RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781067|ref|YP_003065480.1| elongation factor P
[Candidatus Liberibacter asiaticus str. psy62]
(189 letters)
>gnl|CDD|179058 PRK00529, PRK00529, elongation factor P; Validated.
Length = 186
Score = 246 bits (630), Expect = 3e-66
Identities = 70/186 (37%), Positives = 109/186 (58%)
Query: 3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV 62
+ A+ +RKG V+++DG+ Y+VL ++ PGKG + +++ + G V ++ ++V
Sbjct: 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKV 60
Query: 63 ERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVA 122
ERA VE + Q+LY D +G+ FM+ ETY+Q+ V + +GD + +EGMEV ++ + G
Sbjct: 61 ERADVERREMQYLYNDGDGYVFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEP 120
Query: 123 LSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNS 182
+SVE+P V V +TEP KG T + KPA L VP IN G+ I + T
Sbjct: 121 ISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGEKIKVDTRTGE 180
Query: 183 YVERVK 188
YVER K
Sbjct: 181 YVERAK 186
>gnl|CDD|161673 TIGR00038, efp, translation elongation factor P. function:
involved in peptide bond synthesis. stimulate efficient
translation and peptide-bond synthesis on native or
reconstituted 70S ribosomes in vitro. probably functions
indirectly by altering the affinity of the ribosome for
aminoacyl-tRNA, thus increasing their reactivity as
acceptors for peptidyl transferase (by similarity). The
trusted cutoff of this model is set high enough to
exclude members of TIGR02178, an EFP-like protein of
certain Gammaproteobacteria.
Length = 184
Score = 219 bits (560), Expect = 5e-58
Identities = 65/182 (35%), Positives = 108/182 (59%)
Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERA 65
A+ +RKG V+++DG+ Y+VL ++ PGKG +V+++ + G + +R+ E+VE+A
Sbjct: 3 ANDLRKGLVIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKA 62
Query: 66 FVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSV 125
VE++ Q+LY+D + + FM+ ETY+Q+ + ++++GD + +E MEV + + G + V
Sbjct: 63 DVEEREMQYLYKDGDSYVFMDTETYEQIELPKDLLGDAAKFLKENMEVSVTFYNGEPIGV 122
Query: 126 EVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVE 185
E+P V V +TEP KG T + KPA L VP I G+ I + T YVE
Sbjct: 123 ELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFIEEGEKIKVDTRTGEYVE 182
Query: 186 RV 187
R
Sbjct: 183 RA 184
>gnl|CDD|179863 PRK04542, PRK04542, elongation factor P; Provisional.
Length = 189
Score = 105 bits (264), Expect = 8e-24
Identities = 52/184 (28%), Positives = 100/184 (54%), Gaps = 3/184 (1%)
Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGK--GTPITQVEMRRISDGVKVSNRWRTTEQVE 63
A+ ++KG V++ +GKL +V P G + ++ + G+KV R++ + ++
Sbjct: 4 ANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILD 63
Query: 64 RAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGME-VKLLIHEGVA 122
+ + F Y D + + FM+ E Y T ++ I D+ ++ EGM +++L +G
Sbjct: 64 TVDLTRRPVTFSYIDGDEYVFMDNEDYTPYTFKKDQIEDELLFIPEGMPGMQVLTVDGQP 123
Query: 123 LSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNS 182
+++E+P+ V +++T PS KG + +A KPA LS + VP +I+ G+ I I TE+
Sbjct: 124 VALELPQTVDLEIVETAPSIKGASASARTKPATLSTGLVIQVPEYISTGEKIRINTEERK 183
Query: 183 YVER 186
++ R
Sbjct: 184 FMGR 187
>gnl|CDD|183522 PRK12426, PRK12426, elongation factor P; Provisional.
