RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13344
(155 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 = 53.6 bits (129), Expect = 4e-09
Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 3/100 (3%)
Query: 51 IWKIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDER 110
+ +G I+Y D +K+R LNG L V+I ++ R + R
Sbjct: 148 AILLEVDGGR-ILYTGDVKRRKDRLLNGAELPP--CIDVLIVESTYGDRLHPNRDEVERR 204
Query: 111 LMTNILQTLRNNGNVLVAVDTAGRVLELTHMLEQLWRNKD 150
+ ++ L G VL+ GR EL +L +L D
Sbjct: 205 FIESVKAALERGGTVLIPAFALGRAQELLLILRELGFAGD 244
>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 = 41.5 bits (98), Expect = 6e-05
Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 5/97 (5%)
Query: 57 EGEEEIVYGVDFNLKKERHLNGCVLDRFIR-PTVVITDTMSA--IYQQARRRTRDERLMT 113
+G IVY DF +K R L+ V ++F R T+++ T YQ +R ++ L+
Sbjct: 336 DGLYNIVYTGDFKYEKTRLLDPAV-NKFPRVETLIMESTYGGRDDYQPSREEA-EKELIK 393
Query: 114 NILQTLRNNGNVLVAVDTAGRVLELTHMLEQLWRNKD 150
+ +T++ G VL+ V GR E+ +LE+ R
Sbjct: 394 VVNETIKRGGKVLIPVFAVGRAQEVMLVLEEAMRKGL 430
>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 = 38.5 bits (90), Expect = 7e-04
Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 5/96 (5%)
Query: 57 EGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTM---SAIYQQARRRTRDERLMT 113
+G IVY DF +K R L ++F R +I ++ Q R ++ L+
Sbjct: 342 DGLYNIVYTGDFKFEKTRLLEPAN-NKFPRVETLIMESTYGGRDDVQPPREEA-EKELIK 399
Query: 114 NILQTLRNNGNVLVAVDTAGRVLELTHMLEQLWRNK 149
I TL+ G VL+ V GR E+ +LE+ R
Sbjct: 400 VINDTLKRGGKVLIPVFAVGRSQEVMIVLEEAMRKG 435
>gnl|CDD|216812 pfam01963, TraB, TraB family. pAD1 is a hemolysin/bacteriocin
plasmid originally identified in Enterococcus faecalis
DS16. It encodes a mating response to a peptide sex
pheromone, cAD1, secreted by recipient bacteria. Once
the plasmid pAD1 is acquired, production of the
pheromone ceases--a trait related in part to a
determinant designated traB. However a related protein
is found in C. elegans, suggesting that members of the
TraB family have some more general function. This family
also includes the bacterial GumN protein. The family has
a conserved GXXH motif close to the N-terminus, a
conserved glutamate and a conserved arginine that may be
catalytic. The family also includes a second conserved
GXXH motif near the C-terminus.
Length = 261
Score = 29.2 bits (66), Expect = 0.86
Identities = 10/37 (27%), Positives = 13/37 (35%), Gaps = 5/37 (13%)
Query: 107 RDERLMTNILQTLRNNGNVLVAVDTA-----GRVLEL 138
R+ I L++ G V V V VL L
Sbjct: 214 RNRYWAEKIEAALKSGGKVFVVVGAGHLPGEDGVLGL 250
>gnl|CDD|235128 PRK03522, rumB, 23S rRNA methyluridine methyltransferase; Reviewed.
Length = 315
Score = 28.3 bits (64), Expect = 1.5
Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 15/66 (22%)
Query: 50 PIWKIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRP-------TVVITDTMSAIYQQA 102
P+ + EGEEEI L NG + FIRP V + +Y A
Sbjct: 114 PVHMAILEGEEEIFLTEQQAL--PERFNG--VPLFIRPQSFFQTNPAV----AAQLYATA 165
Query: 103 RRRTRD 108
R R+
Sbjct: 166 RDWVRE 171
>gnl|CDD|185439 PTZ00091, PTZ00091, 40S ribosomal protein S5; Provisional.
