RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13232
(111 letters)
>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease
and similar proteins. Oligoribonuclease (Orn) is a
DEDDh-type DnaQ-like 3'-5' exoribonuclease that is
responsible for degrading small oligoribonucleotides to
mononucleotides. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. Orn is essential
for Escherichia coli survival. The human homolog, also
called Sfn (small fragment nuclease), is able to
hydrolyze short single-stranded RNA and DNA oligomers.
It plays a role in cellular nucleotide recycling.
Length = 173
Score = 84.9 bits (211), Expect = 4e-22
Identities = 27/58 (46%), Positives = 40/58 (68%)
Query: 34 YYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
+ +EVL M+EWC E H SGLT+RVRAS+V++ +A+ L +F+ KYV +P+ G
Sbjct: 42 HQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEAELLEFIKKYVPKGKSPLAG 99
>gnl|CDD|235429 PRK05359, PRK05359, oligoribonuclease; Provisional.
Length = 181
Score = 79.8 bits (198), Expect = 4e-20
Identities = 23/56 (41%), Positives = 35/56 (62%)
Query: 36 NEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
++E L M+EW H SGL DRVRAS+VS EA+ + +F+ ++V +P+ G
Sbjct: 48 SDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAEAEAQTLEFLKQWVPAGKSPLCG 103
>gnl|CDD|224860 COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA
processing and modification].
Length = 184
Score = 72.8 bits (179), Expect = 2e-17
Identities = 23/59 (38%), Positives = 38/59 (64%)
Query: 33 LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
++ ++E L M+EW E H SGLT+RV+AS+V+ EA+ + F+ K+V +P+ G
Sbjct: 48 IHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEAEAEAQTLDFLKKWVPKGVSPICG 106
>gnl|CDD|143586 cd07185, OmpA_C-like, Peptidoglycan binding domains similar to
the C-terminal domain of outer-membrane protein OmpA.
OmpA-like domains (named after the C-terminal domain of
Escherichia coli OmpA protein) have been shown to
non-covalently associate with peptidoglycan, a network
of glycan chains composed of disaccharides, which are
crosslinked via short peptide bridges. Well-studied
members of this family include the Escherichia coli
outer membrane protein OmpA, the Escherichia coli
lipoprotein PAL, Neisseria meningitdis RmpM, which
interact with the outer membrane, as well as the
Escherichia coli motor protein MotB, and the Vibrio
flagellar motor proteins PomB and MotY, which interact
with the inner membrane.
Length = 106
Score = 31.0 bits (71), Expect = 0.039
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 2 DNIGNRPSNTALSSM--EQVKAYLQTQG 27
D+ G+ N LS E V YL ++G
Sbjct: 43 DSRGSDAYNQELSERRAEAVADYLVSKG 70
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease. This family includes a variety
of exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 161
Score = 31.6 bits (72), Expect = 0.048
Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 2/58 (3%)
Query: 34 YYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
Y E L + + E H + R S + EA + + V + VG
Sbjct: 38 YVKPERL--ITDEATEFHGITPEMLRNAPSFEEVLEAFLEFLKKLKILVGHNASFDVG 93
>gnl|CDD|128673 smart00391, MBD, Methyl-CpG binding domain. Methyl-CpG binding
domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1)
domain.
Length = 77
Score = 30.0 bits (68), Expect = 0.074
Identities = 7/26 (26%), Positives = 9/26 (34%)
Query: 8 PSNTALSSMEQVKAYLQTQGTCKCGL 33
P L S ++ YL G L
Sbjct: 35 PCGKKLRSKSELARYLHKNGDLSLDL 60
>gnl|CDD|225439 COG2885, OmpA, Outer membrane protein and related
peptidoglycan-associated (lipo)proteins [Cell envelope
biogenesis, outer membrane].
Length = 190
Score = 27.9 bits (62), Expect = 0.85
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 6/30 (20%)
Query: 2 DNIGNRPSNTALSSMEQ----VKAYLQTQG 27
D+ G+ N ALS E+ V YL +QG
Sbjct: 124 DSTGSDEYNQALS--ERRAEAVADYLVSQG 151
>gnl|CDD|217795 pfam03923, Lipoprotein_16, Uncharacterized lipoprotein. The
function of this presumed lipoprotein is unknown. The
family includes E. coli YajG.
Length = 159
Score = 26.8 bits (60), Expect = 1.8
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 60 VRASSVSIEEADKRLHQFVAKYVK 83
+VS+ D R Q+VA+ +
Sbjct: 11 NSNVTVSLSTKDLRSAQYVARIDR 34
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha
and epsilon chain, ribonuclease T and other
exonucleases.
Length = 169
Score = 26.9 bits (60), Expect = 2.2
Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 43 MNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYV 82
+ ++ E H G+T + + + EE + L +F+ +
Sbjct: 46 ITDYATEIH---GITPEMLDDAPTFEEVLEELLEFLRGRI 82
>gnl|CDD|216651 pfam01697, Glyco_transf_92, Glycosyltransferase family 92.
Members of this family act as galactosyltransferases,
belonging to glycosyltransferase family 92. The aligned
region contains several conserved cysteine residues and
several charged residues that may be catalytic
residues. This is supported by the inclusion of this
family in the GT-A glycosyl transferase superfamily.
Length = 266
Score = 26.7 bits (59), Expect = 2.9
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 29 CKCGLYYNEEVLQNMNEWCVEHHNASG 55
C L+ NE + E+ +E+H G
Sbjct: 6 CVAPLFGNEAKWLQLQEF-IEYHKLQG 31
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 26.3 bits (58), Expect = 4.2
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 9 SNTALSSMEQVKAYLQTQGT 28
S TA++ +E+VK +QTQ +
Sbjct: 21 SKTAVAPIERVKMLIQTQDS 40
>gnl|CDD|225598 COG3056, COG3056, Uncharacterized lipoprotein [Cell envelope
biogenesis, outer membrane].
