RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021613
(310 letters)
>gnl|CDD|215333 PLN02618, PLN02618, tryptophan synthase, beta chain.
Length = 410
Score = 469 bits (1208), Expect = e-167
Identities = 198/238 (83%), Positives = 211/238 (88%), Gaps = 5/238 (2%)
Query: 61 ESDPAPWQRPDVFGRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYV 120
SDP +QRPD FGRFG+FGGK+VPETLM ALSELE+A + LA D +FQEEL+GIL+DYV
Sbjct: 4 GSDPTGFQRPDSFGRFGKFGGKYVPETLMTALSELEAAFNALATDPEFQEELAGILKDYV 63
Query: 121 GRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRII 180
GRETPLYFAERLTEHY+R +G GP IYLKREDLNHTGAHKINNAV QALLAKRLGK RII
Sbjct: 64 GRETPLYFAERLTEHYKRADGEGPEIYLKREDLNHTGAHKINNAVAQALLAKRLGKKRII 123
Query: 181 AETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLK 240
AETGAGQHGVATATVCARFGL+CIVYMGAQDMERQALNVFRMRLLGAEVR VHSGTATLK
Sbjct: 124 AETGAGQHGVATATVCARFGLECIVYMGAQDMERQALNVFRMRLLGAEVRPVHSGTATLK 183
Query: 241 DATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFHATSIGEMGWETRCADCMRWW 298
DATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFH+ +G ETR M W
Sbjct: 184 DATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFHSV----IGKETR-RQAMEKW 236
>gnl|CDD|235288 PRK04346, PRK04346, tryptophan synthase subunit beta; Validated.
Length = 397
Score = 464 bits (1198), Expect = e-165
Identities = 155/223 (69%), Positives = 177/223 (79%), Gaps = 9/223 (4%)
Query: 68 QRPDVFGRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRETPLY 127
PD G FG FGG+FVPETLM AL ELE A K +D +FQ EL +L++YVGR TPLY
Sbjct: 3 TLPDENGYFGEFGGRFVPETLMPALEELEEAYEKAKNDPEFQAELDYLLKNYVGRPTPLY 62
Query: 128 FAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQ 187
FAERL+EH GG IYLKREDLNHTGAHKINN +GQALLAKR+GK RIIAETGAGQ
Sbjct: 63 FAERLSEHL-----GGAKIYLKREDLNHTGAHKINNVLGQALLAKRMGKKRIIAETGAGQ 117
Query: 188 HGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAI 247
HGVATAT A GL+C++YMGA+D+ERQALNVFRM+LLGAEV V SG+ TLKDA +EA+
Sbjct: 118 HGVATATAAALLGLECVIYMGAEDVERQALNVFRMKLLGAEVVPVTSGSRTLKDAVNEAL 177
Query: 248 RDWVTNVETTHYILGSVAGPHPYPMMVRDFHATSIGEMGWETR 290
RDWVTNVE THY++GSVAGPHPYP MVRDF + IGE E +
Sbjct: 178 RDWVTNVEDTHYLIGSVAGPHPYPTMVRDFQSV-IGE---EAK 216
>gnl|CDD|223211 COG0133, TrpB, Tryptophan synthase beta chain [Amino acid transport
and metabolism].
Length = 396
Score = 429 bits (1106), Expect = e-151
Identities = 156/221 (70%), Positives = 177/221 (80%), Gaps = 10/221 (4%)
Query: 70 PDVFGRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRETPLYFA 129
PD G FG FGG++VPETLM AL ELE A K +D +FQ EL +L+DY GR TPLYFA
Sbjct: 3 PDEKGYFGEFGGQYVPETLMPALEELEKAYEKAKNDPEFQAELDYLLKDYAGRPTPLYFA 62
Query: 130 ERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHG 189
ERLTEH G IYLKREDLNHTGAHKINNA+GQALLAKR+GKTRIIAETGAGQHG
Sbjct: 63 ERLTEHL------GAKIYLKREDLNHTGAHKINNALGQALLAKRMGKTRIIAETGAGQHG 116
Query: 190 VATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAIRD 249
VATAT A FGL+C++YMGA+D+ERQALNVFRMRLLGAEV V SG+ TLKDA +EA+RD
Sbjct: 117 VATATAAALFGLECVIYMGAEDVERQALNVFRMRLLGAEVVPVTSGSGTLKDAINEALRD 176
Query: 250 WVTNVETTHYILGSVAGPHPYPMMVRDFHATSIGEMGWETR 290
WVTNVE THY++GS AGPHPYP +VRDF + IGE E +
Sbjct: 177 WVTNVEDTHYLIGSAAGPHPYPTIVRDFQSV-IGE---EAK 213
>gnl|CDD|183851 PRK13028, PRK13028, tryptophan synthase subunit beta; Provisional.
Length = 402
Score = 372 bits (957), Expect = e-128
Identities = 132/215 (61%), Positives = 156/215 (72%), Gaps = 6/215 (2%)
Query: 70 PDVFGRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRETPLYFA 129
PD G FG +GG+FVP L AL ELE+A ++ D DF EL +L+ YVGR TPLY A
Sbjct: 9 PDADGFFGEYGGQFVPPELKPALDELEAAYEEIKKDPDFIAELRYLLKHYVGRPTPLYHA 68
Query: 130 ERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHG 189
+RL+E GG IYLKREDLNHTGAHKINN +GQALLAKR+GK R+IAETGAGQHG
Sbjct: 69 KRLSEEL-----GGAQIYLKREDLNHTGAHKINNCLGQALLAKRMGKKRLIAETGAGQHG 123
Query: 190 VATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAIRD 249
VATAT A FGL+C +YMG D+ERQ NVFRM+LLGAEV V G TLK+A A D
Sbjct: 124 VATATAAALFGLECEIYMGEVDIERQHPNVFRMKLLGAEVVPVTRGGRTLKEAVDSAFED 183
Query: 250 WVTNVETTHYILGSVAGPHPYPMMVRDFHATSIGE 284
++ + + THY +GSV GPHP+PMMVRDF + IGE
Sbjct: 184 YLKDPDNTHYAIGSVVGPHPFPMMVRDFQSV-IGE 217
>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 = 365 bits (938), Expect = e-126
Identities = 141/211 (66%), Positives = 160/211 (75%), Gaps = 6/211 (2%)
Query: 74 GRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRETPLYFAERLT 133
G FG FGG++VPETLM AL ELE+A D F EL+ +LR+Y GR TPL FA LT
Sbjct: 1 GYFGDFGGQYVPETLMPALEELEAAFEDAKADPAFWAELNELLRNYAGRPTPLTFAPNLT 60
Query: 134 EHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHGVATA 193
E GG IYLKREDLNHTGAHKINNA+GQALLAKR+GK RIIAETGAGQHGVATA
Sbjct: 61 EAL-----GGAKIYLKREDLNHTGAHKINNALGQALLAKRMGKKRIIAETGAGQHGVATA 115
Query: 194 TVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAIRDWVTN 253
T A GL C VYMGA+D+ERQ NVFRM LLGA+V V SG+ TLKDA +EA+RDWVT+
Sbjct: 116 TAAALLGLDCEVYMGAEDVERQKPNVFRMELLGAKVIPVTSGSGTLKDAVNEALRDWVTS 175
Query: 254 VETTHYILGSVAGPHPYPMMVRDFHATSIGE 284
V+ THY+LGS GPHP+P MVRDF + IGE
Sbjct: 176 VDDTHYVLGSAVGPHPFPTMVRDFQSV-IGE 205
>gnl|CDD|107207 cd06446, Trp-synth_B, Tryptophan synthase-beta: Trptophan synthase
is a bifunctional enzyme that catalyses the last two
steps in the biosynthesis of L-tryptophan via its alpha
and beta reactions. In the alpha reaction, indole
3-glycerol phosphate is cleaved reversibly to
glyceraldehyde 3-phosphate and indole at the active site
of the alpha subunit. In the beta reaction, indole
undergoes a PLP-dependent reaction with L-serine to form
L-tryptophan at the active site of the beta subunit.
Members of this CD, Trp-synth_B, are found in all three
major phylogenetic divisions.