Length = 185
Score = 98.4 bits (245), Expect = 9e-22
Identities = 45/184 (24%), Positives = 91/184 (49%)
Query: 4 VIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVE 63
V++S + G + LY V+ KG +V ++ V V ++ ++V+
Sbjct: 2 VLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVK 61
Query: 64 RAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVAL 123
A E + ++LY + + + F++ YD++ + +E++ D ++ + G+ V L+++G
Sbjct: 62 EAQFEPRNLEYLYLEGDEYLFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVF 121
Query: 124 SVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSY 183
SVE+P + V T+ +++ K A+L + VPP + IGD I + T Y
Sbjct: 122 SVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEVLVPPFVEIGDVIKVDTRTCEY 181
Query: 184 VERV 187
++RV
Sbjct: 182 IQRV 185
>gnl|CDD|131233 TIGR02178, yeiP, elongation factor P-like protein YeiP. This model
represents the family of Escherichia coli protein YeiP,
a close homolog of elongation factor P (TIGR00038) and
probably itself a translation factor. Member of this
family are found only in some Gammaproteobacteria,
including E. coli and Vibrio cholerae.
Length = 186
Score = 96.1 bits (239), Expect = 5e-21
Identities = 48/184 (26%), Positives = 98/184 (53%), Gaps = 3/184 (1%)
Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGK--GTPITQVEMRRISDGVKVSNRWRTTEQVE 63
AS ++KG++++ +GK ++ + P G + M + G KV R++ + ++
Sbjct: 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLD 61
Query: 64 RAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGME-VKLLIHEGVA 122
+ + F Y+D E + FM+ E Y T ++ I D+ ++ EG+ + + + +G
Sbjct: 62 TVELLRREASFSYKDGEEYVFMDEEDYTPYTFDKDAIEDELLFISEGLSGMYVQLIDGSP 121
Query: 123 LSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNS 182
+++E+P+HVV +++T P KG + + KPA L + VP +I G+ I+I T + +
Sbjct: 122 VALELPQHVVLEIVETPPEIKGASASKRPKPAKLITGLVVQVPEYITTGERILINTTERA 181
Query: 183 YVER 186
++ R
Sbjct: 182 FMGR 185
>gnl|CDD|173042 PRK14578, PRK14578, elongation factor P; Provisional.
Length = 187
Score = 93.7 bits (233), Expect = 2e-20
Identities = 56/182 (30%), Positives = 93/182 (51%), Gaps = 2/182 (1%)
Query: 7 SAVRKGNVLDVDGKLYIVLVAKNFHPGK--GTPITQVEMRRISDGVKVSNRWRTTEQVER 64
S +KG V+ +DG ++L P + + + R + G + +R+ ++VE
Sbjct: 5 SDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEE 64
Query: 65 AFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALS 124
A E + QFLY D + FM+ ETY+Q + E+ + +G EV+L + +G ++
Sbjct: 65 ADFERHKGQFLYADGDRGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVN 124
Query: 125 VEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYV 184
V++P V TV DT P K T TA K A+L +R VPP++ G+ I + T D ++
Sbjct: 125 VDLPMTVELTVTDTAPVMKNATATAQTKEAVLETGLRLQVPPYLESGEKIKVDTRDGRFI 184
Query: 185 ER 186
R
Sbjct: 185 SR 186
>gnl|CDD|150075 pfam09285, Elong-fact-P_C, Elongation factor P, C-terminal.
Members of this family of nucleic acid binding domains
are predominantly found in elongation factor P, where
they adopt an OB-fold, with five beta-strands forming a
beta-barrel in a Greek-key topology.
Length = 56
Score = 75.6 bits (187), Expect = 7e-15
Identities = 21/56 (37%), Positives = 27/56 (48%)
Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186
V V++TEP KG T ++ KPA L VP I G+ I + T YV R
Sbjct: 1 VELEVVETEPGVKGDTASSGTKPATLETGAEVQVPLFIEEGEKIKVDTRTGEYVSR 56
>gnl|CDD|129074 smart00841, Elong-fact-P_C, Elongation factor P, C-terminal. These
nucleic acid binding domains are predominantly found in
elongation factor P, where they adopt an OB-fold, with
five beta-strands forming a beta-barrel in a Greek-key
topology PUBMED:15210970.
