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= 040494
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1V2X|A Chain A, Trmh
Length = 194
Score = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 50/156 (32%), Positives = 74/156 (47%), Gaps = 9/156 (5%)
Query: 6 VVVHNIAKRHNVGTLARSATAFGVSEMILV----GRRDFNAFGSHGSTSHVNFRHFHSLS 61
V++ N+ K HN+ + R+ A GV E V G FN S GS V R L
Sbjct: 25 VLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNE-TSGGSHKWVYLRVHPDLH 83
Query: 62 DARVFLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIP 121
+A FLK + + + ++A D + + K TA L G E G+S + + D + IP
Sbjct: 84 EAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIP 143
Query: 122 QYGGGTASLNVTVAASIVL---HHFGVWAGFSERTR 154
G SLNV+VAA+++L + AG +R R
Sbjct: 144 ML-GMVQSLNVSVAAAVILFEAQRQRLKAGLYDRPR 178
>pdb|2HA8|A Chain A, Methyltransferase Domain Of Human Tar (Hiv-1) Rna Binding
Protein 1
pdb|2HA8|B Chain B, Methyltransferase Domain Of Human Tar (Hiv-1) Rna Binding
Protein 1
Length = 184
Score = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 44/148 (29%), Positives = 72/148 (48%), Gaps = 15/148 (10%)
Query: 6 VVVHNIAKRHNVGTLARSATAFGVSEMIL-----VGRRDFNAFGSHGSTSHVNFRHFHSL 60
VV I K N+G L R+ FG S +++ + + F H S S + +
Sbjct: 29 VVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQ----HLSVSAEQWLPLVEV 84
Query: 61 SDARV--FLKSKDCD---ICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICD 115
++ +L+ K + I GVE T ++D+TQ+ F + + LLGNE G+ A + D
Sbjct: 85 KPPQLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLD 144
Query: 116 FFVYIPQYGGGTASLNVTVAASIVLHHF 143
V IPQ G SLNV V+ ++++ +
Sbjct: 145 VCVEIPQQ-GIIRSLNVHVSGALLIWEY 171
>pdb|1ZJR|A Chain A, Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODIFYING
ENZYME
Length = 211
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 62/137 (45%), Gaps = 5/137 (3%)
Query: 10 NIAKRHNVGTLARSATAFGVSEMILV---GRR-DFNAFGSHGSTSHVNFRHFHSLSDARV 65
N+ HN + R+ A GV + G++ N + GS V + +
Sbjct: 32 NVKNEHNFSAIVRTCDAVGVLYLYYYHAEGKKAKINEGITQGSHKWVFIEKVDNPVQKLL 91
Query: 66 FLKSKDCDICGVEITDNAVDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYGG 125
K++ I ++ +V+ + + K T ++GNE G+S + EI D + IP YG
Sbjct: 92 EFKNRGFQIVATWLSKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGM 151
Query: 126 GTASLNVTVAASIVLHH 142
SLNV+VA I+L+
Sbjct: 152 A-QSLNVSVATGIILYE 167
>pdb|1GZ0|A Chain A, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|B Chain B, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|C Chain C, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|D Chain D, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|E Chain E, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|F Chain F, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|G Chain G, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|H Chain H, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
Length = 253
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 61/143 (42%), Gaps = 11/143 (7%)
Query: 5 YVVVHNIAKRHNVGTLARSATAFGVSEMILVGRR--DFNAFGSH---GSTSHVNFRHFHS 59
+++ + HN+G RSA A GV +I+ R NA G+ V +
Sbjct: 107 LLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTN 166
Query: 60 LSDARVFLKSKDCDICGVEITDNAVDVTQHPFKKS--TAFLLGNEGMGLSAKECEICDFF 117
L+ L+ ++ I G T D T + K + A + G EG G E CD
Sbjct: 167 LARTXRXLQEENIWIVG---TAGEADHTLYQSKXTGRLALVXGAEGEGXRRLTREHCDEL 223
