RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 016159
(394 letters)
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 730 bits (1887), Expect = 0.0
Identities = 324/375 (86%), Positives = 353/375 (94%)
Query: 1 MVRGLLNKLVSRSLTVAGQWQQQQLRRLNIHEYQGAELMAKYGINVPKGLAVASVDEVKK 60
M+RGLLNKL SRSL+VAG+WQ QQLRRLNIHEYQGAELM+KYG+NVPKG A +S+DEVKK
Sbjct: 1 MLRGLLNKLASRSLSVAGKWQHQQLRRLNIHEYQGAELMSKYGVNVPKGAAASSLDEVKK 60
Query: 61 AIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGVHIVKKEEVEDLAGKMLGQILVTKQ 120
A++ FPD E+VVKSQILAGGRGLGTFK+GLKGGVHIVKK++ E+LAGKMLGQILVTKQ
Sbjct: 61 ALEKMFPDEGEVVVKSQILAGGRGLGTFKNGLKGGVHIVKKDKAEELAGKMLGQILVTKQ 120
Query: 121 TGPQGKIVSKVYLCEKLSLVNEMYFAIMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIV 180
TGP GK V+KVYLCEK+SLVNEMYFAI+LDR +AGP+II CSKGGTSIEDLAEK+P I+
Sbjct: 121 TGPAGKPVNKVYLCEKMSLVNEMYFAILLDRASAGPLIIACSKGGTSIEDLAEKFPEKII 180
Query: 181 KVPIDVFNGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCESDCTLLEINPLAETS 240
KVPID+F GITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFC+ DCT++EINPLAET+
Sbjct: 181 KVPIDIFKGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCKCDCTMVEINPLAETA 240
Query: 241 GKQLVAADAKLNFDDNAAFRQKEIFALRDPTQEDPREVAAAKADLNYIGLDGEIGCMVNG 300
QLVAADAKLNFDDNAAFRQKEIFALRD +QEDPREVAAAKADLNYIGLDGEIGCMVNG
Sbjct: 241 DGQLVAADAKLNFDDNAAFRQKEIFALRDTSQEDPREVAAAKADLNYIGLDGEIGCMVNG 300
Query: 301 AGLAMATMDIIKLHGGTPANFLDVGGNASEGQVVEAFKILTSDEKVKAILVNIFGGIMKC 360
AGLAMATMDIIKLHGG+PANFLDVGGNASE QVVEAFKILTSD+KVKAILVNIFGGIMKC
Sbjct: 301 AGLAMATMDIIKLHGGSPANFLDVGGNASEQQVVEAFKILTSDDKVKAILVNIFGGIMKC 360
Query: 361 DVIASGIVNAAKQVS 375
DVIASGIVNAAKQV
Sbjct: 361 DVIASGIVNAAKQVG 375
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 460 bits (1187), Expect = e-162
Identities = 174/354 (49%), Positives = 225/354 (63%), Gaps = 24/354 (6%)
Query: 29 NIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKEL-----VVKSQILAGGR 83
N+HEYQ EL AKYG+ VP+G+ + +E +A +EL VVK+Q+ AGGR
Sbjct: 2 NLHEYQAKELFAKYGVPVPRGIVATTPEEAVEAA-------EELGGGVWVVKAQVHAGGR 54
Query: 84 GLGTFKSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNE 142
G GGV + K EE + A ++LG LVT QTGP+G+ V+KV + E + E
Sbjct: 55 GKA-------GGVKLAKSPEEAREFAKQILGMTLVTHQTGPKGQPVNKVLVEEGADIAKE 107
Query: 143 MYFAIMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD-- 200
Y +I+LDR T + + ++GG IE++AE+ P I KV ID G+ A ++
Sbjct: 108 YYLSIVLDRATRRVVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQPFQAREIAFKL 167
Query: 201 GLAPKVADRNDAIEQVKKLYKLFCESDCTLLEINPLAETSGKQLVAADAKLNFDDNAAFR 260
GL + + + LYK F E D +L+EINPL T L+A DAK+NFDDNA FR
Sbjct: 168 GLPGEQV--KQFAKILMGLYKAFVEKDASLVEINPLVVTKDGDLIALDAKINFDDNALFR 225
