RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9059
(269 letters)
>gnl|CDD|131494 TIGR02441, fa_ox_alpha_mit, fatty acid oxidation complex, alpha
subunit, mitochondrial. Members represent alpha subunit
of mitochondrial multifunctional fatty acid degradation
enzyme complex. Subunit activities include: enoyl-CoA
hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA
dehydrogenase (EC 1.1.1.35). Some characterization in
human , pig , and rat. The beta subunit has activity:
acetyl-CoA C-acyltransferase (EC 2.3.1.16).
Length = 737
Score = 257 bits (658), Expect = 6e-81
Identities = 99/149 (66%), Positives = 120/149 (80%)
Query: 120 QTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTT 179
P +IGMHYFSPVDKMQLLEIIT + TS+DT ASAVAVGLKQGKVVI VKDGPGFYTT
Sbjct: 463 SRPEKVIGMHYFSPVDKMQLLEIITHDGTSKDTLASAVAVGLKQGKVVIVVKDGPGFYTT 522
Query: 180 RILSTMLSEAMRILQEGTSPKDLDRLTKQFGFPVGAATLSDEVGIDVGAHIAKDLSKTFG 239
R L ML+E +R+LQEG PK LD+LT +FGFPVGAATL+DEVG+DV H+A+DL K FG
Sbjct: 523 RCLGPMLAEVIRLLQEGVDPKKLDKLTTKFGFPVGAATLADEVGVDVAEHVAEDLGKAFG 582
Query: 240 DRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
+RF GG+ +L+E+V+ G+L K+ G +
Sbjct: 583 ERFGGGSAELLSELVKAGFLGRKSGKGIF 611
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 182 bits (463), Expect = 9e-53
Identities = 69/159 (43%), Positives = 93/159 (58%), Gaps = 9/159 (5%)
Query: 117 IPI-------QTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVIT 169
+PI P +IG+HYFSPV+KM L+E+I +TS +T A+ VA+ KQGK I
Sbjct: 428 LPIGQIAAAAARPEQVIGLHYFSPVEKMPLVEVIPHAKTSAETIATTVALAKKQGKTPIV 487
Query: 170 VKDGPGFYTTRILSTMLSEAMRILQEGTSPKDLDRLTKQFGFPVGAATLSDEVGIDVGAH 229
V+DG GFY RIL+ ++EA R+L EG + +D +FGFPVG TL DEVGIDVG
Sbjct: 488 VRDGAGFYVNRILAPYINEAARLLLEGEPIEHIDAALVKFGFPVGPITLLDEVGIDVGTK 547
Query: 230 IAKDLSKTFGDRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
I L G+RFS ++++ KN G+Y
Sbjct: 548 IIPILEAALGERFSAP--AAFDKLLNDDRKGRKNGRGFY 584
Score = 29.5 bits (67), Expect = 2.2
Identities = 29/80 (36%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 185 MLSEAMRILQEGT--SPKDLDRLTKQF--GFPV---GAATLSDEVGIDVGAHIAKDLSKT 237
ML+EA+R L EG S +D D + F GFP G D +G I + L+
Sbjct: 626 MLNEAVRCLDEGIIRSARDGD-IGAVFGIGFPPFLGGPFRYMDSLGAGEVVAILERLAAQ 684
Query: 238 FGDRFSGGNLNVLNEMVEKG 257
+GDRF+ L EM E+G
Sbjct: 685 YGDRFTPCER--LVEMAERG 702
>gnl|CDD|224170 COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism].
Length = 307
Score = 152 bits (386), Expect = 1e-44
Identities = 60/149 (40%), Positives = 91/149 (61%), Gaps = 2/149 (1%)
Query: 122 PHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRI 181
P IG+H+F+PV M L+E+I E+TS +T V K GK + VKD PGF R+
Sbjct: 133 PERFIGLHFFNPVPLMPLVEVIRGEKTSDETVERVVEFAKKIGKTPVVVKDVPGFIVNRL 192
Query: 182 LSTMLSEAMRILQEGT-SPKDLDRLTKQ-FGFPVGAATLSDEVGIDVGAHIAKDLSKTFG 239
L+ +L+EA+R+L+EG +P+++D +Q G P+G L+D +G+DV HI K L++T G
Sbjct: 193 LAALLNEAIRLLEEGVATPEEIDAAMRQGLGLPMGPFELADLIGLDVMLHIMKVLNETLG 252
Query: 240 DRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
D +L ++VE G L K+ G+Y
Sbjct: 253 DDPYYRPPPLLRKLVEAGRLGRKSGKGFY 281
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 141 bits (357), Expect = 3e-38
Identities = 74/184 (40%), Positives = 103/184 (55%), Gaps = 5/184 (2%)
Query: 86 QQMSERIYMYTYSERLMGSNGLAMVFPL-QEQIPIQTPHLIIGMHYFSPVDKMQLLEIIT 144
QM + I + + SN ++ P+ Q P +IG+HYFSPV+KM L+E+I
Sbjct: 400 HQMVKDIEQECAAHTIFASNTSSL--PIGQIAAAASRPENVIGLHYFSPVEKMPLVEVIP 457
Query: 145 TEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRILSTMLSEAMRILQEGTSPKDLDR 204
TS+ T A+ VA+ KQGK I V D GFY RIL+ ++EA R+L EG + +D+
Sbjct: 458 HAGTSEQTIATTVALAKKQGKTPIVVADKAGFYVNRILAPYMNEAARLLLEGEPVEHIDK 517
Query: 205 LTKQFGFPVGAATLSDEVGIDVGAHIAKDLSKTFGDRFSGGNLNVLNEMVEKGYLDFKNK 264
+FGFPVG TL DEVGIDVGA I+ L G+RF V ++++ KN
Sbjct: 518 ALVKFGFPVGPITLLDEVGIDVGAKISPILEAELGERFKAP--AVFDKLLSDDRKGRKNG 575
Query: 265 DGYY 268
G+Y
Sbjct: 576 KGFY 579
Score = 31.7 bits (72), Expect = 0.48
Identities = 28/81 (34%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 170 VKDGPGFYTTRILSTMLSEAMRILQEGT--SPKDLDRLTKQF--GFPV---GAATLSDEV 222
V R + ML+EA+R L EG SP+D D + F GFP G D +
Sbjct: 604 VDKEASAVAERCVMLMLNEAVRCLDEGVIRSPRDGD-IGAIFGIGFPPFLGGPFRYIDTL 662
