RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15340
(81 letters)
>gnl|CDD|217819 pfam03966, Trm112p, Trm112p-like protein. The function of this
family is uncertain. The bacterial members are about
60-70 amino acids in length and the eukaryotic examples
are about 120 amino acids in length. The C terminus
contains the strongest conservation. Trm112p is
required for tRNA methylation in S. cerevisiae and is
found in complexes with 2 tRNA methylases (TRM9 and
TRM11) also with putative methyltransferase YDR140W.
The zinc-finger protein Ynr046w is plurifunctional and
a component of the eRF1 methyltransferase in yeast. The
crystal structure of Ynr046w has been determined to 1.7
A resolution. It comprises a zinc-binding domain built
from both the N- and C-terminal sequences and an
inserted domain, absent from bacterial and archaeal
orthologs of the protein, composed of three
alpha-helices.
Length = 47
Score = 29.6 bits (67), Expect = 0.029
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 48 EVEVVEGDLECPESGRKFPISSG 70
++ EG+L CPE G +PI G
Sbjct: 25 HYDIEEGELVCPECGLAYPIRDG 47
>gnl|CDD|225391 COG2835, COG2835, Uncharacterized conserved protein [Function
unknown].
Length = 60
Score = 27.6 bits (62), Expect = 0.19
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 47 LEVEVVEGDLECPESGRKFPISSGIPNMLLKE 78
L + + +L CP +PI GIP +L E
Sbjct: 18 LVYDEEKQELICPRCKLAYPIRDGIPVLLPDE 49
>gnl|CDD|222465 pfam13942, Lipoprotein_20, YfhG lipoprotein. This family
includes the YfhG protein from E. coli. Members of this
family have an N-terminal lipoprotein attachment site.
The members of this family are functionally
uncharacterized.
Length = 180
Score = 28.0 bits (63), Expect = 0.38
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 2 IPKLDWS-AFYKATLMLGDAEISIPEK-----LIDSY 32
+P W AF ++ L L +AE + E+ ++SY
Sbjct: 54 VPDDSWQNAFKQSIL-LANAEPTPAERRQMVERLNSY 89
>gnl|CDD|197278 cd09181, PLDc_FAM83A_N, N-terminal phospholipase D-like domain of
the uncharacterized protein, Family with sequence
similarity 83A. N-terminal phospholipase D (PLD)-like
domain of the uncharacterized protein, Family with
sequence similarity 83A (FAM83A), also known as tumor
antigen BJ-TSA-9. FAM83A or BJ-TSA-9 is a novel
tumor-specific gene highly expressed in human lung
adenocarcinoma. Due to this specific expression pattern,
it may serve as a biomarker for lung cancer, especially
in the early detection of micrometastasis for lung
adenocarcinoma patients. Since the N-terminal PLD-like
domain of FAM83 proteins shows only trace similarity to
the PLD catalytic domain and lacks the functionally
important histidine residue, FAM83 proteins may share a
similar three-dimensional fold with PLD enzymes, but are
most unlikely to carry PLD activity.
Length = 276
Score = 27.5 bits (61), Expect = 0.70
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 39 LKKVHHALLEVEVVEGDLECPESGRKF 65
+ H + V VEGD C +SGRKF
Sbjct: 188 INDSHFKNISVRSVEGDTYCAKSGRKF 214
>gnl|CDD|211555 TIGR00138, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase
GidB. GidB (glucose-inhibited division protein B)
appears to be present and in a single copy in nearly all
complete eubacterial genomes. It is missing only from
some obligate intracellular species of various lineages
(Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera,
etc.). GidB shows a methytransferase fold in its the
crystal structure, and acts as a 7-methylguanosine
(m(7)G) methyltransferase, apparently specific to 16S
rRNA [Protein synthesis, tRNA and rRNA base
modification].
