RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3769
(974 letters)
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 452 bits (1166), Expect = e-151
Identities = 166/328 (50%), Positives = 235/328 (71%), Gaps = 6/328 (1%)
Query: 1 MNIYEYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGI 60
MN++EYQ KE+ K+ V +P+GI+ +EA++AA+++GG WV+KAQ+HAGGRGK GG+
Sbjct: 1 MNLHEYQAKELFAKYGVPVPRGIVATTPEEAVEAAEELGGGVWVVKAQVHAGGRGKAGGV 60
Query: 61 KLAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQN 120
KLA+S E+ ++ K+ILGM L+T QT +G+ V VL+EE DI KE Y+S + DR +
Sbjct: 61 KLAKSPEEAREFAKQILGMTLVTHQTGPKGQPVNKVLVEEGADIAKEYYLSIVLDRATRR 120
Query: 121 IIFMGSNKGGMDIEIISKNSPELLYKTIIDPLIGLTKNNIDNISKKISIPKNSLINFYEE 180
++FM S +GGMDIE +++ +PE ++K IDPL GL I+ K+ +P + F +
Sbjct: 121 VVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQPFQAREIAFKLGLPGEQVKQFAKI 180
Query: 181 IQNIYKSYWETDSLLLEINPLVINSKNKIISLDIKFNFDTNALFRHPEIISYQYAHKKYI 240
+ +YK++ E D+ L+EINPLV+ +I+LD K NFD NALFRHP++ + +
Sbjct: 181 LMGLYKAFVEKDASLVEINPLVVTKDGDLIALDAKINFDDNALFRHPDLAELR-----DL 235
Query: 241 NKIDLMEIEASKFDLTYIPLNGNIGCLVNGAGLAMATMDTIKLFGGEPANFLDIGGGATI 300
++ D +E EASK+ L Y+ L+GNIGC+VNGAGLAMATMD IKL+GGEPANFLD+GGGAT
Sbjct: 236 SEEDPLEAEASKYGLNYVKLDGNIGCMVNGAGLAMATMDIIKLYGGEPANFLDVGGGATA 295
Query: 301 KTITEAFKIMMQQNNLKTILVNIF-GIT 327
+ + EAFKI++ N+K ILVNIF GIT
Sbjct: 296 ERVAEAFKIILSDPNVKAILVNIFGGIT 323
>gnl|CDD|180194 PRK05678, PRK05678, succinyl-CoA synthetase subunit alpha;
Validated.
Length = 291
Score = 435 bits (1122), Expect = e-146
Identities = 151/243 (62%), Positives = 182/243 (74%), Gaps = 5/243 (2%)
Query: 325 GITGKTGRFHTNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGATVSVI 384
GITGK G FHT L YG V GV P K G +P+F+TV A TGA SVI
Sbjct: 15 GITGKQGTFHTEQMLAYGT---NIVGGVTPGKGGTTVLGLPVFNTVAEAVEATGANASVI 71
Query: 385 YVPAIFATSAIWEAIESELELVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCPGLIV 444
YVP FA AI EAI++ ++L++CITEGIPV DML +K +++ KT L+GPNCPG+I
Sbjct: 72 YVPPPFAADAILEAIDAGIDLIVCITEGIPVLDMLEVKAYLER--KKTRLIGPNCPGIIT 129
Query: 445 PEEIKIGIMPGNIHKKGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPINGLKYI 504
P E KIGIMPG+IHKKGR+GVVSRSGTLTYE V QLT+LGFGQS+ VGIGGDPING +I
Sbjct: 130 PGECKIGIMPGHIHKKGRVGVVSRSGTLTYEAVAQLTDLGFGQSTCVGIGGDPINGTNFI 189
Query: 505 DILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIKKNMKKPVIGFIAGITAPPGKRMGHAG 564
D+L+ F ED T+A++MIGEIGG E AA +IK N+ KPV+G+IAG+TAPPGKRMGHAG
Sbjct: 190 DVLEAFEEDPETEAIVMIGEIGGSAEEEAAEYIKANVTKPVVGYIAGVTAPPGKRMGHAG 249
Query: 565 ALI 567
A+I
Sbjct: 250 AII 252
>gnl|CDD|130091 TIGR01019, sucCoAalpha, succinyl-CoA synthetase, alpha subunit.
This model describes succinyl-CoA synthetase alpha
subunits but does not discriminate between GTP-specific
and ATP-specific reactions. The model is designated as
subfamily rather than equivalog for that reason. ATP
citrate lyases appear to form an outgroup [Energy
metabolism, TCA cycle].
Length = 286
Score = 371 bits (955), Expect = e-121
Identities = 150/243 (61%), Positives = 181/243 (74%), Gaps = 5/243 (2%)
Query: 325 GITGKTGRFHTNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGATVSVI 384
GITG G FHT L YG V GV P K G +P+FD+VK A ETGA SVI
Sbjct: 13 GITGSQGSFHTEQMLAYGTN---IVGGVTPGKGGTTVLGLPVFDSVKEAVEETGANASVI 69
Query: 385 YVPAIFATSAIWEAIESELELVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCPGLIV 444
+VPA FA AI+EAI++ +EL++CITEGIPV DML +K M S T L+GPNCPG+I
Sbjct: 70 FVPAPFAADAIFEAIDAGIELIVCITEGIPVHDMLKVKRYM--EESGTRLIGPNCPGIIT 127
Query: 445 PEEIKIGIMPGNIHKKGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPINGLKYI 504
P E KIGIMPG+IHK G +G+VSRSGTLTYE V QLT+ GFGQS+ VGIGGDP+NG +I
Sbjct: 128 PGECKIGIMPGHIHKPGNVGIVSRSGTLTYEAVHQLTKAGFGQSTCVGIGGDPVNGTSFI 187
Query: 505 DILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIKKNMKKPVIGFIAGITAPPGKRMGHAG 564
D+L+ F +D T+A++MIGEIGG E AA++IK+NM KPV+GFIAG TAPPGKRMGHAG
Sbjct: 188 DVLEAFEKDPETEAIVMIGEIGGSAEEEAADFIKQNMSKPVVGFIAGATAPPGKRMGHAG 247
Query: 565 ALI 567
A+I
Sbjct: 248 AII 250
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 373 bits (960), Expect = e-121
Identities = 149/327 (45%), Positives = 219/327 (66%), Gaps = 10/327 (3%)
Query: 1 MNIYEYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGI 60
MN++EYQ KE+ K+ + +P G + + +EA +AAK++GG V+KAQ+HAGGRGK GG+
Sbjct: 1 MNLHEYQAKELFAKYGIPVPPGYVATSPEEAEEAAKELGGGPVVVKAQVHAGGRGKAGGV 60
Query: 61 KLAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYID-IKKELYISFMTDRVQQ 119
KLA+S E+ ++ ++ILG QT+ +GE V VL+EE +D IKKE Y+S + DR +
Sbjct: 61 KLAKSPEEAKEAAEEILGK---NYQTDIKGEPVNKVLVEEAVDIIKKEYYLSIVLDRSSR 117
Query: 120 NIIFMGSNKGGMDIEIISKNSPELLYKTIIDPLIGLTKNNIDNISKKISIPKNSLINFYE 179
+ M S +GGMDIE +++ +PE + K +DPL GL ++ K+ + + +
Sbjct: 118 RPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLRPYQARELAFKLGLEGELVKQVAD 177
Query: 180 EIQNIYKSYWETDSLLLEINPLVINSKN-KIISLDIKFNFDTNALFRHPEIISYQYAHKK 238
I+ +YK + E D+ L+EINPLV+ +++LD K D NALFRHP++ A +
Sbjct: 178 IIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNALFRHPDL-----AELR 232
Query: 239 YINKIDLMEIEASKFDLTYIPLNGNIGCLVNGAGLAMATMDTIKLFGGEPANFLDIGGGA 298
++ D E EAS + L Y+ L+GNIGC+VNGAGLAMATMD +KL+GG+PANFLD+GGGA
Sbjct: 233 DESEEDPREAEASGYGLNYVELDGNIGCIVNGAGLAMATMDIVKLYGGKPANFLDVGGGA 292
Query: 299 TIKTITEAFKIMMQQNNLKTILVNIFG 325
T + + EAFK+++ N+K I VNIFG
Sbjct: 293 TAERVKEAFKLILSDPNVKAIFVNIFG 319
>gnl|CDD|223152 COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy
production and conversion].
Length = 293
Score = 368 bits (948), Expect = e-120
Identities = 146/252 (57%), Positives = 177/252 (70%), Gaps = 6/252 (2%)
Query: 321 VNIFGITGKTGRFHTNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGAT 380
V + GITGK G FHT L YG V GV P K GQ +P+F+TV+ A ETGA
Sbjct: 11 VIVQGITGKQGTFHTEQMLAYGT---KIVGGVTPGKGGQTILGLPVFNTVEEAVKETGAN 67
Query: 381 VSVIYVPAIFATSAIWEAIESELELVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCP 440
SVI+VP FA AI EAI++ ++LV+ ITEGIPV DML LK ++ T L+GPNCP
Sbjct: 68 ASVIFVPPPFAADAILEAIDAGIKLVVIITEGIPVLDMLELKRYARE--KGTRLIGPNCP 125
Query: 441 GLIVPEEIKIGIMPGNIHKKGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPING 500
G+I P E KIGIMPGNI+K G IG+VSRSGTLTYE V QLTE G GQS+A+GIGGDPI G
Sbjct: 126 GIITPGECKIGIMPGNIYKPGNIGIVSRSGTLTYEAVSQLTEAGLGQSTAIGIGGDPIPG 185
Query: 501 LKYIDILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIKKNMK-KPVIGFIAGITAPPGKR 559
+ID L++F D T+A++MIGEIGG E AA +IK N KPV+ +IAG TAP GKR
Sbjct: 186 TSFIDALEMFEADPETEAIVMIGEIGGPAEEEAAEYIKANATRKPVVAYIAGRTAPEGKR 245
Query: 560 MGHAGALITEIK 571
MGHAGA+++ K
Sbjct: 246 MGHAGAIVSGGK 257
>gnl|CDD|240307 PTZ00187, PTZ00187, succinyl-CoA synthetase alpha subunit;
Provisional.
