RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022648
(294 letters)
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 429 bits (1105), Expect = e-151
Identities = 190/233 (81%), Positives = 216/233 (92%)
Query: 1 MVRGLLNKLVSRSLTVAGQWQQQQLRRLNIHEYQGAELMAKYGINVPKGLAVASVDEVKK 60
M+RGLLNKL SRSL+VAG+WQ QQLRRLNIHEYQGAELM+KYG+NVPKG A +S+DEVKK
Sbjct: 1 MLRGLLNKLASRSLSVAGKWQHQQLRRLNIHEYQGAELMSKYGVNVPKGAAASSLDEVKK 60
Query: 61 AIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGVHIVKKEEVEDLAGKMLGQILVTKQ 120
A++ FPD E+VVKSQILAGGRGLGTFK+GLKGGVHIVKK++ E+LAGKMLGQILVTKQ
Sbjct: 61 ALEKMFPDEGEVVVKSQILAGGRGLGTFKNGLKGGVHIVKKDKAEELAGKMLGQILVTKQ 120
Query: 121 TGPQGKIVSKVYLCEKLSLVNEMYFAIMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIV 180
TGP GK V+KVYLCEK+SLVNEMYFAI+LDR +AGP+II CSKGGTSIEDLAEK+P I+
Sbjct: 121 TGPAGKPVNKVYLCEKMSLVNEMYFAILLDRASAGPLIIACSKGGTSIEDLAEKFPEKII 180
Query: 181 KVPIDVFNGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCESDCTLLEV 233
KVPID+F GITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFC+ DCT++E+
Sbjct: 181 KVPIDIFKGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCKCDCTMVEI 233
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 202 bits (516), Expect = 5e-65
Identities = 92/208 (44%), Positives = 131/208 (62%), Gaps = 14/208 (6%)
Query: 29 NIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTF 88
N+HEYQ EL+AKYG+ VP+G S +E ++A + K VVK+Q+LAGGRG
Sbjct: 1 NLHEYQAKELLAKYGVPVPRGEVAFSPEEAEEAAKKL--GGKVWVVKAQVLAGGRGKA-- 56
Query: 89 KSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFAI 147
GGV + K EE ++ A +MLG+ LVTKQTGP+GK V+KV + E + + E Y +I
Sbjct: 57 -----GGVKLAKSPEEAKEAAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSI 111
Query: 148 MLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD--GLAPK 205
+LDR + GP++I ++GG IE++A K P I KVPID G+T A ++ GL +
Sbjct: 112 VLDRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLTPYQAREIAFKLGLEGE 171
Query: 206 VADRNDAIEQVKKLYKLFCESDCTLLEV 233
+ + A + +KKLYKLF E D TL+E+
Sbjct: 172 LVKQ--AADIIKKLYKLFVERDATLVEI 197
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 198 bits (507), Expect = 3e-61
Identities = 79/213 (37%), Positives = 116/213 (54%), Gaps = 24/213 (11%)
Query: 29 NIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKEL-----VVKSQILAGGR 83
N+HEYQ EL AKYG+ VP+G+ + +E +A +EL VVK+Q+ AGGR
Sbjct: 2 NLHEYQAKELFAKYGVPVPRGIVATTPEEAVEAA-------EELGGGVWVVKAQVHAGGR 54
Query: 84 GLGTFKSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNE 142
G GGV + K EE + A ++LG LVT QTGP+G+ V+KV + E + E
Sbjct: 55 GKA-------GGVKLAKSPEEAREFAKQILGMTLVTHQTGPKGQPVNKVLVEEGADIAKE 107
