RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8848
(459 letters)
>gnl|CDD|182922 PRK11040, PRK11040, peptidase PmbA; Provisional.
Length = 446
Score = 389 bits (1002), Expect = e-132
Identities = 173/448 (38%), Positives = 273/448 (60%), Gaps = 15/448 (3%)
Query: 15 KSEFQQLAQDMLNYAKKIGASHSSIEFNEGNGFSVFVRKGKIDVIEQNNDKNMNVIIYIQ 74
+ ++ L A + + + ++ G SV R G+++ +E N+D + + +Y Q
Sbjct: 11 RKILEEAVSTALELASG-KSDGAEVAVSKTTGISVSTRYGEVENVEFNSDGALGITVYHQ 69
Query: 75 DGKKMFYGNSSTSDFCKKSLYDTINAAYNIARFTASDNFAGLPDENTLEMNPLDFKLYTP 134
K G++S++D +++ T+ AA +IAR+T+ D AG D+ L + D L+ P
Sbjct: 70 QRK----GSASSTDLSPQAIARTVQAALDIARYTSPDPCAGPADKELLAFDAPDLDLFHP 125
Query: 135 WFLSIDDAKLIAYRCENEAFNFNSLIVNNENTGVTTQQSHF---LLANSHGFMSGYPFSK 191
+ D+A +A R E A + I N E + SH+ + NSHG + Y S+
Sbjct: 126 AEVDPDEAIELAARAEQAALQADKRITNTEGG---SFNSHYGIKVFGNSHGMLQSYCSSR 182
Query: 192 HIISISPIAIKGKEMQRDNWYSSNSDPKKLDQPEIIGFYAAKRTISRLKAKKISTRKCPV 251
H +S IA + +M+RD Y+ L PE +G A+RT+SRL +K+ST K PV
Sbjct: 183 HSLSSCVIAEENGDMERDYAYTIGRAMDDLQTPEWVGAECARRTLSRLSPRKLSTMKAPV 242
Query: 252 LFEAPLAFELLNIFARLISGNSLYRKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSSF 311
+F A +A L ISG S+YRKSTFL+DSLGK+I + I E PH+L S+ F
Sbjct: 243 IFAAEVATGLFGHLVGAISGGSVYRKSTFLLDSLGKQILPEWLTIEEHPHLLKGLASTPF 302
Query: 312 DNEGVKTQKRLVVKNGIIQGYFLSTYSAKKLGMKTTGNSGGAHHLIIISNKTKSSDNLKE 371
D+EGV+T++R ++K+G++Q + L++YSA+KLG+K+TG++GG H+ I + ++
Sbjct: 303 DSEGVRTERRDIIKDGVLQTWLLTSYSARKLGLKSTGHAGGIHNWRIAG----QGLSFEQ 358
Query: 372 MLKKMNTGLLVTELMGDGINYITGDYSKGAFGYWIENGKIQYSVEEITISGKLQNMFKQI 431
MLK+M TGL+VTELMG G++ +TGDYS+GA G+W+ENG+IQY V EITI+G L++M++ I
Sbjct: 359 MLKEMGTGLVVTELMGQGVSAVTGDYSRGAAGFWVENGEIQYPVSEITIAGNLKDMWRNI 418
Query: 432 VAIGSDVLTRNSNTSGSILIENMIIAGK 459
V +G+D+ TR++ GS+L+ M IAG+
Sbjct: 419 VTVGNDIETRSNIQCGSVLLPEMKIAGQ 446
>gnl|CDD|223389 COG0312, TldD, Predicted Zn-dependent proteases and their
inactivated homologs [General function prediction only].
