RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7810
(478 letters)
>gnl|CDD|238765 cd01488, Uba3_RUB, Ubiquitin activating enzyme (E1) subunit UBA3.
UBA3 is part of the heterodimeric activating enzyme
(E1), specific for the Rub family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins. consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin(-like) by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis. UBA3
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 291
Score = 543 bits (1400), Expect = 0.0
Identities = 211/330 (63%), Positives = 247/330 (74%), Gaps = 39/330 (11%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
K+L+IGAGGLGCELLK++AL GF IHVIDMDTID+SNLNRQFLFR+KDIG KAEVAAK
Sbjct: 1 KILVIGAGGLGCELLKNLALSGFRNIHVIDMDTIDVSNLNRQFLFREKDIGKPKAEVAAK 60
Query: 107 FINSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYEEDGQ 166
F+N R+PGV V PHF KIQD D +FY+QF+II+CGLDSI ARRWING L+SLL YE
Sbjct: 61 FVNDRVPGVNVTPHFGKIQDKDEEFYRQFNIIICGLDSIEARRWINGTLVSLLLYE---- 116
Query: 167 VDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQVTYPLCTIASTPRLPEHC 226
D +IIP++DGGTEGFKG+ARVILPG+TACI+C+LDLFPPQVT+PLCTIA+T
Sbjct: 117 -DPESIIPLIDGGTEGFKGHARVILPGITACIECSLDLFPPQVTFPLCTIANT------- 168
Query: 227 IEYVKVTYPLCTIASTPRLPEHCDLPPRLPEHCIEYVKVIQWSKENPFDCPIDGDDPNHI 286
PRLPEHCIEY +IQW KE PF P+DGDDP HI
Sbjct: 169 --------------------------PRLPEHCIEYASLIQWPKEFPFV-PLDGDDPEHI 201
Query: 287 NWIYEKASERASQFNIVGVTYRLVQGVIKNIIPAVASTNAVIAATCATEVFKLATGCATS 346
W+Y+KA ERA+QFNI GVTY L QGV+K IIPAVASTNA+IAA C E K+AT C +
Sbjct: 202 EWLYQKALERAAQFNISGVTYSLTQGVVKRIIPAVASTNAIIAAACCLEALKIATDCYEN 261
Query: 347 LNNYMVFNDVAGIYTYTYEAERKSNCLACG 376
LNNY+++N V G YTYT+E ERK +C C
Sbjct: 262 LNNYLMYNGVDGCYTYTFEHERKEDCPVCS 291
>gnl|CDD|238761 cd01484, E1-2_like, Ubiquitin activating enzyme (E1), repeat
2-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the second repeat of
Ub-E1.
Length = 234
Score = 326 bits (838), Expect = e-110
Identities = 153/294 (52%), Positives = 196/294 (66%), Gaps = 63/294 (21%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KVL++GAGG+GCELLK++ALMGF +IHVIDMDTID+SNLNRQFLFR KDIG K+EVAA+
Sbjct: 1 KVLLVGAGGIGCELLKNLALMGFGQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKSEVAAE 60
Query: 107 FINSRIPGVKVIPHFCKI---QDYDSDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYEE 163
+N R P KV+P+ K+ QD++ F++QFHIIV LD+I+ARR++NGML+ L
Sbjct: 61 AVNDRNPNCKVVPYQNKVGPEQDFNDTFFEQFHIIVNALDNIIARRYVNGMLIFL----- 115
Query: 164 DGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQVTYPLCTIASTPRLP 223
I+P+++ GTEGFKGNA+VILPGMT CI+CTL PPQ +P+CTIAS PRLP
Sbjct: 116 --------IVPLIESGTEGFKGNAQVILPGMTECIECTLY--PPQKNFPMCTIASMPRLP 165
Query: 224 EHCIEYVKVTYPLCTIASTPRLPEHCDLPPRLPEHCIEYVKVIQWSKENPFDCPIDGDDP 283
EHCIE+ ++ +QW DDP
Sbjct: 166 EHCIEWARM---------------------------------LQW------------DDP 180
Query: 284 NHINWIYEKASERASQFNIVGVTYRLVQGVIKNIIPAVASTNAVIAATCATEVF 337
HI +I++ ++ERASQ+NI GVTY L +GV IIPAVA+TNAV+A CA EVF
Sbjct: 181 EHIQFIFQASNERASQYNIRGVTYFLTKGVAGRIIPAVATTNAVVAGVCALEVF 234
>gnl|CDD|238766 cd01489, Uba2_SUMO, Ubiquitin activating enzyme (E1) subunit UBA2.
UBA2 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. UBA2
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 312
Score = 234 bits (600), Expect = 8e-74
Identities = 113/305 (37%), Positives = 170/305 (55%), Gaps = 38/305 (12%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KVL++GAGG+GCELLK++ L GF EIH+ID+DTIDLSNLNRQFLFR+K +G SKA+VA +
Sbjct: 1 KVLVVGAGGIGCELLKNLVLTGFGEIHIIDLDTIDLSNLNRQFLFRKKHVGKSKAQVAKE 60
Query: 107 FINSRIPGVKVIPHFCKIQD--YDSDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYEED 164
+ S P VK++ + I+D ++ +F++QF ++ LD++ ARR +N M L+
Sbjct: 61 AVLSFNPNVKIVAYHANIKDPDFNVEFFKQFDLVFNALDNLAARRHVNKMCLAA------ 114
Query: 165 GQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQVTYPLCTIASTPRLPE 224
+P+++ GT GF G +VI G T C +C T+P+CTI STP P
Sbjct: 115 -------DVPLIESGTTGFLGQVQVIKKGKTECYECQPK--ETPKTFPVCTIRSTPSQPI 165
Query: 225 HCIEYVKVTYPLCT---IASTPRLPEHCDL----PPRLPEHCIEYVKVIQWSKENPFDCP 277
HCI + K + L RL +L P +P + W +
Sbjct: 166 HCIVWAKSLFFLFNKVFKDDIERLLSMEELWKTRKPPVP---------LSWK-----ELT 211
Query: 278 IDGDDPNHINWIYEKASERASQFNIVGVTYRLVQGVIKNIIPAVASTNAVIAATCATEVF 337
D DD + ++++ A+ R+ F I + ++ + NIIPA+A+TNA+IA E
Sbjct: 212 FDKDDQDALDFVAAAANLRSHVFGIPMKSRFDIKQMAGNIIPAIATTNAIIAGLIVLEAL 271
Query: 338 KLATG 342
K+ +G
Sbjct: 272 KVLSG 276
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 149 bits (379), Expect = 2e-43
Identities = 57/155 (36%), Positives = 83/155 (53%), Gaps = 14/155 (9%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+VL++G GGLG E+ ++A G +I +ID DT++LSNLNRQFL RQ DIG KAEVAA+
Sbjct: 1 RVLLVGLGGLGSEIALNLARSGVGKITLIDFDTVELSNLNRQFLARQADIGKPKAEVAAR 60
Query: 107 FINSRIPGVKVIPHFCKIQDY-DSDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYEEDG 165
+N PGV V I + DF +++ +D+I RR +N
Sbjct: 61 RLNELNPGVNVTAVPEGISEDNLDDFLDGVDLVIDAIDNIAVRRALNRAC---------- 110
Query: 166 QVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDC 200
+ IP++D G G G+ +VI G + +
Sbjct: 111 ---KELGIPVIDAGGLGLGGDIQVIDIGSLSAAEA 142
>gnl|CDD|238767 cd01490, Ube1_repeat2, Ubiquitin activating enzyme (E1), repeat 2.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the second repeat of Ub-E1.