Query: 143 MYFAIMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD-- 200
Y +I+LDR T + + ++GG IE++AE+ P I KV ID G+ A ++
Sbjct: 108 YYLSIVLDRATRRVVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQPFQAREIAFKL 167
Query: 201 GLAPKVADRNDAIEQVKKLYKLFCESDCTLLEV 233
GL + + + LYK F E D +L+E+
Sbjct: 168 GLPGEQV--KQFAKILMGLYKAFVEKDASLVEI 198
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 172 bits (438), Expect = 3e-51
Identities = 79/210 (37%), Positives = 121/210 (57%), Gaps = 18/210 (8%)
Query: 28 LNIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGT 87
+N+HEYQ EL AKYGI VP G S +E ++A ++ +VVK+Q+ AGGRG
Sbjct: 1 MNLHEYQAKELFAKYGIPVPPGYVATSPEEAEEAAKEL--GGGPVVVKAQVHAGGRGKA- 57
Query: 88 FKSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKL-SLVNEMYF 145
GGV + K EE ++ A ++LG+ QT +G+ V+KV + E + + E Y
Sbjct: 58 ------GGVKLAKSPEEAKEAAEEILGK---NYQTDIKGEPVNKVLVEEAVDIIKKEYYL 108
Query: 146 AIMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD--GLA 203
+I+LDR + P+++ ++GG IE++AEK P IVKV +D G+ A ++ GL
Sbjct: 109 SIVLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLRPYQARELAFKLGLE 168
Query: 204 PKVADRNDAIEQVKKLYKLFCESDCTLLEV 233
++ + +KKLYKLF E D TL+E+
Sbjct: 169 GELV--KQVADIIKKLYKLFVEKDATLVEI 196
>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 = 158 bits (401), Expect = 8e-46
Identities = 79/209 (37%), Positives = 120/209 (57%), Gaps = 14/209 (6%)
Query: 28 LNIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGT 87
+N+HEYQ ++ AKYGI VP+G SV+E ++ +VVK+Q+ AGGRG
Sbjct: 1 MNLHEYQAKQIFAKYGIPVPRGYVATSVEEAEEIAAKL--GAGPVVVKAQVHAGGRGKA- 57
Query: 88 FKSGLKGGVHIVK-KEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFA 146
GGV + K KEE A K+LG+ LVT QT P G+ V+K+ + E + E Y +
Sbjct: 58 ------GGVKVAKSKEEARAAAEKLLGKELVTNQTDPLGQPVNKILIEEATDIDKEYYLS 111
Query: 147 IMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVD--GLAP 204
I++DR P+I+ ++GG IE++AEK P I+K ID G+ A ++ GL
Sbjct: 112 IVIDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGLLPYQAREIAKKLGLEG 171
Query: 205 KVADRNDAIEQVKKLYKLFCESDCTLLEV 233
++ + I +KKLY++F E D +L+E+
Sbjct: 172 ELVKQVADI--IKKLYQIFLEYDASLVEI 198
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 141 bits (357), Expect = 3e-39
Identities = 69/207 (33%), Positives = 114/207 (55%), Gaps = 10/207 (4%)
Query: 28 LNIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGT 87
++IHEYQ EL+A +G+ VP+G S ++ ++ H VVK+QI +G RG
Sbjct: 1 MDIHEYQAKELLASFGVAVPRGALAYSPEQAVYRARELGGWH--WVVKAQIHSGARGKA- 57
Query: 88 FKSGLKGGVHIVKKE-EVEDLAGKMLGQILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFA 146
GG+ + + EV D A +LG+ LVT QTGP+GK V +VY+ + E+Y
