RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11067
(292 letters)
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 37.0 bits (85), Expect = 0.010
Identities = 35/186 (18%), Positives = 55/186 (29%), Gaps = 8/186 (4%)
Query: 58 SCPIVNCNFTSVNLNTFKIHLLKHFDKRPFKCKLTTANNTPCMWGFFSKHKLLRHM--TS 115
S +S+ + + D K + C F L RH+ +
Sbjct: 254 SSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVN 313
Query: 116 HD-EDKKCYPCDQKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTM----KQY 170
H E K + C C K F+ LK H++ H + L KF +
Sbjct: 314 HSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQ 373
Query: 171 STHLKEHSNVSAPYMCDYKGCGKSFYLMASLKSHQRVHVTNPEDLV-CKGCGKQFKVPCR 229
S + C ++F ++L H H++ C K F
Sbjct: 374 SLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYN 433
Query: 230 LREHYK 235
L H K
Sbjct: 434 LIPHKK 439
Score = 34.3 bits (78), Expect = 0.079
Identities = 27/123 (21%), Positives = 45/123 (36%), Gaps = 1/123 (0%)
Query: 57 WSCPIVNCNFTSVNLNTFKIHLLKHFDKRPFKCKLTTANNTPCMWGFFSKHKLLRHMTSH 116
+SCP C + K H+L H P K KL +++ ++
Sbjct: 322 FSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKF-SPLLNNEPPQSLQQYKD 380
Query: 117 DEDKKCYPCDQKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKE 176
++ K +C + F SNL +H++ H C+ C + F H K
Sbjct: 381 LKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKI 440
Query: 177 HSN 179
H+N
Sbjct: 441 HTN 443
>gnl|CDD|218670 pfam05639, Pup, Pup-like protein. This family consists of
several short bacterial proteins formely known as
(DUF797). It was recently shown that Mycobacterium
tuberculosis contains a small protein, Pup (Rv2111c),
that is covalently conjugated to the e-NH2 groups of
lysines on several target proteins (pupylation) such as
the malonyl CoA acyl carrier protein (FabD). Pupylation
of FabD was shown to result in its recruitment to the
mycobacterial proteasome and subsequent degradation
analogous to eukaryotic ubiquitin-conjugated proteins.
Searches recovered Pup orthologs in all major
actinobacteria lineages including the basal
bifidobacteria and also sporadically in certain other
bacterial lineages. The Pup proteins were all between
50-90 residues in length and a multiple alignment shows
that they all contain a conserved motif with a G [EQ]
signature at the C-terminus. Thus, all of them are
suitable for conjugation via the terminal glutamate or
the deamidated glutamine (as shown in the case of the
Mycobacterium Pup). The conserved globular core of Pup
is predicted to form a bihelical unit with the extreme
C-terminal 6-7 residues forming a tail in the extended
conformation. Thus, Pup is structurally unrelated to
the ubiquitin fold and has convergently evolved the
function of protein modifier.
Length = 66
Score = 30.8 bits (70), Expect = 0.099
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 3 VATASSDSEGKTEELNKEIDDEEDAITEALQSLGINKEYFISS 45
A A++D + E+L +++DD D I + L+ N E F+ S
Sbjct: 20 TAEATADGAERREKLTEDVDDLLDEIDDVLEE---NAEEFVRS 59
>gnl|CDD|222711 pfam14366, DUF4410, Domain of unknown function (DUF4410). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 187 and 238 amino
acids in length.
Length = 119
Score = 31.9 bits (73), Expect = 0.11
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 10/71 (14%)
Query: 7 SSDSEGKTEELNKEIDDE-EDAITEALQSLGINKEYFISSTGGKNSKKQQLWSCPIVNCN 65
S+ K +E K + DA+ + L+S G+ KN+ IV +
Sbjct: 16 DSEEAAKQQEDAKSAPELLADALVKELKSKGLFAVRSDPPPLPKNA-----L---IVEGD 67
Query: 66 FTSVNL-NTFK 75
FT ++ N
Sbjct: 68 FTKIDEGNRAA 78
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 32.4 bits (73), Expect = 0.24
Identities = 27/92 (29%), Positives = 38/92 (41%), Gaps = 15/92 (16%)
Query: 119 DKKCYPCDQKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHS 178
D K Y C + CNK++ + LK HM HG ++L + M +S K
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHM-LHGH----QNQKLHENPSPEKMNIFSAKDK--- 397
Query: 179 NVSAPYMCDYKGCGKSFYLMASLKSHQRVHVT 210
PY C+ C K + + LK H R H
Sbjct: 398 ----PYRCEV--CDKRYKNLNGLKYH-RKHSH 422
Score = 28.5 bits (63), Expect = 4.8
Identities = 24/92 (26%), Positives = 34/92 (36%), Gaps = 19/92 (20%)
Query: 52 KKQQLWSCPIVNCNFTSVNLNTFKIHLLKHFDKRPFKCKLTTANNTPCMWGFFSKHKLLR 111
K + + CP+ CN N N K H+L H + N +P
Sbjct: 345 KDGKPYKCPVEGCNKKYKNQNGLKYHML-HGHQNQ----KLHENPSP------------E 387
Query: 112 HMTSHDEDKKCYPCDQKNCNKRFTTLSNLKMH 143
M K Y C+ C+KR+ L+ LK H
Sbjct: 388 KMNIFSAKDKPYRCEV--CDKRYKNLNGLKYH 417
Score = 27.4 bits (60), Expect = 9.6
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 242 KNFKCTYDGCKLLFSTKSALKRHNKSKHLNMRMFPCP 278
K +KC +GC + ++ LK H H N ++ P
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP 384
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 26.5 bits (59), Expect = 1.6
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 128 KNCNKRFTTLSNLKMHMVRH 147
+C K F+ SNLK H+ H
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
Score = 24.2 bits (53), Expect = 9.0
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 189 KGCGKSFYLMASLKSHQRVH 208
CGKSF ++LK H R H
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 29.5 bits (67), Expect = 1.7
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 4 ATASSDSEGKTEELNKEIDDEEDAITEALQ 33
A A + +EG+ EL +E+D E+ AL
Sbjct: 108 AGAGAAAEGRAGELAQELDSEKQVSARALA 137
>gnl|CDD|219584 pfam07800, DUF1644, Protein of unknown function (DUF1644). This
family consists of sequences found in a number of
hypothetical plant proteins of unknown function. The
region of interest contains nine highly conserved
cysteine residues and is approximately 160 amino acids
in length, and is probably a zinc-binding domain.
