Query 030084
Match_columns 183
No_of_seqs 162 out of 1069
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 08:16:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0694 Thioredoxin-like prote 99.9 1.3E-25 2.9E-30 169.8 9.1 80 75-155 7-89 (93)
2 PF01106 NifU: NifU-like domai 99.9 3.7E-25 8E-30 157.3 8.6 68 82-150 1-68 (68)
3 TIGR03341 YhgI_GntY IscR-regul 99.9 5.5E-24 1.2E-28 176.9 10.4 81 76-157 104-186 (190)
4 PRK11190 Fe/S biogenesis prote 99.9 4E-24 8.7E-29 178.3 9.1 81 77-157 106-188 (192)
5 KOG2358 NifU-like domain-conta 99.8 3.7E-22 8.1E-27 169.2 1.1 154 6-161 44-209 (213)
6 TIGR02000 NifU_proper Fe-S clu 99.8 1.6E-20 3.4E-25 164.8 10.1 71 78-150 220-290 (290)
7 KOG2358 NifU-like domain-conta 98.6 2.2E-08 4.8E-13 85.7 3.6 105 75-179 75-179 (213)
8 PF01883 DUF59: Domain of unkn 93.8 0.41 9E-06 33.1 6.9 65 80-147 2-70 (72)
9 TIGR02159 PA_CoA_Oxy4 phenylac 89.8 1.9 4.1E-05 35.0 7.5 73 97-173 14-86 (146)
10 TIGR02945 SUF_assoc FeS assemb 88.0 4.4 9.6E-05 29.6 7.8 66 79-147 3-73 (99)
11 PF07315 DUF1462: Protein of u 85.5 2.3 4.9E-05 32.8 5.2 52 117-170 11-62 (93)
12 PRK10862 SoxR reducing system 76.0 3.5 7.7E-05 33.4 3.6 26 100-125 6-33 (154)
13 PF04246 RseC_MucC: Positive r 73.9 3.1 6.8E-05 32.2 2.7 24 102-125 1-26 (135)
14 COG1941 FrhG Coenzyme F420-red 71.9 9.5 0.00021 34.0 5.4 29 109-138 6-34 (247)
15 COG2151 PaaD Predicted metal-s 71.3 18 0.00038 28.4 6.3 70 76-148 11-86 (111)
16 TIGR02000 NifU_proper Fe-S clu 65.9 11 0.00024 33.7 4.7 67 115-182 166-243 (290)
17 cd02966 TlpA_like_family TlpA- 64.7 28 0.0006 23.5 5.6 66 96-170 8-75 (116)
18 COG4837 Uncharacterized protei 63.1 14 0.00031 29.0 4.3 52 117-170 18-69 (106)
19 PF09012 FeoC: FeoC like trans 55.5 16 0.00035 25.2 3.2 44 75-128 24-67 (69)
20 PF02061 Lambda_CIII: Lambda P 54.8 16 0.00034 24.8 2.8 26 115-140 7-32 (45)
21 PRK12933 secD preprotein trans 49.5 1.1E+02 0.0024 30.5 8.9 94 77-182 147-251 (604)
22 TIGR03406 FeS_long_SufT probab 48.3 1E+02 0.0022 25.7 7.4 68 77-147 73-149 (174)
23 PRK11670 antiporter inner memb 37.6 1.5E+02 0.0032 27.1 7.3 68 77-147 12-83 (369)
24 PF11718 CPSF73-100_C: Pre-mRN 36.0 1.8E+02 0.004 24.7 7.2 38 101-140 173-210 (216)
25 PRK02114 formylmethanofuran--t 35.2 30 0.00064 31.7 2.3 55 117-181 220-285 (297)
26 cd03018 PRX_AhpE_like Peroxire 35.0 38 0.00082 25.3 2.6 34 96-129 16-52 (149)
27 PF08777 RRM_3: RNA binding mo 34.9 51 0.0011 25.0 3.3 30 87-117 16-47 (105)
28 cd02967 mauD Methylamine utili 34.7 1.6E+02 0.0036 20.7 6.3 35 95-129 8-44 (114)
29 PF04865 Baseplate_J: Baseplat 34.7 1.1E+02 0.0024 25.4 5.5 62 77-142 164-227 (243)
30 cd03377 TPP_PFOR_PNO Thiamine 33.9 16 0.00034 34.1 0.4 14 112-125 3-16 (365)
31 PF01545 Cation_efflux: Cation 32.9 2.4E+02 0.0053 23.5 7.4 58 87-147 208-274 (284)
32 TIGR03119 one_C_fhcD formylmet 32.0 41 0.0009 30.7 2.7 54 117-181 213-277 (287)
33 CHL00123 rps6 ribosomal protei 31.7 41 0.00089 25.2 2.3 26 156-181 16-41 (97)
34 COG3086 RseC Positive regulato 31.0 53 0.0011 27.4 3.0 35 101-136 7-43 (150)
35 PRK14454 ribosomal RNA large s 30.9 2.3E+02 0.005 25.8 7.4 76 96-172 86-176 (342)
36 PF13192 Thioredoxin_3: Thiore 30.8 51 0.0011 22.8 2.5 25 109-138 2-26 (76)
37 PF07045 DUF1330: Protein of u 30.7 1.3E+02 0.0029 20.4 4.6 24 80-103 2-25 (65)
38 PF00274 Glycolytic: Fructose- 30.1 3E+02 0.0065 25.8 8.0 90 75-173 184-275 (348)
39 PRK11325 scaffold protein; Pro 29.4 71 0.0015 24.9 3.4 37 97-135 38-77 (127)
40 TIGR01999 iscU FeS cluster ass 29.1 73 0.0016 24.6 3.4 37 97-135 36-75 (124)
41 TIGR00532 HMG_CoA_R_NAD hydrox 29.1 2.6E+02 0.0057 26.4 7.5 64 79-142 143-214 (393)
42 TIGR03421 FeS_CyaY iron donor 28.2 1.3E+02 0.0029 22.9 4.6 34 81-115 8-41 (102)
43 PRK14726 bifunctional preprote 27.3 3.6E+02 0.0077 28.1 8.7 95 76-182 65-182 (855)
44 PRK11688 hypothetical protein; 27.2 1.7E+02 0.0037 22.9 5.2 44 76-121 7-50 (154)
45 PF10262 Rdx: Rdx family; Int 26.7 94 0.002 21.8 3.3 34 110-148 3-36 (76)
46 PRK00446 cyaY frataxin-like pr 26.5 1.6E+02 0.0034 22.7 4.7 35 81-116 9-44 (105)
47 PF04468 PSP1: PSP1 C-terminal 26.4 1.6E+02 0.0035 21.6 4.6 54 75-134 17-74 (88)
48 COG0342 SecD Preprotein transl 25.4 2.3E+02 0.0049 27.5 6.6 97 77-183 58-154 (506)
49 PRK14565 triosephosphate isome 24.7 1.7E+02 0.0036 25.7 5.1 55 127-182 136-199 (237)
50 PF01250 Ribosomal_S6: Ribosom 24.0 59 0.0013 23.4 1.9 26 156-181 11-36 (92)
51 PLN00107 FAD-dependent oxidore 23.9 1.6E+02 0.0035 26.4 5.0 68 18-96 17-88 (257)
52 smart00044 CYCc Adenylyl- / gu 23.7 1.8E+02 0.0038 22.8 4.7 41 75-117 56-96 (194)
53 PF01591 6PF2K: 6-phosphofruct 23.3 84 0.0018 27.1 3.0 36 71-106 69-104 (222)
54 cd06927 RNAP_L L subunit of Ar 22.5 3.2E+02 0.0069 20.0 6.4 69 100-175 1-79 (83)
55 PF00121 TIM: Triosephosphate 22.1 60 0.0013 28.2 1.9 52 130-181 138-211 (244)
56 PRK00453 rpsF 30S ribosomal pr 22.1 78 0.0017 23.7 2.3 26 156-181 12-37 (108)
57 COG2946 Putative phage replica 22.0 2.9E+02 0.0063 26.3 6.4 61 107-169 127-187 (377)
58 PRK09437 bcp thioredoxin-depen 22.0 70 0.0015 24.3 2.1 34 96-129 19-54 (154)
59 PF00403 HMA: Heavy-metal-asso 22.0 1.3E+02 0.0029 19.4 3.2 45 116-169 7-58 (62)
60 PF13793 Pribosyltran_N: N-ter 21.6 1.1E+02 0.0024 23.6 3.1 35 87-121 14-48 (116)
61 PRK13022 secF preprotein trans 21.4 5E+02 0.011 22.9 7.6 38 98-142 68-106 (289)
62 TIGR02174 CXXU_selWTH selT/sel 21.1 1.2E+02 0.0026 21.3 3.0 23 118-142 6-28 (72)
63 PF08534 Redoxin: Redoxin; In 21.1 37 0.0008 25.4 0.3 34 95-128 16-51 (146)
64 PF02741 FTR_C: FTR, proximal 20.5 99 0.0021 25.8 2.7 55 117-181 75-140 (150)
65 PRK14965 DNA polymerase III su 20.5 4.9E+02 0.011 25.3 7.8 66 79-145 450-517 (576)
66 PLN02536 diaminopimelate epime 20.3 1.4E+02 0.0029 26.1 3.7 40 86-125 165-217 (267)
No 1
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=1.3e-25 Score=169.77 Aligned_cols=80 Identities=43% Similarity=0.748 Sum_probs=73.2
Q ss_pred hhchHHHHHHHHH-hhcchhhhCCCcEEEEEee--CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecc
Q 030084 75 FDLTAKNVDLVLE-DVRPYLIADGGNIDVVSVE--DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVY 151 (183)
Q Consensus 75 ~el~~e~Ve~vLe-~IRP~LqsdGGDVELVdVe--dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~ 151 (183)
.....++|+.+|+ +|||+|+.|||||+|++|+ +|+|+|||.|||+|||||++||+++||++|++.+| ++.+|++++
T Consensus 7 ~~~~~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 7 DAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIP-EVKEVEQVT 85 (93)
T ss_pred cHHHHHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCC-ccceEEEcc
Confidence 3445678899985 9999999999999999998 88999999999999999999999999999999999 699999998
Q ss_pred cccc
Q 030084 152 DEEV 155 (183)
Q Consensus 152 d~e~ 155 (183)
++..
