RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780391|ref|YP_003064804.1| DNA polymerase III subunit chi [Candidatus Liberibacter asiaticus str. psy62] (141 letters) >gnl|CDD|146811 pfam04364, DNA_pol3_chi, DNA polymerase III chi subunit, HolC. The DNA polymerase III holoenzyme (EC:2.7.7.7) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either either the tau or gamma product of gene dnax, complexed to delta.delta' and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi. Length = 136 Score = 98.0 bits (245), Expect = 9e-22 Identities = 40/140 (28%), Positives = 65/140 (46%), Gaps = 8/140 (5%) Query: 1 MRTLLFYRFKNDWEYNLL-VLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPH 59 M + FY D L L + +G RV V+C E ++L+E LWT++ D FLPH Sbjct: 1 MTRVDFYHLTRDPLEALACRLAEKALRQGWRVLVRCEDEEQAEALDELLWTFRPDSFLPH 60 Query: 60 GVDVGDEGDFSSFQPVLLTISSLNANTS-TIRFLVDEASMHIGDVDYYEKVVFIINTDDQ 118 G+ ++ QPVLL N N + +D A +E+V+ ++ DD Sbjct: 61 GL---AGEGPAAGQPVLLGWDGENPNGHADVLINLDGAVP--EFASRFERVIEFVDGDDA 115 Query: 119 GSLEWGRAHWRSLKNSGYAP 138 + + R W++ + +GY Sbjct: 116 -AKQAARERWKAYRAAGYEL 134 >gnl|CDD|32751 COG2927, HolC, DNA polymerase III, chi subunit [DNA replication, recombination, and repair]. Length = 144 Score = 78.8 bits (194), Expect = 5e-16 Identities = 34/140 (24%), Positives = 64/140 (45%), Gaps = 8/140 (5%) Query: 1 MRTLLFYRFKND-WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPH 59 M+ FY L + + G RV +QC E ++L+E+LWT+ + F+PH Sbjct: 1 MKEATFYLLSESTLLAAACRLAEKAWRSGWRVLIQCEDEAQAEALDEHLWTFSAESFIPH 60 Query: 60 GVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIIN--TDD 117 + G+ QP+L+ N N++ + L++ A YE V + + D+ Sbjct: 61 NLA-GEPPPAG--QPILIAWPGGNPNSARVDLLINLAD--EFPDFAYEFVTRVFDFVPDE 115 Query: 118 QGSLEWGRAHWRSLKNSGYA 137 + L+ R W++ + +G+ Sbjct: 116 EALLQLARERWKAYRGAGFQ 135 >gnl|CDD|35738 KOG0518, KOG0518, KOG0518, Actin-binding cytoskeleton protein, filamin [Cytoskeleton]. Length = 1113 Score = 30.3 bits (68), Expect = 0.19 Identities = 12/56 (21%), Positives = 16/56 (28%), Gaps = 6/56 (10%) Query: 51 WKKDGFLPHGVDV-GDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDY 105 K G LP V V G +L T + F+ E + V Sbjct: 287 ASKAGLLPLEVAVCGGRVPVEPVM-----AVALGDGTYNVSFVPSEDGPYTISVRI 337 >gnl|CDD|37636 KOG2425, KOG2425, KOG2425, Nuclear protein involved in cell morphogenesis and cell surface growth [General function prediction only]. Length = 599 Score = 28.2 bits (62), Expect = 0.92 Identities = 8/24 (33%), Positives = 12/24 (50%) Query: 35 CGSERVRDSLNEYLWTWKKDGFLP 58 C E+ +S Y W+K +LP Sbjct: 216 CLWEKANESFVSYFTVWEKARYLP 239 >gnl|CDD|113574 pfam04808, CTV_P23, Citrus tristeza virus (CTV) P23 protein. This family consists of protein P23 from the citrus tristeza virus, which is a member of the Closteroviridae. CTV viruses produce more positive than negative RNA strands, and P23 controls this asymmetrical RNA accumulation. Amino acids 42-180 are essential for function and are thought to contain RNA-binding and zinc finger domains. Length = 209 Score = 27.0 bits (59), Expect = 1.7 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 15/71 (21%) Query: 25 YEKGKRVSVQCGSERVRDSL-------------NEYLWTWKKDGFLP--HGVDVGDEGDF 69 Y K ++++V +ER + L Y + LP + VDVGD D Sbjct: 129 YTKERQLAVDLAAEREKTRLARRHPMRSPEETPEHYKFGMTAKAMLPEINAVDVGDNEDT 188 Query: 70 SSFQPVLLTIS 80 SS PV L++S Sbjct: 189 SSEYPVSLSVS 199 >gnl|CDD|146921 pfam04523, Herpes_U30, Herpes virus tegument protein U30. This family is named after the human herpesvirus protein, but has been characterized in cytomegalovirus as UL47. Cytomegalovirus UL47 is a component of the tegument, which is a protein layer surrounding the viral capsid. UL47 co-precipitates with UL48 and UL69 tegument proteins, and the major capsid protein UL86. A UL47-containing complex is thought to be involved in the release of viral DNA from the disassembling virus particle. Length = 883 Score = 25.4 bits (56), Expect = 5.3 Identities = 8/24 (33%), Positives = 10/24 (41%) Query: 1 MRTLLFYRFKNDWEYNLLVLLQDE 24 MR+ L+ K W L L E Sbjct: 459 MRSYLYIDAKRKWGDILFPLTAPE 482 >gnl|CDD|31489 COG1298, FlhA, Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 696 Score = 25.2 bits (55), Expect = 6.1 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 2/38 (5%) Query: 68 DFSSFQPVLL--TISSLNANTSTIRFLVDEASMHIGDV 103 DFSSF +LL T+ L N ++ R ++ G V Sbjct: 69 DFSSFPTLLLITTLLRLGLNVASTRVILSHGHEAAGKV 106 >gnl|CDD|73263 cd01379, MYSc_type_III, Myosin motor domain, type III myosins. Myosin III has been shown to play a role in the vision process in insects and in hearing in mammals. Myosin III, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.. Length = 653 Score = 25.0 bits (54), Expect = 7.3 Identities = 9/48 (18%), Positives = 28/48 (58%), Gaps = 1/48 (2%) Query: 29 KRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVL 76 +++ + +E+++ N++++ W++ +L GVD ++ +P+L Sbjct: 392 EQLCINIANEQIQYYFNQHIFAWEQQEYLNEGVDA-RLVEYEDNRPLL 438 >gnl|CDD|107208 cd06447, D-Ser-dehyd, D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive antagonist of beta-alanine in the biosynthetic pathway to pentothenate and coenzyme A. D-serine dehydratase is different from other pyridoxal-5'-phosphate-dependent enzymes in that it catalyzes alpha, beta-elimination reactions on amino acids.. Length = 404 Score = 25.0 bits (55), Expect = 7.6 Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 1/22 (4%) Query: 51 WKKDGFLPHGVDVGD-EGDFSS 71 WKKD GV V + E D+S Sbjct: 171 WKKDKLRSKGVTVVEYETDYSK 192 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 0.320 0.138 0.431 Gapped Lambda K H 0.267 0.0753 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,784,972 Number of extensions: 83972 Number of successful extensions: 195 Number of sequences better than 10.0: 1 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 15 Length of query: 141 Length of database: 6,263,737 Length adjustment: 84 Effective length of query: 57 Effective length of database: 4,448,581 Effective search space: 253569117 Effective search space used: 253569117 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 (21.8 bits) S2: 52 (23.8 bits)