RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12143
(443 letters)
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 498 bits (1284), Expect = e-176
Identities = 218/430 (50%), Positives = 292/430 (67%), Gaps = 12/430 (2%)
Query: 1 MLSRSVTVLENVAKNTSLKALSAAPSWS-QQKRNLNVHEHVSYTLLKEGGIPVPPFGVAK 59
ML + L + ++LS A W QQ R LN+HE+ L+ + G+ VP A
Sbjct: 1 MLRGLLNKL-------ASRSLSVAGKWQHQQLRRLNIHEYQGAELMSKYGVNVPKGAAAS 53
Query: 60 TKKEAGEIAKKL--NIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMVDTPEEAEEVAGKMI 117
+ E + +K+ + ++V+K+Q+LAGGRG G FK GLKGGV +V ++AEE+AGKM+
Sbjct: 54 SLDEVKKALEKMFPDEGEVVVKSQILAGGRGLGTFKNGLKGGVHIV-KKDKAEELAGKML 112
Query: 118 GDYLITKQTGEKGRICNAVMVTERKYPRKEYYFAFMMERSFAGPVLIASSQGGVNIEEVA 177
G L+TKQTG G+ N V + E+ E YFA +++R+ AGP++IA S+GG +IE++A
Sbjct: 113 GQILVTKQTGPAGKPVNKVYLCEKMSLVNEMYFAILLDRASAGPLIIACSKGGTSIEDLA 172
Query: 178 AENPSAILYEPVDITVGITKEQALKVADAVGLK-AKRDITAEMLIKMYALFISKDASLIE 236
+ P I+ P+DI GIT E A KV D + K A R+ E + K+Y LF D +++E
Sbjct: 173 EKFPEKIIKVPIDIFKGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCKCDCTMVE 232
Query: 237 INPYAEDATGNFFGLDAKMRFDDNAEFRQKALFDLRDWSQEDAKEVEAAKHSLNYIALDG 296
INP AE A G DAK+ FDDNA FRQK +F LRD SQED +EV AAK LNYI LDG
Sbjct: 233 INPLAETADGQLVAADAKLNFDDNAAFRQKEIFALRDTSQEDPREVAAAKADLNYIGLDG 292
Query: 297 SIGCLVNGAGLAMATMDIIKLHGGEPANFLDVGGGATAAQVKEAFKIITADPKVCAIMVN 356
IGC+VNGAGLAMATMDIIKLHGG PANFLDVGG A+ QV EAFKI+T+D KV AI+VN
Sbjct: 293 EIGCMVNGAGLAMATMDIIKLHGGSPANFLDVGGNASEQQVVEAFKILTSDDKVKAILVN 352
Query: 357 IFGGIMRCDVIAEGIIAAAQELSLKIPIICRLQGTNVDDAKVLIASAAMKILPCDNLDEA 416
IFGGIM+CDVIA GI+ AA+++ LK+P++ RL+GTNVD K ++ + M ++ ++LD+A
Sbjct: 353 IFGGIMKCDVIASGIVNAAKQVGLKVPLVVRLEGTNVDQGKRILKESGMTLITAEDLDDA 412
Query: 417 ARLAVKLSSI 426
A AVK +I
Sbjct: 413 AEKAVKALAI 422
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 494 bits (1275), Expect = e-175
Identities = 200/390 (51%), Positives = 268/390 (68%), Gaps = 8/390 (2%)
Query: 35 NVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKG 94
N+HE+ + L + G+PVP VA T +EA E A++L V+KAQV AGGRGK
Sbjct: 2 NLHEYQAKELFAKYGVPVPRGIVATTPEEAVEAAEELGGGVWVVKAQVHAGGRGKA---- 57
Query: 95 GLKGGVKMVDTPEEAEEVAGKMIGDYLITKQTGEKGRICNAVMVTERKYPRKEYYFAFMM 154
GGVK+ +PEEA E A +++G L+T QTG KG+ N V+V E KEYY + ++
Sbjct: 58 ---GGVKLAKSPEEAREFAKQILGMTLVTHQTGPKGQPVNKVLVEEGADIAKEYYLSIVL 114
Query: 155 ERSFAGPVLIASSQGGVNIEEVAAENPSAILYEPVDITVGITKEQALKVADAVGLKAK-R 213
+R+ V +AS++GG++IEEVA E P I +D G+ QA ++A +GL +
Sbjct: 115 DRATRRVVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQPFQAREIAFKLGLPGEQV 174
Query: 214 DITAEMLIKMYALFISKDASLIEINPYAEDATGNFFGLDAKMRFDDNAEFRQKALFDLRD 273
A++L+ +Y F+ KDASL+EINP G+ LDAK+ FDDNA FR L +LRD
Sbjct: 175 KQFAKILMGLYKAFVEKDASLVEINPLVVTKDGDLIALDAKINFDDNALFRHPDLAELRD 234
Query: 274 WSQEDAKEVEAAKHSLNYIALDGSIGCLVNGAGLAMATMDIIKLHGGEPANFLDVGGGAT 333
S+ED E EA+K+ LNY+ LDG+IGC+VNGAGLAMATMDIIKL+GGEPANFLDVGGGAT
Sbjct: 235 LSEEDPLEAEASKYGLNYVKLDGNIGCMVNGAGLAMATMDIIKLYGGEPANFLDVGGGAT 294
Query: 334 AAQVKEAFKIITADPKVCAIMVNIFGGIMRCDVIAEGIIAAAQELSLKIPIICRLQGTNV 393
A +V EAFKII +DP V AI+VNIFGGI RCDVIAEGIIAA +E+ + +P++ RL+GTNV
Sbjct: 295 AERVAEAFKIILSDPNVKAILVNIFGGITRCDVIAEGIIAAVKEVGVTVPLVVRLEGTNV 354
Query: 394 DDAKVLIASAAMKILPCDNLDEAARLAVKL 423