Length = 56
Score = 74.8 bits (185), Expect = 1e-14
Identities = 23/56 (41%), Positives = 26/56 (46%)
Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186
V V +TEP KG T + KPA L VP IN GD I + T YV R
Sbjct: 1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 56
>gnl|CDD|149330 pfam08207, EFP_N, Elongation factor P (EF-P) KOW-like domain.
Length = 58
Score = 60.5 bits (148), Expect = 3e-10
Identities = 18/57 (31%), Positives = 37/57 (64%)
Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV 62
AS ++KG V+++DG+ Y+VL ++ PGKG + +++ + G KV +++ ++V
Sbjct: 2 ASDLKKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLRTGAKVEKTFKSGDKV 58
>gnl|CDD|129148 TIGR00037, eIF_5A, translation initiation factor eIF-5A. Observed
in eukaryotes and archaea.
Length = 130
Score = 31.3 bits (71), Expect = 0.14
Identities = 31/113 (27%), Positives = 53/113 (46%), Gaps = 7/113 (6%)
Query: 7 SAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERA 65
SA+R G + +DG+ ++ PGK G +V I G K+ +T +VE
Sbjct: 10 SALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVP 69
Query: 66 FVEDQRFQFLYQDQEGFHFMNPETY--DQVTVSEEVIGDQKVYFQEGMEVKLL 116
V+ + +Q L M+ +TY D++ + EE +GD + G EV+ +
Sbjct: 70 IVDRREYQVLAIMGGMVQLMDLDTYETDELPIPEE-LGDS---LEPGFEVEYI 118
>gnl|CDD|181436 PRK08462, PRK08462, biotin carboxylase; Validated.
Length = 445
Score = 28.9 bits (65), Expect = 0.85
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 72 FQFLYQDQEGFHFMNPETYDQV--TVSEEVIG 101
F+FL F+FM T QV TVSE V G
Sbjct: 276 FEFLLDSNLDFYFMEMNTRLQVEHTVSEMVSG 307
>gnl|CDD|184330 PRK13794, PRK13794, hypothetical protein; Provisional.
Length = 479
Score = 28.5 bits (64), Expect = 1.1
Identities = 23/99 (23%), Positives = 34/99 (34%), Gaps = 20/99 (20%)
Query: 96 SEEVIGDQKV----YFQEGM---EVKLLIHEGVALSVEVPRHVVFTVIDTEPSS---KGQ 145
EE+I D V + E ++ EG + + V D P KG
Sbjct: 84 MEEIIVDGAVVGIIRYNEKKHRWKIIPRP-EGARRLIPTAKKKFIVVKDDVPKFIRNKGA 142
Query: 146 TVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYV 184
+V P + I GDD++IL E+ V
Sbjct: 143 SVLR---PGVAE------ASEDIEEGDDVIILDENGDVV 172
>gnl|CDD|180406 PRK06111, PRK06111, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 450
Score = 28.5 bits (64), Expect = 1.2
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 72 FQFLYQDQEGFHFMNPETYDQVT--VSEEVIGDQKVYFQEGMEVKLLIHEGVALSV---E 126
+FL +Q+ F+F+ T QV V+EE+ G V E +L I G LS +
Sbjct: 274 IEFLVDEQKNFYFLEMNTRLQVEHPVTEEITGIDLV------EQQLRIAAGEKLSFTQDD 327
Query: 127 VPRH 130
+ R
Sbjct: 328 IKRS 331
>gnl|CDD|102207 PRK06145, PRK06145, acyl-CoA synthetase; Validated.
