Query 028908
Match_columns 202
No_of_seqs 185 out of 1245
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 04:26:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2358 NifU-like domain-conta 100.0 1.7E-46 3.7E-51 307.1 8.4 200 1-201 10-212 (213)
2 PF08712 Nfu_N: Scaffold prote 100.0 1.3E-33 2.7E-38 206.2 7.4 87 3-89 1-87 (87)
3 COG0694 Thioredoxin-like prote 100.0 1.9E-28 4.2E-33 179.9 9.9 85 109-193 6-90 (93)
4 PF01106 NifU: NifU-like domai 99.9 4.1E-25 8.9E-30 154.3 8.9 68 117-187 1-68 (68)
5 TIGR03341 YhgI_GntY IscR-regul 99.9 5.2E-25 1.1E-29 181.8 10.5 84 108-192 101-184 (190)
6 PRK11190 Fe/S biogenesis prote 99.9 7.5E-25 1.6E-29 181.0 10.0 83 109-192 103-186 (192)
7 TIGR02000 NifU_proper Fe-S clu 99.8 6.7E-20 1.4E-24 160.2 12.3 74 110-187 217-290 (290)
8 KOG2358 NifU-like domain-conta 98.1 9.8E-07 2.1E-11 73.2 1.9 76 115-193 80-155 (213)
9 PF01883 DUF59: Domain of unkn 96.8 0.012 2.6E-07 40.6 8.3 67 115-185 2-71 (72)
10 COG2151 PaaD Predicted metal-s 94.7 0.24 5.2E-06 37.7 7.8 78 111-190 11-91 (111)
11 TIGR02945 SUF_assoc FeS assemb 94.3 0.24 5.3E-06 36.2 7.0 71 113-187 2-76 (99)
12 TIGR03406 FeS_long_SufT probab 91.2 1.1 2.4E-05 36.7 7.4 77 111-189 72-154 (174)
13 PF02061 Lambda_CIII: Lambda P 81.8 1.8 4E-05 27.1 2.7 25 153-177 7-31 (45)
14 TIGR02159 PA_CoA_Oxy4 phenylac 72.3 17 0.00037 28.8 6.6 48 134-186 15-62 (146)
15 PRK11670 antiporter inner memb 70.3 23 0.00049 32.2 7.8 72 113-188 13-87 (369)
16 PF10646 Germane: Sporulation 69.8 30 0.00064 25.3 7.1 78 110-190 23-110 (117)
17 PF08821 CGGC: CGGC domain; I 64.1 13 0.00028 28.0 4.1 23 155-179 45-67 (107)
18 PF07315 DUF1462: Protein of u 62.7 7.8 0.00017 28.5 2.6 27 155-182 11-37 (93)
19 PRK10862 SoxR reducing system 62.7 11 0.00023 30.2 3.7 24 137-162 7-32 (154)
20 PF09012 FeoC: FeoC like trans 57.0 20 0.00043 24.2 3.8 27 133-166 41-67 (69)
21 PF01883 DUF59: Domain of unkn 57.0 46 0.00099 22.3 5.7 48 41-88 16-63 (72)
22 PRK12463 chorismate synthase; 55.8 12 0.00025 34.5 3.1 37 28-67 235-271 (390)
23 PF01264 Chorismate_synt: Chor 55.7 7 0.00015 35.4 1.7 35 27-65 215-249 (346)
24 PF04246 RseC_MucC: Positive r 55.6 12 0.00025 28.8 2.7 20 139-160 2-23 (135)
25 cd07304 Chorismate_synthase Ch 55.4 8.4 0.00018 34.9 2.1 30 37-66 223-252 (344)
26 PRK05382 chorismate synthase; 51.2 10 0.00022 34.6 2.0 31 37-67 221-251 (359)
27 TIGR00033 aroC chorismate synt 50.8 10 0.00023 34.4 2.0 31 37-67 222-252 (351)
28 PF11718 CPSF73-100_C: Pre-mRN 50.3 1.5E+02 0.0033 24.8 11.5 115 59-177 77-209 (216)
29 PLN02754 chorismate synthase 49.8 11 0.00023 35.0 1.9 31 37-67 256-286 (413)
30 PHA02782 hypothetical protein; 48.0 60 0.0013 30.5 6.3 57 111-176 369-428 (503)
31 PF00403 HMA: Heavy-metal-asso 47.7 71 0.0015 20.4 5.3 41 39-79 14-57 (62)
32 PF01545 Cation_efflux: Cation 45.3 1.2E+02 0.0027 25.5 7.7 74 110-188 203-278 (284)
33 COG4837 Uncharacterized protei 44.6 19 0.00041 26.8 2.1 27 155-182 18-44 (106)
34 COG3086 RseC Positive regulato 41.7 31 0.00068 27.6 3.2 34 138-174 8-43 (150)
35 PF13192 Thioredoxin_3: Thiore 39.8 30 0.00064 23.6 2.5 25 148-177 3-27 (76)
36 COG1308 EGD2 Transcription fac 39.6 26 0.00057 27.1 2.4 92 40-136 13-113 (122)
37 PRK15431 ferrous iron transpor 38.0 14 0.0003 26.4 0.6 26 134-164 44-69 (78)
38 COG0082 AroC Chorismate syntha 36.8 20 0.00044 32.7 1.6 30 38-67 228-257 (369)
39 COG5561 Predicted metal-bindin 36.6 42 0.00091 24.8 2.9 31 154-186 34-64 (101)
40 COG2946 Putative phage replica 36.5 87 0.0019 28.6 5.5 51 135-190 117-171 (377)
41 TIGR02174 CXXU_selWTH selT/sel 36.0 66 0.0014 22.0 3.8 25 155-181 5-29 (72)
42 PRK11702 hypothetical protein; 35.7 1.9E+02 0.0041 21.9 6.4 66 110-187 35-100 (108)
43 PF08777 RRM_3: RNA binding mo 35.6 43 0.00092 24.9 2.9 26 129-155 22-47 (105)
44 COG1941 FrhG Coenzyme F420-red 33.3 95 0.0021 26.9 5.0 29 148-177 7-35 (247)
45 cd03026 AhpF_NTD_C TRX-GRX-lik 33.0 1.1E+02 0.0024 21.6 4.7 34 153-191 21-54 (89)
46 PF14424 Toxin-deaminase: The 30.6 89 0.0019 24.3 4.1 52 112-182 75-126 (133)
47 PF08141 SspH: Small acid-solu 29.8 91 0.002 20.9 3.5 41 114-154 3-43 (58)
48 PRK09437 bcp thioredoxin-depen 29.8 87 0.0019 23.8 4.0 59 132-195 19-79 (154)
49 cd02971 PRX_family Peroxiredox 28.7 1.4E+02 0.003 21.9 4.9 61 132-197 11-73 (140)
50 PF13793 Pribosyltran_N: N-ter 28.6 49 0.0011 25.0 2.3 40 110-159 9-48 (116)
51 TIGR03820 lys_2_3_AblA lysine- 27.7 2E+02 0.0043 26.8 6.5 55 41-96 177-252 (417)
52 PRK10503 multidrug efflux syst 27.1 2.6E+02 0.0057 29.0 7.9 114 38-153 73-199 (1040)
53 cd02966 TlpA_like_family TlpA- 25.7 1.3E+02 0.0028 20.4 4.0 60 132-197 8-71 (116)
54 PF02591 DUF164: Putative zinc 25.4 56 0.0012 21.2 1.8 19 146-164 14-33 (56)
55 TIGR02861 SASP_H small acid-so 25.2 1.2E+02 0.0027 20.2 3.5 42 114-155 3-44 (58)
56 PRK01625 sspH acid-soluble spo 24.6 1.3E+02 0.0029 20.2 3.5 42 114-155 3-44 (59)
57 TIGR03421 FeS_CyaY iron donor 24.5 1.9E+02 0.004 21.4 4.7 31 112-153 11-41 (102)
58 COG5429 Uncharacterized secret 24.4 60 0.0013 28.1 2.3 24 145-168 42-65 (261)
59 PRK03174 sspH acid-soluble spo 23.8 1.4E+02 0.003 20.2 3.5 41 114-154 3-43 (59)
60 PF07045 DUF1330: Protein of u 23.7 69 0.0015 21.3 2.1 23 116-139 3-25 (65)
61 PF00578 AhpC-TSA: AhpC/TSA fa 23.4 1.2E+02 0.0026 21.7 3.5 64 131-198 13-77 (124)
62 PF10262 Rdx: Rdx family; Int 22.5 1.3E+02 0.0028 20.6 3.4 33 148-185 3-36 (76)
63 cd03015 PRX_Typ2cys Peroxiredo 22.1 2.1E+02 0.0046 22.3 5.0 52 135-191 21-74 (173)
64 PRK11023 outer membrane lipopr 21.8 3E+02 0.0064 22.4 5.9 67 109-189 46-112 (191)
65 PRK00446 cyaY frataxin-like pr 21.6 2.4E+02 0.0053 21.0 4.9 34 111-154 11-44 (105)
66 cd03018 PRX_AhpE_like Peroxire 21.3 1.6E+02 0.0035 21.9 4.1 34 132-167 16-52 (149)
67 PRK11198 LysM domain/BON super 20.7 1.3E+02 0.0028 23.5 3.4 63 110-188 24-86 (147)
68 PRK10614 multidrug efflux syst 20.6 3E+02 0.0066 28.4 6.9 113 38-153 64-190 (1025)
69 COG1509 KamA Lysine 2,3-aminom 20.4 3.6E+02 0.0078 24.8 6.5 87 39-129 178-285 (369)
70 cd03014 PRX_Atyp2cys Peroxired 20.4 2.2E+02 0.0047 21.2 4.5 53 131-190 14-68 (143)
71 PF04320 DUF469: Protein with 20.3 3.7E+02 0.0081 20.0 5.7 65 110-187 29-94 (101)
No 1
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-46 Score=307.10 Aligned_cols=200 Identities=52% Similarity=0.772 Sum_probs=182.6
Q ss_pred CceeccCCCCCCceeeecCcccC-CCcceecCChhhhcCcHHHHhccCCC-CeeEEEEeCCeEEEEecCC-CChhhhhHH
Q 028908 1 MFIQTQPTPNPSSLMFYPGKPVM-EVGSADFPNARAAMNSPLAKSLYGVD-GITRVFFGSDFITVTKSED-TSWDLLKPE 77 (202)
Q Consensus 1 mfI~~e~TPNP~~lKF~~~~~~~-~~~~~~f~~~~~a~~spLa~~Lf~i~-gV~~Vf~~~dfItVtk~~~-~~W~~l~~~ 77 (202)
||||++.||||+++||.|+.+++ .+++.+|.+...+..+|||+++|.+. ||+++|+++|||||+|... .+|..|+++
T Consensus 10 ~~i~t~~tPn~~Sl~f~p~~~i~~~~~~~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~ 89 (213)
T KOG2358|consen 10 MFIQTQITPNPSSLLFLPGKQILSERGLGDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSVLDPE 89 (213)
T ss_pred hcccccCCCCcccccccCCCcccccccccccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccchhhhHhhhchh
Confidence 89999999999999999999998 56788999988888999999999888 8999999999999999887 899999999
Q ss_pred HHHHHHHHHhcCCCCccchhhhhhhcccCCCCchHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCC
Q 028908 78 IFAAIMDFYSSGQPLFLDSETAAAKDTAINEDDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACS 157 (202)
Q Consensus 78 I~~~I~d~l~sG~pvv~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~ 157 (202)
+...+.|++..|.|.+.+.......+. ..+++.++...|+++|++||||.|+.||||++|+++|.+.|+|+++|+|+|.
