RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7966
(194 letters)
>gnl|CDD|176411 cd01816, Raf_RBD, Ubiquitin domain of Raf serine/threonine
kinases. The Raf serine/threonine kinases are composed
of three conserved regions, CR1, CR2 and CR3. CR1 has
two Ras binding domains (RBD and CRD), CR2 is a
serine/threonine rich domain and CR3 is the catalytic
kinase domain. The RBD of Raf is structurally similar
to ubiquitin with little of no sequence similarity.The
Raf signalling pathway plays an important role in the
proliferation and survival of tumor cells.
Length = 74
Score = 77.4 bits (191), Expect = 2e-19
Identities = 33/73 (45%), Positives = 48/73 (65%), Gaps = 4/73 (5%)
Query: 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY----DSNTGVSLQWDTD 58
L+R LPN+QRT V++R G TL +AL+KA+K+R L+PE C + S+ + + WDTD
Sbjct: 1 LIRVFLPNKQRTVVNVRPGMTLRDALAKALKVRGLQPECCAVFRLGDGSSKKLRIDWDTD 60
Query: 59 SDHLPTTEIRVEV 71
L E++VEV
Sbjct: 61 ISSLIGEELQVEV 73
>gnl|CDD|202147 pfam02196, RBD, Raf-like Ras-binding domain.
Length = 71
Score = 61.6 bits (150), Expect = 4e-13
Identities = 30/70 (42%), Positives = 37/70 (52%)
Query: 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDH 61
R LPN QR+ V +R G T+ +AL+KA K R L P C S L DTD
Sbjct: 1 KTCRVHLPNNQRSVVEVRPGMTVRDALAKACKRRGLNPSACAVRLSGEKKPLDLDTDISS 60
Query: 62 LPTTEIRVEV 71
LP E+RVE+
Sbjct: 61 LPGEELRVEL 70
>gnl|CDD|128731 smart00455, RBD, Raf-like Ras-binding domain.
Length = 70
Score = 61.1 bits (149), Expect = 4e-13
Identities = 24/69 (34%), Positives = 34/69 (49%)
Query: 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHL 62
+ LP+ QRT V +R G+T+ +AL+KA+K R L PE C L + L
Sbjct: 1 TCKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLDLNQPISSL 60
Query: 63 PTTEIRVEV 71
E+ VE
Sbjct: 61 DGQELVVEE 69
>gnl|CDD|176358 cd01760, RBD, Ubiquitin-like domain of RBD-like S/T kinases. The
ras-binding domain (RBD) of the serine/threonine kinase
raf is structurally quite similar to the beta-grasp
fold of ubiquitin. A raf-like RBD is also present in
RGS12 and other members of a family of GTPase
activating proteins and TIAM1, a guanine nucleotide
exchange protein.
Length = 72
Score = 60.3 bits (147), Expect = 8e-13
Identities = 29/71 (40%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY--DSNTGVSLQWDTDSD 60
L R LPN QRT V +R G ++ + L+KA K R L PE C + + L DTDS
Sbjct: 1 LCRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGLDEKKPLDLDTDSS 60
Query: 61 HLPTTEIRVEV 71
L E+ VE
Sbjct: 61 SLAGEELEVEP 71
>gnl|CDD|237996 cd00029, C1, Protein kinase C conserved region 1 (C1) .
Cysteine-rich zinc binding domain. Some members of this
domain family bind phorbol esters and diacylglycerol,
some are reported to bind RasGTP. May occur in tandem
arrangement. Diacylglycerol (DAG) is a second messenger,
released by activation of Phospholipase D. Phorbol
Esters (PE) can act as analogues of DAG and mimic its
downstream effects in, for example, tumor promotion.
Protein Kinases C are activated by DAG/PE, this
activation is mediated by their N-terminal conserved
region (C1). DAG/PE binding may be phospholipid
dependent. C1 domains may also mediate DAG/PE signals in
chimaerins (a family of Rac GTPase activating proteins),
RasGRPs (exchange factors for Ras/Rap1), and Munc13
isoforms (scaffolding proteins involved in exocytosis).