Length = 435
Score = 155 bits (394), Expect = 2e-42
Identities = 97/362 (26%), Positives = 158/362 (43%), Gaps = 85/362 (23%)
Query: 47 KVLIIGAGGLGCELLKDIALMGF-----NEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKA 101
KV ++GAG +GCELLK+ ALMG EI V DMD I+ SNLNRQFLFR D+G K+
Sbjct: 1 KVFLVGAGAIGCELLKNFALMGVGTGESGEITVTDMDNIEKSNLNRQFLFRPHDVGKPKS 60
Query: 102 EVAAKFINSRIPGVKVIPHFCKI-----QDYDSDFYQQFHIIVCGLDSIVARRWINGMLL 156
EVAA + + P +K+ ++ ++ +F+++ + LD++ AR +++ +
Sbjct: 61 EVAAAAVKAMNPDLKITALQNRVGPETEHIFNDEFWEKLDGVANALDNVDARMYVDRRCV 120
Query: 157 SLLQYEEDGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQVTYPLCTI 216
Y P+++ GT G KGN +V++P +T + D PP+ + PLCT+
Sbjct: 121 Y---YR----------KPLLESGTLGTKGNTQVVIPHLTESYSSSRD--PPEKSIPLCTL 165
Query: 217 ASTPRLPEHCIEYVKVTYPLCTIASTPR-----LPEHCDLPPRLPEHCIEYVKVIQ---- 267
+ P EH I++ + + P L E C RL + Q
Sbjct: 166 KNFPNAIEHTIQWARDEFEG-LFKQPPENVNQYLFEDCVRWARLLFEKYFNNNIKQLLHN 224
Query: 268 -------------WSKENPFDCPI--DGDDPNHINWIYEKASERASQFNIVG-------- 304
WS P+ D ++P H++++ A+ A + I G
Sbjct: 225 FPPDAVTSDGAPFWSGPKRCPTPLEFDVNNPLHLDFVLAAANLYAEVYGIPGFEKDDDTN 284
Query: 305 -----VTY-------------------RLVQGVIKNIIPAVASTNAVIAATCATEVFKLA 340
+T + + G IIPA+A+T A + E++K+
Sbjct: 285 FHMDFITAASNLRARNYSIPPADRHKTKRIAG---KIIPAIATTTAAVTGLVCLELYKVV 341
Query: 341 TG 342
G
Sbjct: 342 DG 343
>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 2
[Coenzyme metabolism].
Length = 254
Score = 148 bits (375), Expect = 2e-41
Identities = 59/165 (35%), Positives = 87/165 (52%), Gaps = 15/165 (9%)
Query: 45 SCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVA 104
+VL++GAGGLG K +AL G ++ ++D DT++LSNL RQFLF + D+G KAEVA
Sbjct: 30 DSRVLVVGAGGLGSPAAKYLALAGVGKLTIVDFDTVELSNLQRQFLFTEADVGKPKAEVA 89
Query: 105 AKFINSRIPGVKVIPHFCKIQDYD-SDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYEE 163
AK + P V+V+ + ++ + + + QF +++ D+ R IN
Sbjct: 90 AKALRKLNPLVEVVAYLERLDEENAEELIAQFDVVLDCTDNFETRYLIN----------- 138
Query: 164 DGQVDQSTIIPMVDGGTEGFKGNARVILPG-MTACIDCTLDLFPP 207
IP+V GG GF+G VI+PG T C C PP
Sbjct: 139 --DACVKLGIPLVHGGAIGFEGQVTVIIPGDKTPCYRCLFPEKPP 181
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 135 bits (343), Expect = 3e-38
Identities = 48/147 (32%), Positives = 76/147 (51%), Gaps = 14/147 (9%)
Query: 45 SCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVA 104
S +VL++GAGGLG + +A G ++ ++D DT++LSNLNRQ LF + DIG KAEVA
Sbjct: 1 SSRVLVVGAGGLGSPAAEYLARAGVGKLTLVDFDTVELSNLNRQILFTESDIGKPKAEVA 60
Query: 105 AKFINSRIPGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLDSIVARRWINGMLLSLLQYEE 163
+ + + P V+V + ++ + + + ++V LD+ AR +N
Sbjct: 61 KERLRAINPDVEVEAYPERLTPENLEELLKGVDLVVDALDNFAARYLLN----------- 109
Query: 164 DGQVDQSTIIPMVDGGTEGFKGNARVI 190
IP++ G GF G VI
Sbjct: 110 --DACVKRGIPLISAGALGFDGQVTVI 134
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 127 bits (321), Expect = 3e-31
Identities = 64/197 (32%), Positives = 105/197 (53%), Gaps = 25/197 (12%)
Query: 45 SCKVLIIGAGGLGCELLKDIALMGFN-----EIHVIDMDTIDLSNLNRQFLFRQKDIGSS 99
+ + ++G G +GCE+LK+ ALMG I V D D I+ SNLNRQFLFR IG
Sbjct: 419 NLNIFLVGCGAIGCEMLKNFALMGVGTGKKGMITVTDPDLIEKSNLNRQFLFRPHHIGKP 478
Query: 100 KAEVAAKFINSRIPGVKVIPHFCKIQD-----YDSDFYQQFHIIVCGLDSIVARRWINGM 154
K+ AA P +K+ H ++ ++ +FY++ +++ LD++ ARR+++
Sbjct: 479 KSYTAADATLKINPQIKIDAHQNRVGPETETIFNDEFYEKLDVVINALDNVEARRYVDSR 538
Query: 155 LLSLLQYEEDGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQVTYPLC 214
L+ L+ P+++ GT G KGN +V++P +T + D PP+ P C
Sbjct: 539 CLAFLK-------------PLLESGTLGTKGNTQVVVPHLTESYGSSRD--PPEKEIPFC 583
Query: 215 TIASTPRLPEHCIEYVK 231
T+ S P EH I++ +
Sbjct: 584 TLKSFPAAIEHTIQWAR 600
Score = 47.6 bits (113), Expect = 1e-05
Identities = 23/70 (32%), Positives = 36/70 (51%)
Query: 48 VLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAKF 107
VLI G GGLG E+ K++ L G + + D + +L+ F + D+G ++AE K
Sbjct: 27 VLISGMGGLGLEIAKNLVLAGVKSVTLHDTEKCQAWDLSSNFFLSEDDVGRNRAEAVVKK 86
Query: 108 INSRIPGVKV 117
+ P V V
Sbjct: 87 LAELNPYVHV 96
Score = 35.6 bits (82), Expect = 0.060
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 281 DDPN-HINWIYEKASERASQFNIVGVTYRLVQGVIKNIIPAVASTNAVIAATCATEVFKL 339
DD N HI++I ++ RA ++I + + IIPA+A++ A ++ E+ K+
Sbjct: 810 DDHNGHIDFITAASNLRAKNYSIEPADRFKTKFIAGKIIPAIATSTATVSGLVCLELIKV 869
Query: 340 ATG 342
G
Sbjct: 870 TDG 872
>gnl|CDD|238386 cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like
enzymes involved in molybdopterin and thiamine
biosynthesis family. The common reaction mechanism
catalyzed by MoeB and ThiF, like other E1 enzymes,
begins with a nucleophilic attack of the C-terminal
carboxylate of MoaD and ThiS, respectively, on the
alpha-phosphate of an ATP molecule bound at the active
site of the activating enzymes, leading to the formation
of a high-energy acyladenylate intermediate and
subsequently to the formation of a thiocarboxylate at
the C termini of MoaD and ThiS. MoeB, as the MPT
synthase (MoaE/MoaD complex) sulfurase, is involved in
the biosynthesis of the molybdenum cofactor, a
derivative of the tricyclic pterin, molybdopterin (MPT).
ThiF catalyzes the adenylation of ThiS, as part of the
biosynthesis pathway of thiamin pyrophosphate (vitamin
B1). .
Length = 228
Score = 119 bits (300), Expect = 5e-31
Identities = 47/165 (28%), Positives = 79/165 (47%), Gaps = 14/165 (8%)
Query: 45 SCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVA 104
+ +VL++GAGGLG + +A G ++ ++D D ++LSNL RQ L + D+G KAE A
Sbjct: 21 NARVLVVGAGGLGSPAAEYLAAAGVGKLGLVDDDVVELSNLQRQILHTEADVGQPKAEAA 80
Query: 105 AKFINSRIPGVKVIPHFCKIQDYD-SDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYEE 163
A+ + + P V++ + ++ + + + +++ D+ R IN
Sbjct: 81 AERLRAINPDVEIEAYNERLDAENAEELIAGYDLVLDCTDNFATRYLIN----------- 129
Query: 164 DGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQ 208
D V P+V G GF+G V +PG C C PP
Sbjct: 130 DACVKLG--KPLVSGAVLGFEGQVTVFIPGEGPCYRCLFPEPPPP 172
>gnl|CDD|202124 pfam02134, UBACT, Repeat in ubiquitin-activating (UBA) protein.
