RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1016
(718 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 = 453 bits (1168), Expect = e-157
Identities = 171/256 (66%), Positives = 194/256 (75%), Gaps = 19/256 (7%)
Query: 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIH 60
MGVP FFRWLS +YP +I +E + + EFDNLYLDMNGIIH
Sbjct: 1 MGVPKFFRWLSERYPKIIQPIIEHQIPD------------------EFDNLYLDMNGIIH 42
Query: 61 PCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120
PC+HPEDKP P+ EDEM VAIFE IDRLF IVRPRKLLYMAIDGVAPRAKMNQQRSRRFR
Sbjct: 43 PCSHPEDKPFPETEDEMFVAIFEYIDRLFNIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 102
Query: 121 ASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLHYYIH 180
A+K+ EK AE RE+L +G LP + EK FDSNCITPGTPFMARL+ L YYI
Sbjct: 103 AAKDAKEKEAEAEENREELETEGIKLPEKVEK-EKFDSNCITPGTPFMARLAKALRYYIK 161
Query: 181 DRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIML 240
+LN DP W+ + VILSDA VPGEGEHKIMD+IR QRAQPD+DPNT+HCL G DADLIML
Sbjct: 162 KKLNTDPEWQNLTVILSDAEVPGEGEHKIMDFIRSQRAQPDYDPNTRHCLYGLDADLIML 221
Query: 241 GLATHEPNFTIIREEF 256
GLATHEP+F+++REE
Sbjct: 222 GLATHEPHFSVLREEV 237
>gnl|CDD|227382 COG5049, XRN1, 5'-3' exonuclease [DNA replication, recombination,
and repair / Cell division and chromosome partitioning /
Translation].
Length = 953
Score = 462 bits (1190), Expect = e-150
Identities = 193/379 (50%), Positives = 248/379 (65%), Gaps = 40/379 (10%)
Query: 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIH 60
MGVP+FFRWLS +YP +I +E+K P FDNLYLDMNGI+H
Sbjct: 1 MGVPSFFRWLSERYPKII-QLIEEKQ---------------IPE---FDNLYLDMNGILH 41
Query: 61 PCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120
CTHP D P+ E+EM A+FE ID + +RPRKLLYMA+DGVAPRAKMNQQR+RRFR
Sbjct: 42 NCTHPNDGSPPETEEEMYKAVFEYIDHILLKIRPRKLLYMAVDGVAPRAKMNQQRARRFR 101
Query: 121 ASKET--AEKIAEVAR--IREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLH 176
++K+ A AE I E+ G + + FDSNCITPGTPFM RL+ L
Sbjct: 102 SAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKFDSNCITPGTPFMERLAKVLR 161
Query: 177 YYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADAD 236
YYIH +L++DP W+ +++I S VPGEGEHKIM++IR Q+AQP ++PNT+HC+ G DAD
Sbjct: 162 YYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDAD 221
Query: 237 LIMLGLATHEPNFTIIREE--FKPNQAR--PCDVCGQMGHEMKECVGLDAEPNPESVITF 292
LIMLGL+THEP+F I+RE+ F R C CG+ GH +EC L +P
Sbjct: 222 LIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKVLTHQP-------- 273
Query: 293 GSEVEFIFVRLSVLREYLEKELAMPNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEI 352
F + +S+LREYLE+E P LPF + ER LDDW+F+CFFVGNDFLPHLP L+I
Sbjct: 274 -----FYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDI 328
Query: 353 REGAVDRLVNLYKKTVYKT 371
REGA++ L ++KK++
Sbjct: 329 REGAIETLTEIWKKSLPHM 347
Score = 109 bits (274), Expect = 1e-24
Identities = 46/105 (43%), Positives = 60/105 (57%), Gaps = 3/105 (2%)
Query: 386 RGVKRSFDDVDESSEEE-ESNDEVRLWEDGFKDRYYESKFDVPKDDI-AFRLMVGHEYVL 443
R + + ++ EEE E+ V L G+K+RYY SK D R M EYV