Length = 50
Score = 39.8 bits (93), Expect = 3e-05
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 83 HNITRRTFFAIAFCDACHKLLFS----GHLCRTCGFKFHRACNLAVPYLC 128
H R++FF FCD C K ++ G C C K H+ C VP C
Sbjct: 1 HRFVRKSFFKPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKVPPSC 50
>gnl|CDD|215738 pfam00130, C1_1, Phorbol esters/diacylglycerol binding domain (C1
domain). This domain is also known as the Protein
kinase C conserved region 1 (C1) domain.
Length = 53
Score = 39.0 bits (91), Expect = 6e-05
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 83 HNITRRTFFAIAFCDACHKLLFSGHL----CRTCGFKFHRACNLAVPYLCQ 129
H+ RTF + FCD C + L+ C CG H+ C+ VP C
Sbjct: 1 HHFVHRTFKSPTFCDHCGEFLWGLGKQGLKCSWCGLNVHKRCHSLVPPECG 51
>gnl|CDD|197519 smart00109, C1, Protein kinase C conserved region 1 (C1) domains
(Cysteine-rich domains). Some bind phorbol esters and
diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Length = 50
Score = 38.2 bits (89), Expect = 1e-04
Identities = 16/50 (32%), Positives = 19/50 (38%), Gaps = 4/50 (8%)
Query: 83 HNITRRTFFAIAFCDACHKLLFSGHL----CRTCGFKFHRACNLAVPYLC 128
H RTF FC C K ++ C C K H+ C VP C
Sbjct: 1 HKHVFRTFTKPTFCCVCRKSIWGSFKQGLRCSECKVKCHKKCADKVPKAC 50
>gnl|CDD|117542 pfam08976, DUF1880, Domain of unknown function (DUF1880). This
domain is found predominantly in DJ binding protein. It
has no known function.
Length = 122
Score = 29.8 bits (66), Expect = 0.47
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 148 TSAGILQMPSDYRPGSNTRKHPKTLANLVCYPGIVQRRDCN 188
T + + P D RPG ++ HP T A+ PG ++C+
Sbjct: 67 TRSALSLPPQDLRPGLKSQSHPCTPASTTVIPGTPPLQNCD 107
>gnl|CDD|185698 cd09021, Aldose_epim_Ec_YphB, aldose 1-epimerase, similar to
Escherichia coli YphB. Proteins similar to Escherichia
coli YphB are uncharacterized members of the
aldose-1-epimerase superfamily. Aldose 1-epimerases or
mutarotases are key enzymes of carbohydrate metabolism,
catalyzing the interconversion of the alpha- and
beta-anomers of hexose sugars such as glucose and
galactose. This interconversion is an important step
that allows anomer specific metabolic conversion of
sugars. Studies of the catalytic mechanism of the best
known member of the family, galactose mutarotase, have
shown a glutamate and a histidine residue to be critical
for catalysis; the glutamate serves as the active site
base to initiate the reaction by removing the proton
from the C-1 hydroxyl group of the sugar substrate, and
the histidine as the active site acid to protonate the
C-5 ring oxygen.
Length = 273
Score = 30.3 bits (69), Expect = 0.54
Identities = 8/30 (26%), Positives = 8/30 (26%)
Query: 49 TGVSLQWDTDSDHLPTTEIRVEVQERFPAA 78
W D DHLPT F
Sbjct: 156 ADADGVWLEDEDHLPTGLRPHPPDWDFSQP 185
>gnl|CDD|176413 cd01818, TIAM1_RBD, Ubiquitin domain of Tiam1 guanine nucleotide
exchange factor. Tiam1 (T lymphoma invasion and
metastasis 1) a guanine nucleotide exchange factor that
activates Rac, is an important regulator of Rho GTPase
functions in tumor cells including regulation of cell
shape and invasiveness in epithelial cells and
fibroblasts. TIAM1 has an RBD (Ras-binding domain)
similar to that of Raf kinase as well as PH (pleckstrin
homology), PDZ, and RhoGEF domains.
