Query 028564
Match_columns 207
No_of_seqs 70 out of 72
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 13:29:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02174 CXXU_selWTH selT/sel 99.8 2.4E-18 5.1E-23 124.6 7.6 71 124-202 1-71 (72)
2 PF10262 Rdx: Rdx family; Int 99.7 1.3E-16 2.9E-21 115.4 5.9 73 122-204 1-75 (76)
3 COG3526 Uncharacterized protei 97.9 6.3E-05 1.4E-09 59.0 7.6 76 121-206 5-82 (99)
4 KOG3286 Selenoprotein T [Gener 97.2 0.0016 3.4E-08 57.7 7.5 78 121-206 69-212 (226)
5 PRK13669 hypothetical protein; 75.7 11 0.00024 28.8 5.9 66 124-207 3-73 (78)
6 PF07293 DUF1450: Protein of u 70.8 15 0.00033 27.8 5.6 66 124-207 3-73 (78)
7 PF00403 HMA: Heavy-metal-asso 60.0 43 0.00094 22.2 5.8 26 128-160 8-34 (62)
8 PRK00939 translation initiatio 55.2 28 0.00061 27.2 4.7 29 173-206 35-63 (99)
9 PF10411 DsbC_N: Disulfide bon 47.3 16 0.00034 25.4 2.0 37 142-178 1-38 (57)
10 cd03026 AhpF_NTD_C TRX-GRX-lik 46.6 38 0.00082 25.1 4.1 54 118-177 12-77 (89)
11 PF13453 zf-TFIIB: Transcripti 44.8 16 0.00036 23.6 1.7 25 123-147 16-40 (41)
12 PF14424 Toxin-deaminase: The 44.6 38 0.00082 27.6 4.1 31 121-158 98-130 (133)
13 cd02996 PDI_a_ERp44 PDIa famil 39.1 39 0.00085 24.5 3.1 30 123-152 24-53 (108)
14 PF08494 DEAD_assoc: DEAD/H as 37.7 70 0.0015 26.8 4.8 34 135-173 27-66 (187)
15 COG3581 Uncharacterized protei 37.4 56 0.0012 32.0 4.7 44 115-159 67-112 (420)
16 COG2608 CopZ Copper chaperone 34.3 65 0.0014 23.0 3.6 37 128-173 12-48 (71)
17 COG1326 Uncharacterized archae 33.7 57 0.0012 29.1 3.8 67 122-197 3-73 (201)
18 PRK09381 trxA thioredoxin; Pro 33.7 1.2E+02 0.0026 21.9 4.9 31 118-148 22-52 (109)
19 cd03023 DsbA_Com1_like DsbA fa 33.4 65 0.0014 23.9 3.6 27 129-159 17-43 (154)
20 PF08818 DUF1801: Domain of un 31.3 94 0.002 22.5 4.1 46 135-180 2-52 (103)
21 TIGR01068 thioredoxin thioredo 30.3 83 0.0018 21.5 3.5 27 121-147 18-44 (101)
22 PRK15317 alkyl hydroperoxide r 30.1 1.6E+02 0.0034 28.0 6.3 59 122-184 23-81 (517)
23 PF00085 Thioredoxin: Thioredo 28.2 51 0.0011 22.7 2.2 27 122-148 22-48 (103)
24 PRK14891 50S ribosomal protein 27.4 59 0.0013 27.3 2.7 31 162-193 16-53 (131)
25 cd03005 PDI_a_ERp46 PDIa famil 26.9 67 0.0014 22.4 2.6 28 126-153 25-52 (102)
26 cd02984 TRX_PICOT TRX domain, 26.8 73 0.0016 22.2 2.8 34 122-158 19-53 (97)
27 KOG2536 MAM33, mitochondrial m 26.6 2.7E+02 0.0059 25.8 7.0 50 155-205 162-220 (263)
28 PF11197 DUF2835: Protein of u 25.8 60 0.0013 24.1 2.2 19 163-181 49-67 (68)
29 PTZ00051 thioredoxin; Provisio 24.2 78 0.0017 22.2 2.5 35 121-159 22-57 (98)
30 PF13909 zf-H2C2_5: C2H2-type 24.0 32 0.0007 19.3 0.4 21 128-149 2-22 (24)
31 PF10122 Mu-like_Com: Mu-like 23.8 75 0.0016 22.8 2.3 30 128-169 6-35 (51)
32 cd02973 TRX_GRX_like Thioredox 23.6 1.3E+02 0.0028 19.8 3.4 26 125-154 7-32 (67)
33 cd03331 Macro_Poa1p_like_SNF2 23.3 56 0.0012 27.1 1.9 29 122-153 19-48 (152)
34 cd02995 PDI_a_PDI_a'_C PDIa fa 23.2 64 0.0014 22.4 1.9 35 124-159 25-60 (104)
35 PF04658 TAFII55_N: TAFII55 pr 21.8 1.6E+02 0.0035 24.8 4.3 55 138-194 14-70 (162)
36 smart00678 WWE Domain in Delte 21.8 2.8E+02 0.006 19.4 5.0 51 140-195 21-71 (73)
37 TIGR01158 SUI1_rel translation 21.5 1.5E+02 0.0033 23.1 3.8 29 173-206 36-64 (101)
38 PF12221 HflK_N: Bacterial mem 21.4 78 0.0017 21.5 1.9 17 191-207 19-35 (42)
39 cd02964 TryX_like_family Trypa 21.1 1.8E+02 0.0038 22.0 4.1 34 121-154 17-54 (132)
40 KOG0562 Predicted hydrolase (H 20.2 39 0.00084 29.7 0.3 23 128-150 155-177 (184)
41 TIGR03140 AhpF alkyl hydropero 20.2 2.9E+02 0.0063 26.3 6.1 59 122-184 23-82 (515)
No 1
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=99.76 E-value=2.4e-18 Score=124.56 Aligned_cols=71 Identities=27% Similarity=0.396 Sum_probs=66.0
Q ss_pred EEEcccccchhhHHhHHHHHHHHhccCCCcEEEecCCCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCChHHHHHHH
Q 028564 124 VVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLNPEKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLDMDEVVSDI 202 (207)
Q Consensus 124 VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~D~Vi~~I 202 (207)
|.||||.+|+ |+.||..|++.|+..||+..|.+++.+||+|+|||.++|.++|+.+. ..+|||+++|++.|
T Consensus 1 V~IeyC~~C~-y~~Ra~~l~q~L~~~Fp~~~v~~~~~~~~~G~Fev~~~g~~v~sk~~-------~~~fp~~~~~~~~i 71 (72)
T TIGR02174 1 VEIEYCGSCG-YKPRAAWLKQELLEEFPDLEIEGENTPPTTGAFEVTVNGQLVWSKLR-------GGGFPEPEELKQLI 71 (72)
T ss_pred CEEEECCCCC-ChHHHHHHHHHHHHHCCCCeeEEeeecCCCcEEEEEECCEEEEEecc-------CCCCCCHHHHHHhh
Confidence 6799999998 99999999999999999999999999999999999999978888887 57899999998876
No 2
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=99.66 E-value=1.3e-16 Score=115.44 Aligned_cols=73 Identities=32% Similarity=0.468 Sum_probs=65.7
