RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13041
(81 letters)
>gnl|CDD|221257 pfam11838, DUF3358, Domain of unknown function (DUF3358). This
domain is functionally uncharacterized. This domain is
found in eukaryotes and bacteria. This domain is found
to the C-terminus of an aminopeptidase domain.
Length = 323
Score = 51.5 bits (124), Expect = 2e-09
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 4 DEKNIRSQDYFTVIV-MVAGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGK 62
D+ ++ +QD V+ + N G + W +V++N+D L K+ GR++
Sbjct: 228 DDDSVSNQDIRAVMAGLRRSNQAGRELLWPWVERNFDALAKKLPRGSSALGRVVGLYPSG 287
Query: 63 FTTQERLDEVSE 74
F++ E LDEV
Sbjct: 288 FSSAELLDEVEA 299
>gnl|CDD|198349 cd07771, FGGY_RhuK, L-rhamnulose kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial L-rhamnulose kinases
(RhuK, also known as rhamnulokinase; EC 2.7.1.5), which
are encoded by the rhaB gene and catalyze the
ATP-dependent phosphorylation of L-rhamnulose to produce
L-rhamnulose-1-phosphate and ADP. Some uncharacterized
homologous sequences are also included in this
subfamily. The prototypical member of this subfamily is
Escherichia coli RhuK, which exists as a monomer
composed of two large domains. The ATP binding site is
located in the cleft between the two domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. The presence of divalent Mg2+ or Mn2+
is required for catalysis. Although an intramolecular
disulfide bridge is present in Rhuk, disulfide formation
is not important to the regulation of RhuK enzymatic
activity. Members of this subfamily belong to the FGGY
family of carbohydrate kinases.
Length = 440
Score = 31.7 bits (73), Expect = 0.021
Identities = 7/28 (25%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 31 WDYVKKNWDY-LLKRFGLNHRVFGRIIP 57
D ++WD LL++ G+ +F ++
Sbjct: 179 LDPRTRDWDTELLEKLGIPEELFPPLVE 206
>gnl|CDD|224272 COG1353, COG1353, Predicted CRISPR-associated polymerase [Defense
mechanisms].
Length = 799
Score = 27.8 bits (62), Expect = 0.46
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 2/52 (3%)
Query: 32 DYVKKNWDYLLKRFGLNHRVFGRIIPSVC--GKFTTQERLDEVSEKSLKNLL 81
D + K DY + RVFG +I + E + + L
Sbjct: 471 DELLKQLDYNNSIYEFVFRVFGNVIEYLQLGDDVRELEFEEYAEKSLGTKYL 522
>gnl|CDD|221435 pfam12132, DUF3587, Protein of unknown function (DUF3587). This
protein is found in viruses. Proteins in this family are
typically between 209 and 248 amino acids in length.
Length = 201
Score = 27.7 bits (62), Expect = 0.57
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 7/29 (24%)
Query: 37 NWDYLLKRFGLNHRVFGRIIPSVCGKFTT 65
N D LL +FG I+P +FT+
Sbjct: 93 NVDSLL-------PIFGGIVPPGMDEFTS 114
>gnl|CDD|212131 cd11666, GH38N_Man2A1, N-terminal catalytic domain of Golgi
alpha-mannosidase II and similar proteins; glycoside
hydrolase family 38 (GH38). This subfamily is
represented by Golgi alpha-mannosidase II (GMII, also
known as mannosyl-oligosaccharide 1,3- 1,6-alpha
mannosidase, EC 3.2.1.114, Man2A1), a monomeric,
membrane-anchored class II alpha-mannosidase existing in
the Golgi apparatus of eukaryotes. GMII plays a key role
in the N-glycosylation pathway. It catalyzes the
hydrolysis of the terminal of both alpha-1,3-linked and
alpha-1,6-linked mannoses from the high-mannose
oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield
GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which
is the committed step of complex N-glycan synthesis.
