Query 025028
Match_columns 259
No_of_seqs 97 out of 99
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:24:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025028.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025028hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13225 DUF4033: Domain of un 100.0 8.9E-49 1.9E-53 305.9 6.4 79 154-232 1-86 (86)
2 TIGR00273 iron-sulfur cluster- 59.2 5.1 0.00011 39.7 1.5 42 149-193 251-307 (432)
3 PF14196 ATC_hydrolase: L-2-am 51.5 56 0.0012 26.1 6.2 50 171-222 88-149 (149)
4 PF13187 Fer4_9: 4Fe-4S diclus 47.3 6.4 0.00014 26.8 0.1 28 179-209 1-28 (55)
5 TIGR00397 mauM_napG MauM/NapG 44.7 9.5 0.0002 34.1 0.7 20 173-193 170-189 (213)
6 PF12837 Fer4_6: 4Fe-4S bindin 42.0 6.1 0.00013 24.2 -0.6 16 176-192 5-20 (24)
7 PRK13409 putative ATPase RIL; 41.8 13 0.00029 37.8 1.4 30 163-193 34-63 (590)
8 PRK06273 ferredoxin; Provision 32.4 8.9 0.00019 33.3 -1.4 24 170-194 41-64 (165)
9 PF11342 DUF3144: Protein of u 32.3 58 0.0012 25.6 3.2 40 91-152 6-45 (78)
10 PRK15031 5-carboxymethyl-2-hyd 31.3 7.9 0.00017 32.5 -1.8 30 92-121 59-88 (126)
11 PHA02611 51 baseplate hub asse 31.1 52 0.0011 31.0 3.3 34 90-124 23-56 (249)
12 KOG3196 NADH:ubiquinone oxidor 29.1 18 0.00038 33.5 -0.1 41 121-161 76-116 (233)
13 COG1144 Pyruvate:ferredoxin ox 28.9 36 0.00078 27.7 1.6 38 153-193 43-80 (91)
14 PF13183 Fer4_8: 4Fe-4S diclus 28.3 9.1 0.0002 26.1 -1.6 15 178-193 3-17 (57)
15 PF00037 Fer4: 4Fe-4S binding 26.9 17 0.00037 21.9 -0.4 17 176-193 4-20 (24)
16 COG1245 Predicted ATPase, RNas 26.7 35 0.00076 35.4 1.5 31 163-194 35-65 (591)
17 PF14922 FWWh: Protein of unkn 26.0 83 0.0018 27.4 3.5 50 108-157 98-149 (161)
18 PRK02651 photosystem I subunit 23.8 40 0.00086 24.8 1.0 19 175-194 6-24 (81)
19 PF02671 PAH: Paired amphipath 23.7 1.5E+02 0.0033 19.9 3.8 44 90-135 3-47 (47)
20 PF12798 Fer4_3: 4Fe-4S bindin 21.9 28 0.00061 19.3 -0.1 12 181-193 2-13 (15)
21 PRK09626 oorD 2-oxoglutarate-a 20.7 38 0.00081 26.5 0.3 18 175-193 13-30 (103)
22 PF14697 Fer4_21: 4Fe-4S diclu 20.2 34 0.00074 24.7 0.0 19 174-193 35-53 (59)
23 PF04675 DNA_ligase_A_N: DNA l 20.2 1.6E+02 0.0034 24.6 4.0 47 91-137 3-53 (177)
No 1
>PF13225 DUF4033: Domain of unknown function (DUF4033)
Probab=100.00 E-value=8.9e-49 Score=305.93 Aligned_cols=79 Identities=73% Similarity=1.379 Sum_probs=77.8
Q ss_pred ccccceeeEEEe--ecCeeeeceEEEeec-----CCCcccccccccCcchhhhhhhcCCceeeccCCccceeeEeeCCCC
Q 025028 154 WLVGPSEVVEVE--INGEKQRSGVHIKKC-----SGCVGMCVNMCKFPTQDFFTREFGLPLTMIPNFEDMSCEMVYGQVP 226 (259)
