RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780183|ref|YP_003064596.1| single-strand binding protein (ssb) [Candidatus Liberibacter asiaticus str. psy62] (159 letters) >gnl|CDD|109492 pfam00436, SSB, Single-strand binding protein family. This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA. Length = 104 Score = 125 bits (317), Expect = 4e-30 Identities = 44/106 (41%), Positives = 70/106 (66%), Gaps = 2/106 (1%) Query: 5 LNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEEL 64 +NKVIL+G L DP++R+T +G + N +A + +KD+ E E+T++ V+V+ + L Sbjct: 1 MNKVILVGRLTRDPELRYTPNGNAVANFTLAVNRRFKDQ-NGESDEETDFIRVVVWGK-L 58 Query: 65 CRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVML 110 +YL+KGS VY+EG L+TRK++DQ G RY TEI+ ++ L Sbjct: 59 AENAAEYLKKGSLVYVEGRLRTRKYEDQEGQKRYVTEIVADNVQFL 104 >gnl|CDD|30974 COG0629, Ssb, Single-stranded DNA-binding protein [DNA replication, recombination, and repair]. Length = 167 Score = 123 bits (310), Expect = 2e-29 Identities = 56/168 (33%), Positives = 84/168 (50%), Gaps = 12/168 (7%) Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSE 62 +NKVIL+G L DP++R+T +G +V + A + D + ER E+T+W V+++ Sbjct: 1 MMMNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWG- 59 Query: 63 ELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMR----SMVMLDGRRDSLQ 118 +L +YL+KGS VY+EG LQTRKW+DQ G RY TEI+ S+ ML R+ Sbjct: 60 KLAENAAEYLKKGSLVYVEGRLQTRKWEDQEGQKRYQTEIVTEIVADSVQMLGSRKSGEA 119 Query: 119 GEEQRSEQHSNNLKENVVGNRYSSPRE-------ESVFSDELDDEIPF 159 +S + E + + DD+IPF Sbjct: 120 AGGGGGGSNSPDSPPPAQSAEAPGDDENASPFVVVNAPIEFDDDDIPF 167 >gnl|CDD|72968 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity.. Length = 100 Score = 107 bits (269), Expect = 1e-24 Identities = 42/103 (40%), Positives = 62/103 (60%), Gaps = 3/103 (2%) Query: 8 VILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEELCRI 67 VILIG LG DP++R+T G + +A + KDR +E E+T+W V+ F + L Sbjct: 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDR--DEEEEETDWIRVVAFGK-LAEN 57 Query: 68 VEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVML 110 +YL+KG VY+EG L+TR W+D+ G RY TE++ + L Sbjct: 58 AAKYLKKGDLVYVEGRLRTRSWEDKDGQKRYGTEVVADRIEFL 100 >gnl|CDD|36866 KOG1653, KOG1653, KOG1653, Single-stranded DNA-binding protein [Replication, recombination and repair]. Length = 175 Score = 77.0 bits (189), Expect = 2e-15 Identities = 37/113 (32%), Positives = 60/113 (53%), Gaps = 3/113 (2%) Query: 4 SLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNE--RREKTEWHSVIVFS 61 +NKVIL+G +G DP + ++GR + + T +K R+ + + T+WH V VF+ Sbjct: 54 GVNKVILVGRVGQDPLQKILRNGRPVTIFSVGTGGMFKQRLYQAGDQPQPTQWHRVSVFN 113 Query: 62 EELCRIVEQYLRKGSKVYIEGSLQTRKWQ-DQSGNNRYTTEIIMRSMVMLDGR 113 E L +YL+KGS++Y+EG ++ R D GN + II+ V Sbjct: 114 EVLADYALKYLKKGSRIYVEGKIEYRGENDDIQGNVKRIPTIIIARDVSFLID 166 >gnl|CDD|113557 pfam04791, LMBR1, LMBR1-like membrane protein. Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. A member of this family has been shown to be a lipocalin membrane receptor. Length = 419 Score = 29.3 bits (66), Expect = 0.42 Identities = 9/33 (27%), Positives = 12/33 (36%) Query: 124 SEQHSNNLKENVVGNRYSSPREESVFSDELDDE 156 S L E+V R S E + EL+ Sbjct: 218 SVSLLPRLLEDVNEQRSKSATELGKLTRELNLS 250 >gnl|CDD|33020 COG3207, DIT1, Pyoverdine/dityrosine biosynthesis protein [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 330 Score = 28.5 bits (63), Expect = 0.88 Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 17/66 (25%) Query: 22 HTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEELCRIV-----EQYLRKGS 76 H DG K ++ + T D + T WH V V +E R V E GS Sbjct: 259 HPADGLKFGSLMMPTEDDFL----------TPWHGVAVNTE--DRFVLMKRSEVLELGGS 306 Query: 77 KVYIEG 82 V I G Sbjct: 307 LVQING 312 >gnl|CDD|145480 pfam02353, CMAS, Cyclopropane-fatty-acyl-phospholipid synthase. This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase EC:2.1.1.79 this enzyme catalyse the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid <=> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. Length = 273 Score = 26.5 bits (59), Expect = 2.9 Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 5/54 (9%) Query: 36 TSDSWKDRVTNERREKTEWHSVIVFSEELCRIVEQYLRKGSKVYIEGSLQTRKW 89 T D W + + +++ ++ + SEE R+ YL + + G + ++ Sbjct: 225 TLDLWAENL-QANKDE----AIALQSEEFYRMWMLYLTGCAVAFRVGYIDVHQF 273 >gnl|CDD|37118 KOG1907, KOG1907, KOG1907, Phosphoribosylformylglycinamidine synthase [Nucleotide transport and metabolism]. Length = 1320 Score = 25.3 bits (55), Expect = 7.3 Identities = 13/34 (38%), Positives = 19/34 (55%) Query: 43 RVTNERREKTEWHSVIVFSEELCRIVEQYLRKGS 76 RV E E+ E+H I+FS + I +Q+ RK Sbjct: 413 RVLLENGERREYHKPIMFSGGIGTIRKQHARKEP 446 >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 = 25.2 bits (56), Expect = 8.2 Identities = 7/17 (41%), Positives = 12/17 (70%) Query: 64 LCRIVEQYLRKGSKVYI 80 CR+ E+ LR+G +V + Sbjct: 18 ACRLAEKALRQGWRVLV 34 >gnl|CDD|30929 COG0584, UgpQ, Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]. Length = 257 Score = 25.2 bits (54), Expect = 8.7 Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 5/49 (10%) Query: 2 VASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERRE 50 +A+ G + DV+ T+DG +V I D DR TN Sbjct: 23 LAAFELAAEQGADYIELDVQLTKDG-VLVVIH----DETLDRTTNGLGT 66 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 0.314 0.131 0.371 Gapped Lambda K H 0.267 0.0664 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,864,214 Number of extensions: 86778 Number of successful extensions: 171 Number of sequences better than 10.0: 1 Number of HSP's gapped: 164 Number of HSP's successfully gapped: 27 Length of query: 159 Length of database: 6,263,737 Length adjustment: 86 Effective length of query: 73 Effective length of database: 4,405,363 Effective search space: 321591499 Effective search space used: 321591499 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: 53 (24.3 bits)