RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 038224
(282 letters)
>gnl|CDD|215204 PLN02356, PLN02356, phosphateglycerate kinase.
Length = 423
Score = 526 bits (1356), Expect = 0.0
Identities = 241/281 (85%), Positives = 257/281 (91%)
Query: 1 SQILEALGATVERVRPVSITHRDHFVNVARRRALEANELASKRRRAVDKDGKELEHINGY 60
SQILEALGATVERVRPVSITH+DH+VN+ARRRALEANELASKRR+ + DG LE NG
Sbjct: 143 SQILEALGATVERVRPVSITHKDHYVNIARRRALEANELASKRRKGSETDGIHLEKTNGC 202
Query: 61 GSDGAIQSSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGG 120
S+ ++S F S CTGGFFADQFENLANFRAHYEGTGPEIWEQT G LDAFVAAAGTGG
Sbjct: 203 ISEEEKENSLFSSSCTGGFFADQFENLANFRAHYEGTGPEIWEQTQGNLDAFVAAAGTGG 262
Query: 121 TVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIG 180
T+AGVSRFLQE NPNIKCFLIDPPGS LFNKVTRGVMYT+EEAEGRRLKNPFDTITEGIG
Sbjct: 263 TLAGVSRFLQEKNPNIKCFLIDPPGSGLFNKVTRGVMYTREEAEGRRLKNPFDTITEGIG 322
Query: 181 INRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPG 240
INRLTQNF+MAKLDGAFRGTD+EAVEMSR+L+KNDGLF+GSSSAMNCVGAVRVAQSLGPG
Sbjct: 323 INRLTQNFLMAKLDGAFRGTDKEAVEMSRYLLKNDGLFVGSSSAMNCVGAVRVAQSLGPG 382
Query: 241 HTIVTILCDSGMRHLSKFYDVHYLSQQGLTPAAAGLEFLGI 281
HTIVTILCDSGMRHLSKF+D YLSQ GLTP A GLEFLGI
Sbjct: 383 HTIVTILCDSGMRHLSKFHDPQYLSQHGLTPTATGLEFLGI 423
>gnl|CDD|182672 PRK10717, PRK10717, cysteine synthase A; Provisional.
Length = 330
Score = 265 bits (679), Expect = 4e-88
Identities = 111/270 (41%), Positives = 150/270 (55%), Gaps = 45/270 (16%)
Query: 4 LEALGATVERVRPVSITHRDHFVNVARRRALEANELASKRRRAVDKDGKELEHINGYGSD 63
L ALGA + V + +++V A R A E + +
Sbjct: 106 LRALGAELVLVPAAPYANPNNYVKGAGRLA---------------------EELVASEPN 144
Query: 64 GAIQSSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGTVA 123
GAI +A+QF+N AN AHYE TGPEIWEQT G++D FV A GTGGT+A
Sbjct: 145 GAI-------------WANQFDNPANREAHYETTGPEIWEQTDGKVDGFVCAVGTGGTLA 191
Query: 124 GVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGINR 183
GVSR+L+E NP +K L DP GS+L++ G + +AEG +ITEGIG R
Sbjct: 192 GVSRYLKETNPKVKIVLADPTGSALYSYYKTG----ELKAEG-------SSITEGIGQGR 240
Query: 184 LTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPGHTI 243
+T N A +D A R D EA+ + L++ +GL LG SS +N A+R+A+ LGPGHTI
Sbjct: 241 ITANLEGAPIDDAIRIPDEEALSTAYRLLEEEGLCLGGSSGINVAAALRLARELGPGHTI 300
Query: 244 VTILCDSGMRHLSKFYDVHYLSQQGLTPAA 273
VTILCDSG R+ SK ++ +L ++GL
Sbjct: 301 VTILCDSGERYQSKLFNPDFLREKGLPVPR 330
>gnl|CDD|107204 cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine
beta-synthase (CBS) and Cysteine synthase. CBS is a
unique heme-containing enzyme that catalyzes a pyridoxal
5'-phosphate (PLP)-dependent condensation of serine and
homocysteine to give cystathionine. Deficiency of CBS
leads to homocystinuria, an inherited disease of sulfur
metabolism characterized by increased levels of the
toxic metabolite homocysteine. Cysteine synthase on the
other hand catalyzes the last step of cysteine
biosynthesis. This subgroup also includes an
O-Phosphoserine sulfhydrylase found in hyperthermophilic
archaea which produces L-cysteine from sulfide and the
more thermostable O-phospho-L-serine.
Length = 291
Score = 227 bits (581), Expect = 7e-74
Identities = 90/255 (35%), Positives = 119/255 (46%), Gaps = 56/255 (21%)
Query: 2 QILEALGATVERVRPVSITHRDHFVNVARRRALEANELASKRRRAVDKDGKELEHINGYG 61
++L ALGA V + AR A E
Sbjct: 93 KLLRALGAEVILTPEAEADGMKGAIAKARELA------------------AETP------ 128
Query: 62 SDGAIQSSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGT 121
F+ +QFEN AN AHYE T PEIWEQ G++DAFVA GTGGT
Sbjct: 129 ---------------NAFWLNQFENPANPEAHYETTAPEIWEQLDGKVDAFVAGVGTGGT 173
Query: 122 VAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGI 181
+ GV+R+L+E NPN++ +DP GS LF+ P EGIG
Sbjct: 174 ITGVARYLKEKNPNVRIVGVDPVGSVLFSG-----------------GPPGPHKIEGIGA 216
Query: 182 NRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPGH 241
+ +N + +D R +D EA M+R L + +GL +G SS A+++A+ LGPG
Sbjct: 217 GFIPENLDRSLIDEVVRVSDEEAFAMARRLAREEGLLVGGSSGAAVAAALKLAKRLGPGK 276
Query: 242 TIVTILCDSGMRHLS 256
TIVTIL DSG R+LS
Sbjct: 277 TIVTILPDSGERYLS 291
>gnl|CDD|223110 COG0031, CysK, Cysteine synthase [Amino acid transport and
metabolism].
