RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy460
(117 letters)
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 29.6 bits (67), Expect = 0.30
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 2/78 (2%)
Query: 33 LGLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDKISAEQQTAVPLDSYTRKLVDAQ 92
L I+ + L E+ R EL+ + S L S + + S KL D
Sbjct: 73 LNQIRARISQLKEEIEQKRERIEELKRALAQRRSDLSSASYQLEKRRA--SQLEKLQDEI 130
Query: 93 QKISIVGNILQTTQVAMH 110
++ N L +
Sbjct: 131 KRTRSKLNALHSLLAEKR 148
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, 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 = 314
Score = 28.0 bits (63), Expect = 1.2
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 65 TSQLDKISAEQQTAV---PLDSYTRKLVDAQQ 93
S LD+ + V PL TR L+ A +
Sbjct: 182 LSDLDEALEQADVVVVALPLTKQTRGLIGAAE 213
>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812). This is
a family of fungal proteins whose function is not known.
Length = 126
Score = 27.2 bits (61), Expect = 1.5
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 34 GLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDKISAEQQT 77
++P +D +DE+ A RA E +L E Q ++ ++
Sbjct: 80 SRVQPVLDEIDERAEAQRARDEEKKLDEEEAKRQHEEAKERERE 123
>gnl|CDD|182797 PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase;
Provisional.
Length = 743
Score = 26.7 bits (59), Expect = 3.1
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 29 AEGLLGLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDKISAEQQTAVPLDSYTRK 87
AE L L + + LDE A + L + L SQ +K SAE+Q A L +K
Sbjct: 526 AEKHL-LPRYNFNSLDELLAAIGGGDIRLNQMVNFLQSQFNKPSAEEQDAAALKQLQQK 583
>gnl|CDD|225452 COG2899, COG2899, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 346
Score = 26.2 bits (58), Expect = 4.0
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 59 LQIEALTSQLDKISAEQQTAVPLDSYTRKLVDAQQKISIVG 99
L I A+ + LD I A + P +SY + + DA +I+ G
Sbjct: 90 LVIVAVAAGLDPIRAMKLALEPPESYAKIITDAHPQIAAFG 130
>gnl|CDD|240357 PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
Length = 559
Score = 26.1 bits (58), Expect = 4.8
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 13/71 (18%)
Query: 5 TVSTNTSADDKTEDFCDNPTQDTIAE----GLLGLIKPTVDLLDEKFRATRASQLE-LRL 59
S D F + T T E G+ GL+ PTV+ L++ Q+E L
Sbjct: 13 VPSNARGVDVLRNRFLNKGTAFTAEEREHLGIEGLLPPTVETLEQ--------QVERLWT 64
Query: 60 QIEALTSQLDK 70
Q + + ++K
Sbjct: 65 QFNRIETPINK 75
>gnl|CDD|200948 pfam00038, Filament, Intermediate filament protein.
Length = 312
Score = 26.0 bits (58), Expect = 5.6
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 48 RATRASQLELRLQIEALTSQLD-----KISAEQQTAVPLDSYTRKLVDAQQKISIVGNIL 102
R+ + ELR QI++L +L K S E+Q A + Y +L D Q IS + L
Sbjct: 212 RSAKEEITELRRQIQSLEIELQSLKKQKASLERQLAELEERYELELADYQDTISELEEEL 271
Query: 103 QTT 105
Q
Sbjct: 272 QQL 274
>gnl|CDD|221268 pfam11853, DUF3373, Protein of unknown function (DUF3373). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 472 to 574 amino acids in
length.
