RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780897|ref|YP_003065310.1| trigger factor [Candidatus
Liberibacter asiaticus str. psy62]
(473 letters)
>gnl|CDD|30890 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 232 bits (593), Expect = 2e-61
Identities = 117/450 (26%), Positives = 232/450 (51%), Gaps = 12/450 (2%)
Query: 1 MQVIEKFSEGLKRELDVIIPSNRLTDSFNERIEDIRSKANIKGFRPGKVPLSHIKSLYGK 60
M+V + EGL+ L V +P+ + + ++ ++ + K I GFR GKVP I+ YG+
Sbjct: 1 MKVTVEKLEGLEVRLTVEVPAEEIKKALDKALKKLAKKVKIPGFRKGKVPRKVIEQRYGE 60
Query: 61 SILSETIDEIIKEIVPEILSKRDERAAMRPSITINEGESDITSGLIEGTVDLKLRLSYDI 120
++ + ++E++ E E + + + A +P I I E E D + ++
Sbjct: 61 AVRQDVLNELLPEAFEEAIKEEGLKPAGQPEIEITEFEKG---------EDFEFTAEVEV 111
Query: 121 LPQIEISSFDDLQVTQDICEVDEKEIDRQMAEIAKNNVAFEVKETESEIGDKVTVDYTVS 180
P++E+ + ++V + + EV ++++D ++ ++ K E E +E GD+VT+D+ S
Sbjct: 112 YPEVELGDYKGIEVEKPVVEVTDEDVDEELEKLRKRFATLEPVEGAAENGDRVTIDFEGS 171
Query: 181 VDNVILEDQSKKNVQFIVGSADLFSETTEILVGLKTGDQKEIERFFPEDHSIKDLAGKKV 240
VD E +N +GS + LVG+K G++K+I+ FPED+ ++LAGK+
Sbjct: 172 VDGEEFEGGKAENFSLELGSGRFIPGFEDQLVGMKAGEEKDIKVTFPEDYHAEELAGKEA 231
Query: 241 RLNFSIKEVFSPLPVVVNNDLAVRLG-FESESAMRGLCSQKIKQHSEFLVRQKVKRQILD 299
+KEV ++++ A +LG ++ ++ + +++ + +K K Q+LD
Sbjct: 232 TFKVKVKEVKKRELPELDDEFAKKLGEEDTLEELKEKLRKNLERELKEATLEKRKEQLLD 291
Query: 300 YISNKYTFDVPESLVENEYNGILQKVRFEMSSANQKSQNVDSIDEEDLQ-YYHMLAKRRV 358
+ FD+PESLVE E + +L++ ++ S EE+L+ + A++RV
Sbjct: 292 ALVEANDFDLPESLVEAEIDNLLKQALQQLQQQGIDSLEASGESEEELREEFKEEAEKRV 351
Query: 359 LTGIVLGTIGEKNNIEVTEEEMQSALYQQLGRFPGH-EKKMLDHFQKYPNALAELRAPIF 417
G++L I ++ +EVTEEE+++ + + ++ G ++++ + L L+A I
Sbjct: 352 KLGLLLEEIAKEEKLEVTEEEIKAEIEELARQYGGEQPEEVIKLYYNNQELLDALKADIL 411
Query: 418 EDKVIDHILKSVQIVDRKVTFDQLFDNSSE 447
E+K +D +L + + V K + N +E
Sbjct: 412 EEKAVDLLLANKKKVTEKEVSFEELMNEAE 441
>gnl|CDD|147704 pfam05697, Trigger_N, Bacterial trigger factor protein (TF). In
the E. coli cytosol, a fraction of the newly synthesized
proteins requires the activity of molecular chaperones
for folding to the native state. The major chaperones
implicated in this folding process are the
ribosome-associated Trigger Factor (TF), and the DnaK
and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the N-terminal region of
the protein.