Length = 193
Score = 27.8 bits (62), Expect = 1.9
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 99 YQQAR-RRTR---DERLMTNILQTLRNNGNVLVAVDTAGRVLELTHML 142
YQ+ R R+ + ERL+ +++ RNNG L+AV E+ H+L
Sbjct: 45 YQKKRFRKAQCPIVERLVNSLMFHGRNNGKKLLAVRIVKHAFEIIHLL 92
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 27.9 bits (62), Expect = 2.4
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 95 MSAIYQQARRRTRDE 109
MSA+YQ+AR T DE
Sbjct: 1 MSALYQRARPITFDE 15
>gnl|CDD|234958 PRK01544, PRK01544, bifunctional N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase/tRNA
(m7G46) methyltransferase; Reviewed.
Length = 506
Score = 27.9 bits (62), Expect = 2.4
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 100 QQARRRTRDERLMTNILQT-LRNNGNVLVAVDTAGRVLELTHMLEQ 144
Q+ +R ERL ILQ L++NGN++ A D E +++Q
Sbjct: 434 QKKKRIFNKERL--KILQDKLKDNGNLVFASDIENYFYEAIELIQQ 477
>gnl|CDD|99848 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA
exonuclease 1, -3 and similar eukaryotic proteins.
This subfamily is composed of RNA exonuclease 1 (REX1
or Rex1p), REX3 (or Rex3p), and similar eukaryotic
proteins. In yeast, REX1 and REX3 are required for 5S
rRNA and MRP (mitochondrial RNA processing) RNA
maturation, respectively. They are DEDDh-type DnaQ-like
3'-5' exonucleases containing 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. REX1 is the
major exonuclease responsible for pre-tRNA trail
trimming and may also be involved in nuclear CCA
turnover. REX proteins function in the processing and
maturation of many RNA species, similar to the function
of Escherichia coli RNase T.
Length = 150
Score = 27.1 bits (61), Expect = 2.8
Identities = 10/28 (35%), Positives = 12/28 (42%), Gaps = 7/28 (25%)
Query: 66 VDFNLKKERHLNGCVLDRFIRPTVVITD 93
VD N K VLD ++P I D
Sbjct: 22 VDENGK-------VVLDELVKPDGEIVD 42
>gnl|CDD|182138 PRK09907, PRK09907, toxin MazF; Provisional.
Length = 111
Score = 26.7 bits (59), Expect = 3.1
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 86 RPTVVITDTMSAIYQQARRRTRDERLMTNILQTLRNNGNVLV 127
R V + D + +I +AR T+ + LQ ++ NVL+
Sbjct: 69 RDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVLI 110
>gnl|CDD|129363 TIGR00261, traB, pheromone shutdown-related protein TraB. traB is
a plasmid encoded gene that functions in the shutdown of
the peptide sex pheromone cPD1 which is produced by the
plasmid free recipient cell prior to conjugative
transfer in Enterococcus faecalis. Once the recipient
acquires the plasmid, production of cPD1 is shut down.
The gene product may play another role in the other
species in the family [Unknown function, General].