Q ss_pred ceEEEcccccchhhHHhHHHHHHHHhccCCC--cEEEecCCCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCChHHHH
Q 028564 122 RTVVIEHCKQCNSFKTRANHVKDGLEKGVPG--INVLLNPEKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLDMDEVV 199 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~--~qV~INp~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~D~Vi 199 (207)
++|.||||.+|+ |..||..|.+.|...||+ ++|.++| +++|+|||.++|.++|+.+. ...|||.++|+
T Consensus 1 p~V~IeYC~~C~-~~~~a~~l~~~l~~~fp~~~~~v~~~~--~~~G~FEV~v~g~lI~SK~~-------~g~fP~~~~i~ 70 (76)
T PF10262_consen 1 PKVTIEYCTSCG-YRPRALELAQELLQTFPDRIAEVELSP--GSTGAFEVTVNGELIFSKLE-------SGRFPDPDEIV 70 (76)
T ss_dssp EEEEEEEETTTT-CHHHHHHHHHHHHHHSTTTCSEEEEEE--ESTT-EEEEETTEEEEEHHH-------HTSSS-HHHHH
T ss_pred CEEEEEECCCCC-CHHHHHHHHHHHHHHCCCcceEEEEEe--ccCCEEEEEEccEEEEEehh-------cCCCCCHHHHH
Confidence 479999999997 999999999999999999 8999997 48999999999999999998 55999999999
Q ss_pred HHHHH
Q 028564 200 SDIVA 204 (207)
Q Consensus 200 ~~I~~ 204 (207)
+-|.+
T Consensus 71 ~~I~~ 75 (76)
T PF10262_consen 71 QLIRD 75 (76)
T ss_dssp HHHHH
T ss_pred HHHhc
Confidence 98875
No 3
>COG3526 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=6.3e-05 Score=58.95 Aligned_cols=76 Identities=22% Similarity=0.304 Sum_probs=57.7
Q ss_pred cceEEEcccccchhhHHhHHHHHHHHhccCCC-c-EEEecCCCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCChHHH
Q 028564 121 ERTVVIEHCKQCNSFKTRANHVKDGLEKGVPG-I-NVLLNPEKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLDMDEV 198 (207)
Q Consensus 121 ~~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~-~-qV~INp~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~D~V 198 (207)
.+.|.|=||+||| +.-||.=+.+.|...|.+ + .|.+.|+ --|-|||+.+| ...|- .-+---||+...+
T Consensus 5 ~p~i~I~YCtQCn-WlLRa~WmaQElL~TF~~dlgeV~L~Pg--TGG~FeI~~dg---~~iWe----RKrdGGFP~ak~L 74 (99)
T COG3526 5 KPRIEITYCTQCN-WLLRAAWMAQELLSTFADDLGEVALIPG--TGGVFEITCDG---VLIWE----RKRDGGFPEAKVL 74 (99)
T ss_pred CceEEEEEechhh-HHHHHHHHHHHHHHHHHhhhheEEEecC--CCceEEEEECC---EEEEE----eeccCCCCchHHH
Confidence 5789999999998 666777788888877744 4 7999987 56899999988 45555 1125678888888
Q ss_pred HHHHHHhh
Q 028564 199 VSDIVAKL 206 (207)
Q Consensus 199 i~~I~~aL 206 (207)
-+-|.+.|
T Consensus 75 KQrvRD~i 82 (99)
T COG3526 75 KQRVRDLI 82 (99)
T ss_pred HHHHHhhc
Confidence 77777654
No 4
>KOG3286 consensus Selenoprotein T [General function prediction only]
Probab=97.16 E-value=0.0016 Score=57.70 Aligned_cols=78 Identities=26% Similarity=0.377 Sum_probs=64.1
Q ss_pred cceEEEcccccchhhHHhHHHHHHHHhccCCCcEEEec-------------------------------C------CCC-
Q 028564 121 ERTVVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLN-------------------------------P------EKP- 162 (207)
Q Consensus 121 ~~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~IN-------------------------------p------~KP- 162 (207)
++++.|=+|-+|+ ||.-+.+....|.+.|||++|..- | +.|
T Consensus 69 ~ptl~i~fCvSCg-Yk~af~~~~~~l~ekyPgl~IegaNy~Pp~~kr~lAk~v~v~k~gvIglii~G~~pF~~iGl~~P~ 147 (226)
T KOG3286|consen 69 GPTLEINFCVSCG-YKQAFEQYKKFLKEKYPGLDIEGANYPPPAWKRYLAKVVSVVKMGVIGLIIGGKNPFEFIGLGYPS 147 (226)
T ss_pred CCcEEEEEEEecC-cHHHHHHHHHHHHhhCCCceeecCcCCCchHHHHHHHHHHHHhheeEEEEeccCCccceecCCCcH
Confidence 4679999999996 999999999999999999987642 1 111
Q ss_pred ----------------------------CcceeEEEecCCeeEEEecCCCCCCCCCCCCChHHHHHHHHHhh
Q 028564 163 ----------------------------RRGCFEIREDGGEKFISLLDMKRPFKPMKDLDMDEVVSDIVAKL 206 (207)
Q Consensus 163 ----------------------------RRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~D~Vi~~I~~aL 206 (207)
..|+|||..+|-.+|++|. .-++|-++++.+-|-+-|
T Consensus 148 iwqh~~aNkf~scm~vf~lGN~les~L~StGAFEI~lndepVwSKl~-------~gr~Ps~~el~qlid~~L 212 (226)
T KOG3286|consen 148 IWQHAQANKFYSCMMVFFLGNMLESQLISTGAFEITLNDEPVWSKLE-------SGRLPSPQELVQLIDNQL 212 (226)
T ss_pred HHHHHHhhhHHHHHHHHHHHHHHHHHhhccCcEEEEECCEeeeehhh-------ccCCCCHHHHHHHHHHhh
Confidence 3699999999878888888 889999999887766544
No 5
>PRK13669 hypothetical protein; Provisional
Probab=75.72 E-value=11 Score=28.84 Aligned_cols=66 Identities=23% Similarity=0.336 Sum_probs=44.2
Q ss_pred EEEcccccchhhHHhHHHHHHHHhccCCCcEEEecC-----CCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCChHHH
Q 028564 124 VVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLNP-----EKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLDMDEV 198 (207)
Q Consensus 124 VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp-----~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~D~V 198 (207)
-+||+|.+=-.... ..+-+.| +..|++.|.-.. +.-|++.|-+- +| . ....++.|++
T Consensus 3 piVEfC~sNl~~G~--~~~~~~L-e~dP~~dVie~gCls~CG~C~~~~FAlV-ng-~-------------~V~a~t~eeL 64 (78)
