RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9783
(726 letters)
>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 = 318 bits (817), Expect = e-103
Identities = 127/266 (47%), Positives = 151/266 (56%), Gaps = 85/266 (31%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVARN 80
KVLVVGAGGIGCELLKNLVL+GF I I+DLDTID+SNLNRQFL
Sbjct: 1 KVLVVGAGGIGCELLKNLVLTGFGEIHIIDLDTIDLSNLNRQFL---------------- 44
Query: 81 SALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIIR 140
Sbjct: 44 ------------------------------------------------------------ 44
Query: 141 FLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVM 200
F K+HVGKSKAQVA+ + L+FNP+ IVA+H +I DF V +FKQF LV
Sbjct: 45 ---------FRKKHVGKSKAQVAKEAVLSFNPNVKIVAYHANIKDPDFNVEFFKQFDLVF 95
Query: 201 NALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCYECDPKPAAKTYPGC 260
NALDN AAR HVN+MCLA++VPLIESGT G+ GQV++IKKG+T+CYEC PK KT+P C
Sbjct: 96 NALDNLAARRHVNKMCLAADVPLIESGTTGFLGQVQVIKKGKTECYECQPKETPKTFPVC 155
Query: 261 TIRNTPSEPIHCIVWAKHLFNYLERL 286
TIR+TPS+PIHCIVWAK LF ++
Sbjct: 156 TIRSTPSQPIHCIVWAKSLFFLFNKV 181
Score = 191 bits (488), Expect = 2e-55
Identities = 84/189 (44%), Positives = 101/189 (53%), Gaps = 53/189 (28%)
Query: 379 LFAKFFDADIRYLISMSDLWKTRKAPQPLVWDTLSDAVAGSSKETDGGGLKDQRVWSVAE 438
LF K F DI L+SM +LWKTRK P PL W L
Sbjct: 177 LFNKVFKDDIERLLSMEELWKTRKPPVPLSWKEL-------------------------- 210
Query: 439 CARVFERSVRELKTKFDAAVEKDEHLVWDKDDKPAMDFVAACANIRAHVFSIPEKSRFDI 498
+DKDD+ A+DFVAA AN+R+HVF IP KSRFDI
Sbjct: 211 --------------------------TFDKDDQDALDFVAAAANLRSHVFGIPMKSRFDI 244
Query: 499 KSMAGNIIPAIATSNAIVAGLVVLHAIHVLQARFSSCQTVYLRKKPNHRDQMIVPEKYLT 558
K MAGNIIPAIAT+NAI+AGL+VL A+ VL C+TV+L +PN R +++VP K L
Sbjct: 245 KQMAGNIIPAIATTNAIIAGLIVLEALKVLSGDKEQCRTVFLNLQPNRRKRLLVPCK-LD 303
Query: 559 APNPTCPVC 567
PNP C VC
Sbjct: 304 PPNPNCYVC 312
>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 = 187 bits (477), Expect = 6e-55
Identities = 88/260 (33%), Positives = 118/260 (45%), Gaps = 84/260 (32%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVARN 80
KVL+VGAGGIGCELLKNL L GF I ++D+DTIDVSNLNRQF
Sbjct: 1 KVLLVGAGGIGCELLKNLALMGFGQIHVIDMDTIDVSNLNRQF----------------- 43
Query: 81 SALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIIR 140
LF + +G+ K++VA + + NP+ +V + +
Sbjct: 44 -----------------------LFRPKDIGRPKSEVAAEAVNDRNPNCKVVPYQNKVGP 80
Query: 141 FLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVM 200
DF +F+QF +++
Sbjct: 81 --------------------------------------------EQDFNDTFFEQFHIIV 96
Query: 201 NALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCYECDPKPAAKTYPGC 260
NALDN AR +VN M + VPLIESGT G++G ++I G T+C EC P K +P C
Sbjct: 97 NALDNIIARRYVNGMLIFLIVPLIESGTEGFKGNAQVILPGMTECIECTLYPPQKNFPMC 156
Query: 261 TIRNTPSEPIHCIVWAKHLF 280
TI + P P HCI WA+ L
Sbjct: 157 TIASMPRLPEHCIEWARMLQ 176
Score = 74.9 bits (184), Expect = 4e-15
Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 462 EH-LVWDK----DDKPAMDFVAACANIRAHVFSIPEKSRFDIKSMAGNIIPAIATSNAIV 516
EH + W + DD + F+ +N RA ++I + F K +AG IIPA+AT+NA+V
Sbjct: 166 EHCIEWARMLQWDDPEHIQFIFQASNERASQYNIRGVTYFLTKGVAGRIIPAVATTNAVV 225
Query: 517 AGLVVL 522
AG+ L
Sbjct: 226 AGVCAL 231
>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 = 160 bits (406), Expect = 4e-44
Identities = 86/267 (32%), Positives = 114/267 (42%), Gaps = 97/267 (36%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVARN 80
K+LV+GAGG+GCELLKNL LSGF NI ++D+DTIDVSNLNRQFL
Sbjct: 1 KILVIGAGGLGCELLKNLALSGFRNIHVIDMDTIDVSNLNRQFL---------------- 44
Query: 81 SALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIIR 140
F ++ +GK KA+VA A V
Sbjct: 45 ------------------------FREKDIGKPKAEVA----------AKFV-------- 62
Query: 141 FLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVM 200
N + P N+ H I D +++QF +++
Sbjct: 63 ----NDRV-----------------------PGVNVTPHFGKI--QDKDEEFYRQFNIII 93
Query: 201 NALDNRAARNHVNRMCL--------ASEVPLIESGTAGYEGQVELIKKGETKCYEC--DP 250
LD+ AR +N + S +PLI+ GT G++G +I G T C EC D
Sbjct: 94 CGLDSIEARRWINGTLVSLLLYEDPESIIPLIDGGTEGFKGHARVILPGITACIECSLDL 153
Query: 251 KPAAKTYPGCTIRNTPSEPIHCIVWAK 277
P T+P CTI NTP P HCI +A
Sbjct: 154 FPPQVTFPLCTIANTPRLPEHCIEYAS 180
Score = 46.6 bits (111), Expect = 2e-05
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 467 DKDDKPAMDFVAACANIRAHVFSIPEKSRFDIKSMAGNIIPAIATSNAIVA 517
D DD ++++ A RA F+I + + + IIPA+A++NAI+A
Sbjct: 194 DGDDPEHIEWLYQKALERAAQFNISGVTYSLTQGVVKRIIPAVASTNAIIA 244
>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 = 144 bits (365), Expect = 4e-37
Identities = 79/265 (29%), Positives = 106/265 (40%), Gaps = 87/265 (32%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSN-----IEIVDLDTIDVSNLNRQFLFHKQHVGKSKA 75
KV +VGAG IGCELLKN L G I + D+D I+ SNLNRQFL
Sbjct: 1 KVFLVGAGAIGCELLKNFALMGVGTGESGEITVTDMDNIEKSNLNRQFL----------- 49
Query: 76 QVARNSALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHH 135
F VGK K++VA + NPD I A
Sbjct: 50 -----------------------------FRPHDVGKPKSEVAAAAVKAMNPDLKITA-- 78
Query: 136 TSIIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQ 195
NR VG P+ + F ++++
Sbjct: 79 -------LQNR--------VG---------------PETEHI----------FNDEFWEK 98
Query: 196 FTLVMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCYECDPKPAAK 255
V NALDN AR +V+R C+ PL+ESGT G +G +++ T+ Y P K
Sbjct: 99 LDGVANALDNVDARMYVDRRCVYYRKPLLESGTLGTKGNTQVVIPHLTESYSSSRDPPEK 158
Query: 256 TYPGCTIRNTPSEPIHCIVWAKHLF 280
+ P CT++N P+ H I WA+ F
Sbjct: 159 SIPLCTLKNFPNAIEHTIQWARDEF 183
Score = 78.1 bits (193), Expect = 3e-15
Identities = 31/65 (47%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 467 DKDDKPA--MDFVAACANIRAHVFSIPEKSRFDIKSMAGNIIPAIATSNAIVAGLVVLHA 524
+KDD MDF+ A +N+RA +SIP R K +AG IIPAIAT+ A V GLV L
Sbjct: 278 EKDDDTNFHMDFITAASNLRARNYSIPPADRHKTKRIAGKIIPAIATTTAAVTGLVCLEL 337
Query: 525 IHVLQ 529
V+
Sbjct: 338 YKVVD 342
>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 = 118 bits (297), Expect = 4e-31
Identities = 54/217 (24%), Positives = 80/217 (36%), Gaps = 86/217 (39%)
Query: 19 KSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVA 78