+ K ++A + + I+ D LD+AA+ AV+
Sbjct: 355 ELGKKILAESGLNIIAADTLDDAAQKAVEA 384
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 439 bits (1132), Expect = e-153
Identities = 198/393 (50%), Positives = 273/393 (69%), Gaps = 13/393 (3%)
Query: 34 LNVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFK 93
+N+HE+ + L + GIPVPP VA + +EA E AK+L +V+KAQV AGGRGK
Sbjct: 1 MNLHEYQAKELFAKYGIPVPPGYVATSPEEAEEAAKELGGGPVVVKAQVHAGGRGKA--- 57
Query: 94 GGLKGGVKMVDTPEEAEEVAGKMIGDYLITKQTGEKGRICNAVMVTERK-YPRKEYYFAF 152
GGVK+ +PEEA+E A +++G QT KG N V+V E +KEYY +
Sbjct: 58 ----GGVKLAKSPEEAKEAAEEILG---KNYQTDIKGEPVNKVLVEEAVDIIKKEYYLSI 110
Query: 153 MMERSFAGPVLIASSQGGVNIEEVAAENPSAILYEPVDITVGITKEQALKVADAVGLKAK 212
+++RS PVL+AS++GG++IEEVA + P I+ VD G+ QA ++A +GL+ +
Sbjct: 111 VLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLRPYQARELAFKLGLEGE 170
Query: 213 -RDITAEMLIKMYALFISKDASLIEINPYAEDAT-GNFFGLDAKMRFDDNAEFRQKALFD 270
A+++ K+Y LF+ KDA+L+EINP G+ LDAK+ DDNA FR L +
Sbjct: 171 LVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNALFRHPDLAE 230
Query: 271 LRDWSQEDAKEVEAAKHSLNYIALDGSIGCLVNGAGLAMATMDIIKLHGGEPANFLDVGG 330
LRD S+ED +E EA+ + LNY+ LDG+IGC+VNGAGLAMATMDI+KL+GG+PANFLDVGG
Sbjct: 231 LRDESEEDPREAEASGYGLNYVELDGNIGCIVNGAGLAMATMDIVKLYGGKPANFLDVGG 290
Query: 331 GATAAQVKEAFKIITADPKVCAIMVNIFGGIMRCDVIAEGIIAAAQELSLKIPIICRLQG 390
GATA +VKEAFK+I +DP V AI VNIFGGI RCD +AEGIIAA +E+ + +P++ RL+G
Sbjct: 291 GATAERVKEAFKLILSDPNVKAIFVNIFGGITRCDEVAEGIIAALKEVGVNVPLVVRLEG 350
Query: 391 TNVDDAKVLIASAAMKILPCDNLDEAARLAVKL 423
TNV++ K ++A + + I+ D+LDEAA AV+L
Sbjct: 351 TNVEEGKRILAESGLNIIAADDLDEAAEKAVEL 383
>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 = 402 bits (1035), Expect = e-138
Identities = 181/392 (46%), Positives = 268/392 (68%), Gaps = 8/392 (2%)
Query: 34 LNVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFK 93
+N+HE+ + + + GIPVP VA + +EA EIA KL +V+KAQV AGGRGK
Sbjct: 1 MNLHEYQAKQIFAKYGIPVPRGYVATSVEEAEEIAAKLGAGPVVVKAQVHAGGRGKA--- 57
Query: 94 GGLKGGVKMVDTPEEAEEVAGKMIGDYLITKQTGEKGRICNAVMVTERKYPRKEYYFAFM 153
GGVK+ + EEA A K++G L+T QT G+ N +++ E KEYY + +
Sbjct: 58 ----GGVKVAKSKEEARAAAEKLLGKELVTNQTDPLGQPVNKILIEEATDIDKEYYLSIV 113
Query: 154 MERSFAGPVLIASSQGGVNIEEVAAENPSAILYEPVDITVGITKEQALKVADAVGLKAKR 213
++RS PV++AS++GGV+IEEVA ++P I+ +D G+ QA ++A +GL+ +
Sbjct: 114 IDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGLLPYQAREIAKKLGLEGEL 173
Query: 214 -DITAEMLIKMYALFISKDASLIEINPYAEDATGNFFGLDAKMRFDDNAEFRQKALFDLR 272
A+++ K+Y +F+ DASL+EINP GN LDAK+ DDNA FR L ++R
Sbjct: 174 VKQVADIIKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRHPDLEEMR 233
Query: 273 DWSQEDAKEVEAAKHSLNYIALDGSIGCLVNGAGLAMATMDIIKLHGGEPANFLDVGGGA 332
D+SQED +EV A + LNY+ALDG+IGC+VNGAGLAMATMDIIKL+GGEPANFLDVGGGA
Sbjct: 234 DYSQEDPREVLAKQWGLNYVALDGNIGCMVNGAGLAMATMDIIKLYGGEPANFLDVGGGA 293
Query: 333 TAAQVKEAFKIITADPKVCAIMVNIFGGIMRCDVIAEGIIAAAQELSLKIPIICRLQGTN 392
+A +V+EA K++ +D V + +NIFGGI RCD++A+G++ A +E+ + +P++ RL+GTN
Sbjct: 294 SAERVREALKLVLSDKSVKVVFINIFGGITRCDLVAKGLVEALKEVGVNVPVVVRLEGTN 353
Query: 393 VDDAKVLIASAAMKILPCDNLDEAARLAVKLS 424
V++ K ++A + + I+ +++EAA AV+ +
Sbjct: 354 VEEGKKILAESGLNIIFATSMEEAAEKAVEAA 385
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 357 bits (917), Expect = e-121
