RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 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|30940 COG0595, COG0595, Predicted hydrolase of the metallo-beta-lactamase superfamily [General function prediction only]. Length = 555 Score = 496 bits (1279), Expect = e-141 Identities = 226/557 (40%), Positives = 331/557 (59%), Gaps = 13/557 (2%) Query: 2 KNEELVFLPLGGVGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFI 61 K ++ LGGVGEIG NM + YG I++D G+ FP+DDL GVDL+ PD +++ Sbjct: 5 KKAKIKIFALGGVGEIGKNMYVVEYG----DDIIILDAGLKFPEDDLLGVDLIIPDFSYL 60 Query: 62 MKERKNLMAIFITHAHEDHYGALHDLWS-FLHVPVYASPFAIGLLEAKRVYERVSK-KIP 119 + + + IF+TH HEDH GAL L L P+YASP L++ K + K + Sbjct: 61 EENKDKVKGIFLTHGHEDHIGALPYLLKQVLFAPIYASPLTAALIKEKLKEHGLFKNENE 120 Query: 120 CISFQAGDKVDVGAFSIESVRVNHSIPETMALVIRSPVGNIVHTGDWKLDDDAILGDVTD 179 + G ++ G+F +E V HSIP+++ +VI++P GNIV+TGD+K D + G+ TD Sbjct: 121 LHEVKPGSEIKFGSFEVEFFPVTHSIPDSLGIVIKTPEGNIVYTGDFKFDPTPVDGEPTD 180 Query: 180 KDSLCAIGNEGILALMCDSTNAMREGTCISEKGIKKNIYDIMKNAKGCVLVTTFSSSVSR 239 L IG EG+LAL+ DSTNA G SE + +N+ DI++NAKG V+VTTF+S++ R Sbjct: 181 LARLAEIGKEGVLALISDSTNAENPGFTPSESEVGENLEDIIRNAKGRVIVTTFASNIER 240 Query: 240 IRSIIDIAEQIGRKIVLLGSSLKRVVSVAIDVGIIK-KDQLFLSDESFGLYPREQLIVIA 298 I++IID AE++GRK+V+ G S++R++++A +G +K D+ F+ YP E++++I Sbjct: 241 IQTIIDAAEKLGRKVVVTGRSMERLIAIARRLGYLKLPDESFIEIREVKRYPDEEVLIIC 300 Query: 299 TGSQGEPRSALAQLSRGEMRNVKLAEKDTVIFSSRAIPGNEVAIGHIKNRLVEQGVRVIA 358 TGSQGEP +AL++++ GE R VK+ E DTVIFSS IPGNE A+ + NRL + G +VI Sbjct: 301 TGSQGEPMAALSRMANGEHRYVKIKEGDTVIFSSSPIPGNEAAVYRLLNRLYKAGAKVI- 359 Query: 359 EDAECPVHVSGHPYPNDLKRMYQWIRPQVLVAIHGEPLHLVAHKELALQEGIA--CVPPV 416 + VHVSGH +LK M +RP+ L+ +HGE LVAH +LA +EGI + + Sbjct: 360 TGGDKKVHVSGHASREELKLMINLLRPKYLIPVHGEYRMLVAHAKLAEEEGIPQENIFIL 419 Query: 417 RNGKMLRLFPDPIEIIDEVVHGLFLKDGFLIGKFADLGIAKRRQLSFVGHLSVNVLLD-N 475 RNG +L L +I +V G DG IG + + RRQLS G + V V++D Sbjct: 420 RNGDVLELEGGKARVIGKVPAGDVYIDGNGIGDVGAIVLRDRRQLSEDGIVIVVVVIDKK 479 Query: 476 HYNIFGVPEIVDIGIPAYDGDGGKIHKLLLKTVITTVVDLPQFRRKDLKLLRESISSALR 535 I PEI G Y + K+ + L+ V + Q + D K L+ESI ALR Sbjct: 480 KKKILAGPEISSRGFV-YVKESEKLIEEALELVENALESFLQ-EKFDWKELKESIRRALR 537 Query: 536 SLLKKVWGKKPLVTVFI 552 L K ++PL+ + Sbjct: 538 KFLYKKTKRRPLILPTV 554 >gnl|CDD|36352 KOG1137, KOG1137, KOG1137, mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification]. Length = 668 Score = 78.9 bits (194), Expect = 3e-15 Identities = 97/499 (19%), Positives = 167/499 (33%), Gaps = 50/499 (10%) Query: 8 FLPLGGVGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKN 67 F P G + ++ G ++D + P + ++ Sbjct: 153 FWPYH-AGHVLGACMFMV----EIAGVRLLYTGDYSREEDRHLIAAEMPPTGPDVLITES 207 Query: 68 LMAIFITHAHEDHYGAL----HDL---WSFLHVPVYASPFAIGLLEAKRVYERV---SKK 117 + I E+ G L H + +PV+A A LL Y + Sbjct: 208 TYGVQIHEPREEREGRLTWVIHSTVPRGGRVLIPVFALGRAQELLLILDEYWGNHVDLRD 267 Query: 118 IPCISFQAGDKVDVGAFSIESVRVNHSIPETMALVIRSPV----GNIVHTGDWKLDDDAI 173 IP + K +G F +N I + AL R+P +I+ TGDW D+ Sbjct: 268 IPIYYASSLAKKCMGVFQTYVNMMNDRIRKQSAL--RNPFIFKHVSILRTGDWFDDEGPS 325 Query: 174 LGDVTDKDSLCAIGNEGILALMCDSTNA-MREGTCISEKGIK------KNIYDIMKNAKG 226 + + + E DS NA + G C+ K K I M K Sbjct: 326 VVMASPGMLQSGLSRELFERWCSDSKNAVLIPGYCVEGTLAKDILSEPKEI-MAMNGRKL 384 Query: 227 ----CVLVTTFSSSVSRIRSIIDIAEQIGRKIVLLG------SSLKRVVSVAIDVGIIKK 276 V +F++ V +++ IA+ ++L+ LK + A G + Sbjct: 385 PLRMQVEYISFAAHVDYLQNSEFIADITPPHLILVHGEANEMMRLKSALEAAFRDGKVPI 444 Query: 277 DQLFLSD-ESFGLYPREQLIVIATGSQGE----PRSALAQLSRGEMRNVKLAEKDTVIFS 331 D + E LY + + TGS E R + +S G + L+ +D +++S Sbjct: 445 DVSTPRNCEDVELYFPGEKLAKTTGSLAEVPKEDRVSGILVSYGFSYAI-LSPEDLILYS 503 Query: 332 S-RAIPGNEVAIGHIKNRLVEQGVRVIAEDAECPVHVSGHPYPNDLKRMYQWIRPQVLVA 390 + IP NE + R+ G +I E + S + + Sbjct: 504 DLKTIPLNERQVIPYMGRIALIGPNLIQGKNEM-LETSKKHAYRVELVIKVVKPQEFP-- 560 Query: 391 IHGEPLHLVAHKELALQEGIACVPPVRNGKMLRLFPDPIEIIDEV-VHGLFLKDGFLIGK 449 I E L + LA G + + K ++L D + ++ + LK+ F K Sbjct: 561 IVLEWLSNPENDMLADSIGARILTVSLSPKSVKLMVDKCDEVERKKLLESLLKNQFGDDK 620 Query: 450 FADLGIAKRRQLSFVGHLS 468 + GI V +S Sbjct: 621 TNEYGILVMEVDGMVARIS 639 Score = 39.6 bits (92), Expect = 0.003 Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 18/86 (20%) Query: 3 NEELVFLPLGGVGEIGMNMALYGYGSPSSRKWIMIDCGVSFPK----DDLPGVDLVFPDI 58 +++L F PLG E+G + + Y K IM+DCGV P LP D V Sbjct: 11 SDQLKFTPLGAGNEVGRSCHILEYKG----KTIMLDCGV-HPAYSGMASLPFYDEV---- 61 Query: 59 TFIMKERKNLMAIFITHAHEDHYGAL 84 + + + ITH H DH +L Sbjct: 62 -----DLSAIDPLLITHFHLDHAASL 82 >gnl|CDD|31429 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]. Length = 427 Score = 75.5 bits (185), Expect = 3e-14 Identities = 93/439 (21%), Positives = 161/439 (36%), Gaps = 62/439 (14%) Query: 6 LVFLPLGGVGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKER 65 + LG E+G + L G I++DCG+ ++ Sbjct: 1 MTLRFLGAAREVGRSCVLLETGGTR----ILLDCGLFPGDPS---------PERPLLPPF 47 Query: 66 KNLMAIFITHAHEDHYGALHDLWS-FLHVPVYASPFAIGLLE------------------ 106 + A+ +THAH DH GAL L PVYA+P LL+ Sbjct: 48 PKVDAVLLTHAHLDHIGALPYLVRNGFEGPVYATPPTAALLKVLLGDSLKLAEGPDKPPY 107 Query: 107 AKRVYERVSKKIPCISFQAGDKVDVGAFSIESVRVNHSIPETMALVIRSPVGNIVHTGDW 