T Consensus 86 ~~~~ 89 (93)
T COG0694 86 EHAR 89 (93)
T ss_pred Cccc
Confidence 8754
No 2
>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=3.7e-25 Score=157.32 Aligned_cols=68 Identities=50% Similarity=0.933 Sum_probs=63.2
Q ss_pred HHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084 82 VDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV 150 (183)
Q Consensus 82 Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V 150 (183)
|+.+|++|||+|++||||++|+++++++|+|||+|+|+|||++..||+++||++|++++| ++..|+.|
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 VEEVLEEIRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVP-EVKRVVPV 68 (68)
T ss_dssp HHHHHHHCHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHST-T-SEEEEC
T ss_pred CHHHHHHhChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCC-CCceEEEC
Confidence 678998899999999999999999999999999999999999999999999999999999 57777654
No 3
>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=99.90 E-value=5.5e-24 Score=176.92 Aligned_cols=81 Identities=28% Similarity=0.625 Sum_probs=74.6
Q ss_pred hchHHHHHHHHH-hhcchhhhCCCcEEEEEee-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccc
Q 030084 76 DLTAKNVDLVLE-DVRPYLIADGGNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE 153 (183)
Q Consensus 76 el~~e~Ve~vLe-~IRP~LqsdGGDVELVdVe-dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~ 153 (183)
+.+.++|+.+|+ +|||+|++|||||||++|+ +++|+|||+|+|+|||++.+||+++||++|++++| +|++|+.+++|
T Consensus 104 ~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p-~v~~V~~~~~~ 182 (190)
T TIGR03341 104 APLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFP-ELKGVRDATDH 182 (190)
T ss_pred hHHHHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCC-CcceEEEecCc
Confidence 446788999996 8999999999999999997 57999999999999999999999999999999999 69999999999
Q ss_pred cccc
Q 030084 154 EVRE 157 (183)
Q Consensus 154 e~~e 157 (183)
+...
T Consensus 183 ~~~~ 186 (190)
T TIGR03341 183 TRGE 186 (190)
T ss_pred cccC
Confidence 7643
No 4
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.90 E-value=4e-24 Score=178.28 Aligned_cols=81 Identities=26% Similarity=0.579 Sum_probs=74.9
Q ss_pred chHHHHHHHHH-hhcchhhhCCCcEEEEEee-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccc
Q 030084 77 LTAKNVDLVLE-DVRPYLIADGGNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154 (183)
Q Consensus 77 l~~e~Ve~vLe-~IRP~LqsdGGDVELVdVe-dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e 154 (183)
.+.++|+.+|+ +|||+|++|||||||++|+ +++|+|||+|+|+|||||.+||+++||++|++++|++|++|++|++|.
T Consensus 106 ~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v~~~~ 185 (192)
T PRK11190 106 PLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDLTEHQ 185 (192)
T ss_pred HHHHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEecccc
Confidence 35678999995 9999999999999999997 689999999999999999999999999999999998899999999997
Q ss_pred ccc
Q 030084 155 VRE 157 (183)
Q Consensus 155 ~~e 157 (183)
...
T Consensus 186 ~~~ 188 (192)
T PRK11190 186 RGE 188 (192)
T ss_pred cCC
Confidence 543
No 5
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.84 E-value=3.7e-22 Score=169.23 Aligned_cols=154 Identities=30% Similarity=0.301 Sum_probs=123.1
Q ss_pred cccceeeeecccccCCCCCCccccCccceEEeccCCcceeeccc-eeeecccCCCCC-----CCCCCCCCcc----ccch
Q 030084 6 LTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGS-HETAIRASNPSA-----PAGSSPGLYS----AHQF 75 (183)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-----~~~~~~~l~s----~~~~ 75 (183)
.++.||.+.++ +.++++++++...++.||.+.|++.++..+-. +...+.-+...+ -++....++. ++..
T Consensus 44 ~s~~~s~La~s-~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~ 122 (213)
T KOG2358|consen 44 CSAFFSPLAKS-ILFRDGGVVKVFFGPDFVTVTKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDP 122 (213)
T ss_pred cchhhcHHHHH-HHhhcCCcEEEEecCCeEEEeccchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCCh
Confidence 45667888887 88899999999999999999999995544433 332222222221 1223333333 6667
Q ss_pred hchHHHHHHHHHhhcchhhhCCCcEEEEEeeC--CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccc
Q 030084 76 DLTAKNVDLVLEDVRPYLIADGGNIDVVSVED--GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE 153 (183)
Q Consensus 76 el~~e~Ve~vLe~IRP~LqsdGGDVELVdVed--g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~ 153 (183)
|.+....+.+..+|||.++.||||++++++++ |.|++||+|+|.+||++..||+++||.+|+.++| +|++|+++.|.
T Consensus 123 e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~-eVK~v~qv~d~ 201 (213)
T KOG2358|consen 123 ESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVP-EVKGVIQVPDA 201 (213)
T ss_pred hHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcc-eeeEEEeccCc
Confidence 77777788888999999999999999999998 5999999999999999999999999999999999 89999999999
Q ss_pred ccccccHH
Q 030084 154 EVRETTVE 161 (183)
Q Consensus 154 e~~e~s~E 161 (183)
|.+++..|
T Consensus 202 e~~~v~~e 209 (213)
T KOG2358|consen 202 EVMTVTVE 209 (213)
T ss_pred cceEEeee
Confidence 88777655
No 6
>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=99.83 E-value=1.6e-20 Score=164.82 Aligned_cols=71 Identities=38% Similarity=0.669 Sum_probs=65.5
Q ss_pred hHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084 78 TAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV 150 (183)
Q Consensus 78 ~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V 150 (183)
..++|+.+|++|||+|+.|||||+|++|++++|+|||+|+|+|||++.+||+. ||++|++++| ++..|+.|
T Consensus 220 ~~~~v~~~l~~irP~l~~dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p-~~~~V~~v 290 (290)
T TIGR02000 220 RIQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLG-EFVVVEAV 290 (290)
T ss_pred HHHHHHHHHHHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCC-CceEEEeC
Confidence 34668999999999999999999999999999999999999999999999998 9999999999 57777654
No 7
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=2.2e-08 Score=85.71 Aligned_cols=105 Identities=29% Similarity=0.250 Sum_probs=89.2
Q ss_pred hhchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccc
Q 030084 75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154 (183)
Q Consensus 75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e 154 (183)
+.+++++++.+|...+|++.+|||++-+--+++..+.+++.|+|..||.+++|++.+||..||.++++..-+|..+..+.
T Consensus 75 ~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~ 154 (213)
T KOG2358|consen 75 TKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFET 154 (213)
T ss_pred eccchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccC
Confidence 34566789999999999999999999999999999999999999999999999999999999999996555555554443
Q ss_pred cccccHHHHHHHHHHhhhhhhccCC
Q 030084 155 VRETTVEVSALLLCLISDKRYYYTT 179 (183)
Q Consensus 155 ~~e~s~E~In~al~~Lr~a~~~~~~ 179 (183)
-.++..+.+..|+.-.+.+.-..++
T Consensus 155 g~g~v~lklqgact~cpss~vtlk~ 179 (213)
T KOG2358|consen 155 GLGLVSLKLQGACTECPSSLVTLKN 179 (213)
T ss_pred ccchHHHHHhhhhccCCcccchhhh
Confidence 4589999999999888877655443
No 8
>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=93.77 E-value=0.41 Score=33.08 Aligned_cols=65 Identities=29% Similarity=0.407 Sum_probs=47.5
Q ss_pred HHHHHHH-HhhcchhhhC---CCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084 80 KNVDLVL-EDVRPYLIAD---GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI 147 (183)
Q Consensus 80 e~Ve~vL-e~IRP~Lqsd---GGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V 147 (183)
+.|..+| .-.-|.+..+ =|-|+=+.+++|.|+|.|.-...+|+ ....|+.-|+++|+ .+|. +++|
T Consensus 2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~g-v~~V 70 (72)
T PF01883_consen 2 QAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALPG-VKSV 70 (72)
T ss_dssp HHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT--SEE
T ss_pred HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCC-CceE
Confidence 5567777 3445666544 47788899999999999999999999 77788899999999 5774 5555
No 9
>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=89.83 E-value=1.9 Score=35.02 Aligned_cols=73 Identities=18% Similarity=0.204 Sum_probs=49.7
Q ss_pred CCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHHhhhh
Q 030084 97 GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDK 173 (183)
Q Consensus 97 GGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~Lr~a 173 (183)
=|-|.=++++++.|.|.|.-.=.+||... .|++.|+++|++. + ++.|.-...-.+.=.++=.-++++++||.+
T Consensus 14 LG~Vr~V~v~gd~V~VtIt~Ty~gcpa~e-~L~~~I~~aL~~~-G--v~~V~V~i~~~p~Wt~d~it~~gr~~l~~~ 86 (146)
T TIGR02159 14 LGMVREVDVDGGGVVVKFTPTYSGCPALE-VIRQDIRDAVRAL-G--VEVVEVSTSLDPPWTTDWITEDAREKLREY 86 (146)
T ss_pred cCCeeEEEEECCEEEEEEEeCCCCCchHH-HHHHHHHHHHHhc-C--CCeEEEeEeeCCCCChHHCCHHHHHHHHhc
Confidence 36677778888999999998889999655 7888999999883 4 555533222223344444455667777653
No 10
>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=87.97 E-value=4.4 Score=29.63 Aligned_cols=66 Identities=20% Similarity=0.330 Sum_probs=44.8
Q ss_pred HHHHHHHHH-hhcchhhhC---CCcEEEEEeeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084 79 AKNVDLVLE-DVRPYLIAD---GGNIDVVSVED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI 147 (183)
Q Consensus 79 ~e~Ve~vLe-~IRP~Lqsd---GGDVELVdVed-g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V 147 (183)
.+.|..+|+ -.-|.+..+ =|-|.=+.+++ +.|+|.|.-...+|+.... ++..++++|.. ++ .++.|
T Consensus 3 ~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~~~-l~~~i~~al~~-l~-gv~~v 73 (99)
T TIGR02945 3 KDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGS-MPGEVENAVRA-VP-GVGSV 73 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHH-HHHHHHHHHHh-CC-CCceE
Confidence 456777774 444555542 34555567775 8999999988888886554 77888888876 55 35655
No 11
>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=85.52 E-value=2.3 Score=32.84 Aligned_cols=52 Identities=23% Similarity=0.245 Sum_probs=30.9
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHHh
Q 030084 117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLI 170 (183)
Q Consensus 117 ACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~L 170 (183)
+|.+=|||..|. .++|.+|++++|+.--.+.-|+-+++.+- ++.-+-+.+|+
T Consensus 11 SCVn~PsSkeTy-eWL~aal~RKyp~~~f~~~YiDi~~p~~~-~~~~~~a~~I~ 62 (93)
T PF07315_consen 11 SCVNAPSSKETY-EWLEAALKRKYPDQPFEFTYIDIENPPEN-DHDQQFAERIL 62 (93)
T ss_dssp GGSSS--HHHHH-HHHHHHHHHH-TTS-EEEEEEETTT-----HHHHHHHHHHH
T ss_pred hhcCCCCchhHH-HHHHHHHhCcCCCCceEEEEEecCCCCcc-HHHHHHHHHHH
Confidence 455668899998 79999999999975456666765554333 44444454544
No 12
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=76.02 E-value=3.5 Score=33.44 Aligned_cols=26 Identities=31% Similarity=0.659 Sum_probs=20.4
Q ss_pred EEEEEeeCCEEEEEEc--ccCCCCcchH
Q 030084 100 IDVVSVEDGVVSVKLQ--GACGSCPSST 125 (183)
Q Consensus 100 VELVdVedg~V~VrL~--GACsGCpsS~ 125 (183)
-.+++++++.++|+.. .+|++|.+..
