RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17634
(119 letters)
>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 48.9 bits (117), Expect = 7e-08
Identities = 25/91 (27%), Positives = 45/91 (49%), Gaps = 9/91 (9%)
Query: 5 IKMTSLSGTMDESPPCYLLQVDEFKILLDCG------WDEMFSMDFVKELKRHVHHIDAV 58
+++T+L G + L+ E ++LLDCG ++ F V E + +DAV
Sbjct: 181 VRVTALGGFREVGRSALLVSTPESRVLLDCGVNVAGNGEDAFPYLDVPEFQP--DELDAV 238
Query: 59 LLSYPDVAHLGALPYMVGKCGLSCPIFATIP 89
++++ + H G LP + K G P++ T P
Sbjct: 239 IITHAHLDHCGFLPLLF-KYGYDGPVYCTPP 268
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 44.9 bits (107), Expect = 1e-06
Identities = 25/91 (27%), Positives = 45/91 (49%), Gaps = 9/91 (9%)
Query: 5 IKMTSLSGTMDESPPCYLLQVDEFKILLDCG------WDEMFSMDFVKELKRHVHHIDAV 58
+++T+L G + LL E ++LLDCG D + V E + + +DAV
Sbjct: 175 VRVTALGGFREVGRSALLLSTPESRVLLDCGVNVGADGDNAYPYLDVPEFQ--LDELDAV 232
Query: 59 LLSYPDVAHLGALPYMVGKCGLSCPIFATIP 89
++++ + H G +P + K G P++ T P
Sbjct: 233 VITHAHLDHSGLVPLLF-KYGYDGPVYCTPP 262
>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold
involved in RNA processing [Translation, ribosomal
structure and biogenesis].
Length = 427
Score = 44.0 bits (104), Expect = 3e-06
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 19 PCYLLQVDEFKILLDCGWDEMFSMDFVKELKRHVHHIDAVLLSYPDVAHLGALPYMVGKC 78
C LL+ +ILLDCG + L +DAVLL++ + H+GALPY+V
Sbjct: 15 SCVLLETGGTRILLDCGLFPGDPSP-ERPLLPPFPKVDAVLLTHAHLDHIGALPYLVRN- 72
Query: 79 GLSCPIFATIPVYKMGQMFMYDLF 102
G P++AT P + ++ + D
Sbjct: 73 GFEGPVYATPPTAALLKVLLGDSL 96
>gnl|CDD|216099 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily.
Length = 148
Score = 42.3 bits (99), Expect = 7e-06
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 20 CYLLQVDEFKILLDCGWDEMFSMDFVKELKRHVHHIDAVLLSYPDVAHLGALPY 73
YL++ D +L+D G ++ + L IDA++L++ H+G LP
Sbjct: 8 SYLVEGDGGAVLIDTGLGADDALLLLALLGLDPKDIDAIILTHAHADHIGGLPE 61
>gnl|CDD|223668 COG0595, COG0595, mRNA degradation ribonucleases J1/J2
(metallo-beta-lactamase superfamily) [Translation,
ribosomal structure and biogenesis; Replication,
recombination and repair].
Length = 555
Score = 41.1 bits (97), Expect = 3e-05
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 20 CYLLQVDEFKILLDCGW----DEMFSMDFV----KELKRHVHHIDAVLLSYPDVAHLGAL 71
Y+++ + I+LD G D++ +D + L+ + + + L++ H+GAL
Sbjct: 24 MYVVEYGDDIIILDAGLKFPEDDLLGVDLIIPDFSYLEENKDKVKGIFLTHGHEDHIGAL 83
Query: 72 PYMVGKCGLSCPIFAT 87
PY++ + L PI+A+
Sbjct: 84 PYLLKQ-VLFAPIYAS 98
>gnl|CDD|214854 smart00849, Lactamase_B, Metallo-beta-lactamase superfamily.