T Consensus 90 i~~~~sd~g~~g~pli~g~~~~~~~~~-~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact 168 (213)
T KOG2358|consen 90 IPSLMSDGGNVGLPLIDGNIVVLKLQG-ACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACT 168 (213)
T ss_pred hHHHHhccccccchhhccchhhhhhcc-cccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhc
Confidence 999999999999999987754332222 3467889999999999999999999999999999999766899999999999
Q ss_pred CCcchHHHHHHHHHHHHHhhCCCcceEEecCCcchHHHhhccCC
Q 028908 158 GCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAEDEVATLAGQM 201 (202)
Q Consensus 158 gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~~~~~~~~~~~~ 201 (202)
+|||+..||++||+++|++|+|+|+.|+++.|.+.+..+++-.+
T Consensus 169 ~cpss~vtlk~Gie~mL~~y~~eVK~v~qv~d~e~~~v~~e~~~ 212 (213)
T KOG2358|consen 169 ECPSSLVTLKNGIENMLEIYVPEVKGVIQVPDAEVMTVTVELTK 212 (213)
T ss_pred cCCcccchhhhhHHHHHHhhcceeeEEEeccCccceEEeeeccc
Confidence 99999999999999999999999999999999999888776543
No 2
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=100.00 E-value=1.3e-33 Score=206.16 Aligned_cols=87 Identities=49% Similarity=0.877 Sum_probs=71.1
Q ss_pred eeccCCCCCCceeeecCcccCCCcceecCChhhhcCcHHHHhccCCCCeeEEEEeCCeEEEEecCCCChhhhhHHHHHHH
Q 028908 3 IQTQPTPNPSSLMFYPGKPVMEVGSADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEIFAAI 82 (202)
Q Consensus 3 I~~e~TPNP~~lKF~~~~~~~~~~~~~f~~~~~a~~spLa~~Lf~i~gV~~Vf~~~dfItVtk~~~~~W~~l~~~I~~~I 82 (202)
||+|+|||||+|||+++++++++++++|++.++|..||||++||+|+||++||+++|||||+|.++++|++|+++|++.|
T Consensus 1 I~~e~TPNPn~lKF~~~~~~~~~~s~~f~~~~~a~~spLA~~Lf~i~gV~~Vf~~~dfItVtK~~~~~W~~l~~~I~~~I 80 (87)
T PF08712_consen 1 IQIEPTPNPNALKFVLDEPLLPGGSFEFKSAEEASDSPLAQALFAIPGVKSVFIGDDFITVTKNPDADWEDLKPEIREVI 80 (87)
T ss_dssp EEEEE-SSSSEEEEEESS-SSTS---EEESSS-TTS-HHHHHHHTSTTEEEEEEETTEEEEEE-TTS-HHHHHHHHHHHT
T ss_pred CEeecCCCcccEEEECCceeecCccEEeCChHHcccCHHHHHhcCCCCEeEEEEECCEEEEeeCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcC
Q 028908 83 MDFYSSG 89 (202)
Q Consensus 83 ~d~l~sG 89 (202)
++||.+|
T Consensus 81 ~~~l~sG 87 (87)
T PF08712_consen 81 MEFLESG 87 (87)
T ss_dssp H------
T ss_pred hhhccCC
Confidence 9999886
No 3
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=1.9e-28 Score=179.89 Aligned_cols=85 Identities=51% Similarity=0.837 Sum_probs=80.7
Q ss_pred CchHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecC
Q 028908 109 DDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 188 (202)
Q Consensus 109 ~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~ 188 (202)
.++++.++++.+|+++|||+|++||||++|+++++.+|+|+|||+|||+|||||++|||++||++|++++|++.+|++.+
T Consensus 6 ~~~~~~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v~ 85 (93)
T COG0694 6 TDAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQVT 85 (93)
T ss_pred ccHHHHHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEcc
Confidence 46789999999999999999999999999999998789999999999999999999999999999999999999999999
Q ss_pred CcchH
Q 028908 189 DAEDE 193 (202)
Q Consensus 189 ~~~~~ 193 (202)
++...
T Consensus 86 ~~~~~ 90 (93)
T COG0694 86 EHARG 90 (93)
T ss_pred Ccccc
Confidence 87654
No 4
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=99.92 E-value=4.1e-25 Score=154.27 Aligned_cols=68 Identities=56% Similarity=0.909 Sum_probs=63.6
Q ss_pred HHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 117 IKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 117 i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
|+++|++ |||+|++||||++|++++ +++|+|||+|+|+|||+|..||+++||++|++++|++..|.++
T Consensus 1 V~~~l~~-IrP~L~~dGGdv~lv~v~--~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V~~v 68 (68)
T PF01106_consen 1 VEEVLEE-IRPYLQSDGGDVELVDVD--DGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVVPV 68 (68)
T ss_dssp HHHHHHH-CHHHHHHTTEEEEEEEEE--TTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEEEC
T ss_pred CHHHHHH-hChHHHhcCCcEEEEEec--CCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEEEC
Confidence 6789997 999999999999999999 6799999999999999999999999999999999999999863
No 5
>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.
Probab=99.92 E-value=5.2e-25 Score=181.79 Aligned_cols=84 Identities=31% Similarity=0.589 Sum_probs=78.4
Q ss_pred CCchHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 108 EDDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 108 ~~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
.+++++.++|+++|+++|||+|++|||||+|++++. +++|+|||+|+|+|||||..||+++||++|++++|+|++|+..
T Consensus 101 ~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~-~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~ 179 (190)
T TIGR03341 101 ADDAPLEERINYVLQSEINPQLASHGGKVTLVEITD-DGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDA 179 (190)
T ss_pred ccchHHHHHHHHHHHhccCHHHHhcCCceEEEEEcC-CCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEe
Confidence 346679999999999999999999999999999984 5799999999999999999999999999999999999999999
Q ss_pred CCcch
Q 028908 188 LDAED 192 (202)
Q Consensus 188 ~~~~~ 192 (202)
+++..
T Consensus 180 ~~~~~ 184 (190)
T TIGR03341 180 TDHTR 184 (190)
T ss_pred cCccc
Confidence 98753
No 6
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.92 E-value=7.5e-25 Score=181.03 Aligned_cols=83 Identities=30% Similarity=0.590 Sum_probs=78.2
Q ss_pred CchHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCC-CcceEEec
Q 028908 109 DDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVP-EVKSVEQE 187 (202)
Q Consensus 109 ~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~P-ev~~V~~~ 187 (202)
+++++.++|+++|+++|||+|++|||||+|++++. +|+|+|||+|||+|||||+.||+++||++|++++| +|++|+++
T Consensus 103 ~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~-~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v 181 (192)
T PRK11190 103 DDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITE-DGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDL 181 (192)
T ss_pred ccHHHHHHHHHHHHhccChhHHhcCCcEEEEEEcC-CCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEe
Confidence 46679999999999999999999999999999984 58999999999999999999999999999999999 99999999
Q ss_pred CCcch
Q 028908 188 LDAED 192 (202)
Q Consensus 188 ~~~~~ 192 (202)
+++..
T Consensus 182 ~~~~~ 186 (192)
T PRK11190 182 TEHQR 186 (192)
T ss_pred ccccc
Confidence 98865
No 7
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=99.82 E-value=6.7e-20 Score=160.21 Aligned_cols=74 Identities=36% Similarity=0.637 Sum_probs=68.8
Q ss_pred chHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 110 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
..+..++|+++| ++|||+|++|||||+|++++ +++|+|||+|+|+|||+|++||++ ||++|++++|++..|+.+
T Consensus 217 ~~~~~~~v~~~l-~~irP~l~~dGGdv~lv~v~--~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~~V~~v 290 (290)
T TIGR02000 217 NVQRIQLIQKVL-EEVRPVLQADGGDVELYDVD--GKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred hHHHHHHHHHHH-HHhCchHhhcCCcEEEEEEe--CCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 456778999999 69999999999999999998 689999999999999999999998 999999999999999763
No 8
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=9.8e-07 Score=73.23 Aligned_cols=76 Identities=28% Similarity=0.393 Sum_probs=68.3
Q ss_pred HHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecCCcchH
Q 028908 115 AMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAEDE 193 (202)
Q Consensus 115 ~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~~~~ 193 (202)
+....+|+ ..+|++-+|||+.-+--++ +..+.++++|+|..||.+++++|.+|+..||..+||.-.+++.-+.++.
T Consensus 80 e~~w~~L~-p~i~~~~sd~g~~g~pli~--g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g 155 (213)
T KOG2358|consen 80 ENVWSVLD-PEIPSLMSDGGNVGLPLID--GNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETG 155 (213)
T ss_pred hhhHhhhc-hhhHHHHhccccccchhhc--cchhhhhhcccccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCc
Confidence 45567787 7899999999999998887 6789999999999999999999999999999999999999987777774
No 9
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=96.82 E-value=0.012 Score=40.56 Aligned_cols=67 Identities=24% Similarity=0.431 Sum_probs=51.9
Q ss_pred HHHHHHHHhccchhhhhc---CCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEE
Q 028908 115 AMIKELLETRIRPAVQDD---GGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVE 185 (202)
Q Consensus 115 ~~i~~~l~~~IrP~l~~d---GGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~ 185 (202)
++|.++|.+-.-|.+..+ =|-|.=+.++ +|.|+|.+.-.+.+|| ....|+..|+..|+ .+|++.+|.
T Consensus 2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~--~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~gv~~V~ 71 (72)
T PF01883_consen 2 QAVRDALKQVKDPELGKDIVELGMVRDISIE--GGKVSVSLELPTPACP-AAEPLREEIREALK-ALPGVKSVK 71 (72)
T ss_dssp HHHHHHHTT-BETTTSSBTTTTTSEEEEEEC--TCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT-SEEE
T ss_pred HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEE--CCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCCCceEe
Confidence 577888888888877655 3667777776 7999999999999999 55579999999999 799998886
No 10
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=94.65 E-value=0.24 Score=37.73 Aligned_cols=78 Identities=33% Similarity=0.443 Sum_probs=56.1
Q ss_pred hHHHHHHHHHHHhccchhhhhcC---CCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 111 SETVAMIKELLETRIRPAVQDDG---GDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 111 ~~~~~~i~~~l~~~IrP~l~~dG---Gdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
..+..+|.+.|.+-+-|.|--|= |=|.=+.++.++|.++|+|+..-.|||++.. +..-++++|++ +|.|++|+..
T Consensus 11 ~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~-i~~~v~~al~~-~~~v~~v~V~ 88 (111)
T COG2151 11 KVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEV-IADQVEAALEE-IPGVEDVEVE 88 (111)
T ss_pred hhhHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHH-HHHHHHHHHHh-cCCcceEEEE
Confidence 45677888888888889984442 2222233343255899999999999999986 66789999988 7778877765
Q ss_pred CCc
Q 028908 188 LDA 190 (202)
Q Consensus 188 ~~~ 190 (202)
..-
T Consensus 89 l~~ 91 (111)
T COG2151 89 LTL 91 (111)
T ss_pred EEE
Confidence 443
No 11
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=94.30 E-value=0.24 Score=36.16 Aligned_cols=71 Identities=28% Similarity=0.383 Sum_probs=51.4
Q ss_pred HHHHHHHHHHhccchhhhhcC---CCEEEEEEecCC-CEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 113 TVAMIKELLETRIRPAVQDDG---GDIEYRGFDPET-GTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 113 ~~~~i~~~l~~~IrP~l~~dG---Gdiel~~~d~~~-g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
+.++|.++|.+-.-|.+..+- |-|.=+.++ + +.|+|.+.-...+||... .|++.++..|.. +|++..|...
