RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15984
(68 letters)
>gnl|CDD|214540 smart00164, TBC, Domain in Tre-2, BUB2p, and Cdc16p. Probable
Rab-GAPs. Widespread domain present in Gyp6 and Gyp7,
thereby giving rise to the notion that it performs a
GTP-activator activity on Rab-like GTPases.
Length = 216
Score = 63.5 bits (155), Expect = 3e-14
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 2 SLSKV--TYVWEHLDVGYMQGMCDLVAPILVILDDESLTYSCFCCLMDRMAANFPTTG 57
SL +V Y + +VGY QGM L AP+L++++DE + C LM+R NF
Sbjct: 74 SLRRVLKAYALYNPEVGYCQGMNFLAAPLLLVMEDEEDAFWCLVKLMERYGPNFYLPD 131
>gnl|CDD|215997 pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain. Identification of a
TBC domain in GYP6_YEAST and GYP7_YEAST, which are
GTPase activator proteins of yeast Ypt6 and Ypt7,
implies that these domains are GTPase activator proteins
of Rab-like small GTPases.
Length = 206
Score = 48.5 bits (116), Expect = 1e-08
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 2 SLSKV--TYVWEHLDVGYMQGMCDLVAPILVILDDESLTYSCFCCLMDRMAANF 53
L ++ Y + DVGY QGM + AP+L+++ DE + CF L++ + +F
Sbjct: 64 QLRRILKAYSIYNPDVGYCQGMNFIAAPLLLVVLDEEEAFWCFVSLLEYLLRDF 117
>gnl|CDD|227535 COG5210, COG5210, GTPase-activating protein [General function
prediction only].
Length = 496
Score = 47.9 bits (114), Expect = 3e-08
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 6 VTYVWEHLDVGYMQGMCDLVAPILVILDDESLTYSCFCCLMDR 48
Y + +VGY+QGM L AP+L++L+ E + C L+
Sbjct: 290 KAYSLYNPEVGYVQGMNFLAAPLLLVLESEEQAFWCLVKLLKN 332
>gnl|CDD|215687 pfam00063, Myosin_head, Myosin head (motor domain).
Length = 679
Score = 28.4 bits (64), Expect = 0.20
Identities = 19/70 (27%), Positives = 26/70 (37%), Gaps = 14/70 (20%)
Query: 10 WEHLDVGYM-QGMCDLV----APILVILDDESL----TYSCFC-CLMDRMAANFPT---- 55
W +D G Q DL+ IL +LD+E T F L+D ++ P
Sbjct: 416 WTFIDYGLDNQACIDLIEKKPPGILSLLDEECRFPKATDQTFLEKLLDTFSSKHPHFSKP 475
Query: 56 TGGVMDNHFA 65
G D F
Sbjct: 476 RFGQGDTSFT 485
>gnl|CDD|232875 TIGR00211, glyS, glycyl-tRNA synthetase, tetrameric type, beta
subunit. The glycyl-tRNA synthetases differ even among
the eubacteria in oligomeric structure. In Escherichia
coli and most others, it is a heterodimer of two alpha
chains and two beta chains, encoded by tandem genes. The
genes are similar, but fused, in Chlamydia trachomatis.
By contrast, the glycyl-tRNA synthetases of Thermus
thermophilus and of archaea and eukaryotes differ
considerably; they are homodimeric, mutually similar,
and not detected by this model [Protein synthesis, tRNA
aminoacylation].
Length = 691
Score = 27.8 bits (62), Expect = 0.35
Identities = 7/27 (25%), Positives = 10/27 (37%)
Query: 41 CFCCLMDRMAANFPTTGGVMDNHFANM 67
L+ M FP G+M +A
Sbjct: 395 SKADLVTNMVYEFPELQGIMGEKYARH 421
>gnl|CDD|173978 cd08213, RuBisCO_large_III, Ribulose bisphosphate carboxylase large
chain, Form III. Ribulose bisphosphate carboxylase
(Rubisco) plays an important role in the Calvin
reductive pentose phosphate pathway. It catalyzes the
primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV , which differ in
their taxonomic distribution and subunit composition.
Form III is only found in archaea and forms large
subunit oligomers (dimers or decamers) that do not
include small subunits.
Length = 412
Score = 26.6 bits (59), Expect = 0.93
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 11 EHLDVGY--MQGMCDLVAPILVILDDESLTYSCFCCLMDRMAA 51
EH +V Y + G DLV DDE+LT F +R
Sbjct: 148 EHAEVAYEALVGGVDLVK------DDENLTSQPFNRFEERAKE 184
>gnl|CDD|187599 cd05340, Ycik_SDR_c, Escherichia coli K-12 YCIK-like, classical
(c) SDRs. Escherichia coli K-12 YCIK and related
proteins have a canonical classical SDR
nucleotide-binding motif and active site tetrad. They
are predicted oxoacyl-(acyl carrier protein/ACP)
reductases. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 236
Score = 26.0 bits (57), Expect = 1.3
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 25 VAPILVILDDESLTYSCFCCLMDRMAANFPTTGGVMDN 62
P ILD + T L R+A N+P GV+ N
Sbjct: 54 RQPQWFILDLLTCTSENCQQLAQRIAVNYPRLDGVLHN 91
>gnl|CDD|182116 PRK09856, PRK09856, fructoselysine 3-epimerase; Provisional.
