RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6081
(226 letters)
>gnl|CDD|202558 pfam03159, XRN_N, XRN 5'-3' exonuclease N-terminus. This family
aligns residues towards the N-terminus of several
proteins with multiple functions. The members of this
family all appear to possess 5'-3' exonuclease activity
EC:3.1.11.-. Thus, the aligned region may be necessary
for 5' to 3' exonuclease function. The family also
contains several Xrn1 and Xrn2 proteins. The 5'-3'
exoribonucleases Xrn1p and Xrn2p/Rat1p function in the
degradation and processing of several classes of RNA in
Saccharomyces cerevisiae. Xrn1p is the main enzyme
catalyzing cytoplasmic mRNA degradation in multiple
decay pathways, whereas Xrn2p/Rat1p functions in the
processing of rRNAs and small nucleolar RNAs (snoRNAs)
in the nucleus.
Length = 237
Score = 278 bits (712), Expect = 2e-95
Identities = 112/180 (62%), Positives = 124/180 (68%), Gaps = 20/180 (11%)
Query: 47 NPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMA 106
+ EFDNLYLDMNGIIHPC+HPEDKP P+ EDEM VAIFE IDRLF IVRPRKLLYMA
Sbjct: 24 HQIPDEFDNLYLDMNGIIHPCSHPEDKPFPETEDEMFVAIFEYIDRLFNIVRPRKLLYMA 83
Query: 107 IDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLAD 166
IDGVAPRAKMNQ RSRRFRA+K+ EK AE RE+L +
Sbjct: 84 IDGVAPRAKMNQ-------------------QRSRRFRAAKDAKEKEAEAEENREELETE 124
Query: 167 GCILPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226
G LP + EK FDSNCITPGTPFMA L+ L YYI +LN DP W+ + VILSDA VP
Sbjct: 125 GIKLPEKVEK-EKFDSNCITPGTPFMARLAKALRYYIKKKLNTDPEWQNLTVILSDAEVP 183
>gnl|CDD|227382 COG5049, XRN1, 5'-3' exonuclease [DNA replication, recombination,
and repair / Cell division and chromosome partitioning /
Translation].
Length = 953
Score = 215 bits (548), Expect = 1e-64
Identities = 87/186 (46%), Positives = 109/186 (58%), Gaps = 26/186 (13%)
Query: 45 KPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLY 104
K P FDNLYLDMNGI+H CTHP D P+ E+EM A+FE ID + +RPRKLLY
Sbjct: 24 KQIPE---FDNLYLDMNGILHNCTHPNDGSPPETEEEMYKAVFEYIDHILLKIRPRKLLY 80
Query: 105 MAIDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKE--TAEKIAEVAR--IR 160
MA+DGVAPRAKMNQ R+RRFR++K+ A AE I
Sbjct: 81 MAVDGVAPRAKMNQ-------------------QRARRFRSAKDASAAALKAEPNGEEIP 121
Query: 161 EKLLADGCILPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVIL 220
E+ G + + FDSNCITPGTPFM L+ L YYIH +L++DP W+ +++I
Sbjct: 122 EEKDEIGNEIDTIDVEKKKFDSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIF 181
Query: 221 SDANVP 226
S VP
Sbjct: 182 SGHLVP 187
>gnl|CDD|140234 PTZ00207, PTZ00207, hypothetical protein; Provisional.
Length = 591
Score = 29.8 bits (67), Expect = 1.2
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 82 MMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQPLTV 122
++ +IF C+ F I+ + +Y A+ G AP +N LTV
Sbjct: 358 LLWSIFCCVGAHFVIIFNARFIYTALAGEAPDDALNTLLTV 398
>gnl|CDD|185162 PRK15250, PRK15250, virulence protein SpvD; Provisional.
Length = 216
Score = 28.5 bits (63), Expect = 2.1
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 8/28 (28%)
Query: 179 HFDSNCITPGTPFMACLSACLHYYIHDR 206
H+ NC+ LSACLHY IH R
Sbjct: 68 HYSGNCVL--------LSACLHYNIHHR 87
>gnl|CDD|193129 pfam12652, CotJB, CotJB protein. CotJ is a sigma E-controlled
operon involved in the spore coat of Bacillus subtilis.
This protein has been identified as a spore coat
protein.
Length = 78
Score = 27.1 bits (61), Expect = 2.1
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 8/21 (38%)
Query: 55 NLYLDMNGIIHPCTHPEDKPA 75
NLYLD THP+D+ A
Sbjct: 19 NLYLD--------THPDDQEA 31
>gnl|CDD|114294 pfam05563, SpvD, Salmonella plasmid virulence protein SpvD. This
family consists of several SpvD plasmid virulence
proteins from different Salmonella species.
Length = 216
Score = 28.5 bits (63), Expect = 2.5
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 8/28 (28%)
Query: 179 HFDSNCITPGTPFMACLSACLHYYIHDR 206
H+ NC+ LSACLHY IH R
Sbjct: 68 HYSGNCVL--------LSACLHYNIHHR 87
>gnl|CDD|237170 PRK12677, PRK12677, xylose isomerase; Provisional.
