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= 020213
(329 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 49/212 (23%), Positives = 92/212 (43%), Gaps = 16/212 (7%)
Query: 78 EKLVPMVECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMI 137
+KLV + L+ + P E A+ + R E+ + +L F + +G+ + QLG +
Sbjct: 10 QKLVLLGVDLSKIEKHP-EAANLLLRL------DFEKDIKQMLLFLKDVGIEDNQLGAFL 62
Query: 138 LLNPRLISYSIESKLTETVDFLTSLGLAREGMIGKVLVKHPFIMGYSV---DNRLRPTSE 194
N + S +E+ L V +L S ++ + +++ K PF++ +SV DNRL
Sbjct: 63 TKNHAIFSEDLEN-LKTRVAYLHSKNFSKAD-VAQMVRKAPFLLNFSVERLDNRL---GF 117
Query: 195 FLKSVGLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALVAAYPPILI 254
F K + L + + V+ P +L + + + GF +I ++ P +L
Sbjct: 118 FQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRIPKMLT 177
Query: 255 KSIKNSLEPRIKFLVEVMGRQIDEVADYPDFF 286
+ K L F+ VM + +P F
Sbjct: 178 AN-KMKLTETFDFVHNVMSIPHHIIVKFPQVF 208
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 38/163 (23%), Positives = 70/163 (42%), Gaps = 10/163 (6%)
Query: 7 QNGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYL-KSIGILERKLPNVV 65
+N + + +L + F+ + M ++ L +R + + K + + +K ++V
Sbjct: 74 ENLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLV 133
Query: 66 SKCPKILTLGLNEKLVPMVECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQ- 124
+ P++LT L M LG K E+ ITR P +L+ + + KL F
Sbjct: 134 VRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRIPKMLT-ANKMKLTETFDFVHN 192
Query: 125 ALGVPEKQLGRM-ILLNPRLISYSIESKLTETVDFLTSLGLAR 166
+ +P + + + N RL K+ E FLT LG A+
Sbjct: 193 VMSIPHHIIVKFPQVFNTRLF------KVKERHLFLTYLGRAQ 229
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 78/177 (44%), Gaps = 9/177 (5%)
Query: 113 EEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGMIGK 172
E+ + +L F + +G+ + QLG + N + S +E+ L V +L S ++ + +
Sbjct: 66 EKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSKAD-VAQ 123
Query: 173 VLVKHPFIMGYSV---DNRLRPTSEFLKSVGLKELDLQVVAVKFPEVLCRDVNKILSPNF 229
++ K PF++ +SV DNRL F K + L + + V+ P +L + +
Sbjct: 124 MVRKAPFLLNFSVERLDNRL---GFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMK 180
Query: 230 TFLKRCGFADGQIAALVAAYPPILIKSIKNSLEPRIKFLVEVMGRQIDEVADYPDFF 286
+ GF +I ++ P +L + K L F+ VM + +P F
Sbjct: 181 VYRLELGFKHNEIQHMITRIPKMLTAN-KMKLTETFDFVHNVMSIPHHIIVKFPQVF 236
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 38/163 (23%), Positives = 70/163 (42%), Gaps = 10/163 (6%)
Query: 7 QNGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYL-KSIGILERKLPNVV 65
+N + + +L + F+ + M ++ L +R + + K + + +K ++V
Sbjct: 102 ENLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLV 161
Query: 66 SKCPKILTLGLNEKLVPMVECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQ- 124
+ P++LT L M LG K E+ ITR P +L+ + + KL F
Sbjct: 162 VRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRIPKMLT-ANKMKLTETFDFVHN 220
Query: 125 ALGVPEKQLGRM-ILLNPRLISYSIESKLTETVDFLTSLGLAR 166
+ +P + + + N RL K+ E FLT LG A+
Sbjct: 221 VMSIPHHIIVKFPQVFNTRLF------KVKERHLFLTYLGRAQ 257
>pdb|3MEY|A Chain A, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With Atp
pdb|3MEY|B Chain B, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With Atp
pdb|3MF1|A Chain A, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With An Analogue Of Glycyl Adenylate
pdb|3MF1|B Chain B, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With An Analogue Of Glycyl Adenylate
pdb|3MF2|A Chain A, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With Amp
pdb|3MF2|B Chain B, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With Amp
pdb|3PZC|A Chain A, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With Coenzyme A
pdb|3PZC|B Chain B, Crystal Structure Of Class Ii Aars Homologue (Bll0957)
Complexed With Coenzyme A
Length = 346
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 83 MVECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALG 127
+VE LA L T E + RFPP++S + EK L +F LG
Sbjct: 66 IVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLG 110
>pdb|3GRR|A Chain A, Crystal Structure Of The Complex Between S-Adenosyl
Homocysteine And Methanocaldococcus Jannaschi Dim1.