Identities = 166/389 (42%), Positives = 249/389 (64%), Gaps = 8/389 (2%)
Query: 34 LNVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFK 93
+++HE+ + LL G+ VP +A + ++A A++L V+KAQ+ +G RGK
Sbjct: 1 MDIHEYQAKELLASFGVAVPRGALAYSPEQAVYRARELGGWHWVVKAQIHSGARGKA--- 57
Query: 94 GGLKGGVKMVDTPEEAEEVAGKMIGDYLITKQTGEKGRICNAVMVTERKYPRKEYYFAFM 153
GG+K+ T E + A ++G L+T QTG +G+ V V +E Y F+
Sbjct: 58 ----GGIKLCRTYNEVRDAAEDLLGKKLVTHQTGPEGKPVQRVYVETADPIERELYLGFV 113
Query: 154 MERSFAGPVLIASSQGGVNIEEVAAENPSAILYEPVDITVGITKEQALKVADAVGLKAKR 213
++R +IAS++GG+ IEE+AA+ P AI+ V+ VG+ + QA ++A +GL K+
Sbjct: 114 LDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVGLQQFQAREIAFGLGLDIKQ 173
Query: 214 DITA-EMLIKMYALFISKDASLIEINPYAEDATGNFFGLDAKMRFDDNAEFRQKALFDLR 272
A + ++ Y F DA+++EINP LDAKM FDDNA FR+ + ++R
Sbjct: 174 VSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFRRPNIAEMR 233
Query: 273 DWSQEDAKEVEAAKHSLNYIALDGSIGCLVNGAGLAMATMDIIKLHGGEPANFLDVGGGA 332
D SQED +E +AA+H L+Y+ LDG IGC+VNGAGLAMATMD+IKL GGEPANFLDVGGGA
Sbjct: 234 DPSQEDPREAQAAEHGLSYVGLDGDIGCIVNGAGLAMATMDMIKLAGGEPANFLDVGGGA 293
Query: 333 TAAQVKEAFKIITADPKVCAIMVNIFGGIMRCDVIAEGIIAAAQELSLKIPIICRLQGTN 392
+ +V +AF+++ +D V AI+VNIF GI RCD +AEG++ AA+E+ + +P++ RL GTN
Sbjct: 294 SPERVAKAFRLVLSDRNVKAILVNIFAGINRCDWVAEGVVQAAREVGIDVPLVVRLAGTN 353
Query: 393 VDDAKVLIASAAMKILPCDNLDEAARLAV 421
V++ + ++A + + I+ D L EAA AV
Sbjct: 354 VEEGRKILAESGLPIITADTLAEAAEKAV 382
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 237 bits (606), Expect = 1e-76
Identities = 100/209 (47%), Positives = 142/209 (67%), Gaps = 8/209 (3%)
Query: 35 NVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKG 94
N+HE+ + LL + G+PVP VA + +EA E AKKL K V+KAQVLAGGRGK
Sbjct: 1 NLHEYQAKELLAKYGVPVPRGEVAFSPEEAEEAAKKLGGKVWVVKAQVLAGGRGKA---- 56
Query: 95 GLKGGVKMVDTPEEAEEVAGKMIGDYLITKQTGEKGRICNAVMVTERKYPRKEYYFAFMM 154
GGVK+ +PEEA+E A +M+G L+TKQTG +G+ N V+V E +EYY + ++
Sbjct: 57 ---GGVKLAKSPEEAKEAAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSIVL 113
Query: 155 ERSFAGPVLIASSQGGVNIEEVAAENPSAILYEPVDITVGITKEQALKVADAVGLKAKR- 213
+R+ GPVLIAS++GGV+IEEVAA+NP AI P+D G+T QA ++A +GL+ +
Sbjct: 114 DRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLTPYQAREIAFKLGLEGELV 173
Query: 214 DITAEMLIKMYALFISKDASLIEINPYAE 242
A+++ K+Y LF+ +DA+L+EINP E
Sbjct: 174 KQAADIIKKLYKLFVERDATLVEINPLVE 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 = 123 bits (310), Expect = 6e-34
Identities = 47/128 (36%), Positives = 71/128 (55%), Gaps = 7/128 (5%)
Query: 301 LVNGAGLAMATMDIIKLHGGEPANFLDVGGGA-TAAQVKEAFKIITADPKVCAIMVNIFG 359
LVNG LAM MD+IKL GG P NF+D+GG A T +A K+ ADP+V I+++I
Sbjct: 1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVL 60
Query: 360 GIMRCDVIAEGIIAAAQEL-SLKIPIICRLQGTNVD-----DAKVLIASAAMKILPCDNL 413
G C+ A G++ A +E + ++P++ R+ GT D + +A + + I +N
Sbjct: 61 GYGACEDPAGGLLKAIKEARARELPVVARVCGTEADPQGREEQAKALAESGVLIASSNNQ 120
Query: 414 DEAARLAV 421
A AV
Sbjct: 121 ALRAAGAV 128
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 39.8 bits (93), Expect = 0.003
Identities = 96/400 (24%), Positives = 158/400 (39%), Gaps = 68/400 (17%)
Query: 36 VHEHVSYTLLKE-----GGIPVPPFGVAKTKK-EAGEIAKK---LNIKDIVLKAQVLAGG 86
+ E+ S LLKE GI +P T+ + E+A K L+ +V+K +L G