Length = 365
Score = 361 bits (929), Expect = e-125
Identities = 140/200 (70%), Positives = 155/200 (77%), Gaps = 9/200 (4%)
Query: 91 ALSELESALHKLADDRDFQEELSGILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKR 150
AL ELE K D DF EEL + +DYVGR TPLY A+RL+E+ GG IYLKR
Sbjct: 2 ALEELEQEFSKERYDPDFPEELRELYKDYVGRPTPLYRAKRLSEYL-----GGAKIYLKR 56
Query: 151 EDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQ 210
EDLNHTGAHKINNA+GQALLAKR+GK R+IAETGAGQHGVATAT CA FGL+C +YMGA
Sbjct: 57 EDLNHTGAHKINNALGQALLAKRMGKKRVIAETGAGQHGVATATACALFGLECEIYMGAV 116
Query: 211 DMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAIRDWVTNVETTHYILGSVAGPHPY 270
D+ERQ LNVFRM LLGAEV V SG+ TLKDA SEAIRDWVTNVE THY+LGSV GPHPY
Sbjct: 117 DVERQPLNVFRMELLGAEVVPVPSGSGTLKDAISEAIRDWVTNVEDTHYLLGSVVGPHPY 176
Query: 271 PMMVRDFHATSIGEMGWETR 290
P MVRDF + IGE E +
Sbjct: 177 PNMVRDFQ-SVIGE---EAK 192
>gnl|CDD|237513 PRK13803, PRK13803, bifunctional phosphoribosylanthranilate
isomerase/tryptophan synthase subunit beta; Provisional.
Length = 610
Score = 360 bits (925), Expect = e-121
Identities = 132/215 (61%), Positives = 161/215 (74%), Gaps = 7/215 (3%)
Query: 70 PDVFGRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRETPLYFA 129
D GR+G FGG +VPETLM L EL+ + K+ +FQ+ +L++Y GR TPL A
Sbjct: 218 SDPAGRYGTFGGAYVPETLMANLQELQESYTKIIKSNEFQKTFKRLLQNYAGRPTPLTEA 277
Query: 130 ERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHG 189
+RL++ Y G IYLKREDLNHTG+HKINNA+GQALLAKR+GKTRIIAETGAGQHG
Sbjct: 278 KRLSDIY------GARIYLKREDLNHTGSHKINNALGQALLAKRMGKTRIIAETGAGQHG 331
Query: 190 VATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAIRD 249
VATAT CA FGL+C ++MG +D++RQALNV RM+LLGA V V SG+ TLKDA +EAIRD
Sbjct: 332 VATATACALFGLKCTIFMGEEDIKRQALNVERMKLLGANVIPVLSGSKTLKDAVNEAIRD 391
Query: 250 WVTNVETTHYILGSVAGPHPYPMMVRDFHATSIGE 284
WV +V THY++GS GPHPYP MV F + IGE
Sbjct: 392 WVASVPDTHYLIGSAVGPHPYPEMVAYFQSV-IGE 425
>gnl|CDD|184335 PRK13802, PRK13802, bifunctional indole-3-glycerol phosphate
synthase/tryptophan synthase subunit beta; Provisional.
Length = 695
Score = 278 bits (713), Expect = 8e-89
Identities = 129/209 (61%), Positives = 156/209 (74%), Gaps = 1/209 (0%)
Query: 76 FGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRETPLYFAERLTEH 135
+G+FGG++VPE L+ AL ELE + D +F +EL+ + + YVGR +PL A R E
Sbjct: 279 WGQFGGRYVPEALITALDELERVYTQAKADPEFHKELATLNQRYVGRPSPLTEAPRFAER 338
Query: 136 YRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHGVATATV 195
+ G ++LKREDLNHTGAHKINNA+GQALL KR+GKTR+IAETGAGQHGVATATV
Sbjct: 339 VKEKTGLDARVFLKREDLNHTGAHKINNALGQALLVKRMGKTRVIAETGAGQHGVATATV 398
Query: 196 CARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEAIRDWVTNVE 255
CA GL+C +YMG D RQALNV RMR+LGAEV V G LKDA +EA+RDWVTNV+
Sbjct: 399 CAMLGLKCRIYMGQIDARRQALNVARMRMLGAEVVEVTLGDRILKDAINEALRDWVTNVK 458
Query: 256 TTHYILGSVAGPHPYPMMVRDFHATSIGE 284
THY+LG+VAGPHP+P MVRDF IGE
Sbjct: 459 DTHYLLGTVAGPHPFPAMVRDFQKI-IGE 486
>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 = 137 bits (347), Expect = 6e-39
Identities = 52/160 (32%), Positives = 68/160 (42%), Gaps = 23/160 (14%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLG---KTRII 180
TPL +RL++ GG +IYLK E LN TG+ K A+ LLA+ G K II
Sbjct: 1 TPLVRLKRLSK------LGGANIYLKLEFLNPTGSFKDRGALNLILLAEEEGKLPKGVII 54
Query: 181 AETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLK 240
TG G G+A A AR GL+C + M V +MR LGAEV V
Sbjct: 55 ESTG-GNTGIALAAAAARLGLKCTIVMPEGA---SPEKVAQMRALGAEVVLVPGD---FD 107
Query: 241 DATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFHAT 280
DA + A + +Y+ +P T
Sbjct: 108 DAIALAKELAEED-PGAYYVNQFD---NPA---NIAGQGT 140
>gnl|CDD|237087 PRK12391, PRK12391, tryptophan synthase subunit beta; Reviewed.
Length = 427
Score = 114 bits (289), Expect = 4e-29
Identities = 66/174 (37%), Positives = 81/174 (46%), Gaps = 30/174 (17%)
Query: 110 EELSGILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQAL 169
EE+ I R + R TPL A RL + P IY K E ++ TG+HK N AV QA
Sbjct: 66 EEVREIYR--LWRPTPLIRARRLEKALGTP----AKIYYKYEGVSPTGSHKPNTAVAQAY 119
Query: 170 LAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQDME----RQALNVFRMRLL 225
K+ G R+ ETGAGQ G A A CA FGL+C V+M E R++L M
Sbjct: 120 YNKKEGIKRLTTETGAGQWGSALALACALFGLECTVFMVRVSYEQKPYRRSL----METY 175
Query: 226 GAEVRA-----VHSGTATLKD----------ATSEAIRDWVTNVETTHYILGSV 264
GAEV +G L + A SEA+ D T Y LGSV
Sbjct: 176 GAEVIPSPSDLTEAGRKILAEDPDHPGSLGIAISEAVEDAAKR-PDTKYALGSV 228
>gnl|CDD|224269 COG1350, COG1350, Predicted alternative tryptophan synthase
beta-subunit (paralog of TrpB) [General function
prediction only].
Length = 432
Score = 106 bits (267), Expect = 4e-26
Identities = 63/160 (39%), Positives = 78/160 (48%), Gaps = 20/160 (12%)
Query: 120 VGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRI 179
+GR TPL A+ L E G IY K E + TG+HKIN A+ QA AK+ G R+
Sbjct: 75 IGRPTPLIRAKNLEEAL----GTPARIYYKYEGVTPTGSHKINTALAQAYYAKKEGAKRL 130
Query: 180 IAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHS----- 234
ETGAGQ G A + A FGL+ V+M ++ + M L GAEV S
Sbjct: 131 TTETGAGQWGSALSLAAALFGLKATVFMVRVSYYQKPYRKYLMELYGAEVVPSPSELTEF 190
Query: 235 GTATLKD----------ATSEAIRDWVTNVETTHYILGSV 264
G LK+ A SEAI + N E T Y LGSV
Sbjct: 191 GRKILKEDPDHPGSLGIAISEAIEYALKN-ENTKYSLGSV 229
>gnl|CDD|233403 TIGR01415, trpB_rel, pyridoxal-phosphate dependent TrpB-like
enzyme. This model represents a family of
pyridoxal-phosphate dependent enzyme (pfam00291) closely
related to the beta subunit of tryptophan synthase
(TIGR00263). However, the only case in which a member of
this family replaces a member of TIGR00263 is in
Sulfolobus species which contain two sequences which hit
this model, one of which is proximal to the alpha
subunit. In every other case so far, either the species
appears not to make tryptophan (there is no trp synthase
alpha subunit), or a trp synthase beta subunit matching
TIGR00263 is also found [Unknown function, Enzymes of
unknown specificity].