Length = 317
Score = 351 bits (903), Expect = e-113
Identities = 152/247 (61%), Positives = 179/247 (72%), Gaps = 7/247 (2%)
Query: 325 GITGKTGRFHTNLCLNYGNGKKAFVAGVNPKKNGQKFEE--IPIFDTVKNAKNETGATVS 382
GITGK G FHT + YG V GVNPKK G + +P+F TVK AK TGA S
Sbjct: 36 GITGKQGTFHTEQAIEYGT---KMVGGVNPKKAGTTHLKHGLPVFATVKEAKKATGADAS 92
Query: 383 VIYVPAIFATSAIWEAIESELELVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCPGL 442
VIYVP A SAI EAIE+E+ LV+CITEGIP DM+ +K + +KT L+GPNCPG+
Sbjct: 93 VIYVPPPHAASAIIEAIEAEIPLVVCITEGIPQHDMVKVK-HALLSQNKTRLIGPNCPGI 151
Query: 443 IVPEEIKIGIMPGNIHKKGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPINGLK 502
I P E KIGIMPG+IHKKG+IG+VSRSGTLTYE V Q T +G GQS+ VGIGGDP NG
Sbjct: 152 IKPGECKIGIMPGHIHKKGKIGIVSRSGTLTYEAVAQTTAVGLGQSTCVGIGGDPFNGTN 211
Query: 503 YIDILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIKKN-MKKPVIGFIAGITAPPGKRMG 561
+ID LKLF D T+ +I+IGEIGG E AA WIK N +KKPV+ FIAGITAPPG+RMG
Sbjct: 212 FIDCLKLFLNDPETEGIILIGEIGGTAEEEAAEWIKNNPIKKPVVSFIAGITAPPGRRMG 271
Query: 562 HAGALIT 568
HAGA+I+
Sbjct: 272 HAGAIIS 278
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 349 bits (898), Expect = e-112
Identities = 138/327 (42%), Positives = 217/327 (66%), Gaps = 6/327 (1%)
Query: 1 MNIYEYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGI 60
M+I+EYQ KE+L F V +P+G L + ++A+ A+++GG WV+KAQIH+G RGK GGI
Sbjct: 1 MDIHEYQAKELLASFGVAVPRGALAYSPEQAVYRARELGGWHWVVKAQIHSGARGKAGGI 60
Query: 61 KLAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQN 120
KL ++ +V + +LG +L+T QT EG+ V V +E I++ELY+ F+ DR +
Sbjct: 61 KLCRTYNEVRDAAEDLLGKKLVTHQTGPEGKPVQRVYVETADPIERELYLGFVLDRKSER 120
Query: 121 IIFMGSNKGGMDIEIISKNSPELLYKTIIDPLIGLTKNNIDNISKKISIPKNSLINFYEE 180
+ + S +GGM+IE I+ PE + + +++P +GL + I+ + + + +
Sbjct: 121 VRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVGLQQFQAREIAFGLGLDIKQVSRAVKT 180
Query: 181 IQNIYKSYWETDSLLLEINPLVINSKNKIISLDIKFNFDTNALFRHPEIISYQYAHKKYI 240
I Y+++ + D+ +LEINPLV+ +++++LD K +FD NALFR P I A +
Sbjct: 181 IMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFRRPNI-----AEMRDP 235
Query: 241 NKIDLMEIEASKFDLTYIPLNGNIGCLVNGAGLAMATMDTIKLFGGEPANFLDIGGGATI 300
++ D E +A++ L+Y+ L+G+IGC+VNGAGLAMATMD IKL GGEPANFLD+GGGA+
Sbjct: 236 SQEDPREAQAAEHGLSYVGLDGDIGCIVNGAGLAMATMDMIKLAGGEPANFLDVGGGASP 295
Query: 301 KTITEAFKIMMQQNNLKTILVNIF-GI 326
+ + +AF++++ N+K ILVNIF GI
Sbjct: 296 ERVAKAFRLVLSDRNVKAILVNIFAGI 322
>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 = 343 bits (881), Expect = e-109
Identities = 146/326 (44%), Positives = 217/326 (66%), Gaps = 7/326 (2%)
Query: 1 MNIYEYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGI 60
MN++EYQ K+I K+ + +P+G + +V+EA + A K+G V+KAQ+HAGGRGK GG+
Sbjct: 1 MNLHEYQAKQIFAKYGIPVPRGYVATSVEEAEEIAAKLGAGPVVVKAQVHAGGRGKAGGV 60
Query: 61 KLAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQN 120
K+A+S E+ +K+LG +L+T+QT+ G+ V +LIEE DI KE Y+S + DR +
Sbjct: 61 KVAKSKEEARAAAEKLLGKELVTNQTDPLGQPVNKILIEEATDIDKEYYLSIVIDRSARC 120
Query: 121 IIFMGSNKGGMDIEIISKNSPELLYKTIIDPLIGLTKNNIDNISKKISIPKNSLINFYEE 180
+ M S +GG+DIE +++ SPE + K IDPL GL I+KK+ + + +
Sbjct: 121 PVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGLLPYQAREIAKKLGLEGELVKQVADI 180
Query: 181 IQNIYKSYWETDSLLLEINPLVINSKNKIISLDIKFNFDTNALFRHPEIIS-YQYAHKKY 239
I+ +Y+ + E D+ L+EINPLVI +I+LD K D NALFRHP++ Y+ +
Sbjct: 181 IKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRHPDLEEMRDYSQE-- 238
Query: 240 INKIDLMEIEASKFDLTYIPLNGNIGCLVNGAGLAMATMDTIKLFGGEPANFLDIGGGAT 299
D E+ A ++ L Y+ L+GNIGC+VNGAGLAMATMD IKL+GGEPANFLD+GGGA+
Sbjct: 239 ----DPREVLAKQWGLNYVALDGNIGCMVNGAGLAMATMDIIKLYGGEPANFLDVGGGAS 294
Query: 300 IKTITEAFKIMMQQNNLKTILVNIFG 325
+ + EA K+++ ++K + +NIFG
Sbjct: 295 AERVREALKLVLSDKSVKVVFINIFG 320
>gnl|CDD|215066 PLN00125, PLN00125, Succinyl-CoA ligase [GDP-forming] subunit
alpha.
Length = 300
Score = 304 bits (779), Expect = 1e-95
Identities = 143/245 (58%), Positives = 179/245 (73%), Gaps = 5/245 (2%)
Query: 325 GITGKTGRFHTNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGATVSVI 384
GITGK G FHT + YG V GV PKK G + +P+F+TV AK ET A SVI
Sbjct: 19 GITGKNGTFHTEQAIEYGT---KMVGGVTPKKGGTEHLGLPVFNTVAEAKAETKANASVI 75
Query: 385 YVPAIFATSAIWEAIESELELVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCPGLIV 444
YVP FA +AI EA+E+EL+LV+CITEGIP DM+ +K + + SKT L+GPNCPG+I
Sbjct: 76 YVPPPFAAAAILEAMEAELDLVVCITEGIPQHDMVRVKAALNRQ-SKTRLIGPNCPGIIK 134
Query: 445 PEEIKIGIMPGNIHKKGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPINGLKYI 504
P E KIGIMPG IHK GRIG+VSRSGTLTYE V Q T +G GQS+ VGIGGDP NG ++
Sbjct: 135 PGECKIGIMPGYIHKPGRIGIVSRSGTLTYEAVFQTTAVGLGQSTCVGIGGDPFNGTNFV 194
Query: 505 DILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIKKN-MKKPVIGFIAGITAPPGKRMGHA 563
D L+ F +D T+ +I+IGEIGG E AA +IK++ +KPV+ FIAG+TAPPG+RMGHA
Sbjct: 195 DCLEKFVKDPQTEGIILIGEIGGTAEEDAAAFIKESGTEKPVVAFIAGLTAPPGRRMGHA 254
Query: 564 GALIT 568
GA+++
Sbjct: 255 GAIVS 259
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 278 bits (712), Expect = 2e-84
Identities = 128/334 (38%), Positives = 196/334 (58%), Gaps = 15/334 (4%)
Query: 1 MNIYEYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKI--GGNSWVIKAQIHAGGRGKC- 57
+NI+EYQG E++ K+ V +PKG ++DE KA +K+ V+K+QI AGGRG
Sbjct: 28 LNIHEYQGAELMSKYGVNVPKGAAASSLDEVKKALEKMFPDEGEVVVKSQILAGGRGLGT 87
Query: 58 ------GGIKLAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYIS 111
GG+ + + ++ E+ K+LG L+T QT G+ V V + E + + E+Y +
Sbjct: 88 FKNGLKGGVHIVKK-DKAEELAGKMLGQILVTKQTGPAGKPVNKVYLCEKMSLVNEMYFA 146
Query: 112 FMTDRVQQNIIFMGSNKGGMDIEIISKNSPELLYKTIIDPLIGLTKNNIDNISKKISIPK 171
+ DR + + +KGG IE +++ PE + K ID G+T + + ++
Sbjct: 147 ILLDRASAGPLIIACSKGGTSIEDLAEKFPEKIIKVPIDIFKGITDEDAAKVVDGLAPKV 206
Query: 172 NSLINFYEEIQNIYKSYWETDSLLLEINPLVINSKNKIISLDIKFNFDTNALFRHPEIIS 231
+ E+++ +YK + + D ++EINPL + ++++ D K NFD NA FR EI +
Sbjct: 207 ADRNDAIEQVKKLYKLFCKCDCTMVEINPLAETADGQLVAADAKLNFDDNAAFRQKEIFA 266
Query: 232 YQYAHKKYINKIDLMEIEASKFDLTYIPLNGNIGCLVNGAGLAMATMDTIKLFGGEPANF 291
+ ++ D E+ A+K DL YI L+G IGC+VNGAGLAMATMD IKL GG PANF
Sbjct: 267 -----LRDTSQEDPREVAAAKADLNYIGLDGEIGCMVNGAGLAMATMDIIKLHGGSPANF 321
Query: 292 LDIGGGATIKTITEAFKIMMQQNNLKTILVNIFG 325
LD+GG A+ + + EAFKI+ + +K ILVNIFG
Sbjct: 322 LDVGGNASEQQVVEAFKILTSDDKVKAILVNIFG 355
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 231 bits (592), Expect = 3e-70
Identities = 87/202 (43%), Positives = 134/202 (66%)
Query: 2 NIYEYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIK 61
N++EYQ KE+L K+ V +P+G + + +EA +AAKK+GG WV+KAQ+ AGGRGK GG+K
Sbjct: 1 NLHEYQAKELLAKYGVPVPRGEVAFSPEEAEEAAKKLGGKVWVVKAQVLAGGRGKAGGVK 60
Query: 62 LAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNI 121
LA+S E+ ++ K++LG L+T QT EG+ V VL+EE +DI +E Y+S + DR +
Sbjct: 61 LAKSPEEAKEAAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSIVLDRASRGP 120
Query: 122 IFMGSNKGGMDIEIISKNSPELLYKTIIDPLIGLTKNNIDNISKKISIPKNSLINFYEEI 181
+ + S +GG+DIE ++ +PE ++K IDP GLT I+ K+ + + + I
Sbjct: 121 VLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLTPYQAREIAFKLGLEGELVKQAADII 180
Query: 182 QNIYKSYWETDSLLLEINPLVI 203
+ +YK + E D+ L+EINPLV
Sbjct: 181 KKLYKLFVERDATLVEINPLVE 202
>gnl|CDD|163429 TIGR03717, R_switched_YjbE, integral membrane protein, YjbE family.
