RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781179|ref|YP_003065592.1| D-alanine--D-alanine ligase
[Candidatus Liberibacter asiaticus str. psy62]
(300 letters)
>gnl|CDD|179288 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 407 bits (1049), Expect = e-114
Identities = 134/301 (44%), Positives = 187/301 (62%), Gaps = 6/301 (1%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNVLHGN 61
AVLMGG S+EREVSL+SG A +AL +AG+ ID + L L D FN LHG
Sbjct: 8 AVLMGGTSAEREVSLNSGAAVLAALREAGYDAHPIDPGEDIAAQLKELGFDRVFNALHGR 67
Query: 62 FGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQ 121
GEDG +Q +LELL IPYT SG+LASAL+MDK+R+K V + G+P P I++ R
Sbjct: 68 GGEDGTIQGLLELLGIPYTGSGVLASALAMDKLRTKLVWQAAGLPTPPWIVLTREEDLLA 127
Query: 122 --HLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTC 179
+ P V+KP + GSS+G+ +K++ + L ++ + D++L+E+Y+ G ELT
Sbjct: 128 AIDKLGLPLVVKPAREGSSVGVSKVKEEDELQAAL--ELAFKYDDEVLVEKYIKGRELTV 185
Query: 180 GVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIG 239
V+G +L V EI VP +FY YE KY + + ++ PA +P +I E+Q LA A++A+G
Sbjct: 186 AVLGGKALPVIEI-VPAGEFYDYEAKYLAGGTQYICPAGLPAEIEAELQELALKAYRALG 244
Query: 240 CRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDASCL 299
CRG R DF+ D K + LE+N QPGMT S+ P A AG SF EL+ ++EDA C
Sbjct: 245 CRGWGRVDFMLDE-DGKPYLLEVNTQPGMTSHSLVPMAARAAGISFSELVDRILEDALCD 303
Query: 300 R 300
R
Sbjct: 304 R 304
>gnl|CDD|162248 TIGR01205, D_ala_D_alaTIGR, D-alanine--D-alanine ligase. but a
number of antibiotic resistance proteins score above the
trusted cutoff of this model.
Length = 315
Score = 266 bits (683), Expect = 4e-72
Identities = 113/318 (35%), Positives = 184/318 (57%), Gaps = 28/318 (8%)
Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHL------------ 49
AVL GG S+E E+SL S A AL D G+ V +D+D+ L
Sbjct: 3 AVLFGGKSAEHEISLVSAAAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALLE 62
Query: 50 KPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCP 109
D+ F VLHG +GEDG +Q +LEL+ IPYT SG+LASALSMDK+ +K + + G+P
Sbjct: 63 GIDVVFPVLHGRYGEDGTIQGLLELMGIPYTGSGVLASALSMDKLLTKLLWKALGLPTPD 122
Query: 110 SILVNRF-----TMDSQHLISP---PYVIKPLKGGSSLGIIVIK-KDQSIP-LDLLQSSS 159
I++ + ++ + + P P ++KP + GSS+G+ +K +++ LD
Sbjct: 123 YIVLTQNRASADELECEQVAEPLGFPVIVKPAREGSSVGVSKVKSEEELQAALDEAFE-- 180
Query: 160 WNHGDQLLIEQYVDGIELTCGVMG-DASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAK 218
+ +++L+EQ++ G EL ++G + +L + EI FY YE KY ++ +V+PA
Sbjct: 181 --YDEEVLVEQFIKGRELEVSILGNEEALPIIEIVPEIEGFYDYEAKYLDGSTEYVIPAP 238
Query: 219 IPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMA 278
+ ++ ++++ LA A++A+GCRG++R DF D +++ EIN PGMT +S+FP+ A
Sbjct: 239 LDEELEEKIKELALKAYKALGCRGLARVDFFLDE-EGEIYLNEINTIPGMTAISLFPKAA 297
Query: 279 AYAGYSFRELLLWMVEDA 296
A AG F +L+ ++E A
Sbjct: 298 AAAGIEFSQLVERILELA 315
>gnl|CDD|179356 PRK01966, ddl, D-alanyl-alanine synthetase A; Reviewed.