166 ++ ERV I + + G+ V+VG + H I + A+++ G I++TGD Sbjct: 108 SEEDVERVPDLIRPLPY--GEPVEVGGVKVTFYNAGH-ILGSAAILLEVDGGRILYTGDV 164 Query: 167 KLDDDAILGDVTDKDSLCAIGNEGILALMCDSTNAMREGTCISEKGIKKNIYDIMKNA-- 224 K D +L A I L+ +ST R E ++ + +K A Sbjct: 165 KRRKDRLLN--------GAELPPCIDVLIVESTYGDRLHPNRDEV--ERRFIESVKAALE 214 Query: 225 -KGCVLVTTFSSSVSRIRSIIDIAEQIGRKI---VLLGSSLKRVVSVAID--VGIIKKDQ 278 G VL+ F ++ R + ++ I ++G + + + RV +G+ D Sbjct: 215 RGGTVLIPAF--ALGRAQELLLILRELGFAGDYPIYVDGPIARVALAYAKYPIGLDLPDL 272 Query: 279 LFLSDESFG--LYPREQLIVIATGSQGEPRSALAQLSRGEMRNVKLA----EKDTVIFSS 332 L +++ F R + +A L G R EK+ V+ Sbjct: 273 LKVAESRFRFVESRRNSMREGIDKGPAVVLAAPGMLKGGRSRYYLKHLLSDEKNWVLLPG 332 Query: 333 RAIPG-NEVAIGHIKNRLVEQGVRVIAEDAECPVHVSGHPYPNDLKRMYQWIRPQVLVAI 391 G + + +G+ + + + S H ++L + I P +V + Sbjct: 333 YQAEGTLGRVLLEGGTSVHIKGIEIKVKARVEELDFSAHADGDELLEFIKDISPPKVVLV 392 Query: 392 HGEPLHLVAHKELALQEGI 410 HGEP + A + L+E I Sbjct: 393 HGEPEYGAALRARLLEELI 411 >gnl|CDD|144377 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily. Length = 148 Score = 72.4 bits (177), Expect = 3e-13 Identities = 36/158 (22%), Positives = 54/158 (34%), Gaps = 15/158 (9%) Query: 14 VGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFI 73 G +G N L I+ID G+ L L K++ AI + Sbjct: 1 GGGVGSNSYLVEGD----GGAILIDTGLGADDALLLLAALGLDP--------KDIDAIIL 48 Query: 74 THAHEDHYGALHDLWSFLHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAGDKVDVGA 133 THAH DH G L +L PV A+P L + + +K+ + D Sbjct: 49 THAHADHIGGLPELKEATPAPVVAAPEDAAALLRLGLDDAELRKLVDVLPPDVDLEGGDG 108 Query: 134 FSIESVRVN---HSIPETMALVIRSPVGNIVHTGDWKL 168 + H +V+ P G ++ TGD Sbjct: 109 ILGGGTLLFVTPHPGHGPGHVVVYLPGGKVLFTGDLLF 146 >gnl|CDD|36575 KOG1361, KOG1361, KOG1361, Predicted hydrolase involved in interstrand cross-link repair [Replication, recombination and repair]. Length = 481 Score = 54.2 bits (130), Expect = 8e-08 Identities = 63/305 (20%), Positives = 108/305 (35%), Gaps = 34/305 (11%) Query: 28 SPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNL-----MAIFITHAHEDHYG 82 S S K G+ V V P F + + A F++H H DHY Sbjct: 68 SESIGKSSKDPSGIKVRSRIPLHVIKVLPGGEFSVDAFRYGHIEGCSAYFLSHFHSDHYI 127 Query: 83 ALHDLWSFLHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAGDKVDVGAFSIESVRVN 142 L WS H P+Y SP L+ K + S + +++ + + N Sbjct: 128 GLTKSWS--HPPLYCSPITARLVPLKVSVTKQS----IQALDLNQPLEIPGIQVTLLDAN 181 Query: 143 HSIPETMALVIRSPVGNIVHTGDWKLDDDAILGDVTDKDSLCAIGNEGILALMCDSTNAM 202 H M L S I+HTGD++ D + I L D+T Sbjct: 182 HCPGAVMFLFELSFGPCILHTGDFRASADMS-------KEPALTLEQTIDILYLDTTYCN 