Rfam model RF00080 describes a structured RNA element
called the yybP-ykoY leader, or SraF, which may precede
one or several genes in a genome. Members of this highly
hydrophobic protein family commonly are preceded by a
yybP-ykoY leader, which may serve as a riboswitch. From
the larger group of TerC homologs (pfam03741), this
subfamily contains protein YjbE from Bacillus subtilis.
A transport function is proposed.
Length = 176
Score = 191 bits (487), Expect = 4e-56
Identities = 82/181 (45%), Positives = 120/181 (66%), Gaps = 7/181 (3%)
Query: 583 SIIQIILIDILLGSTDAIIIALACRNLQPNIRTKGIIFGTFGAIAIRIILVIFSINLLNL 642
+++QII ID++LG +A++IALA RNL + R K I +GT GAI +RI+L ++ LL +
Sbjct: 1 ALLQIIAIDLVLGGDNAVVIALAARNLPAHQRKKAIFWGTAGAIVLRILLTAVAVYLLAI 60
Query: 643 KYIKIIGGFLLFWISIKLLSNDHNYTT--IASGKNLIHAIKTIIFADLIMSIDNVLAIAG 700
++K+IGG LL WI KLL + + L AIKTI+ AD +MS+DNVLA+AG
Sbjct: 61 PFLKLIGGLLLLWIGWKLLLEEEEEQGGDVKGSTTLWAAIKTIVIADAVMSLDNVLAVAG 120
Query: 701 TASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSGNMIFS 760
A + L+I G+L SIPII++GS L+L L+++F II + + LLGY++G MI +
Sbjct: 121 AA-----HGHLGLLIFGLLLSIPIIVWGSTLILKLMDRFPWIIYIGAALLGYVAGEMIVT 175
Query: 761 D 761
D
Sbjct: 176 D 176
>gnl|CDD|217707 pfam03741, TerC, Integral membrane protein TerC family. This
family contains a number of integral membrane proteins
that also contains the TerC protein. TerC has been
implicated in resistance to tellurium. This protein may
be involved in efflux of tellurium ions. The
tellurite-resistant Escherichia coli strain KL53 was
found during testing of the group of clinical isolates
for antibiotics and heavy metal ion resistance.
Determinant of the tellurite resistance of the strain
was located on a large conjugative plasmid. Analyses
showed, the genes terB, terC, terD and terE are
essential for conservation of the resistance. The
members of the family contain a number of conserved
aspartates that could be involved in binding to metal
ions.
Length = 184
Score = 129 bits (328), Expect = 2e-34
Identities = 55/190 (28%), Positives = 93/190 (48%), Gaps = 19/190 (10%)
Query: 585 IQIILIDILLGSTDAIIIALACRNLQPNIRTKGIIFGTFGAIAIRIILVIFSINLLNL-K 643
+ + L++I L +A +IAL R L P + K + +G GA+ +RIIL++ LL L
Sbjct: 1 LTLYLLEISLSVDNAFVIALIFRKLPPEQQKKALFWGIIGALVLRIILILLGSALLELFD 60
Query: 644 YIKIIGGFLLFWISIKLLSNDHNY------------TTIASGKNLIHAIKTIIFADLIMS 691
+I +IGG L + +IKLL + + +L A+ I ADL+ S
Sbjct: 61 WILLIGGAFLLYTAIKLLRENEEDDEENKIVRELKKVLPVTSSSLWLAVIQIELADLVFS 120
Query: 692 IDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLG 751
+D+V A G +VI G +F+I + F + L+ LIE+F + L + +LG
Sbjct: 121 LDSVPAAVGITDDP------FIVITGNIFAILGLRFLAFLLAKLIERFPYLKYLAAAILG 174
Query: 752 YLSGNMIFSD 761
++ ++
Sbjct: 175 FIGVKLLLEG 184
Score = 30.5 bits (70), Expect = 3.0
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 13/87 (14%)
Query: 582 ISIIQIILIDILLGSTDAIIIALACRNLQPNIRTKGIIFGTFGAIAIRIILVIFSINLLN 641
+++IQI L D++ S D++ A+ I I T AI + L + L
Sbjct: 107 LAVIQIELADLVF-SLDSVPAAVG-------ITDDPFIVITGNIFAI-LGLRFLAFLLAK 157
Query: 642 L----KYIKIIGGFLLFWISIKLLSND 664
L Y+K + +L +I +KLL
Sbjct: 158 LIERFPYLKYLAAAILGFIGVKLLLEG 184
>gnl|CDD|223930 COG0861, TerC, Membrane protein TerC, possibly involved in
tellurium resistance [Inorganic ion transport and
metabolism].
Length = 254
Score = 123 bits (311), Expect = 2e-31
Identities = 54/221 (24%), Positives = 100/221 (45%), Gaps = 27/221 (12%)
Query: 575 FLTASNGISIIQIILIDILLGSTDAIIIALACRNLQPNIRTKGIIFGTFGAIAIRIILVI 634
+ ++++ +IL++I+LG +AI+IA+ L P R K + G GA+ +RIIL+
Sbjct: 11 LADPAAWVALLTLILLEIVLGIDNAIVIAILASKLPPKQRKKALFIGLAGALVLRIILLA 70
Query: 635 FSINLLNL-KYIKIIGGFLLFWISIKLL------------------SNDHNYTT--IASG 673
LL L + + I G L W IKLL + + +
Sbjct: 71 SISWLLTLTQPLLYIFGLYLLWRDIKLLLGGLFLLFKATKELHERLEGEEFFVNGKLKKA 130
Query: 674 KNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVL 733
AI I ADL+ S+D+V+A G A +++ ++F+I ++ F + L+
Sbjct: 131 TPFWGAIIQIELADLVFSLDSVIAAVGMAGHP------FVMVTAVIFAILVMRFAAFLLA 184
Query: 734 ILIEKFSSIIILCSILLGYLSGNMIFSDQSLTQLQINKLLI 774
L+E+ ++ L ++L ++ +I + I K +
Sbjct: 185 RLLERHPTLKYLALVILLFIGVKLILEGLAHFGFHIPKGYL 225
Score = 33.0 bits (76), Expect = 0.56
Identities = 24/112 (21%), Positives = 46/112 (41%), Gaps = 9/112 (8%)
Query: 582 ISIIQIILIDILLGSTDAIIIALACRNLQPNIRTKGIIFGTFGAIAIRIILVIFSINLLN 641
+IIQI L D++ S D++I A+ P + ++ AI + LL
Sbjct: 135 GAIIQIELADLVF-SLDSVIAAVGMAG-HPFV----MVTAVIFAILVMRFAAFLLARLLE 188
Query: 642 -LKYIKIIGGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSI 692
+K + +L +I +KL+ + K ++ + F+ LI +
Sbjct: 189 RHPTLKYLALVILLFIGVKLILEGLAHFGFHIPKGYLYL--AVGFSVLIELL 238
>gnl|CDD|214881 smart00881, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 100
Score = 94.1 bits (235), Expect = 5e-23
Identities = 40/101 (39%), Positives = 56/101 (55%), Gaps = 2/101 (1%)
Query: 313 QNNLKTILVNIFGITGKTGRFHTNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKN 372
N ++ V G +G G F + N FV GV P K G K + +P++D+V
Sbjct: 2 LNPNTSVAV--VGASGNLGSFGLAVMRNLLEYGTKFVGGVYPGKVGPKVDGVPVYDSVAE 59
Query: 373 AKNETGATVSVIYVPAIFATSAIWEAIESELELVICITEGI 413
A ETG V+VI+VPA A AI EAIE+ ++ ++ ITEGI
Sbjct: 60 APEETGVDVAVIFVPAEAAPDAIDEAIEAGIKGIVVITEGI 100
>gnl|CDD|234650 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 172
Score = 94.4 bits (236), Expect = 3e-22
Identities = 34/126 (26%), Positives = 62/126 (49%), Gaps = 3/126 (2%)
Query: 841 DHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGN 900
+ L+ +G ++ A+GI G + +K F D F + ++I + + H
Sbjct: 5 EDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLL--GKGGEWQEVEIESGRFHKG 62
Query: 901 YVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTV 960
+++ G+ DRN A L+G L + + P+L D +YW +LI V + G+ LG V
Sbjct: 63 FLIVKFEGVDDRNAAEALKGCELFVPRSQLPEL-EEDEYYWHDLIGLEVVDEDGEELGKV 121
Query: 961 TEIIQN 966
T+I++
Sbjct: 122 TDILET 127
>gnl|CDD|233805 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM. This family
consists of the bacterial protein RimM (YfjA, 21K), a
30S ribosomal subunit-binding protein implicated in 16S
ribsomal RNA processing. It has been partially
characterized in Escherichia coli, is found with other
translation-associated genes such as trmD. It is broadly
distributed among bacteria, including some minimal
genomes such the aphid endosymbiont Buchnera aphidicola.
The protein contains a PRC-barrel domain that it shares
with other protein families (pfam05239) and a unique
domain (pfam01782). This model describes the full-length
protein. A member from Arabidopsis (plant) has
additional N-terminal sequence likely to represent a
chloroplast transit peptide [Transcription, RNA
processing].