Length = 66
Score = 93.8 bits (234), Expect = 9e-24
Identities = 25/64 (39%), Positives = 40/64 (62%)
Query: 279 DGDDPNHINWIYEKASERASQFNIVGVTYRLVQGVIKNIIPAVASTNAVIAATCATEVFK 338
D DD +H++++Y A+ RA + I V+G+ NIIPA+A+TNA++A E+ K
Sbjct: 3 DKDDDDHLDFVYAAANLRAQNYGIPPADRFDVKGIAGNIIPAIATTNAIVAGIVVLELLK 62
Query: 339 LATG 342
+ TG
Sbjct: 63 ILTG 66
>gnl|CDD|192164 pfam08825, E2_bind, E2 binding domain. E1 and E2 enzymes play a
central role in ubiquitin and ubiquitin-like protein
transfer cascades. This is an E2 binding domain that is
found on NEDD8 activating E1 enzyme. The domain
resembles ubiquitin, and recruits the catalytic core of
the E2 enzyme Ubc12 in a similar manner to that in which
ubiquitin interacts with ubiquitin binding domains.
Length = 85
Score = 88.1 bits (219), Expect = 2e-21
Identities = 35/84 (41%), Positives = 48/84 (57%), Gaps = 4/84 (4%)
Query: 390 DMKLSELIELLCQHPSYQMKSPGLTTMQDGRNRTLYMSTVRSIEEATRENLKRSLVELGL 449
L ELIE L + P +Q+K P LTT +TLYM + S+EEATR NL + L ELG+
Sbjct: 6 SWTLQELIESLSERPEFQLKKPSLTT----AGKTLYMQSPPSLEEATRPNLSKPLKELGV 61
Query: 450 RDEGIVNVADSTTPNTLEITLRVT 473
D + V D P +L++ L+
Sbjct: 62 SDGQEIVVTDPALPTSLKLRLKFK 85
>gnl|CDD|162820 TIGR02356, adenyl_thiF, thiazole biosynthesis adenylyltransferase
ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF
family of proteins (pfam00899) include a number of
members encoded in the midst of thiamine biosynthetic
operons. This mix of known and putative ThiF proteins
shows a deep split in phylogenetic trees, with the
Escherichia. coli ThiF and the E. coli MoeB proteins
seemingly more closely related than E. coli ThiF and
Campylobacter (for example) ThiF. This model represents
the more widely distributed clade of ThiF proteins such
found in E. coli [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 202
Score = 86.6 bits (215), Expect = 1e-19
Identities = 52/177 (29%), Positives = 73/177 (41%), Gaps = 25/177 (14%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
VLIIGAGGLG +A G I ++D D +DLSNL RQ LF ++D+G K EVAA+
Sbjct: 23 HVLIIGAGGLGSPAALYLAGAGVGTIVIVDDDHVDLSNLQRQILFTEEDVGRPKVEVAAQ 82
Query: 107 FINSRIPGVKVIPHFCKIQDYDS----DFYQQFHIIVCGLDSIVARRWINGMLLSLLQYE 162
+ ++V + + +++ D+ R IN
Sbjct: 83 RLRELNSDIQVTAL---KERVTAENLELLINNVDLVLDCTDNFATRYLIN---------- 129
Query: 163 EDGQVDQSTIIPMVDGGTEGFKGNARVILPGM-TACIDCTLDLFP-PQVTYPLCTIA 217
+ P++ GF G V PG C+ C LFP T P C A
Sbjct: 130 ---DACVALGTPLISAAVVGFGGQLMVFDPGGEGPCLRC---LFPDIADTGPSCATA 180
>gnl|CDD|235528 PRK05600, PRK05600, thiamine biosynthesis protein ThiF; Validated.
Length = 370
Score = 77.2 bits (190), Expect = 2e-15
Identities = 36/99 (36%), Positives = 59/99 (59%), Gaps = 1/99 (1%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+VL+IGAGGLGC ++ +A G I +ID DT+D+SN++RQ LF D+G K EVAA+
Sbjct: 43 RVLVIGAGGLGCPAMQSLASAGVGTITLIDDDTVDVSNIHRQILFGASDVGRPKVEVAAE 102
Query: 107 FINSRIPGVKVIPHFCKIQDYDS-DFYQQFHIIVCGLDS 144
+ P ++V ++ ++ + +++ G DS
Sbjct: 103 RLKEIQPDIRVNALRERLTAENAVELLNGVDLVLDGSDS 141
>gnl|CDD|180204 PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB;
Provisional.
Length = 245
Score = 75.3 bits (186), Expect = 2e-15
Identities = 30/107 (28%), Positives = 51/107 (47%), Gaps = 1/107 (0%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+VL++G GGLGC + +A G + ++D DT+ LSNL RQ L IG K E A
Sbjct: 34 RVLVVGLGGLGCAASQYLAAAGVGTLTLVDFDTVSLSNLQRQVLHDDATIGQPKVESARA 93
Query: 107 FINSRIPGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLDSIVARRWIN 152
+ P + + ++ D + +++ D++ R +N
Sbjct: 94 ALARINPHIAIETINARLDDDELAALIAGHDLVLDCTDNVATRNQLN 140
>gnl|CDD|181156 PRK07878, PRK07878, molybdopterin biosynthesis-like protein MoeZ;
Validated.
Length = 392
Score = 76.3 bits (188), Expect = 5e-15
Identities = 37/107 (34%), Positives = 57/107 (53%), Gaps = 1/107 (0%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+VL+IGAGGLG L +A G + +++ D +D SNL RQ + Q D+G SKA+ A
Sbjct: 44 RVLVIGAGGLGSPTLLYLAAAGVGTLGIVEFDVVDESNLQRQVIHGQSDVGRSKAQSARD 103
Query: 107 FINSRIPGVKVIPHFCKIQ-DYDSDFYQQFHIIVCGLDSIVARRWIN 152
I P V V H ++ + + Q+ +I+ G D+ R +N
Sbjct: 104 SIVEINPLVNVRLHEFRLDPSNAVELFSQYDLILDGTDNFATRYLVN 150
>gnl|CDD|236337 PRK08762, PRK08762, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 376
Score = 75.8 bits (187), Expect = 6e-15
Identities = 49/173 (28%), Positives = 71/173 (41%), Gaps = 37/173 (21%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+VL+IGAGGLG +A G + ++D D +D SNL RQ L + +G K + AA+
Sbjct: 137 RVLLIGAGGLGSPAALYLAAAGVGTLGIVDHDVVDRSNLQRQILHTEDRVGQPKVDSAAQ 196
Query: 107 FINSRIPGVKVIPHFCK---------IQDYDSDFYQQFHIIVCGLDSIVARRWINGMLLS 157
+ + P V+V + +QD D ++V G D+ R +N
Sbjct: 197 RLAALNPDVQVEAVQERVTSDNVEALLQDVD--------VVVDGADNFPTRYLLN----- 243
Query: 158 LLQYEEDGQVDQSTIIPMVDGGTEGFKGNARVILPGMTA----CIDCTLDLFP 206
D V P+V G F+G V G C C LFP
Sbjct: 244 ------DACVKLG--KPLVYGAVFRFEGQVSVFDAGRQRGQAPCYRC---LFP 285
>gnl|CDD|238769 cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit Aos1.
Aos1 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. Aos1
contains part of the adenylation domain.
Length = 197
Score = 70.4 bits (173), Expect = 4e-14
Identities = 30/98 (30%), Positives = 54/98 (55%)
Query: 44 TSCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEV 103
S ++L+IG GLG E+ K++ L G + ++D T+ +L QFL +D+G ++AE
Sbjct: 20 RSARILLIGLKGLGAEIAKNLVLSGIGSLTILDDRTVTEEDLGAQFLIPAEDLGQNRAEA 79
Query: 104 AAKFINSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCG 141
+ + + + P VKV I + +F+ QF ++V
Sbjct: 80 SLERLRALNPRVKVSVDTDDISEKPEEFFSQFDVVVAT 117
>gnl|CDD|238762 cd01485, E1-1_like, Ubiquitin activating enzyme (E1), repeat
1-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. The E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the first repeat of
Ub-E1.