S+VLVVGAGG+G + L +G + +VD DT+++SNLNRQ LF + +GK K
Sbjct: 1 SSRVLVVGAGGLGSPAAEYLARAGVGKLTLVDFDTVELSNLNRQILFTESDIGKPK---- 56
Query: 79 RNSALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSI 138
A+VA+ NPD + A+
Sbjct: 57 ------------------------------------AEVAKERLRAINPDVEVEAYPER- 79
Query: 139 IRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTL 198
++ + K L
Sbjct: 80 ---------------------------------------------LTPENLEELLKGVDL 94
Query: 199 VMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQV 235
V++ALDN AAR +N C+ +PLI +G G++GQV
Sbjct: 95 VVDALDNFAARYLLNDACVKRGIPLISAGALGFDGQV 131
>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 = 123 bits (310), Expect = 6e-29
Identities = 77/277 (27%), Positives = 110/277 (39%), Gaps = 91/277 (32%)
Query: 9 FEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFS-----NIEIVDLDTIDVSNLNRQF 63
F++ L++L + +VG G IGCE+LKN L G I + D D I+ SNLNRQF
Sbjct: 413 FQQKLQNL----NIFLVGCGAIGCEMLKNFALMGVGTGKKGMITVTDPDLIEKSNLNRQF 468
Query: 64 LFHKQHVGKSKAQVARNSALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSAL 123
L F H+GK K+ A ++ L
Sbjct: 469 L----------------------------------------FRPHHIGKPKSYTAADATL 488
Query: 124 NFNPDANIVAHHTSIIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSI 183
NP I A H NR VG +
Sbjct: 489 KINPQIKIDA---------HQNR--------VGPETETI--------------------- 510
Query: 184 ISADFGVNYFKQFTLVMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGET 243
F ++++ +V+NALDN AR +V+ CLA PL+ESGT G +G +++ T
Sbjct: 511 ----FNDEFYEKLDVVINALDNVEARRYVDSRCLAFLKPLLESGTLGTKGNTQVVVPHLT 566
Query: 244 KCYECDPKPAAKTYPGCTIRNTPSEPIHCIVWAKHLF 280
+ Y P K P CT+++ P+ H I WA+ F
Sbjct: 567 ESYGSSRDPPEKEIPFCTLKSFPAAIEHTIQWARDKF 603
Score = 69.9 bits (171), Expect = 3e-12
Identities = 31/62 (50%), Positives = 38/62 (61%)
Query: 467 DKDDKPAMDFVAACANIRAHVFSIPEKSRFDIKSMAGNIIPAIATSNAIVAGLVVLHAIH 526
D D +DF+ A +N+RA +SI RF K +AG IIPAIATS A V+GLV L I
Sbjct: 809 DDDHNGHIDFITAASNLRAKNYSIEPADRFKTKFIAGKIIPAIATSTATVSGLVCLELIK 868
Query: 527 VL 528
V
Sbjct: 869 VT 870
Score = 49.5 bits (118), Expect = 6e-06
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 1/86 (1%)
Query: 19 KSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVA 78
KS VL+ G GG+G E+ KNLVL+G ++ + D + +L+ F + VG+++A+
Sbjct: 24 KSNVLISGMGGLGLEIAKNLVLAGVKSVTLHDTEKCQAWDLSSNFFLSEDDVGRNRAEAV 83
Query: 79 RNSALNFNPDANIYYQVDFHLNRQFL 104
NP ++ N +FL
Sbjct: 84 VKKLAELNPYVHV-SSSSVPFNEEFL 108
>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 = 111 bits (280), Expect = 1e-27
Identities = 58/245 (23%), Positives = 85/245 (34%), Gaps = 87/245 (35%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
+K ++VLVVGAGG+G + L +G + +VD D +++SNL RQ L + VG+ K
Sbjct: 19 LKNARVLVVGAGGLGSPAAEYLAAAGVGKLGLVDDDVVELSNLQRQILHTEADVGQPK-- 76
Query: 77 VARNSALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHT 136
A+ A NPD I A++
Sbjct: 77 --------------------------------------AEAAAERLRAINPDVEIEAYNE 98
Query: 137 SIIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQF 196
+ A N +I +
Sbjct: 99 RL---------------------------DAENAEE----------LI---------AGY 112
Query: 197 TLVMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCYEC-DPKPAAK 255
LV++ DN A R +N C+ PL+ G+EGQV + GE CY C P+P
Sbjct: 113 DLVLDCTDNFATRYLINDACVKLGKPLVSGAVLGFEGQVTVFIPGEGPCYRCLFPEPPPP 172
Query: 256 TYPGC 260
P C
Sbjct: 173 GVPSC 177
>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 2
[Coenzyme metabolism].
Length = 254
Score = 111 bits (279), Expect = 2e-27
Identities = 63/257 (24%), Positives = 91/257 (35%), Gaps = 90/257 (35%)
Query: 8 VFEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHK 67
+ + +K S+VLVVGAGG+G K L L+G + IVD DT+++SNL RQFLF +
Sbjct: 19 GIGGEGQQKLKDSRVLVVGAGGLGSPAAKYLALAGVGKLTIVDFDTVELSNLQRQFLFTE 78
Query: 68 QHVGKSKAQVARNSALNFNPDANIYYQVDFHLNRQFLFHKQHVGKSKAQVARNSALNFNP 127
VGK KA +VA + NP
Sbjct: 79 ADVGKPKA----------------------------------------EVAAKALRKLNP 98
Query: 128 DANIVAHHTSIIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISAD 187
+VA+ + +
Sbjct: 99 LVEVVAYL----------------------------------------------ERLDEE 112
Query: 188 FGVNYFKQFTLVMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGE-TKCY 246
QF +V++ DN R +N C+ +PL+ G G+EGQV +I G+ T CY
Sbjct: 113 NAEELIAQFDVVLDCTDNFETRYLINDACVKLGIPLVHGGAIGFEGQVTVIIPGDKTPCY 172
Query: 247 EC---DPKPAAKTYPGC 260
C + P C
Sbjct: 173 RCLFPEKPPPGLVPTSC 189
>gnl|CDD|202124 pfam02134, UBACT, Repeat in ubiquitin-activating (UBA) protein.
Length = 66
Score = 100 bits (251), Expect = 8e-26
Identities = 38/65 (58%), Positives = 48/65 (73%)
Query: 465 VWDKDDKPAMDFVAACANIRAHVFSIPEKSRFDIKSMAGNIIPAIATSNAIVAGLVVLHA 524
+DKDD +DFV A AN+RA + IP RFD+K +AGNIIPAIAT+NAIVAG+VVL
Sbjct: 1 EFDKDDDDHLDFVYAAANLRAQNYGIPPADRFDVKGIAGNIIPAIATTNAIVAGIVVLEL 60
Query: 525 IHVLQ 529
+ +L
Sbjct: 61 LKILT 65
>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 = 95.8 bits (239), Expect = 3e-23
Identities = 33/71 (46%), Positives = 46/71 (64%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVARN 80
+VL+VG GG+G E+ NL SG I ++D DT+++SNLNRQFL + +GK KA+VA
Sbjct: 1 RVLLVGLGGLGSEIALNLARSGVGKITLIDFDTVELSNLNRQFLARQADIGKPKAEVAAR 60
Query: 81 SALNFNPDANI 91
NP N+
Sbjct: 61 RLNELNPGVNV 71
Score = 74.6 bits (184), Expect = 7e-16
Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 1/95 (1%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
LNRQFL + +GK KA+VA NP N+ A I + ++ LV++A+
Sbjct: 39 LNRQFLARQADIGKPKAEVAARRLNELNPGVNVTAVPEGISEDNL-DDFLDGVDLVIDAI 97
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAGYEGQVELI 238
DN A R +NR C +P+I++G G G +++I
Sbjct: 98 DNIAVRRALNRACKELGIPVIDAGGLGLGGDIQVI 132
>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 = 83.4 bits (207), Expect = 5e-20
Identities = 22/39 (56%), Positives = 27/39 (69%)
Query: 243 TKCYECDPKPAAKTYPGCTIRNTPSEPIHCIVWAKHLFN 281
T+CYEC P P K+ P CT+R+ PS P HCI WA+ LF
Sbjct: 2 TECYECSPDPPEKSIPVCTLRSFPSTPEHCIEWARDLFE 40
>gnl|CDD|236320 PRK08644, PRK08644, thiamine biosynthesis protein ThiF;
Provisional.