T Consensus 2 ~~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~--~~~~v~i~l~l~~p~~~~~~-~l~~~i~~al~~-l~gv~~v~v~ 76 (99)
T TIGR02945 2 LKDAVIEALKTVYDPEIPVNIYELGLIYDIDVD--DDGHVDIQMTLTAPNCPVAG-SMPGEVENAVRA-VPGVGSVTVE 76 (99)
T ss_pred HHHHHHHHHcCCCCCCCCCCeecCCCeeEEEEC--CCCeEEEEEEECCCCCChHH-HHHHHHHHHHHh-CCCCceEEEE
Confidence 356788888888888876543 334333343 4 789999988888888766 488889999975 7888877643
No 12
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=91.22 E-value=1.1 Score=36.66 Aligned_cols=77 Identities=23% Similarity=0.293 Sum_probs=57.0
Q ss_pred hHHHHHHHHHHHhccchhhhhc---CCCEEEEEEec---CCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceE
Q 028908 111 SETVAMIKELLETRIRPAVQDD---GGDIEYRGFDP---ETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSV 184 (202)
Q Consensus 111 ~~~~~~i~~~l~~~IrP~l~~d---GGdiel~~~d~---~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V 184 (202)
....++|.++|.+-.-|.+..+ =|-|.=+.++. +++.|+|.|.-...+|++.. .|+..|+.+|.. +|.+++|
T Consensus 72 ~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~~-~L~~dV~~aL~~-l~gV~~V 149 (174)
T TIGR03406 72 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGP-VLVEDVEDKVLA-VPNVDEV 149 (174)
T ss_pred cccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHH-HHHHHHHHHHHh-CCCceeE
Confidence 3445889999998888887664 35565556664 12289999999999999877 577889999975 7898887
Q ss_pred EecCC
Q 028908 185 EQELD 189 (202)
Q Consensus 185 ~~~~~ 189 (202)
.....
T Consensus 150 ~V~l~ 154 (174)
T TIGR03406 150 EVELV 154 (174)
T ss_pred EEEEE
Confidence 75443
No 13
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=81.78 E-value=1.8 Score=27.14 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=22.1
Q ss_pred ccCCCCCcchHHHHHHHHHHHHHhh
Q 028908 153 QGACSGCPSSSVTLKSGIENMLMHY 177 (202)
Q Consensus 153 ~GaC~gCpss~~Tl~~~Ie~~l~~~ 177 (202)
.++|.|||.-+..|...|-..||.-
T Consensus 7 G~~~~G~~ql~ESLLdrItRklr~g 31 (45)
T PF02061_consen 7 GWPRMGCPQLSESLLDRITRKLRDG 31 (45)
T ss_pred CccccCCchhhHHHHHHHHHHHHHH
Confidence 5899999988888999999999874
No 14
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=72.30 E-value=17 Score=28.84 Aligned_cols=48 Identities=25% Similarity=0.448 Sum_probs=36.8
Q ss_pred CCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEe
Q 028908 134 GDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQ 186 (202)
Q Consensus 134 Gdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~ 186 (202)
|-|.=+.++ ++.|.|.+.-.-.+||... .|++.|+.+|+.. .+.+|..
T Consensus 15 G~Vr~V~v~--gd~V~VtIt~Ty~gcpa~e-~L~~~I~~aL~~~--Gv~~V~V 62 (146)
T TIGR02159 15 GMVREVDVD--GGGVVVKFTPTYSGCPALE-VIRQDIRDAVRAL--GVEVVEV 62 (146)
T ss_pred CCeeEEEEE--CCEEEEEEEeCCCCCchHH-HHHHHHHHHHHhc--CCCeEEE
Confidence 556655666 6789999988889999876 6889999999884 5665554
No 15
>PRK11670 antiporter inner membrane protein; Provisional
Probab=70.34 E-value=23 Score=32.15 Aligned_cols=72 Identities=14% Similarity=0.155 Sum_probs=52.9
Q ss_pred HHHHHHHHHHhccchhhhhc---CCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecC
Q 028908 113 TVAMIKELLETRIRPAVQDD---GGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 188 (202)
Q Consensus 113 ~~~~i~~~l~~~IrP~l~~d---GGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~ 188 (202)
..++|.+.|..-+-|.+..+ -|-|.=+.++ ++.+++.+.-.-.+||... .++..+++.|+. +|++++|....
T Consensus 13 ~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~ 87 (369)
T PRK11670 13 LRAMVAGTLANFQHPTLKHNLTTLKALHHVALL--DDTLHIELVMPFVWNSAFE-ELKEQCSAELLR-ITGAKAIDWKL 87 (369)
T ss_pred hHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEe--CCEEEEEEEECCCCchHHH-HHHHHHHHHHHh-cCCCceEEEEE
Confidence 44778888887788887664 3445444555 6788888887767898766 588899999986 78888776543
No 16
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=69.76 E-value=30 Score=25.28 Aligned_cols=78 Identities=21% Similarity=0.254 Sum_probs=48.0
Q ss_pred chHHHHHHHHHHHhc-------cchhhhhcCCCEEEEEEecC-CCEEEEEeccCCC--CCcchHHHHHHHHHHHHHhhCC
Q 028908 110 DSETVAMIKELLETR-------IRPAVQDDGGDIEYRGFDPE-TGTVKLRMQGACS--GCPSSSVTLKSGIENMLMHYVP 179 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~-------IrP~l~~dGGdiel~~~d~~-~g~v~v~l~GaC~--gCpss~~Tl~~~Ie~~l~~~~P 179 (202)
++...+.++.++... .+|.+ -.++.+.++..+ +++++|.|..+=. .=.+...-+...|-..|.+.++
T Consensus 23 ~~~~~~~v~~L~~gp~~~~~~~~~~~~---p~~~~l~~v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~ 99 (117)
T PF10646_consen 23 EDDAEAAVNALLKGPSDSEGPGLRSAL---PPGTKLNSVTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFP 99 (117)
T ss_pred chHHHHHHHHHHhCCCccccceeeecC---CCccceeeEEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcC
Confidence 455666666666542 23333 344555555544 4599999976432 2222344566778888888899
Q ss_pred CcceEEecCCc
Q 028908 180 EVKSVEQELDA 190 (202)
Q Consensus 180 ev~~V~~~~~~ 190 (202)
+|+.|...-+.
T Consensus 100 ~v~~V~i~vdG 110 (117)
T PF10646_consen 100 GVKKVQILVDG 110 (117)
T ss_pred CccEEEEEECC
Confidence 99999875443
No 17
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=64.07 E-value=13 Score=27.97 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=16.2
Q ss_pred CCCCCcchHHHHHHHHHHHHHhhCC
Q 028908 155 ACSGCPSSSVTLKSGIENMLMHYVP 179 (202)
Q Consensus 155 aC~gCpss~~Tl~~~Ie~~l~~~~P 179 (202)
.|.|||.. .+...++.+++..+.
T Consensus 45 ~CgGCpg~--~~~~~~~~l~~~~~d 67 (107)
T PF08821_consen 45 TCGGCPGR--KLVRRIKKLKKNGAD 67 (107)
T ss_pred eCCCCChh--HHHHHHHHHHHCCCC
Confidence 79999944 455678887766554
No 18
>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues. A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.
Probab=62.67 E-value=7.8 Score=28.50 Aligned_cols=27 Identities=30% Similarity=0.433 Sum_probs=19.1
Q ss_pred CCCCCcchHHHHHHHHHHHHHhhCCCcc
Q 028908 155 ACSGCPSSSVTLKSGIENMLMHYVPEVK 182 (202)
Q Consensus 155 aC~gCpss~~Tl~~~Ie~~l~~~~Pev~ 182 (202)
+|.+-|||..|. .+++.+|.+++|+..
T Consensus 11 SCVn~PsSkeTy-eWL~aal~RKyp~~~ 37 (93)
T PF07315_consen 11 SCVNAPSSKETY-EWLEAALKRKYPDQP 37 (93)
T ss_dssp GGSSS--HHHHH-HHHHHHHHHH-TTS-
T ss_pred hhcCCCCchhHH-HHHHHHHhCcCCCCc
Confidence 455568888776 899999999999863
No 19
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=62.67 E-value=11 Score=30.15 Aligned_cols=24 Identities=29% Similarity=0.617 Sum_probs=17.5
Q ss_pred EEEEEecCCCEEEEEe--ccCCCCCcch
Q 028908 137 EYRGFDPETGTVKLRM--QGACSGCPSS 162 (202)
Q Consensus 137 el~~~d~~~g~v~v~l--~GaC~gCpss 162 (202)
.++.++ ++.++|+. +.+|++|.+.
T Consensus 7 ~Vv~v~--~~~a~Ve~~r~saCg~C~a~ 32 (154)
T PRK10862 7 TVVSWQ--NGIALLRCEVKAGCSSCASR 32 (154)
T ss_pred EEEEEE--CCEEEEEEecCCCCcCcCCC
Confidence 456666 67877776 5899999854
No 20
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=57.04 E-value=20 Score=24.21 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=14.7
Q ss_pred CCCEEEEEEecCCCEEEEEeccCCCCCcchHHHH
Q 028908 133 GGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTL 166 (202)
Q Consensus 133 GGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl 166 (202)
-|-|+=+.... .. .|.|.+|+.....+
T Consensus 41 kG~I~~~~~~~-~~------~~~C~~C~~~~~~~ 67 (69)
T PF09012_consen 41 KGYIRKVDMSS-CC------GGSCSSCGPASKEI 67 (69)
T ss_dssp CTSCEEEEEE---S------SSSSSS-SS-----
T ss_pred CCcEEEecCCC-CC------CCCCCCCCCccccC
Confidence 58888765542 22 89999999877543
No 21
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=56.97 E-value=46 Score=22.35 Aligned_cols=48 Identities=10% Similarity=0.048 Sum_probs=38.4
Q ss_pred HHHhccCCCCeeEEEEeCCeEEEEecCCCChhhhhHHHHHHHHHHHhc
Q 028908 41 LAKSLYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEIFAAIMDFYSS 88 (202)
Q Consensus 41 La~~Lf~i~gV~~Vf~~~dfItVtk~~~~~W~~l~~~I~~~I~d~l~s 88 (202)
+-..|.....|+++.+.++-|+++-.-...|......+.+.|.+.+.+
T Consensus 16 ~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~ 63 (72)
T PF01883_consen 16 LGKDIVELGMVRDISIEGGKVSVSLELPTPACPAAEPLREEIREALKA 63 (72)
T ss_dssp TSSBTTTTTSEEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHHT
T ss_pred CCCCHHHcCCeeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHHh
Confidence 446677778899999999999999998888888888888888888763
No 22
>PRK12463 chorismate synthase; Reviewed
Probab=55.81 E-value=12 Score=34.54 Aligned_cols=37 Identities=11% Similarity=0.311 Sum_probs=29.0
Q ss_pred eecCChhhhcCcHHHHhccCCCCeeEEEEeCCeEEEEecC
Q 028908 28 ADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTKSE 67 (202)
Q Consensus 28 ~~f~~~~~a~~spLa~~Lf~i~gV~~Vf~~~dfItVtk~~ 67 (202)
++|... ..+.||+++|+||.||.|-|+..|=.-.+..