T PRK13669 3 PIVEFCVSNLASGS--QAAFEKL-EKDPNLDVLEYGCLGYCGICSEGLFALV-NG-E-------------VVEGETPEEL 64 (78)
T ss_pred ceeeehhcchhhhH--HHHHHHH-HhCCCceEEEcchhhhCcCcccCceEEE-CC-e-------------EeecCCHHHH
Confidence 47899966432222 2223344 678999976554 66789999764 44 2 2346789999
Q ss_pred HHHHHHhhC
Q 028564 199 VSDIVAKLK 207 (207)
Q Consensus 199 i~~I~~aLk 207 (207)
++.|.+.|+
T Consensus 65 ~~kI~~~i~ 73 (78)
T PRK13669 65 VENIYAHLE 73 (78)
T ss_pred HHHHHHHHh
Confidence 999998874
No 6
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=70.83 E-value=15 Score=27.83 Aligned_cols=66 Identities=23% Similarity=0.369 Sum_probs=45.6
Q ss_pred EEEcccccchhhHHhHHHHHHHHhccCCCcEEEecC-----CCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCChHHH
Q 028564 124 VVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLNP-----EKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLDMDEV 198 (207)
Q Consensus 124 VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp-----~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~D~V 198 (207)
.+||+|.+.-. .-...+...|++ .|++.|.-.. +.-++..|-+- +| .. ...++.|++
T Consensus 3 piVefC~~Nl~--~g~~~~~~~Le~-~p~~~Vie~gCl~~Cg~C~~~pFAlV-nG-~~-------------V~A~t~eeL 64 (78)
T PF07293_consen 3 PIVEFCVSNLA--SGTDQVYEKLEK-DPDIDVIEYGCLSYCGPCAKKPFALV-NG-EI-------------VAAETAEEL 64 (78)
T ss_pred ceEEEcccCch--hhhHHHHHHHhc-CCCccEEEcChhhhCcCCCCCccEEE-CC-EE-------------EecCCHHHH
Confidence 57999988843 334556677764 6999876554 45567777653 44 22 346789999
Q ss_pred HHHHHHhhC
Q 028564 199 VSDIVAKLK 207 (207)
Q Consensus 199 i~~I~~aLk 207 (207)
++.|.+.|+
T Consensus 65 ~~kI~~~i~ 73 (78)
T PF07293_consen 65 LEKIKEKIE 73 (78)
T ss_pred HHHHHHHHh
Confidence 999998874
No 7
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=60.04 E-value=43 Score=22.21 Aligned_cols=26 Identities=35% Similarity=0.736 Sum_probs=20.4
Q ss_pred ccccchhhHHhHHHHHHHHhccCCCc-EEEecCC
Q 028564 128 HCKQCNSFKTRANHVKDGLEKGVPGI-NVLLNPE 160 (207)
Q Consensus 128 hCksC~~FKrRA~eL~~aL~ea~P~~-qV~INp~ 160 (207)
+|..|- ..+.++|..- ||+ .+.+|..
T Consensus 8 ~C~~C~------~~v~~~l~~~-~GV~~v~vd~~ 34 (62)
T PF00403_consen 8 TCEGCA------KKVEKALSKL-PGVKSVKVDLE 34 (62)
T ss_dssp TSHHHH------HHHHHHHHTS-TTEEEEEEETT
T ss_pred ccHHHH------HHHHHHHhcC-CCCcEEEEECC
Confidence 699994 8888888866 888 5888864
No 8
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=55.20 E-value=28 Score=27.20 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=20.1
Q ss_pred CCeeEEEecCCCCCCCCCCCCChHHHHHHHHHhh
Q 028564 173 GGEKFISLLDMKRPFKPMKDLDMDEVVSDIVAKL 206 (207)
Q Consensus 173 gg~v~~sL~gMkRPf~kLKfPD~D~Vi~~I~~aL 206 (207)
++..+....||. +...|+.+++..+...+
T Consensus 35 ~gK~VTiI~Gl~-----~~~~~lk~l~k~lKk~~ 63 (99)
T PRK00939 35 YGKEVTIIEGID-----PKDIDLKELAKKLKSKL 63 (99)
T ss_pred CCceEEEEeCCC-----CcchhHHHHHHHHHHHh
Confidence 456666777773 45578888888877654
No 9
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=47.33 E-value=16 Score=25.41 Aligned_cols=37 Identities=30% Similarity=0.576 Sum_probs=22.7
Q ss_pred HHHHHhccCCCcEEEecCCCCCcceeEEEe-cCCeeEE
Q 028564 142 VKDGLEKGVPGINVLLNPEKPRRGCFEIRE-DGGEKFI 178 (207)
Q Consensus 142 L~~aL~ea~P~~qV~INp~KPRRGsFEV~i-~gg~v~~ 178 (207)
|++.|+..+|++.|.---..|=.|=|||.+ +++..++
T Consensus 1 i~~~l~~~~p~~~v~~v~~spi~GlyeV~~~~~~i~Y~ 38 (57)
T PF10411_consen 1 IKQALKKAFPGLKVESVSPSPIPGLYEVVLKGGGILYV 38 (57)
T ss_dssp CHHHHHCT--T-TCEEEEE-SSTTEEEEEE-TTEEEEE
T ss_pred ChhHHHhhcCCCceeEEEcCCCCCeEEEEECCCeEEEE
Confidence 467899999999654333346789999999 5544444
No 10
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=46.60 E-value=38 Score=25.06 Aligned_cols=54 Identities=9% Similarity=-0.026 Sum_probs=32.5
Q ss_pred CCCcceEEE-cccccchhhHHhHHHHHHHHhccCCCcEEEecC--CCC---------CcceeEEEecCCeeE
Q 028564 118 ESKERTVVI-EHCKQCNSFKTRANHVKDGLEKGVPGINVLLNP--EKP---------RRGCFEIREDGGEKF 177 (207)
Q Consensus 118 ~p~~~~VvI-EhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp--~KP---------RRGsFEV~i~gg~v~ 177 (207)
.|-...+++ ..|.+|. .+.++-+.|...+|++++.+-. ..+ +--+|- ++|..++
T Consensus 12 ~pv~i~~F~~~~C~~C~----~~~~~~~~l~~~~~~i~~~~vd~~~~~e~a~~~~V~~vPt~v--idG~~~~ 77 (89)
T cd03026 12 GPINFETYVSLSCHNCP----DVVQALNLMAVLNPNIEHEMIDGALFQDEVEERGIMSVPAIF--LNGELFG 77 (89)
T ss_pred CCEEEEEEECCCCCCcH----HHHHHHHHHHHHCCCceEEEEEhHhCHHHHHHcCCccCCEEE--ECCEEEE
Confidence 343344444 8899997 5556666677778888754433 223 566774 4665554
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.76 E-value=16 Score=23.61 Aligned_cols=25 Identities=28% Similarity=0.461 Sum_probs=21.3
Q ss_pred eEEEcccccchhhHHhHHHHHHHHh
Q 028564 123 TVVIEHCKQCNSFKTRANHVKDGLE 147 (207)
Q Consensus 123 ~VvIEhCksC~~FKrRA~eL~~aL~ 147 (207)
.|.|.+|.+|++.---+.+|.+.+.