Q Consensus 154 WLvGP~ev~~ve--v~G~~~~sgV~IeKC-----SgC~GmCvN~CKiPTQ~FF~d~~GlpLtM~PNFeD~SCqm~FG~~P 226 (259)
||||||+|+++| .+|.+++|||+|||| |||+|||+|+||+|||+||+|+|||||||+||||||||||+||++|
T Consensus 1 WLvGp~~v~~~e~~~~~~~~~sgV~i~kCRyLEes~C~g~C~N~CK~PtQ~Ff~~~~Glpl~M~PNfed~SC~~~FG~~P 80 (86)
T PF13225_consen 1 WLVGPCEVNEVEENGNGRGQKSGVHIEKCRYLEESGCAGMCVNMCKIPTQTFFKEEFGLPLTMEPNFEDFSCQMIFGQTP 80 (86)
T ss_pred CcccccEeeEeeccCCCccccceEEEEEeEEeecCCceeeeehhcccchHHHHHhccCCceEecCCCcCcEEEEEcCCCC
Confidence 999999999999 788999999999999 9999999999999999999999999999999999999999999999
Q ss_pred CCCCCC
Q 025028 227 PSFEDD 232 (259)
Q Consensus 227 Pp~eeD 232 (259)
||+|||
T Consensus 81 pp~eeD 86 (86)
T PF13225_consen 81 PPIEED 86 (86)
T ss_pred CCCCCC
Confidence 999998
No 2
>TIGR00273 iron-sulfur cluster-binding protein. Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters.
Probab=59.22 E-value=5.1 Score=39.67 Aligned_cols=42 Identities=26% Similarity=0.651 Sum_probs=27.4
Q ss_pred hhhhcccccceeeEEEeecCeeeeceE---------------EEeecCCCcccccccccC
Q 025028 149 VPFFHWLVGPSEVVEVEINGEKQRSGV---------------HIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 149 ~~~f~WLvGP~ev~~vev~G~~~~sgV---------------~IeKCSgC~GmCvN~CKi 193 (259)
+....|.-||+.-.++ +|.++...| ...+|-.| |.|+|.|++
T Consensus 251 ~~y~~~IsGps~t~D~--~GP~e~hvilldngr~~~~~~~~~e~~~CIrC-G~C~~~CPv 307 (432)
T TIGR00273 251 TAYINVLTGPRQEGDV--DGPEEFHLILLDNGRSNILATEFREVLACIRC-GACQNECPV 307 (432)
T ss_pred CcceEEeeCCCCCCCC--CCCcEEEEEEeCCCcchhhhhhhhhHhhCCCC-CCccccCcc
Confidence 3455777888875542 343332222 36789999 899999986
No 3
>PF14196 ATC_hydrolase: L-2-amino-thiazoline-4-carboxylic acid hydrolase
Probab=51.50 E-value=56 Score=26.14 Aligned_cols=50 Identities=16% Similarity=0.404 Sum_probs=34.5
Q ss_pred eeceEEEeec--------CCCcccccccccCcchhhhhhhc--CCceeeccCCc--cceeeEee
Q 025028 171 QRSGVHIKKC--------SGCVGMCVNMCKFPTQDFFTREF--GLPLTMIPNFE--DMSCEMVY 222 (259)
Q Consensus 171 ~~sgV~IeKC--------SgC~GmCvN~CKiPTQ~FF~d~~--GlpLtM~PNFe--D~SCqm~F 222 (259)
..-.+++.+| =||...|.-.|.+ ..-+-+.| |+.|+.+=.-- |--|+|.|
T Consensus 88 ~~~~~~~~~Cp~~~~~k~~G~~e~~~~~C~~--D~~~~~~~~~~~~l~r~~tla~G~~~Cdf~f 149 (149)
T PF14196_consen 88 DEFEFDFTRCPYAEFWKEYGLPELGPIYCDI--DYAMAEGFNPGIRLERTKTLADGDDCCDFRF 149 (149)
T ss_pred CeEEEEEEeChHHHHHHHcCCchHHhHhhhh--hHHHHHhCCCCcEEEEeeEEeCCCCcCccCC
Confidence 3568999999 8889999999999 44466667 88877643221 33455544
No 4
>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J.