Query: 261 QKEIFALRDPTQEDPREVAAAKADLNYIGLDGEIGCMVNGAGLAMATMDIIKLHGGTPAN 320
++ LRD ++EDP E A+K LNY+ LDG IGCMVNGAGLAMATMDIIKL+GG PAN
Sbjct: 226 HPDLAELRDLSEEDPLEAEASKYGLNYVKLDGNIGCMVNGAGLAMATMDIIKLYGGEPAN 285
Query: 321 FLDVGGNASEGQVVEAFKILTSDEKVKAILVNIFGGIMKCDVIASGIVNAAKQV 374
FLDVGG A+ +V EAFKI+ SD VKAILVNIFGGI +CDVIA GI+ A K+V
Sbjct: 286 FLDVGGGATAERVAEAFKIILSDPNVKAILVNIFGGITRCDVIAEGIIAAVKEV 339
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 408 bits (1052), Expect = e-142
Identities = 166/352 (47%), Positives = 227/352 (64%), Gaps = 19/352 (5%)
Query: 28 LNIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGT 87
+N+HEYQ EL AKYGI VP G S +E ++A ++ +VVK+Q+ AGGRG
Sbjct: 1 MNLHEYQAKELFAKYGIPVPPGYVATSPEEAEEAAKEL--GGGPVVVKAQVHAGGRGKA- 57
Query: 88 FKSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKL-SLVNEMYF 145
GGV + K EE ++ A ++LG+ QT +G+ V+KV + E + + E Y
Sbjct: 58 ------GGVKLAKSPEEAKEAAEEILGK---NYQTDIKGEPVNKVLVEEAVDIIKKEYYL 108
Query: 146 AIMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD--GLA 203
+I+LDR + P+++ ++GG IE++AEK P IVKV +D G+ A ++ GL
Sbjct: 109 SIVLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLRPYQARELAFKLGLE 168
Query: 204 PKVADRNDAIEQVKKLYKLFCESDCTLLEINPLAETS-GKQLVAADAKLNFDDNAAFRQK 262
++ + +KKLYKLF E D TL+EINPL T G ++A DAK+ DDNA FR
Sbjct: 169 GELV--KQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNALFRHP 226
Query: 263 EIFALRDPTQEDPREVAAAKADLNYIGLDGEIGCMVNGAGLAMATMDIIKLHGGTPANFL 322
++ LRD ++EDPRE A+ LNY+ LDG IGC+VNGAGLAMATMDI+KL+GG PANFL
Sbjct: 227 DLAELRDESEEDPREAEASGYGLNYVELDGNIGCIVNGAGLAMATMDIVKLYGGKPANFL 286
Query: 323 DVGGNASEGQVVEAFKILTSDEKVKAILVNIFGGIMKCDVIASGIVNAAKQV 374
DVGG A+ +V EAFK++ SD VKAI VNIFGGI +CD +A GI+ A K+V
Sbjct: 287 DVGGGATAERVKEAFKLILSDPNVKAIFVNIFGGITRCDEVAEGIIAALKEV 338
>gnl|CDD|233234 TIGR01016, sucCoAbeta, succinyl-CoA synthetase, beta subunit. This
model is designated subfamily because it does not
discriminate the ADP-forming enzyme ((EC 6.2.1.5) from
the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half
is described by the CoA-ligases model (pfam00549). The
C-terminal half is described by the ATP-grasp model
(pfam02222). This family contains a split seen both in a
maximum parsimony tree (which ignores gaps) and in the
gap pattern near position 85 of the seed alignment.
Eukaryotic and most bacterial sequences are longer and
contain a region similar to TXQTXXXG. Sequences from
Deinococcus radiodurans, Mycobacterium tuberculosis,
Streptomyces coelicolor, and the Archaea are 6 amino
acids shorter in that region and contain a motif
resembling [KR]G [Energy metabolism, TCA cycle].