Query: 223 GIDVGAHIAKDLSKTFGDRFS 243
G D I + L +GDRF+
Sbjct: 663 GADNVVKILERLQTQYGDRFT 683
>gnl|CDD|180269 PRK05808, PRK05808, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 282
Score = 109 bits (275), Expect = 1e-28
Identities = 58/153 (37%), Positives = 86/153 (56%), Gaps = 7/153 (4%)
Query: 120 QTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTT 179
+ P +IGMH+F+PV M+L+EII TS T + A+ K GK + VK+ PGF
Sbjct: 131 KRPDKVIGMHFFNPVPVMKLVEIIRGLATSDATHEAVEALAKKIGKTPVEVKNAPGFVVN 190
Query: 180 RILSTMLSEAMRILQEGT-SPKDLDRLTKQFG--FPVGAATLSDEVGIDVGAHIAKDLSK 236
RIL M++EA+ +L EG + +D+D K G P+G L+D +G+D I + L +
Sbjct: 191 RILIPMINEAIFVLAEGVATAEDIDEGMK-LGCNHPIGPLALADLIGLDTCLAIMEVLYE 249
Query: 237 TFGD-RFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
FGD ++ L L +MV G+L K G+Y
Sbjct: 250 GFGDSKYRPCPL--LRKMVAAGWLGRKTGRGFY 280
>gnl|CDD|236434 PRK09260, PRK09260, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 288
Score = 104 bits (261), Expect = 1e-26
Identities = 60/193 (31%), Positives = 102/193 (52%), Gaps = 7/193 (3%)
Query: 78 EQIPIQTPQQMSERIYMYTYSERLMGSNGLAMVFPLQEQIPIQTPHLIIGMHYFSPVDKM 137
E++ ++ + + E + +E + +N M P + + P +I MH+F+PV KM
Sbjct: 91 EKLELK--KAVFETADAHAPAECYIATNTSTMS-PTEIASFTKRPERVIAMHFFNPVHKM 147
Query: 138 QLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRILSTMLSEAMRILQEGT 197
+L+E+I +TS +T A V + GK + V + PGF T+RI + + +EA +LQEG
Sbjct: 148 KLVELIRGLETSDETVQVAKEVAEQMGKETVVVNEFPGFVTSRISALVGNEAFYMLQEGV 207
Query: 198 -SPKDLDRLTKQ-FGFPVGAATLSDEVGIDVGAHIAKDLSKTFGDRFSGGNLNVLNEMVE 255
+ +D+D+ + FP+G L D VG+D + K L +T G+++ L L + V+
Sbjct: 208 ATAEDIDKAIRLGLNFPMGPLELGDLVGLDTRLNNLKYLHETLGEKYRPAPL--LEKYVK 265
Query: 256 KGYLDFKNKDGYY 268
G L K G Y
Sbjct: 266 AGRLGRKTGRGVY 278
>gnl|CDD|180361 PRK06035, PRK06035, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 291
Score = 104 bits (260), Expect = 2e-26
Identities = 59/152 (38%), Positives = 88/152 (57%), Gaps = 10/152 (6%)
Query: 125 IIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRILST 184
IGMH+F+P M+L+E++ TS++T + V + K GK+ I V D PGF+TTR +
Sbjct: 139 FIGMHWFNPAPVMKLIEVVRAALTSEETFNTTVELSKKIGKIPIEVADVPGFFTTRFIEG 198
Query: 185 MLSEAMRILQEGTSP-KDLDRLTK-QFGFPVGAATLSDEVGIDVGAHIAKDLSKTFGD-R 241
L EA+R + G + KD+D + K FGFP+G L D +GID HIA+ L + GD +
Sbjct: 199 WLLEAIRSFEIGIATIKDIDEMCKLAFGFPMGPFELMDIIGIDTVYHIAEYLYEETGDPQ 258
Query: 242 FSGGNLNVLNEMVEKGYL-----DFKNKDGYY 268
F N L +MV GY+ + +K G++
Sbjct: 259 FIPP--NSLKQMVLNGYVGDKKVKYGSKGGWF 288
>gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 715
Score = 107 bits (269), Expect = 3e-26
Identities = 56/160 (35%), Positives = 86/160 (53%), Gaps = 8/160 (5%)
Query: 117 IPI-------QTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVIT 169
I I + P GMH+F+PV +M L+E+I E+TS +T A+ VA K GK I
Sbjct: 431 ISISLLAKALKRPENFCGMHFFNPVHRMPLVEVIRGEKTSDETIATVVAYASKMGKTPIV 490
Query: 170 VKDGPGFYTTRILSTMLSEAMRILQEGTSPKDLDR-LTKQFGFPVGAATLSDEVGIDVGA 228
V D PGF+ R+L + ++L++G + +D+ + KQFG+P+G A L D VGID
Sbjct: 491 VNDCPGFFVNRVLFPYFAGFSQLLRDGADFRQIDKVMEKQFGWPMGPAYLLDVVGIDTAH 550
Query: 229 HIAKDLSKTFGDRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
H +++ F DR + ++ + E KN G+Y
Sbjct: 551 HAQAVMAEGFPDRMKKDYRDAIDVLFEAKRFGQKNGKGFY 590
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Activities include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 105 bits (264), Expect = 9e-26
Identities = 55/151 (36%), Positives = 85/151 (56%), Gaps = 1/151 (0%)
Query: 119 IQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYT 178
++ P GMH+F+PV +M L+E+I E++S +T A+ VA K GK I V D PGF+
Sbjct: 440 LKRPENFCGMHFFNPVHRMPLVEVIRGEKSSDETIATVVAYASKMGKTPIVVNDCPGFFV 499
Query: 179 TRILSTMLSEAMRILQEGTSPKDLDR-LTKQFGFPVGAATLSDEVGIDVGAHIAKDLSKT 237
R+L ++L++G +D+ + KQFG+P+G A L D VGID G H +++
Sbjct: 500 NRVLFPYFGGFSKLLRDGADFVRIDKVMEKQFGWPMGPAYLLDVVGIDTGHHAQAVMAEG 559
Query: 238 FGDRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
F DR + ++ + E L KN G+Y
Sbjct: 560 FPDRMGKDGRDAIDALFEAKRLGQKNGKGFY 590
>gnl|CDD|216084 pfam00725, 3HCDH, 3-hydroxyacyl-CoA dehydrogenase, C-terminal
domain. This family also includes lambda crystallin.