GMII is activated by zinc or cobalt ions and is strongly
inhibited by swainsonine. Inhibition of GMII provides a
route to block cancer-induced changes in cell surface
oligosaccharide structures. GMII has a pH optimum of
5.5-6.0, which is intermediate between those of acidic
(lysosomal alpha-mannosidase) and neutral (ER/cytosolic
alpha-mannosidase) enzymes. GMII is a retaining glycosyl
hydrolase 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 = 344
Score = 26.8 bits (59), Expect = 1.2
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 40 YLLKRFGLNHRVFGRIIPSVCGKFTTQERLD 70
YLLKR GL++ + R+ SV F+ Q+ L+
Sbjct: 135 YLLKRAGLSNMLIQRVHYSVKKHFSLQKTLE 165
>gnl|CDD|219835 pfam08426, ICE2, ICE2. ICE2 is a fungal ER protein which has been
shown to play an important role in forming/maintaining
the cortical ER. It has also bee identified as a protein
which is necessary for nuclear inner membrane targeting.
Length = 406
Score = 26.2 bits (58), Expect = 2.1
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 13 YFTVIVMVAGNPKGLPVAWDYVKKNWDYLL 42
YF+ + N + + + WD LL
Sbjct: 80 YFSNDELNKKNWVLYLFYYSGLVEPWDTLL 109
>gnl|CDD|220395 pfam09778, Guanylate_cyc_2, Guanylylate cyclase. Members of this
family of proteins catalyze the conversion of guanosine
triphosphate (GTP) to 3',5'-cyclic guanosine
monophosphate (cGMP) and pyrophosphate.
Length = 212
Score = 25.8 bits (57), Expect = 2.7
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 40 YLLKRFGLNHRVFGRII---PSVCGKFTTQERLDE 71
YLLK+FG+ H F + + P+ + ++ D
Sbjct: 53 YLLKKFGVRHSYFTQTLGANPNYSVETFYKKHFDA 87
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 25.0 bits (55), Expect = 4.3
Identities = 6/26 (23%), Positives = 15/26 (57%)
Query: 16 VIVMVAGNPKGLPVAWDYVKKNWDYL 41
V+ A +G+ WD ++++ ++L
Sbjct: 207 VLTTSAVTGEGIDELWDAIEEHREFL 232
>gnl|CDD|190521 pfam03096, Ndr, Ndr family. This family consists of proteins from
different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3.
Their similarity was previously noted. The precise
molecular and cellular function of members of this
family is still unknown. Yet, they are known to be
involved in cellular differentiation events. The Ndr1
group was the first to be discovered. Their expression
is repressed by the proto-oncogenes N-myc and c-myc, and
in line with this observation, Ndr1 protein expression
is down-regulated in neoplastic cells, and is
reactivated when differentiation is induced by chemicals
such as retinoic acid. Ndr2 and Ndr3 expression is not
under the control of N-myc or c-myc. Ndr1 expression is
also activated by several chemicals: tunicamycin and
homocysteine induce Ndr1 in human umbilical endothelial
cells; nickel induces Ndr1 in several cell types.
Members of this family are found in wide variety of
multicellular eukaryotes, including an Ndr1 type protein
in Helianthus annuus (sunflower), known as Sf21.
Interestingly, the highest scoring matches in the noise
are all alpha/beta hydrolases pfam00561, suggesting that
this family may have an enzymatic function (Bateman A
pers. obs.).
Length = 284
Score = 25.0 bits (55), Expect = 4.3
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 40 YLLKRFGLNH--RVFGRIIPSVCGK 62
Y+L RF L H RV G ++ +
Sbjct: 111 YILARFALKHPERVEGLVLINPDPN 135
>gnl|CDD|227012 COG4666, COG4666, TRAP-type uncharacterized transport system, fused
permease components [General function prediction only].
Length = 642
Score = 24.6 bits (54), Expect = 6.3
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 13 YFTVIVMV-----AGNPKGLPV-----AWDYVKKNWDYLL 42
YF VI+MV GLP +K+ W YLL
Sbjct: 317 YFGVILMVHLEAKKDGLPGLPREQLPPLRPTLKEGWYYLL 356
>gnl|CDD|200935 pfam00022, Actin, Actin.