T Consensus 6 ~~Vv~v~~~~a~Ve~~r~saCg~C~a~~ 33 (154)
T PRK10862 6 ATVVSWQNGIALLRCEVKAGCSSCASRA 33 (154)
T ss_pred EEEEEEECCEEEEEEecCCCCcCcCCCC
Confidence 3678999998777765 8999998753
No 13
>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=73.87 E-value=3.1 Score=32.24 Aligned_cols=24 Identities=54% Similarity=0.941 Sum_probs=18.3
Q ss_pred EEEeeCCEEEEEEc--ccCCCCcchH
Q 030084 102 VVSVEDGVVSVKLQ--GACGSCPSST 125 (183)
Q Consensus 102 LVdVedg~V~VrL~--GACsGCpsS~ 125 (183)
+++++++.++|+.. .+|++|.++.
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C~~~~ 26 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSCSASG 26 (135)
T ss_pred CEEEeCCEEEEEEccCCcCcccCCCC
Confidence 47889998888874 7888887433
No 14
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=71.87 E-value=9.5 Score=34.02 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=23.2
Q ss_pred EEEEEEcccCCCCcchHHHHHHHHHHHHHH
Q 030084 109 VVSVKLQGACGSCPSSTTTMSMGIERVLKE 138 (183)
Q Consensus 109 ~V~VrL~GACsGCpsS~~TLk~~IE~~Lre 138 (183)
+.++.|.| |+||.+|-.-|....-..+..
T Consensus 6 va~~~L~g-C~GC~~slldl~E~L~dll~~ 34 (247)
T COG1941 6 VATVWLTG-CSGCHMSLLDLYEKLLDLLED 34 (247)
T ss_pred EEEEEecc-ccchHHHHHhHHHHHHHhhhh
Confidence 44666666 999999999999888877773
No 15
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=71.29 E-value=18 Score=28.45 Aligned_cols=70 Identities=24% Similarity=0.395 Sum_probs=46.9
Q ss_pred hchHHHHHHHH-HhhcchhhhC---CCcEEEEEee--CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHcccccccee
Q 030084 76 DLTAKNVDLVL-EDVRPYLIAD---GGNIDVVSVE--DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIR 148 (183)
Q Consensus 76 el~~e~Ve~vL-e~IRP~Lqsd---GGDVELVdVe--dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~ 148 (183)
+.+.+.|-.+| .-+-|.|--| =|=|.=++++ ++.++|+|+..=.|||++..=. .-|+.+|++ ++ .+++|+
T Consensus 11 ~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~-~~v~~al~~-~~-~v~~v~ 86 (111)
T COG2151 11 KVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIA-DQVEAALEE-IP-GVEDVE 86 (111)
T ss_pred hhhHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccHHHH-HHHHHHHHh-cC-CcceEE
Confidence 34445555566 4556666444 2333335555 4589999999999999998654 789999988 55 377663
No 16
>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=65.90 E-value=11 Score=33.70 Aligned_cols=67 Identities=18% Similarity=0.122 Sum_probs=39.9
Q ss_pred cccCCCCcchHHHHHHHHHHHHHHHcccccc--ceeecccc-----cccccc----HHHHHHHHHHhhhhhhccCCccc
Q 030084 115 QGACGSCPSSTTTMSMGIERVLKEKFGDAIK--DIRQVYDE-----EVRETT----VEVSALLLCLISDKRYYYTTAVP 182 (183)
Q Consensus 115 ~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~--~V~~V~d~-----e~~e~s----~E~In~al~~Lr~a~~~~~~~~~ 182 (183)
++++.+|.+=...++..+++.+.+. +..-. .....-++ .+..++ .+.|+.+|+.+||++..-||.|-
T Consensus 166 t~agt~CG~C~~~~~~il~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~irP~l~~dGGdv~ 243 (290)
T TIGR02000 166 TKAGGGCGSCHEKIEDVLKEVLANK-GATNPANAGGSKPTNKPNSGQKRPLTNVQRIQLIQKVLEEVRPVLQADGGDVE 243 (290)
T ss_pred ccCCCCCcchHHHHHHHHHHHHHhc-cccccccccccCcccccccCcchhcChHHHHHHHHHHHHHhCchHhhcCCcEE
Confidence 4555555555677777777777663 11000 01111001 111244 47899999999999999999874
No 17
>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=64.71 E-value=28 Score=23.54 Aligned_cols=66 Identities=17% Similarity=0.345 Sum_probs=33.7
Q ss_pred CCCcEEEEEeeCCEEEEEEc-ccCCCCcchHHHHHHHHHHHHHHHcc-ccccceeeccccccccccHHHHHHHHHHh
Q 030084 96 DGGNIDVVSVEDGVVSVKLQ-GACGSCPSSTTTMSMGIERVLKEKFG-DAIKDIRQVYDEEVRETTVEVSALLLCLI 170 (183)
Q Consensus 96 dGGDVELVdVedg~V~VrL~-GACsGCpsS~~TLk~~IE~~Lre~~P-~eV~~V~~V~d~e~~e~s~E~In~al~~L 170 (183)
+|..+.+-++.+..+.|-+. ..|..|......+.. +.+.+. +.+. +..|..+. . +.|.+....+..
T Consensus 8 ~g~~~~~~~~~~k~~ll~f~~~~C~~C~~~~~~l~~-----~~~~~~~~~~~-~~~v~~d~--~-~~~~~~~~~~~~ 75 (116)
T cd02966 8 DGKPVSLSDLKGKVVLVNFWASWCPPCRAEMPELEA-----LAKEYKDDGVE-VVGVNVDD--D-DPAAVKAFLKKY 75 (116)
T ss_pred CCCEeehHHcCCCEEEEEeecccChhHHHHhHHHHH-----HHHHhCCCCeE-EEEEECCC--C-CHHHHHHHHHHc
Confidence 45566666665555444444 468888776656643 333342 1222 33332221 1 566666665554
No 18
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.12 E-value=14 Score=28.98 Aligned_cols=52 Identities=15% Similarity=0.096 Sum_probs=33.4
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHHh
Q 030084 117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLI 170 (183)
Q Consensus 117 ACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~L 170 (183)
+|.+-|+|..|. .+.|.+|++++|..--.+.-|+-++ +-.+.-..+.|-+|+
T Consensus 18 SCV~aPtsKdt~-eWLeaalkRKyp~~~F~~~YiDI~n-~~~e~~~~~~aekI~ 69 (106)
T COG4837 18 SCVNAPTSKDTY-EWLEAALKRKYPNQPFKYTYIDITN-PPLEDHDLQFAEKIE 69 (106)
T ss_pred HhcCCCcchhHH-HHHHHHHhccCCCCCcEEEEEEcCC-CccHHHHHHHHHHHh
Confidence 355558888888 7999999999996444555564443 234444444444444
No 19
>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=55.54 E-value=16 Score=25.18 Aligned_cols=44 Identities=25% Similarity=0.567 Sum_probs=23.5
Q ss_pred hhchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHH
Q 030084 75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTM 128 (183)
Q Consensus 75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TL 128 (183)
+....+.|+.+|+.. -+-|.|+-++..... .|.|.+|+.....+
T Consensus 24 ~~~s~~~ve~mL~~l-----~~kG~I~~~~~~~~~-----~~~C~~C~~~~~~~ 67 (69)
T PF09012_consen 24 FGISPEAVEAMLEQL-----IRKGYIRKVDMSSCC-----GGSCSSCGPASKEI 67 (69)
T ss_dssp TT--HHHHHHHHHHH-----HCCTSCEEEEEE--S-----SSSSSS-SS-----
T ss_pred HCcCHHHHHHHHHHH-----HHCCcEEEecCCCCC-----CCCCCCCCCccccC
Confidence 334445556555432 368999977776444 89999999877643
No 20
>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=54.80 E-value=16 Score=24.76 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=22.8
Q ss_pred cccCCCCcchHHHHHHHHHHHHHHHc
Q 030084 115 QGACGSCPSSTTTMSMGIERVLKEKF 140 (183)
Q Consensus 115 ~GACsGCpsS~~TLk~~IE~~Lre~~ 140 (183)
.++|.|||.-...|.+.|-+.||+-.