Length = 386
Score = 377 bits (969), Expect = e-129
Identities = 167/351 (47%), Positives = 226/351 (64%), Gaps = 14/351 (3%)
Query: 28 LNIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGT 87
+N+HEYQ ++ AKYGI VP+G SV+E ++ +VVK+Q+ AGGRG
Sbjct: 1 MNLHEYQAKQIFAKYGIPVPRGYVATSVEEAEEIAAKL--GAGPVVVKAQVHAGGRGKA- 57
Query: 88 FKSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFA 146
GGV + K KEE A K+LG+ LVT QT P G+ V+K+ + E + E Y +
Sbjct: 58 ------GGVKVAKSKEEARAAAEKLLGKELVTNQTDPLGQPVNKILIEEATDIDKEYYLS 111
Query: 147 IMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD--GLAP 204
I++DR P+I+ ++GG IE++AEK P I+K ID G+ A ++ GL
Sbjct: 112 IVIDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGLLPYQAREIAKKLGLEG 171
Query: 205 KVADRNDAIEQVKKLYKLFCESDCTLLEINPLAETSGKQLVAADAKLNFDDNAAFRQKEI 264
++ + I +KKLY++F E D +L+EINPL T L+A DAKL DDNA FR ++
Sbjct: 172 ELVKQVADI--IKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRHPDL 229
Query: 265 FALRDPTQEDPREVAAAKADLNYIGLDGEIGCMVNGAGLAMATMDIIKLHGGTPANFLDV 324
+RD +QEDPREV A + LNY+ LDG IGCMVNGAGLAMATMDIIKL+GG PANFLDV
Sbjct: 230 EEMRDYSQEDPREVLAKQWGLNYVALDGNIGCMVNGAGLAMATMDIIKLYGGEPANFLDV 289
Query: 325 GGNASEGQVVEAFKILTSDEKVKAILVNIFGGIMKCDVIASGIVNAAKQVS 375
GG AS +V EA K++ SD+ VK + +NIFGGI +CD++A G+V A K+V
Sbjct: 290 GGGASAERVREALKLVLSDKSVKVVFINIFGGITRCDLVAKGLVEALKEVG 340
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 349 bits (898), Expect = e-118
Identities = 158/348 (45%), Positives = 226/348 (64%), Gaps = 10/348 (2%)
Query: 28 LNIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGT 87
++IHEYQ EL+A +G+ VP+G S ++ ++ H VVK+QI +G RG
Sbjct: 1 MDIHEYQAKELLASFGVAVPRGALAYSPEQAVYRARELGGWH--WVVKAQIHSGARGKA- 57
Query: 88 FKSGLKGGVHIVKKE-EVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFA 146
GG+ + + EV D A +LG+ LVT QTGP+GK V +VY+ + E+Y
Sbjct: 58 ------GGIKLCRTYNEVRDAAEDLLGKKLVTHQTGPEGKPVQRVYVETADPIERELYLG 111
Query: 147 IMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVDGLAPKV 206
+LDRK+ +I ++GG IE++A K P I++V ++ G+ A ++ GL +
Sbjct: 112 FVLDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVGLQQFQAREIAFGLGLDI 171
Query: 207 ADRNDAIEQVKKLYKLFCESDCTLLEINPLAETSGKQLVAADAKLNFDDNAAFRQKEIFA 266
+ A++ + Y+ F + D T+LEINPL T +++A DAK++FDDNA FR+ I
Sbjct: 172 KQVSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFRRPNIAE 231
Query: 267 LRDPTQEDPREVAAAKADLNYIGLDGEIGCMVNGAGLAMATMDIIKLHGGTPANFLDVGG 326
+RDP+QEDPRE AA+ L+Y+GLDG+IGC+VNGAGLAMATMD+IKL GG PANFLDVGG
Sbjct: 232 MRDPSQEDPREAQAAEHGLSYVGLDGDIGCIVNGAGLAMATMDMIKLAGGEPANFLDVGG 291
Query: 327 NASEGQVVEAFKILTSDEKVKAILVNIFGGIMKCDVIASGIVNAAKQV 374
AS +V +AF+++ SD VKAILVNIF GI +CD +A G+V AA++V
Sbjct: 292 GASPERVAKAFRLVLSDRNVKAILVNIFAGINRCDWVAEGVVQAAREV 339
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 212 bits (542), Expect = 1e-67
Identities = 97/213 (45%), Positives = 135/213 (63%), Gaps = 14/213 (6%)
