RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15417
(176 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 152 bits (385), Expect = 5e-46
Identities = 63/161 (39%), Positives = 90/161 (55%), Gaps = 6/161 (3%)
Query: 18 GHTGDVMSLSLAPDMRTFVSGAC-DASAKLWDIRDGSCKQTFPGHESDINAVTFFPNGWA 76
GHT V S++ +PD TFV+ + D + KLWD+R G C T GH ++N+V F P+G
Sbjct: 133 GHTDWVNSVAFSPD-GTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEK 191
Query: 77 FATGSDDATCRLFDIRADQELAMY-SHDNIICGITSVAFSRSGRLLLAGYDDFNCNVWDS 135
+ S D T +L+D+ + L H+N + SVAFS G LL +G +D VWD
Sbjct: 192 LLSSSSDGTIKLWDLSTGKCLGTLRGHENGVN---SVAFSPDGYLLASGSEDGTIRVWDL 248
Query: 136 MKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
E L+GH N V+ L + DG +A+GS D +RIW+
Sbjct: 249 RTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 120 bits (303), Expect = 8e-34
Identities = 49/159 (30%), Positives = 81/159 (50%), Gaps = 2/159 (1%)
Query: 18 GHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGSCKQTFPGHESDINAVTFFPNGWAF 77
GHTG V ++ +PD + +G+ D + K+WD+ G +T GH + V +G
Sbjct: 7 GHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYL 66
Query: 78 ATGSDDATCRLFDIRADQELAMYSHDNIICGITSVAFSRSGRLLLAGYDDFNCNVWDSMK 137
A+GS D T RL+D+ + + + ++SVAFS GR+L + D VWD
Sbjct: 67 ASGSSDKTIRLWDLETGECVRTLTGHT--SYVSSVAFSPDGRILSSSSRDKTIKVWDVET 124
Query: 138 TERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
+ L GH + V+ + + DG VA+ S D +++W+
Sbjct: 125 GKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWD 163
Score = 113 bits (284), Expect = 5e-31
Identities = 57/160 (35%), Positives = 87/160 (54%), Gaps = 4/160 (2%)
Query: 18 GHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGSCKQTFPGHESDINAVTFFPNGWAF 77
GHT V S++ +PD R S + D + K+WD+ G C T GH +N+V F P+G
Sbjct: 91 GHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFV 150
Query: 78 ATGSDDATCRLFDIRADQELAMYS-HDNIICGITSVAFSRSGRLLLAGYDDFNCNVWDSM 136
A+ S D T +L+D+R + +A + H + SVAFS G LL+ D +WD
Sbjct: 151 ASSSQDGTIKLWDLRTGKCVATLTGHTG---EVNSVAFSPDGEKLLSSSSDGTIKLWDLS 207
Query: 137 KTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
+ G L GH+N V+ + + DG +A+GS D +R+W+
Sbjct: 208 TGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWD 247
Score = 83.9 bits (208), Expect = 6e-20
Identities = 36/124 (29%), Positives = 59/124 (47%), Gaps = 4/124 (3%)
Query: 54 CKQTFPGHESDINAVTFFPNGWAFATGSDDATCRLFDIRADQELA-MYSHDNIICGITSV 112
++T GH + V F P+G ATGS D T +++D+ + L + H + V
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTG---PVRDV 57
Query: 113 AFSRSGRLLLAGYDDFNCNVWDSMKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFL 172
A S G L +G D +WD E L GH + VS + + DG +++ S D +
Sbjct: 58 AASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTI 117
Query: 173 RIWN 176
++W+
Sbjct: 118 KVWD 121
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 94.4 bits (233), Expect = 5e-23
Identities = 55/163 (33%), Positives = 92/163 (56%), Gaps = 6/163 (3%)
Query: 17 SGHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGSCKQ--TFPGHESDINAVTFFPNG 74
SGH+ V+S++ +PD + SG+ D + +LWD+ G T GHE +++++F P+G
Sbjct: 281 SGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDG 340
Query: 75 WAFATG-SDDATCRLFDIRADQELAMYSHDNIICGITSVAFSRSGRLLLAGYDDFNCNVW 133
+G SDD T RL+D+R + L + + SV+FS GR++ +G D +W