T Consensus 7 G~~~~G~~ql~ESLLdrItRklr~gw 32 (45)
T PF02061_consen 7 GWPRMGCPQLSESLLDRITRKLRDGW 32 (45)
T ss_pred CccccCCchhhHHHHHHHHHHHHHHH
Confidence 47999999988999999999998854
No 21
>PRK12933 secD preprotein translocase subunit SecD; Reviewed
Probab=49.54 E-value=1.1e+02 Score=30.47 Aligned_cols=94 Identities=13% Similarity=0.179 Sum_probs=65.6
Q ss_pred chHHHHHHHHHhhcchhhhCCCcEEEEEe--eC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccc-------
Q 030084 77 LTAKNVDLVLEDVRPYLIADGGNIDVVSV--ED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKD------- 146 (183)
Q Consensus 77 l~~e~Ve~vLe~IRP~LqsdGGDVELVdV--ed-g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~------- 146 (183)
...++.+.+.+++|-.|+.. .|.+.++ .+ +.+.+++.-+ .-.+.+++.|++.+|+ +.-
T Consensus 147 ~~~~~~~~~~~~~r~~lr~~--~i~~~~~~~~~~~~i~~~~~~~---------~~~~~a~~~l~~~~~~-~~~~~~~~~~ 214 (604)
T PRK12933 147 VYQEQRDALVDSVRQFLREQ--RIRGVSVRLDDSDQLAVTTPDN---------DARSAVRQFIQQNYPG-WQVTNSDDRG 214 (604)
T ss_pred HHHHHHHHHHHHHHHHHHhC--CCceeeEEecCCCeEEEEeCCH---------HHHHHHHHHHHhhCCC-ceEecCCCce
Confidence 34567777789999999975 3444444 34 6788888752 3456777888888775 321
Q ss_pred e-eeccccccccccHHHHHHHHHHhhhhhhccCCccc
Q 030084 147 I-RQVYDEEVRETTVEVSALLLCLISDKRYYYTTAVP 182 (183)
Q Consensus 147 V-~~V~d~e~~e~s~E~In~al~~Lr~a~~~~~~~~~ 182 (183)
+ ...++.+..++...+++.++.+||.-|..+|-+=|
T Consensus 215 ~~~~~~~~~~~~~~~~av~q~~~iir~Rin~lGv~Ep 251 (604)
T PRK12933 215 LQLKLSQQEKTKFRNLTVQQNLQIMRSRIEELGITEA 251 (604)
T ss_pred EEEEECHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 1 11234445678888999999999999999997755
No 22
>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=48.32 E-value=1e+02 Score=25.70 Aligned_cols=68 Identities=15% Similarity=0.172 Sum_probs=46.5
Q ss_pred chHHHHHHHHH-hhcchhhhC---CCcEEEEEeeC---C--EEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084 77 LTAKNVDLVLE-DVRPYLIAD---GGNIDVVSVED---G--VVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI 147 (183)
Q Consensus 77 l~~e~Ve~vLe-~IRP~Lqsd---GGDVELVdVed---g--~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V 147 (183)
...+.|..+|. -.-|.+..+ =|-|.=+++++ + .|+|.|.-...+|++.. .|+.-|+.+|.. +| .+++|
T Consensus 73 ~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~~-~L~~dV~~aL~~-l~-gV~~V 149 (174)
T TIGR03406 73 DNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGP-VLVEDVEDKVLA-VP-NVDEV 149 (174)
T ss_pred ccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHHH-HHHHHHHHHHHh-CC-CceeE
Confidence 44466778884 445655442 35566567765 5 89999999999999664 466788888876 55 36665
No 23
>PRK11670 antiporter inner membrane protein; Provisional
Probab=37.61 E-value=1.5e+02 Score=27.11 Aligned_cols=68 Identities=15% Similarity=0.023 Sum_probs=47.7
Q ss_pred chHHHHHHHHH-hhcchhhhC---CCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084 77 LTAKNVDLVLE-DVRPYLIAD---GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI 147 (183)
Q Consensus 77 l~~e~Ve~vLe-~IRP~Lqsd---GGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V 147 (183)
...+.|..+|. -.-|.+..+ -|-|.=+.++++.|++.+.-.=.+||... .++..++++|+. +| .++.|
T Consensus 12 ~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~-~~~~~ 83 (369)
T PRK11670 12 ALRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAFE-ELKEQCSAELLR-IT-GAKAI 83 (369)
T ss_pred chHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchHHH-HHHHHHHHHHHh-cC-CCceE
Confidence 45577777885 445666553 45565567788999999987777888655 478899999987 55 35555
No 24
>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=35.98 E-value=1.8e+02 Score=24.74 Aligned_cols=38 Identities=21% Similarity=0.279 Sum_probs=30.2
Q ss_pred EEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHc
Q 030084 101 DVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKF 140 (183)
Q Consensus 101 ELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~ 140 (183)
-.+.+++..+.|.|.--..-|. +..|++.||.+|++-.
T Consensus 173 ~~v~vd~~~A~I~~~t~~Vec~--d~~Lk~rve~~l~r~~ 210 (216)
T PF11718_consen 173 LSVTVDGKVAHIDLSTLEVECE--DEPLKQRVETALKRLH 210 (216)
T ss_pred EEEEeCCcEEEEecCCCceecC--CHHHHHHHHHHHHHHH
Confidence 3456677788888888888888 8889999999998743
No 25
>PRK02114 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional
Probab=35.22 E-value=30 Score=31.72 Aligned_cols=55 Identities=15% Similarity=0.190 Sum_probs=36.5
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHH-hhhhh----------hccCCcc
Q 030084 117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCL-ISDKR----------YYYTTAV 181 (183)
Q Consensus 117 ACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~-Lr~a~----------~~~~~~~ 181 (183)
+-..|| ||+..++ ..++|+++..|-.+.- +.+++|.|++|++- ++.+. -||||-+
T Consensus 220 NdayCP----TLr~~~~---~S~lp~~v~~V~EIVI---dGl~~~aV~~Amr~Gi~Aa~~~~Gv~~IsAGNYGGkL 285 (297)
T PRK02114 220 NDAYCP----TLKGKVE---DSELPEGVNAVYEIVI---DGLDEEAVAEAMRAGIEAACAVPGVVKISAGNYGGKL 285 (297)
T ss_pred CcCcCc----chhcccc---cccCCCCCCeEEEEEE---cCCCHHHHHHHHHHHHHHHhcCCCeEEEecCCCCCcc
Confidence 456777 6775543 5567888888844332 47999999999875 33333 3788853
No 26
>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=35.05 E-value=38 Score=25.29 Aligned_cols=34 Identities=9% Similarity=0.155 Sum_probs=22.9
Q ss_pred CCCcEEEEEeeC-CEEEEEEc-c-cCCCCcchHHHHH
Q 030084 96 DGGNIDVVSVED-GVVSVKLQ-G-ACGSCPSSTTTMS 129 (183)
Q Consensus 96 dGGDVELVdVed-g~V~VrL~-G-ACsGCpsS~~TLk 129 (183)
+|..+.+-++.+ +.+.|-+- + -|..|+.....|.
T Consensus 16 ~g~~v~l~~~~g~k~~vl~f~~~~~c~~C~~~~~~l~ 52 (149)
T cd03018 16 NGQEVRLSEFRGRKPVVLVFFPLAFTPVCTKELCALR 52 (149)
T ss_pred CCCEEeHHHHcCCCeEEEEEeCCCCCccHHHHHHHHH
Confidence 566777777766 66666664 3 4999987666663
No 27
>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=34.91 E-value=51 Score=24.99 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=18.9
Q ss_pred HhhcchhhhCCCcEEEEEeeC--CEEEEEEccc
Q 030084 87 EDVRPYLIADGGNIDVVSVED--GVVSVKLQGA 117 (183)
Q Consensus 87 e~IRP~LqsdGGDVELVdVed--g~V~VrL~GA 117 (183)
+.|+-.++.+| +|.+||+.. ..-+|||..+
T Consensus 16 e~iK~~f~~~g-~V~yVD~~~G~~~g~VRf~~~ 47 (105)
T PF08777_consen 16 EDIKEAFSQFG-EVAYVDFSRGDTEGYVRFKTP 47 (105)
T ss_dssp HHHHHHT-SS---EEEEE--TT-SEEEEEESS-
T ss_pred HHHHHHHHhcC-CcceEEecCCCCEEEEEECCc
Confidence 55666677666 999999964 4899999975
No 28
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=34.74 E-value=1.6e+02 Score=20.72 Aligned_cols=35 Identities=11% Similarity=0.291 Sum_probs=23.8
Q ss_pred hCCCcEEEEEee-CCEEEEEEcc-cCCCCcchHHHHH
Q 030084 95 ADGGNIDVVSVE-DGVVSVKLQG-ACGSCPSSTTTMS 129 (183)
Q Consensus 95 sdGGDVELVdVe-dg~V~VrL~G-ACsGCpsS~~TLk 129 (183)
.+|..+.+-+.. +..+.|-|-+ -|..|......++
T Consensus 8 ~~G~~~~l~~~~~gk~vvl~F~~~wC~~C~~~~p~l~ 44 (114)
T cd02967 8 IDGAPVRIGGISPGRPTLLFFLSPTCPVCKKLLPVIR 44 (114)
T ss_pred CCCCEEEcccccCCCeEEEEEECCCCcchHhHhHHHH
Confidence 357778888886 6767777765 3777776655553
No 29
>PF04865 Baseplate_J: Baseplate J-like protein; InterPro: IPR006949 The temperate bacteriophage P2 has four defined tail genes: V, J, W and I. Their order is the late gene promoter, VWJI, followed by the tail fibre genes H and G and then a transcription terminator. BAP V protein is the small spike at the tip of the tail and basal plate assembly protein J lies at the edge of the baseplate []. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred.
Probab=34.72 E-value=1.1e+02 Score=25.36 Aligned_cols=62 Identities=21% Similarity=0.227 Sum_probs=40.5
Q ss_pred chHHHHHHHH--HhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccc
Q 030084 77 LTAKNVDLVL--EDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGD 142 (183)
Q Consensus 77 l~~e~Ve~vL--e~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~ 142 (183)
.+.++|+..| +.+||. |-++.+.....-.+.|++..-...=+......+..|++.|++++..