Length = 181
Score = 26.8 bits (60), Expect = 1.1
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 28 LIDSYEKDSEFLKKVHHAL-LE-VEVVEGDLECPESGRKFPI 67
L++S K FL++V L L VE+V G E + +F I
Sbjct: 71 LLESNHKKVAFLREVKAELGLNNVEIVNGRAEDFQHEEQFDI 112
>gnl|CDD|234430 TIGR03986, TIGR03986, CRISPR-associated protein. Members of this
protein family, part of the larger RAMP family, are
found exclusively in species with CRISPR systems, in
local contexts containing other RAMP (Repeat-Associated
Mystery Proteins).
Length = 562
Score = 26.6 bits (59), Expect = 1.5
Identities = 10/49 (20%), Positives = 22/49 (44%)
Query: 19 DAEISIPEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKFPI 67
DA I + ++LI+ Y++D ++++ + PE F +
Sbjct: 244 DARIRLDKELIEDYQEDESRQLLQRRDNGSSDLLKEYRKLPEGKPVFYV 292
>gnl|CDD|217086 pfam02527, GidB, rRNA small subunit methyltransferase G. This is a
family of bacterial glucose inhibited division proteins
these are probably involved in the regulation of cell
devision. GidB has been shown to be a methyltransferase
G specific to the rRNA small subunit. Previously
identified as a glucose-inhibited division protein B
that appears to be present and in a single copy in all
complete eubacterial genomes so far sequenced. GidB
specifically methylates the N7 position of a guanosine
in 16S rRNA.
Length = 184
Score = 25.3 bits (56), Expect = 3.2
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 28 LIDSYEKDSEFLKKVHHAL-LE-VEVVEGDLE 57
L++S K FL+++ L LE V +V E
Sbjct: 77 LLESLLKKINFLEELKKELNLENVTIVHARAE 108
>gnl|CDD|223434 COG0357, GidB, Predicted S-adenosylmethionine-dependent
methyltransferase involved in bacterial cell division
[Cell envelope biogenesis, outer membrane].
Length = 215
Score = 25.3 bits (56), Expect = 3.9
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 22 ISIPEK---LIDSYEKDSEFLKKVHHAL-LE-VEVVEGDLE 57
I+ P+ L++S K FL++V L LE VE+V G E
Sbjct: 87 IAFPDLKVTLLESLGKKIAFLREVKKELGLENVEIVHGRAE 127
>gnl|CDD|177972 PLN02338, PLN02338, 3-phosphoshikimate 1-carboxyvinyltransferase.
Length = 443
Score = 25.1 bits (55), Expect = 4.8
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 13 ATLMLGDAEISIPEKLI 29
A L LGD EI I +KLI
Sbjct: 188 APLALGDVEIEIVDKLI 204
>gnl|CDD|197218 cd09119, PLDc_FAM83_N, N-terminal phospholipase D-like domain of
proteins from the Family with sequence similarity 83.
N-terminal phospholipase D (PLD)-like domain of
vetebrate proteins from the Family with sequence
similarity 83 (FAM83), which is comprised of 8 members,
designated FAM83A through FAM83H. Since the N-terminal
PLD-like domain of FAM83 proteins shows only trace
similarity to the PLD catalytic domain and lacks the
functionally important histidine residue, the FAM83
proteins may share a similar three-dimensional fold with
PLD enzymes, but are unlikely to carry PLD activity.
Members of the FAM83 are mostly uncharacterized
proteins. FAM83A, also known as tumor antigen BJ-TSA-9,
is a novel tumor-specific gene highly expressed in human
lung adenocarcinoma. FAM83D, also known as spindle
protein CHICA, is a cell-cycle-regulated spindle
component which localizes to the mitotic spindle and is
both upregulated and phosphorylated during mitosis. The
gene encoding protein FAM83H is the first gene involved
in the etiology of amelogenesis imperfecta (AI), that
encodes a non-secreted protein due to the absence of a
signal peptide. Defects in gene FAM83H cause autosomal
dominant hypocalcified amelogenesis imperfecta (ADHCAI).
FAM83B, FAM83C, FAM83F, and FAM83G are uncharacterized
proteins present across vertebrates while FAM83E is an
uncharacterized protein found only in mammals.
