RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8490
(228 letters)
>gnl|CDD|143944 pfam00178, Ets, Ets-domain.
Length = 85
Score = 118 bits (299), Expect = 6e-35
Identities = 46/62 (74%), Positives = 50/62 (80%), Gaps = 1/62 (1%)
Query: 131 PIQLWQFLLELLTDKTCQAFISWTG-DGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRG 189
IQLWQFLLELLTD+ + FI WTG D EFKL DP+EVAR WGIRKNKP MNY+KLSR
Sbjct: 1 QIQLWQFLLELLTDQDNRDFIRWTGRDKGEFKLVDPEEVARLWGIRKNKPNMNYDKLSRA 60
Query: 190 LR 191
LR
Sbjct: 61 LR 62
>gnl|CDD|197710 smart00413, ETS, erythroblast transformation specific domain.
variation of the helix-turn-helix motif.
Length = 87
Score = 111 bits (281), Expect = 3e-32
Identities = 42/62 (67%), Positives = 44/62 (70%), Gaps = 1/62 (1%)
Query: 131 PIQLWQFLLELLTDKTCQAFISWTG-DGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRG 189
IQLWQFLL+LL D I WT D EFKL DP+EVAR WG RKNKP MNYEKLSR
Sbjct: 1 GIQLWQFLLDLLLDPENSDIIKWTDRDEGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRA 60
Query: 190 LR 191
LR
Sbjct: 61 LR 62
>gnl|CDD|236714 PRK10557, PRK10557, hypothetical protein; Provisional.
Length = 192
Score = 31.5 bits (72), Expect = 0.22
Identities = 17/31 (54%), Positives = 18/31 (58%), Gaps = 8/31 (25%)
Query: 139 LELLTDKT-CQAFISWTGDGWEFKLTDPDEV 168
LE L T CQ G GWE KLTDPDE+
Sbjct: 123 LETLRGATSCQ------GKGWE-KLTDPDEI 146
>gnl|CDD|219648 pfam07929, PRiA4_ORF3, Plasmid pRiA4b ORF-3-like protein. Members
of this family are similar to the protein product of
ORF-3 found on plasmid pRiA4 in the bacterium
Agrobacterium rhizogenes. This plasmid is responsible
for tumourigenesis at wound sites of plants infected by
this bacterium, but the ORF-3 product does not seem to
be involved in the pathogenetic process. Other proteins
found in this family are annotated as being putative
TnpR resolvases, but no further evidence was found to
back this. Moreover, another member of this family is
described as a probable lexA repressor and in fact
carries a LexA DNA binding domain (pfam01726), but no
references were found to expand on this.
Length = 175
Score = 30.4 bits (69), Expect = 0.45
Identities = 29/128 (22%), Positives = 45/128 (35%), Gaps = 18/128 (14%)
Query: 57 FQTVPNGTAAPTGPSEAGGPPAWPSPDV--QFLPTGRGEAPSYYYSSFSDS--------- 105
F+ P G GPP V + TG+G+ +Y Y F D+
Sbjct: 50 FEIGGRRYGIPGGFDFPEGPPVVSEDRVRLSDVVTGKGKTFTYTYD-FGDNWQHRIRLER 108
Query: 106 ---KPPYVQPASMLAGYSGSGPCFTGSGPIQLWQFLLELLT--DKTCQAFISWTGDGWEF 160
+P V+ L G P G G +FL L + + + W GD ++
Sbjct: 109 ILPRPVGVEYPRCLDGKRACPPEDVG-GVWGYEEFLEALADPDHEEHEEMVEWLGDDFDP 167
Query: 161 KLTDPDEV 168
D +E+
Sbjct: 168 AAFDLEEI 175
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 29.9 bits (68), Expect = 0.92
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 138 LLELLTDKTCQAFISWTGDGWEFKLTDPDEVARRWGI 174
LL+L++DK G EF+L P+ V ++G+
Sbjct: 135 LLQLVSDKV-SVLDPTKGIK-EFELYTPENVIEKYGL 169
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 28.3 bits (64), Expect = 1.1
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 12 RLKNIGRAYRSYKSIPLDMELSVKYQVP-SQAE 43
R N+ R + Y SI L +L+ + + E
Sbjct: 44 RELNLRRLAKPYSSISLS-DLAKLLGLSVDEVE 75
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human Gammaherpesvirus
that infects and establishes latency in B lymphocytes in
vivo. The latent membrane protein 2 (LMP2) gene is
expressed in latently infected B cells and encodes two
protein isoforms, LMP2A and LMP2B, that are identical
except for an additional N-terminal 119 aa cytoplasmic
domain which is present in the LMP2A isoform. LMP2A is
thought to play a key role in either the establishment
or the maintenance of latency and/or the reactivation of
productive infection from the latent state. The
significance of LMP2B and its role in pathogenesis
remain unclear.