Length = 198
Score = 68.2 bits (167), Expect = 2e-13
Identities = 39/171 (22%), Positives = 71/171 (41%), Gaps = 26/171 (15%)
Query: 36 SEALSFLQTSCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQK- 94
EA + L+++ KVLIIGAG LG E+ K++ L G + I ++D + +L F +
Sbjct: 11 DEAQNKLRSA-KVLIIGAGALGAEIAKNLVLAGIDSITIVDHRLVSTEDLGSNFFLDAEV 69
Query: 95 -DIGSSKAEVAAKFI---NSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCGLDSIVARRW 150
+ G ++A + +F+ N + V ++ Q+F +++
Sbjct: 70 SNSGMNRAAASYEFLQELNPNVKLSIVEEDSLSNDSNIEEYLQKFTLVI----------- 118
Query: 151 INGMLLSLLQYEEDGQVDQSTI---IPMVDGGTEGFKGNARVILPGMTACI 198
+ YE +V+ IP + T G G A P + A +
Sbjct: 119 -----ATEENYERTAKVNDVCRKHHIPFISCATYGLIGYAFFDFP-IAAFL 163
>gnl|CDD|131408 TIGR02355, moeB, molybdopterin synthase sulfurylase MoeB. This
model describes the molybdopterin biosynthesis protein
MoeB in E. coli and related species. The enzyme
covalently modifies the molybdopterin synthase MoaD by
sulfurylation. This enzyme is closely related to ThiF, a
thiamine biosynthesis enzyme that modifies ThiS by an
analogous adenylation. Both MoeB and ThiF belong to the
HesA/MoeB/ThiF family (pfam00899) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 240
Score = 66.0 bits (161), Expect = 3e-12
Identities = 35/107 (32%), Positives = 54/107 (50%), Gaps = 1/107 (0%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+VLI+G GGLGC + +A G + ++D DT+ LSNL RQ L +IG K E A
Sbjct: 26 RVLIVGLGGLGCAASQYLAAAGVGNLTLLDFDTVSLSNLQRQVLHSDANIGQPKVESAKD 85
Query: 107 FINSRIPGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLDSIVARRWIN 152
+ P + + P K+ D + + I+V D++ R +N
Sbjct: 86 ALTQINPHIAINPINAKLDDAELAALIAEHDIVVDCTDNVEVRNQLN 132
>gnl|CDD|236320 PRK08644, PRK08644, thiamine biosynthesis protein ThiF;
Provisional.
Length = 212
Score = 64.9 bits (159), Expect = 5e-12
Identities = 38/120 (31%), Positives = 56/120 (46%), Gaps = 12/120 (10%)
Query: 47 KVLIIGAGGLGCELLKDIALM----GFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAE 102
KV I GAGGLG +IA+ G + ++D D ++ SNLNRQ F IG K E
Sbjct: 30 KVGIAGAGGLG----SNIAVALARSGVGNLKLVDFDVVEPSNLNRQQYF-ISQIGMPKVE 84
Query: 103 VAAKFINSRI-PGVKVIPHFCKI-QDYDSDFYQQFHIIVCGLDSIVARRWINGMLLSLLQ 160
A K I P V++ H KI +D + ++ I+V D+ + + +L
Sbjct: 85 -ALKENLLEINPFVEIEAHNEKIDEDNIEELFKDCDIVVEAFDNAETKAMLVETVLEHPG 143
>gnl|CDD|224100 COG1179, COG1179, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 1
[Coenzyme metabolism].
Length = 263
Score = 65.4 bits (160), Expect = 6e-12
Identities = 26/90 (28%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 46 CKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAA 105
V ++G GG+G ++ +A G I +IDMD + ++N NRQ DIG K EV
Sbjct: 31 AHVCVVGIGGVGSWAVEALARSGIGRITLIDMDDVCVTNTNRQIHALLGDIGKPKVEVMK 90
Query: 106 KFINSRIPGVKVIPHFCKIQDYDSDFYQQF 135
+ I P +V I + +
Sbjct: 91 ERIKQINPECEVTAINDFI---TEENLEDL 117
>gnl|CDD|238764 cd01487, E1_ThiF_like, E1_ThiF_like. Member of superfamily of
activating enzymes (E1) of the ubiquitin-like proteins.
The common reaction mechanism catalyzed by E1-like
enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of the ubiquitin-like substrate,
on the alpha-phosphate of an ATP molecule bound at the
active site of the activating enzymes, leading to the
formation of a high-energy acyladenylate intermediate
and subsequently to the formation of a thiocarboxylate
at the C termini of the substrate. The exact function of
this family is unknown.
Length = 174
Score = 62.4 bits (152), Expect = 2e-11
Identities = 36/113 (31%), Positives = 53/113 (46%), Gaps = 4/113 (3%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KV I GAGGLG + +A G + ++D D ++ SNLNRQ + IG K E A K
Sbjct: 1 KVGIAGAGGLGSNIAVLLARSGVGNLKLVDFDVVEPSNLNRQQ-YFLSQIGEPKVE-ALK 58
Query: 107 FINSRI-PGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLDSIVARRWINGMLLS 157
I P VK+ KI + + + + I+V D+ + + LL
Sbjct: 59 ENLREINPFVKIEAINIKIDENNLEGLFGDCDIVVEAFDNAETKAMLAESLLG 111
>gnl|CDD|192635 pfam10585, UBA_e1_thiolCys, Ubiquitin-activating enzyme active
site. Ubiquitin-activating enzyme (E1 enzyme) activates
ubiquitin by first adenylating with ATP its C-terminal
glycine residue and thereafter linking this residue to
the side chain of a cysteine residue in E1, yielding an
ubiquitin-E1 thiolester and free AMP. Later the
ubiquitin moiety is transferred to a cysteine residue on
one of the many forms of ubiquitin-conjugating enzymes
(E2). This domain carries the last of five conserved
cysteines that is part of the active site of the enzyme,
responsible for ubiquitin thiolester complex formation,
the active site being represented by the sequence motif
PICTLKNFP.
Length = 44
Score = 58.0 bits (141), Expect = 2e-11
Identities = 17/38 (44%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 194 MTACIDCTLDLFPPQVTYPLCTIASTPRLPEHCIEYVK 231
+T C +C+ D PP+ + P+CT+ S P PEHCIE+ +
Sbjct: 1 VTECYECSPD--PPEKSIPVCTLRSFPSTPEHCIEWAR 36
>gnl|CDD|238384 cd00755, YgdL_like, Family of activating enzymes (E1) of
ubiquitin-like proteins related to the E.coli
hypothetical protein ygdL. The common reaction mechanism
catalyzed by E1-like enzymes begins with a nucleophilic
attack of the C-terminal carboxylate of the
ubiquitin-like substrate, on the alpha-phosphate of an
ATP molecule bound at the active site of the activating
enzymes, leading to the formation of a high-energy
acyladenylate intermediate and subsequently to the
formation of a thiocarboxylate at the C termini of the
substrate. The exact function of this family is unknown.
Length = 231
Score = 62.6 bits (153), Expect = 3e-11
Identities = 34/115 (29%), Positives = 52/115 (45%), Gaps = 9/115 (7%)
Query: 36 SEALSFLQTSCKVLIIGAGGLG---CELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFR 92
E L L+ + V ++G GG+G E L A G ++ +ID D + +SNLNRQ
Sbjct: 3 EEGLEKLRNA-HVAVVGLGGVGSWAAEAL---ARSGVGKLTLIDFDVVCVSNLNRQIHAL 58
Query: 93 QKDIGSSKAEVAAKFINSRIPGVKVIPHFCKIQDYDSDFY--QQFHIIVCGLDSI 145
+G K EV A+ I P +V + +S+ +V +DSI
Sbjct: 59 LSTVGKPKVEVMAERIRDINPECEVDAVEEFLTPDNSEDLLGGDPDFVVDAIDSI 113
>gnl|CDD|169382 PRK08328, PRK08328, hypothetical protein; Provisional.
