32/136 (23%), Positives = 57/136 (41%), Gaps = 20/136 (14%)
Query: 52 IDGYCNKGNLEMAFSFRDEMVKQGIMPTASTYNLLIHELLMERKMVEAD---------DM 102
+D KG++ A DE + G+ + YN+L++ + E+ D+
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 103 LKEMGEKGIVPDSITYNILINGYCRCGNAK----KAFSLHDEMIHKGIQPTMLTYTSLIF 158
K+ +VP+ T+ NG R AK AF + GIQP + +Y +F
Sbjct: 93 FKQXIVDKVVPNEATFT---NG-ARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALF 148
Query: 159 VLSKQNRMIEADQLFE 174
++ +AD+ +E
Sbjct: 149 GFCRKG---DADKAYE 161
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%)
Query: 6 VQPDSYTYGSFVSGMCKEGRLEEASRMLEQMKENGLVPTAVTYNTLIDGYCNKGNLEMAF 65
V P+ T+ + + E A ++Q K G+ P +Y + G+C KG+ + A+
Sbjct: 101 VVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAY 160
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 223 YNTLMHGRCRQGKVEEARRLLDQMKRRGIKPDHISFNPTRLTYNALIQGLCK-NQEGDLA 281
YN +M G RQG +E +L +K G+ PD L+Y A +Q + + +Q+
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPD-------LLSYAAALQCMGRQDQDAGTI 220
Query: 282 EELLREMVSKGI 293
E L +M +G+
Sbjct: 221 ERCLEQMSQEGL 232
>pdb|2LBT|A Chain A, Solution Structure Of The C Domain Of Rv0899(D236a) From
Mycobacterium Tuberculosis
Length = 137
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 46/107 (42%), Gaps = 20/107 (18%)
Query: 188 FNALIDGHCTNGN-----IERAFSLLKEM-DRMKVHPD-EVTYNTLMHGRCRQG-----K 235
NA+ G GN I A+ +L + D++K PD VT N +G
Sbjct: 20 INAVTGGPIAFGNDGASLIPAAYEILNRVADKLKACPDARVTINGYTDNTGSEGINIPLS 79
Query: 236 VEEARRLLDQMKRRGIKPDHI------SFNPTRLTYNALIQGLCKNQ 276
+ A+ + D + RG+ DHI S NP + NA +G KN+
Sbjct: 80 AQRAKIVADYLVARGVAGDHIATVGLGSVNP--IASNATPEGRAKNR 124
>pdb|2L26|A Chain A, Rv0899 From Mycobacterium Tuberculosis Contains Two
Separated Domains
Length = 284
Score = 31.2 bits (69), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 48/115 (41%), Gaps = 20/115 (17%)
Query: 188 FNALIDGHCTNGN-----IERAFSLLKEM-DRMKVHPD-EVTYNTLMHGRCRQG-----K 235
NA+ G GN I + +L + D++K PD VT N +G
Sbjct: 165 INAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGINIPLS 224
Query: 236 VEEARRLLDQMKRRGIKPDHI------SFNPTRLTYNALIQGLCKNQEGDLAEEL 284
+ A+ + D + RG+ DHI S NP + NA +G KN+ ++ L
Sbjct: 225 AQRAKIVADYLVARGVAGDHIATVGLGSVNP--IASNATPEGRAKNRRVEIVVNL 277
>pdb|2LCA|A Chain A, Solution Structure Of The C Domain Of Rv0899 From
Mycobacterium Tuberculosis
Length = 137
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 45/107 (42%), Gaps = 20/107 (18%)
Query: 188 FNALIDGHCTNGN-----IERAFSLLKEM-DRMKVHPD-EVTYNTLMHGRCRQG-----K 235
NA+ G GN I + +L + D++K PD VT N +G
Sbjct: 20 INAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGINIPLS 79
Query: 236 VEEARRLLDQMKRRGIKPDHI------SFNPTRLTYNALIQGLCKNQ 276
+ A+ + D + RG+ DHI S NP + NA +G KN+
Sbjct: 80 AQRAKIVADYLVARGVAGDHIATVGLGSVNP--IASNATPEGRAKNR 124
>pdb|2KGW|A Chain A, Solution Structure Of The Carboxy-Terminal Domain Of
Ompatb, A Pore Forming Protein From Mycobacterium
Tuberculosis
Length = 129
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 45/107 (42%), Gaps = 20/107 (18%)
Query: 188 FNALIDGHCTNGN-----IERAFSLLKEM-DRMKVHPD-EVTYNTLMHGRCRQG-----K 235
NA+ G GN I + +L + D++K PD VT N +G
Sbjct: 18 INAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGINIPLS 77
Query: 236 VEEARRLLDQMKRRGIKPDHI------SFNPTRLTYNALIQGLCKNQ 276
+ A+ + D + RG+ DHI S NP + NA +G KN+
Sbjct: 78 AQRAKIVADYLVARGVAGDHIATVGLGSVNP--IASNATPEGRAKNR 122
>pdb|3O6X|A Chain A, Crystal Structure Of The Type Iii Glutamine Synthetase
From Bacteroides Fragilis
pdb|3O6X|B Chain B, Crystal Structure Of The Type Iii Glutamine Synthetase
From Bacteroides Fragilis
pdb|3O6X|C Chain C, Crystal Structure Of The Type Iii Glutamine Synthetase
From Bacteroides Fragilis
pdb|3O6X|D Chain D, Crystal Structure Of The Type Iii Glutamine Synthetase
From Bacteroides Fragilis
pdb|3O6X|E Chain E, Crystal Structure Of The Type Iii Glutamine Synthetase
From Bacteroides Fragilis
pdb|3O6X|F Chain F, Crystal Structure Of The Type Iii Glutamine Synthetase
From Bacteroides Fragilis
Length = 729
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 30 SRMLEQMKENGLVPTAVTY-NTLIDGYC------NKGNLEMAFSFRDEMVKQGIMPTAST 82
SR+L + N +VP AV+Y N L++ C ++ E+ + R E++K+ I S
Sbjct: 604 SRVLGDLAINHIVPIAVSYQNRLLENLCRMKEIFSEEEYEVMSADRKELIKE-ISHRVSA 662
Query: 83 YNLLIHELLMERKMVEADDMLKE 105
+L+ ++ RK+ + KE
Sbjct: 663 IKVLVRDMTEARKVANHKENFKE 685
>pdb|2PD2|A Chain A, Crystal Structure Of (St0148) Conserved Hypothetical From
Sulfolobus Tokodaii Strain7
pdb|2PD2|B Chain B, Crystal Structure Of (St0148) Conserved Hypothetical From
Sulfolobus Tokodaii Strain7
Length = 108
Score = 27.7 bits (60), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 89 ELLMERKMVEADDMLKEMGEKGIVPDSITYNILINGYCRCGNAKKAFSL-HDEMI 142
E+++ + ++A +LK+ + I+ D I NILI G C N+ ++ +L HD++I
Sbjct: 33 EVVLHQSAIKA--LLKDSDTRSIIEDLIKKNILIVG---CENSIRSQNLSHDQLI 82
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
0.319 0.135 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,231,852
Number of Sequences: 62578
Number of extensions: 365867
Number of successful extensions: 1137
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1106
Number of HSP's gapped (non-prelim): 38
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)