234 Query: 203 REGTCISEKGIKKNIYDIM-----KNAKGCVLVTTFSSSVSRIRSIIDIAEQIGRKIVLL 257 + S++ + + D++ KN + ++V T+S ++ +++IA + KI + Sbjct: 235 PKYDFPSQEESVQEVVDVIRSHASKNDRVLIVVGTYSIGKEKL--LLEIARILNSKIWVE 292 Query: 258 GSSLKRVVSVAIDVGIIKKDQLFLSDESFGLYPREQLIVIATGSQGEPRSALAQLSRGEM 317 L+ + + D + LS + + V+ S S S+ E Sbjct: 293 PRRLRLLQCLGFDD-----ESKLLSIDV----DESSVHVVPMNSLASSPSLKEYESQYED 343 Query: 318 RNVKL 322 KL Sbjct: 344 GYSKL 348 >gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]. Length = 637 Score = 47.2 bits (112), Expect = 1e-05 Identities = 53/192 (27%), Positives = 79/192 (41%), Gaps = 44/192 (22%) Query: 11 LGGVGEIGMNMALYGYGSPSSRKWIMIDCGV--------SFPKDDLPGVDLVFPDITFIM 62 LGG E+G + L +P SR +++DCGV +FP D+P D Sbjct: 186 LGGFREVGRSALLVS--TPESR--VLLDCGVNVAGNGEDAFPYLDVPEFQPDELD----- 236 Query: 63 KERKNLMAIFITHAHEDHYGALHDLWSF-LHVPVYASP-----FAIGLLEAKRVYERVSK 116 A+ ITHAH DH G L L+ + PVY +P + L+ V E+ Sbjct: 237 -------AVIITHAHLDHCGFLPLLFKYGYDGPVYCTPPTRDLMVLLQLDYIEVAEKEGG 289 Query: 117 KIP------------CISFQAGDKVDVGA-FSIESVRVNHSIPETMA-LVIRSPVGNIVH 162 + P I+ G+ D+ + H + MA L I + NIV+ Sbjct: 290 EPPYESKDVRKVLKHTITLDYGEVTDIAPDIRLTFYNAGHILGSAMAHLHIGDGLYNIVY 349 Query: 163 TGDWKLDDDAIL 174 TGD+K + +L Sbjct: 350 TGDFKFEKTRLL 361 >gnl|CDD|30837 COG0491, GloB, Zn-dependent hydrolases, including glyoxylases [General function prediction only]. Length = 252 Score = 44.1 bits (102), Expect = 9e-05 Identities = 29/144 (20%), Positives = 50/144 (34%), Gaps = 19/144 (13%) Query: 31 SRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAHEDHYGALHDLWS- 89 ++ID G G + + ++ AI +TH H DH G L Sbjct: 34 EGGAVLIDTG--------LGDADAEALLEALAALGLDVDAILLTHGHFDHIGGAAVLKEA 85 Query: 90 FLHVPVYASPFAIGLLEAKRVY--------ERVSKKIPCISFQAGDKVDVGAFSIESVRV 141 F PV A LL + + P + + GD++D+G +E + Sbjct: 86 FGAAPVIAPAEVPLLLREEILRKAGVTAEAYAAPGASPLRALEDGDELDLGGLELEVLHT 145 Query: 142 NHSIPETMALVIRSPVGNIVHTGD 165 P + ++ ++ TGD Sbjct: 146 PGHTPGHIVFLLEDG--GVLFTGD 167 >gnl|CDD|36351 KOG1136, KOG1136, KOG1136, Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]. Length = 501 Score = 43.4 bits (102), Expect = 2e-04 Identities = 52/199 (26%), Positives = 76/199 (38%), Gaps = 41/199 (20%) Query: 5 ELVFLPLGGVGEIGMNMALYGYGSPSSRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKE 64 E+ PLG ++G + L G K IM DCG+ +D D FPD ++I K Sbjct: 3 EIKVTPLGAGQDVGRSCILVSIGG----KNIMFDCGMHMGFND----DRRFPDFSYISKS 54 Query: 65 R---KNLMAIFITHAHEDHYGALHDLWSFLHVPVYASPFAIG---------LLEAKR--- 109 + + I+H H DH GAL F V Y P + LLE R Sbjct: 55 