Length = 231
Score = 62.9 bits (153), Expect = 3e-11
Identities = 46/162 (28%), Positives = 75/162 (46%), Gaps = 18/162 (11%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KV ++G GGLG + +A G I +ID T +LSNLNRQ L ++D+G + ++AK
Sbjct: 29 KVAVVGVGGLGSPVAYYLAAAGVGRILLIDEQTPELSNLNRQILHWEEDLGKNPKPLSAK 88
Query: 107 FINSRI-PGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLDSIVARRWINGMLLSLLQYEED 164
+ R +K+ ++ + + D + +IV LD+ R ++
Sbjct: 89 WKLERFNSDIKIETFVGRLSEENIDEVLKGVDVIVDCLDNFETRYLLD------------ 136
Query: 165 GQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFP 206
IP+V G EG G I+PG T + ++FP
Sbjct: 137 -DYAHKKGIPLVHGAVEGTYGQVTTIVPGKTKRLR---EIFP 174
Score = 30.5 bits (69), Expect = 1.6
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 315 KNIIPAVASTNAVIAATCATEVFKLATGCATSLNNYMVFNDVA 357
K P + +T VI + A EV KL TG L N ++ D+A
Sbjct: 180 KGKFPILGATAGVIGSIQAMEVIKLITGYGEPLLNKLLIVDLA 222
>gnl|CDD|238768 cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat 1.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the first repeat of Ub-E1.
Length = 286
Score = 63.1 bits (154), Expect = 6e-11
Identities = 37/119 (31%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 36 SEALSFLQTSCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKD 95
EA+ LQ S VLI G GGLG E+ K++ L G + + D S+L+ QF R++D
Sbjct: 11 HEAMKKLQKS-NVLISGLGGLGVEIAKNLILAGVKSVTLHDTKPCSWSDLSSQFYLREED 69
Query: 96 IGSSKAEVAAKFINSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCGLDSIVARRWINGM 154
IG ++AE + + P V V + +D +F ++V S+ + IN
Sbjct: 70 IGKNRAEASQARLAELNPYVPVTVSTGPL---TTDELLKFQVVVLTDASLEDQLKINEF 125
>gnl|CDD|235526 PRK05597, PRK05597, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 355
Score = 63.0 bits (153), Expect = 9e-11
Identities = 33/75 (44%), Positives = 43/75 (57%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KV +IGAGGLG L +A G I +ID DT+DLSNL+RQ + +G KAE A +
Sbjct: 30 KVAVIGAGGLGSPALLYLAGAGVGHITIIDDDTVDLSNLHRQVIHSTAGVGQPKAESARE 89
Query: 107 FINSRIPGVKVIPHF 121
+ + P VKV
Sbjct: 90 AMLALNPDVKVTVSV 104
>gnl|CDD|183547 PRK12475, PRK12475, thiamine/molybdopterin biosynthesis MoeB-like
protein; Provisional.
Length = 338
Score = 61.7 bits (150), Expect = 2e-10
Identities = 46/164 (28%), Positives = 77/164 (46%), Gaps = 20/164 (12%)
Query: 48 VLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAE-VAAK 106
VLI+GAG LG + + G ++ + D D ++ SNL RQ L+ ++D K + +AAK
Sbjct: 27 VLIVGAGALGAANAEALVRAGIGKLTIADRDYVEWSNLQRQQLYTEEDAKQKKPKAIAAK 86
Query: 107 ----FINSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCGLDSIVARRWINGMLLSLLQYE 162
INS + V V+ +++ + + ++ +I+ D+ R IN
Sbjct: 87 EHLRKINSEVEIVPVVTDVT-VEELE-ELVKEVDLIIDATDNFDTRLLIN---------- 134
Query: 163 EDGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFP 206
+ Q IP + GG G G I+PG T C+ C ++ P
Sbjct: 135 ---DLSQKYNIPWIYGGCVGSYGVTYTIIPGKTPCLRCLMEHVP 175
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 54.6 bits (132), Expect = 4e-08
Identities = 50/170 (29%), Positives = 74/170 (43%), Gaps = 30/170 (17%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDI--GSSKAEVA 104
VLIIGAG LG + + G ++ ++D D ++ SNL RQ L+ + D+ KA VA
Sbjct: 26 HVLIIGAGALGTANAEMLVRAGVGKVTIVDRDYVEWSNLQRQQLYTESDVKNNLPKA-VA 84
Query: 105 AK----FINSRIPGVKVIPHFCKIQDYDSD----FYQQFHIIVCGLDSIVARRWINGMLL 156
AK INS + V+ I +QD ++ +I+ D+ R +N
Sbjct: 85 AKKRLEEINSDVR-VEAI-----VQDVTAEELEELVTGVDLIIDATDNFETRFIVN---- 134
Query: 157 SLLQYEEDGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFP 206
Q IP + G G G + I+PG T C+ C L P
Sbjct: 135 ---------DAAQKYGIPWIYGACVGSYGLSYTIIPGKTPCLRCLLQSIP 175
>gnl|CDD|180967 PRK07411, PRK07411, hypothetical protein; Validated.
Length = 390
Score = 53.6 bits (129), Expect = 1e-07
Identities = 35/114 (30%), Positives = 51/114 (44%), Gaps = 15/114 (13%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
VL IG GGLG LL +A G I ++D D +D SNL RQ + +G K E A
Sbjct: 40 SVLCIGTGGLGSPLLLYLAAAGIGRIGIVDFDVVDSSNLQRQVIHGTSWVGKPKIESAKN 99
Query: 107 FINSRIPGVKVIPHFCKIQDYDS--------DFYQQFHIIVCGLDSIVARRWIN 152
I I +C++ Y++ D + ++V G D+ R +N
Sbjct: 100 RILE-------INPYCQVDLYETRLSSENALDILAPYDVVVDGTDNFPTRYLVN 146
>gnl|CDD|163448 TIGR03736, PRTRC_ThiF, PRTRC system ThiF family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
This family is the PRTRC system ThiF family protein.
Length = 244
Score = 51.6 bits (124), Expect = 2e-07
Identities = 45/187 (24%), Positives = 73/187 (39%), Gaps = 38/187 (20%)
Query: 40 SFLQTSCKVLIIGAGGLGCELLK-----DIALMGFN-----EIHVIDMDTIDLSNLNRQF 89
+ L V+++GAGG G +++ AL + V D DT+ +N+ RQ
Sbjct: 6 ALLSRPVSVVLVGAGGTGSQVIAGLARLHHALKALGHPGGLAVTVYDDDTVSEANVGRQ- 64
Query: 90 LFRQKDIGSSKAEVAAKFINSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCGLDSIVARR 149
F D+G +KA V +N + G H +++ S + I++ +D+ AR
Sbjct: 65 AFYPADVGQNKAIVLVNRLNQAM-GTDWTAHPERVE--RSSTLHRPDIVIGCVDNRAARL 121
Query: 150 WI----------NGMLLSLLQYEEDGQVDQSTIIPMVDGGTEGFKGNARVILPGMTACID 199
I L L +DGQV ++ KG R+ LP
Sbjct: 122 AILRAFEGGYSGYAYWLDLGNRADDGQV-------ILGQVPSRAKGENRLRLP------- 167
Query: 200 CTLDLFP 206
+LFP
Sbjct: 168 HVGELFP 174
>gnl|CDD|238770 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
APPBP1. APPBP1 is part of the heterodimeric activating
enzyme (E1), specific for the Rub family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of a
conjugation cascade to attach Ub or Ubls, covalently to
substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin(-like) by C-terminal adenylation,
and subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis.
ABPP1 contains part of the adenylation domain.
Length = 425
Score = 50.0 bits (120), Expect = 1e-06
Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 3/95 (3%)
Query: 48 VLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAKF 107
V ++ A G E+LK++ L G ++D +D +L F +G S+AE +
Sbjct: 23 VCLLNATATGTEILKNLVLPGIGSFTIVDGSKVDEEDLGNNFFLDASSLGKSRAEATCEL 82
Query: 108 I---NSRIPGVKVIPHFCKIQDYDSDFYQQFHIIV 139
+ N + G V + D D F+ QF +++
Sbjct: 83 LQELNPDVNGSAVEESPEALLDNDPSFFSQFTVVI 117
>gnl|CDD|238763 cd01486, Apg7, Apg7 is an E1-like protein, that activates two
different ubiquitin-like proteins, Apg12 and Apg8, and
assigns them to specific E2 enzymes, Apg10 and Apg3,
respectively. This leads to the covalent conjugation of
Apg8 with phosphatidylethanolamine, an important step in
autophagy. Autophagy is a dynamic membrane phenomenon
for bulk protein degradation in the lysosome/vacuole.