Length = 489
Score = 29.4 bits (66), Expect = 1.8
Identities = 17/85 (20%), Positives = 26/85 (30%), Gaps = 4/85 (4%)
Query: 43 ELPTMNSPYDNTGGFQTVPNGTAAPTGPSEAGGPPAWPS-PDVQFLPTGRGEAPSY---Y 98
E+ + + + G G + P PS G P P + P Y
Sbjct: 5 EMQPLGAGGPRSHGGPDGDEGDSNPYYPSSFGSSWDRPGPPVPEDYDAPSHRPPPYGGSN 64
Query: 99 YSSFSDSKPPYVQPASMLAGYSGSG 123
+P Q S+ AG +G
Sbjct: 65 GDRHGGYQPLGQQDPSLYAGLGQNG 89
>gnl|CDD|225950 COG3416, COG3416, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 233
Score = 28.3 bits (63), Expect = 2.6
Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 3/68 (4%)
Query: 56 GFQTVPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGRGEAPSYYYSSFSDSKPPYVQPASM 115
Q G+ + + G P P+P P AP + SS + QP+
Sbjct: 73 ILQAGEAGSGSFLSNAFKWGTPQEPAPPANAPPPKEPAAPPSWRSSPAGPTT---QPSPA 129
Query: 116 LAGYSGSG 123
A S
Sbjct: 130 AANTRSSS 137
>gnl|CDD|221309 pfam11912, DUF3430, Protein of unknown function (DUF3430). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 209 to 265 amino acids in
length.
Length = 204
Score = 27.9 bits (62), Expect = 3.5
Identities = 9/47 (19%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 95 PSYYYSSFSDSKPPYVQPASMLAGYSGSGPCFTGSGPIQLWQFLLEL 141
SYY S + P + S++ Y C + + + F
Sbjct: 108 GSYYSYISSCTDSPEIPSNSLVTVYYNGSDC-SNDNFLYIEYFTNNT 153
>gnl|CDD|220708 pfam10349, WWbp, WW-domain ligand protein. The WWbp domain is
characterized by several short PY and PT-like motifs of
the PPPPY form. These appear to bind directly to the WW
domains of WWP1 and WWP2 and other such diverse proteins
as dystrophin and YAP (Yes-associated protein). This is
the WW-domain binding protein WWbp via PY and PY_like
motifs. The presence of a phosphotyrosine residue in the
pWBP-1 peptide abolishes WW domain binding which
suggests a potential regulatory role for tyrosine
phosphorylation in modulating WW domain-ligand
interactions. Given the likelihood that WWP1 and WWP2
function as E3 ubiquitin-protein ligases, it is possible
that initial substrate-specific recognition occurs via
WW domain-substrate protein interaction followed by
ubiquitin transfer and subsequent proteolysis. This
domain lies just downstream of the GRAM (pfam02893) in
many members.
