RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter asiaticus str. psy62] (122 letters) >gnl|CDD|31944 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega [Transcription]. Length = 74 Score = 76.1 bits (187), Expect = 2e-15 Identities = 40/74 (54%), Positives = 50/74 (67%), Gaps = 2/74 (2%) Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV--GKDKNTVVALREIASGTL 58 MAR T+ED +DKV NR+ LV++A+ R R L+ GA P VD KDK V+ALREIA G + Sbjct: 1 MARPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKI 60 Query: 59 SPDDLEEDFIHSLQ 72 + L E IHSLQ Sbjct: 61 PIEILRELLIHSLQ 74 >gnl|CDD|144692 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6. Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly. Length = 57 Score = 56.5 bits (137), Expect = 2e-09 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%) Query: 7 EDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVD-VGKDKNTVVALREIASGTLSPD 61 E K NR+ L + + R + LS GA P VD + K V+AL EIA G + P+ Sbjct: 1 ERLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPE 56 >gnl|CDD|144074 pfam00343, Phosphorylase, Carbohydrate phosphorylase. The members of this family catalyse the formation of glucose 1-phosphate from one of the following polyglucoses; glycogen, starch, glucan or maltodextrin. Length = 712 Score = 26.2 bits (58), Expect = 2.2 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 2/63 (3%) Query: 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLE--EDFIHSL 71 +N F+ L A +G + KD L +I SG SP+D + D + SL Sbjct: 589 ENIFIFGLTAEEVEALRKKGYRSREYYKKDPRLRQVLDQIISGFFSPEDPDRFRDILDSL 648 Query: 72 QKH 74 Q Sbjct: 649 QGG 651 >gnl|CDD|143454 cd07136, ALDH_YwdH-P39616, Bacillus subtilis aldehyde dehydrogenase ywdH-like. Uncharacterized Bacillus subtilis ywdH aldehyde dehydrogenase (locus P39616) most closely related to the ALDHs and fatty ALDHs of families 3 and 14, and similar sequences, are included in this CD. Length = 449 Score = 25.9 bits (58), Expect = 2.5 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 14/71 (19%) Query: 33 GAKPTVDVGKDKNTVVALREIASGTL--------SPD------DLEEDFIHSLQKHVEID 78 G K V +D N +A + I G +PD ++E FI L++ ++ Sbjct: 208 GGKSPCIVDEDANLKLAAKRIVWGKFLNAGQTCVAPDYVLVHESVKEKFIKELKEEIKKF 267 Query: 79 EPDSPTENSDF 89 + P E+ D+ Sbjct: 268 YGEDPLESPDY 278 >gnl|CDD|34199 COG4555, NatA, ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]. Length = 245 Score = 25.3 bits (55), Expect = 4.1 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 3/59 (5%) Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK---DKNTVVALREIASG 56 ++R ++ I ++ R L+ R S G K V + + +++ L E SG Sbjct: 105 LSRKEIKARIAELSKRLQLLEYLDRRVGEFSTGMKQKVAIARALVHDPSILVLDEPTSG 163 >gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor) [Signal transduction mechanisms]. Length = 5019 Score = 24.6 bits (53), Expect = 7.6 Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 5/37 (13%) Query: 60 PDDLEE---DFIHSLQKH--VEIDEPDSPTENSDFSW 91 P+++ + DF L H +E+DE + E D S Sbjct: 2001 PEEIRDELLDFHEDLLLHCGIELDEDEEEDEEEDLSI 2037 >gnl|CDD|146797 pfam04347, FliO, Flagellar biosynthesis protein, FliO. FliO is an essential component of the flagellum-specific protein export apparatus. It is an integral membrane protein. Its precise molecular function is unknown. Length = 84 Score = 24.5 bits (54), Expect = 8.1 Identities = 5/25 (20%), Positives = 10/25 (40%) Query: 12 KVDNRFLLVLLASHRTRHLSQGAKP 36 +V + LL+ + + L P Sbjct: 36 EVGGKQLLLGVTPQQITLLHTLDTP 60 >gnl|CDD|133201 cd05070, PTKc_Fyn_Yrk, Catalytic domain of the Protein Tyrosine Kinases, Fyn and Yrk. Protein Tyrosine Kinase (PTK) family; Fyn and Yrk kinases; 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. Fyn and Yrk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. Fyn, together with Lck, plays a critical role in T-cell signal transduction by phosphorylating ITAM (immunoreceptor tyr activation motif) sequences on T-cell receptors, ultimately leading to the proliferation and differentiation of T-cells. In addition, Fyn is involved in the myelination of neurons, and is implicated in Alzheimer's and Parkinson's diseases. Yrk has been detected only in chickens. It is primarily found in neuronal and epithelial cells and in macrophages. It may play a role in inflammation and in response to injury. Length = 260 Score = 24.6 bits (53), Expect = 8.1 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%) Query: 45 NTVVALREIASGTLSPDD-LEEDFIHSLQKH 74 NT VA++ + GT+SP+ LEE I +H Sbjct: 30 NTKVAVKTLKPGTMSPESFLEEAQIMKKLRH 60 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 0.313 0.132 0.380 Gapped Lambda K H 0.267 0.0759 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,466,106 Number of extensions: 68680 Number of successful extensions: 128 Number of sequences better than 10.0: 1 Number of HSP's gapped: 126 Number of HSP's successfully gapped: 20 Length of query: 122 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 40 Effective length of database: 4,491,799 Effective search space: 179671960 Effective search space used: 179671960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (23.4 bits)