Length = 148
Score = 28.1 bits (63), Expect = 3.2
Identities = 28/103 (27%), Positives = 39/103 (37%), Gaps = 17/103 (16%)
Query: 177 HSNVSAPYMCD----YKGCGKSFYLMASLK--SHQRVHVTNPEDLVCKGCG---KQFKVP 227
H PYMCD + C F S K S + + +L C C K + V
Sbjct: 23 HDKGCRPYMCDTSHRHSNCLDQFKKAYSKKRNSGKDSEKEDSTELTCPLCRGEVKGWTVV 82
Query: 228 CRLREHYKAVHESTKNFKCTYDGCKLLFS-TKSALKRHNKSKH 269
R + S C +GC FS T L++H +S+H
Sbjct: 83 EPARRFLNSKKRS-----CMQEGCS--FSGTYRELRKHARSEH 118
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 29.0 bits (65), Expect = 4.0
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 211 NPEDLVCKGCGKQFKVPCRLREHYKAVH 238
NP VC C +F +L EH + H
Sbjct: 70 NPSSYVCNVCMAEFSSMDQLAEHQRTTH 97
>gnl|CDD|239307 cd03009, TryX_like_TryX_NRX, Tryparedoxin (TryX)-like family, TryX
and nucleoredoxin (NRX) subfamily; TryX and NRX are
thioredoxin (TRX)-like protein disulfide oxidoreductases
that alter the redox state of target proteins via the
reversible oxidation of an active center CXXC motif.
TryX is involved in the regulation of oxidative stress
in parasitic trypanosomatids by reducing TryX
peroxidase, which in turn catalyzes the reduction of
hydrogen peroxide and organic hydroperoxides. TryX
derives reducing equivalents from reduced trypanothione,
a polyamine peptide conjugate unique to trypanosomatids,
which is regenerated by the NADPH-dependent flavoprotein
trypanothione reductase. Vertebrate NRX is a 400-amino
acid nuclear protein with one redox active TRX domain
containing a CPPC active site motif followed by one
redox inactive TRX-like domain. Mouse NRX transcripts
are expressed in all adult tissues but is restricted to
the nervous system and limb buds in embryos. Plant NRX,
longer than the vertebrate NRX by about 100-200 amino
acids, is a nuclear protein containing a redox inactive
TRX-like domain between two redox active TRX domains.
Both vertebrate and plant NRXs show thiol oxidoreductase
activity in vitro. Their localization in the nucleus
suggests a role in the redox regulation of nuclear
proteins such as transcription factors.
Length = 131
Score = 27.2 bits (61), Expect = 6.1
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 5/23 (21%)
Query: 227 PCR-----LREHYKAVHESTKNF 244
PCR L E Y+ + ES KNF
Sbjct: 32 PCRAFTPKLVEFYEKLKESGKNF 54
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.7 bits (54), Expect = 6.7
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 123 YPCDQKNCNKRFTTLSNLKMHMVRH 147
Y C + C K F + S L+ HM H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|177497 PHA02913, PHA02913, TGF-beta-like protein; Provisional.
Length = 172
Score = 26.9 bits (59), Expect = 8.8
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 89 CKLTTANNTPCMWGFFSKHKLLRHMTSHDEDKKCYPCDQKNCNKRFTTLSNLKMHMVRHG 148
C ++ M+G KH HM + C P KN + +K +++
Sbjct: 110 CSISNHKKINLMYGTAFKH----HMPDNTIPFCCAPIKMKNFIIAYKEGRKIKTDNIKNF 165
Query: 149 KPLTLCC 155
K L C
Sbjct: 166 KILECAC 172
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
0.320 0.132 0.421
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,544,894
Number of extensions: 1176328
Number of successful extensions: 1312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1304
Number of HSP's successfully gapped: 45
Length of query: 292
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 196
Effective length of database: 6,679,618
Effective search space: 1309205128
Effective search space used: 1309205128
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: 59 (26.7 bits)