Sbjct: 341 SLLVSGGSDDGTIRLWDLRTGKPLKTLEGHS---NVLSVSFSPDGRVVSSGSTDGTVRLW 397
Query: 134 DSMKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
D L GH +RV+ L + DG ++A+GS D+ +R+W+
Sbjct: 398 DLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWD 440
Score = 92.8 bits (229), Expect = 2e-22
Identities = 53/163 (32%), Positives = 84/163 (51%), Gaps = 5/163 (3%)
Query: 17 SGHTGDVMSLSLAPDMRTFVSGAC-DASAKLWDIRDGSCKQTFPGHESDINAVTFFPNG- 74
GH+ V SL+ +PD + SG+ D + KLWD+R G T GH ++++ F P+G
Sbjct: 152 EGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGG 211
Query: 75 WAFATGSDDATCRLFDIRADQELAMYSHDNIICGITSVAFSRSGRLLLAGYDDFNCNVWD 134
A+GS D T RL+D+ + L + ++S FS G LL +G D +WD
Sbjct: 212 LLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSS--FSPDGSLLASGSSDGTIRLWD 269
Query: 135 -SMKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
+ L+GH + V + + DG +A+GS D +R+W+
Sbjct: 270 LRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWD 312
Score = 85.9 bits (211), Expect = 4e-20
Identities = 56/162 (34%), Positives = 87/162 (53%), Gaps = 4/162 (2%)
Query: 17 SGHTGDVMSLSLAPDMRTFVSGACDASAKLWDIR-DGSCKQTFPGHESDINAVTFFPNGW 75
SGH+ V+S S +PD SG+ D + +LWD+R S +T GH S + +V F P+G
Sbjct: 239 SGHSDSVVS-SFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGK 297
Query: 76 AFATGSDDATCRLFDIRADQELAMYSHDNIICGITSVAFSRSG-RLLLAGYDDFNCNVWD 134
A+GS D T RL+D+ + L+ + ++S++FS G L+ G DD +WD
Sbjct: 298 LLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWD 357
Query: 135 SMKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
+ L GH N V + + DG V++GS D +R+W+
Sbjct: 358 LRTGKPLKTLEGHSN-VLSVSFSPDGRVVSSGSTDGTVRLWD 398
Score = 67.4 bits (163), Expect = 1e-13
Identities = 49/167 (29%), Positives = 81/167 (48%), Gaps = 10/167 (5%)
Query: 17 SGHTGDVMSLSLA-PDMRTFVS--GACDASAKLWDIR-DGSCKQTFPGHESDINAVTFFP 72
H V L+L+ PD + + + D + KLWD+ G +T GH + ++ F P
Sbjct: 106 GLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSP 165
Query: 73 NG-WAFATGSDDATCRLFDIRADQELAMYSHDNIICGITSVAFSRSGRLLLAGY-DDFNC 130
+G + S D T +L+D+R + L+ + ++S+AFS G LL+A D
Sbjct: 166 DGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHT--DPVSSLAFSPDGGLLIASGSSDGTI 223
Query: 131 NVWD-SMKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
+WD S L+GH + V + DG +A+GS D +R+W+
Sbjct: 224 RLWDLSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSSDGTIRLWD 269
Score = 63.2 bits (152), Expect = 4e-12
Identities = 56/183 (30%), Positives = 91/183 (49%), Gaps = 12/183 (6%)
Query: 3 DHLDKSALLGSPAASGHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGS-CKQTFPG- 60
D L L S GH + S++ +PD +SG+ D + KLWD+ +G ++ G
Sbjct: 48 DSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGL 107
Query: 61 HESDINAVTFF-PNGWAFAT--GSDDATCRLFDIRADQELAMY--SHDNIICGITSVAFS 115
H+S ++ + P+G + S D T +L+D+ +L H +TS+AFS
Sbjct: 108 HDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSES---VTSLAFS 164
Query: 116 RSGRLLLAG-YDDFNCNVWDSMKTERAGILAGHDNRVSCLGVTEDG-MAVATGSWDSFLR 173
G+LL +G D +WD + LAGH + VS L + DG + +A+GS D +R
Sbjct: 165 PDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIR 224
Query: 174 IWN 176
+W+
Sbjct: 225 LWD 227
Score = 51.6 bits (122), Expect = 4e-08
Identities = 38/165 (23%), Positives = 70/165 (42%), Gaps = 6/165 (3%)
Query: 17 SGHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGSCKQTFPGHESDINAVTFFPNGWA 76