GRFTDAIDCVIISHFHLDHCGALP---YFSEVVGYDGPIYMTYPTKAICPVLLEDYRKVA 111 Query: 110 ----------VYERVS---KKIPCISFQAGDKVDVGAFSIESVRVNHSIPETMALVIRSP 156 + + KK+ I +VD I + H + M I+ Sbjct: 112 VDRKGESNFFTTQDIKNCMKKVVAIDLHQTIQVD-EDLQIRAYYAGHVLGAAM-FYIKVG 169 Query: 157 VGNIVHTGDWKLDDDAILG 175 ++V+TGD+ + D LG Sbjct: 170 DQSVVYTGDYNMTPDRHLG 188 >gnl|CDD|31428 COG1235, PhnP, Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]. Length = 269 Score = 41.2 bits (96), Expect = 8e-04 Identities = 29/135 (21%), Positives = 43/135 (31%), Gaps = 14/135 (10%) Query: 31 SRKWIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAHEDHYGALHDLWSF 90 K ++ID G L L D+ AI +TH H DH L DL Sbjct: 39 GVKTLLIDAGPDLRDQGL---RLGVSDLD----------AILLTHEHSDHIQGLDDLRRA 85 Query: 91 LHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAGDKVDVGAFSIESVRVNHSIPETMA 150 +P+Y +P + + R+ F +G + V H E + Sbjct: 86 YTLPIYVNPGTLRASTSDRLLGGFPYLFRHP-FPPFSLPAIGGLEVTPFPVPHDAIEPVG 144 Query: 151 LVIRSPVGNIVHTGD 165 VI + D Sbjct: 145 FVIIRTGRKLHGGTD 159 >gnl|CDD|31427 COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]. Length = 292 Score = 35.8 bits (82), Expect = 0.033 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 11/89 (12%) Query: 66 KNLMAIFITHAHEDHYGALHDL---WSFLH----VPVYASPFAIGLLEAKRVYERVSKKI 118 + + AIFITH H DH L L SF + +Y P +E Sbjct: 52 RKIDAIFITHLHGDHIAGLPGLLVSRSFRGRREPLKIYGPPGIKEFVETSLRLSYSKLTY 111 Query: 119 PCISFQAGDKVDVGAFSIESVRVNHSIPE 147 G +++ AF +E++ ++H +P Sbjct: 112 E----IIGHEIEEDAFEVEALELDHGVPA 136 >gnl|CDD|31430 COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]. Length = 259 Score = 34.9 bits (80), Expect = 0.057 Identities = 25/117 (21%), Positives = 47/117 (40%), Gaps = 18/117 (15%) Query: 66 KNLMAIFITHAHEDHYGALHDLW--SFLHVPVYASPFAIGLLEAKRVYER---VSKKIPC 120 +++ A+ ++H H DH G L L + +PVYA P A + + Sbjct: 57 RDIDAVVLSHGHYDHTGGLPYLLEENNPGIPVYAHPDAFKAKIEVFREIGIPELEELARL 116 Query: 121 ISFQAGDKVDVGAFSI-ESVRVNH------------SIPETMALVIRSPVGNIVHTG 164 I + D++ G ++ E +V + + AL++ + G +V TG Sbjct: 117 ILSEEPDEIVEGVITLGEIPKVTFEKGGYFEDGEPDPVLDEQALIVETEKGLVVITG 173 >gnl|CDD|48083 cd03466, Nitrogenase_NifN_2, Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein.. Length = 429 Score = 32.2 bits (73), Expect = 0.38 Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 16/116 (13%) Query: 389 VAIHGEPLHLVAHKELALQEGIACVPPVRNGKMLRLFPDPIEIIDEVVHGLFLKDGFLIG 448 AI+GEP +VA L+ G+ V + +L E + E V + DG Sbjct: 303 AAIYGEPDFVVAITRFVLENGMVPVLIATGSESKKLKEKLEEDLKEYVEKCVILDG---A 359 Query: 449 KFADLGIAKRRQLSFVGHLSVNVLLDNHYNIF-----GVPEIVDIGIPAYDGDGGK 