RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3152
(402 letters)
>gnl|CDD|197362 cd09804, Dcp1, mRNA decapping enzyme 1 (Dcp1). mRNA decapping
enzyme 1 (Dcp1), together with Dcp2, is part of the
decapping complex which catalyzes the removal of the 5'
cap structure of mRNA. This decapping reaction is an
essential step in mRNA degradation, by exposing the 5'
end for exonucleolytic digestion. Dcp1 binds to the
N-terminal helical domain of catalytic subunit Dcp2 and
enhances its function by promoting Dsp2's closed
conformation which is catalytically more active.
Length = 121
Score = 180 bits (460), Expect = 2e-56
Identities = 56/117 (47%), Positives = 86/117 (73%)
Query: 8 EVNVSAIRRVDPMVKDLVDSATHVALYSFNGHKSEWDKTNIEGALFVYRRVESPLYSMFI 67
+N+ ++R DP + ++D+A+HVA+Y F+ +EW+KT++EG LFVY+R P Y I
Sbjct: 5 ALNLKVLQRHDPYIVSILDTASHVAVYEFDDDTNEWEKTDVEGTLFVYKRSAEPRYGFII 64
Query: 68 LNRNSPENLLEPVVKELDLQLQNPFILYKNKQGLIYGIWFYNKEDCHRISDILQSLV 124
LNR S ENL+EP+ EL+L+LQ+P+++Y+N G IYGIWFY++ED RI +L+ L+
Sbjct: 65 LNRLSTENLIEPITPELELELQDPYLIYRNANGEIYGIWFYDEEDRERIYKLLERLL 121
>gnl|CDD|241336 cd13182, EVH1-like_Dcp1, Decapping enzyme EVH1-like domain. Dcp1
is a small protein containing an EVH1 domain. The
Dcp1-Dcp2 complex plays a critical step in mRNA
degradation with the removal of the 50 cap structure.
Dcp1 stimulates the activity of Dcp2 by promoting and/or
stabilizing the closed complex. The interface of Dcp1
and Dcp2 is not fully conserved and in higher eukaryotes
it requires an additional factor. The proline-rich
sequence (PRS)-binding sites in Dcp1p indicates that it
belongs to a novel class of EVH1 domains. Dcp1 has 2
prominent sites,one required for the function of the
Dcp1p-Dcp2p complex, and the other, the PRS-binding site
of EVH1 domains, a binding site for decapping regulatory
proteins. It also has a conserved hydrophobic patch is
shown to be critical for decapping. The EVH1 domains are
part of the PH domain superamily.
Length = 116
Score = 172 bits (439), Expect = 2e-53
Identities = 54/116 (46%), Positives = 88/116 (75%)
Query: 9 VNVSAIRRVDPMVKDLVDSATHVALYSFNGHKSEWDKTNIEGALFVYRRVESPLYSMFIL 68
+N+ ++R DP +++++D+A+HV LY F+ +EW+KT++EG LFVY+R +P Y IL
Sbjct: 1 LNLRVLQRHDPYIEEILDTASHVVLYKFDPDSNEWEKTDVEGTLFVYKRSAAPRYGFIIL 60
Query: 69 NRNSPENLLEPVVKELDLQLQNPFILYKNKQGLIYGIWFYNKEDCHRISDILQSLV 124
NR SPEN +EP+ +LD +LQ+PF++Y+N +G IYGIWFY++++ RI +L+ L+
Sbjct: 61 NRLSPENFVEPITPDLDFELQDPFLIYRNAEGEIYGIWFYDEDERERIYKLLEKLL 116
>gnl|CDD|147945 pfam06058, DCP1, Dcp1-like decapping family. An essential step in
mRNA turnover is decapping. In yeast, two proteins have
been identified that are essential for decapping, Dcp1
(this family) and Dcp2 (pfam05026). The precise role of
these proteins in the decapping reaction have not been
established. Evidence suggests that the Dcp1 may enhance
the function of Dcp2.