Length = 333
Score = 240 bits (615), Expect = 4e-64
Identities = 111/332 (33%), Positives = 180/332 (54%), Gaps = 44/332 (13%)
Query: 2 AVLMGGISSEREVSLSSGKACASAL---------------------EDAGFKVSQIDVDR 40
A+L GG S+E EVSL S K+ AL + +++ D D+
Sbjct: 7 ALLFGGRSAEHEVSLVSAKSVLKALDKEKYEVVPIGITKDGRWYLIDADNMELADDDNDK 66
Query: 41 SVGLVLAHLKP-----DLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMR 95
+L D+ F VLHG GEDG +Q +LELL IPY G+LASALSMDK+
Sbjct: 67 EDLSLLILPSGGSEEVDVVFPVLHGPPGEDGTIQGLLELLGIPYVGCGVLASALSMDKIL 126
Query: 96 SKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGI-IVIKKDQ 148
+K+++++ G+PV P +++ R + L + P +KP GSS+GI V +++
Sbjct: 127 TKRLLAAAGIPVAPYVVLTRGDWEEASLAEIEAKLGLPVFVKPANLGSSVGISKVKNEEE 186
Query: 149 SIP-LDLLQSSSWNHGDQLLIEQYVDGIELTCGVMG---DASLDVTEIAVPKSDFYSYEL 204
LDL ++ + ++L+EQ + G E+ C V+G AS+ EI V DFY YE
Sbjct: 187 LAAALDL----AFEYDRKVLVEQGIKGREIECAVLGNDPKASV-PGEI-VKPDDFYDYEA 240
Query: 205 KYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINV 264
KY ++ ++PA + ++ ++++ LA A +A+GC G++R DF +++ EIN
Sbjct: 241 KYLDGSAELIIPADLSEELTEKIRELAIKAFKALGCSGLARVDFFLTE-DGEIYLNEINT 299
Query: 265 QPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
PG TP+S++P++ +G S+ EL+ ++E A
Sbjct: 300 MPGFTPISMYPKLWEASGLSYPELIDRLIELA 331
>gnl|CDD|184751 PRK14571, PRK14571, D-alanyl-alanine synthetase A; Provisional.
Length = 299
Score = 188 bits (478), Expect = 2e-48
Identities = 100/305 (32%), Positives = 159/305 (52%), Gaps = 21/305 (6%)
Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHLKP-DLAFNVLH 59
+A+LMGG+S ERE+SL SG+ ALE G++V+ DVD + LK D+ FNVLH
Sbjct: 3 VALLMGGVSREREISLRSGERVKKALEKLGYEVTVFDVDEDFLKKVDQLKSFDVVFNVLH 62
Query: 60 GNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMD 119
G FGEDG +QAIL+ L I YT S +S + DK+ + + + ++ + F
Sbjct: 63 GTFGEDGTLQAILDFLGIRYTGSDAFSSMICFDKLLTYRFLKG-------TVEIPDFVEI 115
Query: 120 SQHLISPPY----VIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGI 175
+ + + P V+KP + GSS+G+ + + D+ L +++++Y+ G
Sbjct: 116 KEFMKTSPLGYPCVVKPRREGSSIGVFICESDEEFQHAL--KEDLPRYGSVIVQEYIPGR 173
Query: 176 ELTCGVM----GDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLA 231
E+T ++ G L + E+ PK FY Y KY+ + +LPA + + + V+ A
Sbjct: 174 EMTVSILETEKGFEVLPILELR-PKRRFYDYVAKYTKGETEFILPAPLNPEEERLVKETA 232
Query: 232 FLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLW 291
A GCRG R D +F + ++LEIN PG+T +S P A G F EL+
Sbjct: 233 LKAFVEAGCRGFGRVDGIFS--DGRFYFLEINTVPGLTELSDLPASAKAGGIEFEELVDI 290
Query: 292 MVEDA 296
+++ A
Sbjct: 291 IIKSA 295
>gnl|CDD|173036 PRK14572, PRK14572, D-alanyl-alanine synthetase A; Provisional.
Length = 347
Score = 168 bits (428), Expect = 1e-42
Identities = 105/347 (30%), Positives = 162/347 (46%), Gaps = 60/347 (17%)
Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLV--------------- 45
+AV GG S+E +S+ +G + L G V I + G V
Sbjct: 4 IAVFFGGSSTEHSISIRTGCFICATLHTMGHSVKPILLTPDGGWVVPTVYRPSIPDESGN 63
Query: 46 --------------------LAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGIL 85
++ L D+AF LHG GEDG +Q L+ L IPYT SG+L
Sbjct: 64 SEDLFLEEFQKANGVSEPADISQLDADIAFLGLHGGAGEDGRIQGFLDTLGIPYTGSGVL 123
Query: 86 ASALSMDKMRSKQVVSSCGVPVCPSILVNR--FTMDSQHLI------SPPYVIKPLKGGS 137
ASAL+MDK R+ Q+ G V P + + + + + P +KP++GGS
Sbjct: 124 ASALAMDKTRANQIFLQSGQKVAPFFELEKLKYLNSPRKTLLKLESLGFPQFLKPVEGGS 183
Query: 138 SLGIIVIKKDQSIP--LDLLQSSSWNHGDQLLIEQYVDGIELTCGVM--------GDASL 187
S+ I + + L L+ S +++ + ++ G E++CGV+ +L
Sbjct: 184 SVSTYKITNAEQLMTLLALIFESD----SKVMSQSFLSGTEVSCGVLERYRGGKRNPIAL 239
Query: 188 DVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSD 247
TEI VP +F+ +E KY S + PA+I K VQ LA AH+++GC+G SR+D
Sbjct: 240 PATEI-VPGGEFFDFESKYKQGGSEEITPARISDQEMKRVQELAIRAHESLGCKGYSRTD 298
Query: 248 FLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVE 294
F+ + + LE N PGMT S+ P+ A AG + E+ ++E
Sbjct: 299 FII--VDGEPHILETNTLPGMTETSLIPQQAKAAGINMEEVFTDLIE 343
>gnl|CDD|173033 PRK14569, PRK14569, D-alanyl-alanine synthetase A; Provisional.