Sbjct: 58 ------GGIKLCRTYNEVRDAAEDLLGKKLVTHQTGPEGKPVQRVYVETADPIERELYLG 111
Query: 147 IMLDRKTAGPIIIGCSKGGTSIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVDGLAPKV 206
+LDRK+ +I ++GG IE++A K P I++V ++ G+ A ++ GL +
Sbjct: 112 FVLDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVGLQQFQAREIAFGLGLDI 171
Query: 207 ADRNDAIEQVKKLYKLFCESDCTLLEV 233
+ A++ + Y+ F + D T+LE+
Sbjct: 172 KQVSRAVKTIMGCYRAFRDLDATMLEI 198
>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 = 37.6 bits (88), Expect = 0.003
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 17/92 (18%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGV 96
+ M ++GI + +E K I++A VVK+ LA G+ GV
Sbjct: 8 DFMKRHGIPTAEYETFTDPEEAKSYIREAGF---PAVVKADGLAAGK-----------GV 53
Query: 97 HIVKKEEVEDLAGKMLGQILVTKQTGPQGKIV 128
+ E A K + +IL K+ G G+ V
Sbjct: 54 IVAMDNEE---AIKAVDEILEQKKFGEAGEPV 82
>gnl|CDD|233164 TIGR00877, purD, phosphoribosylamine--glycine ligase. Alternate
name: glycinamide ribonucleotide synthetase (GARS). This
enzyme appears as a monofunctional protein in
prokaryotes but as part of a larger, multidomain protein
in eukaryotes [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 422
Score = 35.7 bits (83), Expect = 0.021
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 17/97 (17%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGV 96
+ M +YGI + +E K IQ+ +VVK+ LA G+ GV
Sbjct: 110 DFMKRYGIPTAEYEVFTDPEEAKSYIQEKGA---PIVVKADGLAAGK-----------GV 155
Query: 97 HIVKKEEVEDLAGKMLGQILVTKQTGPQGKIVSKVYL 133
+ K E A K + IL K ++V + +L
Sbjct: 156 IVAKTNEE---AIKAVEDILEQKFGDAGERVVIEEFL 189
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 34.4 bits (79), Expect = 0.060
Identities = 56/224 (25%), Positives = 95/224 (42%), Gaps = 40/224 (17%)
Query: 27 RLNIHEYQGAELMAKY-----GINVPKGLA--VASVDEVKKAIQDAFPDHKELVVKSQIL 79
R I EY L+ ++ GI++P A S D + A ++ + +LVVK +L
Sbjct: 3 RKKIREYDSKRLLKEHLKRLAGIDLPIRSAQVTESTDFNELANKEPWLSSTKLVVKPDML 62
Query: 80 AGGRGLGTFKSGLKGGVHIVKKEEVEDLAGKMLG-QILVTKQTGPQGKIVSKVYLCEKLS 138
G RG KSGL + +V + LG ++ + GP + + ++
Sbjct: 63 FGKRG----KSGLVA--LNLDLAQVATFVKERLGKEVEMGGCKGPITTFIVEPFVPHD-- 114
Query: 139 LVNEMYFAIMLDRKTAGPIIIGCS-----KGGTSIEDLAEKYPNMIVKVPIDVFNGITDE 193
E Y +I+ DR +GCS GG IE+ +K + + +T E
Sbjct: 115 --QEFYLSIVSDR-------LGCSISFSECGGIEIEENWDKVKTIFLPTE----APLTSE 161
Query: 194 DAAKVVDGLAPKVADRNDAIEQ-VKKLYKLFCESDCTLLEVSMN 236
A ++ L ++ IE+ +K ++ +F + D T LE MN
Sbjct: 162 ICAPLIATLPLEI---RGKIEEFIKGVFAVFQDLDFTFLE--MN 200
>gnl|CDD|217645 pfam03629, DUF303, Domain of unknown function (DUF303).
Distribution of this domain seems limited to prokaryotes
and viruses.