Query: 29 NIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTF 88
N+HEYQ EL+AKYG+ VP+G S +E ++A + K VVK+Q+LAGGRG
Sbjct: 1 NLHEYQAKELLAKYGVPVPRGEVAFSPEEAEEAAKKL--GGKVWVVKAQVLAGGRGKA-- 56
Query: 89 KSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFAI 147
GGV + K EE ++ A +MLG+ LVTKQTGP+GK V+KV + E + + E Y +I
Sbjct: 57 -----GGVKLAKSPEEAKEAAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSI 111
Query: 148 MLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD--GLAPK 205
+LDR + GP++I ++GG IE++A K P I KVPID G+T A ++ GL +
Sbjct: 112 VLDRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLTPYQAREIAFKLGLEGE 171
Query: 206 VADRNDAIEQVKKLYKLFCESDCTLLEINPLAE 238
+ + A + +KKLYKLF E D TL+EINPL E
Sbjct: 172 LVKQ--AADIIKKLYKLFVERDATLVEINPLVE 202
>gnl|CDD|215988 pfam00549, Ligase_CoA, CoA-ligase. This family includes the CoA
ligases Succinyl-CoA synthetase alpha and beta chains,
malate CoA ligase and ATP-citrate lyase. Some members of
the family utilise ATP others use GTP.
Length = 128
Score = 97.3 bits (243), Expect = 1e-24
Identities = 35/83 (42%), Positives = 51/83 (61%), Gaps = 1/83 (1%)
Query: 297 MVNGAGLAMATMDIIKLHGGTPANFLDVGGNASEGQVV-EAFKILTSDEKVKAILVNIFG 355
+VNG LAM MD+IKL GG P NF+D+GG+A +A K+ +D +VK IL++I
Sbjct: 1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVL 60
Query: 356 GIMKCDVIASGIVNAAKQVSALD 378
G C+ A G++ A K+ A +
Sbjct: 61 GYGACEDPAGGLLKAIKEARARE 83
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 46.3 bits (110), Expect = 2e-05
Identities = 63/247 (25%), Positives = 105/247 (42%), Gaps = 37/247 (14%)
Query: 27 RLNIHEYQGAELMAKY-----GINVPKGLA--VASVDEVKKAIQDAFPDHKELVVKSQIL 79
R I EY L+ ++ GI++P A S D + A ++ + +LVVK +L
Sbjct: 3 RKKIREYDSKRLLKEHLKRLAGIDLPIRSAQVTESTDFNELANKEPWLSSTKLVVKPDML 62
Query: 80 AGGRGLGTFKSGLKGGVHIVKKEEVEDLAGKMLG-QILVTKQTGPQGKIVSKVYLCEKLS 138
G RG KSGL + +V + LG ++ + GP + + ++
Sbjct: 63 FGKRG----KSGLVA--LNLDLAQVATFVKERLGKEVEMGGCKGPITTFIVEPFVPHD-- 114
Query: 139 LVNEMYFAIMLDRKTAGPIIIGCS-----KGGTSIEDLAEKYPNMIVKVPIDVFNGITDE 193
E Y +I+ DR +GCS GG IE+ +K + + +T E
Sbjct: 115 --QEFYLSIVSDR-------LGCSISFSECGGIEIEENWDKVKTIFLPTE----APLTSE 161
Query: 194 DAAKVVDGLAPKVADRNDAIEQVKKLYKLFCESDCTLLEINPLAETSGKQLVAADAKLNF 253
A ++ L ++ R E +K ++ +F + D T LE+NP G+ D +
Sbjct: 162 ICAPLIATLPLEI--RGKIEEFIKGVFAVFQDLDFTFLEMNPFTLVDGEPY-PLDMRGEL 218
Query: 254 DDNAAFR 260
DD AAF+
Sbjct: 219 DDTAAFK 225
>gnl|CDD|216282 pfam01071, GARS_A, Phosphoribosylglycinamide synthetase, ATP-grasp
(A) domain. Phosphoribosylglycinamide synthetase
catalyzes the second step in the de novo biosynthesis of
purine. The reaction catalyzed by
Phosphoribosylglycinamide synthetase is the ATP-
dependent addition of 5-phosphoribosylamine to glycine
to form 5'phosphoribosylglycinamide. This domain is
related to the ATP-grasp domain of biotin
carboxylase/carbamoyl phosphate synthetase (see
pfam02786).
