RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16443
(412 letters)
>gnl|CDD|147799 pfam05839, Apc13p, Apc13p protein. The anaphase-promoting complex
(APC) is a conserved multi-subunit ubiquitin ligase
required for the degradation of key cell cycle
regulators Members of this family are components of the
anaphase-promoting complex homologous to Apc13p.
Length = 89
Score = 72.2 bits (177), Expect = 6e-16
Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 15/80 (18%)
Query: 84 MDSQ---VQSQGRLLDIVDNEWKEDKLPSDDISVPQNEL------------PDPDSDNGD 128
MDS V I+D+EW++D+LP DD++VP L PD + NG
Sbjct: 1 MDSYFTYVHLHAPHHAILDDEWRKDRLPPDDVAVPMPHLQPVNPEEEEDVVPDQHAANGI 60
Query: 129 SHLTLREQESKWTDLALSQL 148
T +E+E W DL L +L
Sbjct: 61 QKETQKEKEPAWRDLGLEEL 80
>gnl|CDD|201791 pfam01428, zf-AN1, AN1-like Zinc finger. Zinc finger at the
C-terminus of An1, a ubiquitin-like protein in Xenopus
laevis. The following pattern describes the zinc finger.
C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can
be any amino acid, and numbers in brackets indicate the
number of residues.
Length = 43
Score = 57.1 bits (138), Expect = 5e-11
Identities = 16/36 (44%), Positives = 20/36 (55%)
Query: 172 CGEPTCKQLDFLPFQCDLCKNIYCKEHMNPVQHNCT 207
C CK+ DFLPF+C C +C +H P HNC
Sbjct: 1 CSFKGCKKKDFLPFKCRFCGGTFCLKHRLPEDHNCP 36
Score = 38.2 bits (89), Expect = 2e-04
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 228 CSESGCSTLDQVEMLCEQCKHHFCVGHRF---HAC 259
CS GC D + C C FC+ HR H C
Sbjct: 1 CSFKGCKKKDFLPFKCRFCGGTFCLKHRLPEDHNC 35
>gnl|CDD|197545 smart00154, ZnF_AN1, AN1-like Zinc finger. Zinc finger at the
C-terminus of An1, a ubiquitin-like protein in Xenopus
laevis.
Length = 39
Score = 37.8 bits (88), Expect = 3e-04
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 176 TCKQLDFL-PFQCDLCKNIYCKEHMNPVQHNCTE 208
C++ L F+C C N++C EH P H+C
Sbjct: 3 FCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPG 36
Score = 25.4 bits (56), Expect = 6.7
Identities = 8/22 (36%), Positives = 9/22 (40%), Gaps = 3/22 (13%)
Query: 241 MLCEQCKHHFCVGHRF---HAC 259
C C + FC HR H C
Sbjct: 13 FKCRHCGNLFCGEHRLPEDHDC 34
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO modulates
the activity of LIM-homeodomain protein Apterous (Ap),
which regulates the formation of the dorsal-ventral axis
of the Drosophila wing. Biochemical analysis shows that
dLMO protein influences the activity of Apterous by
binding of its cofactor Chip. Further studies shown that
dLMO proteins might function in an evolutionarily
conserved mechanism involved in patterning the
appendages. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 32.1 bits (73), Expect = 0.046
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 243 CEQCKHHFCVGHRFHAC 259
C++C H FCVG RF+ C
Sbjct: 29 CQRCNHRFCVGDRFYLC 45
>gnl|CDD|218311 pfam04888, SseC, Secretion system effector C (SseC) like family.
SseC is a secreted protein that forms a complex together
with SecB and SecD on the surface of Salmonella. All
these proteins are secreted by the type III secretion
system. Many mucosal pathogens use type III secretion
systems for the injection of effector proteins into
target cells. SecB, SseC and SecD are inserted into the
target cell membrane. where they form a small pore or
translocon. In addition to SseC, this family includes
the bacterial secreted proteins PopB, PepB, YopB and
EspD which are thought to be directly involved in pore
formation, and type III secretion system translocon.
Length = 303
Score = 33.2 bits (76), Expect = 0.20
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 268 KMLREQWKIPKEQFKQAKLIADKQIEEKLSKAEIQTENRPLALKLRLMKLKSKAVG 323
K+ +Q K +Q ++A+ +K+ EE + +I+ A + + + SK G
Sbjct: 11 KLAEKQAKSKLQQLERARDKQEKKAEEY--QEQIKKAIEK-AEEAKKSGIFSKIFG 63
>gnl|CDD|114257 pfam05525, Branch_AA_trans, Branched-chain amino acid transport
protein. This family consists of several bacterial
branched-chain amino acid transport proteins which are
responsible for the transport of leucine, isoleucine and
valine via proton motive force.
Length = 428
Score = 31.8 bits (73), Expect = 0.67
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 37 LICLGSANLALTRLLSIS-----LIYITRLAIILLDF 68
LI ANL LT+++SIS LIY + +I+L
Sbjct: 320 LISFLVANLGLTKIISISVPVLVLIYPIAIVLIVLSL 356
>gnl|CDD|226110 COG3582, COG3582, Predicted nucleic acid binding protein containing
the AN1-type Zn-finger [General function prediction
only].