Length = 257
Score = 33.5 bits (77), Expect = 0.096
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 142 EMYFAIMLDRKTAGPI-IIGCSKGGTSIED 170
+FA L ++ PI +I C+ GGT IE
Sbjct: 70 GYFFARKLQQELNVPIGLIPCAWGGTPIEA 99
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 32.9 bits (76), Expect = 0.17
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRG 84
+ M KYGI + +E K I + +VVK+ LA G+G
Sbjct: 109 DFMKKYGIPTAEYEVFTDPEEAKAYIDEKGAP---IVVKADGLAAGKG 153
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 32.8 bits (76), Expect = 0.24
Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 20/89 (22%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQD-AFPDHKELVVKSQILAGGRGLGTFKSGLKGG 95
E M K G+ VP+ S++E + ++ +P ++++ GG G GG
Sbjct: 134 EAMKKIGLPVPRSGIAHSMEEALEVAEEIGYP----VIIRPSFTLGGTG---------GG 180
Query: 96 VHIVKKEEVEDLAGKML-----GQILVTK 119
+ +EE+E++ + L ++L+ +
Sbjct: 181 I-AYNEEELEEIVERGLDLSPVTEVLIEE 208
>gnl|CDD|222215 pfam13549, ATP-grasp_5, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 222
Score = 30.5 bits (70), Expect = 0.85
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 26 RRLNIHEYQGAELMAKYGINVPKGLAVASVDEVKKA 61
R + E + L+A YGI V S +E A
Sbjct: 6 GRTVLTEPEAKALLAAYGIPVVPTRLARSPEEAVAA 41
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 29.6 bits (67), Expect = 2.2
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 25 LRRLNIHEYQGAELMAKYGINVPKGLAVASVDEVKKA-----IQDAFPDHK 70
+ E + EL+ YGI VP +A + V A ++ DHK
Sbjct: 466 GGGTTLDEPEAKELLEAYGIPVPATIASTLDEAVHIAESIGKLRSPDIDHK 516
>gnl|CDD|234856 PRK00885, PRK00885, phosphoribosylamine--glycine ligase;
Provisional.
Length = 420
Score = 29.6 bits (68), Expect = 2.2
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRG 84
+ MA+YGI +E + + +VVK+ LA G+G
Sbjct: 108 DFMARYGIPTAAYETFTDAEEALAYLDEKGAP---IVVKADGLAAGKG 152
>gnl|CDD|237195 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
Provisional.
Length = 326
Score = 29.1 bits (66), Expect = 2.4
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 17/87 (19%)
Query: 33 YQGAELMAKYGINVPKGLAVASVDEVKKAI---QDAFPDHKELVVKSQILAGGRGLGTFK 89
+ E + + GI PK S+++ K A+ + FP L VK + G +G FK
Sbjct: 113 WLTYEFLKENGIPTPKSYLPESLEDFKAALAKGELQFP----LFVKPRD--GSASIGVFK 166
Query: 90 SGLKGGVHIVKKEEVEDLAGKMLGQIL 116
+ KEE+E L + I+
Sbjct: 167 --------VNDKEELEFLLEYVPNLII 185
>gnl|CDD|221251 pfam11832, DUF3352, Protein of unknown function (DUF3352). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 538 to 575
amino acids in length.
Length = 541
Score = 29.3 bits (66), Expect = 2.6
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 20 WQQQQLRRLNIH--EYQGAELMAKYGINVPKGLAVASVDE 57
WQ + L ++ YQG +++ G + + LA A +D+
Sbjct: 144 WQTRSLAGTDLQISTYQGIGIISGQGALLGRPLATALLDD 183
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 28.8 bits (65), Expect = 2.7
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQDA-FPDHKELVVKSQILAGGRG 84
EL+ G+ VP V +++ A ++ FP +V+K + AG G
Sbjct: 10 ELLRAAGLPVPPFFLVDDEEDLDAAAEEIGFP----VVLKPRDGAGSLG 54
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 27.3 bits (61), Expect = 2.7
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 22 QQQLRRLNIHEYQGAELMAKY 42
QQ + +LN HEY+G++L Y
Sbjct: 53 QQAVNKLNGHEYEGSKLKVSY 73
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 29.6 bits (67), Expect = 2.8
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 36 AELMAKYGINVPKGLAVASVDEVKKAIQD-AFPDHKELVVKSQILAGGRGLG 86
E M + G VP+ SV+E A ++ +P ++V+ GG G G
Sbjct: 132 REAMKEIGEPVPESEIAHSVEEALAAAKEIGYP----VIVRPAFTLGGTGGG 179
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 28.9 bits (65), Expect = 3.0
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 167 SIEDLAEKYPNMIVKVPIDVFNGITDEDAA 196
++ DLAEKY + ++ + +DV TD A
Sbjct: 39 TLADLAEKYGDRLLPLALDV----TDRAAV 64
>gnl|CDD|177131 MTH00059, ND2, NADH dehydrogenase subunit 2; Provisional.