Length = 419
Score = 104 bits (262), Expect = 2e-25
Identities = 63/160 (39%), Positives = 81/160 (50%), Gaps = 20/160 (12%)
Query: 120 VGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRI 179
+GR TPL A+ L E G IY K E ++ TG+HKIN A+ QA AK G R+
Sbjct: 65 IGRPTPLIRAKGLEELL----GTPARIYYKYESVSPTGSHKINTAIAQAYYAKIEGAKRL 120
Query: 180 IAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHS----- 234
+ ETGAGQ G A + A FGL+C V+M ++ + M L GAEV S
Sbjct: 121 VTETGAGQWGSALSLAGALFGLECKVFMVRVSFNQKPYRKYLMELYGAEVIPSPSEFTEF 180
Query: 235 GTATLKD----------ATSEAIRDWVTNVETTHYILGSV 264
G LK+ A SEAI +++ E T Y LGSV
Sbjct: 181 GREVLKEDPDHPGSLGIAISEAIEYALSD-EDTKYSLGSV 219
>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 = 88.2 bits (219), Expect = 4e-20
Identities = 44/178 (24%), Positives = 60/178 (33%), Gaps = 19/178 (10%)
Query: 116 LRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLG 175
+ +G TPL G +YLK E LN TG+ K A L A G
Sbjct: 1 ISLGIGP-TPLVRLPSP--------LLGARVYLKLESLNPTGSFKDRGAAYLLLRALERG 51
Query: 176 KTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSG 235
T + E +G G A A AR GL+ + + + MR LGAEV V S
Sbjct: 52 AT--VVEASSGNTGRALAAAAARLGLKVTIVVPE-GASPG--KLLLMRALGAEVILVVSE 106
Query: 236 TATLKDATSEAIRDWVTNVETTHYILGSVAGPHPYPMMVRDFHATSIGEMGWETRCAD 293
+A+ E G + V + T E+ + D
Sbjct: 107 -----GDYDDALELAEEAAELLAAYDGPIPLGQYNNPNVIAGYKTIGLEILEQLGQGD 159
>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 = 63.7 bits (156), Expect = 1e-11
Identities = 33/119 (27%), Positives = 49/119 (41%), Gaps = 16/119 (13%)
Query: 115 ILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRL 174
++ V R TPL + L+E G +YLK E+L TG+ KI A + L
Sbjct: 10 RIKPVV-RRTPLLTSPTLSELL------GAEVYLKCENLQKTGSFKIRGAYNKLLSLSEE 62
Query: 175 GKTR-IIAETGAGQHGVATATVCARFGLQCIVYM--GAQDMERQALNVFRMRLLGAEVR 230
+ + ++A + AG H A G+ + M A + A R GAEV
Sbjct: 63 ERAKGVVAAS-AGNHAQGVAYAAKLLGIPATIVMPETAPAAKVDA-----TRAYGAEVV 115
>gnl|CDD|224092 COG1171, IlvA, Threonine dehydratase [Amino acid transport and
metabolism].
Length = 347
Score = 62.2 bits (152), Expect = 5e-11
Identities = 34/121 (28%), Positives = 48/121 (39%), Gaps = 19/121 (15%)
Query: 115 ILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKIN---NAVGQALLA 171
L+ V TPL + L+E G IYLKRE+L G+ KI N +
Sbjct: 18 RLKGVV-NPTPLQRSPSLSERL------GAEIYLKRENLQPVGSFKIRGAYNKLSSLSEE 70
Query: 172 KRLGKTRIIAETGAGQHGVATATVCARFGLQCIVYM--GAQDMERQALNVFRMRLLGAEV 229
+ +IA + AG H A R G++ + M ++ A R GAEV
Sbjct: 71 EERAAG-VIAAS-AGNHAQGVAYAAKRLGIKATIVMPETTPKIKVDA-----TRGYGAEV 123
Query: 230 R 230
Sbjct: 124 I 124
>gnl|CDD|179673 PRK03910, PRK03910, D-cysteine desulfhydrase; Validated.
Length = 331
Score = 61.4 bits (150), Expect = 1e-10
Identities = 40/134 (29%), Positives = 54/134 (40%), Gaps = 26/134 (19%)
Query: 117 RDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTG-------AHKINNAVGQAL 169
+ G TPL RL+ GP IY+KR+DL TG K+ + AL
Sbjct: 9 LELAGLPTPLEPLPRLSAAL------GPDIYIKRDDL--TGLALGGNKTRKLEFLLADAL 60
Query: 170 LAKRLGKTRIIAETGAGQ--HGVATATVCARFGLQCIVYMGAQDMERQAL-----NVFRM 222
G +I GA Q H TA A+ GL+C++ + NV
Sbjct: 61 ---AQGADTLIT-AGAIQSNHARQTAAAAAKLGLKCVLLLENPVPTEAENYLANGNVLLD 116
Query: 223 RLLGAEVRAVHSGT 236
L GAE+ V +GT
Sbjct: 117 DLFGAEIHVVPAGT 130
>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 = 59.1 bits (144), Expect = 4e-10
Identities = 35/110 (31%), Positives = 45/110 (40%), Gaps = 14/110 (12%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNA---VGQALLAKRLGKTRII 180
TPL RL+ G G IY K E N G+ K A + A L I
Sbjct: 3 TPLVRLNRLSP------GTGAEIYAKLEFFNPGGSVKDRIALYMIEDAEKRGLLKPGTTI 56
Query: 181 AETGAGQHGVATATVCARFGLQCIVYM-GAQDMERQALNVFRMRLLGAEV 229
E +G G+ A V A G + I+ M E++ L +R LGAEV
Sbjct: 57 IEPTSGNTGIGLAMVAAAKGYRFIIVMPETMSEEKRKL----LRALGAEV 102
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 57.4 bits (139), Expect = 2e-09
Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 10/115 (8%)
Query: 116 LRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLG 175
LR V R TPL + L++H G +YLK E L HTG+ K A + L
Sbjct: 14 LRPQV-RVTPLEHSPLLSQH------TGCEVYLKCEHLQHTGSFKFRGASNKLRLLNEAQ 66
Query: 176 KTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVR 230
+ + + +G HG A G+ VY Q A+ + +R LGAEVR
Sbjct: 67 RQQGVITASSGNHGQGVALAAKLAGIPVTVYAPEQ---ASAIKLDAIRALGAEVR 118
>gnl|CDD|225313 COG2515, Acd, 1-aminocyclopropane-1-carboxylate deaminase [Amino
acid transport and metabolism].
Length = 323
Score = 56.6 bits (137), Expect = 3e-09
Identities = 41/139 (29%), Positives = 66/139 (47%), Gaps = 18/139 (12%)
Query: 118 DYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTG-----AHKINNAVGQALLAK 172
+ + TP+ RL+ H G IY+KR+DL K+ +G+AL
Sbjct: 10 ELIFGPTPIQKLPRLSAHL------GVEIYIKRDDLTGLAFGGNKIRKLEFLLGEAL--- 60
Query: 173 RLGKTRIIAETGAGQ--HGVATATVCARFGLQCIVYM-GAQDMERQALNVFRMRLLGAEV 229
R G ++ G Q H TA V A+ GL+C++ + + N+ +L+GAEV
Sbjct: 61 RKGADTLVT-YGGIQSNHVRQTAAVAAKLGLKCVLILENIEANYLLNGNLLLSKLMGAEV 119
Query: 230 RAVHSGTATLKDATSEAIR 248
RAV +GT +A++E +
Sbjct: 120 RAVDAGTDIGINASAEELA 138
>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 = 55.3 bits (134), Expect = 1e-08
Identities = 39/146 (26%), Positives = 59/146 (40%), Gaps = 18/146 (12%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALL---AKRLGKTRII 180
TPL A RL E GG ++Y+K E LN TG+ K G + AK LG +
Sbjct: 23 TPLVRAPRLGE-----RLGGKNLYVKDEGLNPTGSFK---DRGMTVAVSKAKELGVKAVA 74
Query: 181 AETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTATLK 240
+ G + A AR G++C+V++ A L + GA V AV
Sbjct: 75 CAS-TGNTSASLAAYAARAGIKCVVFLPA-GKALGKLA--QALAYGATVLAVEGNFDDAL 130
Query: 241 DATSEAIRD---WVTNVETTHYILGS 263
E + +++N + + G
Sbjct: 131 RLVRELAEENWIYLSNSLNPYRLEGQ 156
>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 = 54.0 bits (130), Expect = 3e-08
Identities = 37/140 (26%), Positives = 56/140 (40%), Gaps = 10/140 (7%)
Query: 110 EELSGILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQAL 169
E L++ V TPL ERL+E Y G +IYLKREDL ++KI A
Sbjct: 4 EAARKRLKEVV-PHTPLQLNERLSEKY------GANIYLKREDLQPVRSYKIRGAYNFLK 56
Query: 170 LAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEV 229
+ + AG H A C G+ V+M A +++ + R+++ G E
Sbjct: 57 QLSDAQLAKGVVCASAGNHAQGFAYACRHLGVHGTVFMPATTPKQK---IDRVKIFGGEF 113
Query: 230 RAVHSGTATLKDATSEAIRD 249
+ T + A
Sbjct: 114 IEIILVGDTFDQCAAAAREH 133
>gnl|CDD|223110 COG0031, CysK, Cysteine synthase [Amino acid transport and
metabolism].