Length = 77
Score = 28.6 bits (64), Expect = 0.55
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 8 LPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDH 61
LP+ Q ++R G ++ + L A K + L P + L++ +H
Sbjct: 6 LPDNQPVLTYLRPGMSVEDFLESACKRKQLDP-------MEHYLRLKFLRMENH 52
>gnl|CDD|219497 pfam07649, C1_3, C1-like domain. This short domain is rich in
cysteines and histidines. The pattern of conservation is
similar to that found in pfam00130.
Length = 30
Score = 27.3 bits (61), Expect = 0.58
Identities = 8/28 (28%), Positives = 10/28 (35%), Gaps = 2/28 (7%)
Query: 95 FCDACHKLLFSGHL--CRTCGFKFHRAC 120
C+AC + C C F H C
Sbjct: 2 TCNACGLPIDGDPFYSCSECDFVLHEDC 29
>gnl|CDD|200417 TIGR04166, methano_MtrB, tetrahydromethanopterin
S-methyltransferase, subunit B. Members of this
protein family are the MtrB protein of the
tetrahydromethanopterin S-methyltransferase complex.
This system is universal in archaeal methanogens
[Energy metabolism, Methanogenesis].
Length = 95
Score = 28.4 bits (64), Expect = 0.84
Identities = 12/57 (21%), Positives = 25/57 (43%)
Query: 39 PEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQERFPAAINIEHNITRRTFFAIAF 95
PE+ D TG+ + D L + E+ + AA ++ +++ RT ++
Sbjct: 7 PELGLVMDPETGIVAEGREDVILLSMDPVNEEIDKLEAAADDLVNSLDPRTTPLGSY 63
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are identified
in a diverse group of proteins with wide variety of
biological functions, including gene expression
regulation, cell fate determination, cytoskeleton
organization, tumor formation and development. LIM
domains function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. They perform
their functions through interactions with other protein
partners. LIM domains are 50-60 amino acids in size and
share two characteristic highly conserved zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. The consensus
sequence of LIM domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 25.7 bits (57), Expect = 3.2
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 96 CDACHKLLFSGHLCRTCGFKFHRAC 120
C C K + L R G K+H C
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPEC 25
>gnl|CDD|204889 pfam12344, UvrB, Ultra-violet resistance protein B. This domain
family is found in bacteria, archaea and eukaryotes,
and is approximately 40 amino acids in length. The
family is found in association with pfam00271,
pfam02151, pfam04851. There are two conserved sequence
motifs: YAD and RRR. This family is the C terminal
region of the UvrB protein which conveys mutational
resistance against UV light to various different
species.
Length = 44
Score = 25.5 bits (57), Expect = 3.4
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 65 TEIRVEVQERFPAAINIEHNITRRT 89
TE R E+Q + N EH IT +T
Sbjct: 17 TERRREIQIAY----NEEHGITPKT 37
>gnl|CDD|220540 pfam10050, DUF2284, Predicted metal-binding protein (DUF2284).
Members of this family of metal-binding hypothetical
bacterial proteins have no known function.
Length = 166
Score = 27.3 bits (61), Expect = 3.9
Identities = 14/67 (20%), Positives = 21/67 (31%), Gaps = 9/67 (13%)
Query: 56 DTDSDHLPTTEIRVEVQERFPAAINIEHNITRRTFFAIAFCDACHKLLFSGH--LCRTCG 113
+ E+ E + + +E R F F A L +G LC TC
Sbjct: 61 PVEDIEDDPEEMFKEKRRVNKILLELE-----RKAFLAGFYKAFA--LGAGPCNLCETCA 113
Query: 114 FKFHRAC 120
+ C
Sbjct: 114 AEKGGPC 120
>gnl|CDD|151909 pfam11470, TUG, GLUT4 regulating protein TUG. TUG is a GLUT4
regulating protein and functions to retain membrane
vesicles containing GLUT4 intracellularly. TUG releases
the GLUT4 containing vesicles to the cellular exocytic
machinery in response to insulin stimulation which
allows translocation to the plasma membrane. TUG has an
N-terminal ubiquitin-like domain (UBL1) which in
similar proteins appears to participate in
protein-protein interactions. The region does have a
area of negative electrostatic potential and increased
backbone motility which leads to suggestions of a
potential protein-protein interaction site.