Sbjct: 508 RKIPDKYVNIIVEEEEENETEKTVNLRFPGWKERYYTSKLHFTTDSEEKIRDMA-KEYVE 566
Query: 444 GLCWVLKYYYQGCRSWKWYFPFHYAPFASDFINIAEVDTNFETGT 488
GL WVL YYY+GC SW WY+P+HYAP A+D +++ D FE GT
Sbjct: 567 GLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFELGT 611
Score = 88.8 bits (220), Expect = 4e-18
Identities = 33/53 (62%), Positives = 39/53 (73%)
Query: 665 DSPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYEKLSVEES 717
SPIIDFYPE+FK+D+NGK +WQ V LLPF+DE RL A+A Y LS EE
Sbjct: 643 KSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDERRLLSAVAVKYPTLSEEER 695
Score = 38.0 bits (88), Expect = 0.020
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 591 GFLTDSGDVKLERVQLIMQDLGMMEDEIFKKRQQTETM-------FKMRNKMKKRRERQM 643
G++T G + L R+++I+ LG ED+IFKK E F +R + K+ +
Sbjct: 349 GYITCDGVINLARLEVILAILGSFEDDIFKKDHIQEERKNESLERFSLRKERKEGLKGMP 408
Query: 644 KMAAQSTKA 652
++ + K
Sbjct: 409 RVVYEQKKL 417
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 34.9 bits (80), Expect = 0.14
Identities = 37/142 (26%), Positives = 52/142 (36%), Gaps = 21/142 (14%)
Query: 304 SVLREYLEKELAMPNL-PFPYSFERALDDWVFMCFF--VGNDFLPHLPSLEIREGAVDRL 360
SVLR + EK + PNL P P + + D +P L LE + L
Sbjct: 261 SVLRRFNEKFV--PNLMPLPGDYNERRGGIILDISLNEFEQDAVPLLVDLERNGNRIKEL 318
Query: 361 ---VNLYKKTVYKTQEQLRQEENGGGGGRGVKRSFDDVDESSEEEESNDEVRLWEDGFKD 417
+ Y E+ K+ D V E S +EES DEV + E ++
Sbjct: 319 ADFGDYY-------------EDIFEVVEVVEKQEGDVVTEESTDEESEDEVEIDESVIEE 365
Query: 418 RYYESKFDVPKDDIAFRLMVGH 439
+V DD+A RL
Sbjct: 366 VAEMELLEVQVDDLAERLAETE 387
>gnl|CDD|110325 pfam01312, Bac_export_2, FlhB HrpN YscU SpaS Family. This family
includes the following members: FlhB, HrpN, YscU, SpaS,
HrcU SsaU and YopU. All of these proteins export
peptides using the type III secretion system. The
peptides exported are quite diverse.
Length = 343
Score = 34.6 bits (80), Expect = 0.16
Identities = 27/119 (22%), Positives = 49/119 (41%), Gaps = 12/119 (10%)
Query: 536 ILKFYVSDNIHLLILLVLRSWLVSLHVFTITYMIVSTMTLAGKASKLFSRMLTYPGFLTD 595
ILK I L +V L + +IV MTL K +L FL
Sbjct: 145 ILKVVAVGLIFYFFLKNDLGTIVRLPGCSPMGIIVIVMTLLKKL------LLVVLLFLLI 198
Query: 596 SG--DVKLERVQLIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRERQMKMAAQSTKA 652
G D +R ++DL M + E+ ++ +++E ++ + RR+ ++A++
Sbjct: 199 VGLLDYLFQRYL-FIKDLKMSKQEVKREYKESEGDPHVKGR---RRQIAREIASERMMQ 253
>gnl|CDD|221111 pfam11443, DUF2828, Domain of unknown function (DUF2828). This is
a uncharacterized domain found in eukaryotes and
viruses.
Length = 414
Score = 33.5 bits (77), Expect = 0.36
Identities = 19/62 (30%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 264 CDVCGQMGHE-MKECVGL-------DAEPNPESVITFGSEVEFIFVRLSVLREYLEKELA 315
CDV G M M C+ L P VITF S + ++ LRE +
Sbjct: 229 CDVSGSMSGPPMDVCIALGLLVSELSEGPFKGRVITFSSNPQLHHIKGDSLREKVSFVRR 288
Query: 316 MP 317
MP
Sbjct: 289 MP 290
>gnl|CDD|151309 pfam10860, DUF2661, Protein of unknown function (DUF2661). This
viral family of proteins have no known function.
