RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780869|ref|YP_003065282.1| beta-lactamase domain-containing protein [Candidatus Liberibacter asiaticus str. psy62] (559 letters) >gnl|CDD|161977 TIGR00649, MG423, conserved hypothetical protein. Contains an ATP-binding domain at the N-terminal end of the protein. Possibly part of a superfamily of beta-lactmases. Length = 422 Score = 314 bits (806), Expect = 4e-86 Identities = 148/429 (34%), Positives = 245/429 (57%), Gaps = 16/429 (3%) Query: 8 FLPLGGVGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKN 67 LGG+GEIG NM + + D G+ FP+D + GVD V PD +++ + + Sbjct: 3 IFALGGLGEIGKNMYVVEIDDDV----FIFDAGILFPEDAMLGVDGVIPDFSYLQENQDK 58 Query: 68 LMAIFITHAHEDHYGALHDLW-SFLHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAG 126 + IFITH HEDH GA+ L+ + P+Y +P I L+++K +++ + + G Sbjct: 59 VKGIFITHGHEDHIGAVPYLFHTVGFPPIYGTPLTIALIKSKIKENKLNVRTDLLEIHEG 118 Query: 127 DKVDVG-AFSIESVRVNHSIPETMALVIRSPVGNIVHTGDWKLDDDAILGDVTDKDSLCA 185 + ++ G +IE +R+ HSIP+++ + +P+G IV+TGD+K D+ ++G+ D + + Sbjct: 119 EPIETGENHTIEFIRITHSIPDSVGFALHTPLGYIVYTGDFKFDNTPVIGEPPDLNRIAE 178 Query: 186 IGNEGILALMCDSTNAMREGTCISEKGIKKNIYDIMKNAKGCVLVTTFSSSVSRIRSIID 245 G +G+L L+ DSTN G SE + + + DI KNAKG V+V TF+S++ R++ +I Sbjct: 179 YGKKGVLLLISDSTNVENPGFTPSEAKVLEQLNDIFKNAKGRVIVATFASNIHRVQQLIQ 238 Query: 246 IAEQIGRKIVLLGSSLKRVVSVAIDVGIIK-KDQLFLSDESFGLYPREQLIVIATGSQGE 304 IA + GRK + G S++ + +A +G+IK F+S + P E ++I TGSQGE Sbjct: 239 IARKQGRKFAVYGRSMEHLFGIARRLGLIKNPHNNFISLKEVNNSPDENYLIITTGSQGE 298 Query: 305 PRSALAQLSRGEMRNVKLAEKDTVIFSSRAIPGNEVAIGH--IKNRLVEQGVRVIAEDAE 362 P +AL +++ E +++ + DTV+FS+ IPGNE + RL E G RVI Sbjct: 299 PYAALTRIANNEHEQIRIRKGDTVVFSAPPIPGNENIAVSILLDIRLNEVGARVIKR--- 355 Query: 363 CPVHVSGHPYPNDLKRMYQWIRPQVLVAIHGEPLHLVAHKELALQEGI--ACVPPVRNGK 420 +HVSGH D K + + ++P+ ++ +HGE L+ H +LA +EG + +RNG Sbjct: 356 --IHVSGHASQEDHKLLLRLLKPKYIIPVHGEYRMLINHTKLAEEEGYPGENIFILRNGD 413 Query: 421 MLRLFPDPI 429 +L + I Sbjct: 414 VLEINGKFI 422 >gnl|CDD|129082 smart00849, Lactamase_B, Metallo-beta-lactamase superfamily. Apart from the beta-lactamases a number of other proteins contain this domain PUBMED:7588620. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor. Length = 183 Score = 82.2 bits (203), Expect = 3e-16 Identities = 44/196 (22%), Positives = 73/196 (37%), Gaps = 31/196 (15%) Query: 14 VGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFI 73 +G +G+N L I+ID G +D L + + P K++ AI + Sbjct: 1 LGGVGVNSYLVEGD----GGAILIDTGPGEAEDLLAELKKLGP---------KDIDAIIL 47 Query: 74 THAHEDHYGALHDLWSFLHVPVYASPFAIGLLEAKRVYERVS-----KKIPCISFQAGDK 128 TH H DH G L +L PVYA LL+ P + + G++ Sbjct: 48 THGHPDHIGGLPELLEAPGAPVYAPEGTAELLKDLLKLGGALGAEAPPPPPDRTLKDGEE 107 Query: 129 VDVGAFSIESVRVNHSIPETMALVIRSPVGNIVHTGDWKLDDDAILGDVTDKDSLCAIGN 188 +D+G +E + P ++ L + G I+ TGD + Sbjct: 108 LDLGGLELEVIHTPGHTPGSIVLYLPE--GKILFTGDLLFSGGI-----------GRTDD 154 Query: 189 EGILALMCDSTNAMRE 204 +G A DS ++ + Sbjct: 155 DGGDASASDSLESLLK 170 >gnl|CDD|132714 TIGR03675, arCOG00543, arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782. Length = 630 Score = 44.5 bits (106), Expect = 7e-05 Identities = 44/147 (29%), Positives = 66/147 (44%), Gaps = 36/147 (24%) Query: 11 LGGVGEIGMNMALYGYGSPSSRKWIMIDCGVS---FPKDDLPGVDLVFPDITFIMKERKN 67 LGG E+G + AL +P SR I++DCGV+ + P +D+ P+ Sbjct: 180 LGGFREVGRS-ALL-LSTPESR--ILLDCGVNVGANGDNAYPYLDV--PEFQL-----DE 228 Query: 68 LMAIFITHAHEDHYGALHDLWSF-LHVPVYASP-----FAIGLLEAKRVYERVSKKIPCI 121 L A+ ITHAH DH G + L+ + PVY +P + L+ V +R KK P Sbjct: 229 LDAVVITHAHLDHSGLVPLLFKYGYDGPVYCTPPTRDLMTLLQLDYIDVAQREGKKPP-- 286 Query: 122 SFQAGDKVDVGAFSIESVR--VNHSIP 146 +S + VR + H+I Sbjct: 287 ------------YSSKDVREALKHTIT 301 >gnl|CDD|148882 pfam07521, RMMBL, RNA-metabolising metallo-beta-lactamase. The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism. Length = 43 Score = 43.6 bits (104), Expect = 1e-04 Identities = 10/31 (32%), Positives = 20/31 (64%) Query: 365 VHVSGHPYPNDLKRMYQWIRPQVLVAIHGEP 395 +H SGH +L + + ++P+ ++ +HGEP Sbjct: 12 LHFSGHADQEELLELLKLLKPKKVILVHGEP 42 >gnl|CDD|163252 TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase. Members of this protein family are hydroxyacylglutathione hydrolase, a detoxification enzyme known as glyoxalase II. It follows lactoylglutathione lyase, or glyoxalase I, and acts to remove the toxic metabolite methylglyoxal and related compounds. This protein belongs to the broader metallo-beta-lactamase family (pfam00753). Length = 248 Score = 43.7 bits (104), Expect = 1e-04 Identities = 22/84 (26%), Positives = 31/84 (36%), Gaps = 17/84 (20%) Query: 56 PDITFIMKERKNLMAIFITHAHEDHYGALHDLWSFLHVPVYASPFAIGLLEAKRVYERVS 115 P + + L AI +TH H DH G + +L PVY Sbjct: 32 PVLDALEARGLTLTAILLTHHHHDHVGGVAELLEAFPAPVYGP---------------AE 76 Query: 116 KKIPCI--SFQAGDKVDVGAFSIE 137 ++IP I + GD V +G E Sbjct: 77 ERIPGITHPVKDGDTVTLGGLEFE 100 >gnl|CDD|179371 PRK02113, PRK02113, putative hydrolase; Provisional. Length = 252 Score = 37.5 bits (87), Expect = 0.010 Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 25/90 (27%) Query: 33 KWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAHEDHYGALHDLWSFLH 92 I+IDCG F + ++ + A+ ITH H DH G L DL F Sbjct: 45 ARILIDCGPDFREQ------MLRLPF-------GKIDAVLITHEHYDHVGGLDDLRPFCR 91 Query: 93 ---VPVYASPFAIGLLEAKRVYERVSKKIP 119 VP+YA + V ER+ ++P Sbjct: 92 FGEVPIYAEQY---------VAERLRSRMP 112 >gnl|CDD|162962 TIGR02651, RNase_Z, ribonuclease Z. Processing of the 3-prime end of tRNA precursors may be the result of endonuclease or exonuclease activity, and differs in different species. Member of this family are ribonuclease Z, a tRNA 3-prime endonuclease that processes tRNAs to prepare for addition of CCA. In species where all tRNA sequences already have the CCA tail, such as E. coli, the need for such an enzyme is unclear. Protein similar to the E. coli enzyme, matched by TIGR02649, are designated ribonuclease BN. Length = 299 Score = 32.2 bits (74), Expect = 0.38 Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 16/94 (17%) Query: 66 KNLMAIFITHAHEDHY----GALHDLWSF--------LHVPVYASPFAIGLLEAKRVYER 113 + IFITH H DH G L SF ++ P F L Y Sbjct: 50 MKIDRIFITHLHGDHILGLPGLLS-TMSFQGRKEPLTIYGPPGIKEFIETSLRV--SYTY 106 Query: 114 VSKKIPCISFQAGDKV-DVGAFSIESVRVNHSIP 146 ++ I + G V + F +E+ ++HSIP Sbjct: 107 LNYPIKIHEIEEGGLVFEDDGFKVEAFPLDHSIP 