Length = 307
Score = 48.9 bits (117), Expect = 2e-06
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDI--GSSKAEVA 104
K L++GAG LGC + +++ G I +D + SN RQ LF +D G KAE A
Sbjct: 1 KCLLLGAGTLGCNVARNLLGWGVRHITFVDSGKVSYSNPVRQSLFTFEDCKGGKPKAEAA 60
Query: 105 AKFINSRIPGV 115
A+ + P +
Sbjct: 61 AERLKEIFPSI 71
>gnl|CDD|162819 TIGR02354, thiF_fam2, thiamine biosynthesis protein ThiF, family 2.
Members of the HesA/MoeB/ThiF family of proteins
(pfam00899) include a number of members encoded in the
midst of thiamine biosynthetic operons. This mix of
known and putative ThiF proteins shows a deep split in
phylogenetic trees, with one the E. coli ThiF and the E.
coli MoeB proteins seemingly more closely related than
E. coli ThiF and Campylobacter (for example) ThiF. This
model represents the divergent clade of putative ThiF
proteins such found in Campylobacter [Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 200
Score = 47.9 bits (114), Expect = 2e-06
Identities = 29/103 (28%), Positives = 53/103 (51%), Gaps = 2/103 (1%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
V I G GGLG + ++A G ++ ++D D ++ SNLNRQ ++ +G K E +
Sbjct: 23 TVAICGLGGLGSNVAINLARAGIGKLILVDFDVVEPSNLNRQ-QYKASQVGEPKTEALKE 81
Query: 107 FINSRIPGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLDSIVAR 148
I+ P ++ + KI + + D F++ I+ D+ A+
Sbjct: 82 NISEINPYTEIEAYDEKITEENIDKFFKDADIVCEAFDNAEAK 124
>gnl|CDD|181302 PRK08223, PRK08223, hypothetical protein; Validated.
Length = 287
Score = 47.8 bits (114), Expect = 5e-06
Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 5/108 (4%)
Query: 46 CKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAA 105
+V I G GG+G L +A +G + + D D +L N NRQ +G KAEV A
Sbjct: 28 SRVAIAGLGGVGGIHLLTLARLGIGKFTIADFDVFELRNFNRQAGAMMSTLGRPKAEVLA 87
Query: 106 KFINSRIPGVKVIPHFCK-IQDYDSD-FYQQFHIIVCGLD--SIVARR 149
+ + P ++ I F + I ++D F + V GLD ARR
Sbjct: 88 EMVRDINPELE-IRAFPEGIGKENADAFLDGVDVYVDGLDFFEFDARR 134
>gnl|CDD|185071 PRK15116, PRK15116, sulfur acceptor protein CsdL; Provisional.
Length = 268
Score = 45.6 bits (108), Expect = 3e-05
Identities = 24/70 (34%), Positives = 40/70 (57%)
Query: 48 VLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAKF 107
+ ++G GG+G + +A G I +IDMD + ++N NRQ + ++G +KAEV A+
Sbjct: 33 ICVVGIGGVGSWAAEALARTGIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKAEVMAER 92
Query: 108 INSRIPGVKV 117
I P +V
Sbjct: 93 IRQINPECRV 102
>gnl|CDD|233388 TIGR01381, E1_like_apg7, E1-like protein-activating enzyme
Gsa7p/Apg7p. This model represents a family of
eukaryotic proteins found in animals, plants, and
yeasts, including Apg7p (YHR171W) from Saccharomyces
cerevisiae and GSA7 from Pichia pastoris. Members are
about 650 to 700 residues in length and include a
central domain of about 150 residues shared with the
ThiF/MoeB/HesA family of proteins. A low level of
similarity to ubiquitin-activating enzyme E1 is
described in a paper on peroxisome autophagy mediated by
GSA7, and is the basis of the name ubiquitin activating
enzyme E1-like protein. Members of the family appear to
be involved in protein lipidation events analogous to
ubiquitination and required for membrane fusion events
during autophagy.
Length = 664
Score = 44.9 bits (106), Expect = 8e-05
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 44 TSCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDI---GSSK 100
+ KVL++GAG LGC + + + G I +D + SN RQ L +D G K
Sbjct: 337 SQLKVLLLGAGTLGCNVARCLIGWGVRHITFVDNGKVSYSNPVRQSLSNFEDCLLGGRGK 396
Query: 101 AEVAAKFINSRIPGVKVIPH 120
AE A K + P ++ H
Sbjct: 397 AETAQKALKRIFPSIQATGH 416
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 41.5 bits (98), Expect = 6e-04
Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 24/96 (25%)
Query: 48 VLIIGAGG-LGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+L+ G G +G EL++ I G ++ V D D N+ ++
Sbjct: 5 ILVTGGAGSIGSELVRQILKFGPKKLIVFDRDE------NKLHELVRE------------ 46
Query: 107 FINSRIPGVKVIPHFCKIQDYDSDFY----QQFHII 138
+ SR P K+ ++D + + I+
Sbjct: 47 -LRSRFPHDKLRFIIGDVRDKERLRRAFKERGPDIV 81
>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
Length = 679
Score = 39.5 bits (92), Expect = 0.004
Identities = 30/98 (30%), Positives = 43/98 (43%), Gaps = 1/98 (1%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KV I G GG+G L + G H+ D D + N+NRQF R G K V +
Sbjct: 45 KVAIPGMGGVGGVHLITMVRTGIGRFHIADFDQFEPVNVNRQFGARVPSFGRPKLAVMKE 104
Query: 107 FINSRIPGVKVIPHFCKIQDYDSD-FYQQFHIIVCGLD 143
S P +++ P I + D F +++ GLD
Sbjct: 105 QALSINPFLEITPFPAGINADNMDAFLDGVDVVLDGLD 142
>gnl|CDD|236122 PRK07877, PRK07877, hypothetical protein; Provisional.
Length = 722
Score = 38.4 bits (90), Expect = 0.009
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 6/48 (12%)
Query: 64 IALMG-FNEIHVIDMDTIDLSNLNR--QFLFRQKDIGSSKAEVAAKFI 108
+A G E+ + D DT++LSNLNR +F D+G +KA VAA+ I
Sbjct: 125 LAAEGLCGELRLADFDTLELSNLNRVPAGVF---DLGVNKAVVAARRI 169
>gnl|CDD|184854 PRK14852, PRK14852, hypothetical protein; Provisional.
Length = 989
Score = 37.8 bits (87), Expect = 0.014
Identities = 40/152 (26%), Positives = 61/152 (40%), Gaps = 20/152 (13%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
+V I G GG+G L +A G ++ D D NLNRQ+ G K +V +
Sbjct: 334 RVAIAGLGGVGGIHLMTLARTGIGNFNLADFDAYSPVNLNRQYGASIASFGRGKLDVMTE 393
Query: 107 FINSRIP--GVKVIPHFCKIQDYDSDFYQQFHIIVCGLDSI---VARRWINGMLLSLLQY 161
S P ++ P + D+ F + ++V G+D + RR N L
Sbjct: 394 RALSVNPFLDIRSFPEGVAAETIDA-FLKDVDLLVDGIDFFALDIRRRLFNRAL------ 446
Query: 162 EEDGQVDQSTIIPMVDGGTEGFKGNARVILPG 193
E G IP++ G G+ V +PG
Sbjct: 447 -ELG-------IPVITAGPLGYSCALLVFMPG 470
>gnl|CDD|239330 cd03032, ArsC_Spx, Arsenate Reductase (ArsC) family, Spx subfamily;
Spx is a unique RNA polymerase (RNAP)-binding protein
present in bacilli and some mollicutes. It inhibits
transcription by binding to the C-terminal domain of the
alpha subunit of RNAP, disrupting complex formation
between RNAP and certain transcriptional activator
proteins like ResD and ComA. In response to oxidative
stress, Spx can also activate transcription, making it a
general regulator that exerts both positive and negative
control over transcription initiation. Spx has been
shown to exert redox-sensitive transcriptional control
over genes like trxA (TRX) and trxB (TRX reductase),
genes that function in thiol homeostasis. This
redox-sensitive activity is dependent on the presence of
a CXXC motif, present in some members of the Spx
subfamily, that acts as a thiol/disulfide switch. Spx
has also been shown to repress genes in a
sulfate-dependent manner independent of the presence of
the CXXC motif.
Length = 115
Score = 33.4 bits (77), Expect = 0.058
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 382 KYLDIESLDMKLSELIELLCQHPS 405
K L+I+ ++ LSELI L+ +HPS
Sbjct: 65 KNLNIDIDELSLSELIRLISEHPS 88
>gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component
regulatory system with EvgA; Provisional.