Length = 212
Score = 76.0 bits (188), Expect = 1e-15
Identities = 30/83 (36%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 9 FEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQ 68
L + +KK+KV + GAGG+G + L SG N+++VD D ++ SNLNRQ F
Sbjct: 18 HTPKLLEKLKKAKVGIAGAGGLGSNIAVALARSGVGNLKLVDFDVVEPSNLNRQQYF-IS 76
Query: 69 HVGKSKAQVARNSALNFNPDANI 91
+G K + + + L NP I
Sbjct: 77 QIGMPKVEALKENLLEINPFVEI 99
Score = 41.8 bits (99), Expect = 5e-04
Identities = 31/104 (29%), Positives = 41/104 (39%), Gaps = 17/104 (16%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
LNRQ F +G K + + + L NP I AH+ I D FK +V+ A
Sbjct: 68 LNRQQYF-ISQIGMPKVEALKENLLEINPFVEIEAHNEK-IDEDNIEELFKDCDIVVEAF 125
Query: 204 DN--------RAARNHVNRMCLASEVPLIESGTAGYEGQVELIK 239
DN H + +A+ SG AGY G IK
Sbjct: 126 DNAETKAMLVETVLEHPGKKLVAA------SGMAGY-GDSNSIK 162
>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 = 71.6 bits (176), Expect = 3e-14
Identities = 23/76 (30%), Positives = 45/76 (59%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
++ +++L++G G+G E+ KNLVLSG ++ I+D T+ +L QFL + +G+++A+
Sbjct: 19 LRSARILLIGLKGLGAEIAKNLVLSGIGSLTILDDRTVTEEDLGAQFLIPAEDLGQNRAE 78
Query: 77 VARNSALNFNPDANIY 92
+ NP +
Sbjct: 79 ASLERLRALNPRVKVS 94
Score = 47.3 bits (113), Expect = 6e-06
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 6/94 (6%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNP--DANIVAHHTSIISADFGVNYFKQFTLVMN 201
L QFL + +G+++A+ + NP ++ S +F F QF +V+
Sbjct: 61 LGAQFLIPAEDLGQNRAEASLERLRALNPRVKVSVDTDDISEKPEEF----FSQFDVVVA 116
Query: 202 ALDNRAARNHVNRMCLASEVPLIESGTAGYEGQV 235
+RA +N +C V +G G G V
Sbjct: 117 TELSRAELVKINELCRKLGVKFYATGVHGLFGFV 150
>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 = 71.6 bits (176), Expect = 3e-14
Identities = 30/75 (40%), Positives = 42/75 (56%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
+ S VL++GAGG+G L +G I IVD D +D+SNL RQ LF ++ VG+ K +
Sbjct: 19 LLNSHVLIIGAGGLGSPAALYLAGAGVGTIVIVDDDHVDLSNLQRQILFTEEDVGRPKVE 78
Query: 77 VARNSALNFNPDANI 91
VA N D +
Sbjct: 79 VAAQRLRELNSDIQV 93
Score = 64.7 bits (158), Expect = 7e-12
Identities = 36/121 (29%), Positives = 52/121 (42%), Gaps = 2/121 (1%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
L RQ LF ++ VG+ K +VA N D + A + + + LV++
Sbjct: 61 LQRQILFTEEDVGRPKVEVAAQRLRELNSDIQVTALKERVTAENL-ELLINNVDLVLDCT 119
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAGYEGQVELI-KKGETKCYECDPKPAAKTYPGCTI 262
DN A R +N C+A PLI + G+ GQ+ + GE C C A T P C
Sbjct: 120 DNFATRYLINDACVALGTPLISAAVVGFGGQLMVFDPGGEGPCLRCLFPDIADTGPSCAT 179
Query: 263 R 263
Sbjct: 180 A 180
>gnl|CDD|224100 COG1179, COG1179, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 1
[Coenzyme metabolism].
Length = 263
Score = 72.7 bits (179), Expect = 5e-14
Identities = 30/88 (34%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 10 EKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQH 69
E LE +K++ V VVG GG+G ++ L SG I ++D+D + V+N NRQ
Sbjct: 22 EDGLE-KLKQAHVCVVGIGGVGSWAVEALARSGIGRITLIDMDDVCVTNTNRQIHALLGD 80
Query: 70 VGKSKAQVARNSALNFNPDANIYYQVDF 97
+GK K +V + NP+ + DF
Sbjct: 81 IGKPKVEVMKERIKQINPECEVTAINDF 108
Score = 44.6 bits (106), Expect = 8e-05
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 2/88 (2%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYF-KQFTLVMNA 202
NRQ +GK K +V + NP+ + A + I+ + + K F V++A
Sbjct: 70 TNRQIHALLGDIGKPKVEVMKERIKQINPECEVTAIN-DFITEENLEDLLSKGFDYVIDA 128
Query: 203 LDNRAARNHVNRMCLASEVPLIESGTAG 230
+D+ A+ + C +++P+I S AG
Sbjct: 129 IDSVRAKVALIAYCRRNKIPVISSMGAG 156
>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 = 71.5 bits (176), Expect = 6e-14
Identities = 27/81 (33%), Positives = 41/81 (50%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
++ + V VVG GG+G + L SG + ++D D + VSNLNRQ VGK K +
Sbjct: 9 LRNAHVAVVGLGGVGSWAAEALARSGVGKLTLIDFDVVCVSNLNRQIHALLSTVGKPKVE 68
Query: 77 VARNSALNFNPDANIYYQVDF 97
V + NP+ + +F
Sbjct: 69 VMAERIRDINPECEVDAVEEF 89
Score = 44.9 bits (107), Expect = 6e-05
Identities = 22/87 (25%), Positives = 37/87 (42%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
LNRQ VGK K +V + NP+ + A + + V++A+
Sbjct: 51 LNRQIHALLSTVGKPKVEVMAERIRDINPECEVDAVEEFLTPDNSEDLLGGDPDFVVDAI 110
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAG 230
D+ A+ + C ++P+I S AG
Sbjct: 111 DSIRAKVALIAYCRKRKIPVISSMGAG 137
>gnl|CDD|181156 PRK07878, PRK07878, molybdopterin biosynthesis-like protein MoeZ;
Validated.
Length = 392
Score = 74.0 bits (182), Expect = 6e-14
Identities = 33/75 (44%), Positives = 48/75 (64%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
+K ++VLV+GAGG+G L L +G + IV+ D +D SNL RQ + + VG+SKAQ
Sbjct: 40 LKNARVLVIGAGGLGSPTLLYLAAAGVGTLGIVEFDVVDESNLQRQVIHGQSDVGRSKAQ 99
Query: 77 VARNSALNFNPDANI 91
AR+S + NP N+
Sbjct: 100 SARDSIVEINPLVNV 114
Score = 57.4 bits (139), Expect = 1e-08
Identities = 35/116 (30%), Positives = 51/116 (43%), Gaps = 8/116 (6%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
L RQ + + VG+SKAQ AR+S + NP N+ H + V F Q+ L+++
Sbjct: 82 LQRQVIHGQSDVGRSKAQSARDSIVEINPLVNVRLHEFR-LDPSNAVELFSQYDLILDGT 140
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAGYEGQV----ELIKKGETKCYEC---DPKP 252
DN A R VN + + P + +EGQ E G Y +P P
Sbjct: 141 DNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGLNYRDLYPEPPP 196
>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 = 71.0 bits (174), Expect = 9e-14
Identities = 30/83 (36%), Positives = 51/83 (61%)
Query: 9 FEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQ 68
F+ D ++ +K S+VL+VG GG+GC + L +G N+ ++D DT+ +SNL RQ L
Sbjct: 14 FDFDGQEALKASRVLIVGLGGLGCAASQYLAAAGVGNLTLLDFDTVSLSNLQRQVLHSDA 73
Query: 69 HVGKSKAQVARNSALNFNPDANI 91
++G+ K + A+++ NP I
Sbjct: 74 NIGQPKVESAKDALTQINPHIAI 96
Score = 61.0 bits (148), Expect = 2e-10
Identities = 30/107 (28%), Positives = 51/107 (47%), Gaps = 2/107 (1%)
Query: 143 HLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNA 202
+L RQ L ++G+ K + A+++ NP I + + A+ + +V++
Sbjct: 63 NLQRQVLHSDANIGQPKVESAKDALTQINPHIAINPINAKLDDAELA-ALIAEHDIVVDC 121
Query: 203 LDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIK-KGETKCYEC 248
DN RN +NR C A++VPL+ EGQV + + CY C
Sbjct: 122 TDNVEVRNQLNRQCFAAKVPLVSGAAIRMEGQVSVFTYQDGEPCYRC 168
>gnl|CDD|235528 PRK05600, PRK05600, thiamine biosynthesis protein ThiF; Validated.
