RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy627
(89 letters)
>gnl|CDD|218273 pfam04800, ETC_C1_NDUFA4, ETC complex I subunit conserved region.
Family of pankaryotic NADH-ubiquinone oxidoreductase
subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of
the electron transport chain initially identified in
Neurospora crassa as a 21 kDa protein.
Length = 101
Score = 111 bits (280), Expect = 6e-34
Identities = 47/86 (54%), Positives = 59/86 (68%), Gaps = 1/86 (1%)
Query: 1 MQSGTHNANNWFIQFDTRERWENPLMGWCSTGDPLSN-LALNFSSKEDAIQYCQKNGWKF 59
MQSG W ++FD RWENPLMGW STGDPLSN + L F +KE AI + ++ GW++
Sbjct: 13 MQSGRARTKKWTLEFDRSARWENPLMGWTSTGDPLSNQMELTFPTKEAAIAFAERQGWEY 72
Query: 60 FVEEPKWKTPKVKSYAFNFSWNKRTR 85
VEEP K K+Y+ NFSWN+RTR
Sbjct: 73 DVEEPNAPKAKPKAYSDNFSWNRRTR 98
>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8. This PCI_Csn8
domain is conserved from plants to humans. It is a
signature protein motif found in components of CSN (COP9
signalosome). It functions as a structural scaffold for
subunit-subunit interactions within the complex and is a
key regulator of photomorphogenic development.
Length = 144
Score = 29.2 bits (66), Expect = 0.16
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 40 LNFSSKEDAIQYCQKNGWK 58
L SS E+ ++ +K GW
Sbjct: 107 LGLSSDEELEKFAKKRGWT 125
>gnl|CDD|233864 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop)
vs. UGG (Trp). In all bacteria, the wobble position of
the tRNA(Ile) recognizing AUA is lysidine, a lysine
derivative of cytidine. This family describes a protein
domain found, apparently, in all bacteria in a single
copy. Eukaryotic sequences appear to be organellar. The
domain archictecture of this protein family is variable;
some, including characterized proteins of E. coli and B.
subtilis known to be tRNA(Ile)-lysidine synthetase,
include a conserved 50-residue domain that many other
members lack. This protein belongs to the ATP-binding
PP-loop family ( pfam01171). It appears in the
literature and protein databases as TilS, YacA, and
putative cell cycle protein MesJ (a misnomer) [Protein
synthesis, tRNA and rRNA base modification].
Length = 189
Score = 28.0 bits (63), Expect = 0.43
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 40 LNFSSKEDAIQYCQKNGWKFFVEE 63
L S K + +Y ++NG +F +E
Sbjct: 149 LGIS-KSEIEEYLKENGLPWFEDE 171
Score = 25.3 bits (56), Expect = 3.9
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 3/31 (9%)
Query: 40 LNFSSKEDA---IQYCQKNGWKFFVEEPKWK 67
L S E+A Q+C+K +++ K
Sbjct: 39 LRPESDEEAEFVQQFCKKLNIPLEIKKVDVK 69
>gnl|CDD|149703 pfam08727, P3A, Poliovirus 3A protein like. This domain is found
in positive-strand RNA viruses. The 3A protein is a
critical component of the poliovirus replication
complex, and is also an inhibitor of host cell ER to
Golgi transport.
Length = 57
Score = 26.9 bits (60), Expect = 0.47
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 46 EDAIQYCQKNGW 57
+ +YC+K GW
Sbjct: 30 PEVREYCEKKGW 41
>gnl|CDD|239429 cd03313, enolase, Enolase: Enolases are homodimeric enzymes that
catalyse the reversible dehydration of
2-phospho-D-glycerate to phosphoenolpyruvate as part of
the glycolytic and gluconeogenesis pathways. The
reaction is facilitated by the presence of metal ions.
Length = 408
Score = 26.7 bits (60), Expect = 1.6
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 47 DAIQYCQKNGWKFFV 61
+AI+ +KNG+ V
Sbjct: 347 EAIKLAKKNGYGVVV 361
>gnl|CDD|131316 TIGR02263, benz_CoA_red_C, benzoyl-CoA reductase, subunit C. This
model describes C subunit of benzoyl-CoA reductase, a
4-subunit enzyme. Many aromatic compounds are
metabolized by way of benzoyl-CoA. This enzyme acts
under anaerobic conditions.