Length = 204
Score = 26.0 bits (57), Expect = 4.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 60 VRASSVSIEEADKRLHQFVAKYVK 83
+ +VSI D+R Q VAK +
Sbjct: 53 LMGVTVSITGKDQRSDQAVAKVTR 76
>gnl|CDD|149640 pfam08653, DASH_Dam1, DASH complex subunit Dam1. The DASH
complex is a ~10 subunit microtubule-binding complex
that is transferred to the kinetochore prior to
mitosis. In Saccharomyces cerevisiae DASH forms both
rings and spiral structures on microtubules in vitro.
Components of the DASH complex, including Dam1, Duo1,
Spc34, Dad1 and Ask1, are essential and connect the
centromere to the plus end of spindle microtubules.
Length = 58
Score = 24.6 bits (54), Expect = 4.5
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 42 NMNEWCVEHHNA 53
MN WCV+ NA
Sbjct: 46 MMNAWCVDFPNA 57
>gnl|CDD|221767 pfam12776, Myb_DNA-bind_3, Myb/SANT-like DNA-binding domain.
This presumed domain appears to be related to other
Myb/SANT like DNA binding domains. In particular
pfam10545 seems most related. This family is greatly
expanded in plants and appears in several proteins
annotated as transposon proteins.
Length = 96
Score = 25.3 bits (56), Expect = 5.2
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 3 NIGNRPSNTALSS---MEQVKAYLQTQGTCKCGLYYNEEVLQN 42
+ GNRP + VK + Q K GL Y ++ L+N
Sbjct: 19 DAGNRPGQGGFTKEGWKNIVKKFNQ-----KTGLKYTKDQLKN 56
>gnl|CDD|233480 TIGR01579, MiaB-like-C, MiaB-like tRNA modifying enzyme. This
clade of sequences is closely related to MiaB, a
modifier of isopentenylated adenosine-37 of certain
eukaryotic and bacterial tRNAs (see TIGR01574). Sequence
alignments suggest that this equivalog performs the same
chemical transformation as MiaB, perhaps on a different
(or differently modified) tRNA base substrate. This
clade is a member of a subfamily (TIGR00089) and spans
low GC Gram positive bacteria, alpha and epsilon
proteobacteria, Campylobacter, Porphyromonas, Aquifex,
Thermotoga, Chlamydia, Treponema and Fusobacterium
[Protein synthesis, tRNA and rRNA base modification].
Length = 414
Score = 25.8 bits (57), Expect = 5.6
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 59 RVRASSVSIEEADKRLHQFVAKYVKPKTAP 88
R+R SS+ E+ D+ L + +A + + P
Sbjct: 222 RIRLSSIDPEDIDEELLEAIAS--EKRLCP 249
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 25.8 bits (56), Expect = 6.0
Identities = 16/67 (23%), Positives = 31/67 (46%)
Query: 8 PSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSI 67
PS +S++E+ A++ + Y EE + + + L +R+R S +
Sbjct: 327 PSPVNMSALERTAAWVLMNSQYEDIEYETEENREEGTQAEKYEQEIARLKERLRVSVRRL 386
Query: 68 EEADKRL 74
EE ++RL
Sbjct: 387 EEYERRL 393
>gnl|CDD|234256 TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group
1. The Pfam domain family pfam00296 is named for
luciferase-like monooxygenases, but the family also
contains several coenzyme F420-dependent enzymes. This
protein family represents a well-resolved clade within
family pfam00296 and shows no restriction to coenzyme
F420-positive species, unlike some other clades within
pfam00296 [Unknown function, Enzymes of unknown
specificity].
Length = 323
Score = 25.5 bits (57), Expect = 6.4
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 5/19 (26%)
Query: 46 WCVEHHNASGLTDRVRASS 64
W EHHN G+ ASS
Sbjct: 38 WVAEHHNMPGI-----ASS 51
>gnl|CDD|173495 PTZ00256, PTZ00256, glutathione peroxidase; Provisional.
Length = 183
Score = 25.1 bits (55), Expect = 7.8
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 3/32 (9%)
Query: 2 DNIGNRPSNTALSSMEQVKAYLQTQGTCKCGL 33
D G LS + KA + CKCGL
Sbjct: 27 DIDGQ---LVQLSKFKGKKAIIVVNVACKCGL 55
>gnl|CDD|223567 COG0493, GltD, NADPH-dependent glutamate synthase beta chain and
related oxidoreductases [Amino acid transport and
metabolism / General function prediction only].
Length = 457
Score = 25.3 bits (56), Expect = 9.0
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 70 ADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFL 107
D+RL V+ K VG T +ELLK+ D
Sbjct: 176 LDRRLELLERSGVEFKLNVRVGRDITLEELLKEYDAVF 213
>gnl|CDD|131459 TIGR02406, ectoine_EctA, diaminobutyrate acetyltransferase. This
enzyme family is the EctA of ectoine biosynthesis.
Ectoine is a compatible solute, analagous to trehalose,
betaines, etc., found often in halotolerant organisms.
EctA is L-2,4-diaminobutyric acid acetyltransferase,
also called DABA acetyltransferase [Cellular processes,
Adaptations to atypical conditions].
Length = 157
Score = 24.7 bits (54), Expect = 9.7
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 61 RASSVSIEEADKRLHQFVAKYVKP 84
+S+ E + FV+ Y++P
Sbjct: 38 ADTSIVAESEGGEIVGFVSGYLRP 61
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 0.128 0.384
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,223,377
Number of extensions: 411909
Number of successful extensions: 408
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 25
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (24.2 bits)