Length = 1197
Score = 35.5 bits (81), Expect = 0.065
Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 8/105 (7%)
Query: 380 QPKYLDIESL------DMKLSELIELLCQHPSYQMKSPGLTTMQDGRNRTLYMSTVRSIE 433
Q ++LDIE+L D++L + I + QH +++ ++ G NRT + R
Sbjct: 1082 QYRHLDIEALKNNTANDLQLMQEILMTFQHETHKDLPAAFHALEAGDNRTFHQCIHRIHG 1141
Query: 434 EATRENLKRSLVELGLRDEGIVNVADSTTPNTLEITLRVTAKMAE 478
A NL++ L+ + + E I V+D + P L++ V +AE
Sbjct: 1142 AANILNLQK-LINISHQLE-ITPVSDDSKPEILQLLNSVKEHIAE 1184
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 34.9 bits (81), Expect = 0.082
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 20/83 (24%)
Query: 48 VLIIGAGG-LGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
VL+ G GG +G EL + I EI + D + +L +
Sbjct: 253 VLVTGGGGSIGSELCRQILKFNPKEIILFSRDE------YKLYLIDME------------ 294
Query: 107 FINSRIPGVKVIPHFCKIQDYDS 129
+ + P +K+ + ++D D
Sbjct: 295 -LREKFPELKLRFYIGDVRDRDR 316
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 33.9 bits (78), Expect = 0.15
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 48 VLIIGAGGLGCELLKDIALMGFNEIHVID 76
V +IGAG +G L+ A G + ID
Sbjct: 133 VAVIGAGFIGLLFLQLAAAAGARRVIAID 161
>gnl|CDD|176202 cd08240, 6_hydroxyhexanoate_dh_like, 6-hydroxyhexanoate
dehydrogenase. 6-hydroxyhexanoate dehydrogenase, an
enzyme of the zinc-dependent alcohol dehydrogenase-like
family of medium chain dehydrogenases/reductases
catalyzes the conversion of 6-hydroxyhexanoate and
NAD(+) to 6-oxohexanoate + NADH and H+.
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. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. 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. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine, the ribose of NAD, a serine, then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 350
Score = 33.0 bits (76), Expect = 0.32
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 6/37 (16%)
Query: 45 SCKVLIIGAGGLGCELLKDIAL---MGFNEIHVIDMD 78
V+IIGAGGLG L +AL +G I V+D+D
Sbjct: 176 DEPVVIIGAGGLG---LMALALLKALGPANIIVVDID 209
>gnl|CDD|113988 pfam05237, MoeZ_MoeB, MoeZ/MoeB domain. This putative domain is
found in the MoeZ protein and the MoeB protein. The
domain has two CXXC motifs that are only partly
conserved.
Length = 77
Score = 30.3 bits (69), Expect = 0.36
Identities = 13/51 (25%), Positives = 20/51 (39%)
Query: 326 AVIAATCATEVFKLATGCATSLNNYMVFNDVAGIYTYTYEAERKSNCLACG 376
I + A E KL TG L+ ++ D ++ R +C CG
Sbjct: 27 GTIGSLQALEAIKLLTGIGEPLSGRLLLFDAWTMHFRKIRLRRDPDCPVCG 77
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 31.8 bits (72), Expect = 0.88
Identities = 9/39 (23%), Positives = 17/39 (43%)
Query: 42 LQTSCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTI 80
+ V+++GAG +G E + A G + D +
Sbjct: 133 AEPPKDVVVVGAGPIGLEAAEAAAKRGKKVTLIEAADRL 171
>gnl|CDD|226713 COG4262, COG4262, Predicted spermidine synthase with an N-terminal
membrane domain [General function prediction only].
Length = 508
Score = 31.7 bits (72), Expect = 0.93
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 38 ALSFLQTSCKVLIIGAG-GLGC-ELLKDIALMGFNEIHVIDMD--TIDLSNLN 86
ALS ++ + VL++G G GL ELLK +I ++D+D I+L++
Sbjct: 283 ALSSVRGARSVLVLGGGDGLALRELLK---YPQVEQITLVDLDPRMIELASHA 332
>gnl|CDD|216573 pfam01564, Spermine_synth, Spermine/spermidine synthase. Spermine
and spermidine are polyamines. This family includes
spermidine synthase that catalyzes the fifth (last) step
in the biosynthesis of spermidine from arginine, and
spermine synthase.
Length = 240
Score = 31.1 bits (71), Expect = 0.95
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 10/48 (20%)
Query: 47 KVLIIGA--GGLGCELLKDIALMGFNEIHVIDMD--TIDLSNLNRQFL 90
KVLIIG GG E++K +I ++++D I+ S ++FL
Sbjct: 78 KVLIIGGGDGGALREVVK---HPSVEKITLVEIDEKVIEFS---KKFL 119
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 31.4 bits (72), Expect = 0.97
Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 42 LQTSCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNL 85
L+ + +VL++G G +G EL D+ G + ++D L++L
Sbjct: 138 LRDAQRVLVVGGGLIGTELAMDLCRAG-KAVTLVDNAASLLASL 180
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms
this enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 31.1 bits (71), Expect = 1.1
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 48 VLIIGAGGLGCELLKDIALMGFNEIHVIDMD 78
VLIIGAGG+G + +A G EI V D
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRS 31
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 31.2 bits (71), Expect = 1.2
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 25/81 (30%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
K L+IGAG +G + K + G +I + NR + +AE AK
Sbjct: 182 KALLIGAGEMGELVAKHLLRKGVGKILI----------ANRTY---------ERAEDLAK 222
Query: 107 FINSRIPGVKVIPHFCKIQDY 127
+ G V F +++Y
Sbjct: 223 ----ELGGEAV--KFEDLEEY 237
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 29.6 bits (67), Expect = 1.4
Identities = 21/115 (18%), Positives = 38/115 (33%), Gaps = 32/115 (27%)
Query: 45 SCKVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKA-EV 103
KVL+IGAG + K + G +I + NR KA E+
Sbjct: 12 GKKVLLIGAGEMARLAAKHLLSKGAKKITIA----------NRTL---------EKAKEL 52
Query: 104 AAKFINSRIPGVKVIPHFCKIQDYDSDFYQQFHIIVCGLDS---IVARRWINGML 155
A +F V + + + + I++ + I+ + + L
Sbjct: 53 AEEF--------PVGGEALPLDEL-EELLAEADIVISATSAPTPIITKEMVEEAL 98
>gnl|CDD|215691 pfam00070, Pyr_redox, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 82
Score = 28.3 bits (64), Expect = 1.8
Identities = 8/46 (17%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 47 KVLIIGAGGLGCEL---LKDIALMGFNEIHVIDMDTIDLSNLNRQF 89
+V+++G G +G E L + ++ V++ L + +
Sbjct: 1 RVVVVGGGYIGLEFASALAKLGS----KVTVVERRDRLLRGFDEEI 42
>gnl|CDD|203593 pfam07200, Mod_r, Modifier of rudimentary (Mod(r)) protein. This
family represents a conserved region approximately 150
residues long within a number of eukaryotic proteins
that show homology with Drosophila melanogaster Modifier
of rudimentary (Mod(r)) proteins. The N-terminal half of
Mod(r) proteins is acidic, whereas the C-terminal half
is basic, and both of these regions are represented in
this family. Members of this family include the Vps37
subunit of the endosomal sorting complex ESCRT-I, a
complex involved in recruiting transport machinery for
protein sorting at the multivesicular body (MVB). The
yeast ESCRT-I complex consists of three proteins (Vps23,
Vps28 and Vps37). The mammalian homologue of Vps37
interacts with Tsg101 (Pfam: PF05743) through its mod(r)
domain and its function is essential for lysosomal
sorting of EGF receptors.