T Consensus 16 ~~~id~C~~C~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 16 DVEIDVCPSCGGIWFDAGELEKLLE 40 (41)
T ss_pred CEEEEECCCCCeEEccHHHHHHHHh
Confidence 3899999999998888888887765
No 12
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=44.57 E-value=38 Score=27.56 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=22.4
Q ss_pred cceEEEcc--cccchhhHHhHHHHHHHHhccCCCcEEEec
Q 028564 121 ERTVVIEH--CKQCNSFKTRANHVKDGLEKGVPGINVLLN 158 (207)
Q Consensus 121 ~~~VvIEh--CksC~~FKrRA~eL~~aL~ea~P~~qV~IN 158 (207)
...||.|. |.+|+ . |-+-++..||+|+|.+.
T Consensus 98 ~i~l~te~~pC~SC~------~-vi~qF~~~~pni~~~v~ 130 (133)
T PF14424_consen 98 TIDLFTELPPCESCS------N-VIEQFKKDFPNIKVNVV 130 (133)
T ss_pred eEEEEecCCcChhHH------H-HHHHHHHHCCCcEEEEe
Confidence 46677665 99996 3 44555667899998876
No 13
>cd02996 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.
Probab=39.08 E-value=39 Score=24.55 Aligned_cols=30 Identities=7% Similarity=0.240 Sum_probs=24.0
Q ss_pred eEEEcccccchhhHHhHHHHHHHHhccCCC
Q 028564 123 TVVIEHCKQCNSFKTRANHVKDGLEKGVPG 152 (207)
Q Consensus 123 ~VvIEhCksC~~FKrRA~eL~~aL~ea~P~ 152 (207)
.++-..|..|..+.+...+|...+...+|+
T Consensus 24 ~F~a~wC~~C~~~~p~~~~~a~~~~~~~~~ 53 (108)
T cd02996 24 NFYADWCRFSQMLHPIFEEAAAKIKEEFPD 53 (108)
T ss_pred EEECCCCHHHHhhHHHHHHHHHHHhhccCC
Confidence 344455999999999999999988877765
No 14
>PF08494 DEAD_assoc: DEAD/H associated; InterPro: IPR013701 This domain is found in ATP-dependent helicases as well as a number of hypothetical proteins together with the helicase conserved C-terminal domain (IPR011545 from INTERPRO) and the IPR001650 from INTERPRO domain. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Probab=37.74 E-value=70 Score=26.76 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=17.6
Q ss_pred hHHhHHHHHH-----HHhccCC-CcEEEecCCCCCcceeEEEecC
Q 028564 135 FKTRANHVKD-----GLEKGVP-GINVLLNPEKPRRGCFEIREDG 173 (207)
Q Consensus 135 FKrRA~eL~~-----aL~ea~P-~~qV~INp~KPRRGsFEV~i~g 173 (207)
|.+++++--. .|...+. .+.+.+|+. .|.|....
T Consensus 27 ~G~~vN~~L~~lla~~l~~~~~~~v~~~~~dy-----gi~l~~~~ 66 (187)
T PF08494_consen 27 FGRRVNEALARLLAYRLSRRYGLSVSVSVDDY-----GIVLSLPE 66 (187)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCeEEEEcCC-----EEEEEcCC
Confidence 7777765333 3333333 456666653 45555544
No 15
>COG3581 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.45 E-value=56 Score=31.98 Aligned_cols=44 Identities=14% Similarity=0.308 Sum_probs=36.2
Q ss_pred CCCCCCcceEEEcccccchhhHHhHHHHHHHHhcc-CCCc-EEEecC
Q 028564 115 DGDESKERTVVIEHCKQCNSFKTRANHVKDGLEKG-VPGI-NVLLNP 159 (207)
Q Consensus 115 ~~d~p~~~~VvIEhCksC~~FKrRA~eL~~aL~ea-~P~~-qV~INp 159 (207)
.-|.-|.-.++.+-|+.|+ |.--...+..+|..+ |+++ .+++|-
T Consensus 67 ~~d~~n~~vlmt~TgGpCR-fgnYi~~~rkaLk~aG~~~V~visLn~ 112 (420)
T COG3581 67 EYDIENDAVLMTQTGGPCR-FGNYIELLRKALKDAGFRDVPVISLNS 112 (420)
T ss_pred CccccccEEEEecCCCCcc-hhhHHHHHHHHHHHcCCCCCcEEEeec
Confidence 4466677888999999998 999999999999977 6888 467773
No 16
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=34.33 E-value=65 Score=22.95 Aligned_cols=37 Identities=24% Similarity=0.359 Sum_probs=27.9
Q ss_pred ccccchhhHHhHHHHHHHHhccCCCcEEEecCCCCCcceeEEEecC
Q 028564 128 HCKQCNSFKTRANHVKDGLEKGVPGINVLLNPEKPRRGCFEIREDG 173 (207)
Q Consensus 128 hCksC~~FKrRA~eL~~aL~ea~P~~qV~INp~KPRRGsFEV~i~g 173 (207)
+|..|- ..+..+|..--+-..|.+|+. .|...|.+++
T Consensus 12 tC~~C~------~~V~~al~~v~gv~~v~v~l~---~~~~~V~~d~ 48 (71)