Probab=47.26 E-value=6.4 Score=26.78 Aligned_cols=28 Identities=39% Similarity=0.726 Sum_probs=16.0
Q ss_pred ecCCCcccccccccCcchhhhhhhcCCceee
Q 025028 179 KCSGCVGMCVNMCKFPTQDFFTREFGLPLTM 209 (259)
Q Consensus 179 KCSgC~GmCvN~CKiPTQ~FF~d~~GlpLtM 209 (259)
||.+| |.|++.| |.+-+..+..+-....
T Consensus 1 kCi~C-g~C~~~C--P~~~~~~~~~~~~~~~ 28 (55)
T PF13187_consen 1 KCIGC-GRCVEAC--PVGVIEFDEDGGKKVV 28 (55)
T ss_dssp C--TT-THHHHHS--TTT-EEEETTTTCEEC
T ss_pred CCCCc-chHHHHC--CccCeEccCccccccc
Confidence 57777 7799999 5555555555544443
No 5
>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein. MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar.
Probab=44.66 E-value=9.5 Score=34.13 Aligned_cols=20 Identities=40% Similarity=1.034 Sum_probs=17.0
Q ss_pred ceEEEeecCCCcccccccccC
Q 025028 173 SGVHIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 173 sgV~IeKCSgC~GmCvN~CKi 193 (259)
-.|+.++|.|| |.|++.|..
T Consensus 170 p~Vd~~~C~gC-G~C~~~CP~ 189 (213)
T TIGR00397 170 PTVDSAKCTGC-GTCEKHCVL 189 (213)
T ss_pred eEEecccCCCc-chhhHhCCC
Confidence 46788999999 899999953
No 6
>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=41.95 E-value=6.1 Score=24.22 Aligned_cols=16 Identities=50% Similarity=1.261 Sum_probs=12.8
Q ss_pred EEeecCCCccccccccc
Q 025028 176 HIKKCSGCVGMCVNMCK 192 (259)
Q Consensus 176 ~IeKCSgC~GmCvN~CK 192 (259)
.-+||.|| |.|+..|+
T Consensus 5 d~~~C~~C-g~C~~~Cp 20 (24)
T PF12837_consen 5 DPDKCIGC-GDCVRVCP 20 (24)
T ss_pred ChhhCcCh-hHHHHhcc
Confidence 34688888 88999887
No 7
>PRK13409 putative ATPase RIL; Provisional
Probab=41.84 E-value=13 Score=37.83 Aligned_cols=30 Identities=33% Similarity=0.915 Sum_probs=23.8
Q ss_pred EEeecCeeeeceEEEeecCCCcccccccccC
Q 025028 163 EVEINGEKQRSGVHIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 163 ~vev~G~~~~sgV~IeKCSgC~GmCvN~CKi 193 (259)
.+|+++...+..+.-+-|.|| |+||.-|++
T Consensus 34 ~~~~~~~~~~~~~~e~~c~~c-~~c~~~cp~ 63 (590)
T PRK13409 34 TIEIDEDDGKPVISEELCIGC-GICVKKCPF 63 (590)
T ss_pred EEEEcCCCCCceeeHhhcccc-ccccccCCc
Confidence 356666665677788899998 999999985
No 8
>PRK06273 ferredoxin; Provisional
Probab=32.38 E-value=8.9 Score=33.31 Aligned_cols=24 Identities=33% Similarity=0.742 Sum_probs=18.3
Q ss_pred eeeceEEEeecCCCcccccccccCc
Q 025028 170 KQRSGVHIKKCSGCVGMCVNMCKFP 194 (259)
Q Consensus 170 ~~~sgV~IeKCSgC~GmCvN~CKiP 194 (259)
++...+.-++|.+| |.|++.|+..