Length = 109
Score = 30.0 bits (68), Expect = 1.4
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 7 FRWLSRKYPSVIVHCVEDK-----PQEVNGQKIPFDSSKPNPNGMEFDNL 51
+ +R Y +V+ VE++ PQ N + I F P N + N+
Sbjct: 26 ILYHARYYKCYVVYYVENEGSLRLPQCENVKFINFKEVYPERNMAKLQNV 75
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 30.6 bits (69), Expect = 2.2
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 258 PNQARPCDVCGQMGHEMKEC 277
+ C CGQ GH ++C
Sbjct: 57 REENPVCFNCGQNGHLRRDC 76
>gnl|CDD|212539 cd11593, Agmatinase-like_2, Agmatinase and related proteins. This
family includes known and predicted bacterial and
archaeal agmatinase (agmatine ureohydrolase; AUH; SpeB;
EC=3.5.3.11), a binuclear manganese metalloenzyme that
belongs to the ureohydrolase superfamily. It is a key
enzyme in the synthesis of polyamine putrescine; it
catalyzes hydrolysis of agmatine to yield urea and
putrescine, the precursor for biosynthesis of higher
polyamines, spermidine, and spermine. As compared to E.
coli where two paths to putrescine exist, via
decarboxylation of an amino acid, ornithine or arginine,
a single path is found in Bacillus subtilis, where
polyamine synthesis starts with agmatine; the speE and
speB encode spermidine synthase and agmatinase,
respectively. The level of agmatinase synthesis is very
low, allowing strict control on the synthesis of
putrescine and therefore, of all polyamines, consistent
with polyamine levels in the cell. This subfamily
belongs to the ureohydrolase superfamily, which includes
arginase, agmatinase, proclavaminate amidinohydrolase,
and formiminoglutamase.
Length = 263
Score = 30.1 bits (69), Expect = 3.7
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 654 SFIPGGQFAP----QDSPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKAL 705
S+ PG +F P + S ++ Y DL F G LP D E++ + +
Sbjct: 13 SYRPGTRFGPAAIREASYQLELYSPYLDRDLEDIPFYDLGDLTLPPGDPEKVLERI 68
>gnl|CDD|237572 PRK13962, PRK13962, bifunctional phosphoglycerate
kinase/triosephosphate isomerase; Provisional.
Length = 645
Score = 30.5 bits (69), Expect = 3.8
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 22/103 (21%)
Query: 190 KGIKVILS-DANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIMLGLATH--- 245
KG +VI+ D NVP + I D R + A P T L A +I L +H
Sbjct: 12 KGKRVIVRVDFNVPLDENGNITDDTRIRAALP-----TIKYLLDHGAKVI---LVSHLGR 63
Query: 246 -----EPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAE 283
+P F++ P R ++ G+ K+ +G DA+
Sbjct: 64 PKGEFDPKFSM-----APVAKRLSELLGKEVIFAKDVIGDDAK 101
>gnl|CDD|233953 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3, subtype
Dpsyc. This model describes a CRISPR-associated
putative DEAH-box helicase, or Cas3, of a subtype found
in Actinomyces naeslundii MG1, Geobacter sulfurreducens
PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea
psychrophila. This protein includes both DEAH and HD
motifs [Mobile and extrachromosomal element functions,
Other].
Length = 862
Score = 30.7 bits (69), Expect = 3.9
Identities = 25/107 (23%), Positives = 46/107 (42%), Gaps = 16/107 (14%)
Query: 606 LIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRE----RQMKMAAQSTKAPSFIPGGQF 661
L+ QD ++ DE ET+F +R++ ++ + R +++ A
Sbjct: 177 LLGQDALIVLDEAHLSPAFQETLFVIRSEQQRLEDFCPLRVVELTATPRTD--------- 227
Query: 662 APQDSPIIDFYPEDFKIDLNGKKFAW-QGVALLPFVDEERLHKALAP 707
P + ED+K GK+ + L P +DE+RLH+ + P
Sbjct: 228 TPDTLTTLR--QEDYKHPTPGKRLDAKKECRLDPQLDEKRLHRDVVP 272
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 29.4 bits (66), Expect = 3.9
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 262 RPCDVCGQMGHEMKEC 277
R C CG+ GH +EC
Sbjct: 53 RSCYNCGKTGHLSREC 68
>gnl|CDD|185162 PRK15250, PRK15250, virulence protein SpvD; Provisional.