Length = 289
Score = 28.7 bits (65), Expect = 3.1
Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 3/52 (5%)
Query: 240 SLVLLICMSLLVGGQVELVI---HLVGGSLCIVLLLLLFSLVDVLVWIFFLF 288
S L+ + + + + S I+ L D+ + FF F
Sbjct: 176 SSATLVVACFCLSIDLCFFLYLYYFFWSSGVIIYFSSLSDSNDLKGYYFFGF 227
>gnl|CDD|233813 TIGR02291, rimK_rel_E_lig, alpha-L-glutamate ligase-related
protein. Members of this protein family contain a
region of homology to the RimK family of
alpha-L-glutamate ligases (TIGR00768), various members
of which modify the Glu-Glu C-terminus of ribosomal
protein S6, or tetrahydromethanopterin, or a form of
coenzyme F420 derivative. Members of this family are
found so far in various Vibrio and Pseudomonas species
and some other gamma and beta Proteobacteria. The
function is unknown.
Length = 317
Score = 28.7 bits (64), Expect = 3.3
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 43 GINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGVH----- 97
GI VP+ V K I + DH + V+K +GG+G+ S G
Sbjct: 49 GITVPELYGVIHNQAEVKTIHNIVKDHPDFVIKPAQGSGGKGILVITSRKDGRYRKPSGA 108
Query: 98 IVKKEEVE 105
+ KEE+E
Sbjct: 109 TINKEEIE 116
>gnl|CDD|178374 PLN02775, PLN02775, Probable dihydrodipicolinate reductase.
Length = 286
Score = 28.8 bits (65), Expect = 3.5
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 114 QILVTKQTGPQGKIVSKVYLCEKLSLVNEMYFAIMLDRKTAG----PI-IIGCSKGGTSI 168
I+V TG G V++ + L LV + T + ++G S+ +
Sbjct: 13 PIMVNGCTGKMGHAVAEAAVSAGLQLVPVSFTGPAGVGVTVEVCGVEVRLVGPSEREAVL 72
Query: 169 EDLAEKYPNMIV 180
+ +YPN+IV
Sbjct: 73 SSVKAEYPNLIV 84
>gnl|CDD|148013 pfam06152, Phage_min_cap2, Phage minor capsid protein 2. Family of
related phage minor capsid proteins.
Length = 361
Score = 28.6 bits (64), Expect = 3.7
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 12 RSLTVAGQWQQQQLRRLN-IHEY--QGAELMAKY-GINVPKGLAVASVDEVKKAIQDAFP 67
+SL +A +Q Q+ +LN + Q +L+AKY G+ + + + K I+D
Sbjct: 38 KSLQLADNVEQWQIEKLNELGLLNKQNIKLIAKYTGVAE-EAITRVIKNAGLKIIKDIDK 96
Query: 68 DHKELVVK 75
E + K
Sbjct: 97 QLSEALNK 104
>gnl|CDD|220420 pfam09815, XK-related, XK-related protein. Members of this family
comprise various XK-related proteins, that are involved
in sodium-dependent transport of neutral amino acids or
oligopeptides. These proteins are responsible for the Kx
blood group system - defects results in McLeod syndrome,
an X-linked multi-system disorder characterized by late
onset abnormalities in the neuromuscular and
hematopoietic systems.
Length = 334
Score = 28.4 bits (64), Expect = 4.1
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 266 LCIVLLLLLFSL----VDVLVWIFFLFWV 290
L + L +F L V +L W+ FWV
Sbjct: 206 LALALFASVFPLYVAAVLLLHWLVMTFWV 234
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 28.7 bits (65), Expect = 4.3
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 38 LMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFK 89
++A+ G VP G S++E F D K +VVK + G G+ FK
Sbjct: 495 ILAEAGFPVPAGDEFTSLEEALADY-SLFAD-KAIVVKPKSTNFGLGISIFK 544
>gnl|CDD|214414 MTH00063, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 522
Score = 28.3 bits (64), Expect = 4.8
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 229 TLLEVSMNFYISLVLLICMSLLVGGQVELVIHLVGG--SLCIVLLLLLF-SLVDVLVWIF 285
+ V N + LV+++C+ L L + L G SL + L F S + V +W+F
Sbjct: 344 SFSSVVFNVSLLLVVILCVFLSYLYSFRLCLILFGVKSSLSSGVRFLFFNSGLMVFLWLF 403
Query: 286 FLFWVRSIL 294
++V +L
Sbjct: 404 INYYVFLLL 412
>gnl|CDD|236887 PRK11259, solA, N-methyltryptophan oxidase; Provisional.