Length = 300
Score = 53.3 bits (129), Expect = 4e-08
Identities = 39/119 (32%), Positives = 49/119 (41%), Gaps = 15/119 (12%)
Query: 118 DYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVG---QALLAKRL 174
D +G TPL RL+ G G IY K E N G+ K A+ A L
Sbjct: 7 DLIGN-TPLVRLNRLSP------GTGVEIYAKLESFNPGGSVKDRIALYMIEDAEKRGLL 59
Query: 175 GKTRIIAETGAGQHGVATATVCARFGLQCIVYM-GAQDMERQALNVFRMRLLGAEVRAV 232
I E +G G+A A V A G + I+ M ER+ L +R LGAEV
Sbjct: 60 KPGGTIVEATSGNTGIALAMVAAAKGYRLIIVMPETMSQERRKL----LRALGAEVILT 114
>gnl|CDD|181319 PRK08246, PRK08246, threonine dehydratase; Provisional.
Length = 310
Score = 50.7 bits (122), Expect = 3e-07
Identities = 38/113 (33%), Positives = 52/113 (46%), Gaps = 13/113 (11%)
Query: 128 FAERLTEHYRR-------PNGGGP-HIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRI 179
A+R+ H RR G GP ++LK E L HTG+ K A LLA + +
Sbjct: 13 AAQRIAPHIRRTPVLEADGAGFGPAPVWLKLEHLQHTGSFKARGAF-NRLLAAPVPAAGV 71
Query: 180 IAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAV 232
+A +G G G+A A A G+ V++ V R+R LGAEV V
Sbjct: 72 VAASG-GNAGLAVAYAAAALGVPATVFVPET---APPAKVARLRALGAEVVVV 120
>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 = 50.5 bits (121), Expect = 3e-07
Identities = 38/126 (30%), Positives = 55/126 (43%), Gaps = 23/126 (18%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGA------HKINNAVGQALLAKRLGKT 177
TP+ + RL+EH GG IY KR+D N A K+ + AL G
Sbjct: 1 TPIQYLPRLSEHL----GGKVEIYAKRDDCNSGLAFGGNKIRKLEYLLPDAL---AKGAD 53
Query: 178 RIIAETGAGQ--HGVATATVCARFGLQCI------VYMGAQDMERQALNVFRMRLLGAEV 229
++ G Q H A V A+ GL+C+ V +R N+ R++GA+V
Sbjct: 54 TLVT-VGGIQSNHTRQVAAVAAKLGLKCVLVQENWVPYSDAVYDRVG-NILLSRIMGADV 111
Query: 230 RAVHSG 235
R V +G
Sbjct: 112 RLVSAG 117
>gnl|CDD|236318 PRK08639, PRK08639, threonine dehydratase; Validated.
Length = 420
Score = 48.6 bits (117), Expect = 2e-06
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 17/97 (17%)
Query: 116 LRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKIN---NAVGQALLAK 172
L+D V ETPL + L+E Y G ++YLKREDL ++K+ NA+ Q L+
Sbjct: 19 LKDVV-PETPLQRNDYLSEKY------GANVYLKREDLQPVRSYKLRGAYNAISQ--LSD 69
Query: 173 RLGKTRIIAETGAGQH--GVATATVCARFGLQCIVYM 207
+ AG H GVA A C G+ +++M
Sbjct: 70 E-ELAAGVVCASAGNHAQGVAYA--CRHLGIPGVIFM 103
>gnl|CDD|236025 PRK07476, eutB, threonine dehydratase; Provisional.
Length = 322
Score = 47.7 bits (114), Expect = 3e-06
Identities = 39/130 (30%), Positives = 55/130 (42%), Gaps = 18/130 (13%)
Query: 122 RETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKI---NNAVGQALLAKRLGKTR 178
R TPL + L+ P ++LK E L TG+ K+ NA+ L A+ +
Sbjct: 18 RRTPLVASASLSARAGVP------VWLKLETLQPTGSFKLRGATNALLS-LSAQERARGV 70
Query: 179 IIAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGTAT 238
+ A TG HG A A G++ + M + V +R LGAEVR V
Sbjct: 71 VTASTG--NHGRALAYAARALGIRATICMSRLVPANK---VDAIRALGAEVRIVGRSQ-- 123
Query: 239 LKDATSEAIR 248
DA +E R
Sbjct: 124 -DDAQAEVER 132
>gnl|CDD|181457 PRK08526, PRK08526, threonine dehydratase; Provisional.
Length = 403
Score = 46.2 bits (110), Expect = 1e-05
Identities = 36/108 (33%), Positives = 54/108 (50%), Gaps = 13/108 (12%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQ-ALLAKRLGKTRIIAE 182
TP +A L++ G +YLK+E+L TGA+KI A + A L++ + +IA
Sbjct: 21 TPFAYAPFLSKI------SGAEVYLKKENLQITGAYKIRGAYNKIANLSEEQKQHGVIAA 74
Query: 183 TGAGQHGVATATVCARFGLQ-CIVYMGAQDMERQALNVFRMRLLGAEV 229
+ AG H A +FG++ IV A + L V + LGAEV
Sbjct: 75 S-AGNHAQGVAISAKKFGIKAVIVMPEATPL----LKVSGTKALGAEV 117
>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 = 44.8 bits (106), Expect = 3e-05
Identities = 40/142 (28%), Positives = 59/142 (41%), Gaps = 22/142 (15%)
Query: 118 DYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGA-----HKINNAVGQALLAK 172
+ +G TP+ + RL+++ G IY+KR+DL K+ + AL
Sbjct: 2 ELIGAPTPIQYLPRLSDYL------GREIYIKRDDLTGLAMGGNKIRKLEFLLADAL--- 52
Query: 173 RLGKTRIIAETGAGQ--HGVATATVCARFGLQCIVYM-----GAQDMERQALNVFRMRLL 225
R G +I GA Q H ATA V A+ GL C++ + + N+ L
Sbjct: 53 RKGADTVIT-AGAIQSNHARATAAVAAKLGLHCVLLLRNPIGTTAENYLLNGNLLLDDLF 111
Query: 226 GAEVRAVHSGTATLKDATSEAI 247
GAE R T DA E +
Sbjct: 112 GAETRIESCEEYTDIDAQLEEL 133
>gnl|CDD|181283 PRK08197, PRK08197, threonine synthase; Validated.
Length = 394
Score = 44.6 bits (106), Expect = 3e-05
Identities = 31/106 (29%), Positives = 44/106 (41%), Gaps = 9/106 (8%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAET 183
TPL RL + G +++K E LN TG+ K AK LG + T
Sbjct: 80 TPLLPLPRLGKAL-----GIGRLWVKDEGLNPTGSFKARGLAVGVSRAKELGVKHLAMPT 134
Query: 184 GAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEV 229
G G A A AR G++ ++M A + + L GAE+
Sbjct: 135 -NGNAGAAWAAYAARAGIRATIFMPA---DAPEITRLECALAGAEL 176
>gnl|CDD|236339 PRK08813, PRK08813, threonine dehydratase; Provisional.
