RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2692
(133 letters)
>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus. This
family represents the C-terminus (approximately 500
residues) of the eukaryotic coatomer alpha subunit.
Coatomer (COPI) is a large cytosolic protein complex
which forms a coat around vesicles budding from the
Golgi apparatus. Such coatomer-coated vesicles have been
proposed to play a role in many distinct steps of
intracellular transport. Note that many family members
also contain the pfam04053 domain.
Length = 421
Score = 155 bits (393), Expect = 1e-46
Identities = 66/148 (44%), Positives = 91/148 (61%), Gaps = 21/148 (14%)
Query: 6 VTSESINKSS---------SFETAFKLLHDQIGVKNFLPYRQMFLNSYLQSRTAYSTLPL 56
V+ N SS SFETA +LLHDQ+GV NF P++ +FL Y SRT+Y LP
Sbjct: 113 VSQIWPNNSSLAADHVAAGSFETAMRLLHDQLGVVNFAPFKDLFLQLYAGSRTSYRALPG 172
Query: 57 LAPVTAFPTRKVDRSSI------------DLIAKIQQCYQLTTSGKFVDAIEKLRNVLIC 104
L V+ +P R S+ L ++Q YQLTT+GKF +A+EK R++L+
Sbjct: 173 LPSVSIYPERNWSESNSKNGPPAVGFKLSQLAKRLQAAYQLTTNGKFGEAVEKFRSILLS 232
Query: 105 IPLLVVTTKKEIEEAKQIINICKEYIVG 132
IPL+VV +K+E+ EA+Q+I IC+EYIVG
Sbjct: 233 IPLIVVDSKQEVAEAQQLITICREYIVG 260
>gnl|CDD|239021 cd02070, corrinoid_protein_B12-BD, B12 binding domain of corrinoid
proteins. A family of small methanogenic corrinoid
proteins that bind methyl-Co(III)
5-hydroxybenzimidazolylcobamide as a cofactor. They play
a role on the methanogenesis from trimethylamine,
dimethylamine or monomethylamine, which is initiated by
a series of corrinoid-dependent methyltransferases.
Length = 201
Score = 30.7 bits (70), Expect = 0.14
Identities = 10/39 (25%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 90 KFVDAIEKLRNVLICIPLLVVTTKKEIEEAKQIINICKE 128
+FV+A+++ + ++ + L+ TT ++E +I KE
Sbjct: 124 EFVEAVKEHKPDILGLSALMTTTMGGMKE---VIEALKE 159
>gnl|CDD|238088 cd00156, REC, Signal receiver domain; originally thought to be
unique to bacteria (CheY, OmpR, NtrC, and PhoB), now
recently identified in eukaroytes ETR1 Arabidopsis
thaliana; this domain receives the signal from the
sensor partner in a two-component systems; contains a
phosphoacceptor site that is phosphorylated by histidine
kinase homologs; usually found N-terminal to a DNA
binding effector domain; forms homodimers.
Length = 113
Score = 27.2 bits (61), Expect = 1.4
Identities = 7/41 (17%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 92 VDAIEKLRNVLICIPLLVVTTKKEIEEAKQIINI-CKEYIV 131
++ + ++R IP++ +T + E+A + + +Y+
Sbjct: 57 LELLRRIRKRGPDIPIIFLTAHGDDEDAVEALKAGADDYLT 97
>gnl|CDD|217274 pfam02896, PEP-utilizers_C, PEP-utilising enzyme, TIM barrel
domain.
Length = 292
Score = 27.2 bits (61), Expect = 2.4
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 100 NVLICIPLLVVTTKKEIEEAKQIINICKE 128
N+ I P+ V T +E+ EAK+II K
Sbjct: 136 NLEIMFPM--VATVEELREAKRIIEEVKA 162
>gnl|CDD|223714 COG0641, AslB, Arylsulfatase regulator (Fe-S oxidoreductase)
[General function prediction only].
Length = 378
Score = 27.0 bits (60), Expect = 3.2
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 72 SIDLIAKIQQCYQLTTSGK-----FVDAIEKLRNVLICIPLLVVTTKKEIEEAKQIINIC 126
SID +I Y++T SGK + +E L+ + L V ++ + ++I +
Sbjct: 120 SIDGPEEIHDKYRVTKSGKGTFDRVMKGLELLQAHGVDFNTLTVVNRQNVLHPEEIYHFL 179
Query: 127 KEYIV 131
K
Sbjct: 180 KSEGS 184
>gnl|CDD|178745 PLN03206, PLN03206, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1307
Score = 27.0 bits (60), Expect = 3.3
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 63 FPTRKVDRSSIDLIAKIQQC 82
F T KVDR L+A+ QQ
Sbjct: 658 FLTTKVDRCVTGLVAQ-QQT 676
>gnl|CDD|233313 TIGR01210, TIGR01210, TIGR01210 family protein. This family of
exclusively archaeal proteins has no characterized close
homologs. Several rounds of PSI-BLAST with a stringent
cutoff of 1e-8 shows apparent similarity of the central
region of this family to the central regions of the
oxygen-independent coproporphyrinogen III dehydrogenase
HemN and to other enzymes [Hypothetical proteins,
Conserved].
