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= 008989
(547 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T11|A Chain A, Trigger Factor
pdb|1T11|B Chain B, Trigger Factor
Length = 392
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 88/390 (22%), Positives = 165/390 (42%), Gaps = 39/390 (10%)
Query: 103 RLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILK 162
RL++ VP A +D+ L + K + GFR GK+P ++ G + V++ + +++
Sbjct: 17 RLNITVPAANIEDAVAAELRNIAKNRRFDGFRKGKVPMKMVAKMYG-KAVRQDVLGEVMQ 75
Query: 163 RTLPHAMTSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKN 222
R H + ++ + + F+ +E L + +V PEV+ G +N
Sbjct: 76 R---HFIEAIVKEKINPAG--APTFAPVE--IGEGKDLVFTATFEVYPEVEL---KGLEN 125
Query: 223 LKIVVEIDNDTXXXXXXXXXLRRRHKSLGSLKIVTDRGLQVGDIAIVDI--SATTIDEDE 280
I VE L K + K V D + G +D S ++ +
Sbjct: 126 --IAVEKPAAEVTDADVAEMLETLRKQQATWKEV-DEAAENGKRVSIDFVGSIDGVEFEG 182
Query: 281 SNVQNIPDAETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQ 340
+N P G +++PGF D I G +G + FPE + E+L+G
Sbjct: 183 GKAENFPLEMGAG---------RMIPGFEDGIVGKTKGMEFVIDVTFPEDYHAENLKGKA 233
Query: 341 AQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKC-REVEQTAKDQATDNA 399
A+F ++ ++ R+LP+L+D + ++ +K + + RE++Q K + + A
Sbjct: 234 AKFAIKVNKVEARELPELNDEFVARFGVAEGGVDALKAEVRKNMERELKQAIKARIKEQA 293
Query: 400 ILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQ 459
I + L K EI +P +L +++ +L+ QA + AA P +E E Q
Sbjct: 294 I-EGLVKENEIQVPSALIDQE------INVLRQQAAQRFGGNVEAAAQLP---RELFEEQ 343
Query: 460 RENITNVIKQNLAVGDIFKRENLQFSTEDL 489
+ V L +G++ + L+ E +
Sbjct: 344 AKRRVVV---GLLLGEVIRTHELKADEEKV 370
>pdb|1W26|A Chain A, Trigger Factor In Complex With The Ribosome Forms A
Molecular Cradle For Nascent Proteins
pdb|1W26|B Chain B, Trigger Factor In Complex With The Ribosome Forms A
Molecular Cradle For Nascent Proteins
pdb|2VRH|A Chain A, Structure Of The E. Coli Trigger Factor Bound To A
Translating Ribosome
Length = 432
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 80/359 (22%), Positives = 157/359 (43%), Gaps = 34/359 (9%)
Query: 103 RLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILK 162
R+++ + + + K L + K+V+I GFR GK+P +++ G +V++ + +
Sbjct: 14 RVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPXNIVAQRYG-ASVRQDVLGDLXS 72
Query: 163 RTLPHAMTSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKN 222
R A+ +++ + + + Y +Y V +V PEV+ +
Sbjct: 73 RNFIDAI-------IKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVELQGLEAIEV 125
Query: 223 LKIVVEI-DNDTXXXXXXXXXLRRRHKSLGSLKIVTDRGLQVGDIAIVDISATTIDEDES 281
K +VE+ D D LR++ + D ++ D +D + + +D +E
Sbjct: 126 EKPIVEVTDADVDGXLDT---LRKQQATWKE----KDGAVEAEDRVTIDFTGS-VDGEEF 177
Query: 282 NVQNIPDAETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQA 341
D F G + +PGF D I G + GE + + FPE + E+L+G A
Sbjct: 178 EGGKASD-----FVLAXGQG-RXIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAA 231
Query: 342 QFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVK-ETLLQKCREVEQTAKDQATDNAI 400
+F + +++ R+LP+L + ++E ++ E RE++ +++ AI
Sbjct: 232 KFAINLKKVEERELPELTAEFIKRFGVEDGSVEGLRAEVRKNXERELKSAIRNRVKSQAI 291
Query: 401 LDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQ 459
+ L K +ID+P +L + + +L+ QA + + AL P +E E Q
Sbjct: 292 -EGLVKANDIDVPAALIDSE------IDVLRRQAAQRFGGNEKQALELP---RELFEEQ 340
>pdb|1L1P|A Chain A, Solution Structure Of The Ppiase Domain From E. Coli
Trigger Factor
Length = 106
