RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17879
(154 letters)
>gnl|CDD|128458 smart00153, VHP, Villin headpiece domain.
Length = 36
Score = 60.8 bits (148), Expect = 1e-13
Identities = 20/36 (55%), Positives = 27/36 (75%)
Query: 119 HLSDVEFETLFLCTRAEFYRLPTWRRNDLKKRARLF 154
+LSD +FE +F TR EFY+LP W++N LKK+ LF
Sbjct: 1 YLSDEDFEEVFGMTREEFYKLPLWKQNQLKKKKGLF 36
>gnl|CDD|202157 pfam02209, VHP, Villin headpiece domain.
Length = 36
Score = 60.8 bits (148), Expect = 1e-13
Identities = 19/36 (52%), Positives = 27/36 (75%)
Query: 119 HLSDVEFETLFLCTRAEFYRLPTWRRNDLKKRARLF 154
+LSD +FE +F T+ EFY+LP W++N LKK+ LF
Sbjct: 1 YLSDEDFEEVFGMTKEEFYKLPAWKQNQLKKKLGLF 36
>gnl|CDD|178406 PLN02810, PLN02810, carbon-monoxide oxygenase.
Length = 231
Score = 30.6 bits (69), Expect = 0.27
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 5 TFKDLIQPYSLFNLHPQLTLFSTFTVSNGSIYDLHSNIHPHHHVPNGGAPELPVSSTYAG 64
T K+LI FNLHP L L + +I S + V L + G
Sbjct: 41 TNKNLI-----FNLHPVLMLIGLIIIGGEAIMSYKS-LPLKKEVKKLIHLVLHAIALILG 94
Query: 65 SLGYAASYSNHIQRSLPNM 83
G A++ NH + + N+
Sbjct: 95 IFGICAAFKNHNESGIANL 113
>gnl|CDD|118503 pfam09974, DUF2209, Uncharacterized protein conserved in archaea
(DUF2209). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 128
Score = 27.8 bits (62), Expect = 1.5
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 122 DVEFETLFLCTRAEFYRLPTWRRNDLKKRA 151
D +FE + + EF+ P WR + +
Sbjct: 65 DKDFEYTIVAEKGEFFNQPEWRVSAMLSAP 94
>gnl|CDD|221329 pfam11938, DUF3456, TLR4 regulator and MIR-interacting MSAP. This
family of proteins, found from plants to humans, is
PRAT4 (A and B), a Protein Associated with Toll-like
receptor 4. The Toll family of receptors - TLRs - plays
an essential role in innate recognition of microbial
products, the first line of defence against bacterial
infection. PRAT4A influences the subcellular
distribution and the strength of TLR responses and
alters the relative activity of each TLR. PRAT4B
regulates TLR4 trafficking to the cell surface and the
extent of its expression there. TLR4 recognizes
lipopolysaccharide (LPS), one of the most
immuno-stimulatory glycolipids constituting the outer
membrane of the Gram-negative bacteria. This family has
also been described as a SAP-like MIR-interacting
protein family.
Length = 151
Score = 27.7 bits (62), Expect = 2.0
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 96 PYHLLIITNYRLPPDVDRKNLERHL--SDVEFETLF--LCTRAEFYRL 139
P + + +RL PD RK +++ S++ L +C R Y L
Sbjct: 23 PKKEVDVGGFRLDPDGKRKGKKKYYARSELRLTELLEGVCDRMLDYNL 70
>gnl|CDD|184847 PRK14843, PRK14843, dihydrolipoamide acetyltransferase;
Provisional.
Length = 347
Score = 27.9 bits (62), Expect = 2.2
Identities = 23/59 (38%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 3 VVTFKDLIQPYSLFNLHPQLTLFSTFTVSNGSIYDLHSNIHPHHHVPNGGAPELPVSST 61
VV FKD+I L P STFT+SN ++ + S P + PN L VSST
Sbjct: 240 VVAFKDVIGRTLDGKLAPSELQNSTFTISNLGMFGVQS-FGPIINQPNSAI--LGVSST 295
>gnl|CDD|217412 pfam03186, CobD_Cbib, CobD/Cbib protein. This family includes CobD
proteins from a number of bacteria, in Salmonella this
protein is called Cbib. Salmonella CobD is a different
protein. This protein is involved in cobalamin
biosynthesis and is probably an enzyme responsible for
the conversion of adenosylcobyric acid to
adenosylcobinamide or adenosylcobinamide phosphate.