T Consensus 235 v~fd~k---Lda~LA~A~msIpAVKgVE~G~Gf~~a~~~G 271 (390)
T PRK12463 235 VHYDRK---LDAKLAGAIMSINAFKGAEIGVGFEAARQPG 271 (390)
T ss_pred cccccc---chHHHHHHhcCcCceeEEEEccchhhhhCCC
Confidence 446522 3578999999999999999999987766544
No 23
>PF01264 Chorismate_synt: Chorismate synthase; InterPro: IPR000453 Chorismate synthase (4.2.3.5 from EC) catalyzes the last of the seven steps in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows a high degree of sequence conservation [, ]. It is a protein of about 360 to 400 amino-acid residues.; GO: 0004107 chorismate synthase activity, 0009073 aromatic amino acid family biosynthetic process; PDB: 4ECD_B 1Q1L_D 1QXO_A 1UMF_B 1UM0_D 1SQ1_A 2O12_A 2O11_A 1ZTB_A 2QHF_A ....
Probab=55.70 E-value=7 Score=35.44 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=26.7
Q ss_pred ceecCChhhhcCcHHHHhccCCCCeeEEEEeCCeEEEEe
Q 028908 27 SADFPNARAAMNSPLAKSLYGVDGITRVFFGSDFITVTK 65 (202)
Q Consensus 27 ~~~f~~~~~a~~spLa~~Lf~i~gV~~Vf~~~dfItVtk 65 (202)
+.-|.+. .+.||+.||+||.||.|.|+..|=....
T Consensus 215 ~p~fdkL----da~la~al~sIpAvKgvEfG~Gf~~a~~ 249 (346)
T PF01264_consen 215 SPVFDKL----DARLAQALMSIPAVKGVEFGDGFEAASM 249 (346)
T ss_dssp BSSCCSH----HHHHHHHHHTSTTEEEEEETTGGGGGGS
T ss_pred CCCcCcH----HHHHHHHhhCCCCeeeEEecCcHHHhhc
Confidence 3336643 4679999999999999999988754433
No 24
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=55.63 E-value=12 Score=28.79 Aligned_cols=20 Identities=20% Similarity=0.564 Sum_probs=14.4
Q ss_pred EEEecCCCEEEEEe--ccCCCCCc
Q 028908 139 RGFDPETGTVKLRM--QGACSGCP 160 (202)
Q Consensus 139 ~~~d~~~g~v~v~l--~GaC~gCp 160 (202)
+.++ ++.++|+. +.+|++|.
T Consensus 2 v~v~--~~~~~V~~~r~saC~~C~ 23 (135)
T PF04246_consen 2 VAVE--GGIAWVEVQRSSACGSCS 23 (135)
T ss_pred EEEe--CCEEEEEEccCCcCcccC
Confidence 3455 67887777 58888887
No 25
>cd07304 Chorismate_synthase Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway. Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway: the conversion of 5- enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a precursor for the biosynthesis of aromatic compounds. This process has an absolute requirement for reduced FMN as a co-factor which is thought to facilitate cleavage of C-O bonds by transiently donating an electron to the substrate, having no overall change its redox state. Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two classes: Enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctiona,l while those that can generate reduced FMN at the expense of NADPH, such as found in fun
Probab=55.41 E-value=8.4 Score=34.90 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=25.7
Q ss_pred cCcHHHHhccCCCCeeEEEEeCCeEEEEec
Q 028908 37 MNSPLAKSLYGVDGITRVFFGSDFITVTKS 66 (202)
Q Consensus 37 ~~spLa~~Lf~i~gV~~Vf~~~dfItVtk~ 66 (202)
..+.||+++|.||.||.|-|+.+|=.-...
T Consensus 223 lda~la~a~~sIpAvKgve~G~Gf~~a~~~ 252 (344)
T cd07304 223 LDARLAQALMSIPAVKGVEIGSGFEAARMR 252 (344)
T ss_pred chHHHHHHhcCcCceeEEEECcchhhhhcc
Confidence 367899999999999999999998766543
No 26
>PRK05382 chorismate synthase; Validated
Probab=51.20 E-value=10 Score=34.58 Aligned_cols=31 Identities=19% Similarity=0.399 Sum_probs=26.7
Q ss_pred cCcHHHHhccCCCCeeEEEEeCCeEEEEecC
Q 028908 37 MNSPLAKSLYGVDGITRVFFGSDFITVTKSE 67 (202)
Q Consensus 37 ~~spLa~~Lf~i~gV~~Vf~~~dfItVtk~~ 67 (202)
..+.||+++|+||.||.|-|+..|=.-....
T Consensus 221 Lda~la~a~msIpAvKgvE~G~Gf~~a~~~G 251 (359)
T PRK05382 221 LDADLAHALMSINAVKGVEIGDGFAAARLRG 251 (359)
T ss_pred chHHHHHHhcCcCceeEEEECcchhhccccC
Confidence 3678999999999999999999987766544
No 27
>TIGR00033 aroC chorismate synthase. Homotetramer (noted in E.coli) suggests reason for good conservation.
Probab=50.77 E-value=10 Score=34.39 Aligned_cols=31 Identities=16% Similarity=0.338 Sum_probs=25.9
Q ss_pred cCcHHHHhccCCCCeeEEEEeCCeEEEEecC
Q 028908 37 MNSPLAKSLYGVDGITRVFFGSDFITVTKSE 67 (202)
Q Consensus 37 ~~spLa~~Lf~i~gV~~Vf~~~dfItVtk~~ 67 (202)
..+.||+++|+||.||.|-|+..|=.-....
T Consensus 222 Lda~La~a~msIpAvKgvE~G~Gf~~a~~~G 252 (351)
T TIGR00033 222 LDARLAHAMMSIPAVKGVEIGDGFELASMRG 252 (351)
T ss_pred chHHHHHHhcCcCceeEEEECcchhhccccc
Confidence 3678999999999999999999986655443
No 28
>PF11718 CPSF73-100_C: Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; InterPro: IPR021718 This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.
Probab=50.28 E-value=1.5e+02 Score=24.82 Aligned_cols=115 Identities=20% Similarity=0.290 Sum_probs=71.9
Q ss_pred CeEEEEecCCC----Chh------hhhHHHHHHHHHHHhcCCCCccchhhhh-----hhcccCCCCchHHHHHHHHHHHh
Q 028908 59 DFITVTKSEDT----SWD------LLKPEIFAAIMDFYSSGQPLFLDSETAA-----AKDTAINEDDSETVAMIKELLET 123 (202)
Q Consensus 59 dfItVtk~~~~----~W~------~l~~~I~~~I~d~l~sG~pvv~~~~~~~-----~~~~~~~~~~~~~~~~i~~~l~~ 123 (202)
+-|+|+..++. +|. .+...|...|.+.-++..++.......+ ........+.....+++..+|..
T Consensus 77 ~~V~v~~~~~~~v~lEW~s~~~nDmiADsv~a~il~~~ssp~svk~~~~~~~h~h~~~~~~~~~~~~~~~~~~l~~~L~~ 156 (216)
T PF11718_consen 77 GCVTVTYDPNEEVVLEWESSPVNDMIADSVVAVILQIDSSPASVKLSSKSCSHSHSHDPNPHEKSDEEERLERLIELLEA 156 (216)
T ss_pred eeEEEEEeCCcEEEEEEcCCcchhHHHHHHHHHHHHHhhCCccccccccccccccccccccccccCHHHHHHHHHHHHHH
Confidence 55777776654 564 4566777777776655443332211000 00011123356677888999988
Q ss_pred ccchhhhhc--CCCE-EEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhh
Q 028908 124 RIRPAVQDD--GGDI-EYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHY 177 (202)
Q Consensus 124 ~IrP~l~~d--GGdi-el~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~ 177 (202)
.-.+....+ +|.. -.+.+| +..+.|.+..-..-|. +..|++.|+..|++-
T Consensus 157 qFG~~~~~~~~~~~~~~~v~vd--~~~A~I~~~t~~Vec~--d~~Lk~rve~~l~r~ 209 (216)
T PF11718_consen 157 QFGDVEVPDIEKPKEPLSVTVD--GKVAHIDLSTLEVECE--DEPLKQRVETALKRL 209 (216)
T ss_pred HcCCCccccccccceeEEEEeC--CcEEEEecCCCceecC--CHHHHHHHHHHHHHH
Confidence 887774444 4443 334455 7789999988888888 667999999999874
No 29
>PLN02754 chorismate synthase
Probab=49.81 E-value=11 Score=35.03 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=26.4
Q ss_pred cCcHHHHhccCCCCeeEEEEeCCeEEEEecC
Q 028908 37 MNSPLAKSLYGVDGITRVFFGSDFITVTKSE 67 (202)
Q Consensus 37 ~~spLa~~Lf~i~gV~~Vf~~~dfItVtk~~ 67 (202)
..+.||++||.||.||.|.|+..|=.-....
T Consensus 256 Lda~LA~Al~SIpAVKGVEfG~GF~~a~~~G 286 (413)
T PLN02754 256 LEAELAKAMMSLPATKGFEIGSGFAGTLLTG 286 (413)
T ss_pred chHHHHHHhcCcCceeEEEEccchhhhhccc
Confidence 3678999999999999999999987666544
No 30
>PHA02782 hypothetical protein; Provisional
Probab=47.95 E-value=60 Score=30.49 Aligned_cols=57 Identities=23% Similarity=0.331 Sum_probs=37.9
Q ss_pred hHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHH---HHHHHHHHh
Q 028908 111 SETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLK---SGIENMLMH 176 (202)
Q Consensus 111 ~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~---~~Ie~~l~~ 176 (202)
..+.++|+++|-++|--+.-.+|| .-|+++|++++.+. ||.+....|+ ..|+..+++
T Consensus 369 kkl~~rIKEiLP~yVSAFANT~GG-yLfIGVdDdt~~Ii--------G~~~e~e~L~~Le~aIe~cI~K 428 (503)
T PHA02782 369 KQLRTRIRQQLPSILSSFANTEGG-YLFIGVDNNTHKVI--------GFTVGQDYLKLVENDIEKYIKR 428 (503)
T ss_pred HHHHHHHHHHhhHHhHhheeCCCC-EEEEEEcCCCCeEe--------eeecCHHHHHHHHHHHHHHHHh
Confidence 358889999999888766666666 77899996434332 6665444443 556665554
No 31
>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=47.74 E-value=71 Score=20.44 Aligned_cols=41 Identities=24% Similarity=0.269 Sum_probs=30.0
Q ss_pred cHHHHhccCCCCeeEEEEe--CCeEEEEecCCC-ChhhhhHHHH
Q 028908 39 SPLAKSLYGVDGITRVFFG--SDFITVTKSEDT-SWDLLKPEIF 79 (202)
Q Consensus 39 spLa~~Lf~i~gV~~Vf~~--~dfItVtk~~~~-~W~~l~~~I~ 79 (202)
..+-+.|.+++||++|-+. .+-++|+-+++. +.+.|...|.
T Consensus 14 ~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~ 57 (62)
T PF00403_consen 14 KKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE 57 (62)
T ss_dssp HHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH
T ss_pred HHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH
Confidence 4566788899999988877 488999988764 5555555443
No 32
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=45.26 E-value=1.2e+02 Score=25.48 Aligned_cols=74 Identities=18% Similarity=0.285 Sum_probs=41.2
Q ss_pred chHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCC--EEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 110 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETG--TVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g--~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
+++..+++++.+++ .|.+..- .++.+..+..+.- .++|++.+.+ .......+.+.|++.|++++|+|.+|...