Length = 454
Score = 299 bits (767), Expect = 4e-97
Identities = 137/461 (29%), Positives = 232/461 (50%), Gaps = 28/461 (6%)
Query: 19 QQLAQDMLNYAKKIGASHSSIEFNEGNGFSVFVRKGKIDVIEQNNDKNMNVIIYIQDGKK 78
+L + +L A K GA + + +G SV +R G+++ + + D+ + V + G
Sbjct: 2 MELLEKLLELALKAGADEAEVRVERSSGESVSLRNGEVETVSFSIDRGVGVRVIKGGGWG 61
Query: 79 MFYGNSSTSDFCKKSLYDTINAAYNIARFTASDNFAGL-PDENTLEMNPLDFKLYTPWFL 137
N + ++L + AA IAR D AGL P E + D L P +
Sbjct: 62 FASTNDLS-----EALEAAVEAALKIARLAGEDEEAGLAPPEPLAPASYPDLDLKDPEDV 116
Query: 138 SIDDAKLIAYRCENEAFNFNSLIVNNENTGVTTQQSHFLLANSHGFMSGYPFSKHIISIS 197
S+++ + R E A + I + + S ++ANS G Y ++ +S+S
Sbjct: 117 SLEEKVELLKRAEAAARAADPRINSVSA-SYSDSVSEVVIANSEGSEVEYERTRVSLSVS 175
Query: 198 PIAIK-GKEMQRDNWYSSNSDPKKL-DQPEIIGFYAAKRTISRLKAKKISTRKCPVLFEA 255
IA + G+ +R + ++L ++PE + AA+R +S L+A+ + + + PV+ +
Sbjct: 176 VIAGEGGRGEERSGRGGGSRGFEELLEEPEEVAEEAARRALSLLEARPVPSGRYPVIL-S 234
Query: 256 PLAFELL--NIFARLISGNSLYRKSTF-LVDSLGKKIFSSHIQIIEDPHILGSFGSSSFD 312
P A +L + G+ +Y+ + L D LGK++ S + II+DP + G GS FD
Sbjct: 235 PEAAGVLLHEALGHALEGDRVYKGESSLLADKLGKRVASELLTIIDDPTLPGGLGSYPFD 294
Query: 313 NEGVKTQKRLVVKNGIIQGYFLSTYSAKKLGMKTTGNS--GGAHHLIIISNK----TKSS 366
+EGV T++ ++++NG+++GY YSA+KLG+++TGN+ G H+ I
Sbjct: 295 DEGVPTRRTVLIENGVLKGYLHDRYSARKLGLESTGNARRGSYAHVPIPRMTNTYIEPGD 354
Query: 367 DNLKEMLKKMNTGLLVTELMGDGINYITGDYS--KGAFGYWIENGKIQYSVEEITISGKL 424
+ +E+++ + GL VT L G G N ITG + GA GY IENG+I Y V+ IT+SG L
Sbjct: 355 YSFEELIEDVKRGLYVTNLWG-GQNDITGGFFRFSGAEGYLIENGEITYPVKGITLSGNL 413
Query: 425 QNMFKQIVAIGSDVL------TRNSNTSGSILIENMIIAGK 459
+ K IVA+G D+ SI + +I+AG
Sbjct: 414 LELLKNIVAVGKDLELDEGRGFCGKVGGPSIRVRGVIVAGG 454
>gnl|CDD|216551 pfam01523, PmbA_TldD, Putative modulator of DNA gyrase. tldD and
pmbA were found to suppress mutations in letD and
inhibitor of DNA gyrase. Therefore it has been
hypothesised that the TldD and PmbA proteins modulate
the activity of DNA gyrase. It has also been suggested
that PmbA may be involved in secretion.
Length = 289
Score = 198 bits (505), Expect = 4e-60
Identities = 85/297 (28%), Positives = 148/297 (49%), Gaps = 15/297 (5%)
Query: 39 IEFNEGNGFSVFVRKGKIDVIEQNNDKNMNVIIYIQDGKKMFYGNSSTSDFCKKSLYDTI 98
+ E SV R GK++ + + D+ + V + DG+ G +STSD +++L +
Sbjct: 5 VRVEESESTSVRFRNGKVENVSSSEDRGVGVRVIK-DGR---VGFASTSDLSEEALKKAV 60
Query: 99 NAAYNIARFTASDNFAGLPDENTLEMNPLDFKLYTPWFLSIDDAKLIAY--RCENEAFNF 156
A +A+ + D AGLPD + L P LY P + + I E A
Sbjct: 61 ERALALAKLSPED-PAGLPDPSPL---PPVPDLYDPDPADLSLEEKIELLKELEEAALAV 116
Query: 157 NSLIVNNENTGVTTQQSHFLLANSHGFMSGYPFSKHIISISPIAIKGKEMQRDNWYSSNS 216
+ I + + S ++ANS G Y ++ +S+S +A G E+Q Y+
Sbjct: 117 DPRIS--ASGSYSDSVSEVIIANSEGLEVEYESTRVSLSVSAVAEDGGEVQSGYSYTGRR 174
Query: 217 DPKKLDQPEIIGFYAAKRTISRLKAKKISTRKCPVLFEAPLAFELLN-IFARLISGNSLY 275
+L PE + AA++ ++ L AK I T K PV+ + A LL+ F + +++
Sbjct: 175 F--ELIDPEELAEEAAEKALALLGAKPIETGKYPVVLDPEAAGSLLHEAFGHALEADNVL 232
Query: 276 RKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSSFDNEGVKTQKRLVVKNGIIQGY 332
+ +FL LG+K+ S + I++DP + G GS FD+EGV T++ ++++NG+++GY
Sbjct: 233 KGRSFLKGKLGEKVASELVTIVDDPTLPGGLGSYPFDDEGVPTRRTVLIENGVLKGY 289
>gnl|CDD|182685 PRK10735, tldD, protease TldD; Provisional.