Length = 349
Score = 44.6 bits (105), Expect = 4e-05
Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 116 LRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLG 175
LR Y+ TPL++AER ++LK E+L TG++K+ A+ L G
Sbjct: 33 LRRYL-SPTPLHYAERFG------------VWLKLENLQRTGSYKVRGALNALLAGLERG 79
Query: 176 KTRIIAETGAGQHGVATATVCARFGLQCIVYM 207
R + AG H A R G+Q I M
Sbjct: 80 DERPVICASAGNHAQGVAWSAYRLGVQAITVM 111
>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 = 43.4 bits (103), Expect = 7e-05
Identities = 33/116 (28%), Positives = 47/116 (40%), Gaps = 15/116 (12%)
Query: 118 DYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVG---QALLAKRL 174
+ +G TPL RL G + K E N +G+ K A+ A L
Sbjct: 3 ELIGN-TPLVRLNRLAP------GCDARVLAKLEGRNPSGSVKDRIALSMIEDAEKRGLL 55
Query: 175 GKTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQ-DMERQALNVFRMRLLGAEV 229
I E +G G+A A V A G + I+ M +ER+ L +R GAE+
Sbjct: 56 KPGDTIIEATSGNTGIALAMVAAAKGYKLILTMPETMSLERRKL----LRAYGAEL 107
>gnl|CDD|235842 PRK06608, PRK06608, threonine dehydratase; Provisional.
Length = 338
Score = 43.2 bits (102), Expect = 8e-05
Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 122 RETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGK--TRI 179
TP+ +E L E G I+ K E L TGA K+ + L K GK +I
Sbjct: 22 HLTPIVHSESLNEML------GHEIFFKVESLQKTGAFKVRGVLNHLLELKEQGKLPDKI 75
Query: 180 IAETGAGQHGVATATVCARFGLQCIVYM 207
+A + G HG A A FG++ +Y+
Sbjct: 76 VAYS-TGNHGQAVAYASKLFGIKTRIYL 102
>gnl|CDD|132036 TIGR02991, ectoine_eutB, ectoine utilization protein EutB. Members
of this protein family are EutB, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti, Silicibacter pomeroyi,
Agrobacterium tumefaciens, and Pseudomonas putida.
Members of this family resemble threonine dehydratases.
Length = 317
Score = 42.9 bits (101), Expect = 1e-04
Identities = 36/131 (27%), Positives = 52/131 (39%), Gaps = 14/131 (10%)
Query: 102 LADDRDFQEELSGILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKI 161
L D +SG + ETPL + L+E P ++LK E TG+ K+
Sbjct: 3 LQDIERAAARISGRVE-----ETPLVESPSLSELCGVP------VHLKLEHRQTTGSFKL 51
Query: 162 NNAVGQALLAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFR 221
A L + + G HG A A A G++ + M + + V
Sbjct: 52 RGATNAVLSLSDTQRAAGVVAASTGNHGRALAYAAAEEGVRATICMSELVPQNK---VDE 108
Query: 222 MRLLGAEVRAV 232
+R LGAEVR V
Sbjct: 109 IRRLGAEVRIV 119
>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 = 42.2 bits (100), Expect = 2e-04
Identities = 37/129 (28%), Positives = 51/129 (39%), Gaps = 21/129 (16%)
Query: 122 RETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVG---QALLAKRLGKTR 178
TPL ERL ++ K E N G+ K A+ A+ R+
Sbjct: 6 GNTPLVKLERLFPDA------PFRLFAKLEGFNPGGSIKDRPALYILEAAIKRGRITPGT 59
Query: 179 IIAETGAGQHGVATATVCARFGLQ--CIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGT 236
I E+ +G G+A A +CA GL+ C+V D N+ +R GAEV V
Sbjct: 60 TIIESSSGNLGIALAMICAYKGLRFICVV-----DPNISPQNLKLLRAYGAEVEKV---- 110
Query: 237 ATLKDATSE 245
T D T
Sbjct: 111 -TEPDETGG 118
>gnl|CDD|223572 COG0498, ThrC, Threonine synthase [Amino acid transport and
metabolism].
Length = 411
Score = 42.3 bits (100), Expect = 2e-04
Identities = 46/174 (26%), Positives = 58/174 (33%), Gaps = 24/174 (13%)
Query: 71 DVFGRFGRFGGKFVPETLMYALSELESALHKLADDRDFQEELSGILRDYVGRE------- 123
+ G F+P Y E L L + E L E
Sbjct: 18 ALLQGLCPDCGLFLPAEYPYFSLEEIDKLLGL----SYPELAWRYLELLPVGEIPAVSLG 73
Query: 124 ---TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRII 180
TPLY A L N +Y+K N TG+ K LAK LG I+
Sbjct: 74 EGGTPLYKAPALAAPLGVLNDN---LYVKELGHNPTGSFKDRGMTVLVSLAKELGAKTIL 130
Query: 181 AETGAGQHGVATATVCARFGLQCIVYM--GAQDMERQALNVFRMRLLGAEVRAV 232
+ +G G + A AR GL+ V G + A M LGA V AV
Sbjct: 131 CAS-SGNTGASAAAYAARAGLKVFVLYPKGKVSPGKLAQ----MLTLGAHVIAV 179
>gnl|CDD|237111 PRK12483, PRK12483, threonine dehydratase; Reviewed.
Length = 521
Score = 40.9 bits (96), Expect = 6e-04
Identities = 39/122 (31%), Positives = 52/122 (42%), Gaps = 13/122 (10%)
Query: 91 ALSELESALHKLADDRDFQEELSGIL--RDY-VGRETPLYFAERLTEHYRRPNGGGPHIY 147
A +E S + L IL R Y V RETPL A L+ +
Sbjct: 2 APTEAVSPTTIAPRAALLADYLRKILAARVYDVARETPLQRAPNLSARLGNQ------VL 55
Query: 148 LKREDLNHTGAHKINNAVGQA--LLAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIV 205
LKREDL + KI A + L A++L + I A G GVA A AR G++ ++
Sbjct: 56 LKREDLQPVFSFKIRGAYNKMARLPAEQLARGVITASAGNHAQGVALAA--ARLGVKAVI 113
Query: 206 YM 207
M
Sbjct: 114 VM 115
>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 = 39.7 bits (93), Expect = 0.001
Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 16/103 (15%)
Query: 135 HYRRPNGGGPHIYLKREDLNHTGAHK-------INNAVGQALLAKRLGKTRIIAETGAGQ 187
R G ++++K E N +G+ K I +A + LL GKT I E +G
Sbjct: 12 RLNRIEGCNANVFVKLEGRNPSGSVKDRIALNMIWDAEKRGLLKP--GKT--IVEPTSGN 67
Query: 188 HGVATATVCARFGLQCIVYMGAQ-DMERQALNVFRMRLLGAEV 229
G+A A V A G + I+ M +ER+ L ++ GAE+
Sbjct: 68 TGIALAMVAAARGYKLILTMPETMSIERRKL----LKAYGAEL 106
>gnl|CDD|107209 cd06448, L-Ser-dehyd, Serine dehydratase is a pyridoxal phosphate
(PLP)-dependent enzyme which catalyzes the conversion of
L- , D-serine, or L-threonine to pyruvate/ketobutyrate
and ammonia.
Length = 316
Score = 39.2 bits (92), Expect = 0.002
Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 15/110 (13%)
Query: 143 GPHIYLKREDLNHTGAHK---INNAVGQALLAKRLGKTRIIAETGAGQHGVATATVCARF 199
G +++LK E+L +G+ K I + ++ ++ +G G G+A A +
Sbjct: 15 GCNVFLKLENLQPSGSFKIRGIGHLCQKSAKQGLNECVHVVCSSG-GNAGLAAAYAARKL 73
Query: 200 GLQCIVYM---GAQDMERQALNVFRMRLLGAEVRAVHSGTATLKDATSEA 246
G+ C + + + V ++R GA V V G +
Sbjct: 74 GVPCTIVVPESTKPRV------VEKLRDEGATV--VVHGKVWWEADNYLR 115
>gnl|CDD|183494 PRK12390, PRK12390, 1-aminocyclopropane-1-carboxylate deaminase;
Provisional.