Length = 485
Score = 26.0 bits (57), Expect = 5.7
Identities = 12/45 (26%), Positives = 22/45 (48%)
Query: 32 LLGLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDKISAEQQ 76
L+ L L A A+ ++L +IEAL +L ++ A+ +
Sbjct: 4 LVSLSLVAALLALSLPAAAAAADIDLLQKIEALKKELAELKAQLK 48
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 25.7 bits (57), Expect = 6.9
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 29 AEGLLGLIKPTVDLLDEKFRATRA-SQLE-LRLQIEALTSQLDKISAEQQTAVPLDSYTR 86
AEG G + +D EK + RA +Q+E L QI AL QL + A LD+ +
Sbjct: 114 AEGRAGELAQELD--SEKQVSARALAQVELLNQQIAALRRQLAALEA------ALDASEK 165
Query: 87 KLVDAQQKISIVGNILQT 104
+ ++Q KI+ +G L
Sbjct: 166 RDRESQAKIADLGRRLNV 183
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 25.4 bits (56), Expect = 8.7
Identities = 8/33 (24%), Positives = 19/33 (57%)
Query: 43 LDEKFRATRASQLELRLQIEALTSQLDKISAEQ 75
+D++F TR + R ++E L +++++ E
Sbjct: 376 VDKEFAETRDELKDYREKLEKLKREINELKREL 408
>gnl|CDD|99741 cd00617, Tnase_like, Tryptophanase family (Tnase). This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to tryptophanase (Tnase) and
tyrosine phenol-lyase (TPL). Tnase and TPL are active as
tetramers and catalyze beta-elimination reactions. Tnase
catalyzes degradation of L-tryptophan to yield indole,
pyruvate and ammonia and TPL catalyzes degradation of
L-tyrosine to yield phenol, pyruvate and ammonia.
Length = 431
Score = 25.4 bits (56), Expect = 9.3
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 74 EQQTAVPLDSYTRKLVDAQQKISIVGNI 101
E AVP+D + DAQ+ I GNI
Sbjct: 109 EANGAVPVDLVIDEAHDAQELIPFKGNI 136
>gnl|CDD|131906 TIGR02859, spore_sigH, RNA polymerase sigma-H factor. Members of
this protein family are RNA polymerase sigma-H factor
for sporulation in endospore-forming bacteria. This
protein is also called Sigma-30 and SigH. Although
rather close homologs in Listeria score above the noise
cutoff to This model, Listeria does not form spores and
the role of the related sigma factor in that genus is in
doubt [Transcription, Transcription factors, Cellular
processes, Sporulation and germination].
Length = 198
Score = 25.1 bits (55), Expect = 9.7
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 25 QDTIAEGLLGLIKPTVDLLDEKFRATRA-SQLELRLQIEALTSQLDKISAEQQTAVPLDS 83
+D I EG++GL K D +K + +A ++L + QI +A +Q +PL+S
Sbjct: 47 EDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIK-----TATRQKHIPLNS 101
Query: 84 Y 84
Y
Sbjct: 102 Y 102
>gnl|CDD|234336 TIGR03734, PRTRC_parB, PRTRC system ParB 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.
It is often found on plasmids. This protein family the
member related to ParB, and is designated PRTRC system
ParB family protein.
Length = 554
Score = 25.4 bits (56), Expect = 9.8
Identities = 13/42 (30%), Positives = 18/42 (42%)
Query: 29 AEGLLGLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDK 70
AE L GL K D + A + + EL+ IE+ L
Sbjct: 153 AELLAGLPKDKQDNVLTAILAEKPTVAELKKMIESAALSLSA 194
>gnl|CDD|181999 PRK09622, porA, pyruvate flavodoxin oxidoreductase subunit alpha;
Reviewed.
Length = 407
Score = 25.1 bits (55), Expect = 9.9
Identities = 21/106 (19%), Positives = 37/106 (34%), Gaps = 21/106 (19%)
Query: 23 PTQDTIAEGLLGLIKPTVDLLDEKFRATRASQLE-----------------LRLQIEALT 65
P D +A +G + +LD T +Q E IE +
Sbjct: 187 PLSDEVAYQFVGEYQTKNSMLDFDKPVTYGAQTEEDWHFEHKAQLHHALMSSSSVIEEVF 246
Query: 66 SQLDKISAEQQTAVPLDSYTRKLVDAQQKISIVGNILQTTQVAMHK 111
+ K++ + V T +L DA+ I +G ++ VA +
Sbjct: 247 NDFAKLTGRKYNLV----ETYQLEDAEVAIVALGTTYESAIVAAKE 288
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
0.313 0.128 0.339
Gapped
Lambda K H
0.267 0.0773 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,476,227
Number of extensions: 456831
Number of successful extensions: 454
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 55
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)