Length = 380
Score = 26.7 bits (59), Expect = 5.7
Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 15/102 (14%)
Query: 51 IWKIVKEGEEEIVYGVDFNLKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDER 110
I + + +I ++ L+++ L + ++ +S I + ++ DER
Sbjct: 134 ISSLFSSTDAKIEDEIEKLLEQD------ALSKIMK-------ELSKISPKVKKVLIDER 180
Query: 111 --LMTNILQTLRNNGNVLVAVDTAGRVLELTHMLEQLWRNKD 150
M N L N N++VAV AG V + L++L
Sbjct: 181 DEFMANKLLEGEGNKNIIVAVVGAGHVSGIMRTLKKLQNKNI 222
>gnl|CDD|187625 cd05367, SPR-like_SDR_c, sepiapterin reductase (SPR)-like,
classical (c) SDRs. Human SPR, a member of the SDR
family, catalyzes the NADP-dependent reduction of
sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to
SPRs, this subgroup also contains Bacillus cereus yueD,
a benzil reductase, which catalyzes the stereospecific
reduction of benzil to (S)-benzoin. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 241
Score = 26.5 bits (59), Expect = 6.0
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 85 IRPTVVITDTMSAIYQQARRRTRDERLMTNILQTLRNNGNVLVAVDTAGRVLEL 138
P VV TD + ++ R + D + ++L+ G +L +A ++ L
Sbjct: 177 YAPGVVDTD----MQREIRETSADPE-TRSRFRSLKEKGELLDPEQSAEKLANL 225
>gnl|CDD|151819 pfam11379, DUF3182, Protein of unknown function (DUF3182). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 355
Score = 26.5 bits (59), Expect = 6.0
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 120 RNNGNVLVAVDTAGRVLELTHMLEQLWR 147
R N +V +D GR +LEQ WR
Sbjct: 269 RRNYDVAQGLDAEGRPR--CGVLEQSWR 294
>gnl|CDD|215073 PLN00142, PLN00142, sucrose synthase.
Length = 815
Score = 26.5 bits (59), Expect = 7.8
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 130 DTAGRVLELTHMLEQL 145
DTA RVLE H+L L
Sbjct: 245 DTAERVLETIHLLLDL 260
>gnl|CDD|172901 PRK14425, PRK14425, acylphosphatase; Provisional.
Length = 94
Score = 25.2 bits (55), Expect = 8.0
Identities = 13/45 (28%), Positives = 20/45 (44%)
Query: 103 RRRTRDERLMTNILQTLRNNGNVLVAVDTAGRVLELTHMLEQLWR 147
R TRDE + +RN + V AG ++ M+E+ R
Sbjct: 22 RDWTRDEAERLGLTGWVRNESDGSVTALIAGPDSAISAMIERFRR 66
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 26.0 bits (58), Expect = 8.9
Identities = 8/30 (26%), Positives = 18/30 (60%)
Query: 116 LQTLRNNGNVLVAVDTAGRVLELTHMLEQL 145
++ + +V VDTAGR+ +++++L
Sbjct: 76 VEKAKAENYDVVLVDTAGRLQNDKNLMDEL 105
>gnl|CDD|183271 PRK11671, mltC, murein transglycosylase C; Provisional.
Length = 359
Score = 26.2 bits (58), Expect = 9.1
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 10/63 (15%)
Query: 67 DFNLKKERHLNGCVLDRFIRPTVVITDTMSAIYQQARRRTRDERLMTNILQTLRNNGNVL 126
D + KE L G VLD +P I + R + L+ N LQ+ N ++
Sbjct: 124 DIPISKEPFLYGQVLDNTGQP----------IRWEGRASNFADYLLQNKLQSRSNGLRII 173
Query: 127 VAV 129
+V
Sbjct: 174 YSV 176
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 26.0 bits (57), Expect = 9.6
Identities = 10/48 (20%), Positives = 14/48 (29%), Gaps = 6/48 (12%)
Query: 81 LDRFI------RPTVVITDTMSAIYQQARRRTRDERLMTNILQTLRNN 122
RF RP V+ D A Y+ + + L N
Sbjct: 183 YRRFEKILEQKRPDFVVIDPFVAFYEGKSISDVQVKEFIKKTRKLARN 230
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
0.321 0.137 0.413
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,074,944
Number of extensions: 740582
Number of successful extensions: 734
Number of sequences better than 10.0: 1
Number of HSP's gapped: 731
Number of HSP's successfully gapped: 34
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
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 (24.9 bits)