Length = 337
Score = 38.9 bits (91), Expect = 0.002
Identities = 41/172 (23%), Positives = 64/172 (37%), Gaps = 52/172 (30%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTR----I 179
TP++ +RL+ H GG +Y KRED N A N KTR +
Sbjct: 16 TPIHPLKRLSAHL----GGKVELYAKREDCNSGLAFGGN-------------KTRKLEYL 58
Query: 180 IAETGAG-------------QHGVATATVCARFGLQCIVYMGAQDMERQAL-----NVFR 221
+ + A H A V A G++C++ A+ N+
Sbjct: 59 VPDALAQGADTLVSIGGVQSNHTRQVAAVAAHLGMKCVLVQENWVNYEDAVYDRVGNILL 118
Query: 222 MRLLGAEVRAVHSG-TATLKDATSEAIRDWVTNVETTHYILGSVAGPHPYPM 272
R++GA+VR V G ++ + +A+ D V AG PY +
Sbjct: 119 SRIMGADVRLVPDGFDIGIRKSWEDALED----VRA--------AGGKPYAI 158
>gnl|CDD|182672 PRK10717, PRK10717, cysteine synthase A; Provisional.
Length = 330
Score = 39.1 bits (92), Expect = 0.002
Identities = 32/95 (33%), Positives = 44/95 (46%), Gaps = 16/95 (16%)
Query: 146 IYLKREDLNHTGAHK-------INNAVGQALLAKRLGKTRIIAETGAGQHGVATATVCAR 198
I K E LN G+ K I +A + LL + G T I E AG G+ A V A
Sbjct: 30 ILGKAEFLNPGGSVKDRAALNIIWDAEKRGLL--KPGGT--IVEGTAGNTGIGLALVAAA 85
Query: 199 FGLQCIVYM-GAQDMERQALNVFRMRLLGAEVRAV 232
G + ++ M Q E++ L +R LGAE+ V
Sbjct: 86 RGYKTVIVMPETQSQEKKDL----LRALGAELVLV 116
>gnl|CDD|236182 PRK08198, PRK08198, threonine dehydratase; Provisional.
Length = 404
Score = 38.2 bits (90), Expect = 0.004
Identities = 42/133 (31%), Positives = 61/133 (45%), Gaps = 22/133 (16%)
Query: 102 LADDRDFQEELSGILRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKI 161
L D + +E L G++R TPL ++ L+E G +YLK E+L TG+ KI
Sbjct: 6 LDDIEEARERLKGVVR-----RTPLEYSRTLSELT------GAEVYLKCENLQRTGSFKI 54
Query: 162 NNA-VGQALLAKRLGKTRIIAETGAGQH--GVATATVCARFGLQCIVYMGAQDMERQAL- 217
A A L++ ++A + AG H GVA A + G++ + M E L
Sbjct: 55 RGAYNKIASLSEEERARGVVAAS-AGNHAQGVAYAA--SLLGIKATIVMP----ETAPLS 107
Query: 218 NVFRMRLLGAEVR 230
V R GAEV
Sbjct: 108 KVKATRSYGAEVV 120
>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 = 37.8 bits (88), Expect = 0.005
Identities = 29/108 (26%), Positives = 46/108 (42%), Gaps = 13/108 (12%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAET 183
TPL ++ L++ G +YLK E+L TG+ KI A+ + + R +
Sbjct: 1 TPLIYSTTLSDIT------GSEVYLKLENLQKTGSFKIRGALNKIANLSEDQRQRGVVAA 54
Query: 184 GAGQHGVATATVCARFGLQCIVYMGAQDMERQA--LNVFRMRLLGAEV 229
AG H A +FG++ ++ M A V + GAEV
Sbjct: 55 SAGNHAQGVAYAAKKFGIKAVIV-----MPESAPPSKVKATKSYGAEV 97
>gnl|CDD|181133 PRK07819, PRK07819, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 286
Score = 36.9 bits (86), Expect = 0.008
Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 184 GAGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSG--TATLKD 241
GAGQ G A VCAR G+ +V+ + + R R+ + RAV G T +D
Sbjct: 12 GAGQMGAGIAEVCARAGVDVLVF----ETTEELATAGRNRIEKSLERAVSRGKLTERERD 67
Query: 242 ATSEAIR 248
A +R
Sbjct: 68 AALARLR 74
>gnl|CDD|236417 PRK09224, PRK09224, threonine dehydratase; Reviewed.
Length = 504
Score = 35.5 bits (83), Expect = 0.034
Identities = 28/86 (32%), Positives = 37/86 (43%), Gaps = 31/86 (36%)
Query: 120 VGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLN--HT----GAH-KI----------- 161
V +ETPL A +L+ R N + LKREDL + GA+ K+
Sbjct: 17 VAQETPLEKAPKLSA--RLGN----QVLLKREDLQPVFSFKLRGAYNKMAQLTEEQLARG 70
Query: 162 -------NNAVGQALLAKRLGKTRII 180
N+A G AL A RLG +I
Sbjct: 71 VITASAGNHAQGVALSAARLGIKAVI 96
>gnl|CDD|232896 TIGR00260, thrC, threonine synthase. Involved in threonine
biosynthesis it catalyses the reaction
O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE +
ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor.
the enzyme is distantly related to the serine/threonine
dehydratases which are also pyridoxal-phosphate
dependent enzymes. the pyridoxal-phosphate binding site
is a Lys (K) residues present at residue 70 of the model
[Amino acid biosynthesis, Aspartate family].
Length = 328
Score = 34.7 bits (80), Expect = 0.051
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 122 RETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALL-AKRLGKTRII 180
TPL+ + L N G ++Y+ N T + K + + AL A LG ++
Sbjct: 22 GVTPLFRSPALVA-----NVGIKNLYVLELFHNPTLSFK-DRGMAVALTKALELGNDTVL 75
Query: 181 AETGAGQHGVATATVCARFGLQCIV 205
+ G G A A + G++ ++
Sbjct: 76 CAS-TGNTGAAAAAYAGKAGVKVVI 99
>gnl|CDD|178165 PLN02550, PLN02550, threonine dehydratase.
Length = 591
Score = 34.5 bits (79), Expect = 0.061
Identities = 45/192 (23%), Positives = 70/192 (36%), Gaps = 47/192 (24%)
Query: 24 SSQSPFKLKKFTASPAKSTSIRCTIARDPVVPMEAKKESDPAPWQRPDVFGRFGRFGGKF 83
++ SP + + S S + +R P A + S P + K
Sbjct: 8 TAGSPLRSHIGSPSKPVVGSTPFSRSRIPAAVDSADETSMAPPPPPSPLPLL------KV 61
Query: 84 VPETLMYALSELESALHKLADDRD------FQEELSGILRDYV---GRETPLYFAERLTE 134
P +L Y L A+ + ++ + E L+ IL V E+PL A++L+E
Sbjct: 62 SPNSLQYPAGYL-GAVPERTNEAENGSIPEAMEYLTNILSAKVYDVAIESPLQLAKKLSE 120
Query: 135 HYRRPNGGGPHIYLKREDLNHTGAHKI-------------------------NNAVGQAL 169
G + LKREDL + K+ N+A G AL
Sbjct: 121 RL------GVKVLLKREDLQPVFSFKLRGAYNMMAKLPKEQLDKGVICSSAGNHAQGVAL 174
Query: 170 LAKRLGKTRIIA 181
A+RLG +IA
Sbjct: 175 SAQRLGCDAVIA 186
>gnl|CDD|136018 PRK06721, PRK06721, threonine synthase; Reviewed.
Length = 352
Score = 34.3 bits (78), Expect = 0.066
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAET 183
TPL +++ G +Y K E N TG+ K V AK G II +
Sbjct: 29 TPLIPLLNISKQL------GIQLYGKYEGANPTGSFKDRGMVMAVAKAKEEGSEAIICAS 82
Query: 184 GAGQHGVATATVCARFGLQCIV 205
G + A AR G++CI+
Sbjct: 83 -TGNTSASAAAYAARLGMKCII 103
>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 = 34.4 bits (79), Expect = 0.068
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 139 PNGGGPHIYLKREDLNHTGAHKINNAVGQALLAKRLGKTR---IIAETGAGQHGVATATV 195
G + K E N G+ K A+ A+ G+ + I E +G G+ A V
Sbjct: 21 SKGIKCELLAKCEFFNPGGSVKDRIALRMIEDAEASGRLKPGDTIIEPTSGNTGIGLALV 80
Query: 196 CARFGLQCIVYMGAQDMERQALNVFRMRLLGAEV 229
A G +CI+ + + M + ++V ++ LGAE+
Sbjct: 81 AAIKGYKCIIVL-PEKMSNEKVDV--LKALGAEI 111
>gnl|CDD|130341 TIGR01274, ACC_deam, 1-aminocyclopropane-1-carboxylate deaminase.
