RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780417|ref|YP_003064830.1| transcriptional regulator CarD family protein [Candidatus Liberibacter asiaticus str. psy62] (188 letters) >gnl|CDD|31520 COG1329, COG1329, Transcriptional regulators, similar to M. xanthus CarD [Transcription]. Length = 166 Score = 192 bits (489), Expect = 6e-50 Identities = 80/165 (48%), Positives = 112/165 (67%) Query: 11 RQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMR 70 + F+ G+H+VYPAHGVG I I+E+E+AG LE++VI F + M + VPV KA +G+R Sbjct: 2 QMAFKIGDHVVYPAHGVGIIQAIEEKEIAGETLEYYVIDFPQSDMTVMVPVAKADSVGLR 61 Query: 71 KLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPE 130 + + ++RAL++++G R K TMWSRR +E + K+ SGD+I IAEVVRDL+R D Q E Sbjct: 62 PVVDQEELDRALQVLQGGEREKPTMWSRRYKENEEKLKSGDIIDIAEVVRDLYRRDKQRE 121 Query: 131 KSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSK 175 SYSER+L E AL + E+A ISE EA ++ L+SKS Sbjct: 122 LSYSERRLLEKALQILAGELALAEGISEEEAKTFLDEVLASKSEA 166 >gnl|CDD|145606 pfam02559, CarD_TRCF, CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. Length = 98 Score = 77.9 bits (193), Expect = 1e-15 Identities = 37/111 (33%), Positives = 55/111 (49%), Gaps = 15/111 (13%) Query: 14 FRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAF-DKDKMCLKVPVGKAIDIGMRKL 72 + G+++V+P HGVG I+ EV G K E++V+ + D DK L VPV + IG Sbjct: 2 LKVGDYVVHPDHGVGRFEGIETIEVGGEKREYYVLEYADGDK--LYVPVDQLDLIGRYIG 59 Query: 73 SEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLH 123 SE V ++ W +R + KI SGD+ AE++R L Sbjct: 60 SEDE--------VPVLDKLGGGTWKKRKR----KIKSGDIDIAAELLRLLA 98 >gnl|CDD|146817 pfam04373, DUF511, Protein of unknown function (DUF511). Bacterial protein of unknown function. Length = 310 Score = 28.8 bits (65), Expect = 0.93 Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 3/73 (4%) Query: 67 IGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTD 126 IG + A +++ + + +R R E + K E + + + Sbjct: 47 IGSDRKELA---KKSPFIKTQEKPPRRYYLKSREDELELKALDEIKSEEDEEQSEAPKAN 103 Query: 127 SQPEKSYSERQLY 139 + + S+ ER L+ Sbjct: 104 KKQKNSFHERDLH 116 >gnl|CDD|133181 cd05050, PTKc_Musk, Catalytic domain of the Protein Tyrosine Kinase, Muscle-specific kinase. Protein Tyrosine Kinase (PTK) family; Muscle-specific kinase (Musk); catalytic (c) domain. 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. Musk is a receptor tyr kinase (RTK) containing an extracellular region with four immunoglobulin-like domains and a cysteine-rich cluster, a transmembrane segment, and an intracellular catalytic domain. Musk is expressed and concentrated in the postsynaptic membrane in skeletal muscle. It is essential for the establishment of the neuromuscular junction (NMJ), a peripheral synapse that conveys signals from motor neurons to muscle cells. Agrin, a large proteoglycan released from motor neurons, stimulates Musk autophosphorylation and activation, leading to the clustering of acetylcholine receptors (AChRs). To date, there is no evidence to suggest that agrin binds directly to Musk. Mutations in AChR, Musk and other partners are responsible for diseases of the NMJ, such as the autoimmune syndrome myasthenia gravis. Length = 288 Score = 28.3 bits (63), Expect = 1.4 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 15/69 (21%) Query: 58 KVPVGKAIDIGMRKLSEAHFVERALK----LVRGKARVK-------RTMWSRRAQEYDAK 106 ++ + K + GM LSE FV R L LV VK R ++S +Y K Sbjct: 132 QLCIAKQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYS---ADY-YK 187 Query: 107 INSGDLIAI 115 + D I I Sbjct: 188 ASENDAIPI 196 >gnl|CDD|37497 KOG2286, KOG2286, KOG2286, Exocyst complex subunit SEC6 [Intracellular trafficking, secretion, and vesicular transport]. Length = 667 Score = 26.4 bits (58), Expect = 4.8 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 2/65 (3%) Query: 87 GKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRM 146 GK R W R E + DL V+ +Y E LY AL+ + Sbjct: 225 GKMRALNKEWQVRLLEVLRFVIREDLRVAKRVLVPCFPPHYNIFSAYLE--LYHQALSDL 282 Query: 147 VREIA 151 +R++A Sbjct: 283 LRDLA 287 >gnl|CDD|34458 COG4849, COG4849, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 269 Score = 26.2 bits (57), Expect = 5.5 Identities = 10/56 (17%), Positives = 22/56 (39%) Query: 93 RTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVR 148 + W+ R +YD + + L+ + H + Q + E+A+ +R Sbjct: 185 KPQWALRRHDYDLETAAAALLGLDVASVASHESKRQIVDMRASVSAPEAAVLATLR 240 >gnl|CDD|35272 KOG0049, KOG0049, KOG0049, Transcription factor, Myb superfamily [Transcription]. Length = 939 Score = 25.9 bits (56), Expect = 6.3 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%) Query: 122 LHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPE 160 + R + +R+ +E L ++R+IA V SE E Sbjct: 174 VARDADITSSNL-DRRQWEMELEDLMRKIAYVREKSEEE 211 >gnl|CDD|30725 COG0376, KatG, Catalase (peroxidase I) [Inorganic ion transport and metabolism]. Length = 730 Score = 26.1 bits (57), Expect = 6.4 Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 3/32 (9%) Query: 88 KARVKRTMWSRRAQEYDAKINSGDLIAIAEVV 119 KAR R +W + ++Y KI+ DLI +A V Sbjct: 139 KAR--RLLWPIK-KKYGRKISWADLIILAGNV 167 >gnl|CDD|145380 pfam02194, PXA, PXA domain. This domain is associated with PX domains pfam00787. Length = 182 Score = 25.7 bits (57), Expect = 7.8 Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 7/35 (20%) Query: 146 MVREIAA-------VNSISEPEAINLIEVNLSSKS 173 ++REI A V+ +S+P+ IN + + L S Sbjct: 148 LLREILACAVLLPLVSKLSDPDFINQLIIKLIETS 182 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 0.315 0.129 0.348 Gapped Lambda K H 0.267 0.0774 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,014,637 Number of extensions: 96693 Number of successful extensions: 236 Number of sequences better than 10.0: 1 Number of HSP's gapped: 235 Number of HSP's successfully gapped: 23 Length of query: 188 Length of database: 6,263,737 Length adjustment: 88 Effective length of query: 100 Effective length of database: 4,362,145 Effective search space: 436214500 Effective search space used: 436214500 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 (21.6 bits) S2: 54 (24.5 bits)