499 F D+ S+ L ++VL+ N Y G+P ++ IG P +D GG+ Sbjct: 360 DFFDIE-------SYAKELKIDVLIGNSYGRRIAEKLGIP-LIRIGFPIHDRLGGQ 407 >gnl|CDD|30775 COG0426, FpaA, Uncharacterized flavoproteins [Energy production and conversion]. Length = 388 Score = 32.1 bits (73), Expect = 0.42 Identities = 62/340 (18%), Positives = 111/340 (32%), Gaps = 57/340 (16%) Query: 71 IFITHAHEDHYGALHDLWS-FLHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAGDKV 129 I + H DH G+L +L + + S A L+ + + + GD + Sbjct: 76 IIVNHTEPDHSGSLPELLELAPNAKIICSKLAARFLKG---FYHDPEWFKIVKT--GDTL 130 Query: 130 DVGAFSIESVRVN--HSIPETMALVIRSPVGNIVHTGDWKLDDDAILGDVTDKDSLCAIG 187 D+G +++ + H P+TM P I+ + D G D Sbjct: 131 DLGGHTLKFIPAPFLHW-PDTMFTYD--PEDKILFSCD-------AFGAHVCDD---YRF 177 Query: 188 NEGILALMCDSTNAMREG-TCI--SEKGIKKNIYDIMKNAK--------GCVLVTTFSSS 236 +E I L+ D MR+ + + +K K G + Sbjct: 178 DEDIEELLPD----MRKYYANLMAPNARLVLWALKKIKLLKIEMIAPSHGPIWRGNPKEI 233 Query: 237 VSRIRSIIDIAEQIGRKIVLL----GSSLKRVVSVAIDVGIIKKDQ----LFLSD----E 284 V R D AE + V L ++ AI G++K+ + L D E Sbjct: 234 VEAYR---DWAEGQPKGKVDLIYDSMYGNTEKMAQAIAEGLMKEGVDVEVINLEDADPSE 290 Query: 285 SFGLYPREQLIVIATGSQGEPRSALAQLSRGEMRNVKLAEKDTVIFSSRAIPGNEVAIGH 344 + +V+ + + Q + G + + K +F S + A+ Sbjct: 291 IVEEILDAKGLVVGSPTINGGAHPPIQTALGYVLALAPKNKLAGVFGSYG--WSGEAVDL 348 Query: 345 IKNRLVEQGVRVIAEDAECPVHVSGHPYPNDLKRMYQWIR 384 I+ +L + G + V P DLK+ + R Sbjct: 349 IEEKLKDLGFEF----GFDGIEVKFRPTEEDLKKCEEAGR 384 >gnl|CDD|37332 KOG2121, KOG2121, KOG2121, Predicted metal-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]. Length = 746 Score = 31.9 bits (72), Expect = 0.51 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 10/64 (15%) Query: 20 NMALYGYGSPSSRKWIMIDCG--VSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAH 77 N++ S I++DCG GV+ V + + L AIFI+H H Sbjct: 460 NVSSILVRIDS-DDSILLDCGEGTLGQLVRHYGVENVDTAL-------RKLRAIFISHLH 511 Query: 78 EDHY 81 DH+ Sbjct: 512 ADHH 515 >gnl|CDD|32402 COG2220, COG2220, Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]. Length = 258 Score = 31.7 bits (71), Expect = 0.52 Identities = 27/110 (24%), Positives = 36/110 (32%), Gaps = 19/110 (17%) Query: 70 AIFITHAHEDHYGA--LHDLWSFLHVPVYASPFAIGLLEAKRVYERVSKKIPCISFQAGD 127 I ITH H DH L L + V A LL V + GD Sbjct: 55 YILITHDHYDHLDDETLIALRTNKAPVVVVPLGAGDLLIRDGV-----EAERVHELGWGD 109 Query: 128 KVDVGAFSIESVRVNHSIPET------------MALVIRSPVGNIVHTGD 165 +++G I +V H + VI +P G + H GD Sbjct: 110 VIELGDLEITAVPAYHVSARHLPGRGIRPTGLWVGYVIETPGGRVYHAGD 159 >gnl|CDD|36031 KOG0813, KOG0813, KOG0813, Glyoxylase [General