Length = 370
Score = 71.4 bits (175), Expect = 3e-13
Identities = 30/72 (41%), Positives = 46/72 (63%)
Query: 20 SKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVAR 79
++VLV+GAGG+GC +++L +G I ++D DT+DVSN++RQ LF VG+ K +VA
Sbjct: 42 ARVLVIGAGGLGCPAMQSLASAGVGTITLIDDDTVDVSNIHRQILFGASDVGRPKVEVAA 101
Query: 80 NSALNFNPDANI 91
PD +
Sbjct: 102 ERLKEIQPDIRV 113
Score = 41.8 bits (98), Expect = 0.001
Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 1/99 (1%)
Query: 143 HLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNA 202
+++RQ LF VG+ K +VA PD + A ++A+ V LV++
Sbjct: 80 NIHRQILFGASDVGRPKVEVAAERLKEIQPDIRVNALRER-LTAENAVELLNGVDLVLDG 138
Query: 203 LDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKG 241
D+ A + V + PL+ + G++ + G
Sbjct: 139 SDSFATKFLVADAAEITGTPLVWGTVLRFHGELAVFNSG 177
>gnl|CDD|180967 PRK07411, PRK07411, hypothetical protein; Validated.
Length = 390
Score = 70.9 bits (174), Expect = 6e-13
Identities = 36/85 (42%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
+K + VL +G GG+G LL L +G I IVD D +D SNL RQ + VGK K +
Sbjct: 36 LKAASVLCIGTGGLGSPLLLYLAAAGIGRIGIVDFDVVDSSNLQRQVIHGTSWVGKPKIE 95
Query: 77 VARNSALNFNPDANIYYQVDFHLNR 101
A+N L NP Y QVD + R
Sbjct: 96 SAKNRILEINP----YCQVDLYETR 116
Score = 40.5 bits (95), Expect = 0.002
Identities = 30/126 (23%), Positives = 52/126 (41%), Gaps = 5/126 (3%)
Query: 138 IIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFT 197
++ +L RQ + VGK K + A+N L NP + + T +S++ ++ +
Sbjct: 72 VVDSSNLQRQVIHGTSWVGKPKIESAKNRILEINPYCQVDLYETR-LSSENALDILAPYD 130
Query: 198 LVMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCYEC---DPKPAA 254
+V++ DN R VN C+ P + +EGQ + Y +P P
Sbjct: 131 VVVDGTDNFPTRYLVNDACVLLNKPNVYGSIFRFEGQATVFNYEGGPNYRDLYPEPPPPG 190
Query: 255 KTYPGC 260
P C
Sbjct: 191 MV-PSC 195
>gnl|CDD|180204 PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB;
Provisional.
Length = 245
Score = 67.9 bits (167), Expect = 1e-12
Identities = 29/74 (39%), Positives = 42/74 (56%)
Query: 18 KKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQV 77
K ++VLVVG GG+GC + L +G + +VD DT+ +SNL RQ L +G+ K +
Sbjct: 31 KAARVLVVGLGGLGCAASQYLAAAGVGTLTLVDFDTVSLSNLQRQVLHDDATIGQPKVES 90
Query: 78 ARNSALNFNPDANI 91
AR + NP I
Sbjct: 91 ARAALARINPHIAI 104
Score = 62.2 bits (152), Expect = 1e-10
Identities = 35/107 (32%), Positives = 50/107 (46%), Gaps = 4/107 (3%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
L RQ L +G+ K + AR + NP I + + D LV++
Sbjct: 72 LQRQVLHDDATIGQPKVESARAALARINPHIAIETI-NARLDDDELAALIAGHDLVLDCT 130
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAG-YEGQVELIK-KGETKCYEC 248
DN A RN +NR C A++ PL+ SG A EGQV + + + CY C
Sbjct: 131 DNVATRNQLNRACFAAKKPLV-SGAAIRMEGQVTVFTYQDDEPCYRC 176
>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 = 62.8 bits (153), Expect = 2e-11
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVARN 80
KV + GAGG+G + L SG N+++VD D ++ SNLNRQ F +G+ K + +
Sbjct: 1 KVGIAGAGGLGSNIAVLLARSGVGNLKLVDFDVVEPSNLNRQQYF-LSQIGEPKVEALKE 59
Query: 81 SALNFNPDANI 91
+ NP I
Sbjct: 60 NLREINPFVKI 70
Score = 35.0 bits (81), Expect = 0.056
Identities = 31/121 (25%), Positives = 48/121 (39%), Gaps = 17/121 (14%)
Query: 138 IIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFT 197
++ +LNRQ F +G+ K + + + NP I A + I + F
Sbjct: 33 VVEPSNLNRQQYF-LSQIGEPKVEALKENLREINPFVKIEAINIKIDENNL-EGLFGDCD 90
Query: 198 LVMNALDNRAARNHVNRMCLASEV------PLI-ESGTAGYEGQVELI--KKGETKCYEC 248
+V+ A DN + M LA + P++ SG AG+ G I KK Y C
Sbjct: 91 IVVEAFDNAETK----AM-LAESLLGNKNKPVVCASGMAGF-GDSNNIKTKKISDNFYIC 144
Query: 249 D 249
Sbjct: 145 G 145
>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 = 62.8 bits (153), Expect = 4e-11
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHV--GKSK 74
++ +KVL++GAG +G E+ KNLVL+G +I IVD + +L F + G ++
Sbjct: 17 LRSAKVLIIGAGALGAEIAKNLVLAGIDSITIVDHRLVSTEDLGSNFFLDAEVSNSGMNR 76
Query: 75 AQVARNSALNFNPDANI 91
A + NP+ +
Sbjct: 77 AAASYEFLQELNPNVKL 93
Score = 37.0 bits (86), Expect = 0.016
Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 5/124 (4%)
Query: 115 AQVARNSALNFNPDANIVAHHTSIIRFLHLNRQFLFHKQHV--GKSKAQVARNSALNFNP 172
A++A+N L IV H L F + G ++A + NP
Sbjct: 32 AEIAKNLVLAGIDSITIVDHRLVSTE--DLGSNFFLDAEVSNSGMNRAAASYEFLQELNP 89
Query: 173 DANIVAHHTSIISADFGVN-YFKQFTLVMNALDNRAARNHVNRMCLASEVPLIESGTAGY 231
+ + +S D + Y ++FTLV+ +N VN +C +P I T G
Sbjct: 90 NVKLSIVEEDSLSNDSNIEEYLQKFTLVIATEENYERTAKVNDVCRKHHIPFISCATYGL 149
Query: 232 EGQV 235
G
Sbjct: 150 IGYA 153
>gnl|CDD|235526 PRK05597, PRK05597, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 355
Score = 63.4 bits (154), Expect = 1e-10
Identities = 33/76 (43%), Positives = 47/76 (61%)
Query: 20 SKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVAR 79
+KV V+GAGG+G L L +G +I I+D DT+D+SNL+RQ + VG+ KA+ AR
Sbjct: 29 AKVAVIGAGGLGSPALLYLAGAGVGHITIIDDDTVDLSNLHRQVIHSTAGVGQPKAESAR 88
Query: 80 NSALNFNPDANIYYQV 95
+ L NPD + V
Sbjct: 89 EAMLALNPDVKVTVSV 104
Score = 33.3 bits (76), Expect = 0.38
Identities = 28/123 (22%), Positives = 53/123 (43%), Gaps = 9/123 (7%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
L+RQ + VG+ KA+ AR + L NPD + ++ ++ + ++++
Sbjct: 68 LHRQVIHSTAGVGQPKAESAREAMLALNPDVKVTV-SVRRLTWSNALDELRDADVILDGS 126
Query: 204 DNRAARNHVNRMCLAS-EVPLIESGTAGYEGQVELIKKGETKCYE----CDPKPAAKTYP 258
DN R H+ A +P + + G++ Q+ + G YE P P + P
Sbjct: 127 DNFDTR-HLASWAAARLGIPHVWASILGFDAQLSVFHAGHGPIYEDLFPTPPPPGS--VP 183
Query: 259 GCT 261