T Consensus 203 ~~~~~~~i~~~i~~--~~~v~~v-~~~~~~~~g~~~~~v~i~v~v~~~~--~v~~~~~i~~~i~~~l~~~~~~i~~v~I~ 277 (284)
T PF01545_consen 203 DPELVEKIRRIIES--VPGVIEV-HDLRVWQVGRNKYVVEIHVQVDPDM--SVEEAHEIRERIEKRLREKFPGIYDVTIH 277 (284)
T ss_dssp HHHHHHHHHHHHHH--TSS-SEE-EEEEEEEETT-EEEEEEEEEETTTS--BHHHHHHHHHHHHHHHHHHSTTCEEEEEE
T ss_pred cccchhHHHHhhcc--CCceEec-cceEEEEecCCcEEEEEEEEeCCCC--CHHHHHHHHHHHHHHHHHhCCCcEEEEEE
Confidence 35566777777764 2222110 1233333321011 3455555655 23334557899999999999999976543
Q ss_pred C
Q 028908 188 L 188 (202)
Q Consensus 188 ~ 188 (202)
.
T Consensus 278 ~ 278 (284)
T PF01545_consen 278 I 278 (284)
T ss_dssp E
T ss_pred E
Confidence 3
No 33
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.62 E-value=19 Score=26.81 Aligned_cols=27 Identities=26% Similarity=0.390 Sum_probs=21.6
Q ss_pred CCCCCcchHHHHHHHHHHHHHhhCCCcc
Q 028908 155 ACSGCPSSSVTLKSGIENMLMHYVPEVK 182 (202)
Q Consensus 155 aC~gCpss~~Tl~~~Ie~~l~~~~Pev~ 182 (202)
+|.+-|+|-.|. .+.|.+|++.+|+..
T Consensus 18 SCV~aPtsKdt~-eWLeaalkRKyp~~~ 44 (106)
T COG4837 18 SCVNAPTSKDTY-EWLEAALKRKYPNQP 44 (106)
T ss_pred HhcCCCcchhHH-HHHHHHHhccCCCCC
Confidence 355558888776 899999999999865
No 34
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=41.72 E-value=31 Score=27.55 Aligned_cols=34 Identities=26% Similarity=0.477 Sum_probs=25.2
Q ss_pred EEEEecCCCEEEEEe--ccCCCCCcchHHHHHHHHHHHH
Q 028908 138 YRGFDPETGTVKLRM--QGACSGCPSSSVTLKSGIENML 174 (202)
Q Consensus 138 l~~~d~~~g~v~v~l--~GaC~gCpss~~Tl~~~Ie~~l 174 (202)
++++. +|.+.|+= +-+|++|++...-- .++.+.|
T Consensus 8 vv~~q--~G~a~V~c~~~S~CgsC~a~~~CG-s~~l~kL 43 (150)
T COG3086 8 VVSWQ--NGQAKVSCQRQSACGSCAARAGCG-SGLLSKL 43 (150)
T ss_pred EEEcc--CCeEEEEeeccCccccchhhcccc-hHHHHHh
Confidence 34444 78888876 68999999988766 5566666
No 35
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=39.84 E-value=30 Score=23.61 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=17.1
Q ss_pred EEEEeccCCCCCcchHHHHHHHHHHHHHhh
Q 028908 148 VKLRMQGACSGCPSSSVTLKSGIENMLMHY 177 (202)
Q Consensus 148 v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~ 177 (202)
+.+ ++-.|..|| .+.+.++..+...
T Consensus 3 I~v-~~~~C~~C~----~~~~~~~~~~~~~ 27 (76)
T PF13192_consen 3 IKV-FSPGCPYCP----ELVQLLKEAAEEL 27 (76)
T ss_dssp EEE-ECSSCTTHH----HHHHHHHHHHHHT
T ss_pred EEE-eCCCCCCcH----HHHHHHHHHHHhc
Confidence 566 666688888 3446677777775
No 36
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=39.65 E-value=26 Score=27.09 Aligned_cols=92 Identities=21% Similarity=0.326 Sum_probs=45.5
Q ss_pred HHHHhc---c-CCCCeeEEEEe-CCeEEEEecCCCChhhhhHHHHHHHHHHHhcCCCCccchhhhh----hhcccCCCCc
Q 028908 40 PLAKSL---Y-GVDGITRVFFG-SDFITVTKSEDTSWDLLKPEIFAAIMDFYSSGQPLFLDSETAA----AKDTAINEDD 110 (202)
Q Consensus 40 pLa~~L---f-~i~gV~~Vf~~-~dfItVtk~~~~~W~~l~~~I~~~I~d~l~sG~pvv~~~~~~~----~~~~~~~~~~ 110 (202)
.+.++| + .++||+.|.|- .|--.|-.+|.+. ..++... .-|--+|.+......... .....++++|
T Consensus 13 k~mkqmGi~~eeld~v~~V~i~~kd~e~vi~~P~V~----~~~~~g~-~~yqi~g~~~~~~~~~~~ee~~~d~~~i~eeD 87 (122)
T COG1308 13 KLMKQMGIDVEELDGVERVIIKLKDTEYVIENPQVT----VMKAMGQ-KTYQISGDPSAKEAVKKPEEKTVDESDISEED 87 (122)
T ss_pred HHHHHhCCCceeccCceEEEEEcCCceEEeeCCcEE----eehhcch-hHHHHhcchhhhcccccchhcccccCCCCHHH
Confidence 445554 2 46788888775 3434555666544 3344444 556566765311111000 0111223333
Q ss_pred hHHHHHHHHHHHhccchhhhhcCCCE
Q 028908 111 SETVAMIKELLETRIRPAVQDDGGDI 136 (202)
Q Consensus 111 ~~~~~~i~~~l~~~IrP~l~~dGGdi 136 (202)
=+|+..=-.+=.+..|-+|..+|||+
T Consensus 88 IkLV~eQa~VsreeA~kAL~e~~GDl 113 (122)
T COG1308 88 IKLVMEQAGVSREEAIKALEEAGGDL 113 (122)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcH
Confidence 23332222233456888999999985
No 37
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=37.95 E-value=14 Score=26.40 Aligned_cols=26 Identities=27% Similarity=0.684 Sum_probs=16.6
Q ss_pred CCEEEEEEecCCCEEEEEeccCCCCCcchHH
Q 028908 134 GDIEYRGFDPETGTVKLRMQGACSGCPSSSV 164 (202)
Q Consensus 134 Gdiel~~~d~~~g~v~v~l~GaC~gCpss~~ 164 (202)
|-|+=+.-+. .|-. +|.|.+||-+..
T Consensus 44 Gkverv~~~~-~gC~----sGsCk~C~e~~~ 69 (78)
T PRK15431 44 GKAVRIQEEP-DGCL----SGSCKSCPEGKA 69 (78)
T ss_pred CCeEeeccCC-CCCC----CCCCCCCCCCcc
Confidence 6666553222 3444 899999998653
No 38
>COG0082 AroC Chorismate synthase [Amino acid transport and metabolism]
Probab=36.76 E-value=20 Score=32.67 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=26.6
Q ss_pred CcHHHHhccCCCCeeEEEEeCCeEEEEecC
Q 028908 38 NSPLAKSLYGVDGITRVFFGSDFITVTKSE 67 (202)
Q Consensus 38 ~spLa~~Lf~i~gV~~Vf~~~dfItVtk~~ 67 (202)
.+.||.+||+|+-||.|-|+..|=+..+..
T Consensus 228 da~lA~AlmsI~AvKGVEiG~GF~~a~~~G 257 (369)
T COG0082 228 DAKLAHALMSIPAVKGVEIGDGFEAARMRG 257 (369)
T ss_pred hHHHHHHhhCCccceeEEeccchhhhhccc
Confidence 578999999999999999999998777654
No 39
>COG5561 Predicted metal-binding protein [Function unknown]
Probab=36.60 E-value=42 Score=24.80 Aligned_cols=31 Identities=19% Similarity=0.341 Sum_probs=20.1
Q ss_pred cCCCCCcchHHHHHHHHHHHHHhhCCCcceEEe
Q 028908 154 GACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQ 186 (202)
Q Consensus 154 GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~ 186 (202)
-.|.|||. .-..+.|+++.....+|..-...
T Consensus 34 ~tCGgCpG--rlvpn~~k~lk~~egaeaihfas 64 (101)
T COG5561 34 ITCGGCPG--RLVPNQIKQLKGKEGAEAIHFAS 64 (101)
T ss_pred EEcCCCCc--chhHHHHHHHhhccccceeeeee
Confidence 47999999 33445666666556677665544
No 40
>COG2946 Putative phage replication protein RstA [DNA replication, recombination, and repair]
Probab=36.52 E-value=87 Score=28.63 Aligned_cols=51 Identities=22% Similarity=0.371 Sum_probs=34.0
Q ss_pred CEEEEEEecCCCEEEEEeccCCCCCcc----hHHHHHHHHHHHHHhhCCCcceEEecCCc
Q 028908 135 DIEYRGFDPETGTVKLRMQGACSGCPS----SSVTLKSGIENMLMHYVPEVKSVEQELDA 190 (202)
Q Consensus 135 diel~~~d~~~g~v~v~l~GaC~gCps----s~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~ 190 (202)
+.-.+.+...++++.+.|.|+ ||-+ ...+|+++.+..+| |-|+.|....|+
T Consensus 117 ~yGkV~~gG~rntvlielsG~--GC~~~~~~we~rl~~fLq~~~r---~riTRvDlA~Dd 171 (377)
T COG2946 117 DYGKVHYGGQRNTVLIELSGT--GCTVAKEGWELRLYQFLQDCGR---PRITRVDLALDD 171 (377)
T ss_pred eEEEEEecCCCceEEEEEecC--ccceecccHHHHHHHHHHHhCC---CceeEEEEeeec
Confidence 344556665567999999997 8844 44455555555554 888888865554
No 41
>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=35.97 E-value=66 Score=22.05 Aligned_cols=25 Identities=16% Similarity=0.450 Sum_probs=19.7
Q ss_pred CCCCCcchHHHHHHHHHHHHHhhCCCc
Q 028908 155 ACSGCPSSSVTLKSGIENMLMHYVPEV 181 (202)
Q Consensus 155 aC~gCpss~~Tl~~~Ie~~l~~~~Pev 181 (202)
-|.+|...... ..+.+.|...+|+.
T Consensus 5 yC~~C~y~~Ra--~~l~q~L~~~Fp~~ 29 (72)
T TIGR02174 5 YCGSCGYKPRA--AWLKQELLEEFPDL 29 (72)
T ss_pred ECCCCCChHHH--HHHHHHHHHHCCCC
Confidence 37788866554 57999999999985
No 42
>PRK11702 hypothetical protein; Provisional
Probab=35.67 E-value=1.9e+02 Score=21.90 Aligned_cols=66 Identities=18% Similarity=0.323 Sum_probs=42.8
Q ss_pred chHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 110 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
.+.+..-+...|++.|.|---+.||.- ...++ |.|...-.|.|. ..-+..|+.=|+.+ ++++|+..