Length = 376
Score = 28.3 bits (64), Expect = 5.4
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 4 GLLNKLVSRSLTVAGQWQQQQLRRLNIHEYQGAELMAKY-GINVPKG 49
G+LN + S +A + + L AE+ ++ +P G
Sbjct: 88 GVLNLGPADSDFLANSIRSARQHGLPHEVLDAAEIRRRFPQFRLPDG 134
>gnl|CDD|185712 cd07902, Adenylation_DNA_ligase_III, Adenylation domain of DNA
Ligase III. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three-step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriophages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
III is not found in lower eukaryotes and is present
both in the nucleus and mitochondria. It has several
isoforms; two splice forms, III-alpha and III-beta,
differ in their carboxy-terminal sequences. DNA ligase
III-beta is believed to play a role in homologous
recombination during meiotic prophase. DNA ligase
III-alpha interacts with X-ray Cross Complementing
factor 1 (XRCC1) and functions in single nucleotide
Base Excision Repair (BER). The mitochondrial form of
DNA ligase III originates from the nucleolus and is
involved in the mitochondrial DNA repair pathway. This
isoform is expressed by a second start site on the DNA
ligase III gene. DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains. The adenylation and
C-terminal oligonucleotide/oligosaccharide binding
(OB)-fold domains comprise a catalytic core unit that
is common to most members of the ATP-dependent DNA
ligase family. The adenylation domain binds ATP and
contains many active site residues. The common
catalytic core unit comprises six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases.
Length = 213
Score = 27.7 bits (62), Expect = 5.5
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 55 VDEVKKAIQDAFPDHKELVVKSQIL 79
V K I AFP +++ S++L
Sbjct: 71 VAHFKDYIPKAFPHGHSMILDSEVL 95
>gnl|CDD|232833 TIGR00118, acolac_lg, acetolactate synthase, large subunit,
biosynthetic type. Two groups of proteins form
acetolactate from two molecules of pyruvate. The type of
acetolactate synthase described in this model also
catalyzes the formation of acetohydroxybutyrate from
pyruvate and 2-oxobutyrate, an early step in the
branched chain amino acid biosynthesis; it is therefore
also termed acetohydroxyacid synthase. In bacteria, this
catalytic chain is associated with a smaller regulatory
chain in an alpha2/beta2 heterotetramer. Acetolactate
synthase is a thiamine pyrophosphate enzyme. In this
type, FAD and Mg++ are also found. Several isozymes of
this enzyme are found in E. coli K12, one of which
contains a frameshift in the large subunit gene and is
not expressed [Amino acid biosynthesis, Pyruvate
family].
Length = 558
Score = 28.2 bits (63), Expect = 6.0
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 9 LVSRSLTVAGQWQQQQLRRLNIHEYQG-----AELMAKYGINVPKGLAVASVDEVKKAIQ 63
L +R L + QWQ+ H + G +L YGI KG+ + +E+ + ++
Sbjct: 464 LNNRYLGMVRQWQELFYEERYSHTHMGSLPDFVKLAEAYGI---KGIRIEKPEELDEKLK 520
Query: 64 DAFPDHKELVV 74
+A E V+
Sbjct: 521 EAL-SSNEPVL 530
>gnl|CDD|178293 PLN02690, PLN02690, Agmatine deiminase.