Length = 144
Score = 109 bits (275), Expect = 2e-24
Identities = 41/153 (26%), Positives = 82/153 (53%), Gaps = 9/153 (5%)
Query: 1 MQVIEKFSEGLKRELDVIIPSNRLTDSFNERIEDIRSKANIKGFRPGKVPLSHIKSLYGK 60
M+V + EGL+ +L V +P+ + ++ ++ ++++ K I GFR GKVP S +K YGK
Sbjct: 1 MKVTVEKLEGLEVKLTVEVPAEEVEEAVDKALKELAKKVKIPGFRKGKVPRSVVKKRYGK 60
Query: 61 SILSETIDEIIKEIVPEILSKRDERAAMRPSITINEGESDITSGLIEGTVDLKLRLSYDI 120
I E ++++++E E L + R +P I E E DL+ +++
Sbjct: 61 EIYQEALEDLLQEAYEEALKEEKLRPIGQPEIEEVELEEG---------KDLEFTAEFEV 111
Query: 121 LPQIEISSFDDLQVTQDICEVDEKEIDRQMAEI 153
P++E+ + L+V + EV ++++D ++ +
Sbjct: 112 YPEVELGDYKGLEVEKPEVEVTDEDVDEELERL 144
>gnl|CDD|147705 pfam05698, Trigger_C, Bacterial trigger factor protein (TF)
C-terminus. In the E. coli cytosol, a fraction of the
newly synthesized proteins requires the activity of
molecular chaperones for folding to the native state.
The major chaperones implicated in this folding process
are the ribosome-associated Trigger Factor (TF), and the
DnaK and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the C-terminal region of
the protein.
Length = 162
Score = 89.6 bits (223), Expect = 2e-18
Identities = 32/152 (21%), Positives = 77/152 (50%), Gaps = 5/152 (3%)
Query: 280 KIKQHSEFLVRQKVKRQILDYISNKYTFDVPESLVENEYNGILQKVRFEMSSANQKSQNV 339
++++ + +++K ILD + ++PESLVE E + +L++ ++ +
Sbjct: 12 QLEEEKKEATAEELKEAILDKLVENAEIELPESLVEEEIDRLLRQFLQQLQGQGLDLEEY 71
Query: 340 DSIDEEDLQYYHM----LAKRRVLTGIVLGTIGEKNNIEVTEEEMQSALYQQLGRFPGHE 395
S+ + A++RV G++L I ++ IEVT+EE++ + + ++
Sbjct: 72 LSLSGSSEEELREEFKEEAEKRVKLGLILEEIAKEEKIEVTDEEIKEEIEELASQYGMEP 131
Query: 396 KKMLDHFQKYPNALAELRAPIFEDKVIDHILK 427
+++ + ++K A L+ + E+K +D +L+
Sbjct: 132 EEVKEFYKKNEQLSA-LKEDLLEEKAVDLLLE 162
>gnl|CDD|144003 pfam00254, FKBP_C, FKBP-type peptidyl-prolyl cis-trans isomerase.
Length = 95
Score = 38.4 bits (90), Expect = 0.004
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 161 EVKETESEIGDKVTVDYTVSVDNVILEDQS---KKNVQFIVGSADLFSETTEILVGLKTG 217
+ + GD VTV YT +++ + D S K +F +GS + E L+G+K G
Sbjct: 1 GDGPRKPKKGDTVTVHYTGKLEDGTVFDSSYDRGKPFEFTLGSGQVIPGWDEGLLGMKVG 60
Query: 218 DQKEIE 223
+++++
Sbjct: 61 EKRKLT 66
>gnl|CDD|31248 COG1047, SlpA, FKBP-type peptidyl-prolyl cis-trans isomerases 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 174
Score = 34.8 bits (80), Expect = 0.049
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 168 EIGDKVTVDYTVSVDNVILEDQSKKNVQ---FIVGSADLFSETTEILVGLKTGDQKEIE 223
E GD V++ YT+ V++ + D + +N FIVG+ L E L+G + G++ +E
Sbjct: 4 EKGDVVSLHYTLKVEDGEVVDTTDENYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVE 62
>gnl|CDD|36139 KOG0921, KOG0921, KOG0921, Dosage compensation complex, subunit MLE
[Transcription].