Length = 275
Score = 25.6 bits (56), Expect = 1.8
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 6 VTYVWEHLDVGYMQGMCDLVAPILVILDDESLTYSCFCCLMDRMA-ANFPTTGGVMDNHF 64
V + + + M D+ AP + E + S F L D++ + + G D H+
Sbjct: 164 VLHALALVPSPRLFSMVDICAP---YVQAEPVM-SYFDKLGDKLRHLHIVDSDGASDTHY 219
>gnl|CDD|234483 TIGR04150, pseudo_rSAM_GG, pseudo-rSAM protein, GG-Bacteroidales
system. Many peptide-modifying radical SAM enzymes
have two 4Fe4S-binding regions, an N-terminal one
recognized by Pfam radical SAM domain-defining model
pfam04055 and a C-terminal one recognized by TIGR04085.
Members of this protein family occur in cassettes with
such a radical SAM family (TIGR04148) and with a
peptide modification target (TIGR04149). Surprisingly,
members of this family show full-length homology to
each other, with several scoring at least borderline
hits to both pfam04055 and TIGR04085, and yet differ in
the presence/absence of a signature CX(3)CX(2)CX(9)C
motif. Instead, members are best-conserved in the
TIGR04085-like C-terminal region. Therefore, this
protein family is designated a pseudo-radical-SAM
protein, which likely works in partnership with a
TIGR04148 family protein.
Length = 407
Score = 25.7 bits (57), Expect = 1.8
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 30 VILDDESLTYSCFCCLMDRMAANF 53
V+LD+E+L + + + F
Sbjct: 52 VLLDEENLRDNEVKEFVSELREKF 75
>gnl|CDD|239125 cd02660, Peptidase_C19D, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin
molecules from polyubiquinated peptides by cleavage of
isopeptide bonds. They hydrolyze bonds involving the
carboxyl group of the C-terminal Gly residue of
ubiquitin. The purpose of the de-ubiquitination is
thought to be editing of the ubiquitin conjugates,
which could rescue them from degradation, as well as
recycling of the ubiquitin. The ubiquitin/proteasome
system is responsible for most protein turnover in the
mammalian cell, and with over 50 members, family C19 is
one of the largest families of peptidases in the human
genome.
Length = 328
Score = 25.8 bits (57), Expect = 1.9
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 38 TYSCFCCLMDRMAANFPTTG 57
SC C MD + F +G
Sbjct: 43 PNSCLSCAMDEIFQEFYYSG 62
>gnl|CDD|214580 smart00242, MYSc, Myosin. Large ATPases. ATPase; molecular motor.
Muscle contraction consists of a cyclical interaction
between myosin and actin. The core of the myosin
structure is similar in fold to that of kinesin.
Length = 677
Score = 25.2 bits (56), Expect = 2.8
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 4/33 (12%)
Query: 10 WEHLDVGYMQGMCDLVAP----ILVILDDESLT 38
W +D Q DL+ IL +LD+E
Sbjct: 422 WTFIDFFDNQDCIDLIEKKPPGILSLLDEECRF 454
>gnl|CDD|217280 pfam02906, Fe_hyd_lg_C, Iron only hydrogenase large subunit,
C-terminal domain.
Length = 272
Score = 24.5 bits (54), Expect = 5.6
Identities = 6/13 (46%), Positives = 6/13 (46%)
Query: 48 RMAANFPTTGGVM 60
F TGGVM
Sbjct: 177 GAGRIFGVTGGVM 189
>gnl|CDD|236731 PRK10658, PRK10658, putative alpha-glucosidase; Provisional.
Length = 665
Score = 24.1 bits (53), Expect = 7.5
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 11 EHLDVGYMQGMCDLVAPI 28
++LD YM G LVAP+
Sbjct: 601 DYLDRQYMLGDSLLVAPV 618
>gnl|CDD|133235 cd05104, PTKc_Kit, Catalytic domain of the Protein Tyrosine Kinase,
Kit. Protein Tyrosine Kinase (PTK) family; Kit (or
c-Kit); catalytic (c) domain. The PTKc family is part of
a larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Kit is a member of the
Platelet Derived Growth Factor Receptor (PDGFR)
subfamily of proteins, which are receptor tyr kinases
(RTKs) containing an extracellular ligand-binding region
with five immunoglobulin-like domains, a transmembrane
segment, and an intracellular catalytic domain. The
binding of Kit to its ligand, the stem-cell factor
(SCF), leads to receptor dimerization, trans
phosphorylation and activation, and intracellular
signaling. Kit is important in the development of
melanocytes, germ cells, mast cells, hematopoietic stem
cells, the interstitial cells of Cajal, and the
pacemaker cells of the GI tract. Kit signaling is
involved in major cellular functions including cell
survival, proliferation, differentiation, adhesion, and
chemotaxis. Mutations in Kit, which result in
constitutive ligand-independent activation, are found in
human cancers such as gastrointestinal stromal tumor
(GIST) and testicular germ cell tumor (TGCT). The
aberrant expression of Kit and/or SCF is associated with
other tumor types such as systemic mastocytosis and
cancers of the breast, neurons, lung, prostate, colon,
and rectum. Although the structure of the human Kit
catalytic domain is known, it is excluded from this
specific alignment model because it contains a deletion
in its sequence.
Length = 375
Score = 23.7 bits (51), Expect = 8.5
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 1 MSLSKV-TYVWEHLDVGYMQGMCDLVAPILVILDDESLTYSCFCCLMD 47
MS KV +Y+ H+++ + G C + P LVI + +CC D
Sbjct: 86 MSELKVLSYLGNHINIVNLLGACTVGGPTLVITE--------YCCYGD 125
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
0.329 0.139 0.457
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,279,587
Number of extensions: 225502
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 14
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.0 bits)