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)