Sbjct: 6 IREYDSKRLLKEHLKRLAGIDLPIRSAQVTESTDFNELANKEPWLSSTKLVVKPDMLFGK 65
Query: 87 RGKGAFKGGLKG-GVKMVDTPEEAEEVAGKMIGDYLITKQTGEKGRICNAVMVTERKYPR 145
RGK GL + + +E GK + + G KG I + E P
Sbjct: 66 RGKS----GLVALNLDLAQVATFVKERLGKEV------EMGGCKGPI--TTFIVEPFVPH 113
Query: 146 K-EYYFAFMMERSFAGPVLIASSQGGVNIEEVAAENPSAILYEPVDITVGITKEQALKVA 204
E+Y + + +R G + S GG+ IEE N + + +T E +
Sbjct: 114 DQEFYLSIVSDR--LGCSISFSECGGIEIEE----NWDKVKTIFLPTEAPLTSEICAPLI 167
Query: 205 DAVGLKAKRDITAEMLIKMYALFISKDASLIEINPYAEDATGNFFGLDAKMRFDDNAEFR 264
+ L+ + I E + ++A+F D + +E+NP+ G + LD + DD A F+
Sbjct: 168 ATLPLEIRGKI-EEFIKGVFAVFQDLDFTFLEMNPFTL-VDGEPYPLDMRGELDDTAAFK 225
Query: 265 QKALFDLRDWSQ-----------EDAKEV-----EAAKHSLNYIALD--GSIGCLVNGAG 306
+ + W + E SL + L+ G I +V G G
Sbjct: 226 -----NFKKWGNIEFPLPFGRVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVAGGG 280
Query: 307 LAMATMDIIKLHG--GEPANFLDVGGGATAAQVKEAFKII----TADPKVCAIMVNIFGG 360
++ D + G E N+ + G +V + +++ TA+P + I GG
Sbjct: 281 ASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATANPDGRKRALLIGGG 340
Query: 361 IMR-CDVIA--EGIIAAAQE-----LSLKIPIICRLQGTN 392
I DV A GII A +E + ++ I R G N
Sbjct: 341 IANFTDVAATFNGIIRALREKESKLKAARMHIFVRRGGPN 380
>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 = 37.8 bits (89), Expect = 0.006
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 24/90 (26%)
Query: 37 HEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAK--------KLNIKDIVLKAQVLAGGRG 88
E + LL GIPV P +A++ +EA A+ K+ DI+ K+ V
Sbjct: 11 TEPEAKALLAAYGIPVVPTRLARSPEEAVAAAEEIGYPVVLKIVSPDILHKSDV------ 64
Query: 89 KGAFKGGLKGGVKM-VDTPEEAEEVAGKMI 117
GGV++ + + EE A +++
Sbjct: 65 ---------GGVRLNLKSAEEVRAAAEEIL 85
>gnl|CDD|223516 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 38.4 bits (90), Expect = 0.006
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 44 LLKEGGIPVPP--FGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVK 101
L+ + G+PV P G +EA IA+++ +++KA GGR G++
Sbjct: 122 LMAKAGVPVVPGSDGAVADNEEALAIAEEIGY-PVIVKAAAGGGGR-----------GMR 169
Query: 102 MVDTPEEAEE 111
+V EE E
Sbjct: 170 VVRNEEELEA 179
>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 = 38.1 bits (89), Expect = 0.008
Identities = 26/103 (25%), Positives = 50/103 (48%), Gaps = 4/103 (3%)
Query: 305 AGLAMATMDIIKLHGGEPANF---LDVGGGATAAQVKEAFKIITADPKVCAIMVNI-FGG 360
A L+ AT + ++ A+ +DV G AT + +A K + D V ++V +
Sbjct: 323 AELSEATKNKLRNILPPEASIKNPVDVLGDATPERYAKALKTVAEDENVDGVVVVLTPTA 382
Query: 361 IMRCDVIAEGIIAAAQELSLKIPIICRLQGTNVDDAKVLIASA 403
+ + +A+GII A++ + K + + G +VD AK ++
Sbjct: 383 MTDPEEVAKGIIEGAKKSNEKPVVAGFMGGKSVDPAKRILEEN 425
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 38.1 bits (89), Expect = 0.010
Identities = 32/114 (28%), Positives = 47/114 (41%), Gaps = 31/114 (27%)
Query: 19 KALSAAPSWSQQKRNL------------NVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGE 66
KALSA + + + L + E + LL+ GIPVP +A T EA
Sbjct: 442 KALSALARYRRWLKKLRETPVFEGGGGTTLDEPEAKELLEAYGIPVPA-TIASTLDEAVH 500
Query: 67 IAK---KLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMVDTPEEAEEVAGKMI 117
IA+ KL DI K++V GGV + T + E+ A ++
Sbjct: 501 IAESIGKLRSPDIDHKSEV---------------GGVMLNRTADAVEKAADDIL 539
Score = 31.9 bits (73), Expect = 0.74
Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 1/89 (1%)
