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)