Length = 300
Score = 202 bits (517), Expect = 4e-64
Identities = 92/256 (35%), Positives = 123/256 (48%), Gaps = 57/256 (22%)
Query: 2 QILEALGATVERVRPVSITHRDHFVNVARRRALEANELASKRRRAVDKDGKELEHINGYG 61
++L ALGA V + R A ELA I GY
Sbjct: 102 KLLRALGAEVILTPG----APGNMKGAIER----AKELA--------------AEIPGYA 139
Query: 62 SDGAIQSSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGT 121
+ +QFEN AN AHYE TGPEIW+QT G++DAFVA GTGGT
Sbjct: 140 -----------------VWLNQFENPANPEAHYETTGPEIWQQTDGKVDAFVAGVGTGGT 182
Query: 122 VAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGI 181
+ GV+R+L+E NPN++ +DP GS L + EG EGIG
Sbjct: 183 ITGVARYLKERNPNVRIVAVDPEGSVLLSG-----------GEGPH-------KIEGIGA 224
Query: 182 NRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPGH 241
+ +N + +D R +D EA+ +R L + +GL +G SS A+++A+ L G
Sbjct: 225 GFVPENLDLDLIDEVIRVSDEEAIATARRLAREEGLLVGISSGAALAAALKLAKELPAGK 284
Query: 242 TIVTILCDSGMRHLSK 257
TIVTIL DSG R+LSK
Sbjct: 285 TIVTILPDSGERYLSK 300
>gnl|CDD|233286 TIGR01136, cysKM, cysteine synthase. This model discriminates
cysteine synthases (EC 2.5.1.47) (both CysK and CysM)
from cystathionine beta-synthase, a protein found
primarily in eukaryotes and carrying a C-terminal CBS
domain lacking from this protein. Bacterial proteins
lacking the CBS domain but otherwise showing
resemblamnce to cystathionine beta-synthases and
considerable phylogenetic distance from known cysteine
synthases were excluded from the seed and score below
the trusted cutoff [Amino acid biosynthesis, Serine
family].
Length = 299
Score = 147 bits (374), Expect = 1e-42
Identities = 77/223 (34%), Positives = 113/223 (50%), Gaps = 21/223 (9%)
Query: 38 ELASKRRRAVDKD-GKELEHING-YGSDGAIQSSKFPSDCTGGFF-ADQFENLANFRAHY 94
E S RR + + G EL G GAI ++ + T + DQFEN AN AHY
Sbjct: 90 ETMSLERRKLLRAYGAELILTPAEEGMKGAIDKAEELAAETNKYVMLDQFENPANPEAHY 149
Query: 95 EGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTR 154
+ TGPEIW T G +D FVA GTGGT+ GV R+L+E NPNIK ++P S +
Sbjct: 150 KTTGPEIWRDTDGRIDHFVAGVGTGGTITGVGRYLKEQNPNIKIVAVEPAESPVL----- 204
Query: 155 GVMYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKN 214
+ G + +GIG + + ++ +D +D +A+E +R L +
Sbjct: 205 --------SGGEPGPHKI----QGIGAGFIPKILDLSLIDEVITVSDEDAIETARRLARE 252
Query: 215 DGLFLGSSSAMNCVGAVRVAQSLG-PGHTIVTILCDSGMRHLS 256
+G+ +G SS A+++A+ L IV IL D+G R+LS
Sbjct: 253 EGILVGISSGAAVAAALKLAKRLENADKVIVAILPDTGERYLS 295
>gnl|CDD|233288 TIGR01139, cysK, cysteine synthase A. This model distinguishes
cysteine synthase A (CysK) from cysteine synthase B
(CysM). CysM differs in having a broader specificity
that also allows the use of thiosulfate to produce
cysteine thiosulfonate [Amino acid biosynthesis, Serine
family].
Length = 298
Score = 138 bits (350), Expect = 2e-39
Identities = 78/223 (34%), Positives = 108/223 (48%), Gaps = 21/223 (9%)
Query: 38 ELASKRRRAVDKD-GKELEHING-YGSDGAIQSSKFPSDCTGG--FFADQFENLANFRAH 93
E S RR + K G EL G G GAI ++ + T F QFEN AN H
Sbjct: 89 ETMSIERRKLLKAYGAELVLTPGAEGMKGAIAKAEEIAASTPNSYFMLQQFENPANPEIH 148
Query: 94 YEGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVT 153
+ TGPEIW T G+LDAFVA GTGGT+ GV L+E PNIK ++P S + +
Sbjct: 149 RKTTGPEIWRDTDGKLDAFVAGVGTGGTITGVGEVLKEQKPNIKIVAVEPAESPVLSGGK 208
Query: 154 RGVMYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLDGAFRGTDREAVEMSRFLVK 213
G + +GIG + +N + +D +D EA+E +R L
Sbjct: 209 PG-------------PHKI----QGIGAGFIPKNLNRSVIDEVITVSDEEAIETARRLAA 251
Query: 214 NDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILCDSGMRHLS 256
+G+ +G SS A+++A+ P IV IL +G R+LS
Sbjct: 252 EEGILVGISSGAAVAAALKLAKRPEPDKLIVVILPSTGERYLS 294
>gnl|CDD|233287 TIGR01137, cysta_beta, cystathionine beta-synthase. Members of
this family closely resemble cysteine synthase but
contain an additional C-terminal CBS domain. The
function of any bacterial member included in this family
is proposed but not proven [Amino acid biosynthesis,
Serine family].
Length = 454
Score = 141 bits (356), Expect = 6e-39
Identities = 68/205 (33%), Positives = 104/205 (50%), Gaps = 17/205 (8%)
Query: 68 SSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSR 127
+ + + G DQ+ N +N AHY+GTGPEI EQ G+LD FVA AGTGGT+ G++R
Sbjct: 130 AKRLVREIPGAHILDQYNNPSNPLAHYDGTGPEILEQCEGKLDMFVAGAGTGGTITGIAR 189
Query: 128 FLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNP--FDTITEGIGINRLT 185
+L+E+NP + DP GS L A+ L EGIG + +
Sbjct: 190 YLKESNPKCRIVGADPEGSIL--------------AQPENLNKTGRTPYKVEGIGYDFIP 235
Query: 186 QNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGP-GHTIV 244
+D + D+E+ +M+R L+K +GL +G SS V A++ A+ IV
Sbjct: 236 TVLDRKVVDEWIKTDDKESFKMARRLIKEEGLLVGGSSGSAVVAALKAAEDELTEDQVIV 295
Query: 245 TILCDSGMRHLSKFYDVHYLSQQGL 269
+L DS +++KF + ++ G
Sbjct: 296 VLLPDSIRNYMTKFLNDEWMKDNGF 320
>gnl|CDD|236972 PRK11761, cysM, cysteine synthase B; Provisional.