Length = 165
Score = 92.7 bits (231), Expect = 1e-21
Identities = 33/125 (26%), Positives = 55/125 (44%), Gaps = 2/125 (1%)
Query: 843 LITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYV 902
L+ +G + +GI G + +K F D F + + ++K+ + N +
Sbjct: 1 LLVVGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGSK-QWQTVKVARVRKQNNKL 59
Query: 903 LANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTE 962
+ GI DR A L+G L + P+L D +YW +LI V G+ LG V E
Sbjct: 60 IVKFEGIDDREAAEALKGLELFVPREALPEL-EEDEYYWTDLIGLEVVTEEGEELGKVVE 118
Query: 963 IIQNK 967
I++
Sbjct: 119 ILETG 123
>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 = 86.9 bits (216), Expect = 4e-20
Identities = 29/108 (26%), Positives = 44/108 (40%), Gaps = 6/108 (5%)
Query: 466 VSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPINGLKYIDILKLFNEDQNTDAVIMIGEI 525
+ GTL E + + G G + + +GGD ID LKL D +++ +
Sbjct: 1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVL 60
Query: 526 G-GLDEIYAANWIK-----KNMKKPVIGFIAGITAPPGKRMGHAGALI 567
G G E A +K + + PV+ + G A P R A AL
Sbjct: 61 GYGACEDPAGGLLKAIKEARARELPVVARVCGTEADPQGREEQAKALA 108
Score = 69.6 bits (171), Expect = 4e-14
Identities = 28/60 (46%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 267 LVNGAGLAMATMDTIKLFGGEPANFLDIGGGATIKT-ITEAFKIMMQQNNLKTILVNIFG 325
LVNG LAM MD IKL GG P NF+D+GG A T +A K+ +K IL++I
Sbjct: 1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVL 60
>gnl|CDD|234588 PRK00040, rpsP, 30S ribosomal protein S16; Reviewed.
Length = 75
Score = 82.5 bits (205), Expect = 2e-19
Identities = 28/55 (50%), Positives = 36/55 (65%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLI 844
DSR+ RDGRFIER+GFYNPLA E++ K+ R YW GA+ + TV L+
Sbjct: 21 VADSRSPRDGRFIERVGFYNPLAKPAEEEVKLDEERVLYWLGQGAQPTDTVRRLL 75
>gnl|CDD|223877 COG0806, RimM, RimM protein, required for 16S rRNA processing
[Translation, ribosomal structure and biogenesis].
Length = 174
Score = 83.0 bits (206), Expect = 3e-18
Identities = 37/124 (29%), Positives = 62/124 (50%), Gaps = 2/124 (1%)
Query: 843 LITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYV 902
L+ +G ++ +GI G + +K F D F W + + + + + H N +
Sbjct: 7 LLLVGKIVSTHGIRGEVRVKSFTDFPESLF-DYGPWLLLKPGGEWQELTVESVRKHKNLL 65
Query: 903 LANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTE 962
+ GI DRN A L+GY + + ++ P+L D FY+ +LI V G+LLG VTE
Sbjct: 66 ILKFKGIDDRNAAEALKGYEIFVDRSELPEL-EEDEFYYHDLIGLEVVTEDGELLGKVTE 124
Query: 963 IIQN 966
I++
Sbjct: 125 ILET 128
>gnl|CDD|202320 pfam02629, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 96
Score = 75.3 bits (186), Expect = 2e-16
Identities = 32/92 (34%), Positives = 50/92 (54%), Gaps = 5/92 (5%)
Query: 323 IFGITGKTGR--FHTNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGAT 380
+ G G + +H L YG V GVNP+K G + IP++ +V + +TG
Sbjct: 8 VIGAGGLGIQGLYHFIQLLGYGI---KMVFGVNPRKGGTEVGGIPVYKSVDELEEDTGVD 64
Query: 381 VSVIYVPAIFATSAIWEAIESELELVICITEG 412
V+VI VPA FA AI E +++ ++ ++ IT G
Sbjct: 65 VAVITVPAPFAQEAIDELVDAGIKGIVNITPG 96
>gnl|CDD|216173 pfam00886, Ribosomal_S16, Ribosomal protein S16.
Length = 61
Score = 73.6 bits (182), Expect = 3e-16
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTS 837
DSR+ RDGRFIE +G YNP+A +E + K+ R YW GA+ +
Sbjct: 14 VADSRSPRDGRFIEELGTYNPIAKPQEPEVKLDEERIKYWLGKGAQPT 61
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 82.6 bits (204), Expect = 4e-16
Identities = 71/247 (28%), Positives = 116/247 (46%), Gaps = 30/247 (12%)
Query: 345 KKAFVAG-VNPKKNG-QKF----EEI--PIFDTVKNA-KNETGATVSVIYVPAIFATSAI 395
+ VAG +NP G QK EEI P+ +++ A K A V + + A ++
Sbjct: 36 ETPSVAGIINPGSEGFQKLFFGQEEIAIPVHGSIEAACKAHPTADVFINFASFRSAAASS 95
Query: 396 WEAIESE-LELVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCPGLIVPEEIKIG--- 451
EA++ + +V I EG+P D L + NN +++GP G I KIG
Sbjct: 96 MEALKQPTIRVVAIIAEGVPESDTKQLIAYARANNK--VVIGPATVGGIQAGAFKIGDTA 153
Query: 452 -----IMPGNIHKKGRIGVVSRSGTLT---YEVVCQLTELGFGQSSAVGIGGDPINGLKY 503
I+ +++ G +G VS+SG ++ Y V+ ++T+ G + IGGD G
Sbjct: 154 GTLDNIIQCKLYRPGSVGFVSKSGGMSNEMYNVIARVTD---GIYEGIAIGGDVFPGSTL 210
Query: 504 IDILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIK-KNMKKPVIGFIAGITA---PPGKR 559
D + FN ++++GE+GG DE +K + KPV+ +++G A +
Sbjct: 211 SDHVLRFNNIPQIKMIVVLGELGGRDEYSLVEALKQGKVSKPVVAWVSGTCARLFKSEVQ 270
Query: 560 MGHAGAL 566
GHAGA
Sbjct: 271 FGHAGAK 277
>gnl|CDD|223306 COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 69.6 bits (171), Expect = 1e-14
Identities = 28/56 (50%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLIT 845
DSR+ RDGRFIER+G YNPL KE++ K+ R YW GA+ S TV L+
Sbjct: 21 VADSRSPRDGRFIERLGTYNPL-LGKEERVKLDEERILYWLSQGAQPSDTVRRLLK 75
>gnl|CDD|172989 PRK14523, rpsP, 30S ribosomal protein S16; Provisional.
Length = 137
Score = 66.4 bits (161), Expect = 7e-13
Identities = 26/53 (49%), Positives = 37/53 (69%)
Query: 792 DSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLI 844
D R RDGRFIER+G+YNP+A ++ + ++ R ++W GA+TSL V HLI
Sbjct: 23 DRRKPRDGRFIERVGYYNPMARGQDIRLQLEKERISHWLNQGAQTSLRVKHLI 75
>gnl|CDD|216696 pfam01782, RimM, RimM N-terminal domain. The RimM protein is
essential for efficient processing of 16S rRNA. The RimM
protein was shown to have affinity for free ribosomal
30S subunits but not for 30S subunits in the 70S
ribosomes. This N-terminal domain is found associated
with a PRC-barrel domain.
Length = 84
Score = 60.6 bits (148), Expect = 2e-11
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 846 IGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLAN 905
+G ++ +G+ G + +K F D F WF + + + + + H ++
Sbjct: 2 VGKIVGTHGLKGEVKVKSFTDFPEAIF-DYGPWFLLKKKGEWKPLTVESVRLHKKGLIVK 60
Query: 906 LYGITDRNLATKLQGYYLKISIND 929
G+ DR+ A L+G L + +D
Sbjct: 61 FEGVDDRDAAEALKGAELYVPRSD 84
>gnl|CDD|129114 TIGR00002, S16, ribosomal protein S16. This model describes
ribosomal S16 of bacteria and organelles [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 78
Score = 59.9 bits (146), Expect = 3e-11
Identities = 26/56 (46%), Positives = 36/56 (64%), Gaps = 2/56 (3%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLIT 845
DSR+ RDGR+IE +GFYNPL KE + K+ + R YW GA+ + TV +L+
Sbjct: 20 VADSRSRRDGRYIEELGFYNPL--TKESRVKLNVERIKYWLSKGAQPTDTVRNLLK 73
>gnl|CDD|172991 PRK14525, rpsP, 30S ribosomal protein S16; Provisional.
Length = 88
Score = 59.2 bits (143), Expect = 6e-11
Identities = 22/55 (40%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLI 844
ATDSRN+RDG+++E +G Y+P +K+ ++ ++ + R +W + GAK S TV ++
Sbjct: 22 ATDSRNARDGKYLEDVGIYDP--TKRPERIELKVERIEHWLKAGAKPSQTVAMIL 74
>gnl|CDD|234326 TIGR03716, R_switched_YkoY, integral membrane protein, YkoY family.
Rfam model RF00080 describes a structured RNA element
called the yybP-ykoY leader, or SraF, which may precede
one or several genes in a genome. Members of this highly
hydrophobic protein family often are preceded by a
yybP-ykoY leader, which may serve as a riboswitch. From
the larger group of TerC homologs (pfam03741), this
subfamily contains proteins YceF and YkoY from Bacillus
subtilis. A transport function is proposed.
Length = 215
Score = 59.2 bits (144), Expect = 1e-09
Identities = 37/188 (19%), Positives = 84/188 (44%), Gaps = 12/188 (6%)
Query: 588 ILIDILLGSTDAIIIALACRNLQPNIRTKGIIFGTFGAIAIRIILVIFSINLLNLKYIKI 647
++++ LL + +A+++A+ ++L R K + +G GA R I + + L+ +IK
Sbjct: 1 VILEGLLSADNALVLAVMVKHLPEKQRKKALFYGLIGAYVFRFIALFLASFLIKFWWIKA 60
Query: 648 IGGFLLFWISIKLLSNDHNYTTI------ASGKNLIHAIKTIIFADLIMSIDNVLAIAGT 701
IG L +++IK + + + D+ S+D++LA
Sbjct: 61 IGALYLLYLAIKHFRKKKKGKEDEEAEKKKAHSGFWRTVLKVELMDIAFSVDSILAAVAL 120
Query: 702 ASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSGNMIFSD 761
+ Q +V +G + I I+ F + + + L+E+F + +L+G++ ++
Sbjct: 121 SGQF------WVVFLGGIIGILIMRFAATIFVKLLERFPELETAAFLLIGWIGVKLLLET 174
Query: 762 QSLTQLQI 769
+ + I
Sbjct: 175 LAHPSIPI 182
>gnl|CDD|180395 PRK06091, PRK06091, membrane protein FdrA; Validated.