T COG2608 12 TCGHCV------KTVEKALEEVDGVASVDVDLE---KGTATVTFDS 48 (71)
T ss_pred CcHHHH------HHHHHHHhcCCCeeEEEEEcc---cCeEEEEEcC
Confidence 699994 888899987755568889876 5666776654
No 17
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=33.74 E-value=57 Score=29.07 Aligned_cols=67 Identities=15% Similarity=0.198 Sum_probs=38.3
Q ss_pred ceEEEcccccchhhHHhHHHHHHHHhccCCCcEEEecCCCCCcceeE--E-EecCC-eeEEEecCCCCCCCCCCCCChHH
Q 028564 122 RTVVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLNPEKPRRGCFE--I-REDGG-EKFISLLDMKRPFKPMKDLDMDE 197 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp~KPRRGsFE--V-~i~gg-~v~~sL~gMkRPf~kLKfPD~D~ 197 (207)
..||| .|.+|+ + -..+|..|+..-+.+-|.|+ -+|.|- + ....- .+-+..+-+.++|+..--+|.++
T Consensus 3 ~~iy~-~Cp~Cg-~---eev~hEVik~~g~~~lvrC~----eCG~V~~~~i~~~k~~~v~viVS~~~~S~~~~vel~~gE 73 (201)
T COG1326 3 EEIYI-ECPSCG-S---EEVSHEVIKERGREPLVRCE----ECGTVHPAIIKTPKPVRVRVIVSRHEESFTKEVELDPGE 73 (201)
T ss_pred ceEEE-ECCCCC-c---chhhHHHHHhcCCceEEEcc----CCCcEeeceeeccccceEEEEEecCCcccceeEecCCCC
Confidence 35788 799997 3 34567777776677777777 566665 1 11111 12234444555565554444443
No 18
>PRK09381 trxA thioredoxin; Provisional
Probab=33.68 E-value=1.2e+02 Score=21.89 Aligned_cols=31 Identities=13% Similarity=0.227 Sum_probs=22.1
Q ss_pred CCCcceEEEcccccchhhHHhHHHHHHHHhc
Q 028564 118 ESKERTVVIEHCKQCNSFKTRANHVKDGLEK 148 (207)
Q Consensus 118 ~p~~~~VvIEhCksC~~FKrRA~eL~~aL~e 148 (207)
.+.-..++-.+|..|..+.+...+|++.+..
T Consensus 22 ~~vvv~f~~~~C~~C~~~~p~~~~l~~~~~~ 52 (109)
T PRK09381 22 GAILVDFWAEWCGPCKMIAPILDEIADEYQG 52 (109)
T ss_pred CeEEEEEECCCCHHHHHHhHHHHHHHHHhCC
Confidence 3333444556699999998888888887754
No 19
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=33.37 E-value=65 Score=23.85 Aligned_cols=27 Identities=19% Similarity=0.524 Sum_probs=17.1
Q ss_pred cccchhhHHhHHHHHHHHhccCCCcEEEecC
Q 028564 129 CKQCNSFKTRANHVKDGLEKGVPGINVLLNP 159 (207)
Q Consensus 129 CksC~~FKrRA~eL~~aL~ea~P~~qV~INp 159 (207)
|..|..|.. .|...+. .++++.|.+.+
T Consensus 17 Cp~C~~~~~---~l~~~~~-~~~~~~~~~~~ 43 (154)
T cd03023 17 CGYCKKLAP---ELEKLLK-EDPDVRVVFKE 43 (154)
T ss_pred ChhHHHhhH---HHHHHHH-HCCCceEEEEe
Confidence 999988764 4444443 35777666543
No 20
>PF08818 DUF1801: Domain of unknown function (DU1801); InterPro: IPR014922 This large entry of bacterial proteins is uncharacterised. They contain a presumed domain about 110 amino acids in length. ; PDB: 2KL4_A 2OC6_B 2I8D_B.
Probab=31.34 E-value=94 Score=22.55 Aligned_cols=46 Identities=11% Similarity=0.089 Sum_probs=32.4
Q ss_pred hHHhHHHHHHHHhccCCCcEEEecCCCC---Ccce--eEEEecCCeeEEEe
Q 028564 135 FKTRANHVKDGLEKGVPGINVLLNPEKP---RRGC--FEIREDGGEKFISL 180 (207)
Q Consensus 135 FKrRA~eL~~aL~ea~P~~qV~INp~KP---RRGs--FEV~i~gg~v~~sL 180 (207)
.+....+|++.+.+.+|+++-.|.=+.| ..|+ .-|.+.....|++|
T Consensus 2 ~r~~~~~lr~li~~~~P~~~e~ikwg~P~y~~~g~~~~~~~~~~~k~~v~l 52 (103)
T PF08818_consen 2 RREILEELRELILEAAPDLEEVIKWGMPAYYYDGKGGPFCGFSAFKNHVSL 52 (103)
T ss_dssp HHHHHHHHHHHHHHHSTTSEEEEETTEEEEEETTE--EEEEEEE-SSEEEE
T ss_pred hHHHHHHHHHHHHHhCcChhheeecceeEEEECCceEEEEEEEecCCeEEE
Confidence 4667899999999999999888876666 4455 66655544444443
No 21
>TIGR01068 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.
Probab=30.32 E-value=83 Score=21.49 Aligned_cols=27 Identities=11% Similarity=0.185 Sum_probs=18.0
Q ss_pred cceEEEcccccchhhHHhHHHHHHHHh
Q 028564 121 ERTVVIEHCKQCNSFKTRANHVKDGLE 147 (207)
Q Consensus 121 ~~~VvIEhCksC~~FKrRA~eL~~aL~ 147 (207)
-..++-.+|..|+.+......|...+.