T Consensus 164 ~l~~~V~~~i~~~~~~p~----~~~v~v~~~~~~~v~v~~~l~~~~~~~~~~~~~~~i~~al~~y~~~ 227 (243)
T PF04865_consen 164 ELLAAVQAYINAEDVRPL----GDRVTVKAPTYVPVDVTATLTVYPGYDTAEVIQAAIKAALRAYFNS 227 (243)
T ss_pred HHHHHHHHHhhhhccCCC----ceEEEEECCEEEEEEEEEEEEECCCCChHHHHHHHHHHHHHHHHHh
Confidence 3446677777 777776 5677777777666666666544422233455555889999988763
No 30
>cd03377 TPP_PFOR_PNO Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). These enzymes are dependent on TPP and a divalent metal cation as cofactors. PFOR and PNO catalyze the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The PFOR from cyanobacterium Anabaena (NifJ) is required for the transfer of electrons from pyruvate to flavodoxin, which reduces nitrogenase. The facultative anaerobic mitochondrion of the photosynthetic protist Euglena gra
Probab=33.89 E-value=16 Score=34.14 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=10.9
Q ss_pred EEEcccCCCCcchH
Q 030084 112 VKLQGACGSCPSST 125 (183)
Q Consensus 112 VrL~GACsGCpsS~ 125 (183)
+.|.|||.||+-..
T Consensus 3 ~ef~gACaGCget~ 16 (365)
T cd03377 3 FEFSGACAGCGETP 16 (365)
T ss_pred ccccccCCCCchHH
Confidence 56889999998643
No 31
>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=32.93 E-value=2.4e+02 Score=23.49 Aligned_cols=58 Identities=24% Similarity=0.362 Sum_probs=36.9
Q ss_pred HhhcchhhhCCCcEEEEEee----CC-----EEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084 87 EDVRPYLIADGGNIDVVSVE----DG-----VVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI 147 (183)
Q Consensus 87 e~IRP~LqsdGGDVELVdVe----dg-----~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V 147 (183)
++++-.+++..|..++.++. +. .++|++.+.+ .......+.+.|++.|++++| ++.+|
T Consensus 208 ~~i~~~i~~~~~v~~v~~~~~~~~g~~~~~v~i~v~v~~~~--~v~~~~~i~~~i~~~l~~~~~-~i~~v 274 (284)
T PF01545_consen 208 EKIRRIIESVPGVIEVHDLRVWQVGRNKYVVEIHVQVDPDM--SVEEAHEIRERIEKRLREKFP-GIYDV 274 (284)
T ss_dssp HHHHHHHHHTSS-SEEEEEEEEEETT-EEEEEEEEEETTTS--BHHHHHHHHHHHHHHHHHHST-TCEEE
T ss_pred hHHHHhhccCCceEeccceEEEEecCCcEEEEEEEEeCCCC--CHHHHHHHHHHHHHHHHHhCC-CcEEE
Confidence 56666676677766666663 33 3555555655 223345578999999999998 47654
No 32
>TIGR03119 one_C_fhcD formylmethanofuran--tetrahydromethanopterin N-formyltransferase. Members of this protein family are the FhcD protein of tetrahydromethanopterin (H4MPT)-dependent C-1 carrier metabolism. In the archaea, FhcD is designated formylmethanofuran--tetrahydromethanopterin N-formyltransferase, while in bacteria it is commonly designated as formyltransferase/hydrolase complex subunit D. FhcD is essential for one-carbon metabolism in at least three groups of prokaryotes: methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria.
Probab=32.04 E-value=41 Score=30.66 Aligned_cols=54 Identities=11% Similarity=0.172 Sum_probs=35.8
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHH-hhhhh----------hccCCcc
Q 030084 117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCL-ISDKR----------YYYTTAV 181 (183)
Q Consensus 117 ACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~-Lr~a~----------~~~~~~~ 181 (183)
+-..|| ||+..+ ..++|+++..|-.+.- +.+++|.|++|++- ++.+. -||||.+
T Consensus 213 NdayCP----TLr~~~----~S~lp~~v~~V~EIVI---dGl~~~aV~~Amr~Gi~Aa~~~~Gv~~IsAGNYGGkL 277 (287)
T TIGR03119 213 NDAYCP----TLKDQV----ESELPEGVNAVYEIVI---DGLNEAAIAEAMRVGILAATEIPGVVKITAGNYGGKL 277 (287)
T ss_pred CcccCc----cccccc----cccCCCCCCeEEEEEE---cCCCHHHHHHHHHHHHHHHhcCCCeEEEecCccCCCC
Confidence 355677 676544 5668888888854432 47899999998774 44443 3888864
No 33
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=31.70 E-value=41 Score=25.16 Aligned_cols=26 Identities=4% Similarity=-0.275 Sum_probs=23.9
Q ss_pred ccccHHHHHHHHHHhhhhhhccCCcc
Q 030084 156 RETTVEVSALLLCLISDKRYYYTTAV 181 (183)
Q Consensus 156 ~e~s~E~In~al~~Lr~a~~~~~~~~ 181 (183)
.++++|.++...+.+...|+..||.+
T Consensus 16 p~l~e~~~~~~~~~~~~~i~~~gg~i 41 (97)
T CHL00123 16 PDLNEEELLKWIENYKKLLRKRGAKN 41 (97)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 57899999999999999999999975
No 34
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=31.03 E-value=53 Score=27.40 Aligned_cols=35 Identities=40% Similarity=0.596 Sum_probs=25.3
Q ss_pred EEEEeeCCEEEEEE--cccCCCCcchHHHHHHHHHHHH
Q 030084 101 DVVSVEDGVVSVKL--QGACGSCPSSTTTMSMGIERVL 136 (183)
Q Consensus 101 ELVdVedg~V~VrL--~GACsGCpsS~~TLk~~IE~~L 136 (183)
.+++.++|.+.|+= +-+|++|++...--. .+...|
T Consensus 7 ~vv~~q~G~a~V~c~~~S~CgsC~a~~~CGs-~~l~kL 43 (150)
T COG3086 7 TVVSWQNGQAKVSCQRQSACGSCAARAGCGS-GLLSKL 43 (150)
T ss_pred EEEEccCCeEEEEeeccCccccchhhcccch-HHHHHh
Confidence 45888899766664 589999999887763 444444
No 35
>PRK14454 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=30.94 E-value=2.3e+02 Score=25.76 Aligned_cols=76 Identities=22% Similarity=0.347 Sum_probs=46.4
Q ss_pred CCCcEEEEEee---CCEEEEEEc----ccCCCCcch------HHHHHHHHHHHHHHH--ccccccceeeccccccccccH
Q 030084 96 DGGNIDVVSVE---DGVVSVKLQ----GACGSCPSS------TTTMSMGIERVLKEK--FGDAIKDIRQVYDEEVRETTV 160 (183)
Q Consensus 96 dGGDVELVdVe---dg~V~VrL~----GACsGCpsS------~~TLk~~IE~~Lre~--~P~eV~~V~~V~d~e~~e~s~ 160 (183)
||-.||-|-+. ..++.|-.+ =.|..|... ..|..+.+++.++.+ +...+..|+-..-.|| -.+.
T Consensus 86 dg~~iE~V~i~~~~~~t~cvSsqvGC~~~C~FC~tg~~G~~rnlt~~EI~~qv~~~~~~~~~~~~gvV~mggGEP-Lln~ 164 (342)
T PRK14454 86 DGNIIESVVMKYKHGNSICVSTQVGCRMGCKFCASTIGGMVRNLTAGEMLDQILAAQNDIGERISNIVLMGSGEP-LDNY 164 (342)
T ss_pred CCCEEEEEEEEEcCCCEEEEEcCCCCCCcCCcCCCCCCCCcccCCHHHHHHHHHHHHHHhcCCCCCEEEECCchh-hcCH
Confidence 33444444442 334545444 346777653 358888888887653 3224666665555554 5788
Q ss_pred HHHHHHHHHhhh
Q 030084 161 EVSALLLCLISD 172 (183)
Q Consensus 161 E~In~al~~Lr~ 172 (183)
|.+-+++++++.
T Consensus 165 d~v~~~l~~l~~ 176 (342)
T PRK14454 165 ENVMKFLKIVNS 176 (342)
T ss_pred HHHHHHHHHHhc
Confidence 889999999885
No 36
>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=30.85 E-value=51 Score=22.78 Aligned_cols=25 Identities=20% Similarity=0.501 Sum_probs=16.3
Q ss_pred EEEEEEcccCCCCcchHHHHHHHHHHHHHH
Q 030084 109 VVSVKLQGACGSCPSSTTTMSMGIERVLKE 138 (183)
Q Consensus 109 ~V~VrL~GACsGCpsS~~TLk~~IE~~Lre 138 (183)
.|.| ++-.|..|+ .+...+++.+.+
T Consensus 2 ~I~v-~~~~C~~C~----~~~~~~~~~~~~ 26 (76)
T PF13192_consen 2 KIKV-FSPGCPYCP----ELVQLLKEAAEE 26 (76)
T ss_dssp EEEE-ECSSCTTHH----HHHHHHHHHHHH
T ss_pred EEEE-eCCCCCCcH----HHHHHHHHHHHh
Confidence 3567 776688888 344566666666
No 37
>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=30.68 E-value=1.3e+02 Score=20.39 Aligned_cols=24 Identities=25% Similarity=0.225 Sum_probs=18.6
Q ss_pred HHHHHHHHhhcchhhhCCCcEEEE
Q 030084 80 KNVDLVLEDVRPYLIADGGNIDVV 103 (183)
Q Consensus 80 e~Ve~vLe~IRP~LqsdGGDVELV 103 (183)
+..+...+.+.|.|+.|||.+-..
