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= 044572
(457 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JJQ|A Chain A, The Crystal Structure Of Pyrococcus Abyssi Trna
(Uracil-54, C5)-Methyltransferase In Complex With
S-Adenosyl-L- Homocysteine
Length = 425
Score = 72.0 bits (175), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 84/346 (24%), Positives = 142/346 (41%), Gaps = 58/346 (16%)
Query: 53 QCPHFQSCSGCTHEFNLHRPIIVDEATDFFKSIGLLDFTFDSCRLYGWRCRAKLAVRGTS 112
+C F C GCT + + + + + +G S +++G R R LA+
Sbjct: 80 RCKAFGKCGGCTLQHLNYDYQLEFKRKKLKRILGFEVEVVPSPKIFGHRNRIDLAI---- 135
Query: 113 TSPLIGLYQEGTH-NVVDIPHCKAHHPRINAAVELLRQGIKELNVEPYDEDDRTGDLRYV 171
T IG + G +VDI C A+E L++ I+E + ++ G LRY+
Sbjct: 136 TKDGIGFRERGKWWKIVDIDECPVFGKTSREAIERLKEFIEEEKISVWNIKKDEGFLRYM 195
Query: 172 QMAVTTYNTSLPASERYRNGKVQITLVWNSRNEKSPNSDKLESLAEFLWRNGGSRSREHY 231
+ R GK E + F+ + G +Y
Sbjct: 196 VL---------------REGKFT-----------------EEVMVNFVTKEGNLPDPTNY 223
Query: 232 IH--SVWANFQTSTNNVIFGNRWRHLLGETDFWENVGGIDISLAPSSFGQANTRAFDILL 289
S++ + S ++V +G+ R G+ E + +D + P+SF Q N+ L+
Sbjct: 224 FDFDSIYWSVNRSKSDVSYGDIER-FWGKEFIRERLDDVDYLIHPNSFFQTNSYQAVNLV 282
Query: 290 RKLQKYVPYGASVTDLYAGAGVIGLSLAAARKCRSVKCVEINKESQLSFEKTVSRLPKSV 349
RK+ + V G + D+Y+G G G+ LA ++ +VK + N+ F ++R
Sbjct: 283 RKVSELVE-GEKILDMYSGVGTFGIYLA--KRGFNVKGFDSNE-----FAIEMARR---- 330
Query: 350 DGNISWHNADNSIEPLS----WLVGSDVLVVDPPRKGLDSSLVHAL 391
N+ +N D E S + G D ++VDPPR GL LV L
Sbjct: 331 --NVEINNVDAEFEVASDREVSVKGFDTVIVDPPRAGLHPRLVKRL 374
>pdb|2VS1|A Chain A, The Crystal Structure Of Pyrococcus Abyssi Trna
(Uracil-54, C5)-Methyltransferase In Complex With
S-Adenosyl-L- Homocysteine
Length = 425
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 83/346 (23%), Positives = 141/346 (40%), Gaps = 58/346 (16%)
Query: 53 QCPHFQSCSGCTHEFNLHRPIIVDEATDFFKSIGLLDFTFDSCRLYGWRCRAKLAVRGTS 112
+C F C GCT + + + + + +G S +++G R R LA+
Sbjct: 80 RCKAFGKCGGCTLQHLNYDYQLEFKRKKLKRILGFEVEVVPSPKIFGHRNRIDLAI---- 135
Query: 113 TSPLIGLYQEGTH-NVVDIPHCKAHHPRINAAVELLRQGIKELNVEPYDEDDRTGDLRYV 171
T IG + G +VDI A+E L++ I+E + ++ G LRY+
Sbjct: 136 TKDGIGFRERGKWWKIVDIDEXPVFGKTSREAIERLKEFIEEEKISVWNIKKDEGFLRYM 195
Query: 172 QMAVTTYNTSLPASERYRNGKVQITLVWNSRNEKSPNSDKLESLAEFLWRNGGSRSREHY 231
+ R GK E + F+ + G +Y
Sbjct: 196 VL---------------REGKFT-----------------EEVMVNFVTKEGNLPDPTNY 223
Query: 232 IH--SVWANFQTSTNNVIFGNRWRHLLGETDFWENVGGIDISLAPSSFGQANTRAFDILL 289
S++ + S ++V +G+ R G+ E + +D + P+SF Q N+ L+
Sbjct: 224 FDFDSIYWSVNRSKSDVSYGDIER-FWGKEFIRERLDDVDYLIHPNSFFQTNSYQAVNLV 282
Query: 290 RKLQKYVPYGASVTDLYAGAGVIGLSLAAARKCRSVKCVEINKESQLSFEKTVSRLPKSV 349
RK+ + V G + D+Y+G G G+ LA ++ +VK + N+ F ++R
Sbjct: 283 RKVSELVE-GEKILDMYSGVGTFGIYLA--KRGFNVKGFDSNE-----FAIEMARR---- 330
Query: 350 DGNISWHNADNSIEPLS----WLVGSDVLVVDPPRKGLDSSLVHAL 391
N+ +N D E S + G D ++VDPPR GL LV L
Sbjct: 331 --NVEINNVDAEFEVASDREVSVKGFDTVIVDPPRAGLHPRLVKRL 374
>pdb|2BH2|A Chain A, Crystal Structure Of E. Coli 5-Methyluridine
Methyltransferase Ruma In Complex With Ribosomal Rna
Substrate And S-Adenosylhomocysteine.
