RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16758
(186 letters)
>gnl|CDD|216874 pfam02099, Josephin, Josephin.
Length = 158
Score = 97.8 bits (244), Expect = 3e-26
Identities = 55/174 (31%), Positives = 76/174 (43%), Gaps = 33/174 (18%)
Query: 15 KQMKELCALHALNNLFQNPKTFSKADLDEICINL--------SPQTW------LNPHRSI 60
+Q +LCA H LNNL Q P FS+ DL I L S + W P ++
Sbjct: 1 RQEGQLCAQHCLNNLLQGP-YFSEFDLASIAKELDQKERNKLSVEHWTPKSFLDEPSHNV 59
Query: 61 LGLGNYDINVIMTALQKKGFE-SNWFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTP 119
GN+ I V+ TAL+ G W R +D G+I N+
Sbjct: 60 DDTGNFSIQVLETALEVWGLSVIPWHSPRVGASSLDPDLERGFICNL------------- 106
Query: 120 IKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKELFVVT 173
HW T+R +NG +YNL+S L PEHI + L +L + S+ +FVV
Sbjct: 107 --SEHWFTIRKVNGTWYNLNSLLAAPEHISKFY-LSAFLDQLKSE-GYSVFVVR 156
>gnl|CDD|188241 TIGR02684, dnstrm_HI1420, probable addiction module antidote
protein. Members of this strictly bacterial protein
family are small, at roughly 100 amino acids. The gene
is almost invariably the downstream member of a gene
pair. It is a predicted DNA-binding protein from a clade
within Pfam helix-turn-helix family pfam01381. These
gene pairs, when found on the bacterial chromosome, are
located often with prophage regions, but also both in
integrated plasmid regions and in housekeeping gene
regions. Analysis suggests that the gene pair may serve
as an addiction module [Mobile and extrachromosomal
element functions, Other].
Length = 89
Score = 28.8 bits (65), Expect = 0.48
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 140 SKLDNPEHIGREEDLVEYLRDVLSDIDKELFV 171
++ D E++ EE + EYL D D
Sbjct: 3 AEFDPAEYLKTEEAIAEYLAQAFEDGDPAYIA 34
>gnl|CDD|224198 COG1279, COG1279, Lysine efflux permease [General function
prediction only].
Length = 202
Score = 28.0 bits (63), Expect = 2.3
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 19/74 (25%)
Query: 22 ALHALNNLFQNPK-----TFSKADLDEI---CINLSPQTWLNPHRSILGLGNYDINVIM- 72
L AL + + P F+K L ++ + + T LNPH L D V++
Sbjct: 84 GLLALKSAPRGPSQLQVAEFTKLKLKKVLLFALAV---TLLNPH-VYL-----DTVVLIG 134
Query: 73 -TALQKKGFESNWF 85
A Q +F
Sbjct: 135 SLAAQLSDEAKWFF 148
>gnl|CDD|129390 TIGR00289, TIGR00289, TIGR00289 family protein. Homologous
proteins related to MJ0570 of Methanococcus jannaschii
include both the apparent orthologs found by this model
above the trusted cutoff, the much longer protein
YLR143W from Saccharomyces cerevisiae, and second
homologous proteins from Archaeoglobus fulgidus and
Pyrococcus horikoshii that appear to represent a second
orthologous group [Hypothetical proteins, Conserved].
Length = 222
Score = 27.9 bits (62), Expect = 2.8
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 69 NVIMTALQKKGFESNWFDRRKDPKCIDQQK 98
VI+ ++ G + +W RR D +CID K
Sbjct: 135 EVIIVSVSAMGLDESWLGRRIDKECIDDLK 164
>gnl|CDD|202036 pfam01902, ATP_bind_4, ATP-binding region. This family of proteins
probably binds ATP. This domain is about 200 amino acids
long with a strongly conserved motif SGGKD at the N
terminus.In some members of this family , this domain is
associated with pfam01042.
Length = 220
Score = 27.8 bits (62), Expect = 2.9
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 69 NVIMTALQKKGFESNWFDRRKDPKCIDQQK 98
V + A+ G +W RR D K ID+ K
Sbjct: 137 EVAIVAVSAYGLGESWLGRRFDRKNIDELK 166
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 26.8 bits (60), Expect = 3.2
Identities = 10/20 (50%), Positives = 11/20 (55%), Gaps = 3/20 (15%)
Query: 20 LCALHALNNLFQNPKTFSKA 39
L AL ALNN NP+ F
Sbjct: 71 LKALRALNN---NPEIFGPD 87
>gnl|CDD|226393 COG3876, COG3876, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 409
Score = 27.8 bits (62), Expect = 3.7
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 6/63 (9%)
Query: 66 YDINVIMTALQKKGFESNWFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHW 125
Y + M A + G E DR P + VEG +L+ + +G Y PI +
Sbjct: 143 YTMAYAMEASAENGKEFIVLDR---PNPMGGNIVEGPLLDPRYKSFVGLY---PIPYCYG 196
Query: 126 LTV 128
+T
Sbjct: 197 MTP 199
>gnl|CDD|204276 pfam09629, YorP, YorP protein. YorP is a 71 residue protein found
in bacteria. As it is also found in a bacteriophage it
might be of viral origin. The structure is of an alpha
helix between two of five beta strands. The function is
unknown.
Length = 71
Score = 26.2 bits (57), Expect = 4.0
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 137 NLDSKLDNPEHIGREEDLVEYLRDVLSDIDKELFVVTRIENSKSYFKEN 185
N +++ P H+GR+ ++E+L D + V+ +YFKE+
Sbjct: 16 NNNARYGCPHHVGRKGKIIEHLHSATYD-----YAVSDETGDITYFKEH 59
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 27.9 bits (62), Expect = 4.1
Identities = 11/60 (18%), Positives = 18/60 (30%), Gaps = 10/60 (16%)
Query: 30 FQNPKTFSKADLDEICINL-----SPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNW 84
+P + I +T+L+ I G + V+ TAL F
Sbjct: 360 ADSPVGQEPPPSEAIFDPSEQGVDPAETYLD---RIFAPGRFSAEVLETALS--IFSRGL 414
>gnl|CDD|189013 cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 546
Score = 27.1 bits (61), Expect = 6.1
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 137 NLDSKLDNPEHIGREEDLVEYLRDVLSDIDKEL 169
++D NP+ G ++LVE + + ++ E
Sbjct: 263 SVDFPGGNPKPFGDADELVEKAKKMYKELSPET 295
>gnl|CDD|178170 PLN02555, PLN02555, limonoid glucosyltransferase.
Length = 480
Score = 26.7 bits (59), Expect = 7.7
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 8 QEIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEIC 45
+EII + M +LC + + LF+ KT + +I
Sbjct: 227 KEIIDY---MSKLCPIKPVGPLFKMAKTPNSDVKGDIS 261
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 26.2 bits (58), Expect = 10.0
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 136 YNLDSKLDNPEHIGREEDLVEYLRDVL 162
+L NP+ + + EDL E++ L
Sbjct: 195 VDLGLTDGNPDKVMQPEDLAEFIVAQL 221
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
0.318 0.137 0.412
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,850,560
Number of extensions: 921035
Number of successful extensions: 860
Number of sequences better than 10.0: 1
Number of HSP's gapped: 857
Number of HSP's successfully gapped: 26
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
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: 56 (25.5 bits)