RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7301
(129 letters)
>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 = 197 bits (503), Expect = 7e-63
Identities = 85/149 (57%), Positives = 92/149 (61%), Gaps = 35/149 (23%)
Query: 1 MDFIVAASNLRAANYGITPADRHTSKLIAGKIIPAIATTTSVVAGLVCLELIKLAKGFTD 60
MDFI AASNLRA NY I PADRH +K IAGKIIPAIATTT+ V GLVCLEL K+ G
Sbjct: 287 MDFITAASNLRARNYSIPPADRHKTKRIAGKIIPAIATTTAAVTGLVCLELYKVVDGKRP 346
Query: 61 IEKYKNGFVNLALPFFGFSEPIAAPK------------DR-------------------- 88
+E YKN F+NLALPFF FSEPI APK DR
Sbjct: 347 LEAYKNAFLNLALPFFAFSEPIPAPKVKYAYDEEWTIWDRFEVKGKQTLQELLIDYFKEK 406
Query: 89 ---AITMLSQGVCMLYSYFMPPAKREERL 114
+TMLSQGV MLYS FMPPAK +ERL
Sbjct: 407 YGLEVTMLSQGVSMLYSSFMPPAKLKERL 435
>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 = 152 bits (385), Expect = 7e-44
Identities = 72/160 (45%), Positives = 88/160 (55%), Gaps = 36/160 (22%)
Query: 1 MDFIVAASNLRAANYGITPADRHTSKLIAGKIIPAIATTTSVVAGLVCLELIKLAKGFTD 60
+DFI AASNLRA NY I PADR +K IAGKIIPAIAT+T+ V+GLVCLELIK+ G
Sbjct: 816 IDFITAASNLRAKNYSIEPADRFKTKFIAGKIIPAIATSTATVSGLVCLELIKVTDGGYK 875
Query: 61 IEKYKNGFVNLALPFFGFSEPIAAPK------------DR-------------------- 88
E YKN F+NLA+P F F+EP K DR
Sbjct: 876 FEVYKNCFLNLAIPLFVFTEPTEVRKTKIRNGISFTIWDRWTLHGDFTLLEFINAVKEKY 935
Query: 89 --AITMLSQGVCMLYSYFMPPAKREERLNLPLVEVVRRSA 126
TM+SQGV +LY MP ERL L + ++V+ +
Sbjct: 936 GLEPTMVSQGVKLLYVPVMP--GHAERLKLKMHKLVKPTT 973
Score = 27.9 bits (62), Expect = 1.7
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 1 MDFIVAASNLRAANYGI-----TPADRHTSKLIAGKIIP 34
+ FI AA+ L A YGI + +++ IP
Sbjct: 714 LSFIQAAAKLYATVYGIPFAEEDLSADALLNILSEVKIP 752
>gnl|CDD|214955 smart00985, UBA_e1_C, Ubiquitin-activating enzyme e1 C-terminal
domain. This presumed domain found at the C terminus of
Ubiquitin-activating enzyme e1 proteins is functionally
uncharacterised.
Length = 128
Score = 97.3 bits (243), Expect = 3e-27
Identities = 44/96 (45%), Positives = 52/96 (54%), Gaps = 35/96 (36%)
Query: 64 YKNGFVNLALPFFGFSEPIAAPK------------DR----------------------- 88
YKN F+NLALPFF FSEPIAAPK DR
Sbjct: 1 YKNAFLNLALPFFAFSEPIAAPKTKYRDKDKWTLWDRLEVPGGDITLKELLDYFEEKYGL 60
Query: 89 AITMLSQGVCMLYSYFMPPAKREERLNLPLVEVVRR 124
+TMLSQGV +LYS FMPP K +ERL+LP+ E+V +
Sbjct: 61 EVTMLSQGVSLLYSSFMPPKKHKERLDLPVTELVEQ 96
>gnl|CDD|202124 pfam02134, UBACT, Repeat in ubiquitin-activating (UBA) protein.
Length = 66
Score = 93.0 bits (232), Expect = 3e-26
Identities = 37/57 (64%), Positives = 45/57 (78%)
Query: 1 MDFIVAASNLRAANYGITPADRHTSKLIAGKIIPAIATTTSVVAGLVCLELIKLAKG 57
+DF+ AA+NLRA NYGI PADR K IAG IIPAIATT ++VAG+V LEL+K+ G
Sbjct: 10 LDFVYAAANLRAQNYGIPPADRFDVKGIAGNIIPAIATTNAIVAGIVVLELLKILTG 66
>gnl|CDD|220201 pfam09358, UBA_e1_C, Ubiquitin-activating enzyme e1 C-terminal
domain. This presumed domain found at the C-terminus of
Ubiquitin-activating enzyme e1 proteins is functionally
uncharacterized.