Length = 296
Score = 127 bits (321), Expect = 6e-35
Identities = 62/185 (33%), Positives = 88/185 (47%), Gaps = 35/185 (18%)
Query: 77 GGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNI 136
G DQF N N AHYE TGPEIW QT G + FV++ GT GT+ GVSR+L+E NP +
Sbjct: 136 EGKVLDQFANPDNPLAHYETTGPEIWRQTEGRITHFVSSMGTTGTIMGVSRYLKEQNPAV 195
Query: 137 KCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGINRLTQNFM-----MA 191
+ + P EG + GI R + ++ +
Sbjct: 196 QIVGLQP-------------------EEGSSIP----------GIRRWPEEYLPKIFDAS 226
Query: 192 KLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILCDSG 251
++D + +EA R L + +G+F G SS A+R+A+ P IV I+CD G
Sbjct: 227 RVDRVLDVSQQEAENTMRRLAREEGIFCGVSSGGAVAAALRIAREN-PNAVIVAIICDRG 285
Query: 252 MRHLS 256
R+LS
Sbjct: 286 DRYLS 290
>gnl|CDD|234409 TIGR03945, PLP_SbnA_fam, 2,3-diaminopropionate biosynthesis protein
SbnA. Members of this family include SbnA, a protein of
the staphyloferrin B biosynthesis operon of
Staphylococcus aureus. SbnA and SbnB together appear to
synthesize 2,3-diaminopropionate, a precursor of certain
siderophores and other secondary metabolites. SbnA is a
pyridoxal phosphate-dependent enzyme [Cellular
processes, Biosynthesis of natural products].
Length = 304
Score = 115 bits (290), Expect = 2e-30
Identities = 54/178 (30%), Positives = 75/178 (42%), Gaps = 19/178 (10%)
Query: 83 QFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLID 142
Q+ N N RAHY GTG EI LD T GT+ G SR L+E PN K +D
Sbjct: 142 QYANPDNPRAHYHGTGREIARAFP-PLDYLFVGVSTTGTLMGCSRRLRERGPNTKVIAVD 200
Query: 143 PPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLDGAFRGTDR 202
GS +F GRR G+G + + + + +D +
Sbjct: 201 AVGSVIFG-----------GPPGRRH-------IPGLGASVVPELLDESLIDDVVHVPEY 242
Query: 203 EAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILCDSGMRHLSKFYD 260
+ V R L + +G+ G SS R+ + PG T+V IL D G R+L Y+
Sbjct: 243 DTVAGCRRLARREGILAGGSSGTVVAAIKRLLPRIPPGSTVVAILPDRGERYLDTVYN 300
>gnl|CDD|178171 PLN02556, PLN02556, cysteine synthase/L-3-cyanoalanine synthase.
Length = 368
Score = 114 bits (287), Expect = 1e-29
Identities = 63/181 (34%), Positives = 92/181 (50%), Gaps = 18/181 (9%)
Query: 77 GGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNI 136
F QF N AN + H+E TGPEIWE T G++D FV G+GGTV+GV ++L+ NPN+
Sbjct: 185 DAFMLQQFSNPANTQVHFETTGPEIWEDTLGQVDIFVMGIGSGGTVSGVGKYLKSKNPNV 244
Query: 137 KCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLDGA 196
K + ++P S++ N G P G+G + M ++
Sbjct: 245 KIYGVEPAESNVLNGGKPG---------------PHHITGNGVGFKPDILD--MDVMEKV 287
Query: 197 FRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQ-SLGPGHTIVTILCDSGMRHL 255
+ +AV M+R L +GL +G SS N V A+R+A+ G IVT+ G R+L
Sbjct: 288 LEVSSEDAVNMARELALKEGLMVGISSGANTVAALRLAKMPENKGKLIVTVHPSFGERYL 347
Query: 256 S 256
S
Sbjct: 348 S 348
>gnl|CDD|130208 TIGR01138, cysM, cysteine synthase B. CysM differs from CysK in
that it can also use thiosulfate instead of sulfide, to
produce cysteine thiosulfonate instead of cysteine.
Alternate name: O-acetylserine (thiol)-lyase [Amino acid
biosynthesis, Serine family].
Length = 290
Score = 111 bits (278), Expect = 7e-29
Identities = 73/224 (32%), Positives = 105/224 (46%), Gaps = 36/224 (16%)
Query: 39 LASKRRRAVDKDGKELEHINGY-GSDGAIQSSKFPSDCTGGFFADQFENLANFRAHYEGT 97
++ +R+ A+ G EL + G +GA + ++ G DQF N N AHY T
Sbjct: 93 MSQERKAAMRAYGAELILVTKEEGMEGARDLALELANRGEGKLLDQFNNPDNPYAHYTST 152
Query: 98 GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVM 157
GPEIW+QTGG + FV++ GT GT+ GVSRFL+E NP ++ + P
Sbjct: 153 GPEIWQQTGGRITHFVSSMGTTGTIMGVSRFLKEQNPPVQIVGLQP-------------- 198
Query: 158 YTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLDGAF--RGTD---REAVEMSRFLV 212
EG + GI R ++ D + R D R+A R L
Sbjct: 199 -----EEGSSIP----------GIRRWPTEYLPGIFDASLVDRVLDIHQRDAENTMRELA 243
Query: 213 KNDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILCDSGMRHLS 256
+G+F G SS A+R+A+ L P +V I+CD G R+LS
Sbjct: 244 VREGIFCGVSSGGAVAAALRLAREL-PDAVVVAIICDRGDRYLS 286
>gnl|CDD|166206 PLN02565, PLN02565, cysteine synthase.
Length = 322
Score = 110 bits (277), Expect = 1e-28
Identities = 66/198 (33%), Positives = 103/198 (52%), Gaps = 19/198 (9%)
Query: 61 GSDGAIQ-SSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTG 119
G GA+Q + + + + QFEN AN + HYE TGPEIW+ TGG++DAFV+ GTG
Sbjct: 124 GMKGAVQKAEEILAKTPNSYILQQFENPANPKIHYETTGPEIWKGTGGKVDAFVSGIGTG 183
Query: 120 GTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGI 179
GT+ G ++L+E NP+IK + ++P S++ + G+ P +GI
Sbjct: 184 GTITGAGKYLKEQNPDIKLYGVEPVESAVLSG-------------GK----PGPHKIQGI 226
Query: 180 GINRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQS-LG 238
G + + LD + + EA+E ++ L +GL +G SS A+++A+
Sbjct: 227 GAGFIPGVLDVDLLDEVVQVSSDEAIETAKLLALKEGLLVGISSGAAAAAAIKIAKRPEN 286
Query: 239 PGHTIVTILCDSGMRHLS 256
G IV I G R+LS
Sbjct: 287 AGKLIVVIFPSFGERYLS 304
>gnl|CDD|177651 PLN00011, PLN00011, cysteine synthase.