Length = 296
Score = 157 bits (399), Expect = 2e-39
Identities = 109/299 (36%), Positives = 165/299 (55%), Gaps = 12/299 (4%)
Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVD-RSVGLVLAHLKPDLAFNVLH 59
+ VL GG S EREVSL SGKA +L G+ +D + + L LKPD F LH
Sbjct: 6 IVVLYGGDSPEREVSLKSGKAVLDSLISQGYDAVGVDASGKELVAKLLELKPDKCFVALH 65
Query: 60 GNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPV-CPSILVNRFTM 118
G GE+G V A+LE+LEI +T S + +S ++MDKM SK+++ +P L ++
Sbjct: 66 GEDGENGRVSALLEMLEIKHTSSSMKSSVITMDKMISKEILMHHRMPTPMAKFLTDKLVA 125
Query: 119 DSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELT 178
+ + IS P +KP GGSS+ +K Q + ++S +G +++IEQ+V G E+T
Sbjct: 126 EDE--ISFPVAVKPSSGGSSIATFKVKSIQELKHAYEEAS--KYG-EVMIEQWVTGKEIT 180
Query: 179 CGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAI 238
++ D I P+++FY YE KYS + H P+ + EV++LA A+ +
Sbjct: 181 VAIVNDEVYSSVWIE-PQNEFYDYESKYSGKSIYHS-PSGLCEQKELEVRQLAKKAYDLL 238
Query: 239 GCRGISRSDFLFDPLSRKVFW-LEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
GC G +R DF++D R F+ +EIN PGMT S+ P+ AA G F + ++E A
Sbjct: 239 GCSGHARVDFIYD--DRGNFYIMEINSSPGMTDNSLSPKSAAAEGVDFDSFVKRIIEQA 295
>gnl|CDD|148851 pfam07478, Dala_Dala_lig_C, D-ala D-ala ligase C-terminus. This
family represents the C-terminal, catalytic domain of
the D-alanine--D-alanine ligase enzyme EC:6.3.2.4.
D-Alanine is one of the central molecules of the
cross-linking step of peptidoglycan assembly. There are
three enzymes involved in the D-alanine branch of
peptidoglycan biosynthesis: the pyridoxal
phosphate-dependent D-alanine racemase (Alr), the
ATP-dependent D-alanine:D-alanine ligase (Ddl), and the
ATP-dependent D-alanine:D-alanine-adding enzyme (MurF).
Length = 201
Score = 138 bits (350), Expect = 2e-33
Identities = 64/207 (30%), Positives = 121/207 (58%), Gaps = 17/207 (8%)
Query: 99 VVSSCGVPVCPSILVNR--FTMDS-QHLISP---PYVIKPLKGGSSLGIIVIKKDQSIPL 152
++ + G+PV P I++ R + + + + + P +KP GSS+GI K S
Sbjct: 1 LLKAAGIPVAPFIVLTREDWVLATIEKVEEKLGYPVFVKPANLGSSVGI---SKVTS--R 55
Query: 153 DLLQSS---SWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIA--VPKSDFYSYELKYS 207
+ LQS+ ++ + +++LIE+ ++G E+ C V+G+ L+V+ + FY YE KY
Sbjct: 56 EELQSAIEEAFQYDNKVLIEEAIEGREIECAVLGNEDLEVSPVGEIRLSGGFYDYEAKYI 115
Query: 208 SLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPG 267
++ ++PA +P ++ +++Q LA A++A+GCRG++R DF +++ E+N PG
Sbjct: 116 LSSAQIIVPADLPEEVEEQIQELALKAYKALGCRGLARIDFFLTE-DGEIYLNEVNTMPG 174
Query: 268 MTPVSIFPEMAAYAGYSFRELLLWMVE 294
T +S++P M A AG S+ +L+ ++E
Sbjct: 175 FTSISLYPRMWAAAGLSYPDLIDQLIE 201
>gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional.