Length = 111
Score = 27.0 bits (60), Expect = 3.6
Identities = 14/62 (22%), Positives = 16/62 (25%), Gaps = 1/62 (1%)
Query: 60 VPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGRGEAPSYYYSSFSDSKPPYVQPASMLAGY 119
P G P A G A P P P P Y + + P Y
Sbjct: 48 PPPGAYVHLEPLPAYGQYAAPPP-YGPPPPYYPAPPGVYPTPPPPNSGYMADPQEPPPPY 106
Query: 120 SG 121
G
Sbjct: 107 PG 108
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 27.5 bits (61), Expect = 4.0
Identities = 15/47 (31%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 52 DNTGGFQTVPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGR--GEAPS 96
D TGG + + A P GP P P+ G GEA S
Sbjct: 5 DGTGGVSSGSSAPAPPAGPGPGPNAPPAPAAPGVDSSAGSSGGEAGS 51
>gnl|CDD|200549 cd10923, CE4_COG5298, Putative NodB-like catalytic domain of
uncharacterized proteins found in bacteria. This family
corresponds to a group of uncharacterized bacterial
proteins with high sequence similarity to the catalytic
domain of the six-stranded barrel rhizobial NodB-like
proteins, which remove N-linked or O-linked acetyl
groups from cell wall polysaccharides and belong to the
larger carbohydrate esterase 4 (CE4) superfamily. Some
family members contain an additional copper amine
oxidase N-terminal domain.
Length = 250
Score = 27.7 bits (62), Expect = 4.3
Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 154 TGDGWEFKLTDPDEVARRWGIRKNKPKMNYEKLSRGLR 191
+GDG+EF D + +++ +GL+
Sbjct: 88 SGDGFEFWDAKNDAPLAE-----DSQAWAEQRVEKGLQ 120
>gnl|CDD|188632 cd00452, KDPG_aldolase, KDPG and KHG aldolase. KDPG and KHG
aldolase. This family belongs to the class I adolases
whose reaction mechanism involves Schiff base formation
between a substrate carbonyl and lysine residue in the
active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG)
aldolase, is best known for its role in the
Entner-Doudoroff pathway of bacteria, where it catalyzes
the reversible cleavage of KDPG to pyruvate and
glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate
(KHG) aldolase, which has enzymatic specificity toward
glyoxylate, forming KHG in the presence of pyruvate, and
is capable of regulating glyoxylate levels in the
glyoxylate bypass, an alternate pathway when bacteria
are grown on acetate carbon sources.
Length = 190
Score = 27.1 bits (61), Expect = 5.7
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 5/26 (19%)
Query: 70 PSEAGGPPAW-----PSPDVQFLPTG 90
P+EA GP P P V+F+PTG
Sbjct: 125 PAEAVGPAYIKALKGPFPQVRFMPTG 150
>gnl|CDD|221789 pfam12818, Tegument_dsDNA, dsDNA viral tegument protein. This is a
family of tegument proteins from double-stranded DNA
herpesvirus and related viral species.
Length = 282
Score = 27.3 bits (61), Expect = 6.3
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 9/63 (14%)
Query: 86 FLPTGRGEAPSYYY--SSFSDSKPPYVQPASMLAGYSGSGPCFTGS----GPIQLWQFLL 139
F PT + P Y Y SS +K + L GPC +GS GP + + LL
Sbjct: 130 FEPTSGPDTPPYLYRDSSLELNK---ILQTLKLFYGLYPGPCISGSIRPPGPASVLEHLL 186
Query: 140 ELL 142
L+
Sbjct: 187 ALV 189
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 27.6 bits (62), Expect = 6.5
Identities = 8/21 (38%), Positives = 9/21 (42%)
Query: 59 TVPNGTAAPTGPSEAGGPPAW 79
AA + A GPPAW
Sbjct: 381 GAGGAAAAAAAGAAAAGPPAW 401
>gnl|CDD|220950 pfam11029, DAZAP2, DAZ associated protein 2 (DAZAP2). DAZ
associated protein 2 has a highly conserved sequence
throughout evolution including a conserved polyproline
region and several SH2/SH3 binding sites. It occurs as
a single copy gene with a four-exon organisation and is
located on chromosome 12. It encodes a ubiquitously
expressed protein and binds to DAZ and DAZL1 through
DAZ repeats.
Length = 136
Score = 26.4 bits (58), Expect = 7.5
Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 9/60 (15%)
Query: 36 YQVPSQAELPTMNSPYDNTGGFQTVPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGRGEAP 95
Y VP QA++P ++PY P + P P + + P G
Sbjct: 16 YVVPPQAQMPQASAPY---------PGPSMYLPMAQVMAVGPQSSHPPMAYYPIGAPPPV 66
>gnl|CDD|130052 TIGR00979, fumC_II, fumarate hydratase, class II. Putative
fumarases from several species (Mycobacterium
tuberculosis, Streptomyces coelicolor, Pseudomonas
aeruginosa) branch deeply, although within the same
branch of a phylogenetic tree rooted by aspartate
ammonia-lyase sequences, and score between the trusted
and noise cutoffs [Energy metabolism, TCA cycle].