140 >gnl|CDD|182327 PRK10241, PRK10241, hydroxyacylglutathione hydrolase; Provisional. Length = 251 Score = 31.7 bits (72), Expect = 0.54 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%) Query: 70 AIFITHAHEDHYGALHDLWS-FLHVPVY 96 AIF+TH H DH G + +L F + VY Sbjct: 48 AIFLTHHHHDHVGGVKELVEKFPQIVVY 75 >gnl|CDD|161839 TIGR00361, ComEC_Rec2, DNA internalization-related competence protein ComEC/Rec2. The role for this protein in species that are not naturally transformable is unknown. Length = 662 Score = 30.6 bits (69), Expect = 1.1 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 4/52 (7%) Query: 33 KWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAHEDHYGAL 84 K I+ D G + + L G ++ P F+ + L A+ ++HA +DH G Sbjct: 460 KGILYDTGEPWREGSL-GEKVIIP---FLTAKGIKLEALILSHADQDHIGGA 507 >gnl|CDD|180093 PRK05452, PRK05452, anaerobic nitric oxide reductase flavorubredoxin; Provisional. Length = 479 Score = 30.5 bits (69), Expect = 1.2 Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 1/33 (3%) Query: 71 IFITHAHEDHYGALHDLWSFL-HVPVYASPFAI 102 I I HA EDH GAL +L + + P+Y + AI Sbjct: 75 IVINHAEEDHAGALTELMAQIPDTPIYCTANAI 107 >gnl|CDD|178829 PRK00055, PRK00055, ribonuclease Z; Reviewed. Length = 270 Score = 29.8 bits (68), Expect = 2.1 Identities = 14/54 (25%), Positives = 16/54 (29%), Gaps = 19/54 (35%) Query: 35 IMIDCG----VSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAHEDHYGAL 84 + DCG K + I IFITH H DH L Sbjct: 32 FLFDCGEGTQRQLLKTGIK-----PRKID----------KIFITHLHGDHIFGL 70 >gnl|CDD|180832 PRK07090, PRK07090, class II aldolase/adducin domain protein; Provisional. Length = 260 Score = 29.6 bits (67), Expect = 2.1 Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 3/37 (8%) Query: 367 VSGHPYPNDLKRMYQWI---RPQVLVAIHGEPLHLVA 400 + G PN R + WI RP V IH P H+ A Sbjct: 92 LDGEGMPNPANRFHSWIYRARPDVNCIIHTHPPHVAA 128 >gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional. Length = 2849 Score = 29.2 bits (65), Expect = 3.2 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 3/64 (4%) Query: 178 TDKDSLCAIGNEGILALMCDSTNAMREGTCISEKGIKKNI--YDIMKNAKGCVLVTTFSS 235 K C NEGI+ + + + + +K I K+I YD K C ++ S Sbjct: 2510 LKKHFACTCDNEGIIHMKIE-KITLDKIKIDEDKRIDKDICKYDSTKKVATCEIIDFIDS 2568 Query: 236 SVSR 239 + Sbjct: 2569 LALK 2572 >gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 420 Score = 28.4 bits (63), Expect = 5.2 Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%) Query: 306 RSALAQLSRGEMRNVKLA-EKDTVIFSSRAIPG 337 R LA S +R VK D VI S++ +PG Sbjct: 4 RKFLAATSHEVLRKVKEELGPDAVILSNKQVPG 36 >gnl|CDD|181927 PRK09522, PRK09522, bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional. Length = 531 Score = 28.1 bits (62), Expect = 6.1 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 3/45 (6%) Query: 272 GIIKKDQLFLSDESFGLYPREQLIVIATGSQGEPRSALAQLSRGE 316 G IK QL D Y +EQL A G+ E R L +L +G+ Sbjct: 438 GEIKSYQLTAEDFGLTPYHQEQL---AGGTPEENRDILTRLLQGK 479 >gnl|CDD|179375 PRK02126, PRK02126, ribonuclease Z; Provisional. Length = 334 Score = 28.0 bits (63), Expect = 6.5 Identities = 6/12 (50%), Positives = 9/12 (75%) Query: 70 AIFITHAHEDHY 81 IF++H H DH+ Sbjct: 50 HIFVSHTHMDHF 61 >gnl|CDD|178929 PRK00208, thiG, thiazole synthase; Reviewed. Length = 250 Score = 28.1 bits (64), Expect = 6.7 Identities = 29/88 (32%), Positives = 39/88 (44%), Gaps = 29/88 (32%) Query: 424 LFPDPIEIID--EVVHGLFLKDGFLIGKF----ADLGIAKRRQLSFVGHLSVNVL----- 472 L PDPIE + E++ +K+GF++ D +AKR L G +V L Sbjct: 105 LLPDPIETLKAAEIL----VKEGFVV--LPYCTDDPVLAKR--LEEAGCAAVMPLGAPIG 156 Query: 473 ----LDNHYNI------FGVPEIVDIGI 490 L N YN+ VP IVD GI Sbjct: 157 SGLGLLNPYNLRIIIEQADVPVIVDAGI 184 >gnl|CDD|130908 TIGR01849, PHB_depoly_PhaZ, polyhydroxyalkanoate depolymerase, intracellular. This model represents an intracellular depolymerase for polyhydroxyalkanoate (PHA), a carbon and energy storing polyester that accumulates in granules in many bacterial species when carbon sources are abundant but other nutrients are limiting. This family is named for PHAs generally, rather than polyhydroxybutyrate (PHB) specificially as in Ralstonia eutropha H16, to avoid overcalling chemical specificity in other species. Note that this family lacks the classic GXSXG lipase motif and instead shows weak similarity to some. Length = 406 Score = 27.4 bits (61), Expect = 8.9 Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 12/81 (14%) Query: 83 ALHDLWSFLHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAGDKVDVGAFSIESVRVN 142 A+ +S+ P+ PFA + ++ER ++ + + I+ V V+ Sbjct: 21 AMASYFSWPPNPLADHPFARRMHAGLELFERFTR-----------RYGKPEWGIDEVEVD 69 Query: 143 -HSIPETMALVIRSPVGNIVH 162 +P +V P ++H Sbjct: 70 GKDVPIRERVVWDKPFCRLIH 90 >gnl|CDD|150558 pfam09899, DUF2126, Putative amidoligase enzyme (DUF2126). Members of this family of bacterial domains are predominantly found in transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown, but they are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes). Length = 817 Score = 27.6 bits (62), Expect = 9.0 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 358 AEDAECPVHVSGHPYPND 375 AE+ PVH+ G+P P D Sbjct: 356 AEELGLPVHIEGYPPPRD 373 >gnl|CDD|183052 PRK11244, phnP, carbon-phosphorus lyase complex accessory protein; Provisional. Length = 250 Score = 27.6 bits (62), Expect = 9.7 Identities = 23/96 (23%), Positives = 37/96 (38%), Gaps = 16/96 (16%) Query: 68 LMAIFITHAHEDHY-GALHDLWSF-LHVPVYASPFAIGLLEAKRVYERVSKKIPCI---- 121 L I +TH H DH G W +PVY P G + ++ K P I Sbjct: 67 LQQILLTHYHMDHVQGLFPLRWGVGDPIPVYGPPDPEGCDD---LF-----KHPGILDFS 118 Query: 122 -SFQAGDKVDVGAFSIESVRVNHSIPETMALVIRSP 156 + + D+G + + +NHS T ++ + Sbjct: 119 HPLEPFEPFDLGGLQVTPLPLNHSKL-TFGYLLETA 153 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.322 0.141 0.415 Gapped Lambda K H 0.267 0.0763 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 9,446,512 Number of extensions: 649986 Number of successful extensions: 1242 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1234 Number of HSP's successfully gapped: 26 Length of query: 559 Length of database: 5,994,473 Length adjustment: 98 Effective length of query: 461 Effective length of database: 3,876,889 Effective search space: 1787245829 Effective search space used: 1787245829 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 (21.9 bits) S2: 60 (26.8 bits)