Length = 193
Score = 36.5 bits (85), Expect = 0.012
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 17/92 (18%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGV 96
+ M ++GI + +E K I++A VVK+ LA G+ GV
Sbjct: 8 DFMKRHGIPTAEYETFTDPEEAKSYIREAGF---PAVVKADGLAAGK-----------GV 53
Query: 97 HIVKKEEVEDLAGKMLGQILVTKQTGPQGKIV 128
+ E A K + +IL K+ G G+ V
Sbjct: 54 IVAMDNEE---AIKAVDEILEQKKFGEAGEPV 82
>gnl|CDD|233164 TIGR00877, purD, phosphoribosylamine--glycine ligase. Alternate
name: glycinamide ribonucleotide synthetase (GARS). This
enzyme appears as a monofunctional protein in
prokaryotes but as part of a larger, multidomain protein
in eukaryotes [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 422
Score = 35.0 bits (81), Expect = 0.060
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 17/97 (17%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGV 96
+ M +YGI + +E K IQ+ +VVK+ LA G+ GV
Sbjct: 110 DFMKRYGIPTAEYEVFTDPEEAKSYIQEKGA---PIVVKADGLAAGK-----------GV 155
Query: 97 HIVKKEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYL 133
+ K E A K + IL K ++V + +L
Sbjct: 156 IVAKTNEE---AIKAVEDILEQKFGDAGERVVIEEFL 189
>gnl|CDD|217645 pfam03629, DUF303, Domain of unknown function (DUF303).
Distribution of this domain seems limited to prokaryotes
and viruses.
Length = 257
Score = 33.1 bits (76), Expect = 0.17
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 142 EMYFAIMLDRKTAGPI-IIGCSKGGTSIED 170
+FA L ++ PI +I C+ GGT IE
Sbjct: 70 GYFFARKLQQELNVPIGLIPCAWGGTPIEA 99
>gnl|CDD|131764 TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP
forming), alpha domain. Although technically
reversible, it is believed that this group of
ADP-dependent acetyl-CoA synthetases (ACS) act in the
direction of acetate and ATP production in the organisms
in which it has been characterized. In most species this
protein exists as a fused alpha-beta domain polypeptide.
In Pyrococcus and related species, however the domains
exist as separate polypeptides. This model represents
the alpha (N-terminal) domain. In Pyrococcus and related
species there appears to have been the development of a
paralogous family such that four other proteins are
close relatives. In reference , one of these (along with
its beta-domain partner) was characterized as ACS-II
showing specificity for phenylacetyl-CoA. This model has
been constructed to exclude these non-ACS-I paralogs.
This may result in new, authentic ACS-I sequences
falling below the trusted cutoff.