Length = 374
Score = 28.1 bits (63), Expect = 6.1
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 35 GAELMAKY--------GINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQ---ILAGG 82
G L A Y GI P+ E + + +AFP+HK + V+S +L GG
Sbjct: 303 GERLAASYVNFYIANGGIVAPQFGDAKWDKEAIEVLSEAFPNHKVVGVESAREIVLGGG 361
>gnl|CDD|233823 TIGR02339, thermosome_arch, thermosome, various subunits, archaeal.
Thermosome is the name given to the archaeal rather
than eukaryotic form of the group II chaperonin
(counterpart to the group I chaperonin, GroEL/GroES, in
bacterial), a torroidal, ATP-dependent molecular
chaperone that assists in the folding or refolding of
nascent or denatured proteins. Various homologous
subunits, one to five per archaeal genome, may be
designated alpha, beta, etc., but phylogenetic analysis
does not show distinct alpha subunit and beta subunit
lineages traceable to ancient paralogs [Protein fate,
Protein folding and stabilization].
Length = 519
Score = 28.1 bits (63), Expect = 6.4
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 55 VDEVKKAIQDAFPDHKELVVKSQILAGG 82
VDE+++++QDA + +++AGG
Sbjct: 379 VDELERSLQDALHVVASALEDGKVVAGG 406
>gnl|CDD|162157 TIGR01013, 2a58, Phosphate:Na+ Symporter (PNaS) Family. [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 456
Score = 27.9 bits (62), Expect = 6.7
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 238 YISLVLLICMSLLVGGQVELVIHLVGGSLCIVLLLLLFSLVDVL-----------VWIFF 286
Y+ L L+ SLL G + L LVG + +L L SL+ VL W F
Sbjct: 386 YLVLNFLLAPSLLFGLDLNLARRLVGVKIPFRILELFSSLLHVLQLRCPRPQSLQTWSFL 445
Query: 287 LFWVRSI 293
W+RS+
Sbjct: 446 PDWLRSL 452
>gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29).
Length = 404
Score = 28.0 bits (63), Expect = 6.9
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 29 NIHEYQGAELMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVV 74
+ +Y AEL+ K G+NV KG V I A + LV
Sbjct: 5 RLEKY--AELLVKVGVNVQKG------QTV--LIS-APVEAAPLVR 39
>gnl|CDD|226404 COG3887, COG3887, Predicted signaling protein consisting of a
modified GGDEF domain and a DHH domain [Signal
transduction mechanisms].
Length = 655
Score = 28.1 bits (63), Expect = 7.0
Identities = 10/62 (16%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 235 MNFY--ISLVLLICMSLLVGGQVELVIHLVGGSLCIVLLLLLFSLVDVLVWIFFLFWVRS 292
MN + L+ I + L+ + +++ + +LL ++V++ FL +
Sbjct: 1 MNKFYHKRLLSYIFLGLIAFSIILIIVSFSFNWWLSAIAVLL-----LVVFLIFLLLAFT 55
Query: 293 IL 294
+
Sbjct: 56 LF 57
>gnl|CDD|200101 TIGR01435, glu_cys_lig_rel, glutamate--cysteine
ligase/gamma-glutamylcysteine synthetase, Streptococcus
agalactiae type. This model represents a bifunctional
protein family for the biosynthesis of glutathione, and
perhaps a range of related gamma-glutamyltripeptides of
the form gamma-Glu-Cys-X(aa). The N-terminal region is
similar to proteobacterial glutamate-cysteine ligase.
The C-terminal region is homologous to cyanophycin
synthetase of cyanobacteria and, more distantly, to
D-alanine-D-alanine ligases. Members of This model
family are found in Listeria and Enterococcus,
Gram-positive lineages in which glutathione is produced
(see PUBMED:8606174), and in Pasteurella multocida, a
Proteobacterium. In Clostridium acetobutylicum, adjacent
genes include separate proteins rather than a fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Glutathione and analogs].