Length = 124
Score = 86.1 bits (214), Expect = 5e-23
Identities = 43/94 (45%), Positives = 50/94 (53%), Gaps = 35/94 (37%)
Query: 64 YKNGFVNLALPFFGFSEPIAAPK-----------DR----------------------AI 90
Y+NGFVNLALPFF FSEPIAAPK DR +
Sbjct: 1 YRNGFVNLALPFFSFSEPIAAPKKKYNDKEFTIWDRWEVNGDLTLQELIDYFEEKYGLEV 60
Query: 91 TMLSQGVCMLYSYFMPPAKREERLNLPLVEVVRR 124
TMLSQGV +LYS F P K++ERLN P+ E+V
Sbjct: 61 TMLSQGVKLLYSSFPP--KKKERLNKPISELVEE 92
>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 = 73.0 bits (179), Expect = 8e-17
Identities = 25/52 (48%), Positives = 34/52 (65%)
Query: 1 MDFIVAASNLRAANYGITPADRHTSKLIAGKIIPAIATTTSVVAGLVCLELI 52
+ FI ASN RA+ Y I +K +AG+IIPA+ATT +VVAG+ LE+
Sbjct: 183 IQFIFQASNERASQYNIRGVTYFLTKGVAGRIIPAVATTNAVVAGVCALEVF 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 = 70.5 bits (173), Expect = 1e-15
Identities = 33/71 (46%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 1 MDFIVAASNLRAANYGITPADRHTSKLIAGKIIPAIATTTSVVAGLVCLELIKLAKGFTD 60
+DF+ AA+NLR+ +GI R K +AG IIPAIATT +++AGL+ LE +K+ G D
Sbjct: 220 LDFVAAAANLRSHVFGIPMKSRFDIKQMAGNIIPAIATTNAIIAGLIVLEALKVLSG--D 277
Query: 61 IEKYKNGFVNL 71
E+ + F+NL
Sbjct: 278 KEQCRTVFLNL 288
>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 = 49.7 bits (119), Expect = 4e-08
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 1 MDFIVAASNLRAANYGITPADRHTSKLIAGKIIPAIATTTSVVAGLVCLELIKLAKGFTD 60
++++ + RAA + I+ ++ + +IIPA+A+T +++A CLE +K+A TD
Sbjct: 201 IEWLYQKALERAAQFNISGVTYSLTQGVVKRIIPAVASTNAIIAAACCLEALKIA---TD 257
Query: 61 IEKYKNGFVN 70
+ N ++
Sbjct: 258 CYENLNNYLM 267
>gnl|CDD|237272 PRK13017, PRK13017, dihydroxy-acid dehydratase; Provisional.
Length = 596
Score = 28.8 bits (65), Expect = 0.86
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 11 RAANYGITPADRHTSKLIAGKIIPAIATTTS 41
R NYG+T + L +GK I IA T S
Sbjct: 32 RYMNYGLTREE-----LQSGKPIIGIAQTGS 57
>gnl|CDD|163144 TIGR03123, one_C_unchar_1, probable H4MPT-linked C1 transfer
pathway protein. This protein family was identified, by
the method of partial phylogenetic profiling, as related
to the use of tetrahydromethanopterin (H4MPT) as a C-1
carrier. Characteristic markers of the H4MPT-linked C1
transfer pathway include formylmethanofuran
dehydrogenase subunits, methenyltetrahydromethanopterin
cyclohydrolase, etc. Tetrahydromethanopterin, a
tetrahydrofolate analog, occurs in methanogenic archaea,
bacterial methanotrophs, planctomycetes, and a few other
lineages [Central intermediary metabolism, One-carbon
metabolism].
Length = 318
Score = 27.7 bits (62), Expect = 1.9
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 14/66 (21%)
Query: 7 ASNLRAANYGITPADRHTSKLIAGKIIPAI-----ATTTSVVAGLVCLELIKLAKGFTDI 61
++ AAN+ T++LIA +I + +TTT ++ ++ AKG TD+
Sbjct: 108 PLDVAAANW------LATAQLIAKRIPECLFVDMGSTTTDII---PIIDGEVAAKGKTDL 158
Query: 62 EKYKNG 67
E+ K G
Sbjct: 159 ERLKTG 164
>gnl|CDD|143413 cd07094, ALDH_F21_LactADH-like, ALDH subfamily: NAD+-dependent,
lactaldehyde dehydrogenase, ALDH family 21 A1, and
related proteins. ALDH subfamily which includes Tortula
ruralis aldehyde dehydrogenase ALDH21A1 (RNP123), and
NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22)
and like sequences.
