RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9123
(118 letters)
>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold
involved in RNA processing [Translation, ribosomal
structure and biogenesis].
Length = 427
Score = 33.6 bits (77), Expect = 0.012
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 50 ESGSVLVPCYPSGVIYDLFECLSSHLDNSSLTQIPMFFISPVADISLAYSNILAEWN 106
G+VL+P + G +L L P++ P+A ++LAY+ +
Sbjct: 215 RGGTVLIPAFALGRAQELLLILREL---GFAGDYPIYVDGPIARVALAYAKYPIGLD 268
>gnl|CDD|214983 smart01027, Beta-Casp, Beta-Casp domain. The beta-CASP domain is
found C terminal to the beta-lactamase domain in
pre-mRNA 3'-end-processing endonuclease. The active site
of this enzyme is located at the interface of these two
domains.
Length = 126
Score = 32.5 bits (75), Expect = 0.015
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 66 DLFECLSSHLDNSSLTQIPMFFISPVADISLAYSNILAEW 105
+L L L +P++ SP+A + EW
Sbjct: 3 ELLLILEELWREGELPNVPIYLDSPMAARATEIYKSYPEW 42
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 30.3 bits (68), Expect = 0.22
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 4 NGDNLDSLIASTASSNGQSKIAVLLHSDLNNITCDEKWMRDIKNQNESGSVL 55
N +NL +I T+ S G+ K A H L+N C WM+ +VL
Sbjct: 653 NPENLAYVI-YTSGSTGKPKGAGNRHRALSNRLC---WMQQAYGLGVGDTVL 700
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 29.1 bits (65), Expect = 0.44
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 12 IASTASSNGQSKIAVLLHSDLNNITCDEKWMRDIKNQNESGSVLV 56
IAST Q+ I V +D+ ++ +W+ D +N+ SVL+
Sbjct: 65 IASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLL 109
>gnl|CDD|169098 PRK07786, PRK07786, long-chain-fatty-acid--CoA ligase; Validated.
Length = 542
Score = 29.0 bits (65), Expect = 0.62
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 10 SLIASTASSNGQSKIAVLLHSDLNN--ITCDEKWMRDIKNQNESGSVLVP 57
+LI T+ + G+ K AVL H++L +TC DI ++ G V VP
Sbjct: 177 ALIMYTSGTTGRPKGAVLTHANLTGQAMTCLRTNGADI--NSDVGFVGVP 224
>gnl|CDD|220932 pfam10996, Beta-Casp, Beta-Casp domain. The beta-CASP domain is
found C terminal to the beta-lactamase domain in
pre-mRNA 3'-end-processing endonuclease. The active site
of this enzyme is located at the interface of these two
domains.
Length = 124
Score = 26.4 bits (59), Expect = 2.8
Identities = 8/40 (20%), Positives = 14/40 (35%)
Query: 66 DLFECLSSHLDNSSLTQIPMFFISPVADISLAYSNILAEW 105
+L L +P++ SP+A + EW
Sbjct: 3 ELLLLLEELWREGIPKDVPIYLDSPMAIKATEIYKSYPEW 42
>gnl|CDD|189052 cd09882, PIN_MtRv0301, PIN domain of the Rv0301 toxin of
Mycobacterium tuberculosis and other uncharacterized,
annotated PilT protein domain proteins. Virulence
associated protein C (VapC)-like PIN (PilT N terminus)
domain of Mycobacterium tuberculosis protein Rv0301 and
similar bacterial proteins are included in this
subfamily. They are PIN domain homologs of the
Mycobacterium tuberculosis VapC and Neisseria
gonorrhoeae FitB toxins of the prokaryotic
toxin/antitoxin operons, VapBC and FitAB, respectively,
which are believed to be involved in growth inhibition
by regulating translation. These toxins are nearly
always co-expressed with an antitoxin, a cognate protein
inhibitor, forming an inert protein complex.
Disassociation of the protein complex activates the
ribonuclease activity of the toxin by an, as yet
undefined mechanism. VapC-like PIN domains are homologs
of flap endonuclease-1 (FEN1)-like PIN domains, but lack
the extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain four
highly conserved acidic residues. These putative active
site residues are thought to bind Mg2+ and/or Mn2+ ions
and be essential for single-stranded ribonuclease
activity.
Length = 128
Score = 26.1 bits (58), Expect = 3.1
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 4/23 (17%)
Query: 9 DSLIASTASSNGQSKIAVLLHSD 31
D LIA+TA +G LLH+D
Sbjct: 94 DLLIAATALEHG----LTLLHND 112
>gnl|CDD|178706 PLN03161, PLN03161, Probable xyloglucan
endotransglucosylase/hydrolase protein; Provisional.
Length = 291
Score = 26.0 bits (57), Expect = 4.9
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 1 MFQNGDNLDSLIASTASSNGQSKIAVLLHS 30
M NGDNL ++ ++ S +SK A L S
Sbjct: 42 MLGNGDNLQLVLDQSSGSGIKSKRAFLFGS 71
>gnl|CDD|184553 PRK14176, PRK14176, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 287
Score = 25.5 bits (56), Expect = 6.7
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 55 LVPCYPSGVIYDLFE 69
LVPC P GVI L E
Sbjct: 143 LVPCTPHGVIRALEE 157
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
0.315 0.130 0.381
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,551,450
Number of extensions: 447631
Number of successful extensions: 360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 15
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)