RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780148|ref|YP_003064561.1| transcription antitermination
protein NusG [Candidatus Liberibacter asiaticus str. psy62]
(177 letters)
>gnl|CDD|180161 PRK05609, nusG, transcription antitermination protein NusG;
Validated.
Length = 181
Score = 225 bits (576), Expect = 4e-60
Identities = 92/178 (51%), Positives = 127/178 (71%), Gaps = 1/178 (0%)
Query: 1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRF 60
M RWY+VQ YS EKK E++ R+ G++ L+ E+ +P+E VV V+ G+K ER+F
Sbjct: 4 MKKRWYVVQTYSGYEKKVKENLENRIETLGMEDLIGEVLVPTEEVVEVKNGKKKKVERKF 63
Query: 61 FPGYVLIKAVMTDKVYHTIKDTPKVIGFLG-TGENPSPVTDSEIEHIMNQVEAAVQRPVS 119
FPGYVL+K VMTD+ +H +++TP V GF+G TG P+P+++ E+E I+ Q++ V++P
Sbjct: 64 FPGYVLVKMVMTDESWHLVRNTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPKP 123
Query: 120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV 177
V FEVGE V V DGPFA FNG V+ VD EKS++ V V IFGR TPVEL ++QVEKI
Sbjct: 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEKID 181
>gnl|CDD|162110 TIGR00922, nusG, transcription termination/antitermination factor
NusG. Archaeal proteins once termed NusG share the KOW
domain but are actually a ribosomal protein
corresponding to L24p in bacterial and L26e in
eukaryotes (TIGR00405).
Length = 172
Score = 190 bits (486), Expect = 1e-49
Identities = 79/172 (45%), Positives = 118/172 (68%), Gaps = 1/172 (0%)
Query: 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGY 64
WY+VQ YS EKK +++ + G+ + E+ +P+E VV ++KG+K ER+ FPGY
Sbjct: 1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGY 60
Query: 65 VLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDS-EIEHIMNQVEAAVQRPVSSVFF 123
VL+K +TD +H +K+TP V GF+G+G P +++ E+++I+N +E +P + F
Sbjct: 61 VLVKMDLTDVSWHLVKNTPGVTGFVGSGGKPKALSEDEEVKNILNALEEGKDKPKPKIDF 120
Query: 124 EVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175
EVGE+V V+DGPFA+F G V+ VD EKS++ V V IFGR TPVEL ++QVEK
Sbjct: 121 EVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172
>gnl|CDD|128977 smart00738, NGN, In Spt5p, this domain may confer affinity for
Spt4p. It possesses a RNP-like fold. In Spt5p, this
domain may confer affinity for Spt4p.Spt4p.
Length = 106
Score = 108 bits (272), Expect = 8e-25
Identities = 41/106 (38%), Positives = 63/106 (59%)
Query: 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPG 63
WY V+ S EK+ E++ + GL+ + I +P+E V +R+G+K ER FPG
Sbjct: 1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERPLFPG 60
Query: 64 YVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQ 109
Y+ ++A + D+V+ I+ TP V GF+G G P+PV D EIE I+
Sbjct: 61 YIFVEADLEDEVWTAIRGTPGVRGFVGGGGKPTPVPDDEIEKILKP 106
>gnl|CDD|131010 TIGR01955, RfaH, transcriptional activator RfaH. This model
represents the transcriptional activator protein, RfaH.
This protein is most closely related to the
transcriptional termination/antitermination protein NusG
(TIGR00922) and contains the KOW motif (pfam00467). This
protein appears to be limited to the gamma
proteobacteria. In E. coli, this gene appears to control
the expression of haemolysin, sex factor and
lipopolysaccharide genes.