function prediction only]. Length = 265 Score = 31.5 bits (71), Expect = 0.63 Identities = 20/89 (22%), Positives = 31/89 (34%), Gaps = 15/89 (16%) Query: 54 VFPDITFIMKERKNLMAIFITHAHEDHYGALHDLWSFLHVPVYASPFAIGLLEAKRVYER 113 V P + + E + L AI TH H DH G D+ + + V Sbjct: 38 VIPSLKKLDDENRRLTAILTTHHHYDHSGGNEDIKREIPYDIK-------------VIGG 84 Query: 114 VSKKIP--CISFQAGDKVDVGAFSIESVR 140 +IP + G+ V VG + + Sbjct: 85 ADDRIPGITRGLKDGETVTVGGLEVRCLH 113 >gnl|CDD|35027 COG5468, COG5468, Predicted secreted (periplasmic) protein [Function unknown]. Length = 172 Score = 31.2 bits (70), Expect = 0.75 Identities = 13/46 (28%), Positives = 17/46 (36%) Query: 283 DESFGLYPREQLIVIATGSQGEPRSALAQLSRGEMRNVKLAEKDTV 328 G R QLI + +G GEP + LS R + V Sbjct: 46 GGRGGQEVRNQLIFLFSGGAGEPANPQYYLSLSVSRFARGVRLVNV 91 >gnl|CDD|37942 KOG2731, KOG2731, KOG2731, DNA alkylation damage repair protein [RNA processing and modification]. Length = 378 Score = 30.0 bits (67), Expect = 1.8 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 10/94 (10%) Query: 115 SKKIPCISFQAGDKVDVGAFSIESVRVNHSIPETMALVIRSPVGNIVHTGDWKLDDDAIL 174 + ++ ++GD V + FS V H+IPE+ +L R + K D+A L Sbjct: 264 GENPDPMTLRSGDVVIMDGFSRL---VEHAIPESRSLPARE-------SNGTKAGDEAPL 313 Query: 175 GDVTDKDSLCAIGNEGILALMCDSTNAMREGTCI 208 D+ + G+ G+ + + R I Sbjct: 314 PDICIVNFYSETGSLGLHQDKAEYLKSSRVNLPI 347 >gnl|CDD|153168 cd04896, ACT_ACR-like_3, ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 75 Score = 28.2 bits (63), Expect = 5.6 Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 7/54 (12%) Query: 206 TCISEKGIKKNIYDIMKNAKGCVLVTT---FSSSVSRIRSI-IDIAEQIGRKIV 255 C+ +KG+ +YDI++ +K C + + FSS V R + + I + G+KI+ Sbjct: 6 RCVDQKGL---LYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQSDGKKIM 56 >gnl|CDD|32198 COG2015, COG2015, Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 655 Score = 28.4 bits (63), Expect = 5.9 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 6/49 (12%) Query: 34 WIMIDCGVSFPKDDLPGVDLVFPDITFIMKERKNLMAIFITHAHEDHYG 82 WI+ID V+ P+ +DL + ++ ++A+ TH+H DH+G Sbjct: 137 WIVIDPLVT-PETAKAALDLYNQH-----RGQRPVVAVIYTHSHSDHFG 179 >gnl|CDD|145414 pfam02248, Como_SCP, Small coat protein. This family contains the small coat protein (SCP) of the comoviridae viral family. Length = 182 Score = 28.2 bits (63), Expect = 6.4 Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 3/47 (6%) Query: 124 QAGDKVDVGAFSIESVRVNHSIPET---MALVIRSPVGNIVHTGDWK 167 K + +F+ + + S T ++ SP+ N++ T WK Sbjct: 19 ADTAKQNFASFTFDLINGTISTDGTGNWNTVLYNSPIANLLRTAAWK 65 >gnl|CDD|176165 