Query: 322 PANFLDVGGGATAAQVKEAFKIITADPKVCAIMV-NIFGGIMRCDVIAEGIIAAAQELSL 380
N +D+ G A A + K+ +I+ D V A++V + + AE II A +
Sbjct: 347 VKNPVDLTGDADAERYKKTLEILLRDENVDALLVIVLPPASADPEETAEAIIRATAKKRG 406
Query: 381 KIPIICRLQGTNVDDAKVLIASAAMKILP 409
K ++ + G + + A+ L+ A + P
Sbjct: 407 KPVVVSSMGGESSEKARRLLEEAGIPTYP 435
>gnl|CDD|216935 pfam02222, ATP-grasp, ATP-grasp domain. This family does not
contain all known ATP-grasp domain members. This family
includes a diverse set of enzymes that possess
ATP-dependent carboxylate-amine ligase activity.
Length = 171
Score = 34.9 bits (81), Expect = 0.033
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 11/69 (15%)
Query: 45 LKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMVD 104
L++ G+P P F A++ +E E ++L VLKA+ G GK G +V
Sbjct: 1 LQKLGLPTPRFAAAESLEELIEAGQELGYP-CVLKARRG-GYDGK---------GQYVVR 49
Query: 105 TPEEAEEVA 113
+ + +
Sbjct: 50 SEADIPQAW 58
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 36.0 bits (84), Expect = 0.038
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMV 103
+K+ GIP + V +EA + IV+KA LA G+G V +
Sbjct: 110 FMKKYGIPTAEYEVFTDPEEAKAYIDEKG-APIVVKADGLAAGKG-----------VIVA 157
Query: 104 DTPEEAEEVAGKMIGDY 120
T EEAE +M+
Sbjct: 158 MTLEEAEAAVDEMLEGN 174
>gnl|CDD|223105 COG0026, PurK, Phosphoribosylaminoimidazole carboxylase (NCAIR
synthetase) [Nucleotide transport and metabolism].
Length = 375
Score = 34.1 bits (79), Expect = 0.14
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 43 TLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKG-GVK 101
L + G+PV PF V + +E A L VLK + +GG G G
Sbjct: 105 QFLDKAGLPVAPFQVVDSAEELDAAAADLGFP-AVLKTR-----------RGGYDGKGQW 152
Query: 102 MVDTPEEAEEVA 113
+ + + E A
Sbjct: 153 RIRSDADLELRA 164
>gnl|CDD|132296 TIGR03252, TIGR03252, uncharacterized HhH-GPD family protein. This
model describes a small, well-conserved bacterial
protein family. Its sequence largely consists of a
domain, HhH-GPD, found in a variety of related base
excision DNA repair enzymes (see pfam00730) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 177
Score = 32.9 bits (75), Expect = 0.19
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 9/47 (19%)
Query: 137 MVTERKYPRKEYYFAFMMERSFAGPVLIASSQGGVNIEEVAAENPSA 183
M+ +++ P MER+FAGP IA G ++ E++A +P A
Sbjct: 25 MLLDQQVP---------MERAFAGPHKIARRMGSLDAEDIAKYDPQA 62
>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 = 33.4 bits (77), Expect = 0.26
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 39 HVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRG 88
LL E GIP P + A + +EA E A ++ +V + VL GGR
Sbjct: 671 EKFSELLDELGIPQPKWKTATSVEEAVEFASEIGYPVLVRPSYVL-GGRA 719
Score = 31.9 bits (73), Expect = 0.93
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 7/72 (9%)
Query: 42 YTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKG------AFKGG 95
+KE G PVP +A + +EA AK++ IV A L GG G G K
Sbjct: 132 REAMKEIGEPVPESEIAHSVEEALAAAKEIGYPVIVRPAFTL-GGTGGGIAYNREELKEI 190
Query: 96 LKGGVKMVDTPE 107
+ + +
Sbjct: 191 AERALSASPINQ 202
>gnl|CDD|217683 pfam03709, OKR_DC_1_N, Orn/Lys/Arg decarboxylase, N-terminal
domain. This domain has a flavodoxin-like fold, and is
termed the "wing" domain because of its position in the
overall 3D structure.