Apart from the beta-lactamases a number of other
proteins contain this domain. These proteins include
thiolesterases, members of the glyoxalase II family,
that catalyse the hydrolysis of S-D-lactoyl-glutathione
to form glutathione and D-lactic acid and a competence
protein that is essential for natural transformation in
Neisseria gonorrhoeae and could be a transporter
involved in DNA uptake. Except for the competence
protein these proteins bind two zinc ions per molecule
as cofactor.
Length = 177
Score = 39.1 bits (91), Expect = 1e-04
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 20 CYLLQVDEFKILLDCGWDEMFSMDFVKELKRH-VHHIDAVLLSYPDVAHLGALPYMVGKC 78
YL++ D IL+D G E + D + ELK+ IDA++L++ H+G LP ++
Sbjct: 2 SYLVRDDGGAILIDTGPGE--AEDLLAELKKLGPKKIDAIILTHGHPDHIGGLPELLEAP 59
Query: 79 GLSCPIFAT 87
G P++A
Sbjct: 60 G--APVYAP 66
>gnl|CDD|237023 PRK11921, PRK11921, metallo-beta-lactamase/flavodoxin
domain-containing protein; Provisional.
Length = 394
Score = 35.1 bits (81), Expect = 0.004
Identities = 19/56 (33%), Positives = 36/56 (64%), Gaps = 4/56 (7%)
Query: 21 YLLQVDEFKILLDCGWDEMFSMDFVKELKRHV--HHIDAVLLSYPDVAHLGALPYM 74
YL++ DE +L+D W + F+ +FV+ LK+ + ID ++ ++ ++ H GALP +
Sbjct: 36 YLIK-DEKTVLIDTVW-QPFAKEFVENLKKEIDLDKIDYIVANHGEIDHSGALPEL 89
>gnl|CDD|179371 PRK02113, PRK02113, putative hydrolase; Provisional.
Length = 252
Score = 32.8 bits (75), Expect = 0.021
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 22 LLQVDEFKILLDCGWDEMFSMDFVKELKRHVHHIDAVLLSYPDVAHLGAL 71
L++ + +IL+DCG D M + IDAVL+++ H+G L
Sbjct: 39 LVETEGARILIDCGPDFREQMLRLP-----FGKIDAVLITHEHYDHVGGL 83
>gnl|CDD|233071 TIGR00649, MG423, conserved hypothetical protein. Contains an
ATP-binding domain at the N-terminal end of the
protein. Possibly part of a superfamily of
beta-lactmases [Hypothetical proteins, Conserved].
Length = 422
Score = 30.8 bits (70), Expect = 0.11
Identities = 23/91 (25%), Positives = 47/91 (51%), Gaps = 9/91 (9%)
Query: 5 IKMTSLSGTMDESPPCYLLQVDEFKILLDCGW----DEMFSMDFV----KELKRHVHHID 56
IK+ +L G + Y++++D+ ++ D G DEM +D V L+ + +
Sbjct: 1 IKIFALGGLGEIGKNMYVVEIDDEIVIFDAGILFPEDEMLGVDGVIPDFTYLQENEDKVK 60
Query: 57 AVLLSYPDVAHLGALPYMVGKCGLSCPIFAT 87
+ +++ H+GA+PY++ + G PI+ T
Sbjct: 61 GIFITHGHEDHIGAVPYLLHQVGFF-PIYGT 90
>gnl|CDD|224158 COG1237, COG1237, Metal-dependent hydrolases of the
beta-lactamase superfamily II [General function
prediction only].