G + + +SL + + S L + D S GHE I ++ F P+G
Sbjct: 21 LGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLS-SLLLRGHEDSITSIAFSPDGEL 79
Query: 77 FATGSDDATCRLFDIR-ADQELAMYS--HDNIICGITSVAFSRSGRLLLAGYDDFNCNVW 133
+GS D T +L+D+ ++ + HD+ + + + + LL + D +W
Sbjct: 80 LLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLW 139
Query: 134 D-SMKTERAGILAGHDNRVSCLGVTEDG-MAVATGSWDSFLRIWN 176
D S + L GH V+ L + DG + + S D +++W+
Sbjct: 140 DLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWD 184
Score = 49.7 bits (117), Expect = 2e-07
Identities = 28/75 (37%), Positives = 46/75 (61%)
Query: 18 GHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGSCKQTFPGHESDINAVTFFPNGWAF 77
+V+S+S +PD R SG+ D + +LWD+ GS + GH S + ++ F P+G +
Sbjct: 368 EGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSL 427
Query: 78 ATGSDDATCRLFDIR 92
A+GS D T RL+D++
Sbjct: 428 ASGSSDNTIRLWDLK 442
Score = 31.6 bits (70), Expect = 0.21
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 99 MYSHDNIICGITSVAFSRSGRLLLAGYDDFNCNVWDSMKTERAGILAGHDNRVSCLGVTE 158
+ S+ S SG LLLA D ++ D + +L GH++ ++ + +
Sbjct: 20 ELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPD----LSSLLLRGHEDSITSIAFSP 75
Query: 159 DGMAVATGSWDSFLRIWN 176
DG + +GS D +++W+
Sbjct: 76 DGELLLSGSSDGTIKLWD 93
Score = 30.4 bits (67), Expect = 0.53
Identities = 17/53 (32%), Positives = 26/53 (49%)
Query: 6 DKSALLGSPAASGHTGDVMSLSLAPDMRTFVSGACDASAKLWDIRDGSCKQTF 58
D S GHT V SL +PD ++ SG+ D + +LWD++ +F
Sbjct: 398 DLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVSF 450
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 45.0 bits (107), Expect = 2e-07
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 51 DGSCKQTFPGHESDINAVTFFPNGWAFATGSDDATCRLFD 90
G +T GH + +V F P+G A+GSDD T +L+D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 35.8 bits (83), Expect = 5e-04
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 143 ILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
L GH V+ + + DG +A+GS D +++W+
Sbjct: 7 TLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 35.0 bits (81), Expect = 0.001
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 17 SGHTGDVMSLSLAPDMRTFVSGACDASAKLWD 48
GHTG V S++ +PD + SG+ D + KLWD
Sbjct: 9 KGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 31.1 bits (71), Expect = 0.030
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 108 GITSVAFSRSGRLLLAGYDDFNCNVWD 134
+TSVAFS G+ L +G DD +WD
Sbjct: 14 PVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 44.3 bits (105), Expect = 4e-07
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 52 GSCKQTFPGHESDINAVTFFPNGWAFATGSDDATCRLFD 90
G +T GH + +V F P+G A+GSDD T R++D
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.9 bits (86), Expect = 2e-04
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 17 SGHTGDVMSLSLAPDMRTFVSGACDASAKLWD 48
GHTG V S++ +PD SG+ D + ++WD
Sbjct: 8 KGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.2 bits (84), Expect = 4e-04
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 142 GILAGHDNRVSCLGVTEDGMAVATGSWDSFLRIWN 176
L GH V+ + + DG +A+GS D +R+W+
Sbjct: 5 RTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 32.3 bits (74), Expect = 0.010
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 108 GITSVAFSRSGRLLLAGYDDFNCNVWD 134
+TSVAFS G LL +G DD VWD