Length = 123
Score = 154 bits (392), Expect = 3e-46
Identities = 57/123 (46%), Positives = 92/123 (74%)
Query: 2 AKLTDSEVNVSAIRRVDPMVKDLVDSATHVALYSFNGHKSEWDKTNIEGALFVYRRVESP 61
K E+N++A++R+DP +++++D ++ VA+Y+FN +EW+KT+IEG FVY+R P
Sbjct: 1 VKKARREINLAALKRIDPYIEEILDVSSFVAVYTFNHAANEWEKTDIEGTFFVYKRSARP 60
Query: 62 LYSMFILNRNSPENLLEPVVKELDLQLQNPFILYKNKQGLIYGIWFYNKEDCHRISDILQ 121
+ I+NR S ENL+EP+ K+L+ QLQ PF+LY+N IYG+WFY+KE+C RI+++L+
Sbjct: 61 YHGFIIMNRLSTENLVEPITKDLEFQLQGPFLLYRNDNQSIYGLWFYDKEECQRIANLLK 120
Query: 122 SLV 124
L+
Sbjct: 121 ELL 123
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 31.5 bits (71), Expect = 1.1
Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 10/105 (9%)
Query: 205 QPPGFVNPPAAIPIIQ-----RPAAYVVPPPAAPVAEVSHPI---IQRIMSNPVHSVEHI 256
Q P + P++Q PAA V+P +P + P + PV V
Sbjct: 1125 QAPVIKSVVTQAPVVQVTISVAPAAPVLPAVVSPPVVSAAPAQSVATAVAMAPVAEVPIA 1184
Query: 257 EKQQRSI--TPQAGGARVKDMAAVPVELENNMLFMRISDSPIPTQ 299
Q+S+ P A + ++ M+ + + PT+
Sbjct: 1185 VPVQQSVDYMPSVAQAAAPQASVNDSAIQQVMMEVVAEKTGYPTE 1229
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 29.7 bits (67), Expect = 2.4
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 234 VAEVSHPIIQRIMSNPVHSVEHIEKQQRSITPQAGGARVKDMAAV 278
+ EVS +Q +++ V V I + G RV+++A V
Sbjct: 252 IQEVSVTPMQTLIAEAVDLVIFIAR-------TPAGRRVQEIAKV 289
>gnl|CDD|165267 PHA02961, PHA02961, hypothetical protein; Provisional.
Length = 658
Score = 29.9 bits (67), Expect = 2.5
Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 15/78 (19%)
Query: 3 KLTDSE-VNVSAIRRV-DPMVK----------DLVDSATHVALYSFNGHKSEWDKTNIEG 50
KL +S +N+S IR + D +K DL+ TH +S + K+ +D +
Sbjct: 106 KLIESNIINLSDIRNIIDNRIKTPIEIALINSDLIIPGTH---FSLDDIKTIFDNKGADN 162
Query: 51 ALFVYRRVESPLYSMFIL 68
+Y+++++P++++ ++
Sbjct: 163 TKELYKKIDTPIHNILLM 180
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 30.1 bits (68), Expect = 2.7
Identities = 13/72 (18%), Positives = 21/72 (29%)
Query: 212 PPAAIPIIQRPAAYVVPPPAAPVAEVSHPIIQRIMSNPVHSVEHIEKQQRSITPQAGGAR 271
AA P A PAAP A + + + ++ P
Sbjct: 396 QAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQA 455
Query: 272 VKDMAAVPVELE 283
+ A+PV +
Sbjct: 456 APETVAIPVRVA 467
>gnl|CDD|165539 PHA03282, PHA03282, envelope glycoprotein E; Provisional.