Length = 259
Score = 28.9 bits (65), Expect = 0.50
Identities = 20/67 (29%), Positives = 34/67 (50%)
Query: 21 YLLQVDEFKILLDCGWDEMFSMDFVKELKRHVHHIDAVLLSYPDVAHLGALPYMVGKCGL 80
L++ + +IL D G D + + L + IDAV+LS+ H G LPY++ +
Sbjct: 25 ALVEDEGTRILFDTGTDSDVLLHNARLLGVDLRDIDAVVLSHGHYDHTGGLPYLLEENNP 84
Query: 81 SCPIFAT 87
P++A
Sbjct: 85 GIPVYAH 91
>gnl|CDD|238945 cd01987, USP_OKCHK, USP domain is located between the N-terminal
sensor domain and C-terminal catalytic domain of this
Osmosensitive K+ channel histidine kinase family. The
family of KdpD sensor kinase proteins regulates the
kdpFABC operon responsible for potassium transport. The
USP domain is homologous to the universal stress protein
Usp Usp is a small cytoplasmic bacterial protein whose
expression is enhanced when the cell is exposed to
stress agents. Usp enhances the rate of cell survival
during prolonged exposure to such conditions, and may
provide a general "stress endurance" activity.
Length = 124
Score = 27.9 bits (63), Expect = 0.91
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 36 WDEMFSMDFVKELKRHVHHIDAVLLS 61
W E+F V L R +ID +++
Sbjct: 99 WRELFRGSLVDRLLRRAGNIDVHIVA 124
>gnl|CDD|225212 COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase
superfamily) [General function prediction only].
Length = 293
Score = 28.1 bits (63), Expect = 1.1
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 22 LLQVDEFKILLDCGWDEMFSMDFVKELKRH-VHHIDAVLLSYPDVAHLGALPYMV 75
L++ + IL D G + M + LK V +D ++L++PD H+G L ++
Sbjct: 58 LIRSEGKTILYDTG-NSMGQDVIIPYLKSLGVRKLDQLILTHPDADHIGGLDEVL 111
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 27.9 bits (63), Expect = 1.4
Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 45 VKELKRHV--HHIDAVLLSYPDVAHLGALPYMVGKCGLSCPIFATIPVYKMGQMFMYDLF 102
+ +L+ + +D V ++ P A + ++ T+ V + +F + L
Sbjct: 180 LDDLEELIREGEVDEVYIALPLAAE-KRILELLDALEDL-----TVDVRLVPDLFDFALL 233
Query: 103 QVRYDTF 109
+ R +
Sbjct: 234 RPRIEEI 240
>gnl|CDD|223855 COG0784, CheY, FOG: CheY-like receiver [Signal transduction
mechanisms].
Length = 130
Score = 26.3 bits (58), Expect = 3.0
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 30 ILLDCGWDEMFSMDFVKELKRHVHHIDAVLLS 61
ILLD M ++ ++ L+ +I +LL+
Sbjct: 55 ILLDINMPGMDGIELLRRLRARGPNIPVILLT 86
>gnl|CDD|234602 PRK00055, PRK00055, ribonuclease Z; Reviewed.
Length = 270
Score = 26.7 bits (60), Expect = 3.2
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 18 PPCYLLQVDEFKILLDCG 35
LL++ L DCG
Sbjct: 20 VSSILLRLGGELFLFDCG 37
>gnl|CDD|223153 COG0075, COG0075, Serine-pyruvate aminotransferase/archaeal
aspartate aminotransferase [Amino acid transport and
metabolism].
Length = 383
Score = 26.4 bits (59), Expect = 3.6
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 30 ILLDCGWDEMFSMDFVKELKRHVHHIDAVLL 60
++L+ W E + V+E I AV +
Sbjct: 107 VVLEVEWGEAVDPEEVEEALDKDPDIKAVAV 137
>gnl|CDD|237595 PRK14050, PRK14050, ferrichrome receptor precursor protein;
Provisional.
Length = 728
Score = 26.3 bits (58), Expect = 5.6
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 75 VGKCGLSCPIFATIPVY--KMGQMFMY 99
V C + PI AT PVY G F+Y
Sbjct: 414 VQACCGATPISATNPVYGTTQGANFVY 440
>gnl|CDD|204080 pfam08840, BAAT_C, BAAT / Acyl-CoA thioester hydrolase C terminal.
This catalytic domain is found at the C terminal of
acyl-CoA thioester hydrolases and bile acid-CoA:amino
acid N-acetyltransferases (BAAT).