Length = 555
Score = 59.7 bits (145), Expect = 5e-09
Identities = 38/185 (20%), Positives = 85/185 (45%), Gaps = 18/185 (9%)
Query: 345 KKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGATVSVIYVPAIFATSAIWEAIESELE 404
++A + Q ++ +D+ + A +++I V +A +A++ L
Sbjct: 86 EEALKQLAQGSGSSQSLTQVRRWDSACQKLPD--ANLALISVAGEYAAELAEQALDRNLN 143
Query: 405 LVICITEGIPVRDMLILKNKMKKNNSKTLLLGPNCPGLIVPEEIKIGIMP---GNIHKKG 461
V+ ++ + + D + LK + ++ L++GP+C + I P N+ +G
Sbjct: 144 -VMMFSDNVTLEDEIRLKTRAREKG--LLVMGPDCGTAM------IAGTPLAFANVMPEG 194
Query: 462 RIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGG----DPINGLKYIDILKLFNEDQNTD 517
IGV+ SGT E+ Q+ G G + A+G+GG + G+ + L++ + D+ ++
Sbjct: 195 NIGVIGASGTGIQELCSQIALAGEGITHAIGLGGRDLSAEVGGISALTALEMLSADEKSE 254
Query: 518 AVIMI 522
+ +
Sbjct: 255 VIAFV 259
>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 = 58.9 bits (143), Expect = 7e-09
Identities = 64/252 (25%), Positives = 107/252 (42%), Gaps = 44/252 (17%)
Query: 335 TNLCLNYG-NGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGATVSVIYVPAIFATS 393
NL + G GK + VNPK + + + +V + ++VI VPA +
Sbjct: 28 KNL-IEGGYKGK---IYPVNPK--AGEILGVKAYPSVLEIPDPV--DLAVIVVPAKYVPQ 79
Query: 394 AIWEAIESELELVICIT--------EGIPVRDMLILKNKMKKNNSKTLLLGPNCPGLIVP 445
+ E E ++ + IT EG + L +K + LLGPNC G+I
Sbjct: 80 VVEECGEKGVKGAVVITAGFKEVGEEGAELEQEL--VEIARKYGMR--LLGPNCLGIINT 135
Query: 446 EEIKI-----GIMPGNIHKKGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPING 500
IK+ MP KKG I +S+SG L ++ + G G S V +G
Sbjct: 136 H-IKLNATFAPTMP----KKGGIAFISQSGALLTALLDWAEKNGVGFSYFVSLGNKAD-- 188
Query: 501 LKYIDILKLFNEDQNTDAVIMIGEIGGLDEIYAANWIKK----NMKKPVIGFIAGITAPP 556
+ D+L+ +D +T +++ E G+ + ++K + KKP++ +G +
Sbjct: 189 IDESDLLEYLADDPDTKVILLYLE--GIKD--GRKFLKTAREISKKKPIVVLKSGTS-EA 243
Query: 557 GKR--MGHAGAL 566
G + H GAL
Sbjct: 244 GAKAASSHTGAL 255
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 54.1 bits (131), Expect = 2e-07
Identities = 36/163 (22%), Positives = 67/163 (41%), Gaps = 33/163 (20%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
K+ ++K+ + + + + +EA + G V+KA A G+ G+ +A +LE+
Sbjct: 108 KDFMKKYGIPTAEYEVFTDPEEAKAYIDEKGAP-IVVKADGLAAGK----GVIVAMTLEE 162
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNIIFM---- 124
E ++L + N G V+IEE++D +E + D + +I M
Sbjct: 163 AEAAVDEML-------EGNAFGSAGARVVIEEFLD-GEEFSLQAFVDG--KTVIPMPTAQ 212
Query: 125 ----------GSNKGGM----DIEIISKNSPELLYKTIIDPLI 153
G N GGM I+ E + I++P +
Sbjct: 213 DHKRAYDGDTGPNTGGMGAYSPAPFITDEVVERAVEEIVEPTV 255
>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
Length = 155
Score = 47.4 bits (113), Expect = 5e-06
Identities = 25/56 (44%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 792 DSRNSRDGRFIERIGFYNPLASKKEKKF-KILLNRFTYWKQVGAKTSLTVDHLITI 846
DSR RDGR IE IG Y+P K+E +I R YW VGA+ + V L+ I
Sbjct: 24 DSRTKRDGRAIEEIGRYHP---KEEPSLIEIDSERAQYWLSVGAQPTEPVLALLKI 76
>gnl|CDD|172990 PRK14524, rpsP, 30S ribosomal protein S16; Provisional.
Length = 94
Score = 45.2 bits (107), Expect = 7e-06
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 792 DSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLR 851
DSR RDG +IE +G+YNPL K+ + K+ + R W GA+ S TV + LR
Sbjct: 23 DSRKRRDGAYIESLGYYNPL--KEPYEIKVDVERAVEWILKGAQPSDTVRDI------LR 74
Query: 852 AYGIF 856
+G+
Sbjct: 75 KFGVM 79
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 49.0 bits (117), Expect = 9e-06
Identities = 57/239 (23%), Positives = 95/239 (39%), Gaps = 35/239 (14%)
Query: 3 IYEYQGKEILR---KFNVTIPKGILCMNVDEAIKAAKKIGGNSW------VIKAQIHAGG 53
I EY K +L+ K I I V E+ + W V+K + G
Sbjct: 6 IREYDSKRLLKEHLKRLAGIDLPIRSAQVTESTDFNELANKEPWLSSTKLVVKPDMLFGK 65
Query: 54 RGKCGGIKLAQSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFM 113
RGK G + L L QV + K+ LG ++ + ++E ++ +E Y+S +
Sbjct: 66 RGKSGLVALNLDLAQVATFVKERLGKEVEMGGCKGP---ITTFIVEPFVPHDQEFYLSIV 122
Query: 114 TDRVQQNIIFMGSNKGGMDIE-------IISKNSPELLYKTIIDPLIGLTKNNIDNISKK 166
+DR+ +I F S GG++IE I + L I PLI
Sbjct: 123 SDRLGCSISF--SECGGIEIEENWDKVKTIFLPTEAPLTSEICAPLIA------------ 168
Query: 167 ISIPKNSLINFYEEIQNIYKSYWETDSLLLEINPLVINSKNKIISLDIKFNFDTNALFR 225
++P E I+ ++ + + D LE+NP + + LD++ D A F+
Sbjct: 169 -TLPLEIRGKIEEFIKGVFAVFQDLDFTFLEMNPFTL-VDGEPYPLDMRGELDDTAAFK 225
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 47.1 bits (112), Expect = 9e-06
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 7/65 (10%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLN--RFTYWKQVGAKTSLTVDHLITI- 846
A DSR RDG+FIE+IG YNP + + LN R YW GA+ + T ++++
Sbjct: 22 AADSRAPRDGKFIEKIGTYNPNTNPA----TVDLNFDRAVYWLMNGAQPTDTARNILSYE 77
Query: 847 GVVLR 851
GV+L+
Sbjct: 78 GVLLK 82
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 49.3 bits (118), Expect = 9e-06
Identities = 61/247 (24%), Positives = 102/247 (41%), Gaps = 33/247 (13%)
Query: 335 TNLCLNYGNGKKAFVAGVNPKKNGQKFEEIPIFDTVKNAKNETGATVSVIYVPAIFATSA 394
NL L YG GK + VNPK + + + +V + + ++VI VPA
Sbjct: 31 RNL-LEYGQGK---IYPVNPKY--DEVLGVKAYTSVADLPDA--PDLAVIVVPAKVVPEI 82
Query: 395 IWEAIESELELVICITEGI--PVRDMLILKNKMKKNNSKTL--LLGPNCPGLIVPEEIKI 450
+ E E ++ I I+ G + + L+ ++ + K ++GPNC GLI I
Sbjct: 83 VHELGEKGVKGAIVISAGFREAGEEGMELEKELVEAARKYGMRIIGPNCLGLI---NPII 139
Query: 451 GIM----PGNIH-KKGRIGVVSRSGTLTYEV--VCQLTELGFGQSSAVGIGGDPINGLKY 503
G+ P + G VS+SG +++ + +GF ++G D
Sbjct: 140 GLNATFDPVFGLGRGGGGAFVSQSGAVSFAILDWANEDGMGFSIKVSLGNAAD----RDE 195
Query: 504 IDILKLFNEDQNTDAVIMI---GEIGGLDEIYAANWIKKNMKKPVIGFIAGITAPPGKRM 560
D+L+ +D T A+ + + G + AA KKP+I AG + K
Sbjct: 196 SDLLEYLADDPRTKAIGLYIEGVKDGRKF-LNAA--RAAERKKPIIALKAGRSEAGAKAA 252
Query: 561 -GHAGAL 566
H G+L
Sbjct: 253 ASHTGSL 259
>gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 165
Score = 46.3 bits (110), Expect = 1e-05
Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 8/122 (6%)
Query: 843 LITIGVVLRAYGIFGWILIKLFLDD-KNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNY 901
LI +GV+ +GI G + IK F +D +NI Y + N+ K+ + ++ N
Sbjct: 2 LICLGVITSPHGIKGHVKIKTFTEDPENISAYGKLT--DGSNTYKISVVSVIGA----NL 55
Query: 902 VLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVT 961
V+A + GI R A L+ L + + P L+ D FY +LI V+ + G +
Sbjct: 56 VIAKISGINSRTEAELLRNKKLYVERSKLPN-LNEDEFYQSDLIGMEVKLEDNTIYGYIK 114
Query: 962 EI 963
+I
Sbjct: 115 KI 116
>gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16.
Length = 82
Score = 43.9 bits (104), Expect = 1e-05
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 10/67 (14%)
Query: 790 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVV 849
A D R+ R+GR +E++GFY+P+ + + + Y+ + GA+ + TV +
Sbjct: 21 AIDVRSRREGRDLEKVGFYDPIK----NQTYLNVPAILYFLEKGAQPTETVYDI------ 70
Query: 850 LRAYGIF 856
L+ +F
Sbjct: 71 LKKAEVF 77
>gnl|CDD|205785 pfam13607, Succ_CoA_lig, Succinyl-CoA ligase like flavodoxin
domain. This domain contains the catalytic domain from
Succinyl-CoA ligase alpha subunit and other related
enzymes. A conserved histidine is involved in phosphoryl
transfer.
