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= psy941
(487 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 35.8 bits (81), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 218 IKAHVDSVRFCGNTIAGLSLLSDSVMKLVDEKTKTQEILVLLKQRSLYVMKDDARYKFTH 277
I AH+D+ + I LSL S+ VM + + V+L +RSL VM ++RY +TH
Sbjct: 211 IPAHIDTHSAFEDEIVSLSLGSEIVMDF--KHPDGIAVPVMLPRRSLLVMTGESRYLWTH 268
Query: 278 EV 279
+
Sbjct: 269 GI 270
Score = 35.8 bits (81), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 414 IKAHVDSVRFCGNTIAGLSLLSDSVMKLVDEKTKTQEILVLLKQRSLYVMKDDARYKFTH 473
I AH+D+ + I LSL S+ VM + + V+L +RSL VM ++RY +TH
Sbjct: 211 IPAHIDTHSAFEDEIVSLSLGSEIVMDF--KHPDGIAVPVMLPRRSLLVMTGESRYLWTH 268
Query: 474 EV 475
+
Sbjct: 269 GI 270
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 164 DHWDDAIHGFRETERSKWNEENTKIIARVQNLAFPPNVTPIQYVHVLDLEQKGYIK 219
D WD+ I FR E + E R++N P V P QYV +L KG ++
Sbjct: 136 DSWDNVIRAFRGNELQNYFE-------RLKNGEIRPVVKP-QYVDLLPKAVKGKVR 183
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 360 DHWDDAIHGFRETERSKWNEENTKIIARVQNLAFPPNVTPIQYVHVLDLEQKGYIK 415
D WD+ I FR E + E R++N P V P QYV +L KG ++
Sbjct: 136 DSWDNVIRAFRGNELQNYFE-------RLKNGEIRPVVKP-QYVDLLPKAVKGKVR 183
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 164 DHWDDAIHGFRETERSKWNEENTKIIARVQNLAFPPNVTPIQYVHVLDLEQKGYIK 219
D WD+ I FR E + E R++N P V P QYV +L KG ++
Sbjct: 150 DSWDNVIRAFRGNELQNYFE-------RLKNGEIRPVVKP-QYVDLLPKAVKGKVR 197
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 360 DHWDDAIHGFRETERSKWNEENTKIIARVQNLAFPPNVTPIQYVHVLDLEQKGYIK 415
D WD+ I FR E + E R++N P V P QYV +L KG ++
Sbjct: 150 DSWDNVIRAFRGNELQNYFE-------RLKNGEIRPVVKP-QYVDLLPKAVKGKVR 197
>pdb|2BZL|A Chain A, Crystal Structure Of The Human Protein Tyrosine
Phosphatase N14 At 1.65 A Resolution
Length = 325
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 221 HVDSVRFCGNTIA--GLSLLSDSVMKLVD--EKTKTQEILVLLKQRSLYVMKDDARYKFT 276
H V C + G+ +LS+ ++ ++ EK + +L LL+++ +++++ A+YKF
Sbjct: 252 HPPIVVHCSAGVGRTGVLILSELMIYCLEHNEKVEVPMMLRLLREQRMFMIQTIAQYKFV 311
Query: 277 HEVL 280
++VL
Sbjct: 312 YQVL 315
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 417 HVDSVRFCGNTIA--GLSLLSDSVMKLVD--EKTKTQEILVLLKQRSLYVMKDDARYKFT 472
H V C + G+ +LS+ ++ ++ EK + +L LL+++ +++++ A+YKF
Sbjct: 252 HPPIVVHCSAGVGRTGVLILSELMIYCLEHNEKVEVPMMLRLLREQRMFMIQTIAQYKFV 311
Query: 473 HEVL 476
++VL
Sbjct: 312 YQVL 315
>pdb|2C1I|A Chain A, Structure Of Streptococcus Pnemoniae Peptidoglycan
Deacetylase (Sppgda) D 275 N Mutant
Length = 431
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 25/42 (59%)
Query: 141 SAEEEQSLLKEINQFIKRQRYEYDHWDDAIHGFRETERSKWN 182
+++ ++ L+KE+ FI+ ++ E D + + F + + S WN
Sbjct: 139 ASKAKEQLIKELTSFIEDKKIEQDQSEQIVKNFSDQDLSAWN 180
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 25/42 (59%)
Query: 337 SAEEEQSLLKEINQFIKRQRYEYDHWDDAIHGFRETERSKWN 378
+++ ++ L+KE+ FI+ ++ E D + + F + + S WN
Sbjct: 139 ASKAKEQLIKELTSFIEDKKIEQDQSEQIVKNFSDQDLSAWN 180
>pdb|2C1G|A Chain A, Structure Of Streptococcus Pneumoniae Peptidoglycan
Deacetylase (Sppgda)
Length = 431
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 25/42 (59%)
Query: 141 SAEEEQSLLKEINQFIKRQRYEYDHWDDAIHGFRETERSKWN 182
+++ ++ L+KE+ FI+ ++ E D + + F + + S WN
Sbjct: 139 ASKAKEQLIKELTSFIEDKKIEQDQSEQIVKNFSDQDLSAWN 180
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 25/42 (59%)
Query: 337 SAEEEQSLLKEINQFIKRQRYEYDHWDDAIHGFRETERSKWN 378
+++ ++ L+KE+ FI+ ++ E D + + F + + S WN
Sbjct: 139 ASKAKEQLIKELTSFIEDKKIEQDQSEQIVKNFSDQDLSAWN 180
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
0.318 0.134 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,998,580
Number of Sequences: 62578
Number of extensions: 495744
Number of successful extensions: 1291
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1278
Number of HSP's gapped (non-prelim): 20
length of query: 487
length of database: 14,973,337
effective HSP length: 103
effective length of query: 384
effective length of database: 8,527,803
effective search space: 3274676352
effective search space used: 3274676352
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)