Some proteins include two copies of this domain.
Length = 97
Score = 95.0 bits (237), Expect = 5e-25
Identities = 39/96 (40%), Positives = 61/96 (63%), Gaps = 3/96 (3%)
Query: 175 GFYTTRILSTMLSEAMRILQEGT-SPKDLDRLTKQ-FGFPVGAATLSDEVGIDVGAHIAK 232
GF R+L+ +L+EA+R+++EG +P+D+D + G P+G LSD VG+DVG HI +
Sbjct: 1 GFVVNRLLAPLLNEAIRLVEEGVATPEDIDAAMRLGLGLPMGPFELSDLVGLDVGYHILE 60
Query: 233 DLSKTFGDRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
L++ FGDR + +L ++VE G L K G+Y
Sbjct: 61 VLAEEFGDRAYRPSP-LLEKLVEAGRLGRKTGKGFY 95
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 93.6 bits (233), Expect = 2e-22
Identities = 53/152 (34%), Positives = 78/152 (51%), Gaps = 5/152 (3%)
Query: 120 QTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTT 179
Q P +IGMH+ +P M+L+EII TS + + A+ + GK V+ +D PGF
Sbjct: 132 QRPQQVIGMHFMNPPPIMKLVEIIRGADTSDEVFDATKALAERFGKTVVCSQDYPGFIVN 191
Query: 180 RILSTMLSEAMRILQEG-TSPKDLDRLTK-QFGFPVGAATLSDEVGIDVGAHIAKDLSKT 237
RIL M++EA L G S +D+D K P+G L+D +G+D I K L +
Sbjct: 192 RILMPMINEAFYALYTGVASKEDIDTGMKLGTNHPMGPLHLADFIGLDTCLSIMKVLHEG 251
Query: 238 FGD-RFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
GD ++ L L + V+ G L K+ G Y
Sbjct: 252 LGDSKYRPCPL--LVQYVDAGRLGRKSGRGVY 281
>gnl|CDD|188207 TIGR02279, PaaC-3OHAcCoADH, 3-hydroxyacyl-CoA dehydrogenase PaaC.
This 3-hydroxyacyl-CoA dehydrogenase is involved in the
degradation of phenylacetic acid, presumably in steps
following the opening of the phenyl ring. The sequences
included in this model are all found in aparrent operons
with other related genes such as paaA, paaB, paaD, paaE,
paaF and paaN. Some genomes contain these other genes
without an apparent paaC in the same operon - possibly
in these cases a different dehydrogenase involved in
fatty acid degradation may fill in the needed activity.
This enzyme has domains which are members of the
pfam02737 and pfam00725 families.
Length = 503
Score = 78.4 bits (193), Expect = 2e-16
Identities = 46/153 (30%), Positives = 72/153 (47%), Gaps = 4/153 (2%)
Query: 119 IQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYT 178
+ P + G+H+F+P M L+E+++ T+ + A L GK + PGF
Sbjct: 132 LARPERVAGLHFFNPAPVMALVEVVSGLATAAEVAEQLYETALAWGKQPVHCHSTPGFIV 191
Query: 179 TRILSTMLSEAMRILQEGTS-PKDLDRLTKQ-FGFPVGAATLSDEVGIDVGAHIAKDLSK 236
R+ +EA+R L+E + P LD + GFP+G L+D +G DV + +
Sbjct: 192 NRVARPYYAEALRALEEQVAAPAVLDAALRDGAGFPMGPFELTDLIGHDVNFAVTCSVFN 251
Query: 237 TF-GDRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
F DR +L V E+V G L K+ G Y
Sbjct: 252 AFWQDRRFLPSL-VQQELVIAGRLGRKSGLGVY 283
Score = 36.5 bits (84), Expect = 0.012
Identities = 22/111 (19%), Positives = 47/111 (42%), Gaps = 4/111 (3%)
Query: 134 VDKMQLLEIITTEQTSQDTAASAVAVGL--KQGKVVITVKDGPGFYTTRILSTMLSEAMR 191
+D I +A+ A+ + GK V+ + D PG R ++ + +EA
Sbjct: 372 LDYSTGKRIAIAAAAVNPDSATRKAIYYLQQAGKKVLQIADYPGLLILRTVAMLANEAAD 431
Query: 192 ILQEGT-SPKDLDRLTKQ-FGFPVGAATLSDEVGIDVGAHIAKDLSKTFGD 240
+ +G S +D+D + +P G + ++G + ++L +G+
Sbjct: 432 AVLQGVASAQDIDTAMRLGVNYPYGPLAWAAQLGWQRILRVLENLQHHYGE 482
>gnl|CDD|235707 PRK06130, PRK06130, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 311
Score = 76.0 bits (187), Expect = 4e-16
Identities = 49/153 (32%), Positives = 77/153 (50%), Gaps = 8/153 (5%)
Query: 122 PHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITV-KDGPGFYTTR 180
P +G H+F+P D + L+E++ ++TS T A+ +A+ GK + V KD PGF R
Sbjct: 130 PERFVGTHFFTPADVIPLVEVVRGDKTSPQTVATTMALLRSIGKRPVLVKKDIPGFIANR 189
Query: 181 ILSTMLSEAMRILQEG-TSPKDLDRLTK-QFGFP---VGAATLSDEVGIDVGAHIAKDLS 235
I + EA+ +L++G S +D+D + K G G D G+DV +A L
Sbjct: 190 IQHALAREAISLLEKGVASAEDIDEVVKWSLGIRLALTGPLEQRDMNGLDVHLAVASYLY 249
Query: 236 KTFGDRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
+ +R +L E VE G L K+ G+Y
Sbjct: 250 QDLENR--TTPSPLLEEKVEAGELGAKSGQGFY 280
>gnl|CDD|181133 PRK07819, PRK07819, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 286
Score = 73.9 bits (182), Expect = 2e-15
Identities = 51/163 (31%), Positives = 82/163 (50%), Gaps = 13/163 (7%)
Query: 117 IPIQT-------PHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVA-VGLKQGKVVI 168
IPI P ++G+H+F+PV + L+E++ T TS+ T A A GK V+
Sbjct: 124 IPIMKLAAATKRPGRVLGLHFFNPVPVLPLVELVPTLVTSEATVARAEEFASDVLGKQVV 183
Query: 169 TVKDGPGFYTTRILSTMLSEAMRILQEG-TSPKDLDR-LTKQFGFPVGAATLSDEVGIDV 226
+D GF +L L A+R+++ G + +D+D+ + P+G LSD VG+D
Sbjct: 184 RAQDRSGFVVNALLVPYLLSAIRMVESGFATAEDIDKAMVLGCAHPMGPLRLSDLVGLDT 243
Query: 227 GAHIAKDLSKTFGD-RFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
IA + + F + ++ L L MVE G L K+ G+Y
Sbjct: 244 VKAIADSMYEEFKEPLYAPPPL--LLRMVEAGLLGKKSGRGFY 284
>gnl|CDD|202367 pfam02737, 3HCDH_N, 3-hydroxyacyl-CoA dehydrogenase, NAD binding
domain. This family also includes lambda crystallin.