Length = 458
Score = 27.4 bits (61), Expect = 8.0
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 173 GIRKNKPKMNYEKLSRGLRRKT------GYEKASRFEKVARRWGI 211
GI NK ++ + L+ L T GY+ A++ K A + GI
Sbjct: 387 GIEPNKERIQ-QLLNNSLMLVTALNPHIGYDNAAKIAKKAHKEGI 430
>gnl|CDD|235577 PRK05718, PRK05718,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 212
Score = 26.7 bits (60), Expect = 8.1
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 6/27 (22%)
Query: 70 PSEA-GGPPAW-----PSPDVQFLPTG 90
P+EA GG P PDV+F PTG
Sbjct: 136 PAEASGGVKMLKALAGPFPDVRFCPTG 162
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 27.0 bits (60), Expect = 9.5
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 39 PSQAELPTMNSPYDNTGGFQTVPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGRGEAPSYY 98
+ + + P ++ G + P+ P+ PS++ PPA PS P P
Sbjct: 176 DADPASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPA-PSSFQSDTP------PPSP 228
Query: 99 YSSFSDSKPPYVQPAS 114
S + S PP
Sbjct: 229 ESPTNPSPPPGPAAPP 244
>gnl|CDD|226832 COG4397, COG4397, Mu-like prophage major head subunit gpT [General
function prediction only].
Length = 308
Score = 26.8 bits (59), Expect = 9.6
Identities = 31/142 (21%), Positives = 38/142 (26%), Gaps = 41/142 (28%)
Query: 52 DNTGGFQTVPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGRGEAPSYYYSSFSDSKPPYVQ 111
D TG V N A TG PAW L R P Y + K +
Sbjct: 148 DGTGQASMVSNIFVAKTGDYSG---PAW-----YLLDCSRALKPLIY----QERKAA--E 193
Query: 112 PASMLAG------------YSGSGPCFTGSGPIQLWQFLLELLT----DKTCQAFISWTG 155
+ Y G G Q+ + LT K A +TG
Sbjct: 194 LVAQTKVDDERVFMDNEFVYGVDARRNVGYGFWQMAYMMQSKLTADALWKAWSAMREFTG 253
Query: 156 DGWEFKLTDPDEVARRWGIRKN 177
DG R+ IR
Sbjct: 254 DG-----------GRKLAIRPT 264
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 27.2 bits (60), Expect = 9.6
Identities = 24/89 (26%), Positives = 30/89 (33%), Gaps = 5/89 (5%)
Query: 37 QVPSQAELPTMNSPYDNTGGFQTVPNGTAAP-TGPSEAGGP-PAWPSPDVQFLPTGRGEA 94
Q Q P P P AP T P+ AG P A P P + L GR
Sbjct: 2918 QPQPQPPPPPQPQPPPPP---PPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAV 2974
Query: 95 PSYYYSSFSDSKPPYVQPASMLAGYSGSG 123
P + + S+ L G+S S
Sbjct: 2975 PRFRVPQPAPSREAPASSTPPLTGHSLSR 3003
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 27.1 bits (60), Expect = 9.9
Identities = 19/72 (26%), Positives = 26/72 (36%)
Query: 60 VPNGTAAPTGPSEAGGPPAWPSPDVQFLPTGRGEAPSYYYSSFSDSKPPYVQPASMLAGY 119
NG ++ GP+ + P SP G G APS +S S S +S +
Sbjct: 274 GWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSS 333
Query: 120 SGSGPCFTGSGP 131
S GP
Sbjct: 334 ESSRGAAVSPGP 345
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 0.134 0.420
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,888,264
Number of extensions: 1113919
Number of successful extensions: 1107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1094
Number of HSP's successfully gapped: 40
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
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 (21.6 bits)
S2: 57 (25.6 bits)