RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11261
(247 letters)
>gnl|CDD|214697 smart00498, FH2, Formin Homology 2 Domain. FH proteins control
rearrangements of the actin cytoskeleton, especially in
the context of cytokinesis and cell polarisation.
Members of this family have been found to interact with
Rho-GTPases, profilin and other actin-assoziated
proteins. These interactions are mediated by the
proline-rich FH1 domain, usually located in front of FH2
(but not listed in SMART). Despite this cytosolic
function, vertebrate formins have been assigned
functions within the nucleus. A set of Formin-Binding
Proteins (FBPs) has been shown to bind FH1 with their WW
domain.
Length = 392
Score = 29.6 bits (67), Expect = 1.5
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 26 ASRDISRKRTQYVLMSLEAMNQILLSCHAHALNLLQKKL-------IQKLLECHEHVLQI 78
AS+D+S K++ + +IL + L +L +KL + +LE E VL +
Sbjct: 55 ASKDVSEKKS-ILKKKASQEFKILDPKRSQNLAILLRKLHMSYEEIKEAILEGDEDVLSV 113
Query: 79 LATQSFVKYANIEED 93
+ +KYA +E+
Sbjct: 114 DLLEQLLKYAPTKEE 128
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 29.5 bits (66), Expect = 1.9
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 105 ISKFSSMCHDSDVELRMAGISGIQGIIRKTVSDDLADNIWKSHH------LDKRWIS 155
I+K SS+ H E+RM GI G GI + T++ L + S +D+ +IS
Sbjct: 193 IAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRL--SRQFQSSVFIDRAFIS 247
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 26.8 bits (60), Expect = 3.5
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 47 QILLSCHAHALNLLQKKLIQKLLECHEHVLQIL----ATQSFVKYANIEEDTPSYHR 99
Q L+ + N + ++ + ++ E + V ++ FV Y++IE+ +Y
Sbjct: 2 QHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDA 58
>gnl|CDD|133237 cd05106, PTKc_CSF-1R, Catalytic domain of the Protein Tyrosine
Kinase, Colony-Stimulating Factor-1 Receptor. Protein
Tyrosine Kinase (PTK) family; Colony-Stimulating
Factor-1 Receptor (CSF-1R); 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. CSF-1R,
also called c-Fms, 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
CSF-1R to its ligand, CSF-1, leads to receptor
dimerization, trans phosphorylation and activation, and
intracellular signaling. CSF-1R signaling is critical in
the regulation of macrophages and osteoclasts. It leads
to increases in gene transcription and protein
translation, and induces cytoskeletal remodeling. CSF-1R
signaling leads to a variety of cellular responses
including survival, proliferation, and differentiation
of target cells. It plays an important role in innate
immunity, tissue development and function, and the
pathogenesis of some diseases including atherosclerosis
and cancer. CSF-1R signaling is also implicated in
mammary gland development during pregnancy and
lactation. Aberrant CSF-1/CSF-1R expression correlates
with tumor cell invasiveness, poor clinical prognosis,
and bone metastasis in breast cancer. Although the
structure of the human CSF-1R catalytic domain is known,
it is excluded from this specific alignment model
because it contains a deletion in its sequence.
Length = 374
Score = 27.9 bits (62), Expect = 5.6
Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 52 CHAHALNLLQKKLIQKLLECHEHVLQILATQSFVKYANIEEDTPSYHRRYDFFISKFSSM 111
C+ LN L+KK + L + +I T S Y NI + ++Y S FSS
Sbjct: 125 CYGDLLNFLRKK-AETFLNFVMALPEISETSS--DYKNITLE-----KKYIRSDSGFSSQ 176
Query: 112 CHDSDVELRMAGISGIQGIIRKTVSDD 138
D+ VE+R S Q K D
Sbjct: 177 GSDTYVEMRPVSSSSSQSSDSKDEEDT 203
>gnl|CDD|224728 COG1815, FlgB, Flagellar basal body protein [Cell motility and
secretion].
Length = 133
Score = 26.5 bits (59), Expect = 7.9
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 2/40 (5%)
Query: 66 QKLLECHEHVLQILATQSFVKYANIEE-DTPSYHRRY-DF 103
+ + L + + + V NI DTP Y + DF
Sbjct: 5 DRAFGLLQKALDVRSLRQEVIANNIANADTPGYKAKDVDF 44
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 27.1 bits (60), Expect = 9.5
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 40 MSL---EAMNQILLS----CHAHALNLLQKKLIQKLLECHEHVLQILATQSFVKYANIEE 92
M L EA+N+++L+ ALN L +L QK+ + +LQ+LA + EE
Sbjct: 112 MDLTQAEAINELILAPNNKVKDIALNKLAGELDQKIEAIRKSLLQLLAQVEV--NIDYEE 169
Query: 93 DTP 95
D
Sbjct: 170 DDD 172
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
0.323 0.137 0.410
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,695,394
Number of extensions: 1199067
Number of successful extensions: 933
Number of sequences better than 10.0: 1
Number of HSP's gapped: 933
Number of HSP's successfully gapped: 17
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (25.9 bits)