T Consensus 2 ~~~~~Y~~~~~~~l~~~GG~~l~~ 25 (65)
T PF07045_consen 2 EAYQEYREAVPPILEKYGGRVLAR 25 (65)
T ss_dssp HHHHHHHHHHHHHHHHTT-EEEEE
T ss_pred hHHHHHHHHHHHHHHHcCCEEEEE
Confidence 445677789999999999987665
No 38
>PF00274 Glycolytic: Fructose-bisphosphate aldolase class-I; InterPro: IPR000741 Fructose-bisphosphate aldolase (4.1.2.13 from EC) [, ] is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms: class I enzymes [] do not require a metal ion, and are characterised by the formation of a Schiff base intermediate between a highly conserved active site lysine and a substrate carbonyl group, while the class II enzymes require an active-site divalent metal ion. This entry represents the class I enzymes. In vertebrates, three forms of this enzyme are found: aldolase A is expressed in muscle, aldolase B in liver, kidney, stomach and intestine, and aldolase C in brain, heart and ovary. The different isozymes have different catalytic functions: aldolases A and C are mainly involved in glycolysis, while aldolase B is involved in both glycolysis and gluconeogenesis. Defects in aldolase B result in hereditary fructose intolerance.; GO: 0004332 fructose-bisphosphate aldolase activity, 0006096 glycolysis; PDB: 1EX5_B 6ALD_D 2QUU_B 3DFN_B 1ADO_B 3DFO_A 1ZAL_A 1J4E_C 3DFP_A 1ZAJ_B ....
Probab=30.14 E-value=3e+02 Score=25.78 Aligned_cols=90 Identities=17% Similarity=0.149 Sum_probs=54.1
Q ss_pred hhchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcc--hHHHHHHHHHHHHHHHccccccceeeccc
Q 030084 75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPS--STTTMSMGIERVLKEKFGDAIKDIRQVYD 152 (183)
Q Consensus 75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCps--S~~TLk~~IE~~Lre~~P~eV~~V~~V~d 152 (183)
++.-.+.-+.+|..+--.|..|+=.++ +-.+.--|--....||. +...+-..--+.|++.+|..|..|.-.+
T Consensus 184 ~~~~~~vt~~vl~~v~~~l~~~~V~Le-----g~llKpnmv~pG~~~~~~~~~~~vA~~T~~~l~~~vP~aVpgIvFLS- 257 (348)
T PF00274_consen 184 IERCAEVTEAVLAAVFKALNDHGVMLE-----GTLLKPNMVTPGKDHPKKASPEEVAEATVRALRRTVPAAVPGIVFLS- 257 (348)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTEEGG-----GEEEEEB-S---TTSSS---HHHHHHHHHHHHHHHSBTTSSEEEEB--
T ss_pred HHHHHHHHHHHHHHHHHhhccCEEEec-----cccccccceeecccCCCCCCHHHHHHHHHHHHHHhcccccceeEecC-
Confidence 333334456667888888888863333 33334444445567775 3344444444789999999999998874
Q ss_pred cccccccHHHHHHHHHHhhhh
Q 030084 153 EEVRETTVEVSALLLCLISDK 173 (183)
Q Consensus 153 ~e~~e~s~E~In~al~~Lr~a 173 (183)
..-|+|.-..+|+-++..
T Consensus 258 ---GGqs~e~At~~Lna~n~~ 275 (348)
T PF00274_consen 258 ---GGQSEEEATANLNAINKM 275 (348)
T ss_dssp ---TTS-HHHHHHHHHHHHHS
T ss_pred ---CCCCHHHHHHHHHHhhCC
Confidence 456777777777777665
No 39
>PRK11325 scaffold protein; Provisional
Probab=29.45 E-value=71 Score=24.88 Aligned_cols=37 Identities=24% Similarity=0.449 Sum_probs=22.8
Q ss_pred CCcEEE-EEee-CC-EEEEEEcccCCCCcchHHHHHHHHHHH
Q 030084 97 GGNIDV-VSVE-DG-VVSVKLQGACGSCPSSTTTMSMGIERV 135 (183)
Q Consensus 97 GGDVEL-VdVe-dg-~V~VrL~GACsGCpsS~~TLk~~IE~~ 135 (183)
|-.|+| +.++ +| +..++|.| .||+.+........|..
T Consensus 38 GD~i~l~l~v~~~~~I~d~~f~~--~GC~is~Asas~~~e~~ 77 (127)
T PRK11325 38 GDVMKLQIKVNDEGIIEDAKFKT--YGCGSAIASSSLVTEWV 77 (127)
T ss_pred ccEEEEEEEECCCCeEEEEEEEe--eCCHHHHHHHHHHHHHH
Confidence 334443 4554 33 78899998 58888877774444433
No 40
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=29.13 E-value=73 Score=24.59 Aligned_cols=37 Identities=22% Similarity=0.408 Sum_probs=22.8
Q ss_pred CCcEEE-EEeeC--CEEEEEEcccCCCCcchHHHHHHHHHHH
Q 030084 97 GGNIDV-VSVED--GVVSVKLQGACGSCPSSTTTMSMGIERV 135 (183)
Q Consensus 97 GGDVEL-VdVed--g~V~VrL~GACsGCpsS~~TLk~~IE~~ 135 (183)
|-.|+| +.+++ .+..++|.|. ||+.+........|..
T Consensus 36 GD~i~l~l~v~~~~~I~d~~f~~~--GC~~s~Asas~~~e~i 75 (124)
T TIGR01999 36 GDVMKLQIKVNDDGIIEDAKFKTF--GCGSAIASSSLATELI 75 (124)
T ss_pred ccEEEEEEEECCCCeEEEEEEEec--CcHHHHHHHHHHHHHH
Confidence 334443 45543 3788999985 8988877764444433
No 41
>TIGR00532 HMG_CoA_R_NAD hydroxymethylglutaryl-CoA reductase, degradative. Most known examples of hydroxymethylglutaryl-CoA reductase are NADP-dependent (EC 1.1.1.34) from eukaryotes and archaea, involved in the biosynthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA. This model, in contrast, is built from the two examples in completed genomes of sequences closely related to the degradative, NAD-dependent hydroxymethylglutaryl-CoA reductase of Pseudomonas mevalonii, a bacterium that can use mevalonate as its sole carbon source.
Probab=29.09 E-value=2.6e+02 Score=26.41 Aligned_cols=64 Identities=14% Similarity=0.275 Sum_probs=42.5
Q ss_pred HHHHHHHHHhhcchhhhCCCcEEEEEe------eCCEEEEEEcccCCCCcchH--HHHHHHHHHHHHHHccc
Q 030084 79 AKNVDLVLEDVRPYLIADGGNIDVVSV------EDGVVSVKLQGACGSCPSST--TTMSMGIERVLKEKFGD 142 (183)
Q Consensus 79 ~e~Ve~vLe~IRP~LqsdGGDVELVdV------edg~V~VrL~GACsGCpsS~--~TLk~~IE~~Lre~~P~ 142 (183)
.+.+..+.+..-|.+.+.||.+.-+++ .++.|+|||.--|.-=..+. .|+.+.+-..|.+.+|.
T Consensus 143 ~~~i~~~a~~~~~~~~~rggg~~~i~~r~~~~~~g~~v~l~~~~dtgDAMGaNmvn~~~Eav~~~i~~~~~~ 214 (393)
T TIGR00532 143 GDEIIERAEECDPMLNNLGGGCKDIEARVIDIIEGGILILHIIVDTCDAMGANALNSIAEKVAEFIELEFGG 214 (393)
T ss_pred HHHHHHHHHHhCHHHHhhcCCeEEEEEEeeecccCCEEEEEEEEecccccccHHHHHHHHHHHHHHHHhCCC
Confidence 344555557888999999998775553 35689999986554333333 33556666777787774
No 42
>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=28.17 E-value=1.3e+02 Score=22.95 Aligned_cols=34 Identities=15% Similarity=0.342 Sum_probs=22.1
Q ss_pred HHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEc
Q 030084 81 NVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQ 115 (183)
Q Consensus 81 ~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~ 115 (183)
.++.+|+.|.-.|...+.|++ ++..+|++.|.|.
T Consensus 8 ~ad~~l~~ie~~ld~~~~d~D-~e~~~gVLti~f~ 41 (102)
T TIGR03421 8 LAEALLDAIEEAIDDADADID-CERAGGVLTLTFE 41 (102)
T ss_pred HHHHHHHHHHHHHhccCCCee-eecCCCEEEEEEC
Confidence 456666666666666666654 2335888888885
No 43
>PRK14726 bifunctional preprotein translocase subunit SecD/SecF; Provisional
Probab=27.31 E-value=3.6e+02 Score=28.07 Aligned_cols=95 Identities=14% Similarity=0.206 Sum_probs=63.0
Q ss_pred hchHHHHHHHHHhhcchhhhCCCcEEEEEe--eCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHcccccc--------
Q 030084 76 DLTAKNVDLVLEDVRPYLIADGGNIDVVSV--EDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIK-------- 145 (183)
Q Consensus 76 el~~e~Ve~vLe~IRP~LqsdGGDVELVdV--edg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~-------- 145 (183)
+...++.+.+.+++|-.|+..+ |.+.++ +++.+.|++.-+ .-.+.+++.|++.+++ +.
T Consensus 65 ~~~~~~~~~~~~~~r~~lr~~~--i~~~~~~~~~~~i~~~~~~~---------~~~~~~~~~l~~~~~~-~~~~~~~~~~ 132 (855)
T PRK14726 65 DIVKDRLEETVANIRNALRDAG--IRYTGLTGNGQTVQVRITDP---------AQTQAAVDALKPLTAP-VSAGGLGGSS 132 (855)
T ss_pred HHHHHHHHHHHHHHHHHHHhCC--CcccceeeeCCEEEEEECCH---------HHHHHHHHHHHhhccc-ccccccccCC
Confidence 3456677777799999999863 334333 467888888852 2345666777776543 21
Q ss_pred --c----------e-eeccccccccccHHHHHHHHHHhhhhhhccCCccc
Q 030084 146 --D----------I-RQVYDEEVRETTVEVSALLLCLISDKRYYYTTAVP 182 (183)
Q Consensus 146 --~----------V-~~V~d~e~~e~s~E~In~al~~Lr~a~~~~~~~~~ 182 (183)
+ + ...++.+..+...+.++.++.+||.-+..+|-+=|
T Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~vir~Rid~lGv~ep 182 (855)
T PRK14726 133 IQELTLQEGGEGQLRLQLTDAGIDYRVSSALTQSIEVVRRRVAELGTTEP 182 (855)
T ss_pred ccceEEeecCCceEEEEECHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 1 1 11233334467788999999999999999987654
No 44
>PRK11688 hypothetical protein; Provisional
Probab=27.22 E-value=1.7e+02 Score=22.90 Aligned_cols=44 Identities=14% Similarity=0.116 Sum_probs=31.3
Q ss_pred hchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCC
Q 030084 76 DLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSC 121 (183)
Q Consensus 76 el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGC 121 (183)
+...+.++..+..-.|+.+..| ++++++++|.+.++|.-.=..|
T Consensus 7 ~~~~~~~~~~~~~~~pf~~~lG--~~~~~~~~g~~~~~l~~~~~~~ 50 (154)
T PRK11688 7 EEALKLVGEIFVYHMPFNRLLG--LELERLEPDFVELSFKMQPELV 50 (154)
T ss_pred HHHHHHHHHHHHhcCCHHHHhC--cEEEEEeCCEEEEEeeCCHHHc
Confidence 3444556666655578888886 7888888999999998655444
No 45
>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=26.65 E-value=94 Score=21.83 Aligned_cols=34 Identities=24% Similarity=0.564 Sum_probs=23.6
Q ss_pred EEEEEcccCCCCcchHHHHHHHHHHHHHHHcccccccee
Q 030084 110 VSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIR 148 (183)
Q Consensus 110 V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~ 148 (183)
|.|.| |.+|.....- ..+++.|...+|+.+.+|.