Sbjct: 13 PVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 36.8 bits (85), Expect = 0.004
Identities = 31/137 (22%), Positives = 48/137 (35%), Gaps = 22/137 (16%)
Query: 18 GHTGDVMSLSLAPD-MRTFVSGACDASAKLWDIRDGSCKQTFPGHESDINAVTFFPNGWA 76
GHT V +S P M S D +WD+ G + H I ++ + +G
Sbjct: 123 GHTKKVGIVSFHPSAMNVLASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSL 182
Query: 77 FATGSDDATCRLFDIRADQELAMYSHDNIICGITSVAFSRSGRLLLAGYDD----FNCN- 131
T S D + D R I+ + + A ++S R L A D C+
Sbjct: 183 LCTTSKDKKLNIIDPR---------DGTIVSSVEAHASAKSQRCLWAKRKDLIITLGCSK 233
Query: 132 -------VWDSMKTERA 141
+WD+ K
Sbjct: 234 SQQRQIMLWDTRKMASP 250
Score = 34.9 bits (80), Expect = 0.014
Identities = 35/124 (28%), Positives = 49/124 (39%), Gaps = 11/124 (8%)
Query: 60 GHESDINAVTFFP-NGWAFATGSDDATCRLFDIRADQELAMYSHDNII--------CGIT 110
G E I V F P + T S+D T + I + L D I+ GI
Sbjct: 73 GQEGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEG-LTQNISDPIVHLQGHTKKVGIV 131
Query: 111 SVAFSRSGRLLLAGYDDFNCNVWDSMKTERAGILAGHDNRVSCLGVTEDGMAVATGSWDS 170
S S L AG D NVWD + + ++ H ++++ L DG + T S D
Sbjct: 132 SFHPSAMNVLASAGADMV-VNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDK 190
Query: 171 FLRI 174
L I
Sbjct: 191 KLNI 194
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 31.9 bits (72), Expect = 0.13
Identities = 35/146 (23%), Positives = 57/146 (39%), Gaps = 33/146 (22%)
Query: 16 ASGHTGDVMSLSLAPDMRTFVSGACDASAKLW--DIRDGSCK--QTFPGHESD----INA 67
A+ H + S+S D T +S A D LW +I DGS P + + I +
Sbjct: 168 ANAHPYHINSISFNSDKETLLS-ADDLRINLWNLEIIDGSFNIVDIKPHNMEELTEVITS 226
Query: 68 VTFFP---NGWAFATGS-------------DDATCRLFDIRADQELAMYSHD---NIICG 108
F P N + +++ D + +LF++ D D I+
Sbjct: 227 AEFHPEMCNVFMYSSSKGEIKLNDLRQSALCDNSKKLFELTIDGV----DVDFFEEIVSS 282
Query: 109 ITSVAFSRSGRLLLAGYDDFNCNVWD 134
I+ FS +GR +L+ D +WD
Sbjct: 283 ISDFKFSDNGRYILS-RDYLTVKIWD 307
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 30.4 bits (68), Expect = 0.57
Identities = 43/160 (26%), Positives = 67/160 (41%), Gaps = 17/160 (10%)
Query: 19 HTGDVMSLSLAP-DMRTFVSGACDASAKLWDIRDGSCKQTFPGHESDINAVTF-FPNGWA 76
H V S+ + D SG+ D S KLW I G T +++I V F +G +
Sbjct: 574 HEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKT-KANICCVQFPSESGRS 632
Query: 77 FATGSDDATCRLFDIRADQ--ELAMYSHDNIICGITSVAFSRSGRLLLAGYDDFNCNVWD 134
A GS D +D+R + M H ++ V F S L+ + D+ +WD
Sbjct: 633 LAFGSADHKVYYYDLRNPKLPLCTMIGHSKT---VSYVRFVDSSTLVSSSTDN-TLKLWD 688
Query: 135 SMKTERAGI-------LAGHDNRVSCLGVTEDGMAVATGS 167
+ +GI GH N + +G++ +ATGS
Sbjct: 689 -LSMSISGINETPLHSFMGHTNVKNFVGLSVSDGYIATGS 727
Score = 27.0 bits (59), Expect = 6.2
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 18 GHTGDVMSLSLAPDMRTFVSGACDASAKLWDIR------DGSCKQTFPGHESDINAVTFF 71
GH+ V + D T VS + D + KLWD+ + + +F GH + N V
Sbjct: 659 GHSKTVSYVRFV-DSSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGHTNVKNFVGLS 717
Query: 72 PNGWAFATGSD 82
+ ATGS+
Sbjct: 718 VSDGYIATGSE 728
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional.
Length = 192
Score = 28.8 bits (65), Expect = 1.1
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 144 LAGHDNRVSCLGVTEDGMAV 163
LAGH RVS + +TEDG A+
Sbjct: 123 LAGHGGRVSLMEITEDGYAI 142
>gnl|CDD|225598 COG3056, COG3056, Uncharacterized lipoprotein [Cell envelope
biogenesis, outer membrane].