Length = 216
Score = 28.9 bits (64), Expect = 7.1
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 8/28 (28%)
Query: 155 HFDSNCITPGTPFMARLSACLHYYIHDR 182
H+ NC+ LSACLHY IH R
Sbjct: 68 HYSGNCVL--------LSACLHYNIHHR 87
>gnl|CDD|130471 TIGR01404, FlhB_rel_III, type III secretion protein, YscU/HrpY
family. This model represents one of several families
of proteins related to bacterial flagellar biosynthesis
proteins and involved in bacterial type III protein
secretion systems. This family is homologous to, but
distinguished from, flagellar biosynthetic protein FlhB
(TIGRFAMs model TIGR00328). This model may not identify
all type III secretion system FlhB homologs [Protein
fate, Protein and peptide secretion and trafficking,
Cellular processes, Pathogenesis].
Length = 342
Score = 29.2 bits (66), Expect = 7.3
Identities = 13/47 (27%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 606 LIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRERQMKMAAQSTKA 652
L M+DL M +DE+ ++ ++ E ++++ KRRE ++ ++ K+
Sbjct: 207 LFMKDLKMSKDEVKREYKEQEGDPEIKS---KRRELHQEILSEQLKS 250
>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 = 28.9 bits (64), Expect = 7.5
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 8/28 (28%)
Query: 155 HFDSNCITPGTPFMARLSACLHYYIHDR 182
H+ NC+ LSACLHY IH R
Sbjct: 68 HYSGNCVL--------LSACLHYNIHHR 87
>gnl|CDD|224340 COG1422, COG1422, Predicted membrane protein [Function unknown].
Length = 201
Score = 28.9 bits (65), Expect = 7.6
Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 572 TMTLAGKASKLFSRMLTYPGFLTDSGDVKLERVQLIMQDLGMMEDEI--FKKRQQTETMF 629
+ +A + L+ +L L D K++ +Q +M++ + E ++ + +
Sbjct: 49 VILVAAVITGLYITILQK--LLIDQ--EKMKELQKMMKEF---QKEFREAQESGDMKKLK 101
Query: 630 KMRNKMKKRRERQMKMAAQSTK 651
K++ K + + Q ++ K
Sbjct: 102 KLQEKQMEMMDDQRELMKMQFK 123
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving DNA
bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 29.1 bits (66), Expect = 7.6
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 12/46 (26%)
Query: 96 KLLYMAI------DGVAPRAKM------NQQRSRRFRASKETAEKI 129
KLL+ I DG AP K QQR + +K+TAEK+
Sbjct: 64 KLLFYGIKPVFVFDGGAPELKRRTLAKRRQQREKAEINAKKTAEKL 109
>gnl|CDD|144881 pfam01452, Rota_NSP4, Rotavirus non structural protein. This
protein has been called NSP4, NSP5, NS28, and NCVP5. The
final steps in the assembly of rotavirus occur in the
lumen of the endoplasmic reticulum (ER). Targeting of
the immature inner capsid particle (ICP) to this
compartment is mediated by the cytoplasmic tail of NSP4,
located in the ER membrane.
Length = 174
Score = 28.3 bits (63), Expect = 9.9
Identities = 21/108 (19%), Positives = 48/108 (44%), Gaps = 18/108 (16%)
Query: 562 VFTITYMIVSTMTLAGKASK------------LFSRMLTYPGFLT-----DSGDVKLER- 603
+FT + TM +A S +F+ +L G+ T D + + R
Sbjct: 43 LFTAHKASIPTMKVAKTTSGCSYKVIKVVVVTIFNTLLRLFGYKTEVTSKDEIEKQASRI 102
Query: 604 VQLIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRERQMKMAAQSTK 651
V+ I + L M+E ++ +Q E + ++ + +K + ++ M+ ++ +
Sbjct: 103 VKEIREQLKMIEKLTTREIEQVELLKRIYDMLKVTSDNEIDMSKETNR 150
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
0.322 0.139 0.429
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,129,946
Number of extensions: 3854260
Number of successful extensions: 3682
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3669
Number of HSP's successfully gapped: 34
Length of query: 718
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 614
Effective length of database: 6,324,786
Effective search space: 3883418604
Effective search space used: 3883418604
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: 63 (28.0 bits)