RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16592
(132 letters)
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 69.9 bits (171), Expect = 7e-17
Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 4/55 (7%)
Query: 68 PRFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAW 122
+ ++K++AVALWSWD+ ++ CAICRNH+M C CQ P + C V W
Sbjct: 1 MKVKIKKWHAVALWSWDIPIDVCAICRNHIMGTCPECQFGMT----PGDECPVVW 51
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to chromosome
metabolism and cell cycle control.
Length = 73
Score = 68.6 bits (168), Expect = 2e-16
Identities = 24/54 (44%), Positives = 33/54 (61%), Gaps = 7/54 (12%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAW 122
R ++K+NAVALWSWD++ + CAICRNH C C++ P + C V W
Sbjct: 1 RVEIKKWNAVALWSWDIEDDVCAICRNHFDGTCPECKS-------PGDDCPVVW 47
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 29.8 bits (67), Expect = 0.13
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 71 TVRKFNAVALWSWDM-DMETCAICR 94
++++NAVA W+WD + C ICR
Sbjct: 4 KIKEWNAVATWTWDTPSDDVCGICR 28
>gnl|CDD|215101 PLN00203, PLN00203, glutamyl-tRNA reductase.
Length = 519
Score = 30.5 bits (69), Expect = 0.22
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 3/40 (7%)
Query: 28 MRKLQIQELINEELQKMKEDRELNRTYKKVLDLRSEYPDV 67
M KL ++ L+++ KM +NR+ ++V LR E+PDV
Sbjct: 277 MGKLLVKHLVSKGCTKMVV---VNRSEERVAALREEFPDV 313
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 29.5 bits (67), Expect = 0.34
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 32 QIQELINEELQKMKEDRELNRTYKK 56
++ +N+ L ++K D L + Y+K
Sbjct: 192 ELLAALNKALAELKADGTLAKLYEK 216
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 28.8 bits (64), Expect = 0.68
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 26 PIMRKLQIQEL---INEELQKMKEDRELNRTYKKVL 58
+RK EL +N+ L+++K D L + K
Sbjct: 228 IALRKGDDPELLEAVNKALKELKADGTLQKISDKWF 263
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 28.4 bits (64), Expect = 0.89
Identities = 9/36 (25%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 23 STWPIMRK--LQIQELINEELQKMKEDRELNRTYKK 56
+RK ++ + IN+ L+++K D L + +K
Sbjct: 182 GYAIAVRKGDPELLDKINKALKELKADGTLKKISEK 217
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 28.5 bits (65), Expect = 1.0
Identities = 9/38 (23%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 28 MRKLQIQELINEELQKMKEDRELNRTYKKVLDLRSEYP 65
M+ +I ELI + L ++ + ++V +L +P
Sbjct: 376 MK--EIAELIADVLDNPDDEAVIEEVKEEVKELCKRFP 411
>gnl|CDD|184619 PRK14322, glmM, phosphoglucosamine mutase; Provisional.
Length = 429
Score = 28.0 bits (62), Expect = 1.6
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 48 RELNRTYKKVLDLRSEYPDVPRFT--VRKFNAVAL 80
R L R+ + + D E PD P+ T VR+ ++L
Sbjct: 340 RVLKRSGRNLSDFAKEIPDYPQITKNVRRTERMSL 374
>gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6. RNA
polymerases catalyze the DNA dependent polymerisation
of RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 6, represents a mobile module of the RNA
polymerase. Domain 6 forms part of the shelf module.
This family appears to be specific to the largest
subunit of RNA polymerase II.
Length = 187
Score = 27.4 bits (62), Expect = 1.7
Identities = 9/27 (33%), Positives = 19/27 (70%)
Query: 27 IMRKLQIQELINEELQKMKEDRELNRT 53
++ ++Q+L++EE +++ EDR L R
Sbjct: 49 LLGDAEVQKLLDEEYEQLLEDRRLLRE 75
>gnl|CDD|219176 pfam06785, UPF0242, Uncharacterized protein family (UPF0242).