T Consensus 41 ~~~~~id~~~CigC-g~C~~aCP~~ 64 (165)
T PRK06273 41 ELPKKVFEELCIGC-GGCANVCPTK 64 (165)
T ss_pred CCCCeECchhCcCh-hHHHHhcCcc
Confidence 34556777899999 6899999743
No 9
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=32.29 E-value=58 Score=25.55 Aligned_cols=40 Identities=23% Similarity=0.356 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCCChHHHHHhhcCCchhHHHHHhhhhhhhh
Q 025028 91 YESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPPGAPAQFRKLFPPTKWAAEFNAALTVPFF 152 (259)
Q Consensus 91 YdglVe~a~~~m~grs~~~q~~~v~~vL~sl~Pp~~~~~fr~lfpp~~~a~e~nA~~T~~~f 152 (259)
-|.||++||+....-.+-+-..+. |+ =++++||++....|
T Consensus 6 aD~fI~lAN~~~~~~~~g~Vsaal------------------ly----AaARfnAf~~a~~~ 45 (78)
T PF11342_consen 6 ADEFIALANEQNKEEDAGQVSAAL------------------LY----AAARFNAFVAASSF 45 (78)
T ss_pred HHHHHHHHHHhhccCCcchHHHHH------------------HH----HHHHHHHHHHHHcc
Confidence 378999999998766444333332 11 26888888877654
No 10
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=31.34 E-value=7.9 Score=32.54 Aligned_cols=30 Identities=27% Similarity=0.390 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Q 025028 92 ESFVDVSKRVMEGRSRQQQQEVVREVLLSM 121 (259)
Q Consensus 92 dglVe~a~~~m~grs~~~q~~~v~~vL~sl 121 (259)
++||.+.-+||.|||.++.+++...+|..|
T Consensus 59 ~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l 88 (126)
T PRK15031 59 YAFVHMTLKIGAGRSLESRQEVGEMLFALI 88 (126)
T ss_pred CcEEEEEeeecCCCCHHHHHHHHHHHHHHH
Confidence 489999999999999999998887766554
No 11
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=31.14 E-value=52 Score=31.02 Aligned_cols=34 Identities=41% Similarity=0.736 Sum_probs=28.6
Q ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCC
Q 025028 90 DYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP 124 (259)
Q Consensus 90 gYdglVe~a~~~m~grs~~~q~~~v~~vL~sl~Pp 124 (259)
+|-+|+ +|+.-|.|+++.+|++++-.++..++|-
T Consensus 23 Ey~~Ll-lar~~me~~~~~Eq~eii~eli~~~~~e 56 (249)
T PHA02611 23 DYRDFL-LVRNDMEGRSPEEQQEILDELLDEYFPE 56 (249)
T ss_pred HHHHHH-hhhhhhcCCChhhHHHHHHHHHHHHhcc
Confidence 577776 4566799999999999999999999754
No 12
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=29.12 E-value=18 Score=33.53 Aligned_cols=41 Identities=22% Similarity=0.181 Sum_probs=22.0
Q ss_pred cCCCChHHHHHhhcCCchhHHHHHhhhhhhhhcccccceee
Q 025028 121 MLPPGAPAQFRKLFPPTKWAAEFNAALTVPFFHWLVGPSEV 161 (259)
Q Consensus 121 l~Pp~~~~~fr~lfpp~~~a~e~nA~~T~~~f~WLvGP~ev 161 (259)
++|..+...+.+++--..--.--.|.+-+.||.|=+|---|
T Consensus 76 WlpiSAM~~VA~~~~v~~mrvyevatfYtmf~r~p~gKy~v 116 (233)
T KOG3196|consen 76 WLPISAMNEVAEVLEVPPMRVYEVATFYTMFFRKPVGKYHV 116 (233)
T ss_pred CcCHHHHHHHHHHHcCChHHHHHHHHHHHHhhccCCCCceE
Confidence 45554444444333211111222567778999999986544
No 13
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=28.92 E-value=36 Score=27.67 Aligned_cols=38 Identities=34% Similarity=0.824 Sum_probs=23.4
Q ss_pred cccccceeeEEEeecCeeeeceEEEeecCCCcccccccccC
Q 025028 153 HWLVGPSEVVEVEINGEKQRSGVHIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 153 ~WLvGP~ev~~vev~G~~~~sgV~IeKCSgC~GmCvN~CKi 193 (259)
=||.=|-.-+..+-+|.. ..|.-..|-|| |+|+|.|+.
T Consensus 43 C~~yCPe~~i~~~~~~~~--~~idYdyCKGC-GICa~vCP~ 80 (91)
T COG1144 43 CWLYCPEPAILEEEGGYK--VRIDYDYCKGC-GICANVCPV 80 (91)
T ss_pred eEEECCchheeeccCCcc--ceeEcccccCc-eechhhCCh
Confidence 355555443333323321 22778889888 899999975
No 14
>PF13183 Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_B 2BS3_B 1QLB_B 2BS2_B 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N ....
