RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780148|ref|YP_003064561.1| transcription antitermination
protein NusG [Candidatus Liberibacter asiaticus str. psy62]
(177 letters)
>gnl|CDD|30599 COG0250, NusG, Transcription antiterminator [Transcription].
Length = 178
Score = 170 bits (432), Expect = 2e-43
Identities = 83/177 (46%), Positives = 117/177 (66%), Gaps = 1/177 (0%)
Query: 1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRF 60
+ RWY+VQ YS EKK E++ + G++ L+ E+ +P+E VV V+ RKV ER+
Sbjct: 1 LMKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKL 60
Query: 61 FPGYVLIKAVMTDKVYHTIKDTPKVIGFLG-TGENPSPVTDSEIEHIMNQVEAAVQRPVS 119
FPGYVL++ MTD+ +H +++TP V GF+G G P P+++ EIEHI+ +E V
Sbjct: 61 FPGYVLVEMDMTDEAWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKP 120
Query: 120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI 176
V FE G+ V + DGPFA F V+ VDEEK ++ VEV IFGR TPVEL ++QVEK+
Sbjct: 121 KVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177
>gnl|CDD|145481 pfam02357, NusG, Transcription termination factor nusG.
Length = 90
Score = 84.3 bits (209), Expect = 2e-17
Identities = 38/99 (38%), Positives = 55/99 (55%), Gaps = 11/99 (11%)
Query: 4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRK-GRKVNSERRFFP 62
+WY+++ S EKK E++ + S L P+E VV VRK G+K ER FP
Sbjct: 2 KWYVLRTKSGQEKKVAENLERQGIESFL---------PTEEVVEVRKNGKKKKVERPLFP 52
Query: 63 GYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDS 101
GYV ++ + D+ + I+ TP V GF+G G P+PV D
Sbjct: 53 GYVFVRMDLNDETWK-IRSTPGVSGFVGFGGKPAPVPDE 90
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 34.3 bits (80), Expect = 0.017
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 125 VGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
G+ V V GPF G V VD+ K+RVHVE
Sbjct: 1 KGDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|37210 KOG1999, KOG1999, KOG1999, RNA polymerase II transcription
elongation factor DSIF/SUPT5H/SPT5 [Transcription].
Length = 1024
Score = 30.7 bits (69), Expect = 0.20
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 125 VGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
+G+ V + GP + GIVK+V+ + +RV +
Sbjct: 687 LGKTVRIRLGPKKGYLGIVKDVNGDTARVELH 718
>gnl|CDD|173961 cd08551, Fe-ADH, iron-containing alcohol dehydrogenases
(Fe-ADH)-like. Large metal-containing alcohol
dehydrogenases (ADH), known as iron-containing alcohol
dehydrogenases. They contain a dehydroquinate
synthase-like protein structural fold and mostly contain
iron. They are distinct from other alcohol
dehydrogenases which contains different protein domains.
There are several distinct families of alcohol
dehydrogenases: Zinc-containing long-chain alcohol
dehydrogenases; insect-type, or short-chain alcohol
dehydrogenases; iron-containing alcohol dehydrogenases,
and others. The iron-containing family has a Rossmann
fold-like topology that resembles the fold of the
zinc-dependent alcohol dehydrogenases, but lacks
sequence homology, and differs in strand arrangement.
ADH catalyzes the reversible oxidation of alcohol to
acetaldehyde with the simultaneous reduction of NAD(P)+
to NAD(P)H.
Length = 370
Score = 26.5 bits (59), Expect = 4.7
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 126 GERVCVSDGPFASFNGIVKNV-DEEKSRVHVEVVIFGRVTPVELAYNQVEKIV 177
G + + P G++ V D K +EVVIF V P + V+ V
Sbjct: 23 GRKALIVTDPGLVKTGVLDKVIDSLKEA-GIEVVIFDGVEP-NPTLSNVDAAV 73
>gnl|CDD|35570 KOG0349, KOG0349, KOG0349, Putative DEAD-box RNA helicase DDX1 [RNA
processing and modification].
Length = 725
Score = 25.8 bits (56), Expect = 6.0
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 7/81 (8%)
Query: 12 SNCEKKAVESIGGRLSRSGLDHLVTEITI----PSERVVSVRKGRKVNSERRFF---PGY 64
SN E +++ IGG L R+ L I P + + KG + RF
Sbjct: 314 SNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFLVLDEAD 373
Query: 65 VLIKAVMTDKVYHTIKDTPKV 85
+L+ DK+Y P +
Sbjct: 374 LLLGQGYDDKIYRFHGQIPHM 394
>gnl|CDD|111185 pfam02263, GBP, Guanylate-binding protein, N-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 264
Score = 25.4 bits (56), Expect = 8.5
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 33 HLVTEITIPSERVVSVRKGRKVNSER--RFFPGYV 65
HLVTE+T S R GR +S FFP +V
Sbjct: 126 HLVTELTELIRAKSSPRYGRVADSAEFVSFFPDFV 160
>gnl|CDD|173644 cd05079, PTKc_Jak1_rpt2, Catalytic (repeat 2) domain of the Protein
Tyrosine Kinase, Janus kinase 1. Protein Tyrosine
Kinase (PTK) family; Janus kinase 1 (Jak1); catalytic
(c) domain (repeat 2). The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Jak1 is a member of the
Janus kinase (Jak) subfamily of proteins, which are
cytoplasmic (or nonreceptor) tyr kinases containing an
N-terminal FERM domain, followed by a Src homology 2
(SH2) domain, a pseudokinase domain, and a C-terminal
tyr kinase domain. Jaks are crucial for cytokine
receptor signaling. They are activated by
autophosphorylation upon cytokine-induced receptor
aggregation, and subsequently trigger downstream
signaling events such as the phosphorylation of signal
transducers and activators of transcription (STATs).
Jak1 is widely expressed in many tissues. Many cytokines
are dependent on Jak1 for signaling, including those
that use the shared receptor subunits common gamma chain
(IL-2, IL-4, IL-7, IL-9, IL-15, IL-21) and gp130 (IL-6,
IL-11, oncostatin M, G-CSF, and IFNs, among others). The
many varied interactions of Jak1 and its ubiquitous
expression suggest many biological roles. Jak1 is
important in neurological development, as well as in
lymphoid development and function. It also plays a role
in the pathophysiology of cardiac hypertrophy and heart
failure. A mutation in the ATP-binding site of Jak1 was
identified in a human uterine leiomyosarcoma cell line,
resulting in defective cytokine induction and antigen
presentation, thus allowing the tumor to evade the
immune system.
Length = 284
Score = 25.3 bits (55), Expect = 8.8
Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 54 VNSERRFFPG-YVLIKAVMTDKVYHTIKD 81
V SE + G + L KA+ TDK Y+T+KD
Sbjct: 142 VESEHQVKIGDFGLTKAIETDKEYYTVKD 170
>gnl|CDD|34765 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 25.4 bits (55), Expect = 8.9
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 112 AAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV 155
++R + +G+ V + G + G+VK+VD +RV +
Sbjct: 341 NELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVEL 384
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
0.318 0.136 0.389
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,110,596
Number of extensions: 105288
Number of successful extensions: 262
Number of sequences better than 10.0: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 21
Length of query: 177
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 89
Effective length of database: 4,362,145
Effective search space: 388230905
Effective search space used: 388230905
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 (24.6 bits)