Length = 295
Score = 27.1 bits (61), Expect = 3.8
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 4/25 (16%)
Query: 43 HPHHHVPNGGAPELPVSSTYAGSLG 67
H PN G PE + AG+LG
Sbjct: 233 ARKHPSPNAGWPE----AAMAGALG 253
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 27.2 bits (61), Expect = 3.8
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 85 QPMSLEPPKIYPYHLLIITNYRLPPDVDRKNLERHLSDVEF 125
Q M PP H+LI T L ++ L DV +
Sbjct: 117 QKMLKNPP-----HILITTPESLAILLNSPKFRELLRDVRY 152
>gnl|CDD|241289 cd01258, PHsplit_syntrophin, Syntrophin Split Pleckstrin homology
(PH) domain. Syntrophins are scaffold proteins that
associate with associate with the Duchenne muscular
dystrophy protein dystrophin and the dystrophin-related
proteins, utrophin and dystrobrevin to form the
dystrophin glycoprotein complex (DGC). There are 5
members: alpha, beta1, beta2, gamma1, and gamma2) all of
which contains a split (also called joined) PH domain
and a PDZ domain (PHN-PDZ-PHC). The split PH domain of
alpha-syntrophin adopts a canonical PH domain fold and
together with PDZ forms a supramodule functioning
synergistically in binding to inositol phospholipids.
The alpha-syntrophin PH-PDZ supramodule showed strong
binding to phosphoinositides PI(3,5)P2 and PI(5)P,
modest binding to PI(3,4)P2 and PI(4,5)P2, and weak
binding to PI(3)P, PI(4)P, and PI(3,4,5)P. There are a
large number of signaling proteins that bind to the PDZ
domain of syntrophins: nitric oxide synthase (nNOS),
aquaporin-4, voltage-gated sodium channels, potassium
channels, serine/threonine protein kinases, and the
ATP-binding cassette transporter A1. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 89
Score = 25.7 bits (57), Expect = 5.5
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 88 SLEPPKIYPYHLLIITNYRLPPDVDRKNLERHLSD 122
+L K P + +T PPD + + LE H D
Sbjct: 27 TLSIEKSIPLKMCYVTRNLTPPDPENRLLELHSPD 61
>gnl|CDD|225324 COG2604, COG2604, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 594
Score = 26.6 bits (59), Expect = 6.5
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 7 KDLIQPYSLFNLHPQLTLFSTFTVSNGSIYDLHSNIH 43
++L + Y L + T+ GS Y+L N+
Sbjct: 21 ENLKENYVLEKDTDNKNILKKETLFMGSKYELERNLE 57
>gnl|CDD|233718 TIGR02089, TTC, tartrate dehydrogenase. Tartrate dehydrogenase
catalyzes the oxidation of both meso- and (+)-tartrate
as well as a D-malate. These enzymes are closely related
to the 3-isopropylmalate and isohomocitrate
dehydrogenases found in TIGR00169 and TIGR02088,
respectively [Energy metabolism, Other].
Length = 352
Score = 26.3 bits (58), Expect = 6.6
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 58 VSSTYAGSLGYAASYSNHIQRSLPNMSQPMSLEPPKI 94
+ + GSLG A S + + + P+M +P+ P I
Sbjct: 251 LGAALMGSLGVAPSANINPEGKFPSMFEPVHGSAPDI 287
>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
motor. This family represents the C-terminal region of
dynein heavy chain. The chain also contains ATPase
activity and microtubule binding ability and acts as a
motor for the movement of organelles and vesicles along
microtubules. Dynein is also involved in cilia and
flagella movement. The dynein subunit consists of at
least two heavy chains and a number of intermediate and
light chains. The 380 kDa motor unit of dynein belongs
to the AAA class of chaperone-like ATPases. The core of
the 380 kDa motor unit contains a concatenated chain of
six AAA modules, of which four correspond to the ATP
binding sites with P-loop signatures described
previously, and two are modules in which the P loop has
been lost in evolution. This C-terminal domain carries
the D6 region of the dynein motor where the P-loop has
been lost in evolution but the general structure of a
potential ATP binding site appears to be retained.