Length = 367
Score = 24.5 bits (54), Expect = 6.5
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 19 MVAGNP--KGLPVAWDYVKKNWDYLLKR 44
+ P G+ WD ++K W++
Sbjct: 58 LEVRYPIEDGIVENWDAMEKIWEHTFFE 85
>gnl|CDD|233737 TIGR02123, TRAP_fused, TRAP transporter, 4TM/12TM fusion protein.
In some species, the 12-transmembrane spanning and
4-transmembrane spanning components of tripartite
ATP-independent periplasmic (TRAP)-type transporters are
fused. This model describes such transporters, found in
the Archaea and in Bacteria [Transport and binding
proteins, Unknown substrate].
Length = 613
Score = 24.5 bits (54), Expect = 6.6
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 10/40 (25%)
Query: 13 YFTVIVMV---------AGNPK-GLPVAWDYVKKNWDYLL 42
+F V + V G K LP +K W L+
Sbjct: 296 FFGVFMQVHLEAKKQGLKGLSKEQLPSPKTVLKAGWYLLI 335
>gnl|CDD|233745 TIGR02141, modB_ABC, molybdate ABC transporter, permease protein.
This model describes the permease protein, ModB, of the
molybdate ABC transporter. This system has been
characterized in E. coli , Staphylococcus carnosus
Rhodobacter capsulatus and Azotobacter vinlandii.
Molybdate is chemically similar to sulfate, thiosulfate,
and selenate. These related substrates, and sometimes
molybdate itself, can be transported by the homologous
sulfate receptor. Some apparent molybdenum transport
operons include a permease related to this ModB,
although less similar than some sulfate permease
proteins and not included in this model [Transport and
binding proteins, Anions].
Length = 208
Score = 24.5 bits (54), Expect = 7.3
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 14 FTVIVMVAGNPKG----LPVA-WDYVKKNWD 39
F +M AGN G +P+A +D V+ +++
Sbjct: 152 FGATLMFAGNIPGETQTIPLAIYDAVESDYE 182
>gnl|CDD|131061 TIGR02006, IscS, cysteine desulfurase IscS. This model represents
IscS, one of several cysteine desulfurases from a larger
protein family designated (misleadingly, in this case)
class V aminotransferases. IscS is one of at least 6
enzymes characteristic of the IscSUA-hscAB-fsx system of
iron-sulfur cluster assembly. Scoring almost as well as
proteobacterial sequences included in the model are
mitochondrial cysteine desulfurases, apparently from an
analogous system in eukaryotes. The sulfur, taken from
cysteine, may be used in other systems as well, such as
tRNA base modification and biosynthesis of other
cofactors [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Protein synthesis, tRNA and rRNA
base modification].
Length = 402
Score = 24.4 bits (53), Expect = 7.6
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 40 YLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEK 75
Y+L+ G+N + I G+FTT+E +D +
Sbjct: 335 YVLRALGINDELAHSSIRFTIGRFTTEEEIDYAVKL 370
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 24.1 bits (53), Expect = 9.1
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 34 VKKNWDYLLKRFGL-NHRVFGRIIPS 58
V ++DY+++R GL + IPS
Sbjct: 684 VNGSFDYIIERLGLEDFYPRTLQIPS 709
>gnl|CDD|184409 PRK13942, PRK13942, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 212
Score = 24.2 bits (53), Expect = 9.8
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 61 GKFTTQERLDEVSEKSLKNLL 81
GK T ER+ E++EK+ K L
Sbjct: 102 GKVVTIERIPELAEKAKKTLK 122
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
0.321 0.139 0.424
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,239,885
Number of extensions: 345121
Number of successful extensions: 357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 357
Number of HSP's successfully gapped: 18
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (21.9 bits)
S2: 53 (24.2 bits)