Length = 180
Score = 70.6 bits (174), Expect = 5e-15
Identities = 22/54 (40%), Positives = 34/54 (62%)
Query: 119 IQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKD 172
+ P IG+H+F+P M L+E++ E+TS +T A+ VA+ K GK + VKD
Sbjct: 126 TKRPERFIGLHFFNPPPLMPLVEVVRGEKTSPETVATVVALAKKIGKTPVVVKD 179
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 70.6 bits (174), Expect = 7e-14
Identities = 35/102 (34%), Positives = 56/102 (54%), Gaps = 2/102 (1%)
Query: 127 GMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRILSTML 186
G+H+F+PV M+L+E+++ T A + A+ GK + KD PGF R
Sbjct: 142 GLHFFNPVPLMKLVEVVSGLATDPAVADALYALARAWGKTPVRAKDTPGFIVNRAARPYY 201
Query: 187 SEAMRILQEG-TSPKDLDRLTK-QFGFPVGAATLSDEVGIDV 226
+EA+R+L+EG P +D + + GF +G L D +G+DV
Sbjct: 202 TEALRVLEEGVADPATIDAILREAAGFRMGPFELMDLIGLDV 243
Score = 51.8 bits (125), Expect = 1e-07
Identities = 28/101 (27%), Positives = 50/101 (49%), Gaps = 2/101 (1%)
Query: 142 IITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRILSTMLSEAMRILQEG-TSPK 200
++ TS +A A+ + GK V ++D PGF R ++ +++EA I Q+G SP
Sbjct: 383 LMAAPATSPAARDAAHALFQQDGKAVSVIRDSPGFVAQRTVAMIVNEAADIAQQGIASPA 442
Query: 201 DLDR-LTKQFGFPVGAATLSDEVGIDVGAHIAKDLSKTFGD 240
D+D + +P+G D +G + ++L +GD
Sbjct: 443 DIDLAMRLGLNYPLGPLAWGDRLGAARILRVLENLQALYGD 483
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 62.7 bits (153), Expect = 2e-11
Identities = 50/151 (33%), Positives = 75/151 (49%), Gaps = 7/151 (4%)
Query: 122 PHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYTTRI 181
P IG+H+ +PV M+L+E+I T + T +A K GK + +D P F RI
Sbjct: 134 PERFIGIHFMNPVPVMKLVELIRGIATDEATFEAAKEFVTKLGKTITVAEDFPAFIVNRI 193
Query: 182 LSTMLSEAMRILQEGT-SPKDLDRLTKQFG--FPVGAATLSDEVGIDVGAHIAKDLSKTF 238
L M++EA+ L EG S + +D K G P+G L+D +G+D I + L
Sbjct: 194 LLPMINEAIYTLYEGVGSVEAIDTAMK-LGANHPMGPLELADFIGLDTCLSIMQVLHDGL 252
Query: 239 GD-RFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
D ++ L L + VE G+L K G+Y
Sbjct: 253 ADSKYRPCPL--LVKYVEAGWLGRKTGRGFY 281
>gnl|CDD|181340 PRK08269, PRK08269, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 314
Score = 52.8 bits (127), Expect = 4e-08
Identities = 39/157 (24%), Positives = 74/157 (47%), Gaps = 10/157 (6%)
Query: 119 IQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITVKDGPGFYT 178
+ P + H+ +P M L+E+ ++ T A+ + GKV + PG+
Sbjct: 127 VAHPERFLNAHWLNPAYLMPLVEVSPSDATDPAVVDRLAALLERIGKVPVVCGPSPGYIV 186
Query: 179 TRILSTMLSEAMRILQEG-TSPKDLDRLTKQFGFPVGAATLS-----DEVGIDVGAHIAK 232
RI + ++EA R+++EG S +D+D+ + GF + A L D G D+ + ++
Sbjct: 187 PRIQALAMNEAARMVEEGVASAEDIDKAIR-TGFGLRFAVLGLLEFIDWGGCDILYYASR 245
Query: 233 DLSKTFG-DRFSGGNLNVLNEMVEKGYLDFKNKDGYY 268
L+ G DRF+ ++ +E+G + G+Y
Sbjct: 246 YLAGEIGPDRFAPP--AIVVRNMEEGRDGLRTGAGFY 280
>gnl|CDD|181359 PRK08293, PRK08293, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 287
Score = 46.5 bits (111), Expect = 5e-06
Identities = 36/144 (25%), Positives = 66/144 (45%), Gaps = 3/144 (2%)
Query: 128 MHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITV-KDGPGFYTTRILSTML 186
+H+ + + K EI+ T + + VA G V I + K+ PG+ +L L
Sbjct: 141 LHFANEIWKNNTAEIMGHPGTDPEVFDTVVAFAKAIGMVPIVLKKEQPGYILNSLLVPFL 200
Query: 187 SEAMRILQEG-TSPKDLDR-LTKQFGFPVGAATLSDEVGIDVGAHIAKDLSKTFGDRFSG 244
S A+ + +G P+ +D+ G P+G + D VG+D +I + ++ D +
Sbjct: 201 SAALALWAKGVADPETIDKTWMIATGAPMGPFGILDIVGLDTAYNITSNWAEATDDENAK 260
Query: 245 GNLNVLNEMVEKGYLDFKNKDGYY 268
+L E ++KG L +G+Y
Sbjct: 261 KAAALLKEYIDKGKLGVATGEGFY 284