Length = 481
Score = 59.0 bits (143), Expect = 2e-09
Identities = 42/172 (24%), Positives = 84/172 (48%), Gaps = 11/172 (6%)
Query: 276 RKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSSFDNEGVKTQKRLVVKNGIIQGYFLS 335
R ++ +G+ + S +++D ++ GS + D+EG Q ++++NGI++GY
Sbjct: 276 RGTSVFSGQVGELVASELCTVVDDGTMVDRRGSVAIDDEGTPGQYNVLIENGILKGYMQD 335
Query: 336 TYSAKKLGMKTTGN---SGGAHHLIIISNKT-----KSSDNLKEMLKKMNTGLLVTELMG 387
+A+ +G+ TGN AH + T KS+ +E+++ + G+ G
Sbjct: 336 KLNARLMGVAPTGNGRRESYAHLPMPRMTNTYMLAGKSTP--QEIIESVEYGIYAPNFGG 393
Query: 388 DGINYITGDYS-KGAFGYWIENGKIQYSVEEITISGKLQNMFKQIVAIGSDV 438
++ +G + + Y IENGK+ V+ T+ G +QI +G+D+
Sbjct: 394 GQVDITSGKFVFSTSEAYLIENGKVTKPVKGATLIGSGIEAMQQISMVGNDL 445
>gnl|CDD|237790 PRK14694, PRK14694, putative mercuric reductase; Provisional.
Length = 468
Score = 30.7 bits (69), Expect = 1.6
Identities = 27/113 (23%), Positives = 50/113 (44%), Gaps = 23/113 (20%)
Query: 257 LAFELLNIFARLISGNSLYRKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSSFDNEGV 316
+A EL FARL S + T L S ++ S EDP + G ++F EG+
Sbjct: 189 VALELAQAFARLGS------RVTVLARS---RVLSQ-----EDPAV-GEAIEAAFRREGI 233
Query: 317 KTQKRLVVKNGIIQGYFLSTYSAKKLGMKTTGNSGGAHHLIIISNKTKSSDNL 369
+ K+ Y+ ++ ++T + A L++ + +T +++NL
Sbjct: 234 EVLKQTQASE--------VDYNGREFILETNAGTLRAEQLLVATGRTPNTENL 278
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 30.8 bits (70), Expect = 1.8
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 6/29 (20%)
Query: 382 VTELMGDGINYITGDYSKGAFGYWIENGK 410
+TEL+ DG GAFGYW E+G+
Sbjct: 174 ITELLKDG------GRIAGAFGYWRESGR 196
>gnl|CDD|182937 PRK11061, PRK11061, fused phosphoenolpyruvate-protein
phosphotransferase PtsP/GAF domain; Provisional.
Length = 748
Score = 29.6 bits (67), Expect = 4.7
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 16 SEFQQLAQDMLN--YAKKIGASHSSIEFNEGNGFSVFVRKGK 55
+E + LAQ L A ++ H F E G +R GK
Sbjct: 709 AEAENLAQRSLEAQLATEV--RHQVAAFMERRGLGGLIRGGK 748
>gnl|CDD|234244 TIGR03527, selenium_YedF, selenium metabolism protein YedF.