Length = 447
Score = 32.7 bits (75), Expect = 0.31
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 301 AGLAMATMDIIKLH---GGTPANFLDVGGNASEGQVVEAFKILTSDEKVKAILVNI-FGG 356
A L+ AT + ++ + N +DV G+A+ + +A K + DE V ++V +
Sbjct: 323 AELSEATKNKLRNILPPEASIKNPVDVLGDATPERYAKALKTVAEDENVDGVVVVLTPTA 382
Query: 357 IMKCDVIASGIVNAAK 372
+ + +A GI+ AK
Sbjct: 383 MTDPEEVAKGIIEGAK 398
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 32.1 bits (74), Expect = 0.44
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRG 84
+ M KYGI + +E K I + +VVK+ LA G+G
Sbjct: 109 DFMKKYGIPTAEYEVFTDPEEAKAYIDEKGAP---IVVKADGLAAGKG 153
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 32.4 bits (75), Expect = 0.46
Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 20/89 (22%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQD-AFPDHKELVVKSQILAGGRGLGTFKSGLKGG 95
E M K G+ VP+ S++E + ++ +P ++++ GG G GG
Sbjct: 134 EAMKKIGLPVPRSGIAHSMEEALEVAEEIGYP----VIIRPSFTLGGTG---------GG 180
Query: 96 VHIVKKEEVEDLAGKML-----GQILVTK 119
+ +EE+E++ + L ++L+ +
Sbjct: 181 I-AYNEEELEEIVERGLDLSPVTEVLIEE 208
>gnl|CDD|222215 pfam13549, ATP-grasp_5, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 222
Score = 30.5 bits (70), Expect = 1.2
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 26 RRLNIHEYQGAELMAKYGINVPKGLAVASVDEVKKA 61
R + E + L+A YGI V S +E A
Sbjct: 6 GRTVLTEPEAKALLAAYGIPVVPTRLARSPEEAVAA 41
>gnl|CDD|221251 pfam11832, DUF3352, Protein of unknown function (DUF3352). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 538 to 575
amino acids in length.
Length = 541
Score = 30.1 bits (68), Expect = 2.6
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 20 WQQQQLRRLNIH--EYQGAELMAKYGINVPKGLAVASVDE 57
WQ + L ++ YQG +++ G + + LA A +D+
Sbjct: 144 WQTRSLAGTDLQISTYQGIGIISGQGALLGRPLATALLDD 183
>gnl|CDD|237195 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
Provisional.
Length = 326
Score = 29.5 bits (67), Expect = 3.0
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 17/87 (19%)
Query: 33 YQGAELMAKYGINVPKGLAVASVDEVKKAI---QDAFPDHKELVVKSQILAGGRGLGTFK 89
+ E + + GI PK S+++ K A+ + FP L VK + G +G FK
Sbjct: 113 WLTYEFLKENGIPTPKSYLPESLEDFKAALAKGELQFP----LFVKPRD--GSASIGVFK 166
Query: 90 SGLKGGVHIVKKEEVEDLAGKMLGQIL 116
+ KEE+E L + I+
Sbjct: 167 --------VNDKEELEFLLEYVPNLII 185
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 26.9 bits (60), Expect = 4.0
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 22 QQQLRRLNIHEYQGAELMAKY 42
QQ + +LN HEY+G++L Y
Sbjct: 53 QQAVNKLNGHEYEGSKLKVSY 73
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 28.4 bits (64), Expect = 4.3
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDA-FPDHKELVVKSQILAGGRG 84
EL+ G+ VP V +++ A ++ FP +V+K + AG G
Sbjct: 10 ELLRAAGLPVPPFFLVDDEEDLDAAAEEIGFP----VVLKPRDGAGSLG 54
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 29.2 bits (66), Expect = 4.4
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 36 AELMAKYGINVPKGLAVASVDEVKKAIQD-AFPDHKELVVKSQILAGGRGLG 86
E M + G VP+ SV+E A ++ +P ++V+ GG G G
Sbjct: 132 REAMKEIGEPVPESEIAHSVEEALAAAKEIGYP----VIVRPAFTLGGTGGG 179
>gnl|CDD|221720 pfam12697, Abhydrolase_6, Alpha/beta hydrolase family. This family
contains alpha/beta hydrolase enzymes of diverse
specificity.