T Consensus 18 vi~f~~~~C~~C~~~~~~l~~~~~~~~ 44 (101)
T TIGR01068 18 LVDFWAPWCGPCKMIAPILEELAKEYE 44 (101)
T ss_pred EEEEECCCCHHHHHhCHHHHHHHHHhc
Confidence 344555679999888777666655443
No 22
>PRK15317 alkyl hydroperoxide reductase subunit F; Provisional
Probab=30.09 E-value=1.6e+02 Score=27.98 Aligned_cols=59 Identities=10% Similarity=0.169 Sum_probs=37.6
Q ss_pred ceEEEcccccchhhHHhHHHHHHHHhccCCCcEEEecCCCCCcceeEEEecCCeeEEEecCCC
Q 028564 122 RTVVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLNPEKPRRGCFEIREDGGEKFISLLDMK 184 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp~KPRRGsFEV~i~gg~v~~sL~gMk 184 (207)
.+++.-.|..|. ...+|-+.|.+.-|.++|..+....|.-+|.|..+|...-+.+.|+|
T Consensus 23 ~~~~~~~~~~~~----~~~~~~~~~~~~s~~i~~~~~~~~~~~p~~~~~~~~~~~~i~f~g~P 81 (517)
T PRK15317 23 LVASLDDSEKSA----ELKELLEEIASLSDKITVEEDSLDVRKPSFSITRPGEDTGVRFAGIP 81 (517)
T ss_pred EEEEeCCCchHH----HHHHHHHHHHHhCCceEEEEccCCCCCCEEEEEcCCccceEEEEecC
Confidence 334444566663 33344444445568899988875557789999766555557777776
No 23
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=28.17 E-value=51 Score=22.72 Aligned_cols=27 Identities=15% Similarity=0.348 Sum_probs=21.2
Q ss_pred ceEEEcccccchhhHHhHHHHHHHHhc
Q 028564 122 RTVVIEHCKQCNSFKTRANHVKDGLEK 148 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~eL~~aL~e 148 (207)
+.++-..|..|..|.+...+|.+.+..
T Consensus 22 v~f~~~~C~~C~~~~~~~~~~~~~~~~ 48 (103)
T PF00085_consen 22 VYFYAPWCPPCKAFKPILEKLAKEYKD 48 (103)
T ss_dssp EEEESTTSHHHHHHHHHHHHHHHHTTT
T ss_pred EEEeCCCCCccccccceeccccccccc
Confidence 444456699999999988888888776
No 24
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=27.40 E-value=59 Score=27.26 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=21.0
Q ss_pred CCcceeEEEecCCeeEEE-------ecCCCCCCCCCCCC
Q 028564 162 PRRGCFEIREDGGEKFIS-------LLDMKRPFKPMKDL 193 (207)
Q Consensus 162 PRRGsFEV~i~gg~v~~s-------L~gMkRPf~kLKfP 193 (207)
|..|.-=|+.+| .+|.- +.-|+|-||+|++-
T Consensus 16 PG~G~~fVR~DG-kvf~FcssKC~k~f~~kRnPRKlkWT 53 (131)
T PRK14891 16 PGTGTMFVRKDG-TVLHFVDSKCEKNYDLGREARDLEWT 53 (131)
T ss_pred CCCCcEEEecCC-CEEEEecHHHHHHHHccCCCccchhH
Confidence 346877788654 55543 34688999999873
No 25
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=26.91 E-value=67 Score=22.44 Aligned_cols=28 Identities=11% Similarity=0.408 Sum_probs=21.2
Q ss_pred EcccccchhhHHhHHHHHHHHhccCCCc
Q 028564 126 IEHCKQCNSFKTRANHVKDGLEKGVPGI 153 (207)
Q Consensus 126 IEhCksC~~FKrRA~eL~~aL~ea~P~~ 153 (207)
-..|..|+.+.+.-.+|...+....+.+
T Consensus 25 a~wC~~C~~~~p~~~~~~~~~~~~~~~~ 52 (102)
T cd03005 25 APWCGHCKRLAPTWEQLAKKFNNENPSV 52 (102)
T ss_pred CCCCHHHHHhCHHHHHHHHHHhccCCcE
Confidence 3449999999998888888887644454
No 26
>cd02984 TRX_PICOT TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli.
Probab=26.81 E-value=73 Score=22.18 Aligned_cols=34 Identities=6% Similarity=0.176 Sum_probs=22.4
Q ss_pred ceEEEcccccchhhHHhHHHHHHHHhccCCCcE-EEec
Q 028564 122 RTVVIEHCKQCNSFKTRANHVKDGLEKGVPGIN-VLLN 158 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~~q-V~IN 158 (207)
+.++-.+|..|+.+.+...+|...+ ++.+. +.+|
T Consensus 19 v~f~~~~C~~C~~~~~~l~~l~~~~---~~~i~~~~vd 53 (97)
T cd02984 19 LHFWAPWAEPCKQMNQVFEELAKEA---FPSVLFLSIE 53 (97)
T ss_pred EEEECCCCHHHHHHhHHHHHHHHHh---CCceEEEEEc
Confidence 4455567999998888777777666 45553 3444
No 27
>KOG2536 consensus MAM33, mitochondrial matrix glycoprotein [Energy production and conversion]
Probab=26.62 E-value=2.7e+02 Score=25.81 Aligned_cols=50 Identities=14% Similarity=0.171 Sum_probs=24.4
Q ss_pred EEecCCCCCcceeEEEec---CCeeEEEecCCCCCCCCCCC------CChHHHHHHHHHh
Q 028564 155 VLLNPEKPRRGCFEIRED---GGEKFISLLDMKRPFKPMKD------LDMDEVVSDIVAK 205 (207)
Q Consensus 155 V~INp~KPRRGsFEV~i~---gg~v~~sL~gMkRPf~kLKf------PD~D~Vi~~I~~a 205 (207)
+.|+-.|+--+|||+... ++..+.+++ |.+|--++.- |+-+++=.+++++
T Consensus 162 lvV~vsK~~~~sLef~cta~pD~i~Idsls-v~~~~d~~~~~l~Y~GP~F~eLDe~Lqd~ 220 (263)
T KOG2536|consen 162 LVVTVSKGDGVSLEFLCTAFPDEIVIDSLS-VRPPIDASEDQLAYEGPSFEELDEELQDS 220 (263)
T ss_pred EEEEEecCCCceEEEEeecCCCceEEeeeE-ecCCCCccchhhhccCCChhHHhHHHHHH
Confidence 333334556677777554 444444443 4444444433 5555554444443
No 28
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=25.80 E-value=60 Score=24.05 Aligned_cols=19 Identities=37% Similarity=0.571 Sum_probs=16.7
Q ss_pred CcceeEEEecCCeeEEEec
Q 028564 163 RRGCFEIREDGGEKFISLL 181 (207)
Q Consensus 163 RRGsFEV~i~gg~v~~sL~ 181 (207)
=+|.|++.++++..|++|.