Length = 1282
Score = 29.5 bits (65), Expect = 2.1
Identities = 15/76 (19%), Positives = 30/76 (39%)
Query: 125 EISSFDDLQVTQDICEVDEKEIDRQMAEIAKNNVAFEVKETESEIGDKVTVDYTVSVDNV 184
++ ++Q I E + + D + +I V + SEI V + V +
Sbjct: 342 PLAFMSMESISQRIMEKERFKRDEALDKITAQREELPVAQYRSEILQAVAENRVVIIKGE 401
Query: 185 ILEDQSKKNVQFIVGS 200
+S + QF++ S
Sbjct: 402 TGCGKSTQVAQFLLES 417
>gnl|CDD|31094 COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation,
ribosomal structure and biogenesis].
Length = 691
Score = 29.4 bits (66), Expect = 2.4
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 377 EEEMQSALYQQLGRFPGHEKKMLDH--FQKYPNALAELRAPI--FEDKVI 422
EE+ + AL++ L + L +Q ALAELR PI F D V+
Sbjct: 608 EEDAEKALFEALQALKPKVAEALAEKDYQDALAALAELRPPIDEFFDNVM 657
>gnl|CDD|32793 COG2974, RdgC, DNA recombination-dependent growth factor C [DNA
replication, recombination, and repair].
Length = 303
Score = 29.1 bits (65), Expect = 2.9
Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 15/76 (19%)
Query: 13 RELDVIIPSNRLTDSFNERIEDIRSKANIKGFRPGKVPLSHIKSLYGKSILSETIDEIIK 72
R+ + I+P++ + D+ +IE+I +K +G + K +K D+++
Sbjct: 68 RKEEKILPASVVKDALEAKIEEIEAK---QGRKLKKKEKDELK------------DDVVH 112
Query: 73 EIVPEILSKRDERAAM 88
E++P S+ + A
Sbjct: 113 ELLPRAFSRSSQTFAW 128
>gnl|CDD|34230 COG4592, FepB, ABC-type Fe2+-enterobactin transport system,
periplasmic component [Inorganic ion transport and
metabolism].
Length = 319
Score = 27.3 bits (60), Expect = 8.5
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 383 ALYQQLGRFPGHEKKMLDHFQKYPNALAELRAPI 416
+L QLG GHEK+ ++ LAE++ I
Sbjct: 154 SLATQLGEATGHEKQAEARIAQFDKQLAEVKQQI 187
>gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 27.1 bits (60), Expect = 9.4
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 120 ILPQIEISSFDDLQVTQDICEVDEKEIDRQMAEIAKNNVAFEVKETESE 168
I P IE + D V + I D +I+++M EIAK N+ E + E
Sbjct: 50 IGPVIEEGFYYDFDVKEPITPEDLLKIEKEMKEIAKENLPIEREVVSRE 98
>gnl|CDD|37967 KOG2756, KOG2756, KOG2756, Predicted Mg2+-dependent
phosphodiesterase TTRAP [Signal transduction
mechanisms].
Length = 349
Score = 27.3 bits (60), Expect = 9.6
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 51 LSHIKSLYGKSILSETIDEIIKEIVPEILSKRDERAAMRPSITINEGESDITSGLIEGTV 110
+ H +LY ++ ++E++P S +R++ IT +E L + V
Sbjct: 122 VCHYLALYSPDVI------FLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRV 175
Query: 111 DLKLRLSYDILP 122
+K S +I+P
Sbjct: 176 KVK---SQEIIP 184
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.314 0.133 0.354
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,383,433
Number of extensions: 287502
Number of successful extensions: 622
Number of sequences better than 10.0: 1
Number of HSP's gapped: 613
Number of HSP's successfully gapped: 26
Length of query: 473
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 376
Effective length of database: 4,167,664
Effective search space: 1567041664
Effective search space used: 1567041664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 59 (26.5 bits)