Length = 313
Score = 26.3 bits (58), Expect = 5.2
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 10/48 (20%)
Query: 90 KFVDAIEKLRN--------VLICIPLLVVTTKKEIEEAKQIINICKEY 129
F+ A E R +L P L + K+ I + I C
Sbjct: 156 DFIRAAELARKYGAGVKAYLLFKPPFL--SEKEAIADMISSIRKCIPV 201
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 26.4 bits (58), Expect = 5.9
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 10/68 (14%)
Query: 54 LPLLAPVTAFPTRKVDRSSIDLIAKIQQCYQLTTSGKFVDAIEKLRNVLICIPLL--VVT 111
LP L P+ +KV ++I L+ I S +++ E +R IC L+ + +
Sbjct: 690 LPSLTPILRNKHQKVVANTIALVGTICM-----NSPEYIGVREWMR---ICFELVDSLKS 741
Query: 112 TKKEIEEA 119
KEI
Sbjct: 742 WNKEIRRN 749
>gnl|CDD|234639 PRK00109, PRK00109, Holliday junction resolvase-like protein;
Reviewed.
Length = 138
Score = 25.9 bits (58), Expect = 6.0
Identities = 6/32 (18%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 106 PLLVVTTKKEIEEAKQIINICKEY-----IVG 132
PL + + ++ + KE+ +VG
Sbjct: 30 PLETIKRNNGTPDWDRLEKLIKEWQPDGLVVG 61
>gnl|CDD|205305 pfam13124, DUF3963, Protein of unknown function (DUF3963). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 42 and 85 amino acids
in length. There is a conserved DIQKW sequence motif.
Length = 40
Score = 24.4 bits (53), Expect = 6.3
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 90 KFVDAIEK-LRNVLICIPLLVVT 111
++ D I+K +RN+ C LLVV
Sbjct: 11 RYFDDIQKWIRNITFCFALLVVV 33
>gnl|CDD|181036 PRK07568, PRK07568, aspartate aminotransferase; Provisional.
Length = 397
Score = 26.0 bits (58), Expect = 7.8
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 77 AKIQQCYQLTTSGKFVDAI-EKLRNVLICIP---LLVVTTKKEIEEAKQIINICKEY 129
KI++ + L + + I K + +LI P VV TK+E+E + I K++
Sbjct: 141 TKIEEGFHLPSKEEIEKLITPKTKAILISNPGNPTGVVYTKEELE---MLAEIAKKH 194
>gnl|CDD|143395 cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase
superfamily. The aldehyde dehydrogenase superfamily
(ALDH-SF) of NAD(P)+-dependent enzymes, in general,
oxidize a wide range of endogenous and exogenous
aliphatic and aromatic aldehydes to their corresponding
carboxylic acids and play an important role in
detoxification. Besides aldehyde detoxification, many
ALDH isozymes possess multiple additional catalytic and
non-catalytic functions such as participating in
metabolic pathways, or as binding proteins, or
osmoregulants, to mention a few. The enzyme has three
domains, a NAD(P)+ cofactor-binding domain, a catalytic
domain, and a bridging domain; and the active enzyme is
generally either homodimeric or homotetrameric. The
catalytic mechanism is proposed to involve cofactor
binding, resulting in a conformational change and
activation of an invariant catalytic cysteine
nucleophile. The cysteine and aldehyde substrate form an
oxyanion thiohemiacetal intermediate resulting in
hydride transfer to the cofactor and formation of a
thioacylenzyme intermediate. Hydrolysis of the
thioacylenzyme and release of the carboxylic acid
product occurs, and in most cases, the reduced cofactor
dissociates from the enzyme. The evolutionary
phylogenetic tree of ALDHs appears to have an initial
bifurcation between what has been characterized as the
classical aldehyde dehydrogenases, the ALDH family
(ALDH) and extended family members or aldehyde
dehydrogenase-like (ALDH-L) proteins. The ALDH proteins
are represented by enzymes which share a number of
highly conserved residues necessary for catalysis and
cofactor binding and they include such proteins as
retinal dehydrogenase, 10-formyltetrahydrofolate
dehydrogenase, non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase,
delta(1)-pyrroline-5-carboxylate dehydrogenases,
alpha-ketoglutaric semialdehyde dehydrogenase,
alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
aldehyde dehydrogenase and succinate-semialdehyde
dehydrogenase. Included in this larger group are all
human, Arabidopsis, Tortula, fungal, protozoan, and
Drosophila ALDHs identified in families ALDH1 through
ALDH22 with the exception of families ALDH18, ALDH19,
and ALDH20 which are present in the ALDH-like group. The
ALDH-like group is represented by such proteins as
gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA
reductase, and coenzyme A acylating aldehyde
dehydrogenase. All of these proteins have a conserved
cysteine that aligns with the catalytic cysteine of the
ALDH group.
Length = 367
Score = 25.7 bits (57), Expect = 8.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 106 PLLVVTTKKEIEEAKQIIN 124
P+L V K+ EEA + N
Sbjct: 276 PVLPVIRFKDEEEAIALAN 294
>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566). Family of
related proteins that is plant specific.
Length = 313
Score = 25.7 bits (56), Expect = 10.0
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 88 SGKFVDAIEKLRNVLICIPLLVVTTKKEIEEAKQIINIC 126
S AIE L+ + +P +V K +++ K+ ++
Sbjct: 236 SSSLSGAIEALKASTLRLP-VVGGAKADMQSLKEAVSSA 273
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.134 0.373
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,439,641
Number of extensions: 555168
Number of successful extensions: 608
Number of sequences better than 10.0: 1
Number of HSP's gapped: 607
Number of HSP's successfully gapped: 25
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.4 bits)