C+
Sbjct: 184 SCS 186
>gnl|CDD|236337 PRK08762, PRK08762, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 376
Score = 63.1 bits (154), Expect = 2e-10
Identities = 27/69 (39%), Positives = 37/69 (53%)
Query: 20 SKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVAR 79
++VL++GAGG+G L +G + IVD D +D SNL RQ L + VG+ K A
Sbjct: 136 ARVLLIGAGGLGSPAALYLAAAGVGTLGIVDHDVVDRSNLQRQILHTEDRVGQPKVDSAA 195
Query: 80 NSALNFNPD 88
NPD
Sbjct: 196 QRLAALNPD 204
Score = 56.9 bits (138), Expect = 2e-08
Identities = 33/125 (26%), Positives = 50/125 (40%), Gaps = 9/125 (7%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMNAL 203
L RQ L + VG+ K A NPD + A +++D + +V++
Sbjct: 175 LQRQILHTEDRVGQPKVDSAAQRLAALNPDVQVEAVQER-VTSDNVEALLQDVDVVVDGA 233
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETK----CYEC---DPKPAAKT 256
DN R +N C+ PL+ +EGQV + G + CY C +P P
Sbjct: 234 DNFPTRYLLNDACVKLGKPLVYGAVFRFEGQVSVFDAGRQRGQAPCYRCLFPEPPPPELA 293
Query: 257 YPGCT 261
P C
Sbjct: 294 -PSCA 297
>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 = 57.3 bits (139), Expect = 1e-08
Identities = 25/74 (33%), Positives = 37/74 (50%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
++ + V ++ A G E+LKNLVL G + IVD +D +L F +GKS+A+
Sbjct: 18 LESAHVCLLNATATGTEILKNLVLPGIGSFTIVDGSKVDEEDLGNNFFLDASSLGKSRAE 77
Query: 77 VARNSALNFNPDAN 90
NPD N
Sbjct: 78 ATCELLQELNPDVN 91
>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 = 55.4 bits (134), Expect = 3e-08
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 7/95 (7%)
Query: 19 KSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVA 78
KS VL+ G GG+G E+ KNL+L+G ++ + D S+L+ QF ++ +GK++A+ +
Sbjct: 19 KSNVLISGLGGLGVEIAKNLILAGVKSVTLHDTKPCSWSDLSSQFYLREEDIGKNRAEAS 78
Query: 79 RNSALNFNPDANIYYQVDFH---LNRQFLFHKQHV 110
+ NP Y V L L Q V
Sbjct: 79 QARLAELNP----YVPVTVSTGPLTTDELLKFQVV 109
Score = 31.5 bits (72), Expect = 1.5
Identities = 18/102 (17%), Positives = 42/102 (41%), Gaps = 5/102 (4%)
Query: 134 HHTSIIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYF 193
H T + L+ QF ++ +GK++A+ ++ NP + + + +
Sbjct: 49 HDTKPCSWSDLSSQFYLREEDIGKNRAEASQARLAELNPYVPVTVSTGPLTT-----DEL 103
Query: 194 KQFTLVMNALDNRAARNHVNRMCLASEVPLIESGTAGYEGQV 235
+F +V+ + + +N C + + I + T G G +
Sbjct: 104 LKFQVVVLTDASLEDQLKINEFCHSPGIKFISADTRGLFGSI 145
>gnl|CDD|185071 PRK15116, PRK15116, sulfur acceptor protein CsdL; Provisional.
Length = 268
Score = 55.2 bits (133), Expect = 3e-08
Identities = 26/82 (31%), Positives = 42/82 (51%)
Query: 16 LIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKA 75
L + + VVG GG+G + L +G I ++D+D + V+N NRQ + +VG +KA
Sbjct: 27 LFADAHICVVGIGGVGSWAAEALARTGIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKA 86
Query: 76 QVARNSALNFNPDANIYYQVDF 97
+V NP+ + DF
Sbjct: 87 EVMAERIRQINPECRVTVVDDF 108
Score = 39.4 bits (92), Expect = 0.004
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 4/93 (4%)
Query: 145 NRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQ-FTLVMNAL 203
NRQ + +VG +KA+V NP+ + I+ D Y F+ V++A+
Sbjct: 71 NRQIHALRDNVGLAKAEVMAERIRQINPECRVTV-VDDFITPDNVAEYMSAGFSYVIDAI 129
Query: 204 DNRAARNHVNRMCLASEVPLIESGTAGYEGQVE 236
D+ + + C +++PL+ +G AG GQ++
Sbjct: 130 DSVRPKAALIAYCRRNKIPLVTTGGAG--GQID 160
>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 = 52.9 bits (127), Expect = 7e-08
Identities = 40/186 (21%), Positives = 74/186 (39%), Gaps = 23/186 (12%)
Query: 13 LEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGK 72
+ ++++ V + G GG+G + NL +G + +VD D ++ SNLNRQ VG+
Sbjct: 15 IVQKLEQATVAICGLGGLGSNVAINLARAGIGKLILVDFDVVEPSNLNRQQYKAS-QVGE 73
Query: 73 SKAQVARNSALNFNP--DANIYYQVDFHLNRQFLFHKQHV-------GKSKAQVARNSAL 123
K + + + NP + Y + N F + ++KA + N+ L
Sbjct: 74 PKTEALKENISEINPYTEIEAYDEKITEENIDKFFKDADIVCEAFDNAEAKAMLV-NAVL 132
Query: 124 NFNPDANIVA-------HHTSIIRFLHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANI 176
D ++A + I+ +++ F G K+ + L P I
Sbjct: 133 EKYKDKYLIAASGLAGYDDANSIKTRKISKHFYL----CGDGKSDAKQGLGL-MAPRVQI 187
Query: 177 VAHHTS 182
A H +
Sbjct: 188 CAAHQA 193
>gnl|CDD|169382 PRK08328, PRK08328, hypothetical protein; Provisional.
Length = 231
Score = 53.3 bits (128), Expect = 1e-07
Identities = 31/85 (36%), Positives = 48/85 (56%), Gaps = 1/85 (1%)
Query: 8 VFEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHK 67
+F + ++ +KK+KV VVG GG+G + L +G I ++D T ++SNLNRQ L +
Sbjct: 16 IFGVEGQEKLKKAKVAVVGVGGLGSPVAYYLAAAGVGRILLIDEQTPELSNLNRQILHWE 75
Query: 68 QHVGK-SKAQVARNSALNFNPDANI 91
+ +GK K A+ FN D I
Sbjct: 76 EDLGKNPKPLSAKWKLERFNSDIKI 100
Score = 40.5 bits (95), Expect = 0.001
Identities = 33/116 (28%), Positives = 49/116 (42%), Gaps = 3/116 (2%)
Query: 143 HLNRQFLFHKQHVGK-SKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMN 201
+LNRQ L ++ +GK K A+ FN D I +S + K ++++
Sbjct: 66 NLNRQILHWEEDLGKNPKPLSAKWKLERFNSDIKIETF-VGRLSEENIDEVLKGVDVIVD 124
Query: 202 ALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCY-ECDPKPAAKT 256
LDN R ++ +PL+ G GQV I G+TK E PK K
Sbjct: 125 CLDNFETRYLLDDYAHKKGIPLVHGAVEGTYGQVTTIVPGKTKRLREIFPKVKKKK 180
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 52.7 bits (127), Expect = 3e-07
Identities = 20/54 (37%), Positives = 33/54 (61%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHV 70
+++ VL++GAG +G + LV +G + IVD D ++ SNL RQ L+ + V
Sbjct: 22 LREKHVLIIGAGALGTANAEMLVRAGVGKVTIVDRDYVEWSNLQRQQLYTESDV 75
>gnl|CDD|181302 PRK08223, PRK08223, hypothetical protein; Validated.