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 45555 7777766664 4788999999997554443
No 46
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=26.53 E-value=1.6e+02 Score=22.71 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=21.5
Q ss_pred HHHHHHHhhcchhhh-CCCcEEEEEeeCCEEEEEEcc
Q 030084 81 NVDLVLEDVRPYLIA-DGGNIDVVSVEDGVVSVKLQG 116 (183)
Q Consensus 81 ~Ve~vLe~IRP~Lqs-dGGDVELVdVedg~V~VrL~G 116 (183)
.++.+|+.|.-.|.. .+.|++ ++..+|+++|.|.+
T Consensus 9 ~ad~~l~~ie~~ld~~~~~d~D-~e~~~gVLti~f~~ 44 (105)
T PRK00446 9 LADALWQAIEEQLDDDGDADID-CERNGGVLTLTFEN 44 (105)
T ss_pred HHHHHHHHHHHHHHhccCCCee-eeccCCEEEEEECC
Confidence 345555555555554 566654 33468888888864
No 47
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=26.41 E-value=1.6e+02 Score=21.57 Aligned_cols=54 Identities=11% Similarity=0.104 Sum_probs=39.5
Q ss_pred hhchHHHHHHHHHhhcchhhhCCCcEEEEEee----CCEEEEEEcccCCCCcchHHHHHHHHHH
Q 030084 75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVE----DGVVSVKLQGACGSCPSSTTTMSMGIER 134 (183)
Q Consensus 75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVe----dg~V~VrL~GACsGCpsS~~TLk~~IE~ 134 (183)
++...+.-+.++...+-.+..+|=+++|++++ +..+++-|.+.. -.-++..|+.
T Consensus 17 ~~~~~~~e~~al~~c~~~~~~~~L~m~lvd~e~~~D~~k~~fyy~a~~------rvDFR~Lvr~ 74 (88)
T PF04468_consen 17 LERLREREEEALKFCRELVKELGLPMKLVDVEYQFDGSKLTFYYTAES------RVDFRELVRD 74 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCeEEEEEEEEcCCCEEEEEEEeCC------cCcHHHHHHH
Confidence 44444555778899999999999999999994 678999998543 2555544443
No 48
>COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion]
Probab=25.44 E-value=2.3e+02 Score=27.54 Aligned_cols=97 Identities=16% Similarity=0.226 Sum_probs=62.9
Q ss_pred chHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccc
Q 030084 77 LTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVR 156 (183)
Q Consensus 77 l~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~ 156 (183)
...+..+.+.+.+|--|...|=.=.-+..+++.+.|++.|+- .+ ...++.++...++ +.-....++.+..
T Consensus 58 ~~~~~~~~~~~~l~~~l~~~~v~~~~~~~~g~~i~v~~~~~~--------~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~ 127 (506)
T COG0342 58 ALKKRLEQLADDLRSRLRKEGVSYSGVRVEGNGITVPLRDAA--------EL-DKARKLLRLLHRG-VVLFLALTEAELD 127 (506)
T ss_pred hHHHHHHHHHHHHHHHHHhcCcccceeeecCceEEEecCChH--------hh-hhhhhhhhhhcCc-ceeeeccchhHHH
Confidence 344566666777777777774322233345668889888852 22 3444555555553 2222334455566
Q ss_pred cccHHHHHHHHHHhhhhhhccCCcccC
Q 030084 157 ETTVEVSALLLCLISDKRYYYTTAVPL 183 (183)
Q Consensus 157 e~s~E~In~al~~Lr~a~~~~~~~~~~ 183 (183)
+.....++.-...+|+.+...|-+.|.
T Consensus 128 ~~~~~~~~q~~~~~~~Rv~~~gv~eP~ 154 (506)
T COG0342 128 EIRKDAVQQNITILRNRVNELGVAEPV 154 (506)
T ss_pred hhhhhhhhhhhhHhhhhccccccCCCe
Confidence 788888889999999999999988884
No 49
>PRK14565 triosephosphate isomerase; Provisional
Probab=24.68 E-value=1.7e+02 Score=25.66 Aligned_cols=55 Identities=9% Similarity=0.006 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHccccccceeeccc-----cccccccHHHHHHHHHHhhhhh----hccCCccc
Q 030084 127 TMSMGIERVLKEKFGDAIKDIRQVYD-----EEVRETTVEVSALLLCLISDKR----YYYTTAVP 182 (183)
Q Consensus 127 TLk~~IE~~Lre~~P~eV~~V~~V~d-----~e~~e~s~E~In~al~~Lr~a~----~~~~~~~~ 182 (183)
.++..+.++|+..++. +..+.--.. ....-.+.|.++++.+.+|... --|||||-
T Consensus 136 ~~~~~~~~Ql~~~l~~-~~~ivIAYEPvWAIGtG~~a~~e~i~~~~~~Ir~~~~~~~IlYGGSV~ 199 (237)
T PRK14565 136 MTKDVLLEQCSNCLPK-HGEFIIAYEPVWAIGGSTIPSNDAIAEAFEIIRSYDSKSHIIYGGSVN 199 (237)
T ss_pred ChHHHHHHHHHHHhcC-CCCEEEEECCHHHhCCCCCCCHHHHHHHHHHHHHhCCCceEEEcCccC
Confidence 3456777888887763 443322111 1233568899999999999753 34999983
No 50
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=24.04 E-value=59 Score=23.36 Aligned_cols=26 Identities=12% Similarity=-0.082 Sum_probs=23.5
Q ss_pred ccccHHHHHHHHHHhhhhhhccCCcc
Q 030084 156 RETTVEVSALLLCLISDKRYYYTTAV 181 (183)
Q Consensus 156 ~e~s~E~In~al~~Lr~a~~~~~~~~ 181 (183)
...+++.++..++.+...|..+||.|
T Consensus 11 ~~~~~~~~~~~~~~~~~~i~~~gg~v 36 (92)
T PF01250_consen 11 PDLSEEEIKKLIERVKKIIEKNGGVV 36 (92)
T ss_dssp TTSCHHHHHHHHHHHHHHHHHTTEEE
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 46789999999999999999999976
No 51
>PLN00107 FAD-dependent oxidoreductase; Provisional
Probab=23.93 E-value=1.6e+02 Score=26.38 Aligned_cols=68 Identities=7% Similarity=0.039 Sum_probs=44.4
Q ss_pred ccCCCCCCccccCccceEEeccCCcceeeccceeeecccCCCCC---CCCCC-CCCccccchhchHHHHHHHHHhhcchh
Q 030084 18 ISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRASNPSA---PAGSS-PGLYSAHQFDLTAKNVDLVLEDVRPYL 93 (183)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~l~s~~~~el~~e~Ve~vLe~IRP~L 93 (183)
.+.-.+|||+--|+ +||.|+.-..+..++..++ ..-.. -.+|.+..+-.-.++...+|.+||-.+
T Consensus 17 ~~~f~g~pv~g~q~-----------~~~~sg~c~~~~~~~~~~~c~wd~r~~~g~~F~E~EyaVP~e~~~~aL~elr~l~ 85 (257)
T PLN00107 17 IPPFPGAAVIGSQD-----------RIMSSGACLDGADDGLITACPWDPRIKHGEFFFQSAISVPLSGAAAFINDIKALR 85 (257)
T ss_pred cccccCCceecccc-----------ccccccccccCccccccccCCCCccccCCcceEEEEEEecHHHHHHHHHHHHHHH
Confidence 44466888887665 5888888655544443332 11112 234667777777888888888888888
Q ss_pred hhC
Q 030084 94 IAD 96 (183)
Q Consensus 94 qsd 96 (183)
..+
T Consensus 86 ~~~ 88 (257)
T PLN00107 86 DIE 88 (257)
T ss_pred HhC
Confidence 777
No 52
>smart00044 CYCc Adenylyl- / guanylyl cyclase, catalytic domain. Present in two copies in mammalian adenylyl cyclases. Eubacterial homologues are known. Two residues (Asn, Arg) are thought to be involved in catalysis. These cyclases have important roles in a diverse range of cellular processes.
Probab=23.66 E-value=1.8e+02 Score=22.85 Aligned_cols=41 Identities=10% Similarity=-0.027 Sum_probs=30.8
Q ss_pred hhchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEccc
Q 030084 75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGA 117 (183)
Q Consensus 75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GA 117 (183)
.+...+.++.+.+.++..+..|||. ++.+.++.+.+-+...