Length = 162
Score = 29.8 bits (67), Expect = 1.6
Identities = 3/35 (8%), Positives = 12/35 (34%)
Query: 183 LPFQCDLCKNIYCKEHMNPVQHNCTEYKDNVLLEK 217
LP + ++ + ++ + + +K
Sbjct: 12 LPSRGNITAKVSSTDNSLTLFSPFKLFIQLCDRKK 46
Score = 28.3 bits (63), Expect = 4.7
Identities = 15/83 (18%), Positives = 24/83 (28%), Gaps = 14/83 (16%)
Query: 124 SDNGDSHLTLREQESKWTDLALSQLILFLNSQQHFVIFIMELPQLGKQCGEPTCKQLDFL 183
S + T + S L I + G+ + L
Sbjct: 64 SAVSNPSNTDTPKRSTRVPL-------NGPFDSGKGITDRCATP--QCTGKGS-----TL 109
Query: 184 PFQCDLCKNIYCKEHMNPVQHNC 206
+C+ C +C EH P H+C
Sbjct: 110 AGKCNYCTGYFCAEHRLPENHDC 132
>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers. the domains occurs
between pairs og RING fingers.
Length = 64
Score = 27.4 bits (61), Expect = 2.3
Identities = 7/32 (21%), Positives = 9/32 (28%), Gaps = 7/32 (21%)
Query: 228 CSESGCSTL-------DQVEMLCEQCKHHFCV 252
C CS + C +C FC
Sbjct: 21 CPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCF 52
>gnl|CDD|233229 TIGR00999, 8a0102, Membrane Fusion Protein cluster 2 (function with
RND porters). [Transport and binding proteins, Other].
Length = 265
Score = 29.7 bits (67), Expect = 2.5
Identities = 13/38 (34%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 266 RRKMLREQWKIPKEQFKQAKL-IADKQIEEKLSKAEIQ 302
R K L EQ IP+++F+ A+ + + Q E + +K+E++
Sbjct: 41 REKKLFEQGVIPRQEFESAEYALEEAQAEVQAAKSELR 78
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 28.9 bits (65), Expect = 4.7
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 266 RRKMLREQWKIPKEQFKQAKLIAD-KQIEEKLSKAEIQT--ENRPLALKLRLMKLKSKAV 322
RRK L + K K+ K+ +A K+I +++++ E + + KLK + +
Sbjct: 288 RRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQRKERGEKKKLKRRKL 347
Query: 323 GDHRIPTAD 331
G H+ P
Sbjct: 348 GKHKYPEPP 356
>gnl|CDD|225951 COG3417, FlgN, Collagen-binding surface adhesin SpaP (antigen I/II
family) [General function prediction only].
Length = 200
Score = 28.7 bits (64), Expect = 4.9
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 4/64 (6%)
Query: 260 HQVETSRRKMLREQWKI-PKEQFKQAKL---IADKQIEEKLSKAEIQTENRPLALKLRLM 315
QVE R + Q I K A +S ++ + + L ++LM
Sbjct: 123 TQVEKQRLSEEKNQLGISEKGTLGSASKAIGGKRNSGAVYVSYSDASGDYKAPTLTMQLM 182
Query: 316 KLKS 319
+++
Sbjct: 183 LVQT 186
>gnl|CDD|223212 COG0134, TrpC, Indole-3-glycerol phosphate synthase [Amino acid
transport and metabolism].
Length = 254
Score = 28.7 bits (65), Expect = 5.0
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 229 SESGCSTLDQVEMLCEQCKHHFCVGHRFHACHQVETSRRKML 270
SESG ST + V L + F VG E + R++L
Sbjct: 212 SESGISTPEDVRRLAKAGADAFLVGEALMRADDPEEALRELL 253
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 28.1 bits (63), Expect = 5.9
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 8/54 (14%)
Query: 237 DQVEMLCEQCKHHF---CVGHRF-----HACHQVETSRRKMLREQWKIPKEQFK 282
Q+ L E H +G + + + R + E WK+PKE F
Sbjct: 121 KQIRALVEHHVHCRRLTALGIKGRYTWPVILNSIPALREVVTGEVWKLPKEHFG 174
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 28.7 bits (65), Expect = 6.6
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 54 SLIYITRLAIILLDFNDLELTSCF-SYATILMDSQVQSQGRLLDIVDNEW 102
++ T ++ DFN +S F + ATI++ +L+ DNEW
Sbjct: 271 GILGYTEDPLVSSDFNGDPHSSIFDASATIVLGGN---LVKLVAWYDNEW 317
>gnl|CDD|239497 cd03403, Band_7_stomatin_like, Band_7_stomatin_like: A subgroup of
the band 7 domain of flotillin (reggie) like proteins
similar to stomatin and podicin (two lipid
raft-associated integral membrane proteins). Individual
proteins of this band 7 domain family may cluster to
form membrane microdomains which may in turn recruit
multiprotein complexes. Stomatin is widely expressed
and, highly expressed in red blood cells. It localizes
predominantly to the plasma membrane and to
intracellular vesicles of the endocytic pathway, where
it is present in higher order homo-oligomeric complexes
(of between 9 and 12 monomers). Stomatin interacts with
and regulates members of the degenerin/epithelia Na+
channel family in mechanosensory cells of Caenorhabditis
elegans and vertebrate neurons and, is implicated in
trafficking of Glut1 glucose transporters. Prohibitin is
a mitochondrial inner-membrane protein hypothesized to
act as a chaperone for the stabilization of
mitochondrial proteins. Podicin localizes to the plasma
membrane of podocyte foot processes and, is found in
higher order oligomers. Podocin plays a role in
regulating glomerular permeability. Mutations in the
podicin gene give rise to autosomal recessive steroid
resistant nephritic syndrome. This group also contains
proteins similar to three Caenorhabditis elegans
proteins: UNC-1, UNC-24 and, MEC-2. Mutations in the
unc-1 and unc-24 genes result in abnormal motion and
altered patterns of sensitivity to volatile anesthetics.