Length = 287
Score = 51.6 bits (124), Expect = 5e-07
Identities = 23/75 (30%), Positives = 35/75 (46%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQ 76
++ S+V + G GG+G L L G I D D ++ N NRQ +G+ KA+
Sbjct: 25 LRNSRVAIAGLGGVGGIHLLTLARLGIGKFTIADFDVFELRNFNRQAGAMMSTLGRPKAE 84
Query: 77 VARNSALNFNPDANI 91
V + NP+ I
Sbjct: 85 VLAEMVRDINPELEI 99
Score = 28.9 bits (65), Expect = 9.4
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 144 LNRQFLFHKQHVGKSKAQVARNSALNFNPDANI 176
NRQ +G+ KA+V + NP+ I
Sbjct: 67 FNRQAGAMMSTLGRPKAEVLAEMVRDINPELEI 99
>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
Length = 679
Score = 52.2 bits (125), Expect = 8e-07
Identities = 26/81 (32%), Positives = 41/81 (50%)
Query: 7 GVFEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFH 66
G+F ++ + ++KV + G GG+G L +V +G I D D + N+NRQF
Sbjct: 31 GLFTPGEQERLAEAKVAIPGMGGVGGVHLITMVRTGIGRFHIADFDQFEPVNVNRQFGAR 90
Query: 67 KQHVGKSKAQVARNSALNFNP 87
G+ K V + AL+ NP
Sbjct: 91 VPSFGRPKLAVMKEQALSINP 111
>gnl|CDD|183547 PRK12475, PRK12475, thiamine/molybdopterin biosynthesis MoeB-like
protein; Provisional.
Length = 338
Score = 46.6 bits (111), Expect = 3e-05
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 17 IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVG--KSK 74
I++ VL+VGAG +G + LV +G + I D D ++ SNL RQ L+ ++ K K
Sbjct: 22 IREKHVLIVGAGALGAANAEALVRAGIGKLTIADRDYVEWSNLQRQQLYTEEDAKQKKPK 81
Query: 75 AQVARNSALNFNPDANI 91
A A+ N + I
Sbjct: 82 AIAAKEHLRKINSEVEI 98
Score = 33.9 bits (78), Expect = 0.29
Identities = 29/107 (27%), Positives = 44/107 (41%), Gaps = 3/107 (2%)
Query: 144 LNRQFLFHKQHVG--KSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMN 201
L RQ L+ ++ K KA A+ N + IV T + + K+ L+++
Sbjct: 64 LQRQQLYTEEDAKQKKPKAIAAKEHLRKINSEVEIVPVVTDVTVEELE-ELVKEVDLIID 122
Query: 202 ALDNRAARNHVNRMCLASEVPLIESGTAGYEGQVELIKKGETKCYEC 248
A DN R +N + +P I G G G I G+T C C
Sbjct: 123 ATDNFDTRLLINDLSQKYNIPWIYGGCVGSYGVTYTIIPGKTPCLRC 169
>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 = 46.2 bits (110), Expect = 3e-05
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHV--GKSKAQVA 78
K L++GAG +GC + +NL+ G +I VD + SN RQ LF + GK KA+ A
Sbjct: 1 KCLLLGAGTLGCNVARNLLGWGVRHITFVDSGKVSYSNPVRQSLFTFEDCKGGKPKAEAA 60
Query: 79 RNSALNFNPDAN 90
P +
Sbjct: 61 AERLKEIFPSID 72
>gnl|CDD|184854 PRK14852, PRK14852, hypothetical protein; Provisional.
Length = 989
Score = 45.8 bits (108), Expect = 8e-05
Identities = 25/73 (34%), Positives = 35/73 (47%)
Query: 19 KSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQVA 78
+S+V + G GG+G L L +G N + D D NLNRQ+ G+ K V
Sbjct: 332 RSRVAIAGLGGVGGIHLMTLARTGIGNFNLADFDAYSPVNLNRQYGASIASFGRGKLDVM 391
Query: 79 RNSALNFNPDANI 91
AL+ NP +I
Sbjct: 392 TERALSVNPFLDI 404
Score = 29.3 bits (65), Expect = 9.1
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 3/92 (3%)
Query: 142 LHLNRQFLFHKQHVGKSKAQVARNSALNFNPDANIVAHHTSIISADFGVNYFKQFTLVMN 201
++LNRQ+ G+ K V AL+ NP +I + + + + K L+++
Sbjct: 370 VNLNRQYGASIASFGRGKLDVMTERALSVNPFLDIRSFPEGVAAETIDA-FLKDVDLLVD 428
Query: 202 ALDNRA--ARNHVNRMCLASEVPLIESGTAGY 231
+D A R + L +P+I +G GY
Sbjct: 429 GIDFFALDIRRRLFNRALELGIPVITAGPLGY 460
>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 = 44.2 bits (104), Expect = 3e-04
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 15 DLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHV---G 71
+ + KVL++GAG +GC + + L+ G +I VD + SN RQ L + + G
Sbjct: 334 ERYSQLKVLLLGAGTLGCNVARCLIGWGVRHITFVDNGKVSYSNPVRQSLSNFEDCLLGG 393
Query: 72 KSKAQVARNS 81
+ KA+ A+ +
Sbjct: 394 RGKAETAQKA 403
>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 = 39.3 bits (92), Expect = 0.004
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 16 LIKKSKVLVVGAGGIGCELLKNLVL-----------SGFSNIEIVDLDTIDVSNLNRQFL 64
L + V++VGAGG G +++ L G + + + D DT+ +N+ RQ
Sbjct: 8 LSRPVSVVLVGAGGTGSQVIAGLARLHHALKALGHPGGLA-VTVYDDDTVSEANVGRQ-A 65
Query: 65 FHKQHVGKSKAQV 77
F+ VG++KA V
Sbjct: 66 FYPADVGQNKAIV 78
>gnl|CDD|178402 PLN02805, PLN02805, D-lactate dehydrogenase [cytochrome].
Length = 555
Score = 34.2 bits (78), Expect = 0.29
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 356 ANGDVVRTSTRAWASACGYDPRKL 379
NGDVV+T++RA SA GYD +L
Sbjct: 263 PNGDVVKTASRARKSAAGYDLTRL 286
>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 = 32.3 bits (74), Expect = 0.35
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 11 KDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIV 49
K + +K KVL++GAG + K+L+ G I I
Sbjct: 4 KKIFGDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIA 42
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(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 DH, 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 = 311
Score = 33.0 bits (76), Expect = 0.49
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 15 DLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIV 49
+K KVLV+GAG +G K+L G + I I
Sbjct: 174 GNLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIA 208
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 33.0 bits (76), Expect = 0.62
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 11 KDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIV 49
K + +K KVLV+GAG +G + K+L G I I
Sbjct: 170 KRIFGSLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIA 208
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (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 DH, 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 = 86
Score = 30.0 bits (68), Expect = 0.75
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 11 KDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTI 54
K +K V+V+GAG +G + K L G + + D D +
Sbjct: 15 KVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCDRDIL 58
>gnl|CDD|147759 pfam05782, ECM1, Extracellular matrix protein 1 (ECM1). This
family consists of several eukaryotic extracellular
matrix protein 1 (ECM1) sequences. ECM1 has been shown
to regulate endochondral bone formation, stimulate the
proliferation of endothelial cells and induce
angiogenesis. Mutations in the ECM1 gene can cause
lipoid proteinosis, a disorder which causes generalised
thickening of skin, mucosae and certain viscera.
Classical features include beaded eyelid papules and
laryngeal infiltration leading to hoarseness.
Length = 419
Score = 31.9 bits (72), Expect = 1.1
Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 7/91 (7%)
Query: 628 PLEHGLIISHRVSARDGPEFEILDQKDLPQPPAPDAAASTTDAAEEKMETNGNGNGDVGT 687
PL L + H V+++ P FE Q ++ PP+P+ EE T N N D
Sbjct: 54 PLSRRLPVDHPVTSQHDPPFE--GQSEVQPPPSPED----IPVYEEDWPTFLNPNVDKAG 107
Query: 688 PDSKKRKVDSSDESLPAKKVRTDEKSTDKVP 718
P + + E LP +V ++K P
Sbjct: 108 PAVPQEAIPLQKE-LPPPQVPIEQKEVKPAP 137
>gnl|CDD|211992 TIGR04269, SAM_SPASM_FxsB, radical SAM/SPASM domain, FxsB family.