Length = 706
Score = 26.5 bits (59), Expect = 8.0
Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 15/84 (17%)
Query: 69 AASYSNHIQRSLPNMSQP--------MSLEPPKIYPYHLL----IITNYRLPPDVDRKNL 116
A S+ +++ L +++ ++ EP P LL ITN PP + NL
Sbjct: 182 APSWLPTLEKKLESLTPGSHPDFRLFLTAEPAPSIPIGLLQNSIKITNE--PPTGLKANL 239
Query: 117 ERHLSDVEFETLFLCTR-AEFYRL 139
R LS ETL +C + AEF R+
Sbjct: 240 LRALSSFTQETLEMCKKPAEFKRI 263
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 26.4 bits (58), Expect = 8.4
Identities = 25/107 (23%), Positives = 38/107 (35%), Gaps = 15/107 (14%)
Query: 25 FSTFTVSNGSIYDLHSNIHPHHHVPNGGAPELPVSSTYAGSLGYAASYSNHIQRS--LPN 82
FS+ SNG Y +I + + P P SST ++ S + S P+
Sbjct: 201 FSSSDTSNGFSYP---SIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSGASLISSNITPS 257
Query: 83 MSQPMSLEP----PKIYPYHL-LIITNYRLPPDVDRKNLERHLSDVE 124
S ++ P IYP L + ++ R L H D
Sbjct: 258 SSNSEAMSTSSKRPYIYPALLSRVAVEFK-----MRLQLGDHKKDGL 299
>gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. The gene
hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found, usually
in a single copy, in nearly all completed genomes, but
varying somewhat in apparent domain architecture. Both
E. coli and H. influenzae have two members rather than
one. The members from the Mycoplasmas have an additional
C-terminal domain [Protein fate, Protein modification
and repair].
Length = 284
Score = 26.2 bits (58), Expect = 8.6
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 100 LIITNYRLPPDVDRKNLERHLSDVEFETL 128
+I++N PP +D ++L + V FE L
Sbjct: 185 IIVSN---PPYIDEEDLADLPNVVRFEPL 210
>gnl|CDD|217109 pfam02567, PhzC-PhzF, Phenazine biosynthesis-like protein.
PhzC/PhzF is involved in dimerisation of two
2,3-dihydro-3-oxo-anthranilic acid molecules to create
PCA by P. fluorescens. This family also contains an
uncharacterized protein Rv2715 from Mycobacterium
tuberculosis, though there is no significant sequence
similarity to pfam00303 members. This family appears to
be distantly related to pfam01678, including containing
a weak internal duplication. However members of this
family do not contain the conserved cysteines that are
hypothesised to be active site residues (Bateman A pers
obs).
Length = 280
Score = 26.2 bits (58), Expect = 8.7
Identities = 17/64 (26%), Positives = 23/64 (35%), Gaps = 14/64 (21%)
Query: 14 SLFNLHPQLT----------LFSTFTVSNGSIYDLHSNIHPHHHVPNGGAPELPVSSTYA 63
+L L P L + S GS D H+ P G E P + + A
Sbjct: 166 ALAALDPDLDAAIADCPDDGVIVGPAASAGSPRDYHA----RMFAPALGIVEDPATGSAA 221
Query: 64 GSLG 67
G+LG
Sbjct: 222 GALG 225
>gnl|CDD|238152 cd00248, Mth938-like, Mth938-like domain. The members of this
family include: Mth938, 2P1, Xcr35, Rpa2829, and several
uncharacterized sequences. Mth938 is a hypothetical
protein encoded by the Methanobacterium
thermoautotrophicum (Mth) genome. This protein
crystallizes as a dimer, although it is monomeric in
solution, with one disulfide bond in each monomer. 2P1
is a partially characterized nuclear protein which is
homologous to E3-3 from rat and known to be alternately
spliced. Xcr35 and Rpa2829 are hypothetical proteins of
unknown function from the Xanthomonas campestris and
Rhodopseudomonas palustris genomes, respectively, for
which the crystal structures have been determined.
Length = 109
Score = 25.3 bits (56), Expect = 8.8
Identities = 12/45 (26%), Positives = 19/45 (42%)
Query: 106 RLPPDVDRKNLERHLSDVEFETLFLCTRAEFYRLPTWRRNDLKKR 150
D+D + L L++ + L + T AE LP R L+
Sbjct: 34 TSLSDLDPEALLPLLAEDRPDILLIGTGAEIAFLPRALRAALRAA 78
>gnl|CDD|177753 PLN00149, PLN00149, potassium transporter; Provisional.
Length = 779
Score = 26.4 bits (58), Expect = 9.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 119 HLSDVEFETLFLCTRAEFYR 138
H D+EFE +C+ AEF R
Sbjct: 608 HKDDMEFEKDLVCSIAEFIR 627
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
0.322 0.138 0.426
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,118,873
Number of extensions: 725634
Number of successful extensions: 636
Number of sequences better than 10.0: 1
Number of HSP's gapped: 634
Number of HSP's successfully gapped: 23
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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: 55 (25.1 bits)