Length = 204
Score = 27.9 bits (62), Expect = 2.2
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 90 DIRADQELAMYSHDNIICGITSVAFSRSGRLLL 122
D R+DQ +A + DN + +T+ SR R LL
Sbjct: 64 DQRSDQAVAKVTRDNQLVKLTA---SRDVRFLL 93
>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI. IscR
(TIGR02010) is an iron-sulfur cluster-binding
transcriptional regulator (see Genome Property
GenProp0138). Members of this protein family include
YhgI, whose expression is under control of IscR, and
show sequence similarity to IscA, a known protein of
iron-sulfur cluster biosynthesis. These two lines of
evidence strongly suggest a role as an iron-sulfur
cluster biosynthesis protein. An older study designated
this protein GntY and suggested a role for it and for
the product of an adjacent gene, based on
complementation studies, in gluconate utilization
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 190
Score = 27.7 bits (62), Expect = 3.0
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 144 LAGHDNRVSCLGVTEDGMAV 163
LA H +V+ + +T+DG+AV
Sbjct: 122 LASHGGKVTLVEITDDGVAV 141
>gnl|CDD|149780 pfam08830, DUF1806, Protein of unknown function (DUF1806). This is
a bacterial family of uncharacterized proteins. The
structure of one of the proteins in this family has been
solved and it adopts a beta barrel-like structure.
Length = 114
Score = 26.1 bits (58), Expect = 6.1
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 108 GITSVAFSRSGRLLLAGYD 126
G+T GRLLLAG+D
Sbjct: 79 GLTHYEVDEEGRLLLAGHD 97
>gnl|CDD|197319 cd09085, Mth212-like_AP-endo, Methanothermobacter
thermautotrophicus Mth212-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes the thermophilic archaeon
Methanothermobacter thermautotrophicus Mth212and related
proteins. These are Escherichia coli exonuclease III
(ExoIII)-like AP endonucleases and they belong to the
large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds. AP endonucleases participate in
the DNA base excision repair (BER) pathway. AP sites are
one of the most common lesions in cellular DNA. During
BER, the damaged DNA is first recognized by DNA
glycosylase. AP endonucleases then catalyze the
hydrolytic cleavage of the phosphodiester bond 5' to the
AP site, and this is followed by the coordinated actions
of DNA polymerase, deoxyribose phosphatase, and DNA
ligase. If left unrepaired, AP sites block DNA
replication, and have both mutagenic and cytotoxic
effects. AP endonucleases can carry out a variety of
excision and incision reactions on DNA, including 3'-5'
exonuclease, 3'-deoxyribose phosphodiesterase,
3'-phosphatase, and occasionally, nonspecific DNase
activities. Different AP endonuclease enzymes catalyze
the different reactions with different efficiences.
Mth212 is an AP endonuclease, and a DNA uridine
endonuclease (U-endo) that nicks double-stranded DNA at
the 5'-side of a 2'-d-uridine residue. After incision at
the 5'-side of a 2'-d-uridine residue by Mth212, DNA
polymerase B takes over the 3'-OH terminus and carries
out repair synthesis, generating a 5'-flap structure
that is resolved by a 5'-flap endonuclease. Finally, DNA
ligase seals the resulting nick. This U-endo activity
shares the same catalytic center as its AP-endo
activity, and is absent from other AP endonuclease
homologues.
Length = 252
Score = 26.9 bits (60), Expect = 6.3
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 97 LAMYSH---DNIICGITSVAFSRSGRLLLAGYDDF 128
+A+YS D++ G+ F GR+L+A +DDF
Sbjct: 68 VALYSKIEPDSVREGLGVEEFDNEGRILIADFDDF 102
>gnl|CDD|223014 PHA03231, PHA03231, glycoprotein BALF4; Provisional.
Length = 829
Score = 26.8 bits (60), Expect = 8.6
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 12/45 (26%)
Query: 8 SALLGSPAASGHTGDVMSLS-----------LAPDMRTFVS-GAC 40
SA+ G P A+ GDV+++S L MR S G C
Sbjct: 482 SAIYGRPVAARLLGDVIAVSKCVEVDQSSVSLQKSMRVPGSPGTC 526
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
0.321 0.134 0.435
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,796,339
Number of extensions: 767316
Number of successful extensions: 522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 36
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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: 56 (25.4 bits)