Length = 187
Score = 28.5 bits (64), Expect = 4.5
Identities = 31/148 (20%), Positives = 54/148 (36%), Gaps = 32/148 (21%)
Query: 148 MLDRKTAGPII-IGCSKGGTSIEDLAEKYPNMIVKV-----PIDVFNGITDEDAAKVVDG 201
+LD GP++ +G S GG A + P + + P+ + DAA ++
Sbjct: 58 LLDALGLGPVVLVGHSLGGAVALAAAARRPERVAGLVLISPPLRDLEELLAADAAALLAL 117
Query: 202 LAPKVADRN--DAIEQVKK--LYKLFCESDCTLLEINPLAETSGKQLVAADAKLNFDDNA 257
L + D + +A+ ++ L + E D + + ++L
Sbjct: 118 LRAALLDADLREALARLTVPVLV-IHGEDD------PLVPPEAARRLA-----------E 159
Query: 258 AFRQKEIFALRD----PTQEDPREVAAA 281
A E+ L P E P EVA A
Sbjct: 160 ALPGAELVVLPGAGHLPHLEHPEEVAEA 187
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 29.2 bits (66), Expect = 4.8
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 25 LRRLNIHEYQGAELMAKYGINVPKGLAVASVDEVKKA-----IQDAFPDHK 70
+ E + EL+ YGI VP +A + V A ++ DHK
Sbjct: 466 GGGTTLDEPEAKELLEAYGIPVPATIASTLDEAVHIAESIGKLRSPDIDHK 516
>gnl|CDD|234856 PRK00885, PRK00885, phosphoribosylamine--glycine ligase;
Provisional.
Length = 420
Score = 28.9 bits (66), Expect = 5.3
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRG 84
+ MA+YGI +E + + +VVK+ LA G+G
Sbjct: 108 DFMARYGIPTAAYETFTDAEEALAYLDEKGAP---IVVKADGLAAGKG 152
>gnl|CDD|233813 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 = 28.7 bits (64), Expect = 5.4
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 43 GINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGVH----- 97
GI VP+ V K I + DH + V+K +GG+G+ S G
Sbjct: 49 GITVPELYGVIHNQAEVKTIHNIVKDHPDFVIKPAQGSGGKGILVITSRKDGRYRKPSGA 108
Query: 98 IVKKEEVE 105
+ KEE+E
Sbjct: 109 TINKEEIE 116
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 28.7 bits (65), Expect = 6.4
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 38 LMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFK 89
++A+ G VP G S++E F D K +VVK + G G+ FK
Sbjct: 495 ILAEAGFPVPAGDEFTSLEEALADY-SLFAD-KAIVVKPKSTNFGLGISIFK 544
>gnl|CDD|185712 cd07902, Adenylation_DNA_ligase_III, Adenylation domain of DNA
Ligase III. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three-step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriophages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
III is not found in lower eukaryotes and is present
both in the nucleus and mitochondria. It has several
isoforms; two splice forms, III-alpha and III-beta,
differ in their carboxy-terminal sequences. DNA ligase
III-beta is believed to play a role in homologous
recombination during meiotic prophase. DNA ligase
III-alpha interacts with X-ray Cross Complementing
factor 1 (XRCC1) and functions in single nucleotide
Base Excision Repair (BER). The mitochondrial form of
DNA ligase III originates from the nucleolus and is
involved in the mitochondrial DNA repair pathway. This
isoform is expressed by a second start site on the DNA
ligase III gene. DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains. The adenylation and
C-terminal oligonucleotide/oligosaccharide binding
(OB)-fold domains comprise a catalytic core unit that
is common to most members of the ATP-dependent DNA
ligase family. The adenylation domain binds ATP and
contains many active site residues. The common
catalytic core unit comprises six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases.
Length = 213
Score = 28.1 bits (63), Expect = 6.6
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 55 VDEVKKAIQDAFPDHKELVVKSQIL 79
V K I AFP +++ S++L
Sbjct: 71 VAHFKDYIPKAFPHGHSMILDSEVL 95
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 28.5 bits (64), Expect = 6.7
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 167 SIEDLAEKYPNMIVKVPIDVFNGITDEDAA 196
++ DLAEKY + ++ + +DV TD A
Sbjct: 39 TLADLAEKYGDRLLPLALDV----TDRAAV 64
>gnl|CDD|178374 PLN02775, PLN02775, Probable dihydrodipicolinate reductase.