pdb|2BH2|B Chain B, Crystal Structure Of E. Coli 5-Methyluridine
Methyltransferase Ruma In Complex With Ribosomal Rna
Substrate And S-Adenosylhomocysteine
Length = 433
Score = 36.2 bits (82), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 64/338 (18%), Positives = 128/338 (37%), Gaps = 57/338 (16%)
Query: 53 QCPHFQSCSGCTHEFNLHRPIIVDEATDFFKSIGLLDFTFDSCRL---YGWRCRAKLAVR 109
+CPHF C GC + H + + + + L+ +G+R RA+L++
Sbjct: 80 RCPHFGVCGGCQQQ---HASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLN 136
Query: 110 --GTSTSPLIGLYQEGTHNVVDIPHCKAHHPRINAAVELLRQGIKELNVEPYDEDDRTGD 167
+ +G + G+ ++VD+ C P++ A + +R + L +
Sbjct: 137 YLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRH-------- 188
Query: 168 LRYVQMAVTTYNTSLPASERYRNGKVQITLVWNSRNEKSPNSDKLESLAEFLWRNGGSRS 227
L +V++ T T + ++ ++ S + +KL
Sbjct: 189 LGHVELVQATSGT--------------LMILRHTAPLSSADREKL--------------- 219
Query: 228 REHYIHSVWANFQTSTNNVIFGNRWRHLLGETDFWENVGGIDISLAPSSFGQANTRAFDI 287
E + HS + + ++ I + GE W + G+ ++ +P F Q N
Sbjct: 220 -ERFSHSEGLDLYLAPDSEILET----VSGEMP-WYDSNGLRLTFSPRDFIQVNAGVNQK 273
Query: 288 LLRKLQKYVPYGAS--VTDLYAGAGVIGLSLAAARKCRSVKCVEINKESQLSFEKTVSRL 345
++ + +++ V DL+ G G L LA + SV VE + + + +RL
Sbjct: 274 MVARALEWLDVQPEDRVLDLFCGMGNFTLPLAT--QAASVVGVE-GVPALVEKGQQNARL 330
Query: 346 PKSVDGNISWHNADNSIEPLSWLV-GSDVLVVDPPRKG 382
+ N + + W G D +++DP R G
Sbjct: 331 NGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAG 368
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 56 HFQSCSGCTHEFNLHRPIIVDEATDFFKSIGLLDFTFDSCRLYGWRCRAKLAVRGTSTS- 114
+FQS +PI+ +E T FK +G+ D ++C GW K+ + +
Sbjct: 19 YFQSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLAL 78
Query: 115 ---PLIGLYQEGT 124
+IGL + G+
Sbjct: 79 QGRDIIGLAETGS 91
>pdb|1UWV|A Chain A, Crystal Structure Of Ruma, The Iron-Sulfur Cluster
Containing E. Coli 23s Ribosomal Rna 5-Methyluridine
Methyltransferase
Length = 433
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 67/341 (19%), Positives = 130/341 (38%), Gaps = 63/341 (18%)
Query: 53 QCPHFQSCSGCTHEFNLHRPIIVDEATDFFKSIGLLDFT-FDSCRL-----YGWRCRAKL 106
+CPHF C GC + H + + + + KS L D + +G+R RA+L
Sbjct: 80 RCPHFGVCGGCQQQ---HASVDLQQRS---KSAALARLXKHDVSEVIADVPWGYRRRARL 133
Query: 107 AVRGTSTSPLI--GLYQEGTHNVVDIPHCKAHHPRINAAVELLRQGIKELNVEPYDEDDR 164
++ + + G + G+ ++VD+ C P++ A + +R + L +
Sbjct: 134 SLNYLPKTQQLQXGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAXRH----- 188
Query: 165 TGDLRYVQMAVTTYNTSLPASERYRNGKVQITLVWNSRNEKSPNSDKLESLAEFLWRNGG 224
L +V++ T T + ++ ++ S + +KL
Sbjct: 189 ---LGHVELVQATSGT--------------LXILRHTAPLSSADREKL------------ 219
Query: 225 SRSREHYIHSVWANFQTSTNNVIFGNRWRHLLGETDFWENVGGIDISLAPSSFGQANTRA 284
E + HS + + ++ I + GE W + G+ ++ +P F Q N
Sbjct: 220 ----ERFSHSEGLDLYLAPDSEILET----VSGEXP-WYDSNGLRLTFSPRDFIQVNAGV 270
Query: 285 FDILLRKLQKYVPYGAS--VTDLYAGAGVIGLSLAAARKCRSVKCVEINKESQLSFEKTV 342
+ + +++ V DL+ G G L LA + SV VE + + +