This model describes a radical SAM (pfam04055)/SPASM
domain (TIGR04085) fusion subfamily distinct from PqqE,
MftC, anaerobic sulfatase maturases, and other peptide
maturases. The combined region described in this model
can itself be fused to another domain, such as
TIGR04267, or stand alone. Members occurring in the same
cassette as a member of family TIGR04268 should be
designated FxsB.
Length = 363
Score = 31.6 bits (72), Expect = 1.3
Identities = 29/112 (25%), Positives = 47/112 (41%), Gaps = 8/112 (7%)
Query: 376 PRKLFAKFFDADIRYLISMSDLWKTRKAPQPL-VWDTLSDAVAGSSKETDGGGLKDQRVW 434
PR+ A R+L+++ D W P P+ +D+L + G T+ GL +
Sbjct: 205 PRRAPDGSPTAYARWLLAVFDRWLADGRPMPVRTFDSLLSTLRGGPSLTEALGLGPVDLA 264
Query: 435 SVAECARVFERSVRELKTKFDAAVEKDEHLVWDKDDKPAMDFVAACANIRAH 486
+ E +E+ + LK +D A V+D +D VAA I A
Sbjct: 265 VI-ETDGTYEQ-LDSLKVAYDGAPATGGD-VFDH----TIDEVAAHPGIAAR 309
>gnl|CDD|172521 PRK14027, PRK14027, quinate/shikimate dehydrogenase; Provisional.
Length = 283
Score = 31.5 bits (71), Expect = 1.5
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 9 FEKDLEDLIKKSK---VLVVGAGGIGCELLKNLVLSGFSNIEIVDLDT 53
F + +E+ + +K V+ VGAGG+G + LV G +++ DLDT
Sbjct: 114 FGRGMEEGLPNAKLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLDT 161
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 31.5 bits (71), Expect = 1.5
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 3/69 (4%)
Query: 657 QPPAPDAAASTTDAAEEKMETNGNGN---GDVGTPDSKKRKVDSSDESLPAKKVRTDEKS 713
+ + AA+ +A + G G D K + +DE V+ ++
Sbjct: 297 EREPAELAAAAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAESVVQVADRD 356
Query: 714 TDKVPEVEE 722
+ P VEE
Sbjct: 357 GESTPAVEE 365
Score = 30.3 bits (68), Expect = 3.7
Identities = 21/92 (22%), Positives = 33/92 (35%), Gaps = 2/92 (2%)
Query: 607 EASGSVIISSEEGETEANNDKPLEHGLIISHRVSARDGPEFEILDQKDLPQPPAPDAAAS 666
E S + I + G+ P H + +A + P + D +P P+ AA
Sbjct: 365 ETSEADIEREQPGDLAG--QAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAP 422
Query: 667 TTDAAEEKMETNGNGNGDVGTPDSKKRKVDSS 698
D A+ D PD +R+ D S
Sbjct: 423 IPDPAKPDELAVAGPGDDPAEPDGIRRQDDFS 454
>gnl|CDD|100021 cd02201, FtsZ_type1, FtsZ is a GTPase that is similar to the
eukaryotic tubulins and is essential for cell division
in prokaryotes. FtsZ is capable of polymerizing in a
GTP-driven process into structures similar to those
formed by tubulin. FtsZ forms a ring-shaped septum at
the site of bacterial cell division, which is required
for constriction of cell membrane and cell envelope to
yield two daughter cells.
Length = 304
Score = 31.3 bits (72), Expect = 1.9
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 12/57 (21%)
Query: 21 KVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQV 77
K+ V+G GG G + ++ SG +E + +T D Q + KSKA
Sbjct: 2 KIKVIGVGGGGGNAVNRMIESGLEGVEFIAANT-DA-----------QALAKSKAPN 46
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 31.1 bits (71), Expect = 2.0
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 19 KSKVLVVGAGGIGCELLKNLVLSGFSNIEIVD 50
K+LV+GAGG+G + L +G + I D
Sbjct: 1 MMKILVIGAGGVGSVVAHKLAQNGDGEVTIAD 32
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 31.3 bits (72), Expect = 2.1
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 10 EKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIV 49
++ DL KVLV+GAG +G + K+L G I +
Sbjct: 174 KQIFGDL-SGKKVLVIGAGEMGELVAKHLAEKGVRKITVA 212
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 322
Score = 31.0 bits (71), Expect = 2.1
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 22/65 (33%)
Query: 6 PGVFEKDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFS----------------NIEIV 49
G+ ++L +L V V+G G IG ++KN LSGF E V
Sbjct: 134 GGLQGRELRNLT----VGVIGTGRIGQAVIKN--LSGFGCKILAYDPYPNEEVKKYAEYV 187
Query: 50 DLDTI 54
DLDT+
Sbjct: 188 DLDTL 192
>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 = 31.0 bits (71), Expect = 2.3
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 11 KDLEDLIKKSKVLVVGAGGIG---CELLKNLVLSGFSNIEIVDLD 52
K L L+ V+++GAGG+G LLK L G +NI +VD+D
Sbjct: 168 KKLMPLVADEPVVIIGAGGLGLMALALLKAL---GPANIIVVDID 209
>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 = 2.4
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 22 VLVVGAGGIGCELLKNLVLSGFSNIEIVD 50
VL++GAGG+G + L G I + D
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVAD 29
>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 = 30.8 bits (70), Expect = 2.6
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 10/40 (25%)
Query: 5 IPGV---FEKDLED-------LIKKSKVLVVGAGGIGCEL 34
IPGV + + D L +V+VVG G IG EL
Sbjct: 118 IPGVEVATLRGVIDSDEILELLELPKRVVVVGGGYIGLEL 157
>gnl|CDD|214779 smart00700, JHBP, Juvenile hormone binding protein domains in
insects. The juvenile hormone exerts pleiotropic
functions during insect life cycles and its binding
proteins regulate these functions.
Length = 224
Score = 30.3 bits (69), Expect = 2.9
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 1 MATKIPGVFEKDLEDLIKKSKVLVVGAGGIGCEL-LKNLVLSGFSNIEIVD--LDTIDVS 57
+ IP L+ L + + +G IG L KN+ + G SN EI +D D
Sbjct: 30 LKNGIPEYGIPPLDPLEIDDLKISIDSGVIGLRLTFKNVKIYGLSNFEITKFKMDLKDKK 89
>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 = 29.5 bits (67), Expect = 3.7
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 9 FEKDLEDL---IKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVD 50
F + LE+ +K KVL++GAGG + L G + I IV+
Sbjct: 6 FVRALEEAGIELKGKKVLILGAGGAARAVAYALAELGAAKIVIVN 50
>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 = 27.9 bits (63), Expect = 3.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 21 KVLVVGAGGIGCEL 34
+V+VVG G IG E
Sbjct: 1 RVVVVGGGYIGLEF 14
>gnl|CDD|219095 pfam06585, JHBP, Haemolymph juvenile hormone binding protein
(JHBP). This family consists of several insect-specific
haemolymph juvenile hormone binding proteins (JHBP).
Juvenile hormone regulates embryogenesis, maintains the
status quo of larval development and stimulates
reproductive maturation in the adult insect. JH is
transported from the sites of its synthesis to target
tissues by a haemolymph carrier called juvenile
hormone-binding protein (JHBP). JHBP protects the JH
molecules from hydrolysis by non-specific esterases
present in the insect haemolymph. The crystal structure
of the JHBP from Galleria mellonella shows an unusual
fold consisting of a long alpha-helix wrapped in a much
curved antiparallel beta-sheet. The folding pattern for
this structure closely resembles that found in some
tandem-repeat mammalian lipid-binding and bactericidal
permeability-increasing proteins, with a similar
organisation of the major cavity and a disulfide bond
linking the long helix and the beta-sheet. It would
appear that JHBP forms two cavities, only one of which,
the one near the N- and C-termini, binds the hormone;
binding induces a conformational change, of unknown
significance. This family now includes DUF233,
pfam03027.