Length = 111
Score = 30.7 bits (70), Expect = 0.42
Identities = 7/52 (13%), Positives = 20/52 (38%), Gaps = 7/52 (13%)
Query: 333 TAAQVKEAFKIITADPKVCAIMVNIFGGIMRCDVIAEGIIAAAQELSLKIPI 384
A + +I + A++++ D A G++ + + +P+
Sbjct: 22 YATSTDDLLSLIENFTDIAAVVLSW-------DDEARGLLDEIRRRNFDLPV 66
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 32.8 bits (75), Expect = 0.45
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGR 87
+L E I P G+A+++ +A IAK++ +V + VL GGR
Sbjct: 709 ILNELKIEQPKGGIARSEADALAIAKRIGYPVVVRPSYVL-GGR 751
>gnl|CDD|234856 PRK00885, PRK00885, phosphoribosylamine--glycine ligase;
Provisional.
Length = 420
Score = 32.3 bits (75), Expect = 0.54
Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 12/76 (15%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMV 103
+ GIP + +EA + IV+KA LA G+ GV +
Sbjct: 109 FMARYGIPTAAYETFTDAEEALAYLDEKG-APIVVKADGLAAGK-----------GVVVA 156
Query: 104 DTPEEAEEVAGKMIGD 119
T EEA+ M+
Sbjct: 157 MTLEEAKAAVDDMLAG 172
>gnl|CDD|233295 TIGR01161, purK, phosphoribosylaminoimidazole carboxylase, PurK
protein. Phosphoribosylaminoimidazole carboxylase is a
fusion protein in plants and fungi, but consists of two
non-interacting proteins in bacteria, PurK and PurE.
This model represents PurK, N5-carboxyaminoimidazole
ribonucleotide synthetase, which hydrolyzes ATP and
converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR.
In the presence of high concentrations of bicarbonate,
PurE is reported able to convert AIR to CAIR directly
and without ATP [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 352
Score = 31.9 bits (73), Expect = 0.68
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 13/71 (18%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKG-GVKM 102
L++ G+PVPPF V K ++E ++L +VLKA+ GG G G
Sbjct: 105 FLQKLGLPVPPFLVIKDEEELDAALQELGFP-VVLKAR-----------TGGYDGRGQYR 152
Query: 103 VDTPEEAEEVA 113
+ + + A
Sbjct: 153 IRNEADLPQAA 163
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 32.0 bits (74), Expect = 0.71
Identities = 13/28 (46%), Positives = 21/28 (75%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKL 71
LL++ GIP PP G A + +EA E+A+++
Sbjct: 676 LLEKLGIPQPPNGTATSVEEALEVAEEI 703
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 31.9 bits (73), Expect = 0.96
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 17/86 (19%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMV 103
L+KE G PVP + + +EA A+K+ IV A L GG G G +
Sbjct: 135 LMKELGEPVPESEIVTSVEEALAFAEKIGFPIIVRPAYTL-GGTGGGIAE---------- 183
Query: 104 DTPEEAEEVAGK-----MIGDYLITK 124
EE E++ + I L+ +
Sbjct: 184 -NLEELEQLFKQGLQASPIHQCLLEE 208
Score = 28.4 bits (64), Expect = 9.2
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 42 YTLLKEGGIPVPPFGVAKTKKEAGEIAKK 70
Y LL E G+P P A ++EA AK+
Sbjct: 675 YQLLDELGLPHVPGLTATDEEEAFAFAKR 703
>gnl|CDD|235674 PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase
subunit; Reviewed.
Length = 372
Score = 30.9 bits (71), Expect = 1.3
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 13/81 (16%)
Query: 43 TLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKG-GVK 101
L + GIPV PF V + ++ L + VLK + +GG G G
Sbjct: 106 QFLDKLGIPVAPFAVVDSAEDLEAALADLGLP-AVLKTR-----------RGGYDGKGQW 153
Query: 102 MVDTPEEAEEVAGKMIGDYLI 122
++ + E+ E + I
Sbjct: 154 VIRSAEDLEAAWALLGSVPCI 174
>gnl|CDD|213332 cd05130, RasGAP_Neurofibromin, Ras-GTPase Activating Domain of
neurofibromin. Neurofibromin is the product of the
neurofibromatosis type 1 gene (NF1) and shares a region
of similarity with catalytic domain of the mammalian
p120RasGAP protein and an extended similarity with the
Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2.
Neurofibromin has been shown to function as a GAP
(GTPase-activating protein) which inhibits low molecular
weight G proteins such as Ras by stimulating their
intrinsic GTPase activity. NF1 is a common genetic
disorder characterized by various symptoms ranging from
predisposition for the development of tumors to learning
disability or mental retardation. Loss of neurofibromin
activity can be correlated to the increase in Ras-GTP
concentration in neurofibromas of NF1 of patients,
supporting the notion that unregulated Ras signaling may
contribute to their development.
Length = 332
Score = 30.8 bits (70), Expect = 1.4
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 394 DDAKVLIASAAMKILPCDNLDEAARLAVKLSS 425
DD ++ IA A ++PC +DE AR+ V L
Sbjct: 20 DDGELPIAMALANVVPCSQMDELARVLVTLFD 51
>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 = 29.6 bits (67), Expect = 2.1
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 42 YTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVK 101
LL+ G+PVPPF + +++ A+++ +VLK + AG GV
Sbjct: 9 RELLRAAGLPVPPFFLVDDEEDLDAAAEEIG-FPVVLKPRDGAGSL-----------GVF 56
Query: 102 MVDTPEEAEEV 112
VD+ E E
Sbjct: 57 RVDSAAELEAA 67
>gnl|CDD|107268 cd06273, PBP1_GntR_like_1, This group includes the ligand-binding
domain of putative DNA transcription repressors which
are highly similar to that of the repressor specific for
gluconate (GntR), a member of the LacI-GalR family of
bacterial transcription regulators. This group includes
the ligand-binding domain of putative DNA transcription
repressors which are highly similar to that of the
repressor specific for gluconate (GntR), a member of the
LacI-GalR family of bacterial transcription regulators.