Query: 118 VYIPQYGGGTASLNVTVAASIVL 140
+ IP G +SLNV+VA I L
Sbjct: 224 ISIP-XAGSVSSLNVSVATGICL 245
>pdb|2I6D|A Chain A, The Structure Of A Putative Rna Methyltransferase Of The
Trmh Family From Porphyromonas Gingivalis
Length = 257
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 66/150 (44%), Gaps = 14/150 (9%)
Query: 6 VVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAF------GSHGSTSHVNFRHFHS 59
+++ + NVGT+ R+A FG+ + L G + F S G+ + V +
Sbjct: 106 LLLDGVQDPGNVGTILRTADWFGIRHVWL-GTGSADVFSPKVVQASXGALARVQPTPLKN 164
Query: 60 LSDARVFLKSKDCDICGVEITDNAVDVTQHP-FKKSTAFLLGNEGMGLSAK-ECEICDFF 117
D + + + + G + ++ P F + +LG+EG G+S + EI D
Sbjct: 165 TVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRL 224
Query: 118 VYIPQYG----GGTASLNVTVAASIVLHHF 143
IP G G T SLNV +A +I+ +
Sbjct: 225 T-IPASGLSVKGHTESLNVAIATAILCSEW 253
>pdb|1X7O|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes
pdb|1X7O|B Chain B, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes
Length = 287
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 50/118 (42%), Gaps = 9/118 (7%)
Query: 16 NVGTLARSATAFGVSEMILVG--------RRDFNAFGSHGSTSHVNFRHFHSLSDARVFL 67
N+G++ RSA A G +I+ G + ++ GS S V + D
Sbjct: 139 NIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVXDWVEAR 198
Query: 68 KSKDCDICGVEITDNA-VDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYG 124
++ I V ++ DV F + T L+GNE GLS +CD+ V IP G
Sbjct: 199 RAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPXAG 256
>pdb|1X7P|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes In Complex With The
Cofactor Adomet
pdb|1X7P|B Chain B, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes In Complex With The
Cofactor Adomet
Length = 287
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 50/118 (42%), Gaps = 9/118 (7%)
Query: 16 NVGTLARSATAFGVSEMILVG--------RRDFNAFGSHGSTSHVNFRHFHSLSDARVFL 67
N+G++ RSA A G +I+ G + ++ GS S V + D
Sbjct: 139 NIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEAR 198
Query: 68 KSKDCDICGVEITDNA-VDVTQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQYG 124
++ I V ++ DV F + T L+GNE GLS +CD+ V IP G
Sbjct: 199 RAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAG 256
>pdb|1IPA|A Chain A, Crystal Structure Of Rna 2'-O Ribose Methyltransferase
Length = 274
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/140 (27%), Positives = 65/140 (46%), Gaps = 5/140 (3%)
Query: 6 VVVHNIAKRHNVGTLARSATAFGVSEMILVGRRDFNAFGSHGSTSHVNFRHFHSL--SDA 63
+V + K N+G + RSA A G +++ G D + +++ V F +L S++
Sbjct: 119 LVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVF-SLRTLAASES 177
Query: 64 RVFLKSKDCDICGVEITDNAVDV-TQHPFKKSTAFLLGNEGMGLSAKECEICDFFVYIPQ 122
V K ++ V T +A + + + A +G E GL A E V IP
Sbjct: 178 EVLDWIKQHNLPLVATTPHAEALYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPM 237
Query: 123 YGGGTASLNVTVAASIVLHH 142
G SLNV+V+A+++L+
Sbjct: 238 QGQAD-SLNVSVSAALLLYE 256
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 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,933,190
Number of Sequences: 62578
Number of extensions: 212421
Number of successful extensions: 432
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 422
Number of HSP's gapped (non-prelim): 10
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
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: 49 (23.5 bits)