Length = 343
Score = 133 bits (337), Expect = 5e-32
Identities = 105/333 (31%), Positives = 151/333 (45%), Gaps = 49/333 (14%)
Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDV---------------------- 38
+ +L GG S E VS+ S A L+ ++ I +
Sbjct: 6 VGILFGGCSEEHPVSVKSAIEVARNLDTEKYEPFYIGITKSGVWKLCDGPCAEWENGSCR 65
Query: 39 ------DRSVG--LVLAH-----LKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGIL 85
DR V LVL ++ D+ F VLHG GEDG +Q +LEL IPY I
Sbjct: 66 PAVLSPDRKVHGLLVLEQGEYETIRLDVVFPVLHGKLGEDGAIQGLLELSGIPYVGCDIQ 125
Query: 86 ASALSMDKMRSKQVVSSCGVPVCPS--ILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIV 143
+SAL MDK + V + G+ P+ + D+ L P +V KP + GSS G V
Sbjct: 126 SSALCMDKSLAYIVAKNAGIAT-PAFWTVTADERPDAATLTYPVFV-KPARSGSSFG--V 181
Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMG-DASL---DVTEIAVPKSDF 199
K + + LD S+ + ++LIE+ V G E+ C V+G A L +V +I + F
Sbjct: 182 SKVNSADELDYAIESARQYDSKVLIEEAVVGSEVGCAVLGNGADLVVGEVDQIRLSHGFF 241
Query: 200 YSY---ELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRK 256
+ E + S NST ++PA I + VQ A ++A+GCRG++R D
Sbjct: 242 RIHQENEPEKGSENSTIIVPADISAEERSRVQETAKAIYRALGCRGLARVDMFLQEDGTV 301
Query: 257 VFWLEINVQPGMTPVSIFPEMAAYAGYSFRELL 289
V E+N PG T S +P M A AG EL+
Sbjct: 302 VL-NEVNTLPGFTSYSRYPRMMAAAGIPLAELI 333
>gnl|CDD|173034 PRK14570, PRK14570, D-alanyl-alanine synthetase A; Provisional.
Length = 364
Score = 128 bits (324), Expect = 1e-30
Identities = 88/337 (26%), Positives = 166/337 (49%), Gaps = 50/337 (14%)
Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAG-FKVSQIDVDRSVGL--------------- 44
+ ++ GG+S E E+SL S SAL + + + +D+ G+
Sbjct: 5 LMLIFGGVSFEHEISLRSAYGIYSALLKLDKYNIYSVFIDKCTGIWYLLDSVPDPPKLIK 64
Query: 45 --VLA---------------HLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILAS 87
VL +L+ D+ F ++HG GEDG +Q L++++IP +GIL S
Sbjct: 65 RDVLPIVSLIPGCGIFVNNKNLEIDVVFPIVHGRTGEDGAIQGFLKVMDIPCVGAGILGS 124
Query: 88 ALSMDKMRSKQVVSSCGVPVCPSILVNRFTM---------DSQHLISPPYVIKPLKGGSS 138
A+S++K K ++ S +P+ P I ++ D + ++ P ++KP GSS
Sbjct: 125 AISINKYFCKLLLKSFNIPLVPFIGFRKYDYFLDKEGIKKDIKEVLGYPVIVKPAVLGSS 184
Query: 139 LGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDV---TEIAVP 195
+GI V + I + ++ + ++IE++++ E+ C V+G+ + + EI V
Sbjct: 185 IGINVAYNENQI--EKCIEEAFKYDLTVVIEKFIEAREIECSVIGNEQIKIFTPGEIVVQ 242
Query: 196 KSDFYSYELKYSSLNSTHV---LPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDP 252
FY Y+ KYS++ + +PA + +++ AFL ++ + RG++R DFL +
Sbjct: 243 DFIFYDYDAKYSTIPGNSIVFNIPAHLDTKHLLDIKEYAFLTYKNLELRGMARIDFLIEK 302
Query: 253 LSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELL 289
+ ++ EIN PG T +S+F +M + G ++ L+
Sbjct: 303 DTGLIYLNEINTIPGFTDISMFAKMCEHDGLQYKSLV 339
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 100 bits (250), Expect = 5e-22
Identities = 92/341 (26%), Positives = 146/341 (42%), Gaps = 53/341 (15%)
Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDR----SVGLVLAHL------- 49
+ ++ GG S E ++SL S K A L + VS ++R L
Sbjct: 454 LGLVCGGKSCEHDISLLSAKNIAKYLSPEFYDVSYFLINRQGLWETVSSLETAIEEDSGK 513
Query: 50 ------------KPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSK 97
K D+ +LHG FGEDG +Q LE++ PYT + SA++MDK+ +K
Sbjct: 514 SVLSSEIAQALAKVDVVLPILHGPFGEDGTMQGFLEIIGKPYTGPSLAFSAIAMDKVLTK 573
Query: 98 QVVSSCGVPVCPSILVNRFTMDS------QHLI---SPPYVIKPLKGGSSLGIIVIKKDQ 148
+ S GVPV P + H++ S P +K GSS+G+ + +
Sbjct: 574 RFASDVGVPVVPYQPLTLAGWKREPELCLAHIVEAFSFPMFVKTAHLGSSIGVFEVHNVE 633
Query: 149 SIPLDLLQSSSWNHGDQLLIEQYVDG---IELTCGVMGDASLDVTEIAVP-----KSDFY 200
+ + S ++ + + +E+ G IE++C +GD S IA P F
Sbjct: 634 ELRDKI--SEAFLYDTDVFVEESRLGSREIEVSC--LGDGS-SAYVIAGPHERRGSGGFI 688
Query: 201 SYELKYSSLNSTHVLPAKIPLDIYKE----VQRLAFLAHQAIGCRGISRSDFLFDPLSRK 256
Y+ KY L+ LD+ KE V LA ++ + +G R DF D
Sbjct: 689 DYQEKY-GLSGKSSAQIVFDLDLSKESQEQVLELAERIYRLLQGKGSCRIDFFLD--EEG 745
Query: 257 VFWL-EINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296
FWL E+N PGMT S F G+++ +++ ++ D
Sbjct: 746 NFWLSEMNPIPGMTEASPFLTAFVRKGWTYEQIVHQLIIDG 786
>gnl|CDD|183732 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
Provisional.