Probab=28.30 E-value=9.1 Score=26.13 Aligned_cols=15 Identities=40% Similarity=1.207 Sum_probs=10.1
Q ss_pred eecCCCcccccccccC
Q 025028 178 KKCSGCVGMCVNMCKF 193 (259)
Q Consensus 178 eKCSgC~GmCvN~CKi 193 (259)
.+|.+| |.|++.|++
T Consensus 3 ~~Ci~C-g~C~~~CP~ 17 (57)
T PF13183_consen 3 SKCIRC-GACTSVCPV 17 (57)
T ss_dssp HC--S--SHHHHCSHH
T ss_pred HHccCc-cChHHHChh
Confidence 578888 999999974
No 15
>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1DUR_A 1H98_A 1BD6_A 1BQX_A 1BWE_A 1BC6_A 3BK7_A 1FCA_A 1FDN_A 2FDN_A ....
Probab=26.93 E-value=17 Score=21.90 Aligned_cols=17 Identities=53% Similarity=1.316 Sum_probs=11.5
Q ss_pred EEeecCCCcccccccccC
Q 025028 176 HIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 176 ~IeKCSgC~GmCvN~CKi 193 (259)
.-++|.+| |.|++.|+.
T Consensus 4 d~~~C~~C-g~C~~~CP~ 20 (24)
T PF00037_consen 4 DPDKCIGC-GRCVEACPF 20 (24)
T ss_dssp ETTTSSS--THHHHHSTT
T ss_pred chHHCCCc-chhhhhccc
Confidence 44677777 788888874
No 16
>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]
Probab=26.74 E-value=35 Score=35.44 Aligned_cols=31 Identities=32% Similarity=0.874 Sum_probs=22.0
Q ss_pred EEeecCeeeeceEEEeecCCCcccccccccCc
Q 025028 163 EVEINGEKQRSGVHIKKCSGCVGMCVNMCKFP 194 (259)
Q Consensus 163 ~vev~G~~~~sgV~IeKCSgC~GmCvN~CKiP 194 (259)
.++++....+....-+-|+|| |+|++-|++=
T Consensus 35 ~I~i~~~~gkpvIsE~lCiGC-GICvkkCPF~ 65 (591)
T COG1245 35 TIEIDEDTGKPVISEELCIGC-GICVKKCPFD 65 (591)
T ss_pred eEEecCCCCCceeEhhhhccc-hhhhccCCcc
Confidence 345544433456777889998 9999999853
No 17
>PF14922 FWWh: Protein of unknown function
Probab=26.02 E-value=83 Score=27.38 Aligned_cols=50 Identities=20% Similarity=0.363 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHhcCCCChHHHHHhhcCCch--hHHHHHhhhhhhhhccccc
Q 025028 108 QQQQEVVREVLLSMLPPGAPAQFRKLFPPTK--WAAEFNAALTVPFFHWLVG 157 (259)
Q Consensus 108 ~~q~~~v~~vL~sl~Pp~~~~~fr~lfpp~~--~a~e~nA~~T~~~f~WLvG 157 (259)
.+-++.+.+++-.++.-.+-..|-..||.++ |..++-..+.-.++.|+.|
T Consensus 98 ~~~kD~~~~~yp~~laqavy~~f~~~FP~s~~~F~~~FK~~l~~~~~~w~sG 149 (161)
T PF14922_consen 98 SHYKDAFFKVYPDCLAQAVYYSFCECFPQSWHLFNEEFKSNLYNTCSEWISG 149 (161)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHCchHHHHHhHHHHHHHHHHHHHHHcC
Confidence 3446678888888888888889999999976 8888999999999999998
No 18
>PRK02651 photosystem I subunit VII; Provisional
Probab=23.78 E-value=40 Score=24.80 Aligned_cols=19 Identities=32% Similarity=0.849 Sum_probs=14.1
Q ss_pred EEEeecCCCcccccccccCc
Q 025028 175 VHIKKCSGCVGMCVNMCKFP 194 (259)
Q Consensus 175 V~IeKCSgC~GmCvN~CKiP 194 (259)
...++|.+| ++|++.|+..