Length = 737
Score = 28.0 bits (62), Expect = 7.1
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 38 LMAKYGINVPKGLAVASVDEVKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSG 91
++ K G NVP+G+ +S+++ +A A ++K +VVK + G G+ FK G
Sbjct: 482 VLQKAGFNVPQGVEFSSLEKAVEAY--ALFENKAIVVKPKSTNYGLGITIFKQG 533
>gnl|CDD|233121 TIGR00768, rimK_fam, alpha-L-glutamate ligases, RimK family. This
family, related to bacterial glutathione synthetases,
contains at least two different alpha-L-glutamate
ligases. One is RimK, as in E. coli, which adds
additional Glu residues to the native Glu-Glu C-terminus
of ribosomal protein S6, but not to Lys-Glu mutants.
Most species with a member of this subfamily lack an S6
homolog ending in Glu-Glu, however. Members in
Methanococcus jannaschii act instead as a
tetrahydromethanopterin:alpha-l-glutamate ligase
(MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase
(MJ1001).
Length = 277
Score = 27.7 bits (62), Expect = 7.2
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 38 LMAKYGINVPKGLAVASVDEVKKAIQDA-FPDHKELVVKSQILAGGRGL 85
L+AK G+ P+ S +E K I++ FP +V+K + GR +
Sbjct: 95 LLAKAGLPQPRTGLAGSPEEALKLIEEIGFP----VVLKPVFGSWGRLV 139
>gnl|CDD|237586 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 27.8 bits (63), Expect = 7.3
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 37 ELMAKYGINVPKGLAVASVDEVKKAIQD-AFPDHKELVVKSQILAGGRG 84
L+A G+ VP+G V S ++ +A ++ +P +VVK GRG
Sbjct: 220 RLLAAAGVPVPEGRVVTSAEDAWEAAEEIGYP----VVVKPLDGNHGRG 264
>gnl|CDD|201826 pfam01493, GXGXG, GXGXG motif. This domain is found in glutamate
synthase, tungsten formylmethanofuran dehydrogenase
subunit c (FwdC) and molybdenum formylmethanofuran
dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G
motif is seen in the alignment.
Length = 198
Score = 27.2 bits (61), Expect = 8.4
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 58 VKKAIQDAFPDHKELVVKSQILAGGRGLGTFKSGLKGGVHIVKKEEVEDLAGKML--GQI 115
KK ++ D E+V + G+ G F +KGGV + + + D GK + G+I
Sbjct: 21 TKKYGEEGLKDTGEIVFN---GSAGQSFGAF---MKGGVTLEVEGDANDYVGKGMSGGEI 74
Query: 116 LVTKQTGPQGKIVSKVY 132
++ G G+ V
Sbjct: 75 VIKGNAGDAGEYVGNGI 91
>gnl|CDD|235269 PRK04284, PRK04284, ornithine carbamoyltransferase; Provisional.
Length = 332
Score = 27.4 bits (61), Expect = 8.4
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 13/55 (23%)
Query: 167 SIEDLAEKYPNMIVKVPIDVFNGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYK 221
++E LA +Y VP V+NG+TDED V +AD A E +KK YK
Sbjct: 113 TVETLA-EYSG----VP--VWNGLTDEDHPTQV------LADFLTAKEHLKKPYK 154
>gnl|CDD|211799 TIGR03247, glucar-dehydr, glucarate dehydratase. Glucarate
dehydratase converts D-glucarate (and L-idarate, a
stereoisomer) to 5-dehydro-4-deoxyglucarate which is
subsequently acted on by GarL, tartronate semialdehyde
reductase and glycerate kinase (, GenProp0716). The E.
coli enzyme has been well-characterized.
Length = 441
Score = 27.5 bits (61), Expect = 8.7
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 80 AGGRGLGTFKSGLKGGVHIVKKEEVE--DLAGKMLGQ 114
AGGRGL TF L+ +H V E DL G+ LG
Sbjct: 92 AGGRGLQTFD--LRTTIHAVTAIESALLDLLGQHLGV 126
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 0.141 0.406
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,987,013
Number of extensions: 1482890
Number of successful extensions: 2329
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2298
Number of HSP's successfully gapped: 101
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
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: 59 (26.4 bits)