Length = 540
Score = 29.5 bits (66), Expect = 3.2
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 190 AKAGVSQGVGENHLPQPPGFVNPP-------AAIPIIQRPAAYVVP-PPAAPVAEVSH 239
A+A V VG +P PPG PP A P P + P P P+AEV+H
Sbjct: 152 ARAVVFLVVGPRPVPTPPGGTPPPDDDEGDEAGAPATPAPPLHPPPAPHPHPIAEVAH 209
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 28.6 bits (64), Expect = 3.6
Identities = 9/37 (24%), Positives = 13/37 (35%)
Query: 204 PQPPGFVNPPAAIPIIQRPAAYVVPPPAAPVAEVSHP 240
PQ G+ P + P + PPP + P
Sbjct: 140 PQYQGYHPMPPQPGMPAPPYSLQYPPPGLLQPQGPPP 176
>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
Length = 679
Score = 29.4 bits (66), Expect = 3.9
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 141 KKPVEQMGNGLIMNMLTKAQEEYNSHKSPMRNDKPRELESAPQSVMDFFAKAGVSQGVGE 200
K P ++ + N+L + ++ + P +S PQ V D+ +AG+ G+
Sbjct: 284 KTPSQRAKLWYVQNVLIRNTDQARV-REPEPPVSVAHFDSLPQGVGDYILQAGIQAPSGD 342
Query: 201 NHLP 204
N P
Sbjct: 343 NVQP 346
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 29.2 bits (66), Expect = 4.1
Identities = 18/104 (17%), Positives = 30/104 (28%), Gaps = 7/104 (6%)
Query: 158 KAQEEYNSHKSPMRNDKPRELESAPQSVMDFFAKAGVSQGVGENHLPQPPGFVNPPAAIP 217
AQ + P + + AP+ A V Q + QP P P
Sbjct: 98 SAQPRQPVQQPP---EAQVPPQHAPRPAQP--APQPVQQPAYQPQPEQPLQQPVSPQVAP 152
Query: 218 IIQRPAAYVVPPPAAPVAEVSHPIIQRIMSNPVHSVEHIEKQQR 261
+ P PA + + P+ ++K +R
Sbjct: 153 --APQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAPVMDKPKR 194
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 29.5 bits (66), Expect = 4.7
Identities = 20/75 (26%), Positives = 26/75 (34%), Gaps = 10/75 (13%)
Query: 169 PMRNDKPRELESAPQSVMDFFAKAGVSQGVGENHLPQPPGFVNPPA-------AIPIIQR 221
P P + P + A S LP P +PPA A+P
Sbjct: 2766 PPAPAPPAAPAAGPPRRLT--RPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAAS 2823
Query: 222 PAAYVVPPPAA-PVA 235
PA + PP +A P A
Sbjct: 2824 PAGPLPPPTSAQPTA 2838
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 29.0 bits (65), Expect = 5.6
Identities = 11/44 (25%), Positives = 12/44 (27%)
Query: 193 GVSQGVGENHLPQPPGFVNPPAAIPIIQRPAAYVVPPPAAPVAE 236
G G G P PA + P P P AE
Sbjct: 702 GPPGGGGGLPPPPDLPAAAGPAPCGSSLIASPTAPPEPEPPGAE 745
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 29.0 bits (65), Expect = 5.9
Identities = 15/108 (13%), Positives = 23/108 (21%), Gaps = 10/108 (9%)
Query: 202 HLPQPPGFVNPPAAIPIIQRPAAYVVPPPAAPVAEVSHPIIQRIMSNPVHSVEHI-EKQQ 260
LPQPP V P P P + P P + +
Sbjct: 171 QLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQ--PPQGHPEQVQPQQFLPAPSQAPA 228
Query: 261 RSITPQAGGARVKDMAAVPVELENNMLFMRI-------SDSPIPTQQF 301
+ P + + + + P P Q
Sbjct: 229 QPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQP 276
>gnl|CDD|225854 COG3317, NlpB, Uncharacterized lipoprotein [Cell envelope
biogenesis, outer membrane].