Length = 323
Score = 107 bits (268), Expect = 3e-27
Identities = 65/198 (32%), Positives = 97/198 (48%), Gaps = 19/198 (9%)
Query: 61 GSDGAIQSSK-FPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGELDAFVAAAGTG 119
G G ++ ++ S GG+ QFEN AN HY TGPEIW + G++D VA GTG
Sbjct: 126 GLKGMLEKAEEILSKTPGGYIPQQFENPANPEIHYRTTGPEIWRDSAGKVDILVAGVGTG 185
Query: 120 GTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGI 179
GT GV +FL+E N +IK +++P S++ + P + +GI
Sbjct: 186 GTATGVGKFLKEKNKDIKVCVVEPVESAVLSG-----------------GQPGPHLIQGI 228
Query: 180 GINRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQS-LG 238
G + N + +D + T EA+E ++ L +GL +G SS A++VA+
Sbjct: 229 GSGIIPFNLDLTIVDEIIQVTGEEAIETAKLLALKEGLLVGISSGAAAAAALKVAKRPEN 288
Query: 239 PGHTIVTILCDSGMRHLS 256
G IV I G R+LS
Sbjct: 289 AGKLIVVIFPSGGERYLS 306
>gnl|CDD|107202 cd00640, Trp-synth-beta_II, Tryptophan synthase beta superfamily
(fold type II); this family of pyridoxal phosphate
(PLP)-dependent enzymes catalyzes beta-replacement and
beta-elimination reactions. This CD corresponds to
aminocyclopropane-1-carboxylate deaminase (ACCD),
tryptophan synthase beta chain (Trp-synth_B),
cystathionine beta-synthase (CBS), O-acetylserine
sulfhydrylase (CS), serine dehydratase (Ser-dehyd),
threonine dehydratase (Thr-dehyd), diaminopropionate
ammonia lyase (DAL), and threonine synthase (Thr-synth).
ACCD catalyzes the conversion of
1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate
and ammonia. Tryptophan synthase folds into a tetramer,
where the beta chain is the catalytic PLP-binding
subunit and catalyzes the formation of L-tryptophan from
indole and L-serine. CBS is a tetrameric hemeprotein
that catalyzes condensation of serine and homocysteine
to cystathionine. CS is a homodimer that catalyzes the
formation of L-cysteine from O-acetyl-L-serine.
Ser-dehyd catalyzes the conversion of L- or D-serine to
pyruvate and ammonia. Thr-dehyd is active as a homodimer
and catalyzes the conversion of L-threonine to
2-oxobutanoate and ammonia. DAL is also a homodimer and
catalyzes the alpha, beta-elimination reaction of both
L- and D-alpha, beta-diaminopropionate to form pyruvate
and ammonia. Thr-synth catalyzes the formation of
threonine and inorganic phosphate from
O-phosphohomoserine.
Length = 244
Score = 102 bits (257), Expect = 3e-26
Identities = 47/178 (26%), Positives = 71/178 (39%), Gaps = 53/178 (29%)
Query: 74 DCTGGFFADQFENLANFRAHYEGTGPEIWEQTGGE-LDAFVAAAGTGGTVAGVSRFLQEN 132
+ G ++ +QF+N AN G EI EQ GG+ DA V G GG +AG++R L+E
Sbjct: 119 EDPGAYYVNQFDNPANIAGQG-TIGLEILEQLGGQKPDAVVVPVGGGGNIAGIARALKEL 177
Query: 133 NPNIKCFLIDPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAK 192
PN+K ++P
Sbjct: 178 LPNVKVIGVEP------------------------------------------------- 188
Query: 193 LDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILCDS 250
+D EA+E R L + +G+ + SSA A+++A+ LG G T+V IL
Sbjct: 189 --EVVTVSDEEALEAIRLLAREEGILVEPSSAAALAAALKLAKKLGKGKTVVVILTGG 244
>gnl|CDD|215840 pfam00291, PALP, Pyridoxal-phosphate dependent enzyme. Members of
this family are all pyridoxal-phosphate dependent
enzymes. This family includes: serine dehydratase
EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16,
tryptophan synthase beta chain EC:4.2.1.20, threonine
synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8
P11096, cystathionine beta-synthase EC:4.2.1.22,
1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.
Length = 295
Score = 102 bits (257), Expect = 7e-26
Identities = 60/252 (23%), Positives = 90/252 (35%), Gaps = 51/252 (20%)
Query: 2 QILEALGATVERVRPVSITHRDHFVNVARRRALEANELASKRRRAVDKDGKELEHINGYG 61
++ ALGA V V VS D + +A A
Sbjct: 91 LLMRALGAEVILV--VSEGDYDDALELAEEAAELLAAYD--------------------- 127
Query: 62 SDGAIQSSKFPSDCTGGFFADQFENLANFRAHYEGTGPEIWEQTG-GELDAFVAAAGTGG 120
G Q+ N N A Y+ G EI EQ G G+ DA V G GG
Sbjct: 128 ---------------GPIPLGQYNN-PNVIAGYKTIGLEILEQLGQGDPDAVVVPVGGGG 171
Query: 121 TVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYTKEE--AEGRRLKNPFDTITEG 178
AG++R L+E P I+ ++P G+ + + G P D
Sbjct: 172 LAAGIARGLKELGPGIRVIGVEPEGAPALARSLEAGRRVPKPTTIAGLGPGIPLDGELAL 231
Query: 179 IGINRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSL- 237
I+ + + +D EA+E R L + +G+ + SSA A+R+A+
Sbjct: 232 ELIDEY--------VGDVYAVSDEEALEAIRLLARREGILVEPSSAAALAAALRLAELEL 283
Query: 238 GPGHTIVTILCD 249
G G +V +L
Sbjct: 284 GKGKRVVVVLTG 295
>gnl|CDD|178587 PLN03013, PLN03013, cysteine synthase.
Length = 429
Score = 99.9 bits (248), Expect = 5e-24
Identities = 62/220 (28%), Positives = 103/220 (46%), Gaps = 19/220 (8%)
Query: 39 LASKRRRAVDKDGKELEHIN-GYGSDGAIQ-SSKFPSDCTGGFFADQFENLANFRAHYEG 96
++ +RR + G EL + G GA+Q + + + + QF+N AN + HYE
Sbjct: 209 MSMERRVLLKAFGAELVLTDPAKGMTGAVQKAEEILKNTPDAYMLQQFDNPANPKIHYET 268
Query: 97 TGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGV 156
TGPEIW+ T G++D FVA GTGGT+ GV RF++E NP + ++P S + +
Sbjct: 269 TGPEIWDDTKGKVDIFVAGIGTGGTITGVGRFIKEKNPKTQVIGVEPTESDILSG----- 323
Query: 157 MYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLDGAFRGTDREAVEMSRFLVKNDG 216
P +GIG + +N +D + EA+E ++ L +G
Sbjct: 324 ------------GKPGPHKIQGIGAGFIPKNLDQKIMDEVIAISSEEAIETAKQLALKEG 371
Query: 217 LFLGSSSAMNCVGAVRVAQSLGPGHTIVTILCDSGMRHLS 256
L +G SS A++VA+ ++ + + R +
Sbjct: 372 LMVGISSGAAAAAAIKVAKRPENAGKLIAVSLFASGRDIY 411
>gnl|CDD|224092 COG1171, IlvA, Threonine dehydratase [Amino acid transport and
metabolism].