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 39.8 bits (93), Expect = 9e-04
Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 125 IIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITV-KDGPGFYTTRILS 183
++G H F+PV + L+E++ E+T+ + +A+ + G + V K+ PGF R+L
Sbjct: 138 VVG-HPFNPVYLLPLVEVLGGERTAPEAVDAAMGIYRALGMRPLHVRKEVPGFIADRLLE 196
Query: 184 TMLSEAMRILQEGTS 198
+ EA+ ++ EG +
Sbjct: 197 ALWREALHLVNEGVA 211
>gnl|CDD|235706 PRK06129, PRK06129, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 308
Score = 37.3 bits (87), Expect = 0.005
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 14/93 (15%)
Query: 118 PIQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAVGLKQGKVVITV-KDGPGF 176
PI P+LI PV +E++ T+ T A A A+ G+ + + ++ GF
Sbjct: 141 PINPPYLI-------PV-----VEVVPAPWTAPATLARAEALYRAAGQSPVRLRREIDGF 188
Query: 177 YTTRILSTMLSEAMRILQEG-TSPKDLDRLTKQ 208
R+ +L EA R++ +G S D+D + +
Sbjct: 189 VLNRLQGALLREAFRLVADGVASVDDIDAVIRD 221
>gnl|CDD|236044 PRK07531, PRK07531, bifunctional 3-hydroxyacyl-CoA
dehydrogenase/thioesterase; Validated.
Length = 495
Score = 32.0 bits (73), Expect = 0.33
Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 112 PLQEQIPIQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVA----VGLKQGKVV 167
P Q + P + H ++PV + L+E++ +TS +T A +G+K V
Sbjct: 121 PSDLQEGMTHPERLFVAHPYNPVYLLPLVELVGGGKTSPETIRRAKEILREIGMK--PVH 178
Query: 168 ITVKDGPGFYTTRILSTMLSEAMRILQEG 196
I K+ F R+L + EA+ ++++G
Sbjct: 179 IA-KEIDAFVGDRLLEALWREALWLVKDG 206
>gnl|CDD|179270 PRK01278, argD, acetylornithine transaminase protein; Provisional.
Length = 389
Score = 31.0 bits (71), Expect = 0.56
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 19/68 (27%)
Query: 210 GFPVGAATLSDEV--GIDVGAHIAKDLSKTFGDRFSGGNL-------NVLNEMVEKGYLD 260
GFP+GA ++E G+ G H T+G GN VL+ ++ G+LD
Sbjct: 249 GFPLGACLATEEAAKGMTPGTH-----GSTYG-----GNPLAMAVGNAVLDVILAPGFLD 298
Query: 261 FKNKDGYY 268
+ G Y
Sbjct: 299 NVQRMGLY 306
>gnl|CDD|216067 pfam00696, AA_kinase, Amino acid kinase family. This family
includes kinases that phosphorylate a variety of amino
acid substrates, as well as uridylate kinase and
carbamate kinase. This family includes: Aspartokinase
EC:2.7.2.4, Acetylglutamate kinase EC:2.7.2.8, Glutamate
5-kinase EC:2.7.2.11, Uridylate kinase EC:2.7.4.-,
Carbamate kinase EC:2.7.2.2.
Length = 230
Score = 30.1 bits (68), Expect = 0.85
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 15/65 (23%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYT--------TRILSTM-LSEAMRILQE-----G 196
DT A+ +A L K++I + D G YT +++ + EA +L G
Sbjct: 149 DTLAALLAEALGADKLII-LTDVDGVYTADPRKNPDAKLIPELSYDEAEELLAAGDVTGG 207
Query: 197 TSPKD 201
K
Sbjct: 208 MKVKH 212
>gnl|CDD|223103 COG0024, Map, Methionine aminopeptidase [Translation, ribosomal
structure and biogenesis].
Length = 255
Score = 29.9 bits (68), Expect = 1.1
Identities = 23/95 (24%), Positives = 35/95 (36%), Gaps = 37/95 (38%)
Query: 180 RILSTMLSEAMRILQEGTSPKDLDRLTKQF--------------GFPVGAATLS------ 219
+I + L E +++ G + +LD + ++F GFP +S
Sbjct: 19 KIAAKALKEVASLVKPGVTTLELDEIAEEFIREKGAYPAFLGYKGFP-FPTCISVNEVVA 77
Query: 220 -------------DEVGIDVGAHI---AKDLSKTF 238
D V IDVGAHI D + TF
Sbjct: 78 HGIPGDKKVLKEGDIVKIDVGAHIDGYIGDTAITF 112
>gnl|CDD|204078 pfam08832, SRC-1, Steroid receptor coactivator. This domain is
found in steroid/nuclear receptor coactivators and
contains two LXXLL motifs that are involved in receptor
binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2,
pCIP/ACTR/GRIP-1/AIB1.
