RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781079|ref|YP_003065492.1| diguanylate cyclase [Candidatus Liberibacter asiaticus str. psy62] (266 letters) >gnl|CDD|143635 cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria. Length = 158 Score = 154 bits (391), Expect = 3e-38 Identities = 63/160 (39%), Positives = 87/160 (54%), Gaps = 10/160 (6%) Query: 105 RIDCLSGLLNHSAF-------ISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAF 157 D L+GL N AF ++ L+++ DID+FKQIND +GH GD+V+ Sbjct: 1 YTDPLTGLPNRRAFEERLERLLARARRSGRPLALLLIDIDHFKQINDTYGHAAGDEVLKE 60 Query: 158 LSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIH 217 ++++L V RLGG+EFA G+ +EA LA LR+ IE + G I Sbjct: 61 VAERLRSSLRESDLVARLGGDEFAILLPGTDLEEAEALAERLREAIE--EPFFIDGQEIR 118 Query: 218 ITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVV 256 +T S GIA E ++ RAD+ALY AK+SGRNRVV Sbjct: 119 VTASIGIATYPEDGEDAEELLRRADEALYRAKRSGRNRVV 158 >gnl|CDD|32381 COG2199, COG2199, FOG: GGDEF domain [Signal transduction mechanisms]. Length = 181 Score = 138 bits (348), Expect = 2e-33 Identities = 64/179 (35%), Positives = 98/179 (54%), Gaps = 11/179 (6%) Query: 89 ILKELFISYNRISQLSRIDCLSGLLNHSAF-------ISSLGSYNEKLSIVFFDIDYFKQ 141 +L L + R+ +L+ D L+GL N AF ++ + E L+++ D+D+FKQ Sbjct: 5 LLTRLRKAEERLERLALHDPLTGLPNRRAFEERLERALARARRHGEPLALLLLDLDHFKQ 64 Query: 142 INDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRK 201 IND +GH GD+V+ ++ +L V RLGG+EFA G+S +EAA LA +R Sbjct: 65 INDTYGHAAGDEVLREVARRLRSNLREGDLVARLGGDEFAVLLPGTSLEEAARLAERIRA 124 Query: 202 IIENSQINISSGPSIHITISAGIAERCHKEPIS--TIIYRADQALYVAKKSGRNRVVCF 258 +E + G + +T+S G+A ++ RAD ALY AK++GRNRVV F Sbjct: 125 ALE--EPFFLGGEELRVTVSIGVALYPEDGSDDAELLLRRADLALYRAKRAGRNRVVVF 181 >gnl|CDD|144545 pfam00990, GGDEF, GGDEF domain. This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Length = 159 Score = 124 bits (314), Expect = 2e-29 Identities = 58/159 (36%), Positives = 85/159 (53%), Gaps = 8/159 (5%) Query: 104 SRIDCLSGLLNHSAFISSLGS------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAF 157 + D L+GL N F L L+++ D+D FK+IND +GH VGD+V+ Sbjct: 1 AAHDPLTGLPNRRYFEEELEQELQRARRQSPLALLLLDLDNFKRINDTYGHAVGDEVLQE 60 Query: 158 LSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS-SGPSI 216 ++ +L V RLGG+EFA +S + A LA +R+++ +I + SG + Sbjct: 61 VAQRLSSSLRRSDLVARLGGDEFAILLPDTSLEGAQELAERIRRLLAALKIPHTLSGLPL 120 Query: 217 HITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNR 254 ++TIS GIA E ++ RADQALY AK GRNR Sbjct: 121 YVTISIGIAAYPNDGEDAEDLLKRADQALYQAKNQGRNR 159 >gnl|CDD|33501 COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]. Length = 435 Score = 124 bits (312), Expect = 3e-29 Identities = 65/177 (36%), Positives = 96/177 (54%), Gaps = 11/177 (6%) Query: 90 LKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSY-------NEKLSIVFFDIDYFKQI 142 ++L S R+ +L+ +D L+GL N F L LS++ DID FK+I Sbjct: 256 ERQLRESLERLQELALVDGLTGLFNRRYFDEHLADLWKRALREGRPLSLLMLDIDDFKEI 315 Query: 143 NDNFGHPVGDKVIAFLSDQLV-VVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRK 201 ND +GH VGD+V+ ++ +L V G + V R GGEEFA + + A +A +R+ Sbjct: 316 NDTYGHDVGDEVLRQVARRLRQTVRGLDL-VARYGGEEFAVVLPDTDLEAAIAIAERIRQ 374 Query: 202 IIENSQINIS-SGPSIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVV 256 I S + +TIS G+AE + ++ I ++ RAD+ALY AK SGRNRVV Sbjct: 375 KINELPFVHELSREPLEVTISIGVAEGKPGEDSIEELLKRADKALYKAKASGRNRVV 431 >gnl|CDD|34606 COG5001, COG5001, Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]. Length = 663 Score = 83.5 bits (206), Expect = 5e-17 Identities = 50/165 (30%), Positives = 78/165 (47%), Gaps = 11/165 (6%) Query: 103 LSRIDCLSGLLNHSAFISSL-------GSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVI 155 L+ +D L+GL N F + L +L + D+D FK +ND FGH GD+++ Sbjct: 227 LANLDSLTGLPNRRRFFAELDARLAAARQSGRRLVLGVIDLDGFKPVNDAFGHATGDRLL 286 Query: 156 AFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS-SGP 214 + +L G P+ RLGG+EFA + ++ A+ R + E+ Q G Sbjct: 287 IEVGRRLKAFDGAPILAARLGGDEFALII--PALEDDALRVAGARALCESLQAPYDLRGV 344 Query: 215 SIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVVCF 258 + + S GIA + + RAD ALY AK++G+ V F Sbjct: 345 RVQVGASIGIAPFPSGADTSEQLFERADYALYHAKQNGKGAAVLF 389 >gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways. Length = 133 Score = 50.4 bits (121), Expect = 5e-07 Identities = 23/127 (18%), Positives = 46/127 (36%), Gaps = 7/127 (5%) Query: 129 LSIVFFDIDYFKQINDNFGHPVGDKVIA-FLSDQLVVVFGTPMFVGRLGGEEFAAAALGS 187 ++I+F DI F + D G GD+++ ++ + + G+EF + Sbjct: 2 VTILFADIVGFTSLADALGPDEGDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSGLD 61 Query: 188 SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAE------RCHKEPISTIIYRAD 241 A A D+R+ + + + + I I G R + ++ A Sbjct: 62 HPAAAVAFAEDMREAVSALNQSEGNPVRVRIGIHTGPVVVGVIGSRPQYDVWGALVNLAS 121 Query: 242 QALYVAK 248 + AK Sbjct: 122 RMESQAK 128 >gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with two other accessory proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 216 Score = 31.0 bits (71), Expect = 0.36 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 8/62 (12%) Query: 84 YISGSILKELFISYNRISQLSRIDCLSGLLNHS-----AFISSLG---SYNEKLSIVFFD 135 YIS +L + N IS + I + +L+ ++ ++G Y KL +F Sbjct: 71 YISAKMLARTKYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPG 130 Query: 136 ID 137 I Sbjct: 131 IK 132 >gnl|CDD|35751 KOG0531, KOG0531, KOG0531, Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]. Length = 414 Score = 29.8 bits (66), Expect = 0.76 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 9/89 (10%) Query: 55 LTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLN 114 L+ LE + + + + I LL + L+ L +S+N+I++L + L+ L Sbjct: 91 LSKLKSLEALDLYDNKIE----KIENLLSSLVN--LQVLDLSFNKITKLEGLSTLTLLKE 144 Query: 115 ---HSAFISSLGSYNEKLSIVFFDIDYFK 140 IS + S+ D+ Y + Sbjct: 145 LNLSGNLISDISGLESLKSLKLLDLSYNR 173 >gnl|CDD|30108 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins. 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 = 767 Score = 29.2 bits (65), Expect = 1.2 Identities = 19/89 (21%), Positives = 30/89 (33%), Gaps = 14/89 (15%) Query: 170 MFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCH 229 +F GR G A E SQ + SI T ++ A Sbjct: 563 LFQGRAGLAPVCLGAGAGLEGT--------------SQQALRRSSSIRRTFTSSTAAVKR 608 Query: 230 KEPISTIIYRADQALYVAKKSGRNRVVCF 258 K P + + D + ++SG + V C+ Sbjct: 609 KSPCVQVKLQVDALIDTLRRSGLHFVHCY 637 >gnl|CDD|112616 pfam03812, KdgT, 2-keto-3-deoxygluconate permease. Length = 314 Score = 28.6 bits (64), Expect = 1.6 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 2/75 (2%) Query: 19 LESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLT-PFYGLEYILVENLSLVIISIT 77 +F+P YF F + I + I ++ F +G + F IL ++ +LV+ I Sbjct: 25 CNTFAPGAGK-YFGSFTNGLITGTLPILAVWFFCMGASIDFRATGTILRKSGTLVVTKIA 83 Query: 78 ISLLLGYISGSILKE 92 + ++ I+ + + Sbjct: 84 FAWVVAVIAAQFIPD 98 >gnl|CDD|37725 KOG2514, KOG2514, KOG2514, Uncharacterized conserved protein [Function unknown]. Length = 861 Score = 28.0 bits (62), Expect = 2.9 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 5/78 (6%) Query: 17 KNLESFSPHTFMIYFSIFFSIFIATVIF-IANIFLFYIGLTPFYGLEYILVENLSLVIIS 75 L SFS FMI ++ FS + +++ I+ + F L + VII+ Sbjct: 385 AMLASFSFVLFMI--AVVFSAVLGVILYRISMVAALQ--CGKFTTSHAWLSATATAVIIN 440 Query: 76 ITISLLLGYISGSILKEL 93 + + ++L I ++ L Sbjct: 441 LVVIMILNAIYSNLASRL 458 >gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]. Length = 709 Score = 27.5 bits (61), Expect = 4.4 Identities = 25/146 (17%), Positives = 54/146 (36%), Gaps = 19/146 (13%) Query: 34 FFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKEL 93 F + I T+I L ++ + Y + L+ V+ +I +++L+ I +L+ Sbjct: 266 FLTGSILTLIIDLLFALIFLAVMFLYSWKLTLI-----VLAAIPLNVLITLIFQPLLRRK 320 