Length = 347
Score = 41.4 bits (98), Expect = 2e-04
Identities = 35/158 (22%), Positives = 59/158 (37%), Gaps = 13/158 (8%)
Query: 96 GT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGS-SLFNKVT 153
GT EI EQ DA G GG ++G++ L+ +P IK ++P G+ S++ +
Sbjct: 162 GTIALEILEQLPDLPDAVFVPVGGGGLISGIATALKALSPEIKVIGVEPEGAPSMYASLK 221
Query: 154 RGVMYTKEEAEGRRLKNPFDTITEGIG---INRLTQNFMMAKLDGAFRGTDREAVEMSRF 210
G + TI +G+ LT + +D + E R
Sbjct: 222 AGKIVVVLPDV--------GTIADGLAVKRPGDLTFEILRELVDDIVLVDEDEICAAMRD 273
Query: 211 LVKNDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILC 248
L + + + A+ + G T+V IL
Sbjct: 274 LFERTKIIAEPAGALALAALLAGKIEPLQGKTVVVILS 311
>gnl|CDD|107205 cd01562, Thr-dehyd, Threonine dehydratase: The first step in amino
acid degradation is the removal of nitrogen. Although
the nitrogen atoms of most amino acids are transferred
to alpha-ketoglutarate before removal, the alpha-amino
group of threonine can be directly converted into NH4+.
The direct deamination is catalyzed by threonine
dehydratase, in which pyridoxal phosphate (PLP) is the
prosthetic group. Threonine dehydratase is widely
distributed in all three major phylogenetic divisions.
Length = 304
Score = 38.2 bits (90), Expect = 0.003
Identities = 40/158 (25%), Positives = 66/158 (41%), Gaps = 16/158 (10%)
Query: 96 GT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTR 154
GT G EI EQ +LDA G GG +AG++ ++ +PN K ++P G+
Sbjct: 153 GTIGLEILEQVP-DLDAVFVPVGGGGLIAGIATAVKALSPNTKVIGVEPEGAPA------ 205
Query: 155 GVMYTKEEAEGRRLKNP-FDTITEGIGINR---LTQNFMMAKLDGAFRGTDREAVEMSRF 210
M A G+ + P DTI +G+ + R LT + +D ++ E
Sbjct: 206 --MAQSLAA-GKPVTLPEVDTIADGLAVKRPGELTFEIIRKLVDDVVTVSEDEIAAAMLL 262
Query: 211 LVKNDGLFLGSSSAMNCVGAVRVAQSLGPGHTIVTILC 248
L + + L + A+ + L G +V +L
Sbjct: 263 LFEREKLVAEPAGALALAALLSGKLDL-KGKKVVVVLS 299
>gnl|CDD|233712 TIGR02079, THD1, threonine dehydratase. This model represents
threonine dehydratase, the first step in the pathway
converting threonine into isoleucine. At least two other
clades of biosynthetic threonine dehydratases have been
charcterized (TIGR01124 and TIGR01127). Those sequences
described by this model are exclusively found in species
containg the rest of the isoleucine pathway and which
are generally lacking in members of the those other two
clades of threonine dehydratases. Members of this clade
are also often gene clustered with other elements of the
isoleucine pathway [Amino acid biosynthesis, Pyruvate
family].
Length = 409
Score = 35.1 bits (81), Expect = 0.029
Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 10/100 (10%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVT 153
+GT EI +Q + D V G GG ++G++ +L +P K ++P G+
Sbjct: 154 QGTVAAEILDQLPEKPDYVVVPVGGGGLISGLTTYLAGTSPKTKIIGVEPEGAP------ 207
Query: 154 RGVMYTKEEAEGRRLKNPFDTITEGIGINRL-TQNFMMAK 192
+ + E E L D +G + R+ NF K
Sbjct: 208 -SMKASLEAGEVVTLDK-IDNFVDGAAVKRVGDLNFKALK 245
>gnl|CDD|236318 PRK08639, PRK08639, threonine dehydratase; Validated.
Length = 420
Score = 34.4 bits (80), Expect = 0.059
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 100 EIWEQTG--GELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPG 145
EI EQ G D G GG ++GV+ +L+E +P K ++P G
Sbjct: 169 EILEQLEKEGSPDYVFVPVGGGGLISGVTTYLKERSPKTKIIGVEPAG 216
>gnl|CDD|130194 TIGR01124, ilvA_2Cterm, threonine ammonia-lyase, biosynthetic, long
form. This model describes a form of threonine
ammonia-lyase, a pyridoxal-phosphate dependent enzyme,
with two copies of the threonine dehydratase C-terminal
domain (pfam00585). Members with known function
participate in isoleucine biosynthesis and are inhibited
by isoleucine. Alternate name: threonine deaminase,
threonine dehydratase. Forms scoring between the trusted
and noise cutoff tend to branch with this subgroup of
threonine ammonia-lyase phylogenetically but have only a
single copy of the C-terminal domain [Amino acid
biosynthesis, Pyruvate family].
Length = 499
Score = 34.3 bits (79), Expect = 0.062
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGS 146
+GT EI Q LDA G GG AGV+ +++ P IK ++P S
Sbjct: 152 QGTLALEILRQVANPLDAVFVPVGGGGLAAGVAALIKQLMPEIKVIGVEPTDS 204
>gnl|CDD|178165 PLN02550, PLN02550, threonine dehydratase.
Length = 591
Score = 34.1 bits (78), Expect = 0.085
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDP 143
+GT G EI Q G L A G GG +AG++ +++ P +K ++P
Sbjct: 244 QGTVGMEIVRQHQGPLHAIFVPVGGGGLIAGIAAYVKRVRPEVKIIGVEP 293
>gnl|CDD|172537 PRK14045, PRK14045, 1-aminocyclopropane-1-carboxylate deaminase;
Provisional.
Length = 329
Score = 32.6 bits (74), Expect = 0.22
Identities = 30/127 (23%), Positives = 49/127 (38%), Gaps = 24/127 (18%)
Query: 100 EIWEQT---GGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGV 156
EI Q G D+ V A G+GGT+AG+S G ++ N R V
Sbjct: 173 EIATQVKKLGVRFDSIVVAVGSGGTLAGLSL-----------------GLAILNAEWRVV 215
Query: 157 ---MYTKEEAEGRRLKNPFDTITEGIGINRLTQNFMMAKLD-GAFRGTDREAVEMSRFLV 212
+ + E ++KN E +G+ Q + G + +E ++ R +
Sbjct: 216 GIAVGSFGEKMKEKVKNLVKKTKELLGVKVKVQEPELYDYSFGEYGKITKEVAKLIRSVG 275
Query: 213 KNDGLFL 219
+GL L
Sbjct: 276 TMEGLIL 282
>gnl|CDD|236417 PRK09224, PRK09224, threonine dehydratase; Reviewed.
