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= 039512
(154 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GBS|A Chain A, Nmr Structure Of Rpa0253 From Rhodopseudomonas Palustris.
Northeast Structural Genomics Consortium Target Rpr3
Length = 145
Score = 63.2 bits (152), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 38/130 (29%), Positives = 54/130 (41%), Gaps = 1/130 (0%)
Query: 7 YWLLKTEPGEWSWEDQAANGGVTK-WDGVKNKQAQKNMKAMRLNELCFFYHXXXXXXXXX 65
YWL+K+EP WSW+ Q A G + W GV+N A+ +M AMR + F+YH
Sbjct: 3 YWLVKSEPSVWSWDQQVAKGAAGEAWTGVRNHSAKLHMVAMRRGDRAFYYHSNEGKEIVG 62
Query: 66 XXXXXLREWYXXXXXXXXXXXXXXXXXXMMRRAVDLKEMKRDQELKGWALFRQPRLSVVN 125
+ ++ V L +K + L AL + RLSV
Sbjct: 63 IAEIIREAYPDPTDASGKFVCVDIKADKPLKTPVTLAAVKAEPRLADMALMKYSRLSVQP 122
Query: 126 VEKKVWDRVC 135
V + W VC
Sbjct: 123 VTAEEWKLVC 132
>pdb|2AR1|A Chain A, Structure Of Hypothetical Protein From Leishmania Major
Length = 172
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 41/136 (30%), Positives = 58/136 (42%), Gaps = 16/136 (11%)
Query: 6 QYWLLKTEPGEWSWEDQAANGGVTKWDGVKNKQAQKNMKAMRLNELCFFYHXXXXXXXXX 65
YWLLK+EP ++S +D A + WDGV+N A+ NM+AM + + FYH
Sbjct: 20 HYWLLKSEPHKFSIDD-LAKQKTSPWDGVRNYAARNNMRAMSVGDKVLFYHSNTKEPGVA 78
Query: 66 XXXXXLREWYXXXXXXXXXXXXXXXXXXMMR---RAVDLK------------EMKRDQEL 110
+R Y + + VD+K E+K +EL
Sbjct: 79 GLAEVVRLAYDDFTALDKTSEYFDPKATKEKNPWKMVDVKFVARWDTVLTLHELKSRREL 138
Query: 111 KGWALFRQPRLSVVNV 126
+ ALF Q RLSV V
Sbjct: 139 QKMALFTQRRLSVQPV 154
>pdb|1ZCE|A Chain A, X-Ray Crystal Structure Of Protein Atu2648 From
Agrobacteriu Tumefaciens. Northeast Structural Genomics
Consortium Targe
Length = 155
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 39/132 (29%), Positives = 58/132 (43%), Gaps = 2/132 (1%)
Query: 6 QYWLLKTEPGEWSWEDQAANGGVT-KWDGVKNKQAQKNMKAMRLNELCFFYHXXXXXXXX 64
YWL K+EP +WSWE Q A G +W GV+N QA+ N +A ++ + FFYH
Sbjct: 3 NYWLYKSEPFKWSWEXQKAKGETGEEWTGVRNYQARNNXRAXKIGDKGFFYHSNEGLDVV 62
Query: 65 XXXXX-XLREWYXXXXXXXXXXXXXXXXXXMMRRAVDLKEMKRDQELKGWALFRQPRLSV 123
L + V LK++K + +L+ +L RLSV
Sbjct: 63 GIVEVCALSHPDSTAEGDLKWDCVDIRAVCDXPQPVSLKDVKANPKLEKXSLVTSXRLSV 122
Query: 124 VNVEKKVWDRVC 135
V ++ + VC
Sbjct: 123 QPVTEEEYLEVC 134
>pdb|3EOP|A Chain A, Crystal Structure Of The Duf55 Domain Of Human Thymocyte
Nuclear Protein 1
pdb|3EOP|B Chain B, Crystal Structure Of The Duf55 Domain Of Human Thymocyte
Nuclear Protein 1
Length = 176
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/161 (26%), Positives = 64/161 (39%), Gaps = 33/161 (20%)
Query: 7 YWLLKTEPGE---------WSWED-QAANGGVTKWDGVKNKQAQKNMKAMRLNELCFFYH 56
+WL+K+EP +S ED +A T WDGV+N QA+ ++AM+L E FFYH
Sbjct: 3 HWLMKSEPESRLEKGVDVKFSIEDLKAQPKQTTCWDGVRNYQARNFLRAMKLGEEAFFYH 62
Query: 57 XXXXXXXXXXXXXXLREWYXXXXXXXXXXXXXXXXXX---------------MMRRAVDL 101
++E Y MM+R + L
Sbjct: 63 SNCKEPGIAGLMKIVKEAYPDHTQFEKNNPHYDPSSKEDNPKWSMVDVQFVRMMKRFIPL 122
Query: 102 KEMKRDQE--------LKGWALFRQPRLSVVNVEKKVWDRV 134
E+K + LK LF + RLS+ + ++ +D V
Sbjct: 123 AELKSYHQAHKATGGPLKNMVLFTRQRLSIQPLTQEEFDFV 163
>pdb|2G2X|A Chain A, X-ray Crystal Structure Protein Q88ch6 From Pseudomonas
Putida. Northeast Structural Genomics Consortium Target
Ppr72.
pdb|2G2X|B Chain B, X-ray Crystal Structure Protein Q88ch6 From Pseudomonas
Putida. Northeast Structural Genomics Consortium Target
Ppr72.
pdb|2G2X|C Chain C, X-ray Crystal Structure Protein Q88ch6 From Pseudomonas
Putida. Northeast Structural Genomics Consortium Target
Ppr72
Length = 157
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 7 YWLLKTEPGEWSWEDQAANGGVTKWDGVKNKQAQKNMKAMRLNELCFFYH 56
YWL K+EP E S E A G +WDGV+N QA+ ++A + + FFYH
Sbjct: 3 YWLXKSEPDELSIE-ALARLGEARWDGVRNYQARNFLRAXSVGDEFFFYH 51
>pdb|2EVE|A Chain A, X-Ray Crystal Structure Of Protein Pspto5229 From
Pseudomona Syringae. Northeast Structural Genomics
Consortium Target P
Length = 157
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 7 YWLLKTEPGEWSWEDQAANGGVTKWDGVKNKQAQKNMKAMRLNELCFFYH 56
YWL K+EP E+S D G +WDGV+N QA+ ++ + FFYH
Sbjct: 3 YWLXKSEPDEFSISD-LQRLGKARWDGVRNYQARNFLRTXAEGDEFFFYH 51
>pdb|1U1H|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
pdb|1U1J|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
pdb|1U1U|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
pdb|1U22|A Chain A, A. Thaliana Cobalamine Independent Methionine Synthase
Length = 765
Score = 25.8 bits (55), Expect = 9.7, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 94 MMRRAVDL-KEMKRDQELKGWALFRQPRLSVVNVEKK 129
++ AVDL E K D E+K W F ++ VN K
Sbjct: 330 LLHTAVDLINETKLDDEIKSWXAFAAQKVVEVNALAK 366
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
0.321 0.134 0.450
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,165,253
Number of Sequences: 62578
Number of extensions: 82451
Number of successful extensions: 183
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 169
Number of HSP's gapped (non-prelim): 9
length of query: 154
length of database: 14,973,337
effective HSP length: 90
effective length of query: 64
effective length of database: 9,341,317
effective search space: 597844288
effective search space used: 597844288
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: 47 (22.7 bits)