Length = 138
Score = 41.7 bits (99), Expect = 3e-04
Identities = 30/116 (25%), Positives = 47/116 (40%), Gaps = 19/116 (16%)
Query: 460 KGRIGVVSRSGTLTYEVVCQLTELGFGQSSAVGIGGDPING--LKYIDILKLFNEDQNTD 517
G + +VS+SG L ++ G G S V +G N + + D+L +D T
Sbjct: 1 PGGVALVSQSGALGAALLDWAARRGIGFSHFVSLG----NEADVDFADLLDYLADDPETR 56
Query: 518 AVIM-IGEIGG----LDEIYAANWIKKNMKKPVIGFIAGITAPPGKRMG--HAGAL 566
+++ + I L A KKPV+ +G + G R H GAL
Sbjct: 57 VILLYLEGIRDGRRFLRAARRA-----ARKKPVVVLKSGRS-EAGARAAASHTGAL 106
>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 = 42.7 bits (101), Expect = 0.001
Identities = 30/114 (26%), Positives = 55/114 (48%), Gaps = 16/114 (14%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
+E +++ +P+ + +V+EA+ AAK+I G +++ GG G GGI A + E+
Sbjct: 132 REAMKEIGEPVPESEIAHSVEEALAAAKEI-GYPVIVRPAFTLGGTG--GGI--AYNREE 186
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNII 122
+++ ++ L S NQ VL+E+ + KE+ M D I
Sbjct: 187 LKEIAERALSA----SPINQ-------VLVEKSLAGWKEIEYEVMRDSNDNCIT 229
Score = 30.7 bits (70), Expect = 5.0
Identities = 23/111 (20%), Positives = 52/111 (46%), Gaps = 26/111 (23%)
Query: 10 EILRKFNVTIPKGILCMNVDEAIKAAKKIG-----GNSWVIKAQIHAGGRGKCGGIKLAQ 64
E+L + + PK +V+EA++ A +IG S+V+ GGR +++
Sbjct: 675 ELLDELGIPQPKWKTATSVEEAVEFASEIGYPVLVRPSYVL------GGR----AMEIVY 724
Query: 65 SLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTD 115
+ E++ +Y ++ + + VLI++Y++ E+ + ++D
Sbjct: 725 NEEELRRY------LEEAVEVSPE-----HPVLIDKYLEDAVEVDVDAVSD 764
>gnl|CDD|190425 pfam02786, CPSase_L_D2, Carbamoyl-phosphate synthase L chain, ATP
binding domain. Carbamoyl-phosphate synthase catalyzes
the ATP-dependent synthesis of carbamyl-phosphate from
glutamine or ammonia and bicarbonate. This important
enzyme initiates both the urea cycle and the
biosynthesis of arginine and/or pyrimidines. The
carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes
is a heterodimer of a small and large chain. The small
chain promotes the hydrolysis of glutamine to ammonia,
which is used by the large chain to synthesise carbamoyl
phosphate. See pfam00988. The small chain has a GATase
domain in the carboxyl terminus. See pfam00117. The ATP
binding domain (this one) has an ATP-grasp fold.
Length = 211
Score = 41.1 bits (97), Expect = 0.001
Identities = 27/120 (22%), Positives = 48/120 (40%), Gaps = 15/120 (12%)
Query: 9 KEILRKFNVTIPKGILCM--NVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSL 66
K +++ V G +EA+ AAK+I G +IKA GG G+ +A++
Sbjct: 6 KAAMKEAGVPTVPGTAGPVETEEEALAAAKEI-GYPVIIKAAFGGGGL----GMGIARNE 60
Query: 67 EQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNIIFMGS 126
E++ + L Q VL+E+ + K + + D N I + +
Sbjct: 61 EELAELFALALAEAPAAFGNPQ-------VLVEKSLKGPKHIEYQVLRDA-HGNCITVCN 112
>gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 171
Score = 39.8 bits (93), Expect = 0.002
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 8/128 (6%)
Query: 844 ITIGVVLRAYGIFGWILIKLFLDDKNIFFYAR----KIWFFDPNSLKLFSIKILNKKNHG 899
I++G + + +GI GW+ ++ + + + K+ DP I +L + HG
Sbjct: 1 ISLGQLGKPFGIKGWL--RVNVRGETLHTLKAPATLKLGKEDPQ-FPESEIALLEIRPHG 57
Query: 900 NYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLG- 958
L G A K +G L + PK+ + FY +LI + GK L
Sbjct: 58 GKFLVRFEGYDTPEEAVKWRGGSLFLPQELLPKIETKGEFYSEDLIGLQAIDETGKPLNW 117
Query: 959 TVTEIIQN 966
+T++ N
Sbjct: 118 KLTDVQDN 125
>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 = 40.0 bits (94), Expect = 0.002
Identities = 26/125 (20%), Positives = 46/125 (36%), Gaps = 25/125 (20%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
+E+LR + +P L + ++ AA++IG V+K + AG G + S +
Sbjct: 9 RELLRAAGLPVPPFFLVDDEEDLDAAAEEIGF-PVVLKPRDGAGSLG----VFRVDSAAE 63
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYID----------IKKELYISFMTDRVQ 118
+E + E E+ L+EEYID EL ++ +
Sbjct: 64 LEAALAAL----------AAEVEDTREYLVEEYIDGDEYHVDGLVDDGELVFLGVSRYLG 113
Query: 119 QNIIF 123
Sbjct: 114 PPPPD 118
>gnl|CDD|172988 PRK14522, rpsP, 30S ribosomal protein S16; Provisional.
Length = 116
Score = 37.7 bits (87), Expect = 0.004
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 792 DSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLR 851
D + RDG++IE +G+Y+P E+ +++ R YW GA+ + L+ G
Sbjct: 24 DVESPRDGKYIELLGWYDP---HSEQNYQLKSERIFYWLNQGAELTEKAGALVKQG---- 76
Query: 852 AYGIFGWILIK 862
A G++ ++ K
Sbjct: 77 APGVYSELMAK 87
>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 = 37.4 bits (88), Expect = 0.017
Identities = 32/138 (23%), Positives = 62/138 (44%), Gaps = 16/138 (11%)
Query: 5 EYQGKEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQ----IHAGGRGKCGGI 60
E + K +L + + + L + +EA+ AA++IG V+K +H + GG+
Sbjct: 12 EPEAKALLAAYGIPVVPTRLARSPEEAVAAAEEIGY-PVVLKIVSPDILH---KSDVGGV 67
Query: 61 KLA-QSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIK-KELYISFMTDRVQ 118
+L +S E+V ++IL + + + VL++ +EL + D V
Sbjct: 68 RLNLKSAEEVRAAAEEILE----RVRRYRPDARIEGVLVQPMAPRGGRELIVGVTRDPVF 123
Query: 119 QNIIFMGSNKGGMDIEII 136
+I G GG +E++
Sbjct: 124 GPVIMFGL--GGTAVEVL 139
>gnl|CDD|184351 PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 161
Score = 36.5 bits (85), Expect = 0.021
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 19/100 (19%)
Query: 876 KIWFF--DPNSL------------KLFSIKILNK-KNHGNYVLANLYGITDRNLATKLQG 920
++ F DP ++ + F++ + K+ ++A L G+ R A L+G
Sbjct: 6 RLKSFTEDPLAIADYGPLTTEDGARSFTVALARPAKDG---LVARLKGVATREAAEALRG 62
Query: 921 YYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTV 960
L + + P+L D FY +LI + G LLG V
Sbjct: 63 LELYVPRDRLPEL-DDDEFYHADLIGLAAVDTGGALLGRV 101
>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 = 38.1 bits (89), Expect = 0.021
Identities = 30/137 (21%), Positives = 58/137 (42%), Gaps = 30/137 (21%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
K+ ++++ + + + + +EA ++ G V+KA A G+ G+ +A++ E+
Sbjct: 109 KDFMKRYGIPTAEYEVFTDPEEAKSYIQEKG-APIVVKADGLAAGK----GVIVAKTNEE 163
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNIIFM---- 124
K + IL Q + V+IEE++D +E + D + +I M
Sbjct: 164 AIKAVEDIL------EQKFGDAGER--VVIEEFLD-GEEFSLLAFVDG--KTVIPMPPAQ 212
Query: 125 ----------GSNKGGM 131
G N GGM
Sbjct: 213 DHKRALEGDKGPNTGGM 229
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 36.2 bits (85), Expect = 0.10
Identities = 27/94 (28%), Positives = 51/94 (54%), Gaps = 16/94 (17%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
KE ++K + +P+ + +++EA++ A++IG +I+ GG G GGI A + E+
Sbjct: 133 KEAMKKIGLPVPRSGIAHSMEEALEVAEEIGYPV-IIRPSFTLGGTG--GGI--AYNEEE 187
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYI 102
+E+ ++ G+ L S + VLIEE +
Sbjct: 188 LEEIVER--GLDL--SPVTE-------VLIEESL 210
Score = 30.8 bits (71), Expect = 4.3
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 10 EILRKFNVTIPKGILCMNVDEAIKAAKKIG 39
++L K + P +V+EA++ A++IG
Sbjct: 675 KLLEKLGIPQPPNGTATSVEEALEVAEEIG 704
>gnl|CDD|227557 COG5232, SEC62, Preprotein translocase subunit Sec62 [Intracellular
trafficking and secretion].
