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= 012091
(471 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 47/209 (22%), Positives = 90/209 (43%), Gaps = 15/209 (7%)
Query: 270 GLSDQEIFRIFLVFPAVISASRERKLRPRIDFLKQCGLGSEDIFKFLTKAPLFLALSFDN 329
G+ D ++ A+ S E L+ R+ +L D+ + + KAP L S +
Sbjct: 80 GIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVER 138
Query: 330 IAIKLGFLVKIGYEC---RTRELAAAMGSVTRTSCENLQKVIGLF-LSYGLSFADIYIMS 385
+ +LGF K E +TR+L + + S E +++ + ++ L G +I M
Sbjct: 139 LDNRLGFFQK-ELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMI 197
Query: 386 KKHPQILQYNHKSLEEKMEYLIVGMGREVGELLAFPAFLGYKLDDRIKHRY--------E 437
+ P++L N L E +++ M ++ FP +L ++K R+
Sbjct: 198 TRIPKMLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRL-FKVKERHLFLTYLGRA 256
Query: 438 AKRKTLGDGLSINKLLSVSVERFSTKIKK 466
+ +S++KL+S+ E F +I K
Sbjct: 257 QYDPAKPNYISLDKLVSIPDEIFCEEIAK 285
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 47/210 (22%), Positives = 90/210 (42%), Gaps = 15/210 (7%)
Query: 269 AGLSDQEIFRIFLVFPAVISASRERKLRPRIDFLKQCGLGSEDIFKFLTKAPLFLALSFD 328
G+ D ++ A+ S E L+ R+ +L D+ + + KAP L S +
Sbjct: 51 VGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVE 109
Query: 329 NIAIKLGFLVKIGYEC---RTRELAAAMGSVTRTSCENLQKVIGLF-LSYGLSFADIYIM 384
+ +LGF K E +TR+L + + S E +++ + ++ L G +I M
Sbjct: 110 RLDNRLGFFQK-ELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHM 168
Query: 385 SKKHPQILQYNHKSLEEKMEYLIVGMGREVGELLAFPAFLGYKLDDRIKHRY-------- 436
+ P++L N L E +++ M ++ FP +L ++K R+
Sbjct: 169 ITRIPKMLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRL-FKVKERHLFLTYLGR 227
Query: 437 EAKRKTLGDGLSINKLLSVSVERFSTKIKK 466
+ +S++KL+S+ E F +I K
Sbjct: 228 AQYDPAKPNYISLDKLVSIPDEIFCEEIAK 257
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 36/130 (27%), Positives = 62/130 (47%), Gaps = 12/130 (9%)
Query: 206 LIVRCPKILN--YDLDTQLIPKVRV--LSELGGDDVDSTAAIVWKFPAILSYSLEHIGKH 261
L+ P+ + DL+ Q++ ++ LS D D I++K PAIL S + + +
Sbjct: 143 LLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNPAILIQSTKRVKAN 202
Query: 262 VEFLRSFAGLSDQEIFRIFLVFPAV----ISASRERKLRPRI-DFLKQCGLGSEDIFKFL 316
+EFLRS L+ +E+ + + P +S R+ I + L G E++ KF+
Sbjct: 203 IEFLRSTFNLNSEELL-VLICGPGAEILDLSNDAARRSYANIKEKLFSLGCTEEEVQKFV 261
Query: 317 TKAP--LFLA 324
P +FLA
Sbjct: 262 LSYPDVIFLA 271
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 61/130 (46%), Gaps = 12/130 (9%)
Query: 206 LIVRCPKILN--YDLDTQLIPKVRV--LSELGGDDVDSTAAIVWKFPAILSYSLEHIGKH 261
L+ P+ + DL+ Q++ ++ LS D D I++K P IL S + + +
Sbjct: 143 LLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQSTKRVKAN 202
Query: 262 VEFLRSFAGLSDQEIFRIFLVFPAV----ISASRERKLRPRI-DFLKQCGLGSEDIFKFL 316
+EFLRS L+ +E+ + + P +S R+ I + L G E++ KF+
Sbjct: 203 IEFLRSTFNLNSEELL-VLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFV 261
Query: 317 TKAP--LFLA 324
P +FLA
Sbjct: 262 LSYPDVIFLA 271
>pdb|3N6S|A Chain A, Crystal Structure Of Human Mitochondrial Mterf In Complex
With A 15- Mer Dna Encompassing The Trnaleu(Uur) Binding
Sequence
Length = 353