Sbjct: 271 NQKXVARALEWLDVQPEDRVLDLFCGXGNFTLPLAT--QAASVVGVE-GVPALVEKGQQN 327
Query: 343 SRLPKSVDGNISWHNADNSIEPLSWLV-GSDVLVVDPPRKG 382
+RL + N + + W G D +++DP R G
Sbjct: 328 ARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAG 368
>pdb|3BT7|A Chain A, Structure Of E. Coli 5-Methyluridine Methyltransferase
Trma In Complex With 19 Nucleotide T-Arm Analogue
pdb|3BT7|B Chain B, Structure Of E. Coli 5-Methyluridine Methyltransferase
Trma In Complex With 19 Nucleotide T-Arm Analogue
Length = 369
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 38/135 (28%), Positives = 57/135 (42%), Gaps = 21/135 (15%)
Query: 275 SSFGQANTRAFDILLRKLQKYVPYGAS--VTDLYAGAGVIGLSLAAARKCRSVKCVEINK 332
+SF Q N A +I + + V G+ + +LY G G SLA AR V EI K
Sbjct: 189 NSFTQPNA-AMNIQMLEWALDVTKGSKGDLLELYCGNG--NFSLALARNFDRVLATEIAK 245
Query: 333 ESQLSFEKTVSRLPKSVD-------GNISWHNADNSIEPLSWLVGSDV-------LVVDP 378
S + + ++ +D + A N + + L G D+ + VDP
Sbjct: 246 PSVAAAQYNIA--ANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDP 303
Query: 379 PRKGLDSSLVHALQS 393
PR GLDS +Q+
Sbjct: 304 PRSGLDSETEKMVQA 318
>pdb|4DZR|A Chain A, The Crystal Structure Of Protein-(Glutamine-N5)
Methyltransferase (Release Factor-Specific) From
Alicyclobacillus Acidocaldarius Subsp. Acidocaldarius
Dsm 446
Length = 215
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 291 KLQKYVPYGASVTDLYAGAGVIGLSLAAARKCRSVKCVEINKESQLSFEKTVSRLPKSVD 350
+ K P G V D+ G+G I +S+A A SV V+++ ++ + R VD
Sbjct: 23 RFLKRXPSGTRVIDVGTGSGCIAVSIALACPGVSVTAVDLSXDALAVARRNAERFGAVVD 82
Query: 351 GNISWHNADNSIEPLSWLV 369
W AD + WL+
Sbjct: 83 ----WAAADG----IEWLI 93
>pdb|3P9N|A Chain A, Rv2966c Of M. Tuberculosis Is A Rsmd-Like
Methyltransferase
Length = 189
Score = 31.6 bits (70), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 12/97 (12%)
Query: 299 GASVTDLYAGAGVIGLSLAAARKCRSVKCVEINKESQLSFEKTVSRLPKS----VDGNIS 354
G +V DLYAG+G +GL A +R SV VE ++ S + + L S G ++
Sbjct: 45 GLAVLDLYAGSGALGLE-ALSRGAASVLFVESDQRSAAVIARNIEALGLSGATLRRGAVA 103
Query: 355 WHNADNSIEPLSWLVGSDVLVVDPPRKGLDSSLVHAL 391
A + P+ D+++ DPP +DS+ V A+
Sbjct: 104 AVVAAGTTSPV------DLVLADPPYN-VDSADVDAI 133
>pdb|3LMK|A Chain A, Ligand Binding Domain Of Metabotropoc Glutamate Receptor
Mglur5 Complexed With Glutamate
pdb|3LMK|B Chain B, Ligand Binding Domain Of Metabotropoc Glutamate Receptor
Mglur5 Complexed With Glutamate
Length = 492
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 267 GIDISLAPSSFGQANTRAFDILLRKLQKYVPYGASVTDLYAGAGVIGLSLAAAR 320
GI I+ + + A ++FD LL+KL ++P V G V GL +A R
Sbjct: 226 GISIAHSYKIYSNAGEQSFDKLLKKLTSHLPKARVVACFCEGMTVRGLLMAMRR 279
>pdb|3L76|A Chain A, Crystal Structure Of Aspartate Kinase From Synechocystis
pdb|3L76|B Chain B, Crystal Structure Of Aspartate Kinase From Synechocystis
Length = 600
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 62/138 (44%), Gaps = 21/138 (15%)
Query: 260 DFWENVGGIDISLAPS--SFGQANTRAFDILLRKLQKYVPYGASVTDLYAGAGVIGLSLA 317