MEC-2 and UNC-24 proteins interact with MEC-4 which is
part of the degenerin channel complex required for
response to gentle body touch.
Length = 215
Score = 28.3 bits (64), Expect = 6.7
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 282 KQAKLI---ADKQIEEKLSKAEIQTENRPLALKLRLM 315
K+AK+I ++Q L++A Q P AL+LR +
Sbjct: 160 KRAKIIEAEGERQAAILLAEAAKQAAINPAALQLREL 196
>gnl|CDD|214993 smart01047, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterised by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C.
Length = 49
Score = 25.8 bits (57), Expect = 7.2
Identities = 5/10 (50%), Positives = 7/10 (70%)
Query: 243 CEQCKHHFCV 252
C +CK FC+
Sbjct: 23 CTKCKQVFCI 32
>gnl|CDD|233143 TIGR00834, ae, anion exchange protein. The Anion Exchanger (AE)
Family (TC 2.A.31)Characterized protein members of the
AE family are found only in animals.They preferentially
catalyze anion exchange (antiport) reactions, typically
acting as HCO3-:Cl- antiporters, but also transporting a
range of other inorganic and organic anions.
Additionally, renal Na+:HCO3- cotransporters have been
found to be members of the AE family. They catalyze the
reabsorption of HCO3- in the renal proximal tubule
[Transport and binding proteins, Anions].
Length = 900
Score = 28.6 bits (64), Expect = 8.7
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 71 LELTSCFSYATILMDSQVQSQGRLLD-IVDNEWKEDKLPSDD 111
LEL CF+ IL+D S + + +VD+ ++ +D
Sbjct: 51 LELRRCFAKGAILLDLAATSLPGVANMVVDHLIYSGQIRPED 92
>gnl|CDD|226213 COG3688, COG3688, Predicted RNA-binding protein containing a PIN
domain [General function prediction only].
Length = 173
Score = 27.7 bits (62), Expect = 8.8
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 259 CHQVETSRRKMLREQWKIPKEQFKQAKLIADKQIEEKLSK 298
+VET ++ + KI KE+ ++ D +I EKL K
Sbjct: 129 YQEVETIEARISKSSRKISKEKPL-TRIALDPEILEKLEK 167
>gnl|CDD|161904 TIGR00507, aroE, shikimate 5-dehydrogenase. This model finds
proteins from prokaryotes and functionally equivalent
domains from larger, multifunctional proteins of fungi
and plants. Below the trusted cutoff of 180, but above
the noise cutoff of 20, are the putative shikimate
dehydrogenases of Thermotoga maritima and Mycobacterium
tuberculosis, and uncharacterized paralogs of shikimate
dehydrogenase from E. coli and H. influenzae. The
related enzyme quinate 5-dehydrogenase scores below the
noise cutoff. A neighbor-joining tree, constructed with
quinate 5-dehydrogenases as the outgroup, shows the
Clamydial homolog as clustering among the shikimate
dehydrogenases, although the sequence is unusual in the
degree of sequence divergence and the presence of an
additional N-terminal domain [Amino acid biosynthesis,
Aromatic amino acid family].
Length = 270
Score = 28.2 bits (63), Expect = 8.9
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 218 PTTTSIVSYKCSESGCSTLDQVEMLCEQCKHHF 250
P T ++ G T+D + ML Q F
Sbjct: 217 PLETPFLAE-AKSLGTKTIDGLGMLVYQAALSF 248
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
0.320 0.137 0.412
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,287,391
Number of extensions: 1899190
Number of successful extensions: 1494
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1490
Number of HSP's successfully gapped: 34
Length of query: 412
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 313
Effective length of database: 6,546,556
Effective search space: 2049072028
Effective search space used: 2049072028
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: 60 (26.9 bits)