Length = 342
Score = 28.2 bits (63), Expect = 8.1
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 8/47 (17%)
Query: 206 PPGFVNPPA----AIPII----QRPAAYVVPPPAAPVAEVSHPIIQR 244
P G + P AIP A + PPA P+A +S +R
Sbjct: 48 PAGVILPQQDGLYAIPQGNGTGAVGKALDIRPPAQPLALISGSRAER 94
>gnl|CDD|234383 TIGR03895, protease_PatA, cyanobactin maturation protease,
PatA/PatG family. This model describes a protease
domain associated with the maturation of various members
of the cyanobactin family of ribosomally produced,
heavily modified bioactive metabolites. Members include
the PatA protein and C-terminal domain of the PatG
protein of Prochloron didemni, TenA and a region of TenG
from Nostoc spongiaeforme var. tenue, etc.
Length = 602
Score = 28.5 bits (64), Expect = 8.2
Identities = 17/77 (22%), Positives = 22/77 (28%)
Query: 196 QGVGENHLPQPPGFVNPPAAIPIIQRPAAYVVPPPAAPVAEVSHPIIQRIMSNPVHSVEH 255
QG E+ P A I A PAA E+S ++ +S
Sbjct: 252 QGTIESSTSVIPPGRAAEPAPVSIPVAAPGEGATPAAAQIELSAGVLPNAISPATPVRPA 311
Query: 256 IEKQQRSITPQAGGARV 272
S P A V
Sbjct: 312 SNGVTPSQAPSAEPQLV 328
>gnl|CDD|235315 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
Length = 903
Score = 28.4 bits (64), Expect = 8.9
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 10/68 (14%)
Query: 264 TPQAGGA--RVKDMAAVPVELENNMLFMRISDSPIPTQQFFNSNLSQPVDALHMNGL-EL 320
P G A RV+D +E+ + L + QQFF+ LS P++A + L +
Sbjct: 162 LPPLGIANLRVRDQL---LEIGSQQLAFDHQE----AQQFFDQRLSSPIEAAESSRLCDD 214
Query: 321 VESNKSAL 328
VE +AL
Sbjct: 215 VEGWATAL 222
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 28.3 bits (63), Expect = 9.0
Identities = 18/77 (23%), Positives = 22/77 (28%), Gaps = 5/77 (6%)
Query: 206 PPGFVNPPAAIPIIQRPAAYVVPPPAAPVAEVSHPIIQ--RIMSNPVHSVEHIEKQQRSI 263
P P AA P P A P A A + + S P +Q +
Sbjct: 386 APAAAAPAAAAPAPAAPPA--APAAAPAAAAAARAVAAAPARRS-PAPEALAAARQASAR 442
Query: 264 TPQAGGARVKDMAAVPV 280
P A AA P
Sbjct: 443 GPGGAPAPAPAPAAAPA 459
>gnl|CDD|217310 pfam02993, MCPVI, Minor capsid protein VI. This minor capsid
protein may act as a link between the external capsid
and the internal DNA-protein core. The C-terminal 11
residues may function as a protease cofactor leading to
enzyme activation.
Length = 238
Score = 27.8 bits (62), Expect = 9.0
Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 1/36 (2%)
Query: 202 HLPQPPGFVNPPAAIPIIQRPAAYV-VPPPAAPVAE 236
P+P V + P+ + P APV E
Sbjct: 129 LQPRPRPDVEEVLVPAAPEPPSYEETIKPGPAPVEE 164
>gnl|CDD|222908 PHA02612, 27, baseplate hub subunit; Provisional.
Length = 372
Score = 27.8 bits (62), Expect = 9.8
Identities = 14/49 (28%), Positives = 22/49 (44%)
Query: 351 ILGAEPIPPKHIEPLTKNQIVQAVSHLLKHDADFVNKLHEAYLNSFKDV 399
IL EPIP EP Q +Q V + D +++ K + +K+
Sbjct: 202 ILNQEPIPMIVGEPRLIGQYIQMVDNPFVFDFEWLTKANYHTRKPYKNA 250
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 0.131 0.378
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,359,837
Number of extensions: 1956571
Number of successful extensions: 2034
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1982
Number of HSP's successfully gapped: 51
Length of query: 402
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 303
Effective length of database: 6,546,556
Effective search space: 1983606468
Effective search space used: 1983606468
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 (21.5 bits)
S2: 60 (27.1 bits)