Length = 326
Score = 45.6 bits (109), Expect = 1e-05
Identities = 44/214 (20%), Positives = 87/214 (40%), Gaps = 36/214 (16%)
Query: 89 LSMDKMRSKQVVSSCGVPVCPSILVN----RFTMDSQHLISPPYVIKPLKGGSSLGI-IV 143
+ DK + + + G+P S L ++ + P +KP G +S+G+ V
Sbjct: 108 ICNDKWLTYEFLKENGIPTPKSYLPESLEDFKAALAKGELQFPLFVKPRDGSASIGVFKV 167
Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIAVPKSDFYSYE 203
K++ L+ L + L+I+++++G E T V+ D + +V I K E
Sbjct: 168 NDKEE---LEFLLE----YVPNLIIQEFIEGQEYTVDVLCDLNGEVISIVPRK----RIE 216
Query: 204 LKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEIN 263
++ + + +++K +RLA +A+G RG + + EIN
Sbjct: 217 VRAGETSKGVTVKDP---ELFKLAERLA----EALGARGPLNIQCFVTD--GEPYLFEIN 267
Query: 264 VQP---GMTPVSIFPEMAAYAGYSFRELLLWMVE 294
P G P+S AG + + ++ +
Sbjct: 268 --PRFGGGYPLS------YMAGANEPDWIIRNLL 293
>gnl|CDD|162681 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions.
Length = 864
Score = 39.4 bits (92), Expect = 0.001
Identities = 44/207 (21%), Positives = 83/207 (40%), Gaps = 32/207 (15%)
Query: 10 SEREVSLSSGKA----CASALEDAGFKVSQ-------IDVDRSVG-----LVLAHLKPDL 53
S +V +G+ SA++D F + Q + D S+G +V K +
Sbjct: 114 SHEQVGRYAGRLAVDLVRSAIDDGPFDLEQALQRLRDLVADASLGPSTAAIVDEAEKRGI 173
Query: 54 AFNVL-HGN---FGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCP 109
+ L G+ G G Q ++ E T +A ++ DK +K+++S GVPV
Sbjct: 174 PYMRLSAGSLVQLGY-GSRQKRIQATETDRT--SAIAVEIACDKDLTKEILSDAGVPVPE 230
Query: 110 SILVNRF--TMDSQHLISPPYVIKPLKGGSSLGI---IVIKKDQSIPLDLLQSSSWNHGD 164
+V ++ + P VIKP G G+ I+ + + +
Sbjct: 231 GTVVQSAEDAWEAAQDLGYPVVIKPYDGNHGRGVTINILTRDEIESAYEAAV----EESS 286
Query: 165 QLLIEQYVDGIELTCGVMGDASLDVTE 191
+++E+++ G + V+G + V E
Sbjct: 287 GVIVERFITGRDHRLLVVGGKVVAVAE 313
>gnl|CDD|162082 TIGR00877, purD, phosphoribosylamine--glycine ligase. This enzyme
appears as a monofunctional protein in prokaryotes but
as part of a larger, multidomain protein in eukaryotes.
Length = 423
Score = 37.3 bits (87), Expect = 0.004
Identities = 35/136 (25%), Positives = 63/136 (46%), Gaps = 21/136 (15%)
Query: 64 EDGLVQAILELLE---IPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDS 120
E LV +++ LE IP A+ L K +K + G+P + FT D
Sbjct: 73 EAPLVLGLVDALEEAGIPVFGPTKEAAQLEGSKAFAKDFMKRYGIP---TAEYEVFT-DP 128
Query: 121 QHLIS-------PPYVIKP--LKGGSSLGIIVIK-KDQSIPL--DLLQSSSWNHGDQLLI 168
+ +S P V+K L G G+IV K +++I ++L+ + G++++I
Sbjct: 129 EEALSYIQEKGAPAIVVKADGLAAGK--GVIVAKTNEEAIKAVEEILEQKFGDAGERVVI 186
Query: 169 EQYVDGIELTCGVMGD 184
E+++DG E++ D
Sbjct: 187 EEFLDGEEVSLLAFVD 202
>gnl|CDD|167327 PRK02186, PRK02186, argininosuccinate lyase; Provisional.