Length = 78
Score = 28.3 bits (63), Expect = 1.2
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 184 TMLSEAMRIL----QEGTSPKDLDRLT 206
+ L E +IL Q G+SP DL +LT
Sbjct: 50 SSLKEKHKILHRLLQNGSSPVDLAKLT 76
>gnl|CDD|239783 cd04250, AAK_NAGK-C, AAK_NAGK-C: N-Acetyl-L-glutamate kinase -
cyclic (NAGK-C) catalyzes the phosphorylation of the
gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in
the second step of arginine biosynthesis found in some
bacteria and photosynthetic organisms using the
non-acetylated, cyclic route of ornithine biosynthesis.
In this pathway, glutamate is first N-acetylated and
then phosphorylated by NAGK to give phosphoryl NAG,
which is converted to NAG-ornithine. There are two
variants of this pathway. In one, typified by the
pathway in Thermotoga maritima and Pseudomonas
aeruginosa, the acetyl group is recycled by reversible
transacetylation from acetylornithine to glutamate. The
phosphorylation of NAG by NAGK is feedback inhibited by
arginine. In photosynthetic organisms, NAGK is the
target of the nitrogen-signaling protein PII. Hexameric
formation of NAGK domains appears to be essential to
both arginine inhibition and NAGK-PII complex formation.
NAGK-C are members of the Amino Acid Kinase Superfamily
(AAK).
Length = 279
Score = 29.8 bits (68), Expect = 1.5
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYT-----TRILSTM-LSEAMRILQEGT 197
DTAA A+A LK K+++ + D G ++S + L EA ++ +G
Sbjct: 180 DTAAGAIAAALKAEKLIL-LTDVAGVLDDPNDPGSLISEISLKEAEELIADGI 231
>gnl|CDD|118101 pfam09565, RE_NgoFVII, NgoFVII restriction endonuclease. This
family includes the NgoFVII (recognises GCSGC but
cleavage site unknown) restriction endonuclease.
Length = 296
Score = 29.7 bits (67), Expect = 1.6
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 113 LQEQIPIQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAV--GLK-QGKVVIT 169
L E I LI+GM+ + Q + +D+ V V + GK+ I
Sbjct: 29 LVENHHILKITLIVGMYPSEGLSASQHNSLEKLHDKLKDSDRGDVYVVPNPEYHGKIYIF 88
Query: 170 VKDG 173
KDG
Sbjct: 89 HKDG 92
>gnl|CDD|227135 COG4798, COG4798, Predicted methyltransferase [General function
prediction only].
Length = 238
Score = 29.0 bits (65), Expect = 2.0
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 160 GLKQGKVVITVKDGPGFYTTRILSTMLSEAMRILQEGTSPKDLDRLTKQFGFPVGAAT 217
GLK G VI + G G++ TRI S + ++ P +L + K+ G + AA
Sbjct: 45 GLKPGATVIDLIPGGGYF-TRIFSPAVGPKGKVY--AYVPAELTKFAKREGPRLNAAA 99
>gnl|CDD|233076 TIGR00657, asp_kinases, aspartate kinase. Aspartate kinase
catalyzes a first step in the biosynthesis from Asp of
Lys (and its precursor diaminopimelate), Met, and Thr.
In E. coli, a distinct isozyme is inhibited by each of
the three amino acid products. The Met-sensitive (I) and
Thr-sensitive (II) forms are bifunctional enzymes fused
to homoserine dehydrogenases and form homotetramers,
while the Lys-sensitive form (III) is a monofunctional
homodimer.The Lys-sensitive enzyme of Bacillus subtilis
resembles the E. coli form but is an alpha 2/beta 2
heterotetramer, where the beta subunit is translated
from an in-phase alternative initiator at Met-246. This
may be a feature of a number of closely related forms,
including a paralog from B. subtilis [Amino acid
biosynthesis, Aspartate family].
Length = 441
Score = 29.2 bits (66), Expect = 2.1
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYTT--RILSTMLSEAMRI 192
D A+ +A LK + I D G YTT RI + +A RI
Sbjct: 194 DYTAALLAAALKADECEI-YTDVDGIYTTDPRI----VPDARRI 232
>gnl|CDD|239771 cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate kinase
(NAGK)-like . Included in this CD are the Escherichia
coli and Pseudomonas aeruginosa type NAGKs which
catalyze the phosphorylation of N-acetyl-L-glutamate
(NAG) by ATP in the second step of arginine biosynthesis
found in bacteria and photosynthetic organisms using
either the acetylated, noncyclic (NC), or
non-acetylated, cyclic (C) route of ornithine
biosynthesis. Also included in this CD is a distinct
group of uncharacterized (UC) bacterial and archeal
NAGKs. Members of this CD belong to the Amino Acid
Kinase Superfamily (AAK).
Length = 256
Score = 29.0 bits (66), Expect = 2.2
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYT--TRILSTM-LSEAMRILQEGT 197
DTAA A+A LK K+++ + D PG ++S + EA ++++G
Sbjct: 160 DTAAGAIAAALKAEKLIL-LTDVPGVLDDPGSLISELTPKEAEELIEDGV 208
>gnl|CDD|237252 PRK12896, PRK12896, methionine aminopeptidase; Reviewed.
Length = 255
Score = 28.6 bits (65), Expect = 3.0
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 33/83 (39%)
Query: 180 RILSTMLSEAMRILQEGTSPKDLDRLTKQF--------------GFPVGAATLS------ 219
RI++T L E + ++ G + K+LDR+ ++ GFP G+ +S
Sbjct: 24 RIVATALKEMGKAVEPGMTTKELDRIAEKRLEEHGAIPSPEGYYGFP-GSTCISVNEEVA 82
Query: 220 ------------DEVGIDVGAHI 230
D V IDV A++
Sbjct: 83 HGIPGPRVIKDGDLVNIDVSAYL 105
>gnl|CDD|130652 TIGR01591, Fdh-alpha, formate dehydrogenase, alpha subunit,
archaeal-type. This model describes a subset of formate
dehydrogenase alpha chains found mainly archaea but also
in alpha and gamma proteobacteria and a small number of
gram positive bacteria. The alpha chain contains domains
for molybdopterin dinucleotide binding and molybdopterin
oxidoreductase (pfam01568 and pfam00384, respectively).