This pyridoxal phosphate-dependent enzyme degrades
1-aminocyclopropane-1-carboxylate, which in plants is a
precursor of the ripening hormone ethylene, to ammonia
and alpha-ketoglutarate. This model includes all members
of this family for which function has been demonstrated
experimentally, but excludes a closely related family
often annotated as putative members of this family
[Central intermediary metabolism, Other].
Length = 337
Score = 34.0 bits (78), Expect = 0.069
Identities = 37/158 (23%), Positives = 61/158 (38%), Gaps = 17/158 (10%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALL---AKRLGKTRII 180
+P++ RL++H GG +Y KRED N A N L A+ G T ++
Sbjct: 15 SPIHPLPRLSQHL----GGKVTLYAKREDCNSGLAFGGNKTRKLEYLIPDAQAQGCTTLV 70
Query: 181 AETG-AGQHGVATATVCARFGLQCI------VYMGAQDMERQALNVFRMRLLGAEVRAVH 233
+ G A V A G++C+ V +R N+ R++GA+VR
Sbjct: 71 SIGGIQSNQTRQVAAVAAHLGMKCVLVQENWVNYSDAVYDRVG-NIQLSRIMGADVRLDP 129
Query: 234 SGTAT-LKDATSEAIRDWVTNVETTHYILGSVAGPHPY 270
G +++ A+ + + I HP
Sbjct: 130 DGFDIGHRNSWERALEEVRGAGGKPYPIPAG-CSDHPL 166
>gnl|CDD|235789 PRK06381, PRK06381, threonine synthase; Validated.
Length = 319
Score = 33.5 bits (77), Expect = 0.11
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 146 IYLKREDLNHTGAHKINNAVGQALLAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIV 205
IYLK E N TG K A A RLG + I T G +G + A +GL+ ++
Sbjct: 33 IYLKFEGANPTGTQKDRIAEAHVRRAMRLGYSGITVGT-CGNYGASIAYFARLYGLKAVI 91
Query: 206 YM 207
++
Sbjct: 92 FI 93
>gnl|CDD|236317 PRK08638, PRK08638, threonine dehydratase; Validated.
Length = 333
Score = 33.6 bits (77), Expect = 0.11
Identities = 35/126 (27%), Positives = 47/126 (37%), Gaps = 22/126 (17%)
Query: 110 EELSGILRDYVGRETPL----YFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAV 165
E L + R+TPL Y +ER I+LK E++ TG+ KI A
Sbjct: 15 IEAKQRLAGRI-RKTPLPRSNYLSERC----------KGEIFLKLENMQRTGSFKIRGAF 63
Query: 166 GQALLAKRLGKTRIIAETGAGQHGVATATVCARFGLQCIVYM--GAQDMERQALNVFRMR 223
+ K + + AG H A CA G+ V M GA + A
Sbjct: 64 NKLSSLTDAEKRKGVVACSAGNHAQGVALSCALLGIDGKVVMPKGAPKSKVAA-----TC 118
Query: 224 LLGAEV 229
GAEV
Sbjct: 119 GYGAEV 124
>gnl|CDD|235757 PRK06260, PRK06260, threonine synthase; Validated.
Length = 397
Score = 33.7 bits (78), Expect = 0.11
Identities = 28/84 (33%), Positives = 35/84 (41%), Gaps = 10/84 (11%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINN-AVGQALLAKRLGKTRII-A 181
TPLY L + G +Y+K E N TG+ K VG A LG + A
Sbjct: 68 TPLYRCPNLEKEL-----GVKELYVKHEGANPTGSFKDRGMTVGVT-KALELGVKTVACA 121
Query: 182 ETGAGQHGVATATVCARFGLQCIV 205
T G + A AR GL+C V
Sbjct: 122 ST--GNTSASLAAYAARAGLKCYV 143
>gnl|CDD|236013 PRK07409, PRK07409, threonine synthase; Validated.
Length = 353
Score = 31.7 bits (73), Expect = 0.40
Identities = 31/89 (34%), Positives = 40/89 (44%), Gaps = 21/89 (23%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHK---INNAVGQALLAKRLGKTRII 180
TPL A L+E G +Y+K E LN TG+ K + AV + AK G +I
Sbjct: 32 TPLIPAPNLSELL------GVEVYVKYEGLNPTGSFKDRGMTMAVTK---AKEEGAKAVI 82
Query: 181 -AETG---AGQHGVATATVCARFGLQCIV 205
A TG A + A AR GL+ V
Sbjct: 83 CASTGNTSA-----SAAAYAARAGLKAFV 106
>gnl|CDD|236065 PRK07591, PRK07591, threonine synthase; Validated.
Length = 421
Score = 31.5 bits (72), Expect = 0.54
Identities = 35/117 (29%), Positives = 53/117 (45%), Gaps = 25/117 (21%)
Query: 124 TPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVGQALL-AKRLGKTRI-IA 181
TPL A+RL G ++Y+K + +N T + K + V AL A+ LG T + A
Sbjct: 90 TPLVKADRLAREL-----GLKNLYIKDDSVNPTHSFK-DRVVSVALTAARELGFTTVACA 143
Query: 182 ETG--AGQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVRAVHSGT 236
TG A + A AR GL V++ A D+E +++G V+ T
Sbjct: 144 STGNLAN----SVAAHAARAGLDSCVFIPA-DLEAG-------KIVGT---LVYGPT 185
>gnl|CDD|129194 TIGR00086, smpB, SsrA-binding protein. This model describes the
SsrA-binding protein, also called tmRNA binding protein,
small protein B, and SmpB. The small, stable RNA SsrA
(also called tmRNA or 10Sa RNA) recognizes stalled
ribosomes such as occur during translation from message
that lacks a stop codon. It becomes charged with Ala
like a tRNA, then acts as mRNA to resume translation
started with the defective mRNA. The short C-terminal
peptide tag added by the SsrA system marks the
abortively translated protein for degradation. SmpB
binds SsrA after its aminoacylation but before the
coupling of the Ala to the nascent polypeptide chain and
is an essential part of the SsrA peptide tagging system.
SmpB has been associated with the survival of bacterial
pathogens in conditions of stress. It is universal in
the first 100 sequenced bacterial genomes [Protein
synthesis, Other].
Length = 144
Score = 30.3 bits (69), Expect = 0.61
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 224 LLGAEVRAVHSGTATLKDATSEAIRD--WVTNVETTHYILGSVAGPHP 269
L G+EV+++ +G +LKD+ + W+ N+ Y G+ P
Sbjct: 24 LKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPYKFGNYFNHDP 71
>gnl|CDD|215204 PLN02356, PLN02356, phosphateglycerate kinase.
Length = 423
Score = 30.7 bits (69), Expect = 1.1
Identities = 39/130 (30%), Positives = 57/130 (43%), Gaps = 15/130 (11%)
Query: 116 LRDYVGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKINNAVG---QALLAK 172
L D +G TPL L+E G I K E LN G+ K AV +AL +
Sbjct: 47 LIDAIG-NTPLIRINSLSE------ATGCEILGKCEFLNPGGSVKDRVAVKIIEEALESG 99
Query: 173 RLGKTRIIAETGAGQHGVATATVCARFGLQC-IVYMGAQDMERQALNVFRMRLLGAEVRA 231
+L ++ E AG ++ ATV +G +C +V +E+ + + LGA V
Sbjct: 100 QLFPGGVVTEGSAGSTAISLATVAPAYGCKCHVVIPDDVAIEKSQI----LEALGATVER 155
Query: 232 VHSGTATLKD 241
V + T KD
Sbjct: 156 VRPVSITHKD 165
>gnl|CDD|201913 pfam01668, SmpB, SmpB protein.