Length = 286
Score = 28.1 bits (63), Expect = 8.1
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 114 QILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFAIMLDRKTAG----PI-IIGCSKGGTSI 168
I+V TG G V++ + L LV + T + ++G S+ +
Sbjct: 13 PIMVNGCTGKMGHAVAEAAVSAGLQLVPVSFTGPAGVGVTVEVCGVEVRLVGPSEREAVL 72
Query: 169 EDLAEKYPNMIV 180
+ +YPN+IV
Sbjct: 73 SSVKAEYPNLIV 84
>gnl|CDD|237243 PRK12875, ubiA, prenyltransferase; Reviewed.
Length = 282
Score = 28.1 bits (63), Expect = 8.7
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 15/62 (24%)
Query: 153 TAGPIIIGCSKGGTSIEDLAEKYPNMIV-----KVPIDVF----NGITDEDAAKVVDGLA 203
AGP+++G + S+ DL P + P +VF N + D D D L
Sbjct: 23 LAGPVVVGVAYAADSVADLFS--PAAVALFAYFLFPANVFLYGVNDVFDAD----TDELN 76
Query: 204 PK 205
PK
Sbjct: 77 PK 78
>gnl|CDD|148013 pfam06152, Phage_min_cap2, Phage minor capsid protein 2. Family of
related phage minor capsid proteins.
Length = 361
Score = 28.2 bits (63), Expect = 8.9
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 12 RSLTVAGQWQQQQLRRLN-IHEY--QGAELMAKY-GINVPKGLAVASVDEVKKAIQDAFP 67
+SL +A +Q Q+ +LN + Q +L+AKY G+ + + + K I+D
Sbjct: 38 KSLQLADNVEQWQIEKLNELGLLNKQNIKLIAKYTGVAE-EAITRVIKNAGLKIIKDIDK 96
Query: 68 DHKELVVK 75
E + K
Sbjct: 97 QLSEALNK 104
>gnl|CDD|236398 PRK09185, PRK09185, 3-oxoacyl-(acyl carrier protein) synthase I;
Reviewed.
Length = 392
Score = 28.3 bits (64), Expect = 9.0
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 301 AGLAMATMDIIKLHG-GTPANFLDVGGNASEGQVVEA 336
AGLA A + I LHG TP N +A E + V A
Sbjct: 273 AGLAPADIGYINLHGTATPLN------DAMESRAVAA 303
>gnl|CDD|233108 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
subunit. [Amino acid biosynthesis, Histidine family].
Length = 254
Score = 27.7 bits (62), Expect = 9.8
Identities = 32/121 (26%), Positives = 52/121 (42%), Gaps = 22/121 (18%)
Query: 168 IEDLAEKYPNMIVKVPIDVFNGITD-EDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCES 226
+E AE V +P+ V GI ED K++ A KV+ A++ + +Y+L
Sbjct: 66 VERTAET-----VFIPLTVGGGIKSIEDVDKLLRAGADKVSINTAAVKNPELIYEL---- 116
Query: 227 DCTLLEINPLAETSGKQ--LVAADAKLNFDDNAAFRQKEIFALRDPTQEDPREVAAAKAD 284
A+ G Q +VA DAK + ++ + + I+ R+ T D E A
Sbjct: 117 ----------ADRFGSQCIVVAIDAKRVYVNSYCWYEVYIYGGRESTGLDAVEWAKEVEK 166
Query: 285 L 285
L
Sbjct: 167 L 167
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.137 0.391
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,064,002
Number of extensions: 2014452
Number of successful extensions: 2148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2128
Number of HSP's successfully gapped: 62
Length of query: 394
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 295
Effective length of database: 6,546,556
Effective search space: 1931234020
Effective search space used: 1931234020
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 (21.7 bits)
S2: 60 (26.6 bits)