RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4580
(72 letters)
>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 = 28.9 bits (65), Expect = 0.16
Identities = 17/70 (24%), Positives = 39/70 (55%)
Query: 2 KSKLEERERDIKDLKILLRSKQEEIGEISVRKDLAESKLANAIRDKDYQEQKLKCVTNRI 61
K +++ E++I++L +EE+ E+ ES+L + +++D E +L+ + +I
Sbjct: 846 KEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKI 905
Query: 62 NQLEEVVDLK 71
+LE ++ K
Sbjct: 906 EELEAQIEKK 915
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 25.4 bits (56), Expect = 2.6
Identities = 9/53 (16%), Positives = 28/53 (52%)
Query: 1 MKSKLEERERDIKDLKILLRSKQEEIGEISVRKDLAESKLANAIRDKDYQEQK 53
+++++EE ++++K L+ + + EI + + A++K + K ++
Sbjct: 93 IEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYD 145
>gnl|CDD|237956 PRK15398, PRK15398, aldehyde dehydrogenase EutE; Provisional.
Length = 465
Score = 25.2 bits (56), Expect = 3.3
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 5 LEERERDIKDLKILLRSKQEEIGEISVRKDLAESKLANAIRDK 47
L R+R I ++ L EE+ E++V E+ + + DK
Sbjct: 57 LAMRQRIIDAIREALLPHAEELAELAV----EETGMGR-VEDK 94
>gnl|CDD|132472 TIGR03431, PhnD, phosphonate ABC transporter, periplasmic
phosphonate binding protein. This model is a subset of
the broader subfamily of phosphate/phosphonate binding
protein ABC transporter components, TIGR01098. In this
model all members of the seed have support from genomic
context for association with pathways for the metabolims
of phosphonates, particularly the C-P lyase system,
GenProp0232. This model includes the characterized phnD
gene from E. coli. Note that this model does not
identify all phnD-subfamily genes with evident
phosphonate context, but all sequences above the trusted
context may be inferred to bind phosphonate compounds
even in the absence of such context. Furthermore, there
is ample evidence to suggest that many other members of
the TIGR01098 subfamily have a different primary
function.
Length = 288
Score = 25.0 bits (55), Expect = 3.3
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 12 IKDLKILLRSKQEEIGEISVRKDLAESKLANAIRD 46
++DL+I+ +S G I RKDL L IR
Sbjct: 211 MEDLRIIWKSPLIPNGPIVYRKDLPAD-LKAKIRK 244
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 25.1 bits (56), Expect = 3.3
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 5 LEERERDIKDLKILLRSKQEEIGEISVRK 33
LE R + L L +++GE SVR+
Sbjct: 165 LEGRLEYREALLRYLDKHLDKLGEDSVRR 193
>gnl|CDD|235773 PRK06291, PRK06291, aspartate kinase; Provisional.
Length = 465
Score = 24.9 bits (55), Expect = 4.3
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 10/60 (16%)
Query: 9 ERDIKDLKILLRSKQEEIGEISVRKDLAESKLANAIRDKDYQEQKLKCVTNRINQLEEVV 68
RDI +K + I ++ R A + AI+D D +E+ K + +RI +LE+ +
Sbjct: 59 VRDIAKVK-------DFIADLRERHYKA---IEEAIKDPDIREEVSKTIDSRIEELEKAL 108
>gnl|CDD|178479 PLN02891, PLN02891, IMP cyclohydrolase.
Length = 547
Score = 24.7 bits (54), Expect = 5.3
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 13 KDLKILLRSKQEEIGEISVRKDLAESKLANAIRDKDYQEQKLKCVTNRINQLEEVVDLK 71
K L+IL +K + G +S+R+ + LA D ++ V+ ++ E+ D K
Sbjct: 381 KTLRIL-EAKPRKKGRLSLRQ-VGGGWLAQDSDDLTPEDITFTVVSEKVPTESELEDAK 437
>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 = 24.6 bits (54), Expect = 5.5
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 1 MKSKLEERERDIKDLKILLRSKQEEIGEISVRKDLAESKLANAIRDKDYQEQKLKCVTNR 60
+K ++ ++ + ++ + +EEI R+ + E K A A R D + R
Sbjct: 62 LKLEVARKKERLNQIRARISQLKEEI--EQKRERIEELKRALAQRRSDLSSASYQLEKRR 119
Query: 61 INQLEEVVD 69
+QLE++ D
Sbjct: 120 ASQLEKLQD 128
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
0.310 0.129 0.322
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,536,546
Number of extensions: 275907
Number of successful extensions: 495
Number of sequences better than 10.0: 1
Number of HSP's gapped: 487
Number of HSP's successfully gapped: 130
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
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 (21.7 bits)
S2: 53 (24.1 bits)