Length = 504
Score = 32.4 bits (75), Expect = 0.24
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 96 GT-GPEIWEQTGGELDA-FVAAAGTGGTVAGVSRFLQENNPNIK 137
GT EI +Q LDA FV G GG +AGV+ ++++ P IK
Sbjct: 156 GTIAMEILQQHPHPLDAVFVPVGG-GGLIAGVAAYIKQLRPEIK 198
>gnl|CDD|130197 TIGR01127, ilvA_1Cterm, threonine ammonia-lyase, medium form. A
form of threonine dehydratase with two copies of the
C-terminal domain pfam00585 is described by TIGR01124.
This model describes a phylogenetically distinct form
with a single copy of pfam00585. This form branches with
the catabolic threonine dehydratase of E. coli; many
members are designated as catabolic for this reason.
However, the catabolic form lacks any pfam00585 domain.
Many members of this model are found in species with
other Ile biosynthetic enzymes [Amino acid biosynthesis,
Pyruvate family].
Length = 380
Score = 32.4 bits (74), Expect = 0.27
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLF 149
+GT G EI E ++D + G GG ++GV+ ++ NPN+K ++ G+
Sbjct: 135 QGTIGLEIMED-IPDVDTVIVPVGGGGLISGVASAAKQINPNVKVIGVEAEGAPSM 189
>gnl|CDD|237111 PRK12483, PRK12483, threonine dehydratase; Reviewed.
Length = 521
Score = 32.1 bits (73), Expect = 0.31
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGS 146
+GT EI Q G LDA G GG +AG++ +++ P IK ++P S
Sbjct: 172 QGTVAMEILRQHPGPLDAIFVPVGGGGLIAGIAAYVKYVRPEIKVIGVEPDDS 224
>gnl|CDD|107210 cd06449, ACCD, Aminocyclopropane-1-carboxylate deaminase (ACCD):
Pyridoxal phosphate (PLP)-dependent enzyme which
catalyzes the conversion of
1-aminocyclopropane-L-carboxylate (ACC), a precursor of
the plant hormone ethylene, to alpha-ketobutyrate and
ammonia.
Length = 307
Score = 32.0 bits (73), Expect = 0.33
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 103 EQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSS--LFNKVTRGVMYTK 160
E+ G + D+ V + TG T AG+S L + ID +V R + K
Sbjct: 169 EELGFKFDSIVVCSVTGSTHAGLSVGLAALGRQRRVIGIDASAKPEKTKAQVLR-IAQAK 227
Query: 161 EEAEGRRLK 169
EG +K
Sbjct: 228 LAEEGLEVK 236
>gnl|CDD|233338 TIGR01275, ACC_deam_rel, pyridoxal phosphate-dependent enzymes,
D-cysteine desulfhydrase family. This model represents
a family of pyridoxal phosphate-dependent enzymes
closely related to (and often designated as putative
examples of) 1-aminocyclopropane-1-carboxylate
deaminase. It appears that members of this family
include both D-cysteine desulfhydrase (EC 4.4.1.15) and
1-aminocyclopropane-1-carboxylate deaminase (EC
3.5.99.7).
Length = 318
Score = 31.7 bits (72), Expect = 0.37
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 100 EIWEQTGGEL--DAFVAAAGTGGTVAGVSRFLQENNPNI 136
EI +Q E+ D+ V A+G+GGT+AG+S L P++
Sbjct: 166 EIAQQLESEVKFDSIVVASGSGGTIAGLSLGLSHLMPDV 204
>gnl|CDD|181457 PRK08526, PRK08526, threonine dehydratase; Provisional.
Length = 403
Score = 30.8 bits (70), Expect = 0.69
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 108 ELDAFVAAAGTGGTVAGVSRFLQENNPNIK 137
+LD V G GG ++G++ ++ NPNIK
Sbjct: 168 DLDMVVVPVGGGGLISGIASAAKQINPNIK 197
>gnl|CDD|215524 PLN02970, PLN02970, serine racemase.
Length = 328
Score = 30.4 bits (69), Expect = 0.91
Identities = 28/120 (23%), Positives = 51/120 (42%), Gaps = 14/120 (11%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVT 153
+GT E EQ ELD + GG ++G++ + P+IK +P G+ +
Sbjct: 162 QGTIALEFLEQVP-ELDVIIVPISGGGLISGIALAAKAIKPSIKIIAAEPKGA---DDAA 217
Query: 154 RGVMYTKEEAEGRRLKNPF-DTITEGI--GINRLTQNFMMAKLDGAFRGTDREAVEMSRF 210
+ +A G + P +TI +G+ + LT + +D D+E +E +
Sbjct: 218 Q------SKAAGEIITLPVTNTIADGLRASLGDLTWPVVRDLVDDVITVDDKEIIEAMKL 271
>gnl|CDD|205605 pfam13427, DUF4111, Domain of unknown function (DUF4111). Although
the exact function of this domain is not known it
frequently appears downstream of the family,
Nucleotidyltransferase, pfam01909. It is also found in
species associated with methicillin-resistant bacteria.
Length = 106
Score = 29.1 bits (66), Expect = 0.93
Identities = 10/27 (37%), Positives = 11/27 (40%)
Query: 87 LANFRAHYEGTGPEIWEQTGGELDAFV 113
L RA Y G + EL AFV
Sbjct: 73 LRAARAAYLGQEEDDLAGREDELAAFV 99
>gnl|CDD|236182 PRK08198, PRK08198, threonine dehydratase; Provisional.
Length = 404
Score = 29.7 bits (68), Expect = 1.6
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 96 GT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIK 137
GT G EI E ++D V G GG ++GV+ ++ P ++
Sbjct: 158 GTIGLEILEDLP-DVDTVVVPIGGGGLISGVATAVKALRPEVR 199
>gnl|CDD|136018 PRK06721, PRK06721, threonine synthase; Reviewed.
Length = 352
Score = 29.7 bits (66), Expect = 1.8
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 200 TDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQS--LGPGHTIVTILCDSGMR 253
+D E + R L K++G+F S + G ++ QS + G T+V +L +G++
Sbjct: 264 SDEEILHAYRLLAKSEGVFAEPGSNASLAGVMKHVQSGKIKKGETVVAVLTGNGLK 319
>gnl|CDD|179673 PRK03910, PRK03910, D-cysteine desulfhydrase; Validated.