Length = 269
Score = 25.0 bits (55), Expect = 4.9
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 43 HHALLEVEVVEGDLECPESGRKF 65
H + V V G C SG+KF
Sbjct: 190 HLKNMRVRSVGGKTYCSRSGKKF 212
>gnl|CDD|234000 TIGR02760, TraI_TIGR, conjugative transfer relaxase protein TraI.
This protein is a component of the relaxosome complex. In
the process of conjugative plasmid transfer the
realaxosome binds to the plasmid at the oriT (origin of
transfer) site. The relaxase protein TraI mediates the
single-strand nicking and ATP-dependent unwinding
(relaxation, helicase activity) of the plasmid molecule.
These two activities reside in separate domains of the
protein.
Length = 1960
Score = 24.9 bits (54), Expect = 5.4
Identities = 8/41 (19%), Positives = 14/41 (34%), Gaps = 2/41 (4%)
Query: 1 MIPKLDWSAFYKATLMLGDAEISIPEKLIDSYEKDSEFLKK 41
+ K S +K L + + IP+ S + L
Sbjct: 1621 IEAKKGLS--FKEALNQAASLLGIPQHYQLSINIKAPQLSN 1659
>gnl|CDD|152822 pfam12387, Peptidase_C74, Pestivirus NS2 peptidase. The pestivirus
NS2 peptidase is responsible for single cleavage between
NS2 and NS3 of the bovine viral diarrhea virus
polyprotein, a cleavage that is correlated with
cytopathogenicity. The peptidase is activated by its
interaction with 'J-domain protein interacting with
viral protein' - Jiv.
Length = 200
Score = 24.7 bits (54), Expect = 6.4
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 7 WSAFYKATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHALLEVEVVEGDLECPESGRKFP 66
W Y L++ + + K+I+ + FL ++ AL+E+ + E + F
Sbjct: 55 WQVVYLLYLII-ELSYYMHRKIIEEIAGGTNFLSRLIAALIELNWAFDEEESKGLKKFFL 113
Query: 67 ISSGIPNMLLK 77
+SS + N+++K
Sbjct: 114 LSSRVKNLIIK 124
>gnl|CDD|189015 cd09608, M3B_PepF_3, Peptidase family M3B Oligopeptidase F
(PepF). Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7
and 17 amino acids with fairly broad specificity. The
PepF gene is duplicated in L. lactis on the plasmid
that bears it, while a shortened second copy is found
in Bacillus subtilis. Most bacterial PepFs are
cytoplasmic endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 538
Score = 24.7 bits (55), Expect = 6.5
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 22 ISIPEKLIDSYEKDSEFLKKVHHALLEV 49
+++PE+ ++S+ K+ LK H L E+
Sbjct: 61 LALPEEKLESFLKEEPELKDYRHYLEEI 88
>gnl|CDD|234215 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 387
Score = 24.6 bits (54), Expect = 6.9
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 13 ATLMLGDAEISIPEKLIDSYEKDSEFLKKVHHALLEVE-----VVEGDLECP 59
L L + E P L D+ F +V AL EVE VV ++CP
Sbjct: 195 GNLELMEFEHETPRALSRGQGGDTIFFARVGEALAEVEDDYDVVV---IDCP 243
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 24.8 bits (54), Expect = 7.2
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 22 ISIPEKLIDSYEKDSEF 38
+SI EKL+ S EKD ++
Sbjct: 361 LSIVEKLVKSEEKDGDW 377
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 24.5 bits (54), Expect = 8.9
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 9 AFYKATLMLGDAEISIPEKLIDSYEK 34
F K T G+ +PEKL+D+ E
Sbjct: 583 IFEKET---GEEPFDLPEKLLDAIEA 605
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 0.137 0.393
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,250,187
Number of extensions: 337700
Number of successful extensions: 241
Number of sequences better than 10.0: 1
Number of HSP's gapped: 241
Number of HSP's successfully gapped: 21
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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: 42 (22.0 bits)
S2: 53 (24.2 bits)