Length = 380
Score = 26.5 bits (58), Expect = 1.7
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 20 RWENPLMGWCSTGDPLSNLALNF--SSKEDAIQY 51
R+EN + GDPL NLAL F S A +Y
Sbjct: 271 RFENNDVA--LAGDPLQNLALAFLHDSISTAAKY 302
>gnl|CDD|234785 PRK00509, PRK00509, argininosuccinate synthase; Provisional.
Length = 399
Score = 25.4 bits (57), Expect = 3.9
Identities = 5/16 (31%), Positives = 11/16 (68%)
Query: 41 NFSSKEDAIQYCQKNG 56
+ S+E+ I Y +++G
Sbjct: 148 DLKSREELIAYAEEHG 163
>gnl|CDD|221087 pfam11340, DUF3142, Protein of unknown function (DUF3142). This
bacterial family of proteins has no known function.
Length = 178
Score = 25.5 bits (56), Expect = 3.9
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 25 LMGWCSTGDPLSNLA 39
L+ W S+GD L+ L
Sbjct: 82 LLDWLSSGDWLNALP 96
>gnl|CDD|238639 cd01314, D-HYD, D-hydantoinases (D-HYD) also called
dihydropyrimidases (DHPase) and related proteins;
DHPases are a family of enzymes that catalyze the
reversible hydrolytic ring opening of the amide bond in
five- or six-membered cyclic diamides, like
dihydropyrimidine or hydantoin. The hydrolysis of
dihydropyrimidines is the second step of reductive
catabolism of pyrimidines in human. The hydrolysis of
5-substituted hydantoins in microorganisms leads to
enantiomerically pure N-carbamyl amino acids, which are
used for the production of antibiotics, peptide
hormones, pyrethroids, and pesticides. HYDs are
classified depending on their stereoselectivity. This
family also includes collapsin response regulators
(CRMPs), cytosolic proteins involved in neuronal
differentiation and axonal guidance which have strong
homology to DHPases, but lack most of the active site
residues.
Length = 447
Score = 25.6 bits (57), Expect = 4.3
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 43 SSKE--DAIQYCQKNGWKFFVE 62
SSKE D I +K G + E
Sbjct: 239 SSKEAADEIARARKKGLPVYGE 260
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 25.1 bits (56), Expect = 4.7
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 44 SKEDAIQYCQKNGWKFF 60
S E+A Q+ ++NG FF
Sbjct: 124 STEEAQQFAKENGLLFF 140
>gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional.
Length = 404
Score = 25.1 bits (55), Expect = 6.0
Identities = 5/16 (31%), Positives = 10/16 (62%)
Query: 41 NFSSKEDAIQYCQKNG 56
+ +ED I+Y +K+
Sbjct: 152 DIKGREDLIEYAKKHN 167
>gnl|CDD|238360 cd00673, AlaRS_core, Alanyl-tRNA synthetase (AlaRS) class II core
catalytic domain. AlaRS is a homodimer. It is
responsible for the attachment of alanine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its predicted structure and the presence of
three characteristic sequence motifs.
Length = 232
Score = 24.6 bits (54), Expect = 7.1
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 4/37 (10%)
Query: 35 LSNLALNFSSKEDAIQYCQKNGWKFFVEEPKWKTPKV 71
L N + KE+AI + W+ E ++
Sbjct: 86 LGNFSFGDYFKEEAIAFA----WELLTEVLGLPKDRL 118
>gnl|CDD|184783 PRK14662, acpS, 4'-phosphopantetheinyl transferase; Provisional.
Length = 120
Score = 24.4 bits (53), Expect = 9.0
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 33 DPLSNLALNFSSKEDAIQYC--QKNGWK 58
DP +LA F++KE A Q C + +GW+
Sbjct: 44 DPAPSLAARFAAKE-AFQKCWPESHGWR 70
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
0.317 0.129 0.443
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,296,773
Number of extensions: 313164
Number of successful extensions: 320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 319
Number of HSP's successfully gapped: 19
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
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: 53 (24.1 bits)