T Consensus 35 ~e~~D~~vD~fIde~Ie~ngL~f~G~G-~~~~e---G~vc~~~~gs~t------Ee~R~~V~~WL~~r--~v~~v~vs 100 (108)
T PRK11702 35 EEQIDATVDAFIDEVIEPNGLAFDGSG-YLAWE---GLICLQKIGKCT------EEHRALVKKWLEGR--KLTDVEVS 100 (108)
T ss_pred HHHHHHHHHHHHHHHHhcCCceecCCc-ceeEE---EEEeecccCCCC------HHHHHHHHHHHHhC--CCceEEee
Confidence 345566677777767777644444432 22333 677766667664 56677899999998 88888753
No 43
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=35.58 E-value=43 Score=24.86 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=15.8
Q ss_pred hhhcCCCEEEEEEecCCCEEEEEeccC
Q 028908 129 VQDDGGDIEYRGFDPETGTVKLRMQGA 155 (202)
Q Consensus 129 l~~dGGdiel~~~d~~~g~v~v~l~Ga 155 (202)
++.+| +|.+++|..++..-+|||..+
T Consensus 22 f~~~g-~V~yVD~~~G~~~g~VRf~~~ 47 (105)
T PF08777_consen 22 FSQFG-EVAYVDFSRGDTEGYVRFKTP 47 (105)
T ss_dssp T-SS---EEEEE--TT-SEEEEEESS-
T ss_pred HHhcC-CcceEEecCCCCEEEEEECCc
Confidence 33344 999999998778999999875
No 44
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=33.27 E-value=95 Score=26.88 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=22.8
Q ss_pred EEEEeccCCCCCcchHHHHHHHHHHHHHhh
Q 028908 148 VKLRMQGACSGCPSSSVTLKSGIENMLMHY 177 (202)
Q Consensus 148 v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~ 177 (202)
.++.| ++|+||-.|-.-|..++-..|..+
T Consensus 7 a~~~L-~gC~GC~~slldl~E~L~dll~~~ 35 (247)
T COG1941 7 ATVWL-TGCSGCHMSLLDLYEKLLDLLEDA 35 (247)
T ss_pred EEEEe-ccccchHHHHHhHHHHHHHhhhhh
Confidence 34444 469999999999999998888844
No 45
>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=32.99 E-value=1.1e+02 Score=21.63 Aligned_cols=34 Identities=12% Similarity=0.290 Sum_probs=18.8
Q ss_pred ccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecCCcc
Q 028908 153 QGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAE 191 (202)
Q Consensus 153 ~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~~ 191 (202)
+..|..||....- ++ .|.+..|.++-.....++.
T Consensus 21 ~~~C~~C~~~~~~----~~-~l~~~~~~i~~~~vd~~~~ 54 (89)
T cd03026 21 SLSCHNCPDVVQA----LN-LMAVLNPNIEHEMIDGALF 54 (89)
T ss_pred CCCCCCcHHHHHH----HH-HHHHHCCCceEEEEEhHhC
Confidence 3679999865433 33 3334568776444433333
No 46
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=30.59 E-value=89 Score=24.27 Aligned_cols=52 Identities=17% Similarity=0.337 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcc
Q 028908 112 ETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVK 182 (202)
Q Consensus 112 ~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~ 182 (202)
+-+.+|-+-|...+..-....||.|.+..- ...|.+|. .|-..++..+|.|+
T Consensus 75 DsE~KiL~~ia~~l~~~~~~~~G~i~l~te-----------~~pC~SC~--------~vi~qF~~~~pni~ 126 (133)
T PF14424_consen 75 DSEYKILEDIAKKLGDNPDPSGGTIDLFTE-----------LPPCESCS--------NVIEQFKKDFPNIK 126 (133)
T ss_pred cHHHHHHHHHHHHhccccccCCceEEEEec-----------CCcChhHH--------HHHHHHHHHCCCcE
Confidence 345666666666776655555677766432 24777775 24445666789886
No 47
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=29.79 E-value=91 Score=20.92 Aligned_cols=41 Identities=24% Similarity=0.217 Sum_probs=31.9
Q ss_pred HHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEecc
Q 028908 114 VAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQG 154 (202)
Q Consensus 114 ~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~G 154 (202)
.+|++++++....--+.=.|=-|=+.++|+++++++|...+
T Consensus 3 ~~RAkeI~~S~~~i~V~y~G~pV~Ie~vde~~~tA~V~~l~ 43 (58)
T PF08141_consen 3 VQRAKEIAESPDMIEVTYNGVPVWIEHVDEENGTARVHPLD 43 (58)
T ss_pred HHHHHHHHcCCceEEEEECCEEEEEEEEcCCCCeEEEEECC
Confidence 46788888866555566667778888899889999999874
No 48
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=29.75 E-value=87 Score=23.83 Aligned_cols=59 Identities=17% Similarity=0.290 Sum_probs=29.5
Q ss_pred cCCCEEEEEEecCCCEEEEEecc--CCCCCcchHHHHHHHHHHHHHhhCCCcceEEecCCcchHHH
Q 028908 132 DGGDIEYRGFDPETGTVKLRMQG--ACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAEDEVA 195 (202)
Q Consensus 132 dGGdiel~~~d~~~g~v~v~l~G--aC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~~~~~~ 195 (202)
+|..+.+..+. +..+.|-+-+ -|..|+.....+.+ ..+.++. ..+.-|-...|..++.+
T Consensus 19 ~G~~~~l~~~~--gk~~ll~f~~~~~~p~C~~~~~~l~~-~~~~~~~--~~v~vi~Is~d~~~~~~ 79 (154)
T PRK09437 19 DGEQVSLTDFQ--GQRVLVYFYPKAMTPGCTVQACGLRD-NMDELKK--AGVVVLGISTDKPEKLS 79 (154)
T ss_pred CCCEEeHHHhC--CCCEEEEEECCCCCCchHHHHHHHHH-HHHHHHH--CCCEEEEEcCCCHHHHH
Confidence 45556665554 4455555643 36678876655533 3333443 23443334444444433
No 49
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=28.71 E-value=1.4e+02 Score=21.88 Aligned_cols=61 Identities=13% Similarity=0.243 Sum_probs=33.2
Q ss_pred cCCCEEEEEEecCCCEEEEEe--ccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecCCcchHHHhh
Q 028908 132 DGGDIEYRGFDPETGTVKLRM--QGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAEDEVATL 197 (202)
Q Consensus 132 dGGdiel~~~d~~~g~v~v~l--~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~~~~~~~~ 197 (202)
+|..+.+..+. +..+.|-+ ..-|..|+.....|.. +.+.++. ..+.-|-...+..+..+..
T Consensus 11 ~g~~~~l~~~~--gk~~ll~f~~~~~c~~C~~~~~~l~~-~~~~~~~--~~~~~i~is~d~~~~~~~~ 73 (140)
T cd02971 11 DGGEVSLSDFK--GKWVVLFFYPKDFTPVCTTELCAFRD-LAEEFAK--GGAEVLGVSVDSPFSHKAW 73 (140)
T ss_pred CCcEEehHHhC--CCeEEEEEeCCCCCCcCHHHHHHHHH-HHHHHHH--CCCEEEEEeCCCHHHHHHH
Confidence 46667777663 44444444 3568889888766644 3444433 3454444444444444443
No 50
>PF13793 Pribosyltran_N: N-terminal domain of ribose phosphate pyrophosphokinase; PDB: 2JI4_A 1DKU_B 1IBS_B 1DKR_B 3MBI_C 3LRT_B 3LPN_B 3NAG_B 2H07_B 2H06_B ....
Probab=28.62 E-value=49 Score=25.01 Aligned_cols=40 Identities=23% Similarity=0.317 Sum_probs=23.8
Q ss_pred chHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCC
Q 028908 110 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGC 159 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gC 159 (202)
..++.++|.+.|. ..-|.+++..|- +|..+||+.+.+.|+
T Consensus 9 ~~~La~~ia~~L~--------~~~~~~~~~~F~--dGE~~v~i~~~v~g~ 48 (116)
T PF13793_consen 9 SQDLAERIAEALG--------IPLGKVETKRFP--DGETYVRIPESVRGK 48 (116)
T ss_dssp GHHHHHHHHHHTT--------S-EE-EEEEE-T--TS-EEEEESS--TTS
T ss_pred CHHHHHHHHHHhC--------CceeeeEEEEcC--CCCEEEEecccccCC
Confidence 3456666666664 223568888887 799999999876653
No 51
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=27.67 E-value=2e+02 Score=26.80 Aligned_cols=55 Identities=13% Similarity=0.105 Sum_probs=34.1
Q ss_pred HHHhccCCCCeeEEEEeCCeE---------------------EEEecCCCChhhhhHHHHHHHHHHHhcCCCCccch
Q 028908 41 LAKSLYGVDGITRVFFGSDFI---------------------TVTKSEDTSWDLLKPEIFAAIMDFYSSGQPLFLDS 96 (202)
Q Consensus 41 La~~Lf~i~gV~~Vf~~~dfI---------------------tVtk~~~~~W~~l~~~I~~~I~d~l~sG~pvv~~~ 96 (202)
+...|-+||+|+.+-++.+.- .|.-+-+. ..++-++++++|.....+|-++....
T Consensus 177 iL~~L~~IphV~~IRI~TR~pvv~P~RIT~ell~~Lk~~~~~~v~~h~nh-p~Eit~~a~~Al~~L~~aGI~l~nQs 252 (417)
T TIGR03820 177 ILTELRAIPHVEVIRIGTRVPVVLPQRITDELVAILKKHHPVWLNTHFNH-PREITASSKKALAKLADAGIPLGNQS 252 (417)
T ss_pred HHHHHhhcCCCceEEEeeccccccccccCHHHHHHHHhcCCeEEEEeCCC-hHhChHHHHHHHHHHHHcCCEEEeec
Confidence 355666788888777775522 22111122 25678888888888888887665544
No 52
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=27.06 E-value=2.6e+02 Score=28.95 Aligned_cols=114 Identities=17% Similarity=0.300 Sum_probs=68.1
Q ss_pred CcHHHHhccCCCCeeEEEEe----CCeEEEEecCCCChhhhhHHHHHHHHHH---HhcCC---CCccchhhhh--hhccc
Q 028908 38 NSPLAKSLYGVDGITRVFFG----SDFITVTKSEDTSWDLLKPEIFAAIMDF---YSSGQ---PLFLDSETAA--AKDTA 105 (202)
Q Consensus 38 ~spLa~~Lf~i~gV~~Vf~~----~dfItVtk~~~~~W~~l~~~I~~~I~d~---l~sG~---pvv~~~~~~~--~~~~~ 105 (202)
-.|+=++|-+++||+.+--. ...|+|+-..+.+|+....+|++.|.+. |..+. |++....... ...-.
T Consensus 73 t~piE~~l~~v~gv~~i~S~S~~G~s~i~v~f~~g~d~~~a~~ev~~~i~~~~~~LP~~~~~~p~~~~~~~~~~pv~~~~ 152 (1040)
T PRK10503 73 TAPLERQFGQMSGLKQMSSQSSGGASVITLQFQLTLPLDVAEQEVQAAINAATNLLPSDLPNPPVYSKVNPADPPIMTLA 152 (1040)
T ss_pred HHHHHHHhcCCCCccEEEEEecCCeEEEEEEEECCCChHHHHHHHHHHHHHHHHhCCCccCCCCEEEEeCCCCCceEEEE
Confidence 58999999999999888764 3457788888889888888888888764 33221 2222110000 00000
Q ss_pred CCCCchHHHHHHHHHHHhccchhhhhcCCCEEEEEEecC-CCEEEEEec
Q 028908 106 INEDDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPE-TGTVKLRMQ 153 (202)
Q Consensus 106 ~~~~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~-~g~v~v~l~ 153 (202)
...+ ..-...++++.+++|+|.|..--| +.-+.+... ...+.|.+-
T Consensus 153 l~~~-~~~~~~L~~~~~~~l~~~L~~i~g-V~~V~~~G~~~~ei~V~vd 199 (1040)
T PRK10503 153 VTST-AMPMTQVEDMVETRVAQKISQVSG-VGLVTLSGGQRPAVRVKLN 199 (1040)
T ss_pred EEcC-CCCHHHHHHHHHHHHHHHhcCCCC-ceEEEecCCCceEEEEEEC
Confidence 1111 112356778888889999998877 333334311 235777773
No 53
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=25.68 E-value=1.3e+02 Score=20.38 Aligned_cols=60 Identities=18% Similarity=0.337 Sum_probs=31.0
Q ss_pred cCCCEEEEEEecCCCEEEEEe-ccCCCCCcchHHHHHHHHHHHHHhh-CCCcceEEecCCc--chHHHhh
Q 028908 132 DGGDIEYRGFDPETGTVKLRM-QGACSGCPSSSVTLKSGIENMLMHY-VPEVKSVEQELDA--EDEVATL 197 (202)
Q Consensus 132 dGGdiel~~~d~~~g~v~v~l-~GaC~gCpss~~Tl~~~Ie~~l~~~-~Pev~~V~~~~~~--~~~~~~~ 197 (202)
+|..+.+.++. +..+.|-+ ...|..|......+.. ..+++ -+.+.-+....+. .++++..