Length = 150
Score = 29.2 bits (66), Expect = 2.6
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 10/63 (15%)
Query: 390 DMKLSELIELLCQHPSYQ---MKSPGLTTMQDGRNRTLYMSTVRSIEEATRENLKR--SL 444
D+ L EL ELL + ++ P + + ++ L E ENL++ L
Sbjct: 3 DLSLDELKELLQDEDALLEFVLELPQVQDLNLEKDALL-----AQNESLAEENLEKEPQL 57
Query: 445 VEL 447
EL
Sbjct: 58 EEL 60
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 29.6 bits (67), Expect = 3.7
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNR 87
++ IIG GG G +L +A EIH+ D D N R
Sbjct: 178 RIAIIGLGGTGSYILDLVAKTPVREIHLFDGDDFLQHNAFR 218
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 29.3 bits (67), Expect = 4.3
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQF 89
K++I+GAG +G L ++++ N++ VID D L L +
Sbjct: 2 KIIIVGAGQVGYTLAENLSGEN-NDVTVIDTDEERLRRLQDRL 43
>gnl|CDD|131585 TIGR02533, type_II_gspE, type II secretion system protein E. This
family describes GspE, the E protein of the type II
secretion system, also called the main terminal branch
of the general secretion pathway. This model separates
GspE from the PilB protein of type IV pilin biosynthesis
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 486
Score = 29.3 bits (66), Expect = 4.7
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 432 IEEATRENLKRSLVELGLRDEGIVNVADSTTPNTLEITLRVT 473
I+E R R+ LRD+G+ V T T+E LRVT
Sbjct: 452 IKEIARAAGMRT-----LRDDGLRKVLAGIT--TIEEVLRVT 486
>gnl|CDD|202320 pfam02629, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 96
Score = 27.5 bits (62), Expect = 5.1
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 47 KVLIIGAGGLGCELLKD-IALMGFNEIHVID 76
KV +IGAGGLG + L I L+G+ V
Sbjct: 5 KVAVIGAGGLGIQGLYHFIQLLGYGIKMVFG 35
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. 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 have 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. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. 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.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 29.1 bits (66), Expect = 5.6
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMD 78
VL+IG GGLG ++ MG + +D+
Sbjct: 168 TVLVIGLGGLGLNAVQIAKAMG-AAVIAVDIK 198
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 29.1 bits (66), Expect = 5.8
Identities = 18/74 (24%), Positives = 24/74 (32%), Gaps = 25/74 (33%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
V ++GAGGLG ++ MG E+ I K E+A K
Sbjct: 169 WVAVVGAGGLGHMAVQYAKAMGA-EVIAI-------------------TRSEEKLELAKK 208
Query: 107 F-----INSRIPGV 115
INS
Sbjct: 209 LGADHVINSSDSDA 222
>gnl|CDD|149194 pfam07979, Intimin_C, Intimin C-type lectin domain. This domain is
found at the C-terminus of intimin. Its structure has
been solved and shown to have a C-lectin type of
structure. Intimin is a bacterial adhesion molecule
involved in intimate attachment of enteropathogenic and
enterohemorrhagic Escherichia coli to mammalian host
cells. Intimin targets the translocated intimin receptor
(Tir), which is exported by the bacteria and integrated
into the host cell plasma membrane.
Length = 101
Score = 27.4 bits (61), Expect = 6.2
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 284 NHIN-WIYEKASERASQFNIVGVTYRLVQGVIKNIIPAVASTNAVIAATCA 333
N I WI + +S++ S V TY LV +N + V A A C
Sbjct: 56 NSITAWIKQTSSDKKSG---VSSTYDLV---TQNPLTNVNVNAANAYAVCV 100
>gnl|CDD|219100 pfam06597, Clostridium_P47, Clostridium P-47 protein. This family
consists of several P-47 proteins from various
Clostridium species as well as two related sequences
from Pseudomonas putida. The function of this family is
unknown.
Length = 449
Score = 28.9 bits (65), Expect = 6.5
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 172 IIPMVDGGTEGFKGNARVILPGMTACIDCTLDLFPPQ 208
IP+ G + K L G+ + LD FPP+
Sbjct: 60 KIPIKKGTFKSGK-GGTYDLSGVNPVVQIKLDFFPPK 95
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 28.5 bits (64), Expect = 6.8
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 35 SSEALSFLQTSCKVLIIGAGGLGCEL---LKDIALMGFNEIHVIDM 77
S E L L+ +V+++G G +G EL L + E+ V++
Sbjct: 132 SDEILELLELPKRVVVVGGGYIGLELAAALAKLGK----EVTVVER 173
>gnl|CDD|215321 PLN02592, PLN02592, ent-copalyl diphosphate synthase.
Length = 800
Score = 29.1 bits (65), Expect = 7.5
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 17 WNHLRKVLERPGPFCTSPSSEALSFLQT 44
W L K+ + G F SPSS A + +QT
Sbjct: 255 WEKLLKLQCQDGSFLFSPSSTAFALMQT 282
>gnl|CDD|100106 cd01425, RPS2, Ribosomal protein S2 (RPS2), involved in formation
of the translation initiation complex, where it might
contact the messenger RNA and several components of the
ribosome. It has been shown that in Escherichia coli
RPS2 is essential for the binding of ribosomal protein
S1 to the 30s ribosomal subunit. In humans, most likely
in all vertebrates, and perhaps in all metazoans, the
protein also functions as the 67 kDa laminin receptor
(LAMR1 or 67LR), which is formed from a 37 kDa
precursor, and is overexpressed in many tumors. 67LR is
a cell surface receptor which interacts with a variety
of ligands, laminin-1 and others. It is assumed that the
ligand interactions are mediated via the conserved
C-terminus, which becomes extracellular as the protein
undergoes conformational changes which are not well
understood. Specifically, a conserved palindromic motif,
LMWWML, may participate in the interactions. 67LR plays
essential roles in the adhesion of cells to the basement
membrane and subsequent signalling events, and has been
linked to several diseases. Some evidence also suggests
that the precursor of 67LR, 37LRP is also present in the
nucleus in animals, where it appears associated with
histones.
Length = 193
Score = 27.9 bits (63), Expect = 7.9
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 22/87 (25%)
Query: 70 NEIHVIDMD-TIDLSNLNRQFLFRQKDIGSSKAEVAAKFINSRIPGVKVIPHFCKIQDYD 128
N IH+ID++ T++ L F+ +I + ++ F+ ++ + + F +
Sbjct: 28 NGIHIIDLEKTLEKLRLALNFI---ANIAAKGGKIL--FVGTKPQAQRAVKKFAE----- 77
Query: 129 SDFYQQFHIIVCGLDSIVARRWINGML 155
G V RW+ G L
Sbjct: 78 ----------RTG-SFYVNGRWLGGTL 93
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 27.6 bits (62), Expect = 8.1
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 19/82 (23%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDMDTIDLSNLNRQFLFRQKDIGSSKAEVAAK 106
KVLI+GAGG + +A +G +I + +NR KA+ A+
Sbjct: 21 KVLILGAGGAARAVAYALAELGAAKIVI----------VNRTL---------EKAKALAE 61
Query: 107 FINSRIPGVKVIPHFCKIQDYD 128
+ + + + D
Sbjct: 62 RFGELGIAIAYLDLEELLAEAD 83
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 28.5 bits (64), Expect = 8.6
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 47 KVLIIGAGGLGCELLKDIALMGFNEIHVIDM 77
+V + G G +GC ++ + +G EI D+
Sbjct: 172 RVFVSGVGPIGCLIVAAVKTLGAAEIVCADV 202
>gnl|CDD|188398 TIGR03882, cyclo_dehyd_2, bacteriocin biosynthesis cyclodehydratase
domain. This model describes a ThiF-like domain of a
fusion protein found in clusters associated with the
production of TOMMs (thiazole/oxazole-modified
microcins), small bacteriocins with characteristic
heterocycle modifications. This domain is presumed to
act as a cyclodehydratase, as do members of the SagC
family modeled by TIGR03603.
Length = 164
Score = 27.7 bits (62), Expect = 8.9
Identities = 13/64 (20%), Positives = 23/64 (35%)
Query: 318 IPAVASTNAVIAATCATEVFKLATGCATSLNNYMVFNDVAGIYTYTYEAERKSNCLACGP 377
+ A +AA A E+ K G L ++ D+A + + + C CG
Sbjct: 58 PWLTPAALAAVAALAAAELAKWLAGERGRLEGAVLTLDLATLTVSRHPLLPRPQCPVCGD 117
Query: 378 ANQP 381
+
Sbjct: 118 LPED 121
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.136 0.413
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,019,501
Number of extensions: 2305535
Number of successful extensions: 2181
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2135
Number of HSP's successfully gapped: 82
Length of query: 478
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 377
Effective length of database: 6,457,848
Effective search space: 2434608696
Effective search space used: 2434608696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.1 bits)