Length = 159
Score = 61.3 bits (149), Expect = 1e-10
Identities = 44/171 (25%), Positives = 76/171 (44%), Gaps = 13/171 (7%)
Query: 5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGY 64
WY++ E++A E L R + E +P V + +G++ FP Y
Sbjct: 1 WYLLYCKPRQEQRAQEH----LERQAV-----ECYLPMITVEKIVRGKRQAVSEPLFPNY 51
Query: 65 VLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHI-MNQVEAAVQRPVSSVFF 123
+ I+ + TI+ T V F+ G +P+PV D I + + + +V P ++
Sbjct: 52 LFIEFDPEVDSWTTIRSTRGVSRFVRFGGHPAPVPDDLIHQLRQYEPKDSV--PPATTLP 109
Query: 124 EVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVE 174
G++V ++DG FA F I D EK R + + + G+ V + VE
Sbjct: 110 YKGDKVRITDGAFAGFEAIFLEPDGEK-RSMLLLNMIGKQIKVSVPNTSVE 159
>gnl|CDD|162624 TIGR01956, NusG_myco, NusG family protein. This model represents a
family of Mycoplasma proteins orthologous to the
bacterial transcription termination/antitermination
factor NusG. These sequences from Mycoplasma are notably
diverged (long branches in a Neighbor-joining
phylogenetic tree) from the bacterial species. And
although NusA and ribosomal protein S10 (NusE) appear to
be present, NusB may be absent in Mycoplasmas calling
into question whether these species have a functional
Nus system including this family as a member.
Length = 258
Score = 53.0 bits (127), Expect = 4e-08
Identities = 28/140 (20%), Positives = 58/140 (41%), Gaps = 31/140 (22%)
Query: 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSV--------------- 48
+WYI + E + +E+I ++ GL++ +++ I ER +
Sbjct: 1 QWYIATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEKVFEPKNGQAPRSMK 60
Query: 49 -------------RKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGT---G 92
+ + SE+ + GY+ IK +MT+ + I++T V G +G+ G
Sbjct: 61 NTATTKWETLDETKYKKTKISEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKG 120
Query: 93 ENPSPVTDSEIEHIMNQVEA 112
P P++ + M + +
Sbjct: 121 AKPIPISADADKLKMLKGIS 140
Score = 36.9 bits (85), Expect = 0.003
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175
F VG V + DGPF G +K +D+EK + VEV I G+ V+L + ++
Sbjct: 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLNFKHLKL 258
>gnl|CDD|181467 PRK08559, nusG, transcription antitermination protein NusG;
Validated.
Length = 153
Score = 38.3 bits (90), Expect = 0.001
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 12/96 (12%)
Query: 63 GYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVF 122
GYVL++A V I+ P V G + P ++ E+EH +
Sbjct: 47 GYVLVEAESKGAVEEAIRGIPHVRGVV-----PGEISFEEVEHFLKPKPIVEG------- 94
Query: 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVV 158
+ G+ V + GPF V VDE K V VE++
Sbjct: 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130
>gnl|CDD|129499 TIGR00405, L26e_arch, ribosomal protein L24p/L26e, archaeal. This
protein contains a KOW domain, shared by bacterial NusG
and the L24p/L26e family of ribosomal proteins. Although
called archaeal NusG in several publications, it is the
only close homolog of eukaryotic L26e in archaeal
genomes, shares an operon with L11 in many genomes, and
has been sequenced from purified ribosomes. It is here
designated as a ribosomal protein for these reasons.
Length = 145
Score = 37.2 bits (86), Expect = 0.003
Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 12/114 (10%)
Query: 63 GYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVF 122
GY+L++A + + I P V G + + EIE + +
Sbjct: 39 GYILVEAETKIDMRNPIIGVPHVRGVV-----EGEIDFEEIERFLTPKKIIES------- 86
Query: 123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176
+ G+ V + GPF V VDE K V +E++ PV + +QV I
Sbjct: 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRII 140
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 32.3 bits (75), Expect = 0.065
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 123 FEVGERVCVSDGPFASFNGIVKNVDEE 149
FEVG+ V V GPF G V VD E
Sbjct: 2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|163584 TIGR03872, cytochrome_MoxG, cytochrome c(L), periplasmic. This
model describes a periplasmic c-type cytochrome that
serves as the primary electron acceptor for the
quinoprotein methanol dehydrogenase, a PQQ enzyme. The
member from Paracoccus denitrificans is also
characterized as an electron acceptor for methylamine
dehydrogenase, a tryptophan tryptophylquinone enzyme.
This protein is called cytochrome c(L) in
methylotrophic bacteria such Methylobacterium
extorquens, but c551i in Paracoccus denitrificans.
Length = 133
Score = 27.4 bits (61), Expect = 1.9
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 81 DTPKVIGFLGTGENP 95
DTP V FL TGENP
Sbjct: 22 DTPAVKQFLETGENP 36
>gnl|CDD|130152 TIGR01080, rplX_A_E, ribosomal protein L24p/L26e,
archaeal/eukaryotic. This model represents the archaeal
and eukaryotic branch of the ribosomal protein L24p/L26e
family. Bacterial and organellar forms are represented
by the related TIGR01079.