The LacI-GalR family repressors are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 268
Score = 29.9 bits (68), Expect = 2.3
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 19/62 (30%)
Query: 365 DVIAEGIIAAAQELSLKIPIICRLQGTNVDDAKVLIASAAMKILPCDNLDEAARLAVKLS 424
DV+A G + A+ L L +P + I+ D++D +A L L+
Sbjct: 187 DVLALGALYEARRLGLSVP-------------------EDLSIVGFDDIDGSAELEPALT 227
Query: 425 SI 426
++
Sbjct: 228 TV 229
>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 = 29.5 bits (67), Expect = 2.5
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 16/88 (18%)
Query: 44 LLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKMV 103
+K GIP + +EA ++ V+KA LA G+ GV +
Sbjct: 9 FMKRHGIPTAEYETFTDPEEAKSYIREAGFP-AVVKADGLAAGK-----------GVIVA 56
Query: 104 DTPEEAEEVAGKMIGDYLITKQTGEKGR 131
EEA + +++ K+ GE G
Sbjct: 57 MDNEEAIKAVDEILEQ----KKFGEAGE 80
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 29.6 bits (67), Expect = 3.1
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 41 SYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFK 93
+ LL + GIPVPP + + EA E + +VLK L G G+G F
Sbjct: 123 TTQLLAKAGIPVPPTLITRDPDEAAEFVAEHLGFPVVLK--PLDGSGGRGVFL 173
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 28.5 bits (65), Expect = 3.8
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 58 AKTKKEAGEIAKKLNIKDIVLKAQVLAGGR 87
A+ EA +A+KL + +KA+ G+
Sbjct: 59 AEELAEAEALAEKLEGLTVTIKAKAGEDGK 88
>gnl|CDD|238858 cd01820, PAF_acetylesterase_like, PAF_acetylhydrolase (PAF-AH)_like
subfamily of SGNH-hydrolases. Platelet-activating factor
(PAF) and PAF-AH are key players in inflammation and in
atherosclerosis. PAF-AH is a calcium independent
phospholipase A2 which exhibits strong substrate
specificity towards PAF, hydrolyzing an acetyl ester at
the sn-2 position. PAF-AH also degrades a family of
oxidized PAF-like phospholipids with short sn-2
residues. In addition, PAF and PAF-AH are associated
with neural migration and mammalian reproduction.
Length = 214
Score = 29.2 bits (66), Expect = 4.0
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 17/67 (25%)
Query: 347 DPKVCAIMV--NIFGGIMRCDVIAEGIIAAAQELSLKIPIICRLQGTNVDDAKVLIASAA 404
+PKV +++ N G + IAEGI+A +E+ K+P +AK+L+
Sbjct: 89 NPKVVVLLIGTNNIGHTTTAEEIAEGILAIVEEIREKLP-----------NAKILL---- 133
Query: 405 MKILPCD 411
+ +LP
Sbjct: 134 LGLLPRG 140
>gnl|CDD|132312 TIGR03268, methan_mark_3, putative methanogenesis marker protein 3.
A single member of this protein family is found in each
of the first ten complete genome sequences of archaeal
methanogens, and nowhere else. This protein family was
detected by the method of partial phylogenetic profiling
(see Haft, et al., 2006). The functions of proteins in
this family are unknown, but their role is likely one
essential to methanogenesis [Energy metabolism,
Methanogenesis].
Length = 503
Score = 29.3 bits (66), Expect = 4.9
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 187 EPVDITVGITKEQALKVADA--------VGLKAKRDITAEMLIKMYALFISKDASLIEIN 238
E V + G T ALK +DA +K +++ E K Y + +K +IE+
Sbjct: 6 EEVTVPDGSTVRDALKASDAPYIEGATIGIIKGVQELERE--TKEYLIKTTKGEVVIELT 63
Query: 239 PYAEDA 244
P E
Sbjct: 64 PNTEAG 69
>gnl|CDD|227536 COG5211, SSU72, RNA polymerase II-interacting protein involved in
transcription start site selection [Transcription].
Length = 197
Score = 28.7 bits (64), Expect = 5.6
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 28 SQQKRNLNVHEHVSYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNI 73
S Q R++ H+ +L + G PV FG + GE K N+
Sbjct: 15 SNQNRSMETHD-----VLAKAGYPVKSFGTGSAVRLPGESIDKPNV 55
>gnl|CDD|107270 cd06275, PBP1_PurR, Ligand-binding domain of purine repressor,
PurR, which functions as the master regulatory protein
of de novo purine nucleotide biosynthesis in Escherichia
coli. Ligand-binding domain of purine repressor, PurR,
which functions as the master regulatory protein of de
novo purine nucleotide biosynthesis in Escherichia coli.