The holo-enzyme also contains beta and gamma subunits.
The enzyme catalyzes the oxidation of formate (produced
from pyruvate during anaerobic growth) to carbon dioxide
with the concomitant release of two electrons and two
protons. The enzyme's purpose is to allow growth on
formate in some circumstances and, in the case of FdhH
in gamma proteobacteria, to pass electrons to
hydrogenase (by which process acid is neutralized). This
model is well-defined, with only a single fragmentary
sequence falling between trusted and noise. The alpha
subunit of a version of nitrate reductase is closely
related.
Length = 671
Score = 29.0 bits (65), Expect = 3.1
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 11/61 (18%)
Query: 62 ERLMGSNGLAMVFPLQEQIPIQTPQQMSERIYMYTYSERLMGSNGLAMVFPLQEQIPIQT 121
ERL L +P + T Y+Y ++ +G A PL+ PI+
Sbjct: 507 ERLDELGSLQ--WPCNDSDASPTS-------YLYK--DKFATPDGKAKFIPLEWVAPIEE 555
Query: 122 P 122
P
Sbjct: 556 P 556
>gnl|CDD|223601 COG0527, LysC, Aspartokinases [Amino acid transport and
metabolism].
Length = 447
Score = 28.8 bits (65), Expect = 3.1
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYTT 179
D +A+A+A L +V I D G YT
Sbjct: 200 DYSAAALAAALGADEVEI-WTDVDGVYTA 227
>gnl|CDD|197274 cd09177, PLDc_RE_NgoFVII, Putative catalytic domain of type II
restriction enzyme NgoFVII and similar proteins.
Putative catalytic domain of type II restriction enzyme
NgoFVII (EC 3.1.21.4), which shows high sequence
similarity to type IIs restriction endonuclease BfiI.
Type II restriction endonucleases are components of
restriction modification (RM) systems that protect
bacteria and archaea against invading foreign DNA. They
usually function as homodimers or homotetramers that
cleave DNA at defined sites of 4 to 8 bp in length, and
they require Mg2+, not ATP or GTP, for catalysis. The
prototype of this subfamily is the NgoFVII restriction
endonuclease from Neisseria gonorrhoeae. It plays an
essential role in the endonucleolytic cleavage of DNA to
give specific double-stranded fragments with terminal
5'-phosphates. It recognizes the double-stranded
sequence GCSGC and cleaves after G-4. Members of this
subfamily contain one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) per protein chain and have been classified into
the phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 143
Score = 27.7 bits (62), Expect = 3.9
Identities = 27/112 (24%), Positives = 44/112 (39%), Gaps = 16/112 (14%)
Query: 106 GLAMVFPLQEQIPIQTPHLIIGMHYFSPVDKMQLLEIITTEQTSQDTAASAVAV--GLK- 162
L + L E+ I T L IGM++ + ++Q I Q+ V + K
Sbjct: 26 SLQELDKLVEEHNISTIKLTIGMYFIEGMPELQYNTAIRLNDKWQEEGIGGVYIVPFFKY 85
Query: 163 QGKVVITVKDGPGFYTTRILSTMLS------------EAMRILQEGTSPKDL 202
GK+ + KDG F + I S L E IL++ + P ++
Sbjct: 86 HGKLYLFKKDGKPF-SAIIGSANLGAIWLTASTRRQYETSVILEDISEPAEI 136
>gnl|CDD|233075 TIGR00656, asp_kin_monofn, aspartate kinase, monofunctional class.
This model describes a subclass of aspartate kinases.
These are mostly Lys-sensitive and not fused to
homoserine dehydrogenase, unlike some Thr-sensitive and
Met-sensitive forms. Homoserine dehydrogenase is part of
Thr and Met but not Lys biosynthetic pathways. Aspartate
kinase catalyzes a first step in the biosynthesis from
Asp of Lys (and its precursor diaminopimelate), Met, and
Thr. In E. coli, a distinct isozyme is inhibited by each
of the three amino acid products. The Met-sensitive (I)
and Thr-sensitive (II) forms are bifunctional enzymes
fused to homoserine dehydrogenases and form
homotetramers, while the Lys-sensitive form (III) is a
monofunctional homodimer. The Lys-sensitive enzyme of
Bacillus subtilis resembles the E. coli form but is an
alpha 2/beta 2 heterotetramer, where the beta subunit is
translated from an in-phase alternative initiator at
Met-246. The protein slr0657 from Synechocystis PCC6803
is extended by a duplication of the C-terminal region
corresponding to the beta chain. Incorporation of a
second copy of the C-terminal domain may be quite common
in this subgroup of aspartokinases [Amino acid
biosynthesis, Aspartate family].
Length = 401
Score = 28.5 bits (64), Expect = 4.3
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYTT--RILST 184
D A+ +A LK +V I D PG YTT R++
Sbjct: 155 DYTAALLAAALKADRVDI-YTDVPGVYTTDPRVVEA 189
>gnl|CDD|216550 pfam01522, Polysacc_deac_1, Polysaccharide deacetylase. This
domain is found in polysaccharide deacetylase. This
family of polysaccharide deacetylases includes NodB
(nodulation protein B from Rhizobium) which is a
chitooligosaccharide deacetylase. It also includes
chitin deacetylase from yeast, and endoxylanases which
hydrolyses glucosidic bonds in xylan.