Length = 887
Score = 36.0 bits (83), Expect = 0.011
Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 3/102 (2%)
Query: 86 ASALSMDKMRSKQVVSSCGVPVCPSILVNRFT--MDSQHLISPPYVIKPLKGGSSLGIIV 143
A DK R + + G+ V + + +D+ ++ P V+KP G S+G+ +
Sbjct: 101 AIRTCRDKKRLARTLRDHGIDVPRTHALALRAVALDALDGLTYPVVVKPRMGSGSVGVRL 160
Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDA 185
+ L++ YV+G E + + A
Sbjct: 161 CASVAEAA-AHCAALRRAGTRAALVQAYVEGDEYSVETLTVA 201
>gnl|CDD|180883 PRK07206, PRK07206, hypothetical protein; Provisional.
Length = 416
Score = 35.8 bits (83), Expect = 0.015
Identities = 43/227 (18%), Positives = 71/227 (31%), Gaps = 65/227 (28%)
Query: 16 LSSGKACASALEDAGFKVSQIDVDRSVGLVL----AHLKPDLAFNVLHGNFGEDGLVQAI 71
SSGK A A + G + + S L+ A V+ +G + +
Sbjct: 11 FSSGKFLAPAFKKRGIEPIAV---TSSCLLDPYYYASFDTSDFIEVII-----NGDIDDL 62
Query: 72 LELLE-------IPYTHSGI-LASALS-----------------MDKMRSKQVVSSCGVP 106
+E L I SG+ LA L+ +K ++ G+P
Sbjct: 63 VEFLRKLGPEAIIAGAESGVELADRLAEILTPQYSNDPALSSARRNKAEMINALAEAGLP 122
Query: 107 VCPSILVNRFT-----MDSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQ-SSSW 160
I + + LI P VIKPL+ S G+ +
Sbjct: 123 AARQINTADWEEAEAWLRENGLIDRPVVIKPLESAGSDGVFICPAKGDWKHAFNAILGKA 182
Query: 161 NH----GDQLLIEQYVDGIELTCGVMGDASLDVTEIAVPKSDFYSYE 203
N + +L+++Y+ G TE V +F S +
Sbjct: 183 NKLGLVNETVLVQEYLIG---------------TEYVV---NFVSLD 211
>gnl|CDD|179511 PRK02948, PRK02948, cysteine desulfurase; Provisional.
Length = 381
Score = 34.7 bits (80), Expect = 0.027
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 8/68 (11%)
Query: 13 EVSLSSGKACASALEDAGFKVSQIDVDRSVGLV-----LAHLKPDLAF-NVLHGNFGEDG 66
+ +S + +LE G+ V++I VD+S GL+ + PD ++ H N E G
Sbjct: 95 PMEHASIHSYFQSLESQGYTVTEIPVDKS-GLIRLVDLERAITPDTVLASIQHAN-SEIG 152
Query: 67 LVQAILEL 74
+Q I E+
Sbjct: 153 TIQPIAEI 160
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase.
Length = 353
Score = 34.0 bits (78), Expect = 0.044
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 23 ASALEDAGFKVSQIDVDRS----VGLVLAHLKPD-LAFNVLHGNFGEDGLVQAILELLEI 77
ALE GF V+ + VD S V + ++PD L +++H N E G +Q I E+ E+
Sbjct: 105 IRALERNGFTVTYLPVDESGRIDVDELADAIRPDTLLVSIMHVN-NETGSIQPIREIAEV 163
>gnl|CDD|184454 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 34.0 bits (79), Expect = 0.045
Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 17/105 (16%)
Query: 81 HSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLK 134
+ +A ++ DK +K+++++ GVPV +V ++ I P V+KPL
Sbjct: 203 QTSAIAVDIACDKELTKRLLAAAGVPVPEGRVVT----SAEDAWEAAEEIGYPVVVKPLD 258
Query: 135 GGSSLGIIV-IKKDQSI--PLDLLQSSSWNHGDQLLIEQYVDGIE 176
G G+ V I + I + +++E+Y+ G +
Sbjct: 259 GNHGRGVTVNITTREEIEAAYAVAS----KESSDVIVERYIPGKD 299
>gnl|CDD|132147 TIGR03103, trio_acet_GNAT, GNAT-family acetyltransferase TIGR03103.
Members of this protein family belong to the GNAT
family of acetyltransferases. Each is part of a
conserved three-gene cassette sparsely distributed
across at least twenty different species known so far,
including alpha, beta, and gamma Proteobacteria,
Mycobacterium, and Prosthecochloris, which is a member
of the Chlorobi. The other two members of the cassette
are a probable protease and an asparagine synthetase
family protein.