Length = 114
Score = 27.1 bits (60), Expect = 2.3
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 125 VGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYN 171
G++V + G F G V VD ++ R++VE V +V E+
Sbjct: 44 KGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTEVPVP 90
>gnl|CDD|151890 pfam11451, DUF3202, Protein of unknown function (DUF3202). This
archaeal family of proteins has no known function.
Length = 67
Score = 27.2 bits (60), Expect = 2.5
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 126 GERVCVSDGPFASFNGIVKNVDEE 149
G +V V G SF+GI+++ DEE
Sbjct: 13 GHKVAVGIGGDHSFSGILEDFDEE 36
>gnl|CDD|180401 PRK06105, PRK06105, aminotransferase; Provisional.
Length = 460
Score = 26.5 bits (59), Expect = 3.5
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 63 GYVLIKAV-MTDKVYHTIKDTPKVIGFLGTG 92
Y + AV M +KVY I D IG G G
Sbjct: 292 SYQPLSAVLMNEKVYDPIADESGKIGTFGHG 322
>gnl|CDD|180601 PRK06520, PRK06520,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase; Provisional.
Length = 368
Score = 26.2 bits (58), Expect = 4.3
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 25 RLSRSGLDHLVTEITIPSERVVSVRKGRKV 54
R +S ++TIPS V+ R GRK
Sbjct: 123 RFLKSISGDATPKMTIPSPSVLHFRGGRKA 152
>gnl|CDD|180330 PRK05965, PRK05965, hypothetical protein; Provisional.
Length = 459
Score = 26.2 bits (58), Expect = 5.0
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 63 GYVLIKAV-MTDKVYHTIKD 81
GYV + AV M+D VY I D
Sbjct: 289 GYVPMGAVLMSDHVYQGIAD 308
>gnl|CDD|148576 pfam07041, DUF1327, Protein of unknown function (DUF1327). This
family consists of several hypothetical bacterial
proteins of around 115 residues in length which seem to
be specific to Escherichia coli. The function of this
family is unknown.
Length = 113
Score = 25.8 bits (56), Expect = 5.9
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 111 EAAVQRPVSSVFFEVGERVCVSDGP 135
EAA +R VF +V +C D P
Sbjct: 54 EAAARRSARQVFLDVAAGLCEGDEP 78
>gnl|CDD|185471 PTZ00136, PTZ00136, eukaryotic translation initiation factor 6-like
protein; Provisional.
Length = 247
Score = 25.5 bits (56), Expect = 8.9
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 75 VYHTIKDTPKVIGFLGTGEN-----PSPVTDSEIEHIMNQV--EAAVQR 116
V+ TI T +VIG L G PS TD E++H+ N + VQR
Sbjct: 49 VHTTIGGT-RVIGRLTVGNRKGLLVPSICTDQELQHLRNSLPDSVKVQR 96
>gnl|CDD|162372 TIGR01458, HAD-SF-IIA-hyp3, HAD-superfamily subfamily IIA
hydrolase, TIGR01458. This hypothetical equivalog is a
member of the IIA subfamily (TIGR01460) of the haloacid
dehalogenase superfamily of aspartate-nucleophile
hydrolases. One sequence (GP|10716807) has been
annotated as a "phospholysine phosphohistidine
inorganic pyrophosphatase," probably in reference to
studies on similarly described (but unsequenced)
enzymes from bovine and rat tissues. However, the
supporting information for this annotation has never
been published.
Length = 257
Score = 25.2 bits (55), Expect = 9.3
Identities = 10/48 (20%), Positives = 23/48 (47%)
Query: 7 IVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKV 54
V+ +N K++ + + RL R G D E+ P+ + + +++
Sbjct: 39 KVRFVTNTTKESKQDLLERLQRLGFDISEDEVFTPAPAARQLLEEKQL 86
>gnl|CDD|183546 PRK12473, PRK12473, hypothetical protein; Provisional.
Length = 198
Score = 25.2 bits (55), Expect = 9.8
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 63 GYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPS 96
Y + A++ D Y IK K +G L ++PS
Sbjct: 143 KYTDMYAIVDDATYAKIKGDEKTVGVLSFDKDPS 176
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 0.136 0.389
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,897,448
Number of extensions: 178826
Number of successful extensions: 355
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 31
Length of query: 177
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 90
Effective length of database: 4,114,577
Effective search space: 370311930
Effective search space used: 370311930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.7 bits)