Length = 384
Score = 28.8 bits (65), Expect = 2.7
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 129 RGNYSTWQLM--RSRRFRASKETAEKIAE--VARIREKLLADGCILPPEKEKGSHFDS 182
T+ ++ ++ FRA E E +A V + + LA G S F+
Sbjct: 301 AACMRTYLILKEKAAAFRADPEVQEALAAARVDELAQPTLAAGETYADLLADRSAFED 358
>gnl|CDD|183934 PRK13270, treF, trehalase; Provisional.
Length = 549
Score = 28.2 bits (63), Expect = 4.0
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 145 ASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDS 182
A+ E A+++A +R +LL G IL E E G +D
Sbjct: 427 ANHEQADRLANA--VRSRLLTPGGILASEYETGEQWDK 462
>gnl|CDD|100003 cd05844, GT1_like_7, Glycosyltransferases catalyze the transfer of
sugar moieties from activated donor molecules to
specific acceptor molecules, forming glycosidic bonds.
The acceptor molecule can be a lipid, a protein, a
heterocyclic compound, or another carbohydrate residue.
This group of glycosyltransferases is most closely
related to the previously defined glycosyltransferase
family 1 (GT1). The members of this family may transfer
UDP, ADP, GDP, or CMP linked sugars. The diverse
enzymatic activities among members of this family
reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility.
Length = 367
Score = 28.0 bits (63), Expect = 4.9
Identities = 34/95 (35%), Positives = 41/95 (43%), Gaps = 16/95 (16%)
Query: 92 RLFRIVRPRKLLYMA---IDGV--APRAK-MNQPLTVY------SVLYDRGNYSTWQLMR 139
RL R RP L A DGV P A+ + PL V + S W L
Sbjct: 76 RLLRRHRPD--LVHAHFGFDGVYALPLARRLGVPLVVTFHGFDATTSLALLLRSRWALYA 133
Query: 140 SRRFRASKETAEKIAEVARIREKLLADGCILPPEK 174
RR R ++ A IA IR++LLA G PPEK
Sbjct: 134 RRRRRLARRAALFIAVSQFIRDRLLALGF--PPEK 166
>gnl|CDD|193515 cd03895, M20_ArgE_DapE_like2, M20 Peptidases with similarity to
acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze
analogous reactions and share a common activator, the
metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad
range of substrates, including N-acetylornithine,
alpha-N-acetylmethionine and alpha-N-formylmethionine,
while DapE catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly bacterial, and have been inferred
by homology as being related to both ArgE and DapE.
Length = 399
Score = 27.5 bits (62), Expect = 5.5
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 144 RASKETAEKIAEVARIREKLLADGCILPPEKE-KGSHFDSNCITPGTPFMACLSAC 198
A E + IAE A + LA+ PPE E G + + P + L+A
Sbjct: 278 EAKAEIEDAIAEAAA-ADPWLAE---HPPEVEWFGFQAEGGELDLDHPLVQALAAA 329
>gnl|CDD|222968 PHA03065, PHA03065, Hypothetical protein; Provisional.
Length = 438
Score = 27.6 bits (62), Expect = 6.1
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 128 DRGNYSTWQLMRSRRFRASKET-AEKIAEVARIR 160
DRG+ Q +R +R +ASK T K E+ ++
Sbjct: 74 DRGSIPIKQSLREKRRKASKNTIKRKREEIEKLE 107
>gnl|CDD|217017 pfam02399, Herpes_ori_bp, Origin of replication binding protein.
This Pfam family represents the herpesvirus origin of
replication binding protein, probably involved in DNA
replication.
Length = 829
Score = 27.3 bits (61), Expect = 7.6
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 13/66 (19%)
Query: 50 GMEFDNLYLD-MNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAID 108
G+ FD + M + P D MV++++ + R+ + R L+YM D
Sbjct: 339 GLSFDPSHFHSMFAYVKPMKGGPD----------MVSVYQSLGRVRSLRRNELLIYM--D 386
Query: 109 GVAPRA 114
R+
Sbjct: 387 ASGARS 392
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 27.0 bits (60), Expect = 8.5
Identities = 11/30 (36%), Positives = 12/30 (40%), Gaps = 3/30 (10%)
Query: 118 QPLTVYSVLYDRGNYSTWQLMRSRRFRASK 147
V D Y WQ+ SRRFR K
Sbjct: 294 HNDKQSDVAVD---YGDWQIPLSRRFRILK 320
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
0.318 0.135 0.414
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,585,474
Number of extensions: 1081058
Number of successful extensions: 995
Number of sequences better than 10.0: 1
Number of HSP's gapped: 991
Number of HSP's successfully gapped: 20
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
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 (21.7 bits)
S2: 57 (25.7 bits)