Length = 547
Score = 30.9 bits (70), Expect = 0.41
Identities = 29/101 (28%), Positives = 50/101 (49%), Gaps = 12/101 (11%)
Query: 85 LASALSM----DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISP--PYVIKPLKGGSS 138
L SA++M DK ++++VS G+ V P + + ++ V+KP++G
Sbjct: 286 LTSAVAMSLCDDKRLTRRLVSEAGLQV-PEQQLAGNGEAVEAFLAEHGAVVVKPVRGEQG 344
Query: 139 LGIIVIKKDQSIPLDLLQ--SSSWNHGDQLLIEQYVDGIEL 177
GI V D P DL + + D++L+E+YV G +L
Sbjct: 345 KGISV---DVRTPDDLEAAIAKARQFCDRVLLERYVPGEDL 382
>gnl|CDD|162020 TIGR00747, fabH, 3-oxoacyl-(acyl-carrier-protein) synthase III.
Active site residues include Cys112, His244 and Asn274
of E. coli FabH. Cys-112 is the site of acyl group
attachment.
Length = 318
Score = 30.8 bits (70), Expect = 0.47
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 8 ISSEREVSLSSG-KACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAF 55
I+++ E S + G +A A+E+AG ID +++A PD AF
Sbjct: 44 IAADDETSSTMGFEAAKRAIENAGISKDDID-----LIIVATTTPDHAF 87
>gnl|CDD|162798 TIGR02291, rimK_rel_E_lig, alpha-L-glutamate ligase-related
protein. Members of this protein family contain a
region of homology to the RimK family of
alpha-L-glutamate ligases (TIGR00768), various members
of which modify the Glu-Glu C-terminus of ribosomal
protein S6, or tetrahydromethanopterin, or a form of
coenzyme F420 derivative. Members of this family are
found so far in various Vibrio and Pseudomonas species
and some other gamma and beta Proteobacteria. The
function is unknown.
Length = 317
Score = 30.2 bits (68), Expect = 0.66
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 92 DKMRSKQVVSSCG--VPVCPSILVNRFTMDSQHLI---SPPYVIKPLKGGSSLGIIVI 144
DK+++K + + G VP ++ N+ + + H I P +VIKP +G GI+VI
Sbjct: 37 DKLKTKIIAQAAGITVPELYGVIHNQAEVKTIHNIVKDHPDFVIKPAQGSGGKGILVI 94
>gnl|CDD|177971 PLN02337, PLN02337, lipoxygenase.
Length = 866
Score = 30.0 bits (68), Expect = 0.82
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 9/40 (22%)
Query: 147 DQSIPLDLL------QSSSWNHGDQLLIEQY---VDGIEL 177
+Q++P DL+ + S HG +LLIE Y VDG+E+
Sbjct: 601 EQALPADLIKRGVAVEDPSSPHGVRLLIEDYPYAVDGLEI 640
>gnl|CDD|180150 PRK05586, PRK05586, biotin carboxylase; Validated.
Length = 447
Score = 29.7 bits (67), Expect = 1.1
Identities = 19/94 (20%), Positives = 44/94 (46%), Gaps = 16/94 (17%)
Query: 92 DKMRSKQVVSSCGVPVCP----SILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKKD 147
+K +++++ GVPV P I ++ I P ++K GG GI +++ +
Sbjct: 115 NKSNAREIMIKAGVPVVPGSEGEIENEEEALEIAKEIGYPVMVKASAGGGGRGIRIVRSE 174
Query: 148 QSIPLDLLQS-------SSWNHGD-QLLIEQYVD 173
+ +L+++ + GD + IE++++
Sbjct: 175 E----ELIKAFNTAKSEAKAAFGDDSMYIEKFIE 204
>gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this
protein family are NifS, one of several related families
of cysteine desulfurase involved in iron-sulfur (FeS)
cluster biosynthesis. NifS is part of the NIF system,
usually associated with other nif genes involved in
nitrogenase expression and nitrogen fixation. The
protein family is given a fairly broad interpretation
here. It includes a clade nearly always found in
extended nitrogen fixation genomic regions, plus a
second clade more closely related to the first than to
IscS and also part of NifS-like/NifU-like systems. This
model does not extend to a more distantly clade found in
the epsilon proteobacteria such as Helicobacter pylori,
also named NifS in the literature, built instead in
TIGR03403.
Length = 379
Score = 28.7 bits (65), Expect = 1.8
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 26 LEDAGFKVSQIDVDRSVGLVLAHLK----PDLAF-NVLHGNFGEDGLVQAILELLEI 77
LE G+KV+ + VD L L L+ D A +V+ N E G + I E+ EI
Sbjct: 106 LEKQGYKVTYLPVDEEGRLDLEELRAAITDDTALVSVMWAN-NETGTIFPIEEIGEI 161
>gnl|CDD|179527 PRK03011, PRK03011, butyrate kinase; Provisional.