This dimeric PurR belongs to the LacI-GalR family of
transcription regulators and is activated to bind to DNA
operator sites by initially binding either of high
affinity corepressors, hypoxanthine or guanine. PurR is
composed of two functional domains: aan N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the sugar-binding domain
of ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the purine transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 269
Score = 28.4 bits (64), Expect = 7.0
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 365 DVIAEGIIAAAQELSLKIP 383
D++A G + AAQE L++P
Sbjct: 187 DLMAMGALCAAQEAGLRVP 205
>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX. The family
of proteins found in this equivalog include the
characterized LysX from Thermus thermophilus which is
part of a well-organized lysine biosynthesis gene
cluster. LysX is believed to carry out an ATP-dependent
acylation of the amino group of alpha-aminoadipate in
the prokaryotic version of the fungal AAA lysine
biosynthesis pathway. No species having a sequence in
this equivalog contains the elements of the more common
diaminopimelate lysine biosythesis pathway, and none has
been shown to be a lysine auxotroph. These sequences
have mainly recieved the name of the related enzyme,
"ribosomal protein S6 modification protein RimK". RimK
has been characterized in E. coli, and acts by
ATP-dependent condensation of S6 with glutamate
residues.
Length = 280
Score = 28.5 bits (64), Expect = 7.2
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 41 SYTLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGR 87
+Y L + G+P P +A ++ A ++A+ L +VLK + + GR
Sbjct: 91 TYLKLAKAGVPTPRTYLAFDREAALKLAEALGYP-VVLKPVIGSWGR 136
>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 = 28.4 bits (64), Expect = 7.3
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 43 TLLKEGGIPVPPFGVAKTKKEAGEIAKKLNIKDIVLKAQVLAGGRGKGAFKGGLKGGVKM 102
+K GIP + V +EA ++ IV+KA LA G+G V +
Sbjct: 110 DFMKRYGIPTAEYEVFTDPEEAKSYIQEKGAP-IVVKADGLAAGKG-----------VIV 157
Query: 103 VDTPEEAEEVAGKMI 117
T EEA + ++
Sbjct: 158 AKTNEEAIKAVEDIL 172
>gnl|CDD|107250 cd01537, PBP1_Repressors_Sugar_Binding_like, Ligand-binding domain
of the LacI-GalR family of transcription regulators and
the sugar-binding domain of ABC-type transport systems.
Ligand-binding domain of the LacI-GalR family of
transcription regulators and the sugar-binding domain of
ABC-type transport systems, all of which contain the
type I periplasmic binding protein-like fold. Their
specific ligands include lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars.
The LacI family of proteins consists of transcriptional
regulators related to the lac repressor; in general the
sugar binding domain in this family binds a sugar, which
in turn changes the DNA binding activity of the
repressor domain. The core structure of the periplasmic
binding proteins is classified into two types and they
differ in number and order of beta strands in each
domain: type I, which has six beta strands, and type II,
which has five beta strands. These two distinct
structural arrangements may have originated from a
common ancestor.
Length = 264
Score = 28.1 bits (63), Expect = 7.8
Identities = 23/110 (20%), Positives = 39/110 (35%), Gaps = 15/110 (13%)
Query: 282 VEAAKHSLNYIA--LDGSIGCLVNGAGLAMAT------MDIIKLHGGEPANFLDVGGGAT 333
+A + ++A I L G + A D +K G + G
Sbjct: 103 EQAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAGPIEIVLVQEGDWDA 162
Query: 334 AAQVKEAFKIITADPKVCAIMVNIFGGIMRCDVIAEGIIAAAQELSLKIP 383
+ A +++TA P AI D +A G + A +E L++P
Sbjct: 163 EKGYQAAEELLTAHPDPTAI---FAAN----DDMALGALRALREAGLRVP 205
>gnl|CDD|235083 PRK02889, tolB, translocation protein TolB; Provisional.
Length = 427
Score = 28.4 bits (64), Expect = 9.3
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 83 LAGGRGKGAF------KGGLKGGVKMVDTPEEAEEVAGKMIGDYLITKQTGEKG 130
LA GR F KG GG+ + T ++ A + I DY+ K TGE+G
Sbjct: 108 LADGRYDVRFRLYDTVKGQSLGGLSLTVTEDQLRLAAHR-IADYIYEKLTGERG 160
>gnl|CDD|107291 cd06296, PBP1_CatR_like, Ligand-binding domain of a LacI-like
transcriptional regulator, CatR which is involved in
catechol degradation. This group includes the
ligand-binding domain of a LacI-like transcriptional
regulator, CatR which is involved in catechol
degradation. This group belongs to the the LacI-GalR
family repressors that are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the sugar-binding domain of ABC-type
transport systems that contain the type I periplasmic
binding protein-like fold. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 270
Score = 28.0 bits (63), Expect = 9.3
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 365 DVIAEGIIAAAQELSLKIP 383
D++A G+ AA+E L+IP
Sbjct: 187 DLMALGVYEAARERGLRIP 205
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
0.318 0.134 0.375
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: 22,687,701
Number of extensions: 2306693
Number of successful extensions: 2456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2420
Number of HSP's successfully gapped: 73
Length of query: 443
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 343
Effective length of database: 6,502,202
Effective search space: 2230255286
Effective search space used: 2230255286
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.0 bits)