Length = 401
Score = 27.6 bits (61), Expect = 2.3
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 30 KLQIQELINEELQKMKEDRELNRTYKKVL----DLRSEY 64
++Q+ L+ E +K++E++ELNR + L +L EY
Sbjct: 147 QIQLDALVQECNEKIEENQELNRELAETLAYQQELNDEY 185
>gnl|CDD|217630 pfam03592, Terminase_2, Terminase small subunit. Packaging of
double-stranded viral DNA concatemers requires
interaction of the prohead with virus DNA. This process
is mediated by a phage-encoded DNA recognition and
terminase protein. The terminase enzymes described so
far, which are hetero-oligomers composed of a small and
a large subunit, do not have a significant level of
sequence homology. The small terminase subunit is
thought to form a nucleoprotein structure that helps to
position the terminase large subunit at the packaging
initiation site.
Length = 141
Score = 26.9 bits (60), Expect = 2.5
Identities = 4/27 (14%), Positives = 14/27 (51%)
Query: 28 MRKLQIQELINEELQKMKEDRELNRTY 54
+ K +I+ I+E +++ ++ +
Sbjct: 40 LTKPKIKAYIDELMKEREKRTIITADE 66
>gnl|CDD|220999 pfam11144, DUF2920, Protein of unknown function (DUF2920). This
bacterial family of proteins has no known function.
Length = 403
Score = 27.2 bits (61), Expect = 3.1
Identities = 7/24 (29%), Positives = 17/24 (70%)
Query: 32 QIQELINEELQKMKEDRELNRTYK 55
+I E +N++++++K+ L+ YK
Sbjct: 118 EIFEYLNKKIKELKQAGILDENYK 141
>gnl|CDD|213273 cd05905, Dip2, Disco-interacting protein 2 (Dip2). Dip2 proteins
show sequence similarity to other members of the
adenylate forming enzyme family, including insect
luciferase, acetyl CoA ligases and the adenylation
domain of nonribosomal peptide synthetases (NRPS).
However, its function may have diverged from other
members of the superfamily. In mouse embryo, Dip2
homolog A plays an important role in the development of
both vertebrate and invertebrate nervous systems. Dip2A
appears to regulate cell growth and the arrangement of
cells in organs. Biochemically, Dip2A functions as a
receptor of FSTL1, an extracellular glycoprotein, and
may play a role as a cardiovascular protective agent.
Length = 556
Score = 26.7 bits (59), Expect = 3.8
Identities = 14/109 (12%), Positives = 29/109 (26%), Gaps = 22/109 (20%)
Query: 5 SEPFHK-KPKTPSAQTFSRSTWPIMRKLQIQELINEELQKMKEDRELNRTYKKVLDLRSE 63
SE K + + WP ++ + E K ++ N + +L +
Sbjct: 96 SEACLKGLRSKTTGEILKFKGWP-----RLVWFVTEIKTLKKPIKDWN-PHLPPANLDTA 149
Query: 64 YPDVPRFTVRKFNAVALWSWDMDMETC-----AICRNHLMDECILCQAR 107
Y + + M + C+ C + R
Sbjct: 150 YIEY---------KTSKEGSVMGVTVTHQALLTHCQALKQ-ACQYTEGR 188
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD.
Length = 218
Score = 26.2 bits (58), Expect = 6.2
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 14 TPSAQTFSRSTWPIMRKLQ--IQELINEELQKMKEDRELNRTYKK 56
PS + K + + +N+ L++++ D EL + KK
Sbjct: 172 GPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKK 216
>gnl|CDD|233054 TIGR00615, recR, recombination protein RecR. All proteins in this
family for which functions are known are involved in the
initiation of recombination and recombinational repair.