T Consensus 6 ~~~~~Ci~C-~~C~~~CP~~ 24 (81)
T PRK02651 6 KIYDTCIGC-TQCVRACPLD 24 (81)
T ss_pred cccccCCCc-chHHHHCCcc
Confidence 334889887 5899999743
No 19
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=23.65 E-value=1.5e+02 Score=19.91 Aligned_cols=44 Identities=27% Similarity=0.484 Sum_probs=25.8
Q ss_pred ChHHHHHHHHHHhcC-CCHHHHHHHHHHHHHhcCCCChHHHHHhhcC
Q 025028 90 DYESFVDVSKRVMEG-RSRQQQQEVVREVLLSMLPPGAPAQFRKLFP 135 (259)
Q Consensus 90 gYdglVe~a~~~m~g-rs~~~q~~~v~~vL~sl~Pp~~~~~fr~lfp 135 (259)
-|+.|+++-+...++ .+..+-.+.|...|..- |-+...|+.++|
T Consensus 3 ~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~h--pdLl~~F~~FlP 47 (47)
T PF02671_consen 3 VYNEFLKILNDYKKGRISRSEVIEEVSELLRGH--PDLLEEFNRFLP 47 (47)
T ss_dssp HHHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT---HHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHccC--HHHHHHHHhhCc
Confidence 599999999888875 46666555543333221 124445555544
No 20
>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=21.86 E-value=28 Score=19.27 Aligned_cols=12 Identities=50% Similarity=1.431 Sum_probs=8.1
Q ss_pred CCCcccccccccC
Q 025028 181 SGCVGMCVNMCKF 193 (259)
Q Consensus 181 SgC~GmCvN~CKi 193 (259)
.+| +.|++.|+.
T Consensus 2 ~~C-~~C~~~Cp~ 13 (15)
T PF12798_consen 2 TGC-GACVEVCPT 13 (15)
T ss_pred CCc-hHHHHHhcC
Confidence 456 778888763
No 21
>PRK09626 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed
Probab=20.72 E-value=38 Score=26.54 Aligned_cols=18 Identities=33% Similarity=1.038 Sum_probs=14.6
Q ss_pred EEEeecCCCcccccccccC
Q 025028 175 VHIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 175 V~IeKCSgC~GmCvN~CKi 193 (259)
+...+|.+| |.|+..|+.
T Consensus 13 id~~~Ci~C-~~Cv~aCP~ 30 (103)
T PRK09626 13 VDESRCKAC-DICVSVCPA 30 (103)
T ss_pred ECcccccCC-cchhhhcCh
Confidence 345789999 899999963
No 22
>PF14697 Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B ....
Probab=20.24 E-value=34 Score=24.67 Aligned_cols=19 Identities=47% Similarity=1.219 Sum_probs=11.1
Q ss_pred eEEEeecCCCcccccccccC
Q 025028 174 GVHIKKCSGCVGMCVNMCKF 193 (259)
Q Consensus 174 gV~IeKCSgC~GmCvN~CKi 193 (259)
-|..++|.|| |+|++.|++
T Consensus 35 ~v~~~~C~GC-g~C~~~CPv 53 (59)
T PF14697_consen 35 PVNPDKCIGC-GLCVKVCPV 53 (59)
T ss_dssp ECE-TT--S--SCCCCCSSS
T ss_pred EeccccCcCc-CcccccCCC
Confidence 4667888888 788888864
No 23
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=20.16 E-value=1.6e+02 Score=24.57 Aligned_cols=47 Identities=15% Similarity=0.257 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCC----ChHHHHHhhcCCc
Q 025028 91 YESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP----GAPAQFRKLFPPT 137 (259)
Q Consensus 91 YdglVe~a~~~m~grs~~~q~~~v~~vL~sl~Pp----~~~~~fr~lfpp~ 137 (259)
|..|+++..++..-.+..+-.+++.+.|.++.+. .+-.+++.+||+.
T Consensus 3 F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~ 53 (177)
T PF04675_consen 3 FSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEY 53 (177)
T ss_dssp HHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTT
T ss_pred HHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccch
Confidence 6678888888887777778888999999998766 3556778888874
Done!