Length = 65
Score = 25.6 bits (57), Expect = 4.2
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 9 PNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGV--SLQW 55
N +R +V + TL + L +A K L P T + + SL +
Sbjct: 4 YNFRRVTVKVTPSTTLNQVLEEACKKFGLDPSEYTLKHNRKPLDLSLPF 52
>gnl|CDD|117316 pfam08746, zf-RING-like, RING-like domain. This is a zinc finger
domain that is related to the C3HC4 RING finger domain
(pfam00097).
Length = 43
Score = 25.1 bits (55), Expect = 4.9
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 96 CDACHKLLFSGHLC--RTCGFKFHRAC 120
C+ CH+++ G C R C ++H C
Sbjct: 1 CEVCHEIVTQGQRCGNRDCNIRWHVDC 27
>gnl|CDD|222758 pfam14446, Prok-RING_1, Prokaryotic RING finger family 1. RING
finger family found sporadically in bacteria and
archaea, and associated in gene neighborhoods with other
components of the ubiquitin-based signaling and
degradation system, including ubiquitin, the E1 and E2
proteins and the JAB-like metallopeptidase. The
bacterial versions contain transmembrane helices.
Length = 55
Score = 25.1 bits (55), Expect = 5.4
Identities = 10/28 (35%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 96 CDACHKLLFSGHL---CRTCGFKFHRAC 120
C C K G C CG +HR C
Sbjct: 8 CPVCGKKFKPGDDIVVCPECGAPYHREC 35
>gnl|CDD|205940 pfam13767, DUF4168, Domain of unknown function (DUF4168).
Length = 78
Score = 25.6 bits (57), Expect = 5.8
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 129 QVERIQQTYYQMLLASNAETSAGILQMPSDYR 160
+E I+Q YYQ + AE A + + +
Sbjct: 15 AIEPIRQEYYQEI--QAAEDPAEAQALQQEAQ 44
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 25.1 bits (55), Expect = 6.2
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 95 FCDACHKLLFSGHL--CRTCGFKFHRAC 120
+C C K+ G L C C FH AC
Sbjct: 1 YCAVCGKVDDDGELLLCDGCDRWFHLAC 28
>gnl|CDD|227944 COG5657, CSE1, CAS/CSE protein involved in chromosome segregation
[Cell division and chromosome partitioning].
Length = 947
Score = 27.1 bits (60), Expect = 6.6
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 113 GFKFHRACNLAVPYLCQVERIQQTYYQMLLASNAETSAGILQMPS 157
F C + +P L + +L E + +LQ+ S
Sbjct: 608 VFLKSGMCEITIPTLVLAL--VPEFPVLLSEDATELWSYVLQLLS 650
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 24.9 bits (54), Expect = 7.0
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 95 FCDACHKLLFSGHL--CRTCGFKFHRAC 120
+C C K G L C C +H+ C
Sbjct: 1 YCSVCGKPDDGGELLQCDGCDRWYHQTC 28
>gnl|CDD|223410 COG0333, RpmF, Ribosomal protein L32 [Translation, ribosomal
structure and biogenesis].
Length = 57
Score = 24.9 bits (55), Expect = 7.2
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 87 RRTFFA-----IAFCDACHKLLFSGHLCRTCGF 114
RR+ A ++ C C + +C CG+
Sbjct: 16 RRSHDALKAPTLSVCPNCGEYKLPHRVCLKCGY 48
>gnl|CDD|233239 TIGR01031, rpmF_bact, ribosomal protein L32. This protein
describes bacterial ribosomal protein L32. The noise
cutoff is set low enough to include the equivalent
protein from mitochondria and chloroplasts. No related
proteins from the Archaea nor from the eukaryotic
cytosol are detected by this model. This model is a
fragment model; the putative L32 of some species shows
similarity only toward the N-terminus [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 55
Score = 24.6 bits (54), Expect = 9.2
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 92 AIAFCDACHKLLFSGHLCRTCGF 114
+ C C + +C +CG+
Sbjct: 25 TLVVCPNCGEFKLPHRVCPSCGY 47
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
0.324 0.135 0.418
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,443,096
Number of extensions: 818848
Number of successful extensions: 891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 886
Number of HSP's successfully gapped: 35
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.3 bits)