Length = 259
Score = 34.9 bits (80), Expect = 0.16
Identities = 29/136 (21%), Positives = 50/136 (36%), Gaps = 19/136 (13%)
Query: 527 GLDEIYAANWIKKNMKKPVIGFIAGITAPPGKRMGHAGALITEIKK-----MTFLTASNG 581
GLDE+ A I + M VI + L + + ++ A
Sbjct: 94 GLDELQA-RLIMQEMLNEVIKL------KVHINKRNTKELDVVLDQKFQEDQHYVWAYEP 146
Query: 582 ISIIQIILIDILLGSTDAIIIALACRNLQPNIRTKG---IIFGTFGAIAIRIILVIFSIN 638
S I ++L + + + +AL L P +G + +G G I +L I +
Sbjct: 147 TSNISLVLCGVFV----LVTLALVLFPLWPRNMRQGLFYMSYGLGGFITFFFVLAILRLI 202
Query: 639 LLNLKYIKIIGGFLLF 654
L ++ Y+ G LF
Sbjct: 203 LFSITYLLYPSGIWLF 218
>gnl|CDD|236307 PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 451
Score = 34.8 bits (81), Expect = 0.24
Identities = 26/101 (25%), Positives = 48/101 (47%), Gaps = 22/101 (21%)
Query: 9 KEILRKFNV-TIP--KGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQS 65
K ++K V +P G + + +EA+ AK+I G +IKA AGG G+ G+++ ++
Sbjct: 120 KATMKKAGVPVVPGSDGPV-DDEEEALAIAKEI-GYPVIIKAT--AGGGGR--GMRVVRT 173
Query: 66 LEQVEKYTKKILGMQLITSQTNQEGENVF---CVLIEEYID 103
++EK E + F V +E+Y++
Sbjct: 174 EAELEKAFS----------MARAEAKAAFGNPGVYMEKYLE 204
>gnl|CDD|223516 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 34.5 bits (80), Expect = 0.26
Identities = 22/102 (21%), Positives = 45/102 (44%), Gaps = 24/102 (23%)
Query: 9 KEILRKFNVTIPKGILCM--NVDEAIKAAKKIGGNSW--VIKAQIHAGGRGKCGGIKLAQ 64
+ ++ K V + G + +EA+ A++IG + ++KA GGR G+++ +
Sbjct: 120 RRLMAKAGVPVVPGSDGAVADNEEALAIAEEIG---YPVIVKAAAGGGGR----GMRVVR 172
Query: 65 SLEQVEKYTKKILGMQLITSQTNQEGENVF---CVLIEEYID 103
+ E++E E E F V +E++I+
Sbjct: 173 NEEELEA----------AFEAARGEAEAAFGNPRVYLEKFIE 204
>gnl|CDD|129605 TIGR00514, accC, acetyl-CoA carboxylase, biotin carboxylase
subunit. This model represents the biotin carboxylase
subunit found usually as a component of acetyl-CoA
carboxylase. Acetyl-CoA carboxylase is designated EC
6.4.1.2 and this component, biotin carboxylase, has its
own designation, EC 6.3.4.14. Homologous domains are
found in eukaryotic forms of acetyl-CoA carboxylase and
in a number of other carboxylases (e.g. pyruvate
carboxylase), but seed members and trusted cutoff are
selected so as to exclude these. In some systems, the
biotin carboxyl carrier protein and this protein (biotin
carboxylase) may be shared by different
carboxyltransferases. However, this model is not
intended to identify the biotin carboxylase domain of
propionyl-coA carboxylase. The model should hit the full
length of proteins, except for chloroplast transit
peptides in plants. If it hits a domain only of a longer
protein, there may be a problem with the identification
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 449
Score = 34.4 bits (79), Expect = 0.27
Identities = 32/123 (26%), Positives = 59/123 (47%), Gaps = 23/123 (18%)
Query: 9 KEILRKFNV-TIP--KGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQS 65
E ++K V +P G++ + +E ++ AK+I G +IKA GGR G+++ +
Sbjct: 120 IETMKKAGVPCVPGSDGLV-EDEEENVRIAKRI-GYPVIIKATAGGGGR----GMRVVRE 173
Query: 66 LEQVEKYTKKILGMQLITSQTNQEGENVF---CVLIEEYIDIKKELYISFMTDRVQQNII 122
+++ K S T E + F V IE+YI+ + + I + D+ N I
Sbjct: 174 PDELVK----------SISMTRAEAKAAFGNDGVYIEKYIENPRHVEIQVLADK-YGNAI 222
Query: 123 FMG 125
++G
Sbjct: 223 YLG 225
>gnl|CDD|184352 PRK13829, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 162
Score = 32.8 bits (75), Expect = 0.37
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 898 HGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLL 957
G ++ +L G+T R A L G + D P L ++Y+ L V + G+ L
Sbjct: 49 VGPELVLHLAGVTSREGAEALVGLRVYADDADLPP-LEEGSYYYHELRGLPVY-VDGEPL 106
Query: 958 GTVTEI 963
G V ++
Sbjct: 107 GEVVDV 112
>gnl|CDD|223534 COG0458, CarB, Carbamoylphosphate synthase large subunit (split
gene in MJ) [Amino acid transport and metabolism /
Nucleotide transport and metabolism].
Length = 400
Score = 33.8 bits (78), Expect = 0.39
Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 21/116 (18%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSW--VIKAQIHAGGRGKCGGIKLAQSL 66
KE +R+ + +P I +V+EA + A +IG + ++K GG G GGI A +
Sbjct: 121 KEAMREIGIPVPSRI-AHSVEEADEIADEIG---YPVIVKPSFGLGGSG--GGI--AYNE 172
Query: 67 EQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNII 122
E++E+ ++ L S + VLIEE I KE + D I+
Sbjct: 173 EELEEIIEEGLRA----SPVEE-------VLIEESIIGWKEFEYEVVRDGKDNCIV 217
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 33.4 bits (77), Expect = 0.80
Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 28/103 (27%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIG-----GNSWVIKAQIHAGGRGKCGGIKLA 63
++L + + G+ + +EA AK+IG S+VI GG+ G+ +
Sbjct: 675 YQLLDELGLPHVPGLTATDEEEAFAFAKRIGYPVLIRPSYVI------GGQ----GMAVV 724
Query: 64 QSLEQVEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKK 106
+E Y + ++ +LI+++ID K+
Sbjct: 725 YDEPALEAYLA-------------ENASQLYPILIDQFIDGKE 754
Score = 32.2 bits (74), Expect = 1.5
Identities = 35/118 (29%), Positives = 58/118 (49%), Gaps = 17/118 (14%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
+ ++++ +P+ + +V+EA+ A+KIG V A GG G GGI A++LE+
Sbjct: 133 RALMKELGEPVPESEIVTSVEEALAFAEKIGFPIIVRPAY-TLGGTG--GGI--AENLEE 187
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTDRVQQNIIFMGS 126
+E+ K+ L S +Q L+EE I KE+ M DR N I + +
Sbjct: 188 LEQLFKQ----GLQASPIHQ-------CLLEESIAGWKEIEYEVMRDR-NGNCITVCN 233
>gnl|CDD|237586 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 32.4 bits (75), Expect = 1.2
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRG 55
K +L V +P+G + + ++A +AA++IG V+K GRG
Sbjct: 219 KRLLAAAGVPVPEGRVVTSAEDAWEAAEEIGY-PVVVKPLDGNHGRG 264
>gnl|CDD|216782 pfam01914, MarC, MarC family integral membrane protein. Integral
membrane protein family that includes the antibiotic
resistance protein MarC. These proteins may be
transporters.
Length = 203
Score = 31.5 bits (72), Expect = 1.7
Identities = 35/154 (22%), Positives = 62/154 (40%), Gaps = 23/154 (14%)
Query: 619 IFGTFGAIAIRIILVIFSINLLNLKYIKIIGGFLLFWISIKLLSND-HNYTTIASGKNLI 677
+F FG ++IL +F I++ + I GG LLF I+I +L T S K
Sbjct: 53 LFLVFG----KLILKLFGISIDAFR---IAGGILLFLIAIDMLFGKQSKEKTSKSEKEES 105
Query: 678 HAIKTIIFADLIM-------SIDNVLAIAGTASQISNKYQMLLVIIGILFSIPI----II 726
I I L + +I + + I + VI+ IL + I ++
Sbjct: 106 EDIDEIAVVPLAIPLIAGPGAITTTMVLMAEHGTIG---LKIAVILAILLAWLITFLILL 162
Query: 727 FGSKLVLILIEKFSSIII-LCSILLGYLSGNMIF 759
S ++ +L + + + +LL ++ MI
Sbjct: 163 SSSFIIRLLGRTGINALTRIMGLLLAAIAVQMIV 196
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 31.8 bits (73), Expect = 2.0
Identities = 28/174 (16%), Positives = 61/174 (35%), Gaps = 16/174 (9%)
Query: 617 GIIFGTFGAIAIRIILVIFSINLLNLKYIKIIGGFLLFWISIKLLSNDHNYTTIASGKNL 676
+ I + I + I L+ ++ + S + + + K
Sbjct: 289 FLYSWKLTLIVLAAIPLNVLITLIFQPLLRRKT------RKLIEESAEQQSFLVETIKG- 341
Query: 677 IHAIKTI-IFADLIMSIDNVLAIAGTAS----QISNKYQMLLVIIGILFSIPIIIFGSKL 731
I +K + DN LA +++ + ++ L S+ I+ FG+ L
Sbjct: 342 IETVKALAAEPRFRSQWDNRLAKQVNIGFKTEKLALILNTIKSLLQQLSSVLILWFGAIL 401
Query: 732 VLILIEKFS-SIIILCSILLGYLSGNMIFSDQSLTQLQINKLLIKNI-FIFNME 783
V L + + ++ ++L GY + Q T Q K+ ++ + I +
Sbjct: 402 V--LEGELTLGQLVAFNMLAGYFISPITRLSQLWTDFQQAKVALERLGDILDTP 453
>gnl|CDD|179654 PRK03818, PRK03818, putative transporter; Validated.
Length = 552
Score = 31.4 bits (72), Expect = 2.5
Identities = 19/43 (44%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 691 SIDNVLAIAGTASQISNKYQMLLVIIGI-----LFSIPIIIFG 728
+ID V + G A Q + QML V IGI L SIP I G
Sbjct: 351 AIDAVANVLGNAQQKLQQVQMLPVFIGIGLGVLLGSIPFFIPG 393
>gnl|CDD|218519 pfam05239, PRC, PRC-barrel domain. The PRC-barrel is an all beta
barrel domain found in photosystem reaction centre
subunit H of the purple bacteria and RNA metabolism
proteins of the RimM group. PRC-barrels are
approximately 80 residues long, and found widely
represented in bacteria, archaea and plants. This domain
is also present at the carboxyl terminus of the
pan-bacterial protein RimM, which is involved in
ribosomal maturation and processing of 16S rRNA. A
family of small proteins conserved in all known
euryarchaea are composed entirely of a single
stand-alone copy of the domain.
Length = 78
Score = 28.5 bits (64), Expect = 3.9
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 937 DTFYWFNLIDCIVENIHGKLLGTVTEIIQNKLTG 970
D FY +LI V G+ LG V +++ ++ G
Sbjct: 2 DEFYASDLIGLEVYTEDGEKLGKVKDVVIDEGEG 35
>gnl|CDD|236325 PRK08654, PRK08654, pyruvate carboxylase subunit A; Validated.