T Consensus 8 ~g~~~~~~~~~--~k~~ll~f~~~~C~~C~~~~~~l~~----~~~~~~~~~~~~~~v~~d~~~~~~~~~~ 71 (116)
T cd02966 8 DGKPVSLSDLK--GKVVLVNFWASWCPPCRAEMPELEA----LAKEYKDDGVEVVGVNVDDDDPAAVKAF 71 (116)
T ss_pred CCCEeehHHcC--CCEEEEEeecccChhHHHHhHHHHH----HHHHhCCCCeEEEEEECCCCCHHHHHHH
Confidence 45556665553 34444444 4578888765555543 22222 2666655555555 4444443
No 54
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.37 E-value=56 Score=21.17 Aligned_cols=19 Identities=37% Similarity=0.735 Sum_probs=11.8
Q ss_pred CEEEEEe-ccCCCCCcchHH
Q 028908 146 GTVKLRM-QGACSGCPSSSV 164 (202)
Q Consensus 146 g~v~v~l-~GaC~gCpss~~ 164 (202)
|.+.+++ .|.|+||-+.-.
T Consensus 14 g~~va~v~~~~C~gC~~~l~ 33 (56)
T PF02591_consen 14 GVAVARVEGGTCSGCHMELP 33 (56)
T ss_pred CcEEEEeeCCccCCCCEEcC
Confidence 3334444 379999987543
No 55
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=25.18 E-value=1.2e+02 Score=20.25 Aligned_cols=42 Identities=19% Similarity=0.169 Sum_probs=32.1
Q ss_pred HHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccC
Q 028908 114 VAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGA 155 (202)
Q Consensus 114 ~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~Ga 155 (202)
.+|++++++....--+-=.|=-|-+..+|+++++++|.+.+.
T Consensus 3 ~~RAkeI~~S~~~i~V~Y~G~pV~Ie~vde~~~tA~V~~l~~ 44 (58)
T TIGR02861 3 VQRAKEIAASPEMINVTYKGVPVYIEHVDEQSGTARVYSLDN 44 (58)
T ss_pred HHHHHHHHcCccceEEEECCEEEEEEEEcCCCCeEEEEECCC
Confidence 367888888655555666677788888998889999998763
No 56
>PRK01625 sspH acid-soluble spore protein H; Provisional
Probab=24.56 E-value=1.3e+02 Score=20.23 Aligned_cols=42 Identities=19% Similarity=0.262 Sum_probs=31.7
Q ss_pred HHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccC
Q 028908 114 VAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGA 155 (202)
Q Consensus 114 ~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~Ga 155 (202)
.+|++++++....--+-=+|=-|-+-.+|+++++.+|...+.
T Consensus 3 ~~RAkeI~~S~~~i~V~Y~G~pV~Iq~vde~~~tA~V~~~~~ 44 (59)
T PRK01625 3 VKRVKQILSSSSRIDVTYEGVPVWIESCDEQSGVAQVYDVSN 44 (59)
T ss_pred HHHHHHHHcCCcceEEEECCEEEEEEEEcCCCCeEEEEecCC
Confidence 367788887666666666677788888898889999988753
No 57
>TIGR03421 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set.
Probab=24.54 E-value=1.9e+02 Score=21.44 Aligned_cols=31 Identities=23% Similarity=0.483 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEec
Q 028908 112 ETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQ 153 (202)
Q Consensus 112 ~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~ 153 (202)
.+..+|++.|+ ..+.|+++ +..+|+++|.+.
T Consensus 11 ~~l~~ie~~ld--------~~~~d~D~---e~~~gVLti~f~ 41 (102)
T TIGR03421 11 ALLDAIEEAID--------DADADIDC---ERAGGVLTLTFE 41 (102)
T ss_pred HHHHHHHHHHh--------ccCCCeee---ecCCCEEEEEEC
Confidence 34455555555 34555544 223677777774
No 58
>COG5429 Uncharacterized secreted protein [Function unknown]
Probab=24.40 E-value=60 Score=28.13 Aligned_cols=24 Identities=33% Similarity=0.685 Sum_probs=18.7
Q ss_pred CCEEEEEeccCCCCCcchHHHHHH
Q 028908 145 TGTVKLRMQGACSGCPSSSVTLKS 168 (202)
Q Consensus 145 ~g~v~v~l~GaC~gCpss~~Tl~~ 168 (202)
-++|.|--+-.|++||-++.-|..
T Consensus 42 ~~VVELfTSQGCsSCPPAd~~l~k 65 (261)
T COG5429 42 LGVVELFTSQGCSSCPPADANLAK 65 (261)
T ss_pred ceEEEEeecCCcCCCChHHHHHHH
Confidence 356777778899999999977654
No 59
>PRK03174 sspH acid-soluble spore protein H; Provisional
Probab=23.83 E-value=1.4e+02 Score=20.17 Aligned_cols=41 Identities=20% Similarity=0.219 Sum_probs=31.4
Q ss_pred HHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEecc
Q 028908 114 VAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQG 154 (202)
Q Consensus 114 ~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~G 154 (202)
.+|++++++....--+-=+|=-|=+-.+|+++++++|.+.+
T Consensus 3 ~~RAkeI~~Sp~~i~VtY~G~pV~Ie~vde~~~tA~I~~l~ 43 (59)
T PRK03174 3 TQRAQEIAESPDMANVTYNGVPIYIQHVDEQNGTARIHPLD 43 (59)
T ss_pred HHHHHHHHcCccceEEEECCEEEEEEEEcCCCCeEEEEECC
Confidence 36778888766666666667778888888888999998875
No 60
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=23.66 E-value=69 Score=21.30 Aligned_cols=23 Identities=26% Similarity=0.442 Sum_probs=16.9
Q ss_pred HHHHHHHhccchhhhhcCCCEEEE
Q 028908 116 MIKELLETRIRPAVQDDGGDIEYR 139 (202)
Q Consensus 116 ~i~~~l~~~IrP~l~~dGGdiel~ 139 (202)
..++..+ .+.|.|+.+||.+-..
T Consensus 3 ~~~~Y~~-~~~~~l~~~GG~~l~~ 25 (65)
T PF07045_consen 3 AYQEYRE-AVPPILEKYGGRVLAR 25 (65)
T ss_dssp HHHHHHH-HHHHHHHHTT-EEEEE
T ss_pred HHHHHHH-HHHHHHHHcCCEEEEE
Confidence 4455665 7899999999987766
No 61
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=23.38 E-value=1.2e+02 Score=21.69 Aligned_cols=64 Identities=16% Similarity=0.262 Sum_probs=36.3
Q ss_pred hcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHh-hCCCcceEEecCCcchHHHhhc
Q 028908 131 DDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMH-YVPEVKSVEQELDAEDEVATLA 198 (202)
Q Consensus 131 ~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~-~~Pev~~V~~~~~~~~~~~~~~ 198 (202)
.+|+.+.+-++. +..+.|-+- +...||.+...+.. +++...+ .-..+.-+-...|..++++...
T Consensus 13 ~~g~~~~l~~l~--gk~~vl~f~-~~~~c~~c~~~l~~-l~~~~~~~~~~~~~vi~is~d~~~~~~~~~ 77 (124)
T PF00578_consen 13 SDGKTVSLSDLK--GKPVVLFFW-PTAWCPFCQAELPE-LNELYKKYKDKGVQVIGISTDDPEEIKQFL 77 (124)
T ss_dssp TTSEEEEGGGGT--TSEEEEEEE-STTTSHHHHHHHHH-HHHHHHHHHTTTEEEEEEESSSHHHHHHHH
T ss_pred CCCCEEEHHHHC--CCcEEEEEe-CccCccccccchhH-HHHHhhhhccceEEeeecccccccchhhhh
Confidence 457777777663 445555543 23345555556643 5555544 2346776666677776666543
No 62
>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=22.47 E-value=1.3e+02 Score=20.57 Aligned_cols=33 Identities=21% Similarity=0.523 Sum_probs=22.5
Q ss_pred EEEEeccCCCCCcchHHHHHHHHHHHHHhhCCC-cceEE
Q 028908 148 VKLRMQGACSGCPSSSVTLKSGIENMLMHYVPE-VKSVE 185 (202)
Q Consensus 148 v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pe-v~~V~ 185 (202)
|.|.| |.+|...... ..+++.|...+|+ +.+|.
T Consensus 3 V~IeY---C~~C~~~~~a--~~l~~~l~~~fp~~~~~v~ 36 (76)
T PF10262_consen 3 VTIEY---CTSCGYRPRA--LELAQELLQTFPDRIAEVE 36 (76)
T ss_dssp EEEEE---ETTTTCHHHH--HHHHHHHHHHSTTTCSEEE
T ss_pred EEEEE---CCCCCCHHHH--HHHHHHHHHHCCCcceEEE
Confidence 45554 6677766654 5799999999998 33444
No 63
>cd03015 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric
Probab=22.10 E-value=2.1e+02 Score=22.31 Aligned_cols=52 Identities=12% Similarity=0.154 Sum_probs=28.2
Q ss_pred CEEEEEEecCCCEEEEEec--cCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecCCcc
Q 028908 135 DIEYRGFDPETGTVKLRMQ--GACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDAE 191 (202)
Q Consensus 135 diel~~~d~~~g~v~v~l~--GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~~ 191 (202)
.+.+..+. +..+.|-+. +-|..|+.....|. .+...++. ..+.-|-...|..
T Consensus 21 ~~~l~~~~--Gk~vvl~F~~~~~c~~C~~~l~~l~-~~~~~~~~--~~v~vv~Is~d~~ 74 (173)
T cd03015 21 EISLSDYK--GKWVVLFFYPLDFTFVCPTEIIAFS-DRYEEFKK--LNAEVLGVSTDSH 74 (173)
T ss_pred EEehHHhC--CCEEEEEEECCCCCCcCHHHHHHHH-HHHHHHHH--CCCEEEEEecCCH
Confidence 45555443 456666664 45899999766553 24444433 3454444444443
No 64
>PRK11023 outer membrane lipoprotein; Provisional
Probab=21.85 E-value=3e+02 Score=22.44 Aligned_cols=67 Identities=21% Similarity=0.324 Sum_probs=44.1
Q ss_pred CchHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecC
Q 028908 109 DDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 188 (202)
Q Consensus 109 ~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~ 188 (202)
+|..+..+|+..|.. .|.+.. +.+|.+..++ |.|+| .|.= .+...+...++..+ .+|.|++|....