Members of this protein family are about 200 amino acids
in size, and include the uncharacterized YedF protein of
Escherichia coli. This family shares an N-terminal
domain, modeled by pfam01206, with the sulfurtransferase
TusA (also called SirA). The C-terminal domain includes
a typical redox-active disulfide motif, CGXC. This
protein family found only among those genomes that also
carry the selenium donor protein SelD, and its
connection to selenium metabolism is indicated by the
method of partial phylogenetic profiling vs. SelD. Its
gene typically is found next to selD. Members of this
family are found even when selenocysteine and
selenouridine biosynthesis pathways are, except for
SelD, completely absent, as in Enterococcus faecalis.
Its role in selenium metabolism is unclear, but may
include either detoxification or a role in labile
selenoprotein biosynthesis.
Length = 194
Score = 28.7 bits (65), Expect = 5.0
Identities = 25/112 (22%), Positives = 38/112 (33%), Gaps = 26/112 (23%)
Query: 351 GGAHHLIIISNKTKSSDNLKEMLKKMNTGLLVTELMGDGINYITGDYSKGAFGYWI---- 406
G L +I + + +N+ + + + V E GYWI
Sbjct: 23 GEEGVLTVIVDNEAAKENVSKFATSLGYEVEVEEKEE---------------GYWILIIK 67
Query: 407 -ENGKIQYSVEEITISGKLQNMFKQIVAIGSDVLTRNSNTSGSILIENMIIA 457
G + S +E GKL +V I SD L G IL++ I
Sbjct: 68 KGEGAAEASPDEAAKEGKL------VVVITSDKLGEGDEELGRILMKGFIYT 113
>gnl|CDD|133132 cd06601, GH31_lyase_GLase, GLases (alpha-1,4-glucan lyases) are
glycosyl hydrolase family 31 (GH31) enzymes that degrade
alpha-1,4-glucans and maltooligosaccharides via a
nonhydrolytic pathway to yield 1,5-D-anhydrofructose
from the nonreducing end. GLases cleave the bond between
C1 and O1 of the nonreducing sugar residue of
alpha-glucans to generate a monosaccharide product with
a double bond between C1 and C2. This family corresponds
to subgroup 2 in the Ernst et al classification of GH31
enzymes.
Length = 332
Score = 29.0 bits (65), Expect = 5.1
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 83 NSSTSDFCKKSLYDTINAAYNIARFTASD--NFAGLPDENTLEMNPLDFKLYTPWF 136
NSS+ DF + ++ +N + SD F EN+++ + +L W+
Sbjct: 218 NSSSWDFLQINIAQVLNLGMSGLPIAGSDIGGFTSYDGENSIQRTWCNPELLIRWY 273
>gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional.
Length = 188
Score = 28.3 bits (64), Expect = 6.2
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 9/34 (26%)
Query: 339 AKKLGMKT---TGNSGG-----AHHLIII-SNKT 363
A++LGMKT TG GG HL+I+ S+ T
Sbjct: 129 ARELGMKTIGLTGRDGGKMKELCDHLLIVPSDDT 162
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC, C-terminal
domain. This model describes the C-terminal domain, or
longer subunit, of the Firmicutes type VII secretion
protein EssC. This protein (homologous to EccC in
Actinobacteria) and the WXG100 target proteins are the
only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 28.8 bits (65), Expect = 8.9
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 355 HLIIISNK---TKSSDNLKEMLKKMNTGLLVTELMGDGINYITGDYSKGA----FGYWIE 407
H I+ +KS D + + +K++ TG+L + S+ GY++
Sbjct: 1226 HFIVAGTHSELSKSYDGVPKEIKQLRTGILGMRKSDQSFFKLPFTRSEKELEPGEGYFVV 1285
Query: 408 NGKIQ 412
NGK Q
Sbjct: 1286 NGKYQ 1290
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
0.317 0.134 0.378
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,167,253
Number of extensions: 2281655
Number of successful extensions: 1837
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1820
Number of HSP's successfully gapped: 24
Length of query: 459
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 359
Effective length of database: 6,502,202
Effective search space: 2334290518
Effective search space used: 2334290518
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: 61 (27.3 bits)