Length = 497
Score = 28.3 bits (63), Expect = 1.3
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 56 WRTTEQVERAFVED--QRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKV 105
W+ E+ AF D + Y D+EGF ++ D + E I +V
Sbjct: 360 WKDPEKTAEAFYGDWFRSGDVGYLDEEGFLYLTDRKKDMIISGGENIASSEV 411
>gnl|CDD|129605 TIGR00514, accC, acetyl-CoA carboxylase, biotin carboxylase
subunit. This model represents the biotin carboxylase
subunit found usually as a component of acetyl-CoA
carboxylase. Acetyl-CoA carboxylase is designated EC
6.4.1.2 and this component, biotin carboxylase, has its
own designation, EC 6.3.4.14. Homologous domains are
found in eukaryotic forms of acetyl-CoA carboxylase and
in a number of other carboxylases (e.g. pyruvate
carboxylase), but seed members and trusted cutoff are
selected so as to exclude these. In some systems, the
biotin carboxyl carrier protein and this protein (biotin
carboxylase) may be shared by different
carboxyltransferases. However, this model is not
intended to identify the biotin carboxylase domain of
propionyl-coA carboxylase. The model should hit the full
length of proteins, except for chloroplast transit
peptides in plants. If it hits a domain only of a longer
protein, there may be a problem with the identification.
Length = 449
Score = 27.8 bits (62), Expect = 1.8
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 72 FQFLYQDQEGFHFMNPETYDQV--TVSEEVIG 101
+FL F+FM T QV V+E + G
Sbjct: 274 VEFLLDKNGEFYFMEMNTRIQVEHPVTEMITG 305
>gnl|CDD|181492 PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 451
Score = 27.1 bits (61), Expect = 2.7
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 72 FQFLYQDQEGFHFMNPETYDQV--TVSEEVIG 101
+FLY+ F+F+ T QV V+E + G
Sbjct: 274 IEFLYEKNGEFYFIEMNTRIQVEHPVTEMITG 305
>gnl|CDD|185215 PRK15315, PRK15315, outer membrane protein RatA; Provisional.
Length = 1865
Score = 26.9 bits (59), Expect = 2.9
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 10/73 (13%)
Query: 78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQE----GME--VKLLIHEGVALSVEVPRHV 131
D EG +PE Y VT +V G + + G+E +++++ + +VE+P V
Sbjct: 533 DSEGMSASSPEHYTGVT---DVNGQAHLTLKHNSGLGVETPIRIVMPDDEGGNVELPFSV 589
Query: 132 VFTVIDTEPSSKG 144
+FTV+ T P G
Sbjct: 590 IFTVV-TSPDVDG 601
>gnl|CDD|132676 TIGR03637, cas1_YPEST, CRISPR-associated endonuclease Cas1, YPEST
subtype. The CRISPR-associated protein Cas1 is
virtually universal to CRISPR systems. CRISPR, an
acronym for Clustered Regularly Interspaced Short
Palindromic Repeats, is prokaryotic immunity system for
foreign DNA, mostly from phage. CRISPR systems belong
to different subtypes, distinguished by both nature of
the repeats, the makeup of the cohort of associated Cas
proteins, and by molecular phylogeny within the more
universal Cas proteins such as this one. This model is
of type EXCEPTION and provides more specific
information than the EQUIVALOG model TIGR00287. It
describes the Cas1 protein particular to the YPEST
subtype of CRISPR/Cas system.
Length = 307
Score = 25.9 bits (57), Expect = 6.7
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 33 GKGTPITQVEMRRISD-GVKV 52
G GT ITQ MR ++ GV V
Sbjct: 50 GTGTSITQAAMRELAKAGVMV 70
>gnl|CDD|178660 PLN03113, PLN03113, DNA ligase 1; Provisional.
Length = 744
Score = 25.7 bits (56), Expect = 8.1
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 144 GQTVTASYKPAILSNDIRTTVPPHI 168
GQT+ A+ A + N+ +T PP+I
Sbjct: 298 GQTLLAALGQAAVYNEEHSTPPPNI 322
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.318 0.135 0.381
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,056,477
Number of extensions: 186333
Number of successful extensions: 380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 376
Number of HSP's successfully gapped: 32
Length of query: 189
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 101
Effective length of database: 4,092,969
Effective search space: 413389869
Effective search space used: 413389869
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.7 bits)