Length = 331
Score = 29.0 bits (66), Expect = 2.5
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 100 EIWEQ---TGGELDAFVAAAGTGGTVAGVSRFLQENNPNIK 137
EI +Q G + DA V A+G+GGT AG++ L P+I
Sbjct: 172 EIAQQLAEGGVDFDAVVVASGSGGTHAGLAAGLAALGPDIP 212
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 28.4 bits (64), Expect = 2.8
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 10/40 (25%)
Query: 220 GSSSAMNC-VGAVRVAQSLGPGHT--IVTI-------LCD 249
G SS +N VG+ +V+ S PG T TI LCD
Sbjct: 94 GKSSLINALVGSKKVSVSSTPGKTKHFQTIFLEPGITLCD 133
>gnl|CDD|178923 PRK00194, PRK00194, hypothetical protein; Validated.
Length = 90
Score = 27.1 bits (61), Expect = 3.1
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 120 GTVAGVSRFLQENNPNI 136
G +AGVS L E N NI
Sbjct: 15 GIIAGVSTVLAELNVNI 31
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 28.9 bits (65), Expect = 3.1
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 95 EGT-GPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIK 137
+GT G E+ EQ LDA A G GG ++G++ +L+ +P +
Sbjct: 155 QGTIGMELVEQQPD-LDAVFVAVGGGGLISGIATYLKTLSPKTE 197
>gnl|CDD|130646 TIGR01584, citF, citrate lyase, alpha subunit. This is a model of
the alpha subunit of the holoenzyme citrate lyase (EC
4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC
4.1.3.34), and acyl carrier protein subunits in a
stoichiometric relationship of 6:6:6. Citrate lyase is
an enzyme which converts citrate to oxaloacetate. In
bacteria, this reaction is involved in citrate
fermentation. The alpha subunit catalyzes the reaction
Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The
seed contains an experimentally characterized member
from Lactococcus lactis subsp. lactis. The model covers
both Gram positive and Gram negative bacteria. It is
quite robust with queries scoring either quite well or
quite poorly against the model. There are currently no
hits in between the noise cutoff and trusted cutoff
[Energy metabolism, Fermentation].
Length = 492
Score = 28.7 bits (64), Expect = 3.7
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 110 DAFVAAAGTGGTVAGVSRFLQEN--NPNIK 137
D F GTGG V+RFL+E + NIK
Sbjct: 251 DGFSFQTGTGGAALAVTRFLKEKMIDHNIK 280
>gnl|CDD|153144 cd04872, ACT_1ZPV, ACT domain proteins similar to the yet
uncharacterized Streptococcus pneumoniae ACT domain
protein. This CD, ACT_1ZPV, includes those single ACT
domain proteins similar to the yet uncharacterized
Streptococcus pneumoniae ACT domain protein (pdb
structure 1ZPV). Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 88
Score = 26.8 bits (60), Expect = 4.0
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 120 GTVAGVSRFLQENNPNI 136
G VAGVS L E N NI
Sbjct: 13 GIVAGVSTKLAELNVNI 29
>gnl|CDD|180539 PRK06352, PRK06352, threonine synthase; Validated.
Length = 351
Score = 28.5 bits (63), Expect = 4.2
Identities = 42/174 (24%), Positives = 68/174 (39%), Gaps = 24/174 (13%)
Query: 100 EIWEQTGGELDAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVMYT 159
EI EQ G D G G ++ + +E N + S L R +
Sbjct: 168 EICEQLGSAPDVLAIPVGNAGNISAYWKGFKEWN--------EAKASGL----PRMHGFE 215
Query: 160 KEEA----EGRRLKNPFDTITEGIGI-NRLTQNFMMAKLD--GAF--RGTDREAVEMSRF 210
E A +G+ + NP +TI I I N + A D G + TD E V +
Sbjct: 216 AEGAAAIVQGKPIDNP-ETIATAIRIGNPASWGLAEAARDESGGYIHSVTDDEIVNAYKK 274
Query: 211 LVKNDGLFLGSSSAMNCVGAVRVAQS--LGPGHTIVTILCDSGMRHLSKFYDVH 262
+ DG+F+ SA + G ++ + + G T+V + +G++ VH
Sbjct: 275 IAAQDGVFIEPGSAASLAGVIQHVANGTIKKGETVVCVFTGNGLKDPDTAMSVH 328
>gnl|CDD|225313 COG2515, Acd, 1-aminocyclopropane-1-carboxylate deaminase [Amino
acid transport and metabolism].
Length = 323
Score = 28.5 bits (64), Expect = 4.4
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 11/64 (17%)
Query: 100 EIWEQTGGEL--DAFVAAAGTGGTVAGVSRFLQENNPNIKCFLIDPPGSSLFNKVTRGVM 157
EI EQ L D+ V A G+GGT AG+ L + P+++ ID V+
Sbjct: 170 EIAEQAEQLLKFDSVVVAPGSGGTHAGLLVGLAQLGPDVEVIGID---------VSADPE 220
Query: 158 YTKE 161
KE
Sbjct: 221 KLKE 224
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 27.9 bits (63), Expect = 4.6
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 114 AAAGTGGTVAGVSRFLQENN--PNIKCFLIDPPG 145
+ A G GV++ +QE + ++K L+D PG
Sbjct: 139 SRACNVGATPGVTKSMQEVHLDKHVK--LLDSPG 170
>gnl|CDD|224372 COG1455, CelB, Phosphotransferase system cellobiose-specific
component IIC [Carbohydrate transport and metabolism].
Length = 432
Score = 28.3 bits (64), Expect = 4.9
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 87 LANFRAHYEG-TGPEIWEQTGGELDAFVAAAGTGGTVA 123
L N A+ G P I T LD+FV G+G T+
Sbjct: 262 LENAAAYQAGEPLPHII--TTPFLDSFVFIGGSGATLG 297
>gnl|CDD|107206 cd01563, Thr-synth_1, Threonine synthase is a pyridoxal phosphate
(PLP) dependent enzyme that catalyses the last reaction
in the synthesis of threonine from aspartate. It
proceeds by converting O-phospho-L-homoserine (OPH) into
threonine and inorganic phosphate. In plants, OPH is an
intermediate between the methionine and
threonine/isoleucine pathways. Thus threonine synthase
competes for OPH with cystathionine-gamma-synthase, the
first enzyme in the methionine pathway. These enzymes
are in general dimers. Members of this CD, Thr-synth_1,
are widely distributed in bacteria, archaea and higher
plants.