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 61/130 (46%), Gaps = 12/130 (9%)
Query: 206 LIVRCPKILN--YDLDTQLIPKVRV--LSELGGDDVDSTAAIVWKFPAILSYSLEHIGKH 261
L+ P+ + DL+ Q++ ++ LS D D I++K P IL S + + +
Sbjct: 144 LLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQSTKRVKAN 203
Query: 262 VEFLRSFAGLSDQEIFRIFLVFPAV----ISASRERKLRPRI-DFLKQCGLGSEDIFKFL 316
+EFLRS L+ +E+ + + P +S R+ I + L G E++ KF+
Sbjct: 204 IEFLRSTFNLNSEELL-VLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFV 262
Query: 317 TKAP--LFLA 324
P +FLA
Sbjct: 263 LSYPDVIFLA 272
>pdb|3N7Q|A Chain A, Crystal Structure Of Human Mitochondrial Mterf Fragment
(Aa 99-399) In Complex With A 12-Mer Dna Encompassing
The Trnaleu(Uur) Binding Sequence
Length = 310
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 61/130 (46%), Gaps = 12/130 (9%)
Query: 206 LIVRCPKILN--YDLDTQLIPKVRV--LSELGGDDVDSTAAIVWKFPAILSYSLEHIGKH 261
L+ P+ + DL+ Q++ ++ LS D D I++K P IL S + + +
Sbjct: 101 LLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQSTKRVKAN 160
Query: 262 VEFLRSFAGLSDQEIFRIFLVFPAV----ISASRERKLRPRI-DFLKQCGLGSEDIFKFL 316
+EFLRS L+ +E+ + + P +S R+ I + L G E++ KF+
Sbjct: 161 IEFLRSTFNLNSEELL-VLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFV 219
Query: 317 TKAP--LFLA 324
P +FLA
Sbjct: 220 LSYPDVIFLA 229
>pdb|2WM8|A Chain A, Crystal Structure Of Human Magnesium-Dependent Phosphatase
1 Of The Haloacid Dehalogenase Superfamily (Mgc5987)
Length = 187
Score = 32.0 bits (71), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 2/90 (2%)
Query: 92 LQSVGIKGMAFCRLISKDSNVLLAEEIDRLICFVRDDLDGNIEPMKLERLLTSTETKF-- 149
LQS+G+ G A R + L E D FV ++ + ERL T F
Sbjct: 80 LQSLGVPGAAASRTSEIEGANQLLELFDLFRYFVHREIYPGSKITHFERLQQKTGIPFSQ 139
Query: 150 LVGFDQKVRLLLQLGVPQETILHVLNNINL 179
++ FD + R ++ + T +H+ N +NL
Sbjct: 140 MIFFDDERRNIVDVSKLGVTCIHIQNGMNL 169
>pdb|4FZV|B Chain B, Crystal Structure Of The Human Mterf4:nsun4:sam Ternary
Complex
Length = 239
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 60 IGLNEKEVDSLLEKNPTLRVTPLDKMRSRILSLQSVGI 97
+GLN + V +L+K+P L P+ +MR R LQ +G+
Sbjct: 43 LGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGL 80
>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 = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 60 IGLNEKEVDSLLEKNPTLRVTPLDKMRSRILSLQSVGI 97
+GLN + V +L+K+P L P+ +MR R LQ +G+
Sbjct: 88 LGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGL 125
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 0.140 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,574,440
Number of Sequences: 62578
Number of extensions: 503275
Number of successful extensions: 1243
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1227
Number of HSP's gapped (non-prelim): 20
length of query: 471
length of database: 14,973,337
effective HSP length: 102
effective length of query: 369
effective length of database: 8,590,381
effective search space: 3169850589
effective search space used: 3169850589
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: 53 (25.0 bits)