Length = 211
Score = 25.7 bits (57), Expect = 5.7
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 48 LKRHVHHIDAVLLSYPDVAHLGALPYMV 75
LK+H ++ +L+YP HL PY
Sbjct: 140 LKKHGKKVEVQVLTYPGAGHLIEPPYFP 167
>gnl|CDD|184689 PRK14459, PRK14459, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 373
Score = 26.0 bits (58), Expect = 6.1
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 8/42 (19%)
Query: 55 IDAVLLSYPDVAHLGALPYMVGKCGLSCPIFATIPVYKMGQM 96
+++VL+ YPD A L + G CG++CP AT GQ
Sbjct: 110 VESVLMRYPDRATL-CISSQAG-CGMACPFCAT------GQG 143
>gnl|CDD|224156 COG1235, PhnP, Metal-dependent hydrolases of the beta-lactamase
superfamily I [General function prediction only].
Length = 269
Score = 25.9 bits (57), Expect = 6.4
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 40 FSMDFVKELKRH-VHHIDAVLLSYPDVAHLGALPYMVGKCGLSCPIFATIPVYK 92
D + R V +DA+LL++ H+ L + PI+ +
Sbjct: 47 AGPDLRDQGLRLGVSDLDAILLTHEHSDHIQGLDDLRRAYT--LPIYVNPGTLR 98
>gnl|CDD|234559 TIGR04358, XXXCH_domain, XXXCH domain. Members of this family
show C-terminal sequence similarity, perhaps indicating
distant homology, to cytochrome c-prime (see
pfam01322). However, the motif CxxCH is replaced by
xxxCH. Genes for this protein occur in a sporadically
distributed genome context, largely in
deltaProteobacteria, in which an ATP-grasp family
glutamate ligase homolog and a CofD (LPPG:FO
2-phospho-L-lactate transferase) homolog suggest a
novel biosynthesis.
Length = 90
Score = 25.0 bits (55), Expect = 6.5
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 6 KMTSLSGTMDESPPCYLLQVDEFKILLDCGWDE--MFSMDFVKELKRHVH 53
+M S G DE +L D+ + + G E + ++D +++ K+ H
Sbjct: 39 RMVSYPGKGDEYYEAFLALADQLQAAVKNGDLEAAVAAVDELEQAKKFCH 88
>gnl|CDD|239800 cd04272, ZnMc_salivary_gland_MPs, Zinc-dependent metalloprotease,
salivary_gland_MPs. Metalloproteases secreted by the
salivary glands of arthropods.
Length = 220
Score = 25.4 bits (56), Expect = 7.0
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 9 SLSGTMDESPPCYLLQVDEFKILLDCGWDEMFSMDFVKELKRH 51
L D SPP V LDC WD+ + M +V +R
Sbjct: 156 LLGAPHDGSPPPSW--VKGHPGSLDCPWDDGYIMSYVVNGERQ 196
>gnl|CDD|233963 TIGR02651, RNase_Z, ribonuclease Z. Processing of the 3-prime
end of tRNA precursors may be the result of
endonuclease or exonuclease activity, and differs in
different species. Member of this family are
ribonuclease Z, a tRNA 3-prime endonuclease that
processes tRNAs to prepare for addition of CCA. In
species where all tRNA sequences already have the CCA
tail, such as E. coli, the need for such an enzyme is
unclear. Protein similar to the E. coli enzyme, matched
by TIGR02649, are designated ribonuclease BN
[Transcription, RNA processing].
Length = 299
Score = 25.6 bits (57), Expect = 7.8
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 18 PPCYLLQVDEFKILLDCG 35
P L+++ L DCG
Sbjct: 18 LPSIALKLNGELWLFDCG 35
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
0.329 0.143 0.448
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,026,801
Number of extensions: 521758
Number of successful extensions: 525
Number of sequences better than 10.0: 1
Number of HSP's gapped: 520
Number of HSP's successfully gapped: 35
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.4 bits)