Length = 68
Score = 27.8 bits (63), Expect = 1.4
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 224 LLGAEVRAVHSGTATLKDA-----TSEAIRDWVTNVETTHYILGS 263
L G EV+++ +G LKD+ EA W+ N + Y +
Sbjct: 25 LTGTEVKSLRAGKVNLKDSYVRIKNGEA---WLINAHISPYKQAN 66
>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 = 29.7 bits (67), Expect = 2.1
Identities = 23/86 (26%), Positives = 31/86 (36%), Gaps = 31/86 (36%)
Query: 120 VGRETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTGAHKI------------------ 161
+ETPL A +L+E I +KREDL + K+
Sbjct: 14 AAQETPLQKAAKLSERLGN------RILIKREDLQPVFSFKLRGAYNKMAQLSPEQKARG 67
Query: 162 -------NNAVGQALLAKRLGKTRII 180
N+A G A A RLG +I
Sbjct: 68 VIAASAGNHAQGVAFSAARLGLKALI 93
>gnl|CDD|234459 TIGR04082, rSAM_for_selen, selenobiotic family peptide radical SAM
maturase. Members of this protein family are radical
SAM (rSAM) enzymes similar in sequence to others with
known or postulated roles in peptide modification, and
regularly found adjacent to members of the GSU_1558
peptide family described by model TIGR04081. GSU_1558
and several other members of that family appear to be
selenoproteins, hence the term selenobiotic.
Length = 516
Score = 29.3 bits (66), Expect = 3.1
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 51 DPVVPMEAKKESDPAPWQRPDVFGRFGRFGGK--FVPETLMYALSELESALHKLA 103
D + D +P PD+ R F+P+ L+ LE ALH +A
Sbjct: 10 DDEALSRLLGDQDKSPEAFPDLLDSLVRELALPPFLPD-----LARLELALHTVA 59
>gnl|CDD|99996 cd04300, GT1_Glycogen_Phosphorylase, This is a family of
oligosaccharide phosphorylases. It includes yeast and
mammalian glycogen phosphorylases, plant starch/glucan
phosphorylase, as well as the maltodextrin
phosphorylases of bacteria. The members of this family
catalyze the breakdown of oligosaccharides into
glucose-1-phosphate units. They are important allosteric
enzymes in carbohydrate metabolism. The allosteric
control mechanisms of yeast and mammalian members of
this family are different from that of bacterial
members. The members of this family belong to the GT-B
structural superfamily of glycoslytransferases, which
have characteristic N- and C-terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two
domains includes the catalytic center and permits a high
degree of flexibility.
Length = 797
Score = 29.4 bits (67), Expect = 3.4
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 92 LSELESALHKLADDRDFQEELSGI-------LRDYVGRET 124
L +L+ L ADD F +E I L Y+ + T
Sbjct: 484 LDQLK-KLEPFADDPAFLKEFRAIKQANKERLAAYIKKTT 522
>gnl|CDD|187755 cd09294, SmpB, Small protein B (SmpB) is a component of the
trans-translation system in prokaryotes for releasing
stalled ribosome from damaged messenger RNAs. Small
protein B (SmpB) is a component of the trans-translation
system in prokaryotes for releasing stalled ribosome
from damaged messenger RNAs and targeting incompletely
synthesized protein fragments for degradation.
Trans-translation system is composed of a
ribonucleoprotein complex of tmRNA, a specialized RNA
with properties of both tRNA and mRNA, and SmpB. SmpB is
highly conserved and present in all bacterial kingdoms
and is also found in some chloroplasts and mitochondria.
This is suggesting Trans-translation arose early in
bacterial evolution and its mechanism is a quality
control for protein synthesis in spite of challenges
such as transcription errors, mRNA damage, and
translation frame shifting. SmpB deletion results in
phage development defects phenotype and absence of
tagged proteins translated from defective mRNAs.
Length = 116
Score = 27.3 bits (62), Expect = 4.7
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 224 LLGAEVRAVHSGTATLKDA-----TSEAIRDWVTNVETTHYILGSVAGPHP 269
LLG EV+++ +G LKD+ EA W+ N + Y + P
Sbjct: 20 LLGTEVKSLRAGKVNLKDSYVRIKNGEA---WLLNAHISPYEFANRFNHDP 67
>gnl|CDD|236186 PRK08206, PRK08206, diaminopropionate ammonia-lyase; Provisional.
Length = 399
Score = 28.3 bits (64), Expect = 6.2
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 186 GQHGVATATVCARFGLQCIVYM--GAQDMERQALNVFRMRLLGAEV 229
G HG A + G + ++YM G+ + A +R LGAE
Sbjct: 125 GNHGRGVAWAAQQLGQKAVIYMPKGSSEERVDA-----IRALGAEC 165
>gnl|CDD|191103 pfam04821, TIMELESS, Timeless protein. The timeless gene in
Drosophila melanogaster and its homologues in a number
of other insects and mammals (including human) are
involved in circadian rhythm control. This family
includes a related proteins from a number of fungal
species.
Length = 266
Score = 28.0 bits (63), Expect = 6.5
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 26 QSPFKLKKFTASPAKSTSIRCTIARDPVVPMEAKKESDPAPWQRPDVFGRFGRFGGKFV 84
Q P KL F S +S S + + K+ES + R RFGG +
Sbjct: 210 QDPEKL--FNDSEQRSLSEKSEDEEELTSLR--KRESADKRPYAKNPPTRHSRFGGMYW 264
>gnl|CDD|232882 TIGR00222, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase.
Members of this family are 3-methyl-2-oxobutanoate
hydroxymethyltransferase, the first enzyme of the
pantothenate biosynthesis pathway. An alternate name is
ketopantoate hydroxymethyltransferase [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pantothenate
and coenzyme A].
Length = 263
Score = 27.8 bits (62), Expect = 7.1
Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 6/65 (9%)
Query: 52 PVVPMEAKKESDPAPWQRPDVFGRFGRFGGKFVPETLMYALSEL-ESALHKLADD---RD 107
PV+ + A D D G KF L A +E +A+ + +
Sbjct: 197 PVIGIGAGNVCDGQILVMHDALGITVGHIPKFAKNYL--AETETIRAAVRQYMAEVRSGV 254
Query: 108 FQEEL 112
F E
Sbjct: 255 FPGEE 259
>gnl|CDD|223326 COG0248, GppA, Exopolyphosphatase [Nucleotide transport and
metabolism / Inorganic ion transport and metabolism].
Length = 492
Score = 28.0 bits (63), Expect = 7.1
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 212 MER--QALNVFRMRLLGAEVRAVHS-GTATLKDAT 243
+ER AL F L G V T+ L+DA
Sbjct: 54 IERALSALKRFAELLDGFGAEEVRVVATSALRDAP 88
>gnl|CDD|172537 PRK14045, PRK14045, 1-aminocyclopropane-1-carboxylate deaminase;
Provisional.
Length = 329
Score = 27.5 bits (61), Expect = 8.3
Identities = 24/115 (20%), Positives = 45/115 (39%), Gaps = 19/115 (16%)
Query: 123 ETPLYFAERLTEHYRRPNGGGPHIYLKREDLNHTG-----AHKINNAVGQALLAKRLGKT 177
ETP+ + ++ G +Y+KR+DL G K+ +G AL
Sbjct: 21 ETPIQYLPNISREL------GADVYVKRDDLTGLGIGGNKIRKLEYLLGDALSR----GA 70
Query: 178 RIIAETGA--GQHGVATATVCARFGLQCIVYMGAQDMERQALNVFRMRLLGAEVR 230
++ GA H T + GL ++ + ++ + N +++G E R
Sbjct: 71 DVVITVGAVHSNHAFVTGLAAKKLGLDAVLVLRGKEELKG--NYLLDKIMGIETR 123
>gnl|CDD|215129 PLN02216, PLN02216, protein SRG1.
Length = 357
Score = 27.9 bits (62), Expect = 8.4
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 54 VPMEAKKESDPAPWQRPDVFGRFGR 78
+PME KK+ WQRP FG+
Sbjct: 109 LPMEEKKKL----WQRPGEIEGFGQ 129
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
0.321 0.134 0.425
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,669,477
Number of extensions: 1505693
Number of successful extensions: 1479
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1429
Number of HSP's successfully gapped: 79
Length of query: 310
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 213
Effective length of database: 6,635,264
Effective search space: 1413311232
Effective search space used: 1413311232
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 (21.9 bits)
S2: 59 (26.6 bits)