Length = 246
Score = 30.0 bits (68), Expect = 3.9
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 1 MATKIPGVFEKDLEDLIKKSKVLVVGAGGIGCEL-LKNLVLSGFSNIEIVDLDTIDVSNL 59
+A IP + L+ L+ + G+G IG + KNL + G SN I L +
Sbjct: 52 LAKGIPELGIPPLDPLVIDDLKISQGSGPIGLKANFKNLKIYGLSNFTIKKL---KLDLD 108
Query: 60 NRQFLFH 66
+F
Sbjct: 109 KLKFELK 115
>gnl|CDD|232805 TIGR00065, ftsZ, cell division protein FtsZ. This family
consists of cell division protein FtsZ, a GTPase found
in bacteria, the chloroplast of plants, and in
archaebacteria. Structurally similar to tubulin, FtsZ
undergoes GTP-dependent polymerization into filaments
that form a cytoskeleton involved in septum synthesis
[Cellular processes, Cell division].
Length = 349
Score = 30.0 bits (68), Expect = 4.7
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 12/59 (20%)
Query: 19 KSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHVGKSKAQV 77
K+K+ V+G GG G + ++ G +E + ++T QH+ +KA
Sbjct: 17 KAKIKVIGVGGGGNNTVNRMLEEGVEGVEFIAINT------------DAQHLKTTKADK 63
>gnl|CDD|193256 pfam12780, AAA_8, P-loop containing dynein motor region D4. The
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D4 ATP-binding region of
the motor.
Length = 268
Score = 29.9 bits (67), Expect = 4.9
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 386 ADIRYLISMSDLWKTRKAPQPLVWDTLSDAVAGSSKETDGGGLKDQRVWSVAECARVF-E 444
AD ++L+ ++DL + + P + D + + ++ E GL D R C + F +
Sbjct: 101 ADEQFLVLINDLLASGEIPDLFMDDEVENIISSVRNEVKSLGLNDTR----ENCWKFFID 156
Query: 445 RSVRELKT 452
R R+LK
Sbjct: 157 RVRRQLKV 164
>gnl|CDD|132802 cd06892, PX_SNX5_like, The phosphoinositide binding Phox Homology
domain of Sorting Nexins 5 and 6. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. Members of this subfamily
include SNX5, SNX6, and similar proteins. They contain a
Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane
curvature, C-terminal to the PX domain, similar to other
sorting nexins including SNX1-2. The PX-BAR structural
unit helps determine the specific membrane-targeting of
some SNXs. SNX5 and SNX6 may be components of the
retromer complex, a membrane coat multimeric complex
required for endosomal retrieval of lysosomal hydrolase
receptors to the Golgi, acting as a mammalian equivalent
of yeast Vsp17p.
Length = 141
Score = 28.9 bits (65), Expect = 5.1
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 656 PQPPAPDAAASTTDAAEEKMETNGNGNGDVGTPDSKKRKVDSSDESLPAKK--VRTDEKS 713
P PP PD DA+ EK++ G G G + + +K K + E L K V E
Sbjct: 64 PAPPKPD-----FDASREKLQKLGEGEGSMTKEEFEKMKQELEAEYLAIFKKTVAMHEVF 118
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 29.9 bits (68), Expect = 5.3
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 21 KVLVVGAGGIGCELLKNLVLSG 42
+VLVVG G IG EL +L +G
Sbjct: 143 RVLVVGGGLIGTELAMDLCRAG 164
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 29.9 bits (68), Expect = 5.6
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 11 KDLEDLIKKSKVLVVGAGG-IGCELLKNLVLSGFSNIEIVD-----LDTIDVSNLNRQF 63
+ + ++ VLV G GG IG EL + ++ I + L ID L +F
Sbjct: 242 ELIGAMLTGKTVLVTGGGGSIGSELCRQILKFNPKEIILFSRDEYKLYLID-MELREKF 299
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 29.5 bits (67), Expect = 5.6
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 9 FEKDLEDLIKKSKVLVVGAGGIGCELLKNLV 39
E DL L++ S V +VGAGGIG L+ L
Sbjct: 115 EEDDLVTLLRGSTVAIVGAGGIGRALIPLLA 145
>gnl|CDD|173310 PTZ00005, PTZ00005, phosphoglycerate kinase; Provisional.
Length = 417
Score = 29.7 bits (67), Expect = 6.9
Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 32/110 (29%)
Query: 571 PQRTIGLDVTKMTVAEFEEAVLK-KTL---------NMS-------AMVDVMVEA--SGS 611
P +GLD ++ EF EA+L+ KT+ M AM+D +V+A G+
Sbjct: 308 PDGWMGLDAGPKSIEEFAEAILRAKTIVWNGPQGVFEMPNFAKGSIAMLDAVVKATEKGA 367
Query: 612 VII-----SSEEGETEANNDKPLEHGLIISHRVSARDGPEFEILDQKDLP 656
+ I ++ E +K +SH VS G E+L+ K+LP
Sbjct: 368 ITIVGGGDTASLVEKTGAANK-------VSH-VSTGGGASLELLEGKELP 409
>gnl|CDD|182519 PRK10526, PRK10526, acyl-CoA thioesterase II; Provisional.
Length = 286
Score = 29.3 bits (66), Expect = 7.1
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 627 KPLEHGLIISHRVSARDGPEFEILDQKDLPQPPAPDAAASTTDAA 671
+++G I + ++ PE QK +P PAPD S TD A
Sbjct: 93 AAIQNGKPIFYMTASFQAPEAGFEHQKTMPSAPAPDGLPSETDIA 137
>gnl|CDD|221866 pfam12935, Sec16_N, Vesicle coat trafficking protein Sec16
N-terminus. Sec16 is a multi-domain vesicle coat
protein. The overall function of Sec16 is in mediating
the movement of protein-cargo between the organelles of
the secretory pathway. Over-expression of truncated
mutants of only the N-terminus are lethal, and this
portion does not appear to be essential for function so
may act as a stabilising region.
Length = 246
Score = 29.1 bits (65), Expect = 7.3
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 3/74 (4%)
Query: 648 EILDQKDLPQPPAPDAAASTTDAAEEKMETNGNGNGDV--GTPDSKKRKVDSSDESLPAK 705
++LD P + + AS N G P+S+ + SS+E L A+
Sbjct: 106 QVLDSLG-LNPDSLSSPASAEPLDPTAQNEFSNVLAASTDGNPESESQSEPSSEEELAAR 164
Query: 706 KVRTDEKSTDKVPE 719
+D++S E
Sbjct: 165 AELSDDESESTPTE 178
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and have 2 tightly
bound zinc atoms per subunit. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 29.0 bits (66), Expect = 7.8
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 20 SKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLD 52
VLV GAG IG L + L L+G S + + + +
Sbjct: 161 DSVLVFGAGPIGLLLAQLLKLNGASRVTVAEPN 193
>gnl|CDD|223075 PHA03398, PHA03398, viral phosphatase superfamily protein;
Provisional.
Length = 303
Score = 29.1 bits (66), Expect = 8.3
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 186 ADFGVNYFKQFTLVMNALDN 205
GVNYFK TLV + N
Sbjct: 245 RKKGVNYFKTITLVDDLKSN 264
>gnl|CDD|140272 PTZ00245, PTZ00245, ubiquitin activating enzyme; Provisional.
Length = 287
Score = 28.9 bits (64), Expect = 9.8
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 1/82 (1%)
Query: 11 KDLEDLIKKSKVLVVGAGGIGCELLKNLVLSGFSNIEIVDLDTIDVSNLNRQFLFHKQHV 70
K + + + V + G G E KNLVL+G + + D + +++ +L +
Sbjct: 18 KSTQQQLMHTSVALHGVAGAAAEAAKNLVLAGVRAVAVADEGLVTDADVCTNYLMQGE-A 76
Query: 71 GKSKAQVARNSALNFNPDANIY 92
G ++ A + NP ++Y
Sbjct: 77 GGTRGARALGALQRLNPHVSVY 98
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
0.318 0.132 0.385
Gapped
Lambda K H
0.267 0.0886 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,425,986
Number of extensions: 3545752
Number of successful extensions: 3499
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3465
Number of HSP's successfully gapped: 150
Length of query: 726
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 622
Effective length of database: 6,324,786
Effective search space: 3934016892
Effective search space used: 3934016892
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (27.8 bits)