pdb|3GRU|A Chain A, Crystal Structure Of The Complex Between Amp And
Methanocaldococcus Jannaschi Dim1
pdb|3GRV|A Chain A, Crystal Structure Of The Complex Between Adenosine And
Methanocaldococcus Jannaschi Dim1
pdb|3GRY|A Chain A, Crystal Structure Of The Complex Between S-Adenosyl
Methionine And Methanocaldococcus Jannaschi Dim1
Length = 295
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 59/137 (43%), Gaps = 28/137 (20%)
Query: 129 PEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGMIGKVLVKHP-FIMGYSVDN 187
P+K+LG+ L++ ++ ++ES D + +GL + G++ + L K+ + +D
Sbjct: 24 PKKKLGQCFLIDKNFVNKAVESANLTKDDVVLEIGLGK-GILTEELAKNAKKVYVIEIDK 82
Query: 188 RLRPTSEFLKS--------------VGLKELDLQVVAVKFPEVLCRDVNKILSP-NFTFL 232
L P + LK V L +LD V P +I SP F +
Sbjct: 83 SLEPYANKLKELYNNIEIIWGDALKVDLNKLDFNKVVANLPY-------QISSPITFKLI 135
Query: 233 KRCGFADGQIAALVAAY 249
KR GF +A L+ Y
Sbjct: 136 KR-GF---DLAVLMYQY 148
>pdb|1T11|A Chain A, Trigger Factor
pdb|1T11|B Chain B, Trigger Factor
Length = 392
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 210 AVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALVAAYPPILIKSIKNSLEPRIK 266
A+K +V R++ ++ N F+ R G A+G + AL A + + +K +++ RIK
Sbjct: 237 AIKVNKVEARELPEL---NDEFVARFGVAEGGVDALKAEVRKNMERELKQAIKARIK 290
>pdb|4FP9|B Chain B, Human Mterf4-Nsun4 Protein Complex
pdb|4FP9|E Chain E, Human Mterf4-Nsun4 Protein Complex
pdb|4FP9|G Chain G, Human Mterf4-Nsun4 Protein Complex
pdb|4FP9|H Chain H, Human Mterf4-Nsun4 Protein Complex
Length = 335
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 61/134 (45%), Gaps = 6/134 (4%)
Query: 143 LISYSIESKLTETVDFLTS---LGLAREGMIGKVLVKHPFIMGYSVDNRLRPTSEFLKSV 199
L+S + L + +D ++ LGL E + VL K P ++ + ++R S +L+ +
Sbjct: 66 LLSVRRGASLQQLLDIISEFILLGLNPEP-VCVVLKKSPQLLKLPI-MQMRKRSSYLQKL 123
Query: 200 GLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALVAAYPPILIKSIKN 259
GL E L+ V PE+ I ++C F Q+ ++ + P +L + +
Sbjct: 124 GLGEGKLKRVLYCCPEIFTMRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDL-G 182
Query: 260 SLEPRIKFLVEVMG 273
LE + ++ MG
Sbjct: 183 QLEYKFQYAYFRMG 196
>pdb|4FZV|B Chain B, Crystal Structure Of The Human Mterf4:nsun4:sam Ternary
Complex
Length = 239
Score = 27.7 bits (60), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 2/101 (1%)
Query: 173 VLVKHPFIMGYSVDNRLRPTSEFLKSVGLKELDLQVVAVKFPEVLCRDVNKILSPNFTFL 232
VL K P ++ + ++R S +L+ +GL E L+ V PE+ I
Sbjct: 53 VLKKSPQLLKLPI-MQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMRQQDINDTVRLLK 111
Query: 233 KRCGFADGQIAALVAAYPPILIKSIKNSLEPRIKFLVEVMG 273
++C F Q+ ++ + P +L + + LE + ++ MG
Sbjct: 112 EKCLFTVQQVTKILHSCPSVLREDL-GQLEYKFQYAYFRMG 151
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
0.324 0.141 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,673,711
Number of Sequences: 62578
Number of extensions: 327215
Number of successful extensions: 769
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 756
Number of HSP's gapped (non-prelim): 11
length of query: 329
length of database: 14,973,337
effective HSP length: 99
effective length of query: 230
effective length of database: 8,778,115
effective search space: 2018966450
effective search space used: 2018966450
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)