Query: 94 F---ISYNRISQLSRIDCLSGLL------NHSAFISSLGSYNEKLSIVFFDIDYFKQIND 144 I + Q ++ + G+ F S + K + F + I + Sbjct: 321 TRKLIEESAEQQSFLVETIKGIETVKALAAEPRFRSQWDNRLAKQVNIGFKTEKLALILN 380 Query: 145 NFGHPVGDKVIAFLSDQLVVVFGTPM 170 ++ LS L++ FG + Sbjct: 381 TIK-----SLLQQLSSVLILWFGAIL 401 >gnl|CDD|143609 cd07585, nitrilase_7, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Length = 261 Score = 26.9 bits (60), Expect = 5.3 Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 1/35 (2%) Query: 217 HITISAGIAERCHKEP-ISTIIYRADQALYVAKKS 250 +TI AG+ E+ P + ++ D ++ +K Sbjct: 75 GLTILAGLIEKAGDRPYNTYLVCLPDGLVHRYRKL 109 >gnl|CDD|100006 cd02199, YjgF_YER057c_UK114_like_1, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.. Length = 142 Score = 26.7 bits (60), Expect = 6.6 Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 5/42 (11%) Query: 155 IAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILA 196 + ++S QL V G ++ G++G + QEAA L Sbjct: 25 LLYVSGQLPRVDGKLVYTGKVGADLSVEEG-----QEAARLC 61 >gnl|CDD|145484 pfam02361, CbiQ, Cobalt transport protein. This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system. Length = 217 Score = 26.5 bits (59), Expect = 7.5 Identities = 16/102 (15%), Positives = 33/102 (32%), Gaps = 5/102 (4%) Query: 21 SFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISL 80 ++ + + ++ I+T + LF TP L L + ++ + L Sbjct: 88 GIGITSWGLLRGLLLALRISTSLSAL---LFLALTTPPAELTSGLRRLGVPLELAEILLL 144 Query: 81 LLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSL 122 YI +L E + + D G+ + L Sbjct: 145 AYRYI--PLLLEEAQRIMQAQKSRGGDSKGGIRRRWRSLGLL 184 >gnl|CDD|177219 MTH00163, ND4, NADH dehydrogenase subunit 4; Provisional. Length = 445 Score = 26.3 bits (59), Expect = 8.8 Identities = 14/68 (20%), Positives = 34/68 (50%), Gaps = 5/68 (7%) Query: 27 FMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYIS 86 +++ +F F+ ++F + + I F+GL+ + + L+++S I +L+ S Sbjct: 22 WLVQSLLFLLSFLFMLLFSLSFYFSNISY--FFGLDLL---SFGLILLSFWICMLMILSS 76 Query: 87 GSILKELF 94 S+ K+ Sbjct: 77 ESVYKKNN 84 >gnl|CDD|32052 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]. Length = 380 Score = 26.0 bits (57), Expect = 9.8 Identities = 10/42 (23%), Positives = 17/42 (40%) Query: 163 VVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIE 204 V P+++G L EEF L +E K+++ Sbjct: 266 KVHLAGPLWLGPLHDEEFIEEMLEIAEGLELGTKKRALKLLK 307 >gnl|CDD|145704 pfam02687, FtsX, Predicted permease. This is a family of predicted permeases and hypothetical transmembrane proteins. The lipoprotein-releasing system transmembrane protein lolC from Buchnera aphidicola has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both lolC and an ATP-binding cassette transporter-like protein from Streptococcus cristatus have been shown to require ATP. Length = 174 Score = 26.2 bits (58), Expect = 9.8 Identities = 17/103 (16%), Positives = 37/103 (35%), Gaps = 13/103 (12%) Query: 18 NLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYI-------------GLTPFYGLEYI 64 S ++ + + + ++ + N+ I G + + + Sbjct: 41 LDLLLSNSIILLLSLLAVLLLLLALLILLNLLSISIAERRREIGILKALGASKKQIFKLL 100 Query: 65 LVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRID 107 L+E L L +I + LLLG++ +L ++ S ID Sbjct: 101 LLEALLLGLIGSLLGLLLGFLLAYLLSSAIGYFSGFSLPLVID 143 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 0.326 0.142 0.409 Gapped Lambda K H 0.267 0.0585 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,234,444 Number of extensions: 182585 Number of successful extensions: 1192 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1118 Number of HSP's successfully gapped: 199 Length of query: 266 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 174 Effective length of database: 4,275,709 Effective search space: 743973366 Effective search space used: 743973366 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 56 (25.7 bits)