cd08476, PBP2_CrgA_like_7, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 28.0 bits (63), Expect = 7.6 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 12/53 (22%) Query: 385 PQVLVAIHGEPLHLVAHKELALQ-EGIACVP------PVRNGKMLRLFPDPIE 430 P LV + E L E ALQ GIAC+P + +G+++ + D +E Sbjct: 124 PTALVCNNIEAL-----IEFALQGLGIACLPDFSVREALADGRLVTVLDDYVE 171 >gnl|CDD|32484 COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]. Length = 293 Score = 27.6 bits (61), Expect = 8.7 Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 5/68 (7%) Query: 71 IFITHAHEDHYGALHDLWSFLHVP-VYASPFAIGLLEAKRVYERVSKKIPCISFQAGDKV 129 + +TH DH G L ++ + VP ++ ++ + IP S +AGD Sbjct: 94 LILTHPDADHIGGLDEVLKTIKVPELWIY----AGSDSTSTFVLRDAGIPVRSCKAGDSW 149 Query: 130 DVGAFSIE 137 G + Sbjct: 150 QWGGVVFQ 157 >gnl|CDD|111050 pfam02112, PDEase_II, cAMP phosphodiesterases class-II. Length = 323 Score = 27.9 bits (62), Expect = 8.9 Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 19/98 (19%) Query: 67 NLMAIFITHAHEDHYGAL-----HDLWSFLHVPVYASPFAIGLLE-------------AK 108 + ITH+H DH L +Y P+ I L+ + Sbjct: 79 RIKNYLITHSHLDHVCGLVINSPGFYKQMSKKTIYGLPYTINALQKHLFNNLVWPNLPSF 138 Query: 109 RVYERVSK-KIPCISFQAGDKVDVGAFSIESVRVNHSI 145 + + K K+ +S +K+ S+ VNH Sbjct: 139 GIVNLIYKVKMFDLSPGEFNKLTETTMSVVPFPVNHGG 176 >gnl|CDD|147701 pfam05690, ThiG, Thiazole biosynthesis protein ThiG. This family consists of several bacterial thiazole biosynthesis protein G sequences. ThiG, together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway. Length = 246 Score = 27.6 bits (62), Expect = 9.2 Identities = 28/86 (32%), Positives = 37/86 (43%), Gaps = 25/86 (29%) Query: 424 LFPDPIEIID--EVVHGLFLKDGF--LIGKFADLGIAKRRQLSFVGHLSVNVL------- 472 L PDPIE + E++ +K+GF L D +A+R L G +V L Sbjct: 104 LLPDPIETLKAAEIL----VKEGFTVLPYTTDDPVLARR--LEEAGCAAVMPLGAPIGSG 157 Query: 473 --LDNHYNI------FGVPEIVDIGI 490 L N N+ VP IVD GI Sbjct: 158 LGLRNPENLRIIIEEADVPVIVDAGI 183 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 0.322 0.141 0.415 Gapped Lambda K H 0.267 0.0785 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 6,950,117 Number of extensions: 392645 Number of successful extensions: 864 Number of sequences better than 10.0: 1 Number of HSP's gapped: 847 Number of HSP's successfully gapped: 29 Length of query: 559 Length of database: 6,263,737 Length adjustment: 99 Effective length of query: 460 Effective length of database: 4,124,446 Effective search space: 1897245160 Effective search space used: 1897245160 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)