Length = 324
Score = 27.6 bits (62), Expect = 7.6
Identities = 40/177 (22%), Positives = 71/177 (40%), Gaps = 27/177 (15%)
Query: 94 YEGT---GPEIWEQTGGEL-DAFVAAAGTGGTVAGVSRFLQE--------NNPNIKCFLI 141
EG EI EQ G E+ D V G GG + + + +E P + +
Sbjct: 153 LEGQKTIAFEIAEQLGWEVPDYVVVPVGNGGNITAIWKGFKELKELGLIDRLP--RMVGV 210
Query: 142 DPPGSSLFNKVTRGVMYTKEEAEGRRLKNPFDTITEGIGI-NRLTQNFMMAKL---DGAF 197
G + R K++ E ++NP +TI I I N + + + G
Sbjct: 211 QAEG---AAPIVRAFKEGKDDIE--PVENP-ETIATAIRIGNPASGPKALRAVRESGGTA 264
Query: 198 RG-TDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQS--LGPGHTIVTILCDSG 251
+D E +E + L + +G+F+ +SA + G ++ + + G +V +L G
Sbjct: 265 VAVSDEEILEAQKLLARTEGIFVEPASAASLAGLKKLREEGIIDKGERVVVVLTGHG 321
>gnl|CDD|225614 COG3072, CyaA, Adenylate cyclase [Nucleotide transport and
metabolism].
Length = 853
Score = 27.8 bits (62), Expect = 7.7
Identities = 24/99 (24%), Positives = 34/99 (34%), Gaps = 19/99 (19%)
Query: 32 RALEANELASKRRRAVDKDGKELEHINGYGSDGAIQSSKFPSDCTGGFFADQFENLANFR 91
AL N+L + D K ++G+ S+G IQ FF D E N
Sbjct: 711 GALSTNKLDGLSVQVEDNHRKLPPVVDGFASEGIIQF----------FFEDTSEKSFNIY 760
Query: 92 AHYEGTGPEIWEQTGGELDAFVAAAGTGGTVAGVSRFLQ 130
E E++ G + V V+RF Q
Sbjct: 761 ILDESNRVEVYRHCEGSKEELVRD---------VNRFYQ 790
>gnl|CDD|132189 TIGR03145, cyt_nit_nrfE, cytochrome c nitrate reductase biogenesis
protein NrfE. Members of this protein family closely
resemble the CcmF protein of the CcmABCDEFGH system, or
system I, for c-type cytochrome biogenesis
(GenProp0678). Members are found, as a rule, next to
closely related paralogs of CcmG and CcmH and always
located near other genes associated with the cytochrome
c nitrite reductase enzyme complex. As a rule, members
are found in species that also encode bona fide members
of the CcmF, CcmG, and CcmH families.
Length = 628
Score = 27.4 bits (61), Expect = 9.2
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 64 GAIQSSKFPSDCTGGFFADQFENLANFRAHYEGTGPEI 101
GAI S F S+ Q + L + Y+G I
Sbjct: 499 GAIMVSYFGSEIGVRLAPQQQQPLGGYEFRYQGFENVI 536
>gnl|CDD|232897 TIGR00263, trpB, tryptophan synthase, beta subunit. Tryptophan
synthase catalyzes the last step in the biosynthesis of
tryptophan. the beta chain contains the functional
domain for or the synthesis of tryptophan from indole
and serine. The enzyme requires pyridoxal-phosphate as a
cofactor. The pyridoxal-P attachment site is contained
within the conserved region
[LIVM]-x-H-x-G-[STA]-H-K-x-N] [K is the pyridoxal-P
attachment site] which is present between residues
90-100 of the model [Amino acid biosynthesis, Aromatic
amino acid family].
Length = 385
Score = 27.3 bits (61), Expect = 9.2
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 200 TDREAVEMSRFLVKNDGLF--LGSSSAMNCVGAVRVAQSLGPGHTIVTILCDSG 251
TD EA+E + L +N+G+ L SS A+ + ++A +L +V L G
Sbjct: 323 TDDEALEAFKLLSRNEGIIPALESSHALAHL--EKIAPTLPKDQIVVVNLSGRG 374
>gnl|CDD|143488 cd06813, PLPDE_III_DSD_D-TA_like_2, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes Similar to D-Serine Dehydratase
and D-Threonine Aldolase, Unknown Group 2. This
subfamily is composed of uncharacterized bacterial
proteins with similarity to eukaryotic D-serine
dehydratases (DSD) and D-threonine aldolases (D-TA). DSD
catalyzes the dehydration of D-serine to aminoacrylate,
which is rapidly hydrolyzed to pyruvate and ammonia.
D-TA reversibly catalyzes the aldol cleavage of
D-threonine into glycine and acetaldehyde, and the
synthesis of D-threonine from glycine and acetaldehyde.
DSD and D-TA are fold type III PLP-dependent enzymes,
similar to bacterial alanine racemase (AR), which
contains an N-terminal PLP-binding TIM barrel domain and
a C-terminal beta-sandwich domain. AR exists as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. Based on
their similarity to AR, it is possible members of this
family also form dimers in solution.
Length = 388
Score = 27.2 bits (61), Expect = 9.3
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 28 VARRRALEANELASKRRRAVD---KDGKELEHINGYGSDGAIQSS 69
+ + ELA +R V +G++LE +NG G G+++S+
Sbjct: 202 IRLLKKRSIKELAERRAAVVAALRAEGEDLEFVNG-GGTGSLEST 245
>gnl|CDD|176250 cd08290, ETR, 2-enoyl thioester reductase (ETR). 2-enoyl thioester
reductase (ETR) catalyzes the NADPH-dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains, at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. Candida tropicalis
enoyl thioester reductase (Etr1p) catalyzes the
NADPH-dependent reduction of trans-2-enoyl thioesters in
mitochondrial fatty acid synthesis. Etr1p forms
homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 341
Score = 27.2 bits (61), Expect = 9.4
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 3/25 (12%)
Query: 224 AMNCVG---AVRVAQSLGPGHTIVT 245
A+NCVG A +A+ L PG T+VT
Sbjct: 225 ALNCVGGKSATELARLLSPGGTMVT 249
>gnl|CDD|215723 pfam00109, ketoacyl-synt, Beta-ketoacyl synthase, N-terminal
domain. The structure of beta-ketoacyl synthase is
similar to that of the thiolase family (pfam00108) and
also chalcone synthase. The active site of beta-ketoacyl
synthase is located between the N and C-terminal
domains. The N-terminal domain contains most of the
structures involved in dimer formation and also the
active site cysteine.
Length = 243
Score = 27.2 bits (61), Expect = 9.9
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 3/54 (5%)
Query: 195 GAFRGTDREAVEMSRFLVKNDGLFLGSSSAMNCVGAVRVAQSL---GPGHTIVT 245
G+ G E + + + M V A R++ L GP T+ T
Sbjct: 109 GSGSGDYAELQALDSAGGPRRVSPYLTGAWMPSVAAGRISYRLGLRGPSVTVDT 162
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.397
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: 14,848,547
Number of extensions: 1443268
Number of successful extensions: 1455
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1430
Number of HSP's successfully gapped: 80
Length of query: 282
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 186
Effective length of database: 6,679,618
Effective search space: 1242408948
Effective search space used: 1242408948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.0 bits)