RecF is also required. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 195
Score = 25.8 bits (57), Expect = 6.8
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 86 DMETCAICRNHLMDECILCQARDAQD 111
D E C IC + D ++C D +D
Sbjct: 64 DQEVCNICSDERRDNSVICVVEDPKD 89
>gnl|CDD|212101 cd10789, GH38N_AMII_ER_cytosolic, N-terminal catalytic domain of
endoplasmic reticulum(ER)/cytosolic class II
alpha-mannosidases; glycoside hydrolase family 38
(GH38). The subfamily is represented by Saccharomyces
cerevisiae vacuolar alpha-mannosidase Ams1, rat
ER/cytosolic alpha-mannosidase Man2C1, and similar
proteins. Members in this family share high sequence
similarity. None of them have any classical signal
sequence or membrane spanning domains, which are
typical of sorting or targeting signals. Ams1 functions
as a second resident vacuolar hydrolase in S.
cerevisiae. It aids in recycling macromolecular
components of the cell through hydrolysis of terminal,
non-reducing alpha-d-mannose residues. Ams1 utilizes
both the cytoplasm to vacuole targeting (Cvt,
nutrient-rich conditions) and autophagic (starvation
conditions) pathways for biosynthetic delivery to the
vacuole. Man2C1is involved in oligosaccharide
catabolism in both the ER and cytosol. It can catalyze
the cobalt-dependent cleavage of alpha 1,2-, alpha
1,3-, and alpha 1,6-linked mannose residues. Members in
this family are retaining glycosyl hydrolases of family
GH38 that employs a two-step mechanism involving the
formation of a covalent glycosyl-enzyme complex. Two
carboxylic acids positioned within the active site act
in concert: one as a catalytic nucleophile and the
other as a general acid/base catalyst.
Length = 252
Score = 25.9 bits (58), Expect = 7.6
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 48 RELNRTYKKVLDLRSEYPDVPRFTVRKFNAVALWSW 83
R+ RT+ VLDL EYPD FT + L+ W
Sbjct: 23 RKAARTFSTVLDLMEEYPD-FVFT---QSQAQLYEW 54
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase.
This family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 25.3 bits (56), Expect = 8.3
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 51 NRTYKKVLDLRSEYPDV 67
NRT +K +L E+P
Sbjct: 43 NRTLEKAKELAEEFPVG 59
>gnl|CDD|171895 PRK13196, PRK13196, pyrrolidone-carboxylate peptidase;
Provisional.
Length = 211
Score = 25.7 bits (56), Expect = 8.4
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 6 EPFHKKPKTPSAQ 18
EPFH P PSAQ
Sbjct: 10 EPFHTHPVNPSAQ 22
>gnl|CDD|114536 pfam05814, DUF843, Baculovirus protein of unknown function
(DUF843). This family consists of several Baculovirus
proteins of around 85 residues long with no known
function.
Length = 83
Score = 24.6 bits (54), Expect = 8.6
Identities = 6/26 (23%), Positives = 16/26 (61%)
Query: 34 QELINEELQKMKEDRELNRTYKKVLD 59
+L E+ +K+K+ ++L + +L+
Sbjct: 53 ADLYTEKAKKIKKKQDLEDAFDAILN 78
>gnl|CDD|132867 cd07229, Pat_TGL3_like, Triacylglycerol lipase 3. Triacylglycerol
lipase 3 (TGL3) are responsible for all the TAG lipase
activity of the lipid particle. Triacylglycerol (TAG)
lipases are also necessary for the mobilization of TAG
stored in lipid particles. TGL3 contains the consensus
sequence motif GXSXG, which is found in lipolytic
enzymes. This family includes Tgl3p from Saccharomyces
cerevisiae.
Length = 391
Score = 25.7 bits (57), Expect = 9.6
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 22 RSTWPIMRKLQIQELINEELQKM 44
R WP + L+++ + EL
Sbjct: 364 RGVWPALAALRVRCAVEFELDDG 386
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
0.319 0.131 0.414
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,524,124
Number of extensions: 547411
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 679
Number of HSP's successfully gapped: 39
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.8 bits)
S2: 53 (24.2 bits)