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 36/56 (64%)
Query: 303 KVLPGFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELFYRDLPKL 358
+++PGF D I G + GE + + FPE + E+L+G A+F + +++ R+LP+L
Sbjct: 50 RMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELPEL 105
>pdb|2D3O|1 Chain 1, Structure Of Ribosome Binding Domain Of The Trigger Factor
On The 50s Ribosomal Subunit From D. Radiodurans
Length = 112
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 99 NSTVRLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVE 158
+ V V VP A +Y +V L + V++PGFRPGK P V+ E V K VE
Sbjct: 9 GNKVEFKVSVPAAEVNRAYDQVWAGLARDVRVPGFRPGKAPRKVI-----ENRVGKGYVE 63
Query: 159 SILKRTL 165
S ++ L
Sbjct: 64 SQVRDRL 70
>pdb|2AAR|7 Chain 7, Structure Of Trigger Factor Binding Domain In Biologically
Homologous Complex With Eubacterial Ribosome
Length = 113
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 99 NSTVRLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVE 158
+ V V VP A +Y +V L + V++PGFRPGK P V+ E V K VE
Sbjct: 8 GNKVEFKVSVPAAEVNRAYDQVWAGLARDVRVPGFRPGKAPRKVI-----ENRVGKGYVE 62
Query: 159 SILKRTL 165
S ++ L
Sbjct: 63 SQVRDRL 69
>pdb|3GTY|X Chain X, Promiscuous Substrate Recognition In Folding And Assembly
Activities Of The Trigger Factor Chaperone
Length = 433
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 46/81 (56%)
Query: 338 GVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKCREVEQTAKDQATD 397
G + + +E E++ R LP++ D LA + T+EQ+KE+L ++ +E+ ++
Sbjct: 213 GKKYTYKLEVEEVYKRTLPEIGDELAKSVNNEFETLEQLKESLKKEGKEIYDVEMKESMR 272
Query: 398 NAILDQLYKMVEIDIPQSLFE 418
+L++L ++VEI+I E
Sbjct: 273 EQLLEKLPEIVEIEISDRTLE 293
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 27/40 (67%), Gaps = 3/40 (7%)
Query: 111 AVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQ 150
A +D R LN ++V+IPGFR G+IP++VL +GE+
Sbjct: 25 AQAEDKAVRYLN---QRVEIPGFRKGRIPKNVLKMKLGEE 61
>pdb|3GU0|A Chain A, Promiscuous Substrate Recognition In Folding And Assembly
Activities Of The Trigger Factor Chaperone
Length = 412
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 46/81 (56%)
Query: 338 GVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKCREVEQTAKDQATD 397
G + + +E E++ R LP++ D LA + T+EQ+KE+L ++ +E+ ++
Sbjct: 213 GKKYTYKLEVEEVYKRTLPEIGDELAKSVNNEFETLEQLKESLKKEGKEIYDVEMKESMR 272
Query: 398 NAILDQLYKMVEIDIPQSLFE 418
+L++L ++VEI+I E
Sbjct: 273 EQLLEKLPEIVEIEISDRTLE 293
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 27/40 (67%), Gaps = 3/40 (7%)
Query: 111 AVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQ 150
A +D R LN ++V+IPGFR G+IP++VL +GE+
Sbjct: 25 AQAEDKAVRYLN---QRVEIPGFRKGRIPKNVLKMKLGEE 61
>pdb|2NSB|A Chain A, Structures Of And Interactions Between Domains Of Trigger
Factor From Themotoga Maritima
pdb|2NSC|A Chain A, Structures Of And Interactions Between Domains Of Trigger
Factor From Themotoga Maritima
Length = 109
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 49/88 (55%), Gaps = 14/88 (15%)
Query: 111 AVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILKRTLPHAMT 170
A +D R LN+ +V+IPGFR G+IP++VL +GE+ ++ T++ ++ +P +
Sbjct: 25 AQAEDKAVRYLNQ---RVEIPGFRKGRIPKNVLKMKLGEE-FQEYTLDFLMD-LIPDTLK 79
Query: 171 S--------VTGRALRD-SVRIVTKFSE 189
VT R L+D + R+V + E
Sbjct: 80 DRKLILSPIVTERELKDVTARVVVEVHE 107
>pdb|1W2B|5 Chain 5, Trigger Factor Ribosome Binding Domain In Complex With 50s
Length = 144
Score = 32.3 bits (72), Expect = 0.64, Method: Composition-based stats.