T Consensus 46 dD~~i~~~V~~aL~~--~~~l~~-~~~I~V~v~~---G~V~L--~G~V-----~~~~~k~~A~~ia~-~v~GV~~V~N~l 111 (191)
T PRK11023 46 DDGTLELRVNNALSK--DEQIKK-EARINVTAYQ---GKVLL--TGQS-----PNAELSERAKQIAM-GVEGVNEVYNEI 111 (191)
T ss_pred hhHHHHHHHHHHHhh--CcccCc-CceEEEEEEC---CEEEE--EEEe-----CCHHHHHHHHHHHh-cCCCceeeccee
Confidence 467788999988864 777754 5678888774 76655 4542 22346666655544 489998887443
Q ss_pred C
Q 028908 189 D 189 (202)
Q Consensus 189 ~ 189 (202)
.
T Consensus 112 ~ 112 (191)
T PRK11023 112 R 112 (191)
T ss_pred e
Confidence 3
No 65
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=21.62 E-value=2.4e+02 Score=20.95 Aligned_cols=34 Identities=21% Similarity=0.379 Sum_probs=19.0
Q ss_pred hHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEecc
Q 028908 111 SETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQG 154 (202)
Q Consensus 111 ~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~G 154 (202)
+++...|++.|++. .+.|+++ +..+|+++|.+.+
T Consensus 11 d~~l~~ie~~ld~~-------~~~d~D~---e~~~gVLti~f~~ 44 (105)
T PRK00446 11 DALWQAIEEQLDDD-------GDADIDC---ERNGGVLTLTFEN 44 (105)
T ss_pred HHHHHHHHHHHHhc-------cCCCeee---eccCCEEEEEECC
Confidence 44556666666631 3445443 2336788887753
No 66
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=21.32 E-value=1.6e+02 Score=21.86 Aligned_cols=34 Identities=18% Similarity=0.317 Sum_probs=19.8
Q ss_pred cCCCEEEEEEecCC-CEEEEEec--cCCCCCcchHHHHH
Q 028908 132 DGGDIEYRGFDPET-GTVKLRMQ--GACSGCPSSSVTLK 167 (202)
Q Consensus 132 dGGdiel~~~d~~~-g~v~v~l~--GaC~gCpss~~Tl~ 167 (202)
+|..+.+-.+. + +.+.|-+- .-|..|+.....+.
T Consensus 16 ~g~~v~l~~~~--g~k~~vl~f~~~~~c~~C~~~~~~l~ 52 (149)
T cd03018 16 NGQEVRLSEFR--GRKPVVLVFFPLAFTPVCTKELCALR 52 (149)
T ss_pred CCCEEeHHHHc--CCCeEEEEEeCCCCCccHHHHHHHHH
Confidence 46666666554 3 45555553 34888876555553
No 67
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=20.71 E-value=1.3e+02 Score=23.53 Aligned_cols=63 Identities=14% Similarity=0.284 Sum_probs=33.9
Q ss_pred chHHHHHHHHHHHhccchhhhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEecC
Q 028908 110 DSETVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQEL 188 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~ 188 (202)
.+.+..+|...|.. .-+. .+++.+. ++ +|+|+|+ |...+...+..+..+... +|.|+.|...+
T Consensus 24 ~~~~~~~i~~~i~~---~~~~--~~~i~V~-v~--~G~v~l~-------G~v~s~~~~~~~~~aa~~-v~GV~~V~d~l 86 (147)
T PRK11198 24 NEDAADALKEHISK---QGLG--DADVNVQ-VE--DGKATVS-------GDAASQEAKEKILLAVGN-IQGIASVDDQV 86 (147)
T ss_pred hHHHHHHHHHHHHh---cCCC--cCCceEE-Ee--CCEEEEE-------EEeCCHHHHHHHHHHhcc-CCCcceecccc
Confidence 34555666555542 1221 2334332 34 7999985 334444555555555544 78888777543
No 68
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=20.64 E-value=3e+02 Score=28.42 Aligned_cols=113 Identities=17% Similarity=0.237 Sum_probs=58.7
Q ss_pred CcHHHHhccCCCCeeEEEE----eCCeEEEEecCCCC----hhhhhHHHHHHHHHHHhcC---CCCccchhhhh--hhcc
Q 028908 38 NSPLAKSLYGVDGITRVFF----GSDFITVTKSEDTS----WDLLKPEIFAAIMDFYSSG---QPLFLDSETAA--AKDT 104 (202)
Q Consensus 38 ~spLa~~Lf~i~gV~~Vf~----~~dfItVtk~~~~~----W~~l~~~I~~~I~d~l~sG---~pvv~~~~~~~--~~~~ 104 (202)
..|+=++|-+++||+.+-- +.-.|+++-+.+.+ |.+++..|-++. +.|..+ .|.+....... ....
T Consensus 64 t~piE~~l~~i~gv~~i~S~s~~G~s~i~l~f~~~~d~~~a~~~v~~~v~~~~-~~LP~~~~~~p~~~~~~~~~~pv~~~ 142 (1025)
T PRK10614 64 ATPLERSLGRIAGVNEMTSSSSLGSTRIILQFDFDRDINGAARDVQAAINAAQ-SLLPSGMPSRPTYRKANPSDAPIMIL 142 (1025)
T ss_pred HHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECCCChHHHHHHHHHHHHHHH-hhCCCccCCCCEEEecCCCccceeEE
Confidence 5788888999999999842 33556666666665 555555543322 223222 23222110000 0000
Q ss_pred cCCCCchHHHHHHHHHHHhccchhhhhcCCCEEEEEEec-CCCEEEEEec
Q 028908 105 AINEDDSETVAMIKELLETRIRPAVQDDGGDIEYRGFDP-ETGTVKLRMQ 153 (202)
Q Consensus 105 ~~~~~~~~~~~~i~~~l~~~IrP~l~~dGGdiel~~~d~-~~g~v~v~l~ 153 (202)
.... ++.-...++++.++.++|.|+.--|--++. +.. ....++|++.
T Consensus 143 ~~~~-~~~~~~~L~~~~~~~l~~~L~~i~GV~~V~-~~G~~~~ei~V~vd 190 (1025)
T PRK10614 143 TLTS-DTYSQGQLYDFASTQLAQTISQIDGVGDVD-VGGSSLPAVRVGLN 190 (1025)
T ss_pred EEEc-CCCCHHHHHHHHHHHHHHHhcCCCCceEEE-ecCCCceEEEEEeC
Confidence 0111 111234667777778899999887744433 321 1235777763
No 69
>COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism]
Probab=20.42 E-value=3.6e+02 Score=24.79 Aligned_cols=87 Identities=18% Similarity=0.268 Sum_probs=53.6
Q ss_pred cHHHHhccCCCCeeEEEEeCCeEEEEecC-------------C--------CChhhhhHHHHHHHHHHHhcCCCCccchh
Q 028908 39 SPLAKSLYGVDGITRVFFGSDFITVTKSE-------------D--------TSWDLLKPEIFAAIMDFYSSGQPLFLDSE 97 (202)
Q Consensus 39 spLa~~Lf~i~gV~~Vf~~~dfItVtk~~-------------~--------~~W~~l~~~I~~~I~d~l~sG~pvv~~~~ 97 (202)
..|..+|.+||.|+.|=|+..-..|.-.- . ..-.+|.++.+++.......|-++.++..
T Consensus 178 ~~ll~~L~~IpHv~iiRi~TR~pvv~P~RIt~~L~~~l~~~~~~v~~~tH~NHp~Eit~e~~~A~~~L~~aGv~l~NQsV 257 (369)
T COG1509 178 EWLLKRLRAIPHVKIIRIGTRLPVVLPQRITDELCEILGKSRKPVWLVTHFNHPNEITPEAREACAKLRDAGVPLLNQSV 257 (369)
T ss_pred HHHHHHHhcCCceeEEEeecccceechhhccHHHHHHHhccCceEEEEcccCChhhcCHHHHHHHHHHHHcCceeecchh
Confidence 45788999999999999997655443211 0 12345555565555555555655555442
Q ss_pred hhhhhcccCCCCchHHHHHHHHHHHhccchhh
Q 028908 98 TAAAKDTAINEDDSETVAMIKELLETRIRPAV 129 (202)
Q Consensus 98 ~~~~~~~~~~~~~~~~~~~i~~~l~~~IrP~l 129 (202)
.. -.++++.+-+.+..+++.+..|+|+=
T Consensus 258 LL----rGVND~~evl~~L~~~L~~~gV~PYY 285 (369)
T COG1509 258 LL----RGVNDDPEVLKELSRALFDAGVKPYY 285 (369)
T ss_pred ee----cccCCCHHHHHHHHHHHHHcCCcceE
Confidence 11 11344455556777888888899975
No 70
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=20.39 E-value=2.2e+02 Score=21.17 Aligned_cols=53 Identities=8% Similarity=0.147 Sum_probs=28.5
Q ss_pred hcCCCEEEEEEecCCCEEEEE-eccC-CCCCcchHHHHHHHHHHHHHhhCCCcceEEecCCc
Q 028908 131 DDGGDIEYRGFDPETGTVKLR-MQGA-CSGCPSSSVTLKSGIENMLMHYVPEVKSVEQELDA 190 (202)
Q Consensus 131 ~dGGdiel~~~d~~~g~v~v~-l~Ga-C~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~~~~ 190 (202)
.+|+.+.+..+. ++.+.|- +.+. |..|......|. +..++ ++++.-|-...|.
T Consensus 14 ~~g~~~~l~~~~--gk~vvl~f~~~~~c~~C~~e~~~l~----~~~~~-~~~~~vi~Is~d~ 68 (143)
T cd03014 14 SDLSEVSLADFA--GKVKVISVFPSIDTPVCATQTKRFN----KEAAK-LDNTVVLTISADL 68 (143)
T ss_pred CCCcEEeHHHhC--CCeEEEEEEcCCCCCcCHHHHHHHH----HHHHh-cCCCEEEEEECCC
Confidence 346667776664 4444444 4667 577877654443 33333 4666544444443
No 71
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=20.33 E-value=3.7e+02 Score=20.02 Aligned_cols=65 Identities=28% Similarity=0.524 Sum_probs=42.0
Q ss_pred chHHHHHHHHHHHhccchh-hhhcCCCEEEEEEecCCCEEEEEeccCCCCCcchHHHHHHHHHHHHHhhCCCcceEEec
Q 028908 110 DSETVAMIKELLETRIRPA-VQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSVEQE 187 (202)
Q Consensus 110 ~~~~~~~i~~~l~~~IrP~-l~~dGGdiel~~~d~~~g~v~v~l~GaC~gCpss~~Tl~~~Ie~~l~~~~Pev~~V~~~ 187 (202)
.++.-.-+.+.|+ .|.|. |.-+||+ ...++ |.|...-.|.|. ..-+..|+.-|.. -|++.+|+..
T Consensus 29 ~e~~D~~~D~fId-~Ie~~gL~~~Ggg--~~~~e---G~vc~~~~gs~t------ee~R~~v~~WL~~-~~ev~~v~vs 94 (101)
T PF04320_consen 29 EEQIDAFVDAFID-VIEPNGLAFGGGG--YEQWE---GFVCLQRYGSCT------EEDRAAVEAWLKA-RPEVSDVEVS 94 (101)
T ss_pred HHHHHHHHHHHHH-HHHhCCCEEecCC--ccCEe---EEEEeccCCCCC------HHHHHHHHHHHHh-CCCcceEEec
Confidence 4555566667776 66664 3444444 33343 777777667664 5666778888877 6888888753
Done!