T Consensus 49 v~G~F~l~~d~~~kf~sle 67 (68)
T PF11197_consen 49 VHGRFRLEFDDNNKFVSLE 67 (68)
T ss_pred ceEEEEEEECCCCCEEEeE
Confidence 4799999999999998874
No 29
>PTZ00051 thioredoxin; Provisional
Probab=24.21 E-value=78 Score=22.16 Aligned_cols=35 Identities=11% Similarity=0.161 Sum_probs=23.5
Q ss_pred cceEEEcccccchhhHHhHHHHHHHHhccCCCcE-EEecC
Q 028564 121 ERTVVIEHCKQCNSFKTRANHVKDGLEKGVPGIN-VLLNP 159 (207)
Q Consensus 121 ~~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~~q-V~INp 159 (207)
-..++-..|..|+.|......|.+ .++++. +.+|-
T Consensus 22 li~f~~~~C~~C~~~~~~l~~l~~----~~~~~~~~~vd~ 57 (98)
T PTZ00051 22 IVDFYAEWCGPCKRIAPFYEECSK----EYTKMVFVKVDV 57 (98)
T ss_pred EEEEECCCCHHHHHHhHHHHHHHH----HcCCcEEEEEEC
Confidence 345666789999988877666665 456663 45554
No 30
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=24.02 E-value=32 Score=19.34 Aligned_cols=21 Identities=24% Similarity=0.700 Sum_probs=13.9
Q ss_pred ccccchhhHHhHHHHHHHHhcc
Q 028564 128 HCKQCNSFKTRANHVKDGLEKG 149 (207)
Q Consensus 128 hCksC~~FKrRA~eL~~aL~ea 149 (207)
.|..|+ |..+...|...++..
T Consensus 2 ~C~~C~-y~t~~~~l~~H~~~~ 22 (24)
T PF13909_consen 2 KCPHCS-YSTSKSNLKRHLKRH 22 (24)
T ss_dssp E-SSSS--EESHHHHHHHHHHH
T ss_pred CCCCCC-CcCCHHHHHHHHHhh
Confidence 388897 887777788777654
No 31
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=23.77 E-value=75 Score=22.77 Aligned_cols=30 Identities=27% Similarity=0.413 Sum_probs=20.2
Q ss_pred ccccchhhHHhHHHHHHHHhccCCCcEEEecCCCCCcceeEE
Q 028564 128 HCKQCNSFKTRANHVKDGLEKGVPGINVLLNPEKPRRGCFEI 169 (207)
Q Consensus 128 hCksC~~FKrRA~eL~~aL~ea~P~~qV~INp~KPRRGsFEV 169 (207)
+|+.|| +.|..+-.-..|.|. =||.|++-.
T Consensus 6 RC~~Cn----------klLa~~g~~~~leIK--CpRC~tiN~ 35 (51)
T PF10122_consen 6 RCGHCN----------KLLAKAGEVIELEIK--CPRCKTINH 35 (51)
T ss_pred eccchh----------HHHhhhcCccEEEEE--CCCCCccce
Confidence 699998 666654333456666 679998744
No 32
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=23.55 E-value=1.3e+02 Score=19.82 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=16.3
Q ss_pred EEcccccchhhHHhHHHHHHHHhccCCCcE
Q 028564 125 VIEHCKQCNSFKTRANHVKDGLEKGVPGIN 154 (207)
Q Consensus 125 vIEhCksC~~FKrRA~eL~~aL~ea~P~~q 154 (207)
+-..|..|. ++..+-+.|....+++.
T Consensus 7 ~~~~C~~C~----~~~~~l~~l~~~~~~i~ 32 (67)
T cd02973 7 VSPTCPYCP----DAVQAANRIAALNPNIS 32 (67)
T ss_pred ECCCCCCcH----HHHHHHHHHHHhCCceE
Confidence 457899996 44444444555567775
No 33
>cd03331 Macro_Poa1p_like_SNF2 Macro domain, Poa1p_like family, SNF2 subfamily. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. Members of this subfamily contain a C-terminal macro domain that show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. In addition, they also contain an SNF2 domain, defined by the presence of seven
Probab=23.27 E-value=56 Score=27.08 Aligned_cols=29 Identities=17% Similarity=0.311 Sum_probs=21.6
Q ss_pred ceEEEcccccchhhHHhHH-HHHHHHhccCCCc
Q 028564 122 RTVVIEHCKQCNSFKTRAN-HVKDGLEKGVPGI 153 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~-eL~~aL~ea~P~~ 153 (207)
+.|+| || ||.|.+... =+..+|...+|.+
T Consensus 19 ~~iI~-H~--cN~~G~WG~gGia~al~~k~p~~ 48 (152)
T cd03331 19 DAIIV-HC--VDDSGHWGRGGLFTALEKRSDQP 48 (152)
T ss_pred CeEEE-EE--ECCCCCCCcchHHHHHHHhCCcH
Confidence 45666 77 777888775 4888888888877
No 34
>cd02995 PDI_a_PDI_a'_C PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticu
Probab=23.20 E-value=64 Score=22.44 Aligned_cols=35 Identities=9% Similarity=0.272 Sum_probs=24.5
Q ss_pred EEEcccccchhhHHhHHHHHHHHhccCCCcE-EEecC
Q 028564 124 VVIEHCKQCNSFKTRANHVKDGLEKGVPGIN-VLLNP 159 (207)
Q Consensus 124 VvIEhCksC~~FKrRA~eL~~aL~ea~P~~q-V~INp 159 (207)
++-..|..|+.|.+...+|.+.+.. .+.+. ..||-
T Consensus 25 f~~~~C~~C~~~~~~~~~~~~~~~~-~~~~~~~~id~ 60 (104)
T cd02995 25 FYAPWCGHCKALAPIYEELAEKLKG-DDNVVIAKMDA 60 (104)
T ss_pred EECCCCHHHHHHhhHHHHHHHHhcC-CCCEEEEEEeC
Confidence 4446799999999999999888765 23442 34554
No 35
>PF04658 TAFII55_N: TAFII55 protein conserved region; InterPro: IPR006751 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits its acetyltransferase activity. The exact role of TAFII55 is currently unknown. The conserved region is situated towards the N-terminal of the protein [].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005669 transcription factor TFIID complex
Probab=21.84 E-value=1.6e+02 Score=24.77 Aligned_cols=55 Identities=22% Similarity=0.340 Sum_probs=35.8
Q ss_pred hHHHHHHHHhccCCC--cEEEecCCCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCC
Q 028564 138 RANHVKDGLEKGVPG--INVLLNPEKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLD 194 (207)
Q Consensus 138 RA~eL~~aL~ea~P~--~qV~INp~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD 194 (207)
.|..|++.|.+...+ +.|.+.....|+|.|-|. |..-.-+|..||=.-=++|-+|
T Consensus 14 ~ad~lr~~i~~~~~~~~~~I~~~~~d~R~~~v~i~--~~~y~a~LvDLP~IvEs~KT~D 70 (162)
T PF04658_consen 14 DADRLREAIEEGDINEKLDIDFKFKDGRRAVVRIG--GQIYSAKLVDLPCIVESHKTLD 70 (162)
T ss_pred HHHHHHHHHHcCCCCCCceEEEecCCCCEEEEEEC--CEEcceEEeecCceeeEEeecc
Confidence 578899999977554 556666445688877664 4444477777775444444444
No 36
>smart00678 WWE Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
Probab=21.80 E-value=2.8e+02 Score=19.35 Aligned_cols=51 Identities=6% Similarity=0.040 Sum_probs=37.0
Q ss_pred HHHHHHHhccCCCcEEEecCCCCCcceeEEEecCCeeEEEecCCCCCCCCCCCCCh
Q 028564 140 NHVKDGLEKGVPGINVLLNPEKPRRGCFEIREDGGEKFISLLDMKRPFKPMKDLDM 195 (207)
Q Consensus 140 ~eL~~aL~ea~P~~qV~INp~KPRRGsFEV~i~gg~v~~sL~gMkRPf~kLKfPD~ 195 (207)
..|.++.+..-|.+.|.|.. ..|.|-+..-..+...+|-.||-+...++..