Length = 358
Score = 28.6 bits (65), Expect = 1.8
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 242 GISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFP---EMAAYA 281
G++ S L + + +V ++ PV ++P EM A A
Sbjct: 304 GLAYSKRLVERIKERVSFI--------APVIVYPGEDEMEALA 338
>gnl|CDD|178963 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 28.5 bits (65), Expect = 2.0
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 22 CASALEDAGFKVSQID 37
C AL+DAG VS ID
Sbjct: 313 CKQALKDAGLSVSDID 328
>gnl|CDD|180313 PRK05928, hemD, uroporphyrinogen-III synthase; Reviewed.
Length = 249
Score = 28.8 bits (65), Expect = 2.0
Identities = 20/73 (27%), Positives = 26/73 (35%), Gaps = 9/73 (12%)
Query: 19 GKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFN----VLHGNFG----EDGLVQA 70
G+ A AL+ G KV + D +L L L L GN G D L +
Sbjct: 88 GEKTALALKKLGGKVVFVPEDGESSELLLELPELLLKGKRVLYLRGNGGREVLGDTLEER 147
Query: 71 ILELLE-IPYTHS 82
E+ E Y
Sbjct: 148 GAEVDECEVYERV 160
>gnl|CDD|181436 PRK08462, PRK08462, biotin carboxylase; Validated.
Length = 445
Score = 28.2 bits (63), Expect = 2.6
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 86 ASALSMDKMRSKQVVSSCGVPVCP-SILVNRFTMDSQHL---ISPPYVIKPLKGGSSLGI 141
AL DK ++K+V+ GVPV P S + +++ + I P ++K GG G+
Sbjct: 111 VMALMSDKSKAKEVMKRAGVPVIPGSDGALKSYEEAKKIAKEIGYPVILKAAAGGGGRGM 170
Query: 142 IVIKKDQSIPLDLLQSSS 159
V++ + + L + S
Sbjct: 171 RVVEDESDLENLYLAAES 188
>gnl|CDD|181732 PRK09258, PRK09258, 3-oxoacyl-(acyl carrier protein) synthase III;
Reviewed.
Length = 338
Score = 28.3 bits (64), Expect = 2.7
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 4 LMGGISSER----EVSLSSG--KACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNV 57
+ GI R LS G A AL +AG S I + + + +L+P A V
Sbjct: 45 ALTGIRERRWWPEGTQLSDGAIAAGRKALAEAGIDPSDIGLLINTSVCRDYLEPATACRV 104
Query: 58 LHGNFG 63
H N G
Sbjct: 105 -HHNLG 109
>gnl|CDD|173003 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion
protein; Provisional.
Length = 230
Score = 28.0 bits (62), Expect = 3.0
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 30 GFKVSQIDVDRSVGLVLAHLKPD 52
G ++++D++R V LAHL+P+
Sbjct: 82 GLALAKVDINRKVLSDLAHLQPE 104
>gnl|CDD|183765 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 27.2 bits (61), Expect = 5.8
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 12/73 (16%)
Query: 123 LISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVM 182
LI P YVI GG G+ V+ + ++ L +++S + +LI+Q++DG E
Sbjct: 709 LIRPSYVI----GG--QGMAVVYDEPALEAYLAENASQLY--PILIDQFIDGKEYEV--- 757
Query: 183 GDASLDVTEIAVP 195
DA D ++ +P
Sbjct: 758 -DAISDGEDVTIP 769
>gnl|CDD|162895 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha
chain. This model represents a small clade of
ribonucleoside-diphosphate reductase, alpha chains which
are sufficiently divergent from the usual Class I RNR
alpha chains (NrdE or NrdA, TIGR02506) as to warrant
their own model. The genes from Thermus thermophilus,
Dichelobacter and Salinibacter are adjacent to the usual
RNR beta chain.
Length = 571
Score = 26.9 bits (59), Expect = 7.2
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 190 TEIAVPKSDFYSYELKYSSLNSTH 213
TEIA+P D S+ SSLN H
Sbjct: 263 TEIALPSDDEESFTCCLSSLNLLH 286
>gnl|CDD|184035 PRK13406, bchD, magnesium chelatase subunit D; Provisional.
Length = 584
Score = 26.5 bits (59), Expect = 8.4
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 7 GISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAH 48
GI+S R L+ A A+A V + D+ + LVLA
Sbjct: 212 GIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARLVLAP 253
>gnl|CDD|179724 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 26.4 bits (59), Expect = 9.5
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 218 KIPLDIYKEVQRLA 231
K+P + KE+QR A
Sbjct: 57 KLPPEEQKELQREA 70
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
0.320 0.137 0.401
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,879,593
Number of extensions: 305748
Number of successful extensions: 678
Number of sequences better than 10.0: 1
Number of HSP's gapped: 631
Number of HSP's successfully gapped: 40
Length of query: 300
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 207
Effective length of database: 3,984,929
Effective search space: 824880303
Effective search space used: 824880303
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 (21.8 bits)
S2: 57 (25.7 bits)