Length = 124
Score = 27.2 bits (61), Expect = 4.4
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 158 AVGLKQGKVVITVKDGPGFYTTRILSTM 185
+ V +T DGP T RIL +
Sbjct: 1 KGDTPKKSVALTFDDGPPDNTPRILDVL 28
>gnl|CDD|239767 cd04234, AAK_AK, AAK_AK: Amino Acid Kinase Superfamily (AAK),
Aspartokinase (AK); this CD includes the N-terminal
catalytic domain of aspartokinase
(4-L-aspartate-4-phosphotransferase;). AK is the first
enzyme in the biosynthetic pathway of the aspartate
family of amino acids (lysine, threonine, methionine,
and isoleucine) and the bacterial cell wall component,
meso-diaminopimelate. It also catalyzes the conversion
of aspartate and ATP to aspartylphosphate and ADP. One
mechanism for the regulation of this pathway is by the
production of several isoenzymes of aspartokinase with
different repressors and allosteric inhibitors. Pairs of
ACT domains are proposed to specifically bind amino
acids leading to allosteric regulation of the enzyme. In
Escherichia coli, three different aspartokinase
isoenzymes are regulated specifically by lysine,
methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII
(MetL) are bifunctional enzymes that consist of an
N-terminal AK and a C-terminal homoserine dehydrogenase
(HSDH). ThrA and MetL are involved in threonine and
methionine biosynthesis, respectively. The third
isoenzyme, AKIII (LysC), is monofunctional and is
involved in lysine synthesis. The three Bacillus
subtilis isoenzymes, AKI (DapG), AKII (LysC), and AKIII
(YclM), are feedback-inhibited by meso-diaminopimelate,
lysine, and lysine plus threonine, respectively. The E.
coli lysine-sensitive AK is described as a homodimer,
whereas, the B. subtilis lysine-sensitive AK is
described as a heterodimeric complex of alpha- and beta-
subunits that are formed from two in-frame overlapping
genes. A single AK enzyme type has been described in
Pseudomonas, Amycolatopsis, and Corynebacterium. The
fungal aspartate pathway is regulated at the AK step,
with L-Thr being an allosteric inhibitor of the
Saccharomyces cerevisiae AK (Hom3). At least two
distinct AK isoenzymes can occur in higher plants, one
is a monofunctional lysine-sensitive isoenzyme, which is
involved in the overall regulation of the pathway and
can be synergistically inhibited by
S-adenosylmethionine. The other isoenzyme is a
bifunctional, threonine-sensitive AK-HSDH protein. Also
included in this CD is the catalytic domain of the
Methylomicrobium alcaliphilum ectoine AK, the first
enzyme of the ectoine biosynthetic pathway, found in
this bacterium, and several other
halophilic/halotolerant bacteria.
Length = 227
Score = 27.8 bits (63), Expect = 4.7
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 10/65 (15%)
Query: 151 DTAASAVAVGLKQGKVVITVKDGPGFYTT--RILSTMLSEAMRILQEGTSPKDLDRLTKQ 208
D +A+A+A L +V I D G YT RI + EA R++ E S + L
Sbjct: 139 DYSAAALAAALGADEVEI-WTDVDGIYTADPRI----VPEA-RLIPE-ISYDEALELAY- 190
Query: 209 FGFPV 213
FG V
Sbjct: 191 FGAKV 195
>gnl|CDD|179812 PRK04293, PRK04293, adenylosuccinate synthetase; Provisional.
Length = 333
Score = 27.9 bits (63), Expect = 5.0
Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 19/64 (29%)
Query: 148 TSQDTAASAVA--VGLKQGKV--VITVKDGPGF--YTTRI----LSTMLS----EAMRIL 193
TS+DT AS +A VG+ KV VI V F Y TR+ T LS E + ++
Sbjct: 191 TSKDTTASGIASDVGVGPTKVDEVIVV-----FKSYPTRVGEGPFPTELSLEEAEKLGLV 245
Query: 194 QEGT 197
+ GT
Sbjct: 246 EYGT 249
>gnl|CDD|180142 PRK05578, PRK05578, cytidine deaminase; Validated.
Length = 131
Score = 27.2 bits (61), Expect = 5.7
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 210 GFPVGAATLSDEVGIDVGAHI 230
FPVGAA L+D+ I G +I
Sbjct: 23 KFPVGAALLTDDGRIYTGCNI 43
>gnl|CDD|189013 cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 546
Score = 27.9 bits (63), Expect = 5.9
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 8/35 (22%)
Query: 232 KDLSKTFGDRFSGGNLNVLNEMVEKGYLDFKNKDG 266
K+LS G+ F + M E G LD +++ G
Sbjct: 289 KELSPETGEFF--------DFMRENGLLDLESRKG 315
>gnl|CDD|226840 COG4409, NanH, Neuraminidase (sialidase) [Carbohydrate transport
and metabolism].
Length = 728
Score = 27.9 bits (62), Expect = 6.5
Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 1/64 (1%)
Query: 36 TVYALCTTVPLVSTSHTGITYLYTYS-ERLMGSNGLAMVFPLQEQIPIQTPQQMSERIYM 94
T Y+ + L H I + G L ++ I + Q + +I
Sbjct: 622 TQYSSISYRQLGDGEHAVIVSTPNGNIGGKDGRYRLGLINSSDNPIDWKYHQDVDYKIGG 681
Query: 95 YTYS 98
Y YS
Sbjct: 682 YAYS 685
>gnl|CDD|223182 COG0104, PurA, Adenylosuccinate synthase [Nucleotide transport and
metabolism].
Length = 430
Score = 28.0 bits (63), Expect = 6.5
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 148 TSQDTAASAVAVGL-----KQGKVVITVKDGPGFYTTRI 181
TS +T A VA G K V+ K YTTR+
Sbjct: 240 TSSNTTAGGVATGSGVGPTKIDYVIGVFKA----YTTRV 274
>gnl|CDD|234869 PRK00942, PRK00942, acetylglutamate kinase; Provisional.
Length = 283
Score = 27.4 bits (62), Expect = 7.6
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 10/53 (18%)
Query: 151 DTAASAVAVGLKQGK-VVIT----VKDGPGFYTTRILSTM-LSEAMRILQEGT 197
DTAA A+A L K +++T V D G +++S + SEA ++++G
Sbjct: 184 DTAAGAIAAALGAEKLILLTDVPGVLDDKG----QLISELTASEAEELIEDGV 232
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
0.320 0.137 0.396
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,839,755
Number of extensions: 1308622
Number of successful extensions: 1230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1209
Number of HSP's successfully gapped: 57
Length of query: 269
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 174
Effective length of database: 6,723,972
Effective search space: 1169971128
Effective search space used: 1169971128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.2 bits)