T Consensus 21 ~~IE~ay~~~~~~~~v~~~g-----~~Y~IdF~~m~Q~n~~t~~~R~VrR~~~~~~ 71 (73)
T smart00678 21 EDIEEAYAAGKKLCELSICG-----FPYTIDFNAMTQYNQATGTTRKVRRVTYSPY 71 (73)
T ss_pred HHHHHHHHcCCCeEEEEECC-----eEEEEECcCCEEECCCCCCccceEeccCCCC
Confidence 45666666666778888872 6899988776677777888888877776543
No 37
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=21.52 E-value=1.5e+02 Score=23.08 Aligned_cols=29 Identities=17% Similarity=0.416 Sum_probs=20.5
Q ss_pred CCeeEEEecCCCCCCCCCCCCChHHHHHHHHHhh
Q 028564 173 GGEKFISLLDMKRPFKPMKDLDMDEVVSDIVAKL 206 (207)
Q Consensus 173 gg~v~~sL~gMkRPf~kLKfPD~D~Vi~~I~~aL 206 (207)
++..+....|| .+...|+++++..+...+
T Consensus 36 ~gK~VTvV~Gl-----~~~~~~l~~l~k~LKk~~ 64 (101)
T TIGR01158 36 KGKGVTIIEGL-----DLSDIDLKELAKELKSKC 64 (101)
T ss_pred CCCEEEEEeCC-----cCchhhHHHHHHHHHHHh
Confidence 45667777777 356678888888776654
No 38
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=21.35 E-value=78 Score=21.53 Aligned_cols=17 Identities=29% Similarity=0.413 Sum_probs=14.5
Q ss_pred CCCChHHHHHHHHHhhC
Q 028564 191 KDLDMDEVVSDIVAKLK 207 (207)
Q Consensus 191 KfPD~D~Vi~~I~~aLk 207 (207)
.-||+|+|+.++.+.|.
T Consensus 19 gPPDLdel~r~l~~kl~ 35 (42)
T PF12221_consen 19 GPPDLDELFRKLQDKLG 35 (42)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 36999999999998873
No 39
>cd02964 TryX_like_family Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.
Probab=21.11 E-value=1.8e+02 Score=22.02 Aligned_cols=34 Identities=18% Similarity=0.380 Sum_probs=23.4
Q ss_pred cceEEEcc----cccchhhHHhHHHHHHHHhccCCCcE
Q 028564 121 ERTVVIEH----CKQCNSFKTRANHVKDGLEKGVPGIN 154 (207)
Q Consensus 121 ~~~VvIEh----CksC~~FKrRA~eL~~aL~ea~P~~q 154 (207)
+..|+|-. |..|......-.+|.+.+...+++++
T Consensus 17 Gk~vll~F~atwC~~C~~~~p~l~~l~~~~~~~~~~v~ 54 (132)
T cd02964 17 GKTVGLYFSASWCPPCRAFTPKLVEFYEKLKEEGKNFE 54 (132)
T ss_pred CCEEEEEEECCCCchHHHHHHHHHHHHHHHhhcCCCeE
Confidence 34455554 99998777777777777776556664
No 40
>KOG0562 consensus Predicted hydrolase (HIT family) [General function prediction only]
Probab=20.25 E-value=39 Score=29.71 Aligned_cols=23 Identities=22% Similarity=0.505 Sum_probs=20.9
Q ss_pred ccccchhhHHhHHHHHHHHhccC
Q 028564 128 HCKQCNSFKTRANHVKDGLEKGV 150 (207)
Q Consensus 128 hCksC~~FKrRA~eL~~aL~ea~ 150 (207)
.|-.|++|.+...+|++.|+..+
T Consensus 155 rC~~Cq~~~~~~~kLK~Hl~~~~ 177 (184)
T KOG0562|consen 155 RCWRCQTFGPHFPKLKAHLREEY 177 (184)
T ss_pred eehhhhhcccccHHHHHHHHHHH
Confidence 49999999999999999999764
No 41
>TIGR03140 AhpF alkyl hydroperoxide reductase, F subunit. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP.
Probab=20.18 E-value=2.9e+02 Score=26.26 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=35.7
Q ss_pred ceEEEcccccchhhHHhHHHHHHHHhccCCCcEEEecC-CCCCcceeEEEecCCeeEEEecCCC
Q 028564 122 RTVVIEHCKQCNSFKTRANHVKDGLEKGVPGINVLLNP-EKPRRGCFEIREDGGEKFISLLDMK 184 (207)
Q Consensus 122 ~~VvIEhCksC~~FKrRA~eL~~aL~ea~P~~qV~INp-~KPRRGsFEV~i~gg~v~~sL~gMk 184 (207)
.+++...|.+|. ...+|-+.|.+.-|.++|.... +..|.-+|.|..+|...-+.+.|+|
T Consensus 23 ~~~~~~~~~~~~----~~~~~~~~~~~~s~ki~~~~~~~~~~~~p~~~~~~~~~~~~i~f~g~P 82 (515)
T TIGR03140 23 LVLSAGSHEKSK----ELLELLDEIASLSDKISLTQNTADTLRKPSFTILRDGADTGIRFAGIP 82 (515)
T ss_pred EEEEeCCCchhH----HHHHHHHHHHHhCCCeEEEEecCCcCCCCeEEEecCCcccceEEEecC
Confidence 344555576664 3333444444556888887766 3457889999755444446667766
Done!