Length = 499
Score = 30.3 bits (69), Expect = 5.3
Identities = 33/127 (25%), Positives = 62/127 (48%), Gaps = 31/127 (24%)
Query: 9 KEILRKFNVTI----PKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQ 64
K++++K V + +GI +++EA + A++I G +IKA AGG G G+++
Sbjct: 120 KKLMKKAGVPVLPGTEEGI--EDIEEAKEIAEEI-GYPVIIKAS--AGGGGI--GMRVVY 172
Query: 65 S---LEQVEKYTKKILGMQLITSQTNQEGENVF---CVLIEEYIDIKKELYISFMTDRVQ 118
S LE + T+ I ++ F V IE+Y++ + + I + D+
Sbjct: 173 SEEELEDAIESTQSI-------------AQSAFGDSTVFIEKYLEKPRHIEIQILADK-H 218
Query: 119 QNIIFMG 125
N+I +G
Sbjct: 219 GNVIHLG 225
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 30.5 bits (70), Expect = 5.5
Identities = 27/109 (24%), Positives = 42/109 (38%), Gaps = 16/109 (14%)
Query: 86 TNQEGENVFCVLIEEYIDIKKEL--YISFMTDRVQQNIIFMGSNKGGMDIEIISKNSPEL 143
+ EG + IE+Y I KEL Y + +R Q I+ NK MD+ +N E
Sbjct: 247 SGSEGRDP----IEDYEKINKELKLYNPRLLERPQ--IVVA--NK--MDLPEAEENLEEF 296
Query: 144 LYKTIID--PLIGLTKNNIDNISKKIS--IPKNSLINFYEEIQNIYKSY 188
K P+ LT +D + ++ + + EE Y
Sbjct: 297 KEKLGPKVFPISALTGQGLDELLYAVAELLEETPEFPLEEEEVEEEVYY 345
>gnl|CDD|233160 TIGR00869, sec62, protein translocation protein, Sec62 family.
Members of the NSCC2 family have been sequenced from
various yeast, fungal and animals species including
Saccharomyces cerevisiae, Drosophila melanogaster and
Homo sapiens. These proteins are the Sec62 proteins,
believed to be associated with the Sec61 and Sec63
constituents of the general protein secretary systems of
yeast microsomes. They are also the non-selective cation
(NS) channels of the mammalian cytoplasmic membrane. The
yeast Sec62 protein has been shown to be essential for
cell growth. The mammalian NS channel proteins has been
implicated in platelet derived growth factor(PGDF)
dependent single channel current in fibroblasts. These
channels are essentially closed in serum deprived
tissue-culture cells and are specifically opened by
exposure to PDGF. These channels are reported to exhibit
equal selectivity for Na+, K+ and Cs+ with low
permeability to Ca2+, and no permeability to anions
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 232
Score = 29.9 bits (67), Expect = 6.0
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 599 AIIIALACRNLQPNIRTKGIIF---GTFGAIAIRIILVIFSINLLNLKYIKIIGGFLLF 654
+II+AL L P +G + G G I + I + L L I + G +F
Sbjct: 128 SIILALVLFPLWPRFMRRGSWYLSLGALGIIGGFFAVAILRLILFVLTLIVVKPGIWIF 186
>gnl|CDD|236254 PRK08384, PRK08384, thiamine biosynthesis protein ThiI;
Provisional.
Length = 381
Score = 29.9 bits (67), Expect = 6.3
Identities = 34/124 (27%), Positives = 57/124 (45%), Gaps = 37/124 (29%)
Query: 97 LIEEYIDIKKELYI----SFM----TDRVQQNI----IFMGSNKGGM------DIEIISK 138
+I++ ++KKE Y FM DR+ + I MG + G + ++ I+S+
Sbjct: 251 IIQKLKELKKENYTCVFCKFMMVKHADRIAKEFGAKGIVMGDSLGQVASQTLENMYIVSQ 310
Query: 139 NSPELLYKTIIDPLIGLTKNNIDNISKKIS--------------IPKNSLI-NFYEEIQN 183
S +Y+ PLIG+ K I I+K I IPK+ +I +EE +
Sbjct: 311 ASDLPIYR----PLIGMDKEEIVAIAKTIGTFELSTLPEDEIPFIPKHPVIRGSWEEFRK 366
Query: 184 IYKS 187
+YK+
Sbjct: 367 LYKA 370
>gnl|CDD|215412 PLN02769, PLN02769, Probable galacturonosyltransferase.
Length = 629
Score = 30.0 bits (68), Expect = 6.6
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 863 LFLDDKNIFFYARKIWFFDPNSLKLFSIKILN-----KKNHGNYVLANLY 907
+ D +N +YA K W FD NS K ++++LN K+ + L L
Sbjct: 364 VLTDAQN--YYAMKHW-FDRNSYKEAAVQVLNIEDLILKDLDKFALKQLS 410
>gnl|CDD|132931 cd07020, Clp_protease_NfeD_1, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon
partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair, causing
NfeD to be previously named STOPP (stomatin operon
partner protein). NfeD homologs can be divided into two
groups: long and short forms. Long-form homologs have a
putative ClpP-class serine protease domain while the
short form homologs do not. Downstream from the
ClpP-class domain is the so-called NfeD or DUF107
domain. N-terminal region of the NfeD homolog PH1510
(1510-N or PH1510-N) from Pyrococcus horikoshii has been
shown to possess serine protease activity and has a
Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 187
Score = 29.4 bits (67), Expect = 6.7
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 512 EDQNTDAVIMIGEI---GGLDEIYAANWIKK---NMKKPVIGFIAGITAPPGKRMGHAGA 565
E+ DA+I+ E+ GGL + + I + PV+ ++ P G R AG
Sbjct: 26 EEGGADALII--ELDTPGGLLD--STREIVQAILASPVPVVVYVY----PSGARAASAGT 77
Query: 566 LIT 568
I
Sbjct: 78 YIL 80
>gnl|CDD|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin is
an insoluble storage polymer for carbon, nitrogen, and
energy, found in most Cyanobacteria. The polymer has a
backbone of L-aspartic acid, with most Asp side chain
carboxyl groups attached to L-arginine. The polymer is
made by this enzyme, cyanophycin synthetase, and
degraded by cyanophycinase. Heterologously expressed
cyanophycin synthetase in E. coli produces a closely
related, water-soluble polymer with some Arg replaced by
Lys. It is unclear whether enzymes that produce soluble
cyanophycin-like polymers in vivo in non-Cyanobacterial
species should be designated as cyanophycin synthetase
itself or as a related enzyme. This model makes the
designation as 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 [Cellular
processes, Biosynthesis of natural products].
Length = 864
Score = 30.1 bits (68), Expect = 6.9
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRG 55
KEIL V +P+G + + ++A +AA+ +G VIK GRG
Sbjct: 218 KEILSDAGVPVPEGTVVQSAEDAWEAAQDLGY-PVVIKPYDGNHGRG 263
>gnl|CDD|216716 pfam01810, LysE, LysE type translocator. This family consists of
various hypothetical proteins and an l-lysine exporter
LysE from Corynebacterium glutamicum which is proposed
to be the first of a novel family of translocators. LysE
exports l-lysine from the cell into the surrounding
medium and is predicted to span the membrane six times.
The physiological function of the exporter is to excrete
excess l-Lysine as a result of natural flux imbalances
or peptide hydrolysis; and also after artificial
deregulation of l-Lysine biosynthesis as used by the
biotechnology. industry for the production of l-lysine.
Length = 191
Score = 29.2 bits (66), Expect = 7.0
Identities = 33/144 (22%), Positives = 53/144 (36%), Gaps = 12/144 (8%)
Query: 618 IIFGTFGAIAIRIILVIFSI-NLLN-----LKYIKIIGGFLLFWISIKLLSNDHNYTTIA 671
+ G A+ I+L +F + LL L +++ GG L W+ I L
Sbjct: 29 VGLGAMLGDAVLILLGLFGLATLLGASPILLALLRLAGGAYLLWLGILTL-RAAWSPKNE 87
Query: 672 SGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKL 731
S + ++K L++S+ N I S S + I F + L
Sbjct: 88 SLSSSEASLKKSFLRGLLVSLSNPKVILFWLSVGS-----AFLDKQQYGDAGRIAFAAGL 142
Query: 732 VLILIEKFSSIIILCSILLGYLSG 755
V+ + FS + L S L LS
Sbjct: 143 VVASLIWFSLLAFLASRLARRLST 166
>gnl|CDD|184699 PRK14478, PRK14478, nitrogenase molybdenum-cofactor biosynthesis
protein NifE; Provisional.
Length = 475
Score = 30.0 bits (68), Expect = 7.1
Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 14/78 (17%)
Query: 107 ELY-ISFMTDRVQQNIIFMGSNKGGMDI-EIISKNSPEL--LYKTIIDPLIGLTKNNIDN 162
ELY SF TD + +++F G K I EII K +P +Y+T + LIG ++ID
Sbjct: 84 ELYRTSFTTDLSETDVVFGGEKKLFKAIDEIIEKYAPPAVFVYQTCVVALIG---DDIDA 140
Query: 163 ISKKIS-------IPKNS 173
+ K+ + IP NS
Sbjct: 141 VCKRAAEKFGIPVIPVNS 158
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 29.9 bits (67), Expect = 7.8
Identities = 32/95 (33%), Positives = 47/95 (49%), Gaps = 25/95 (26%)
Query: 110 ISFMTDRVQQNIIFMGSNKGGMDI-EIISKNSPELL---YKTIIDPLIGLTKNNIDNISK 165
+SFM +Q I+F S G+ I ++I + E L K++IDP DN SK
Sbjct: 220 LSFM----EQAIVFTDSKLTGVKIRKMIGYHGIEFLTSFIKSLIDP---------DNHSK 266
Query: 166 KISIPKNSLINFYEEIQNIYKSYWE----TDSLLL 196
+ I L + Y+E Q+IYK W+ T +L L
Sbjct: 267 SLEI----LESLYQEGQDIYKFLWDSIEFTHTLNL 297
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 29.7 bits (67), Expect = 9.2
Identities = 31/107 (28%), Positives = 46/107 (42%), Gaps = 15/107 (14%)
Query: 9 KEILRKFNVTIPKGILCMNVDEAIKAAKKIGGNSWVIKAQIHAGGRGKCGGIKLAQSLEQ 68
K+ + K + P + +DE + A+ IG +I+ GG G GGI A + E+
Sbjct: 149 KQAMEKIGLKTPPSGIATTLDECFEIAEDIGEFPLIIRPAFTLGGTG--GGI--AYNKEE 204
Query: 69 VEKYTKKILGMQLITSQTNQEGENVFCVLIEEYIDIKKELYISFMTD 115
E K L ITSQ VL+E+ + KE + M D
Sbjct: 205 FETICKAGLAAS-ITSQ----------VLVEKSLLGWKEYELEVMRD 240
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
0.323 0.142 0.409
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 51,009,045
Number of extensions: 5396119
Number of successful extensions: 6367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6158
Number of HSP's successfully gapped: 326
Length of query: 974
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 868
Effective length of database: 6,236,078
Effective search space: 5412915704
Effective search space used: 5412915704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 64 (28.2 bits)