Identities = 26/129 (20%), Positives = 59/129 (45%), Gaps = 8/129 (6%)
Query: 103 RLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILK 162
R+++ + + + K L + K+V+I GFR GK+P +++ G +V++ + ++
Sbjct: 14 RVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPMNIVAQRYG-ASVRQDVLGDLMS 72
Query: 163 RTLPHAMTSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKN 222
R A+ +++ + + + Y +Y V +V PEV+ +
Sbjct: 73 RNFIDAI-------IKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVELQGLEAIEV 125
Query: 223 LKIVVEIDN 231
K +VE+ +
Sbjct: 126 EKPIVEVTD 134
>pdb|1T5B|A Chain A, Structural Genomics, A Protein From Salmonella Typhimurium
Similar To E. Coli Acyl Carrier Protein
Phosphodiesterase
pdb|1T5B|B Chain B, Structural Genomics, A Protein From Salmonella Typhimurium
Similar To E. Coli Acyl Carrier Protein
Phosphodiesterase
Length = 201
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 313 SGIQRGETKSFRLA--FPESWRQEHLRGVQAQFTVECRELFYRDLPKLDDSLAGKLLPG 369
S I G ++S +L F E WR++H V + TV R+L +P LD L G + PG
Sbjct: 9 SSILAGYSQSGQLTDYFIEQWREKH---VADEITV--RDLAANPVPVLDGELVGAMRPG 62
>pdb|4HN9|A Chain A, Crystal Structure Of Iron Abc Transporter Solute-Binding
Protein From Eubacterium Eligens
pdb|4HN9|B Chain B, Crystal Structure Of Iron Abc Transporter Solute-Binding
Protein From Eubacterium Eligens
Length = 335
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 85 RLPADIEVTESPEPNSTVR----LSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGK 137
+LP +IE +SP P S + SV PE V KD Y+ + + + GF P K
Sbjct: 281 KLPNNIEAWDSPVPGSFLGSIYIASVLHPEKVTKDFYETCVTKFYESFY--GFTPAK 335
>pdb|1HXV|A Chain A, Ppiase Domain Of The Mycoplasma Genitalium Trigger Factor
Length = 113
Score = 30.0 bits (66), Expect = 3.3, Method: Composition-based stats.
Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 7/98 (7%)
Query: 248 KSLGSLKIVTDRGLQVGDIAIVDISATTIDEDESNVQNIPDAETKGFHFDTEDGDKVLPG 307
K+ ++ V+D+ L GDIAI+D + + + + A + + T + + G
Sbjct: 17 KTKSTMVDVSDKKLANGDIAIIDFTGIV------DNKKLASASAQNYEL-TIGSNSFIKG 69
Query: 308 FLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTV 345
F + ++ + K+ L FP + + L+ F V
Sbjct: 70 FETGLIAMKVNQKKTLALTFPSDYHVKELQSKPVTFEV 107
>pdb|1OMS|A Chain A, Structure Determination By Mad: E.Coli Trigger Factor
Binding At The Ribosomal Exit Tunnel.
pdb|1OMS|B Chain B, Structure Determination By Mad: E.Coli Trigger Factor
Binding At The Ribosomal Exit Tunnel.
pdb|1OMS|C Chain C, Structure Determination By Mad: E.Coli Trigger Factor
Binding At The Ribosomal Exit Tunnel
Length = 121
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 23/111 (20%), Positives = 51/111 (45%), Gaps = 8/111 (7%)
Query: 103 RLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILK 162
R+++ + + + K L + K+V+I GFR GK+P +++ G +V++ + +
Sbjct: 17 RVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPXNIVAQRYG-ASVRQDVLGDLXS 75
Query: 163 RTLPHAMTSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVK 213
R A+ +++ + + + Y +Y V +V PEV+
Sbjct: 76 RNFIDAI-------IKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVE 119
>pdb|2F1S|A Chain A, Crystal Structure Of A Viral Flip Mc159
Length = 186
Score = 28.9 bits (63), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 368 PGCTTIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLF---EEQGRQL 424
PGCTT+ Q +L Q + + T A+++ LY + +D+ +S F +E QL
Sbjct: 40 PGCTTVTQALCSLSQ---------QRKLTLAALVEMLYVLQRMDLLKSRFGLSKEGAEQL 90
Query: 425 YGAQL------LQMQAGMKLNEQQLAAL 446
G L + G +L+ +L AL
Sbjct: 91 LGTSFLTRYRKLMVCVGEELDSSELRAL 118
>pdb|2BBR|A Chain A, Crystal Structure Of Mc159 Reveals Molecular Mechanism Of
Disc Assembly And Vflip Inhibition
Length = 195
Score = 28.5 bits (62), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 368 PGCTTIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLF---EEQGRQL 424
PGCTT+ Q +L Q + + T A+++ LY + +D+ +S F +E QL
Sbjct: 37 PGCTTVTQALCSLSQ---------QRKLTLAALVEMLYVLQRMDLLKSRFGLSKEGAEQL 87
Query: 425 YGAQL------LQMQAGMKLNEQQLAAL 446
G L + G +L+ +L AL
Sbjct: 88 LGTSFLTRYRKLMVCVGEELDSSELRAL 115
>pdb|2BBZ|A Chain A, Crystal Structure Of Mc159 Reveals Molecular Mechanism Of
Disc Assembly And Vflip Inhibition
pdb|2BBZ|B Chain B, Crystal Structure Of Mc159 Reveals Molecular Mechanism Of
Disc Assembly And Vflip Inhibition
pdb|2BBZ|C Chain C, Crystal Structure Of Mc159 Reveals Molecular Mechanism Of
Disc Assembly And Vflip Inhibition
pdb|2BBZ|D Chain D, Crystal Structure Of Mc159 Reveals Molecular Mechanism Of
Disc Assembly And Vflip Inhibition
Length = 249
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 368 PGCTTIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLF---EEQGRQL 424
PGCTT+ Q +L Q + + T A+++ LY + +D+ +S F +E QL
Sbjct: 37 PGCTTVTQALCSLSQ---------QRKLTLAALVEMLYVLQRMDLLKSRFGLSKEGAEQL 87
Query: 425 YGAQL------LQMQAGMKLNEQQLAAL 446
G L + G +L+ +L AL
Sbjct: 88 LGTSFLTRYRKLMVCVGEELDSSELRAL 115
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
0.316 0.132 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,671,924
Number of Sequences: 62578
Number of extensions: 576601
Number of successful extensions: 1777
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1748
Number of HSP's gapped (non-prelim): 37
length of query: 547
length of database: 14,973,337
effective HSP length: 104
effective length of query: 443
effective length of database: 8,465,225
effective search space: 3750094675
effective search space used: 3750094675
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)