D + ++AP+ S+ +A+ A I+ + + K AGAG+IG
Sbjct: 321 DLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIAKIA---------IAGAGMIGRPGI 371
Query: 318 AARKCRSVKCVEINKESQLSFEKTVSRLPKSVDGNISWHNADNSIEPLSWLVGSDVLVVD 377
AA+ +++ V +N E + E VS + I +AD +I LS G + +
Sbjct: 372 AAKMFKTLADVGVNIEMISTSEVKVSCV-------IDQRDADRAIAALSNAFG---VTLS 421
Query: 378 PPRKGLDSSLVHALQSIG 395
PP+ D+S + A++ +
Sbjct: 422 PPKNQTDTSHLPAVRGVA 439
>pdb|3IJI|A Chain A, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJI|B Chain B, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJL|A Chain A, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Pro-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJL|B Chain B, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Pro-D-Glu;
Nonproductive Substrate Binding.
pdb|3IJQ|A Chain A, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu; Productive
Substrate Binding.
pdb|3IJQ|B Chain B, Structure Of Dipeptide Epimerase From Bacteroides
Thetaiotaomicron Complexed With L-Ala-D-Glu; Productive
Substrate Binding
Length = 338
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 29/55 (52%)
Query: 325 VKCVEINKESQLSFEKTVSRLPKSVDGNISWHNADNSIEPLSWLVGSDVLVVDPP 379
VK N + + ++V+ LP +VD N W + +++ + WL +++++ P
Sbjct: 154 VKLGRDNDKEMIETIRSVTDLPIAVDANQGWKDRQYALDMIHWLKEKGIVMIEQP 208
>pdb|2R7A|A Chain A, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|B Chain B, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|C Chain C, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|D Chain D, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2RG7|A Chain A, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|B Chain B, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|C Chain C, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|D Chain D, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
Length = 256
Score = 28.9 bits (63), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 33/92 (35%), Positives = 44/92 (47%), Gaps = 8/92 (8%)
Query: 293 QKYVPYGASVTDL-YA-GAG--VIGLSLAAARKCRSVKCVEINKESQLSFEKTVSRLPKS 348
++ V G S+T+L YA GAG V+G+ + + K I QLS E +S P S
Sbjct: 3 ERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDS 62
Query: 349 VDGNISWHNADNSIEPLSWLVGSDVLVVDPPR 380
V I+W +A I L L V VV PR
Sbjct: 63 V---ITWQDAGPQIV-LDQLRAQKVNVVTLPR 90
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 0.134 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,784,374
Number of Sequences: 62578
Number of extensions: 488823
Number of successful extensions: 1070
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1056
Number of HSP's gapped (non-prelim): 18
length of query: 457
length of database: 14,973,337
effective HSP length: 102
effective length of query: 355
effective length of database: 8,590,381
effective search space: 3049585255
effective search space used: 3049585255
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)