Length = 453
Score = 27.4 bits (61), Expect = 2.1
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 16 GITPADRHTSKLIAGKIIPAIATTTSVV------AGLVCLELIKL 54
ITP + L+A K+ PAIAT VV L LEL K+
Sbjct: 129 AITPFN-FPLNLVAHKLAPAIATGCPVVLKPASKTPLSALELAKI 172
>gnl|CDD|143463 cd07145, ALDH_LactADH_F420-Bios, Methanocaldococcus jannaschii
NAD+-dependent lactaldehyde dehydrogenase-like.
NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22)
involved the biosynthesis of coenzyme F(420) in
Methanocaldococcus jannaschii through the oxidation of
lactaldehyde to lactate and generation of NAPH, and
similar sequences are included in this CD.
Length = 456
Score = 26.5 bits (59), Expect = 4.3
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 16 GITPADRHTSKLIAGKIIPAIATTTSVV------AGLVCLELIKL 54
ITP + + L A KI PAIA SVV L +EL K+
Sbjct: 129 AITPFN-FPANLFAHKIAPAIAVGNSVVVKPSSNTPLTAIELAKI 172
>gnl|CDD|132294 TIGR03250, PhnAcAld_DH, putative phosphonoacetaldehyde
dehydrogenase. This family of genes are members of the
pfam00171 NAD-dependent aldehyde dehydrogenase family.
These genes are observed in Ralstonia eutropha JMP134,
Sinorhizobium meliloti 1021, Burkholderia mallei ATCC
23344, Burkholderia thailandensis E264, Burkholderia
cenocepacia AU 1054, Burkholderia pseudomallei K96243
and 1710b, Burkholderia xenovorans LB400, Burkholderia
sp. 383 and Polaromonas sp. JS666 in close proximity to
the PhnW gene (TIGR02326) encoding 2-aminoethyl
phosphonate aminotransferase (which generates
phosphonoacetaldehyde) and PhnA (TIGR02335) encoding
phosphonoacetate hydrolase (not to be confused with the
alkylphosphonate utilization operon protein PhnA modeled
by TIGR00686). Additionally, transporters believed to be
specific for 2-aminoethyl phosphonate are often present.
PhnW is, in other organisms, coupled with PhnX
(TIGR01422) for the degradation of phosphonoacetaldehyde
(GenProp0238), but PhnX is apparently absent in each of
the organisms containing this aldehyde reductase. PhnA,
characterized in a strain of Pseudomonas fluorescens
that has not het been genome sequenced, is only rarely
found outside of the PhnW and aldehyde dehydrogenase
context. For instance in Rhodopseudomonas and Bordetella
bronchiseptica, where it is adjacent to transporters
presumably specific for the import of phosphonoacetate.
It seems reasonably certain then, that this enzyme
catalyzes the NAD-dependent oxidation of
phosphonoacetaldehyde to phosphonoacetate, bridging the
metabolic gap between PhnW and PhnA. We propose the name
phosphonoacetaldehyde dehydrogenase and the gene symbol
PhnY for this enzyme.
Length = 472
Score = 26.7 bits (59), Expect = 4.6
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 10 LRAANYGITPADRHTSKLIAGKIIPAIATTTSVV 43
L ITP + H +A KI PAIAT +V
Sbjct: 139 LLGVISAITPFN-HPMNQVAHKIAPAIATNNRMV 171
>gnl|CDD|152304 pfam11868, DUF3388, Protein of unknown function (DUF3388). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 261 to 275 amino acids in
length. This protein is found associated with
pfam01842.
Length = 192
Score = 25.9 bits (57), Expect = 5.9
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 22 RHTSKLIAGKIIPAIATTTSVVAGLVC 48
R KLI + +P + T S+VA VC
Sbjct: 51 REGHKLIGIRGMPRVGKTESIVAASVC 77
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
0.324 0.138 0.399
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,738,209
Number of extensions: 595997
Number of successful extensions: 616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 615
Number of HSP's successfully gapped: 32
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.1 bits)