T Consensus 56 ~~~~~~~l~~~~~~~~~~i~~~gg~--v~~~~Gd~~l~~F~~~ 96 (194)
T smart00044 56 PEQVVTLLNDLYSRFDRIIDRHGGY--KVKTIGDAYMVVSGLP 96 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCeE--EEEEeCCEEEEEECCC
Confidence 3445566788889999999999985 5667788787777653
No 53
>PF01591 6PF2K: 6-phosphofructo-2-kinase; InterPro: IPR013079 6-Phosphofructo-2-kinase (2.7.1.105 from EC, 3.1.3.46 from EC) is a bifunctional enzyme that catalyses both the synthesis and the degradation of fructose-2, 6-bisphosphate. The fructose-2,6-bisphosphatase reaction involves a phosphohistidine intermediate. The catalytic pathway is: ATP + D-fructose 6-phosphate = ADP + D-fructose 2,6-bisphosphate D-fructose 2,6-bisphosphate + H2O = 6-fructose 6-phosphate + Pi The enzyme is important in the regulation of hepatic carbohydrate metabolism and is found in greatest quantities in the liver, kidney and heart. In mammals, several genes often encode different isoforms, each of which differs in its tissue distribution and enzymatic activity []. The family described here bears a resemblance to the ATP-driven phospho-fructokinases, however, they share little sequence similarity, although a few residues seem key to their interaction with fructose 6-phosphate []. This domain forms the N-terminal region of this enzyme, while IPR013078 from INTERPRO forms the C-terminal domain.; GO: 0003873 6-phosphofructo-2-kinase activity, 0005524 ATP binding, 0006000 fructose metabolic process; PDB: 2DWO_A 3QPW_A 3QPV_A 3QPU_A 2I1V_B 2DWP_A 2AXN_A 1K6M_B 3BIF_A 2BIF_A ....
Probab=23.31 E-value=84 Score=27.06 Aligned_cols=36 Identities=19% Similarity=0.364 Sum_probs=26.0
Q ss_pred cccchhchHHHHHHHHHhhcchhhhCCCcEEEEEee
Q 030084 71 SAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVE 106 (183)
Q Consensus 71 s~~~~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVe 106 (183)
|.+..++..+....+|+++--+|+.+||+|-+.|-.
T Consensus 69 n~~~~~~R~~~a~~~l~dl~~~l~~~~G~VAI~DAT 104 (222)
T PF01591_consen 69 NEEAKKLREQIAKEALEDLIEWLQEEGGQVAIFDAT 104 (222)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHTS--SEEEEES-
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHhcCCCeEEEEeCC
Confidence 445556666677888899999999999999999854
No 54
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=22.53 E-value=3.2e+02 Score=20.04 Aligned_cols=69 Identities=12% Similarity=0.082 Sum_probs=44.1
Q ss_pred EEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHH---------cccccc-ceeeccccccccccHHHHHHHHHH
Q 030084 100 IDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEK---------FGDAIK-DIRQVYDEEVRETTVEVSALLLCL 169 (183)
Q Consensus 100 VELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~---------~P~eV~-~V~~V~d~e~~e~s~E~In~al~~ 169 (183)
+++++-+++.+.+.+.|- +-||-+.+...|.+. +|..+. .+........+..-.|++..|++.
T Consensus 1 ikvi~~~~n~~~~~i~~E-------DHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~ 73 (83)
T cd06927 1 LKVIEKEDNELELEIEGE-------DHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKR 73 (83)
T ss_pred CeEEEcCCCEEEEEEeCC-------CchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHH
Confidence 467778899999999996 459999999999882 111111 111111111124567888888888
Q ss_pred hhhhhh
Q 030084 170 ISDKRY 175 (183)
Q Consensus 170 Lr~a~~ 175 (183)
|..-+.
T Consensus 74 l~~~~~ 79 (83)
T cd06927 74 LIDLCE 79 (83)
T ss_pred HHHHHH
Confidence 876543
No 55
>PF00121 TIM: Triosephosphate isomerase; InterPro: IPR000652 Triosephosphate isomerase (5.3.1.1 from EC) (TIM) [] is the glycolytic enzyme that catalyses the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production. It is present in eukaryotes as well as in prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism [, ]. The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure. The TIM barrel fold occurs ubiquitously and is found in numerous other enzymes that can be involved in energy metabolism, macromolecule metabolism, or small molecule metabolism []. The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder [].; GO: 0004807 triose-phosphate isomerase activity, 0008152 metabolic process; PDB: 2YPI_A 1YPI_A 1NEY_B 1NF0_B 1I45_A 7TIM_A 3YPI_B 2H6R_H 2Y63_A 1N55_A ....
Probab=22.11 E-value=60 Score=28.20 Aligned_cols=52 Identities=19% Similarity=0.210 Sum_probs=32.5
Q ss_pred HHHHHHHHHHccc----cccceeeccc-----cccccccHHHHHHHHHHhhhhhhc-------------cCCcc
Q 030084 130 MGIERVLKEKFGD----AIKDIRQVYD-----EEVRETTVEVSALLLCLISDKRYY-------------YTTAV 181 (183)
Q Consensus 130 ~~IE~~Lre~~P~----eV~~V~~V~d-----~e~~e~s~E~In~al~~Lr~a~~~-------------~~~~~ 181 (183)
..+..+|+..+.. +.+.+.--.. ....-.+.|.+++..+.+|..++. |||||
T Consensus 138 ~~l~~Ql~~~l~~i~~~~~~~~iIAYEPvWAIGtG~~as~~~~~~~~~~Ir~~l~~~~~~~~~~~~~ILYGGSV 211 (244)
T PF00121_consen 138 EVLKRQLKSILKGIDKEELKNIIIAYEPVWAIGTGKTASPEQIQEVHAFIREILAELYGEEVANNIRILYGGSV 211 (244)
T ss_dssp HHHHHHHHHHHTTSSGGGGTCEEEEEEEGGGTSSSS-CCHHHHHHHHHHHHHHHHHHTHHHHHHHSEEEEESSE
T ss_pred HHHHHHHHHHHhccccccccceEEEEcccccccCCCCCCHHHHHHHHHHHHHHHHHhccccccCceeEEECCcC
Confidence 5677777765542 1123322211 123457899999999999998754 89997
No 56
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=22.06 E-value=78 Score=23.69 Aligned_cols=26 Identities=8% Similarity=-0.089 Sum_probs=23.6
Q ss_pred ccccHHHHHHHHHHhhhhhhccCCcc
Q 030084 156 RETTVEVSALLLCLISDKRYYYTTAV 181 (183)
Q Consensus 156 ~e~s~E~In~al~~Lr~a~~~~~~~~ 181 (183)
.++++|.++..++.+...|.++||.|
T Consensus 12 ~~~~~~~~~~~~~~~~~~i~~~gg~i 37 (108)
T PRK00453 12 PDLSEEQVKALVERFKGVITENGGTI 37 (108)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 46899999999999999999999975
No 57
>COG2946 Putative phage replication protein RstA [DNA replication, recombination, and repair]
Probab=22.04 E-value=2.9e+02 Score=26.25 Aligned_cols=61 Identities=15% Similarity=0.133 Sum_probs=40.4
Q ss_pred CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHH
Q 030084 107 DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCL 169 (183)
Q Consensus 107 dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~ 169 (183)
+++|.|.|.|. ||..+..+-+..+-+-|....-+-|+.|..-.|.=+.+-+.|.-.+|.+-
T Consensus 127 rntvlielsG~--GC~~~~~~we~rl~~fLq~~~r~riTRvDlA~Ddf~Gey~pe~a~~a~~n 187 (377)
T COG2946 127 RNTVLIELSGT--GCTVAKEGWELRLYQFLQDCGRPRITRVDLALDDFNGEYGPEQAKKARDN 187 (377)
T ss_pred CceEEEEEecC--ccceecccHHHHHHHHHHHhCCCceeEEEEeeecccCccCHHHHHHhhhC
Confidence 56899999995 88555444433333444443323588887666666788888887777664
No 58
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=22.02 E-value=70 Score=24.33 Aligned_cols=34 Identities=15% Similarity=0.269 Sum_probs=22.0
Q ss_pred CCCcEEEEEeeCCEEEEEEcc--cCCCCcchHHHHH
Q 030084 96 DGGNIDVVSVEDGVVSVKLQG--ACGSCPSSTTTMS 129 (183)
Q Consensus 96 dGGDVELVdVedg~V~VrL~G--ACsGCpsS~~TLk 129 (183)
+|..+.+-++.+..+.|-+-. -|..|+.....+.
T Consensus 19 ~G~~~~l~~~~gk~~ll~f~~~~~~p~C~~~~~~l~ 54 (154)
T PRK09437 19 DGEQVSLTDFQGQRVLVYFYPKAMTPGCTVQACGLR 54 (154)
T ss_pred CCCEEeHHHhCCCCEEEEEECCCCCCchHHHHHHHH
Confidence 455566666666667777754 3667887666553
No 59
>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=22.02 E-value=1.3e+02 Score=19.44 Aligned_cols=45 Identities=16% Similarity=0.317 Sum_probs=24.1
Q ss_pred ccCCCCcchHHHHHHHHHHHHHHHccccccceee-ccc------cccccccHHHHHHHHHH
Q 030084 116 GACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQ-VYD------EEVRETTVEVSALLLCL 169 (183)
Q Consensus 116 GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~-V~d------~e~~e~s~E~In~al~~ 169 (183)
-.|.+|. ..|+++|.. +| .|..|.- ... ..++.++.+.|.++++.
T Consensus 7 m~C~~C~-------~~v~~~l~~-~~-GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 7 MTCEGCA-------KKVEKALSK-LP-GVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp TTSHHHH-------HHHHHHHHT-ST-TEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred cccHHHH-------HHHHHHHhc-CC-CCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHH
Confidence 4566664 467788877 44 3554421 111 11233677777777665
No 60
>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=21.61 E-value=1.1e+02 Score=23.62 Aligned_cols=35 Identities=17% Similarity=0.199 Sum_probs=21.3
Q ss_pred HhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCC
Q 030084 87 EDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSC 121 (183)
Q Consensus 87 e~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGC 121 (183)
++|.-.|...-|.+++-.+-||..+||+.+.+.|+
T Consensus 14 ~~ia~~L~~~~~~~~~~~F~dGE~~v~i~~~v~g~ 48 (116)
T PF13793_consen 14 ERIAEALGIPLGKVETKRFPDGETYVRIPESVRGK 48 (116)
T ss_dssp HHHHHHTTS-EE-EEEEE-TTS-EEEEESS--TTS
T ss_pred HHHHHHhCCceeeeEEEEcCCCCEEEEecccccCC
Confidence 44555555566678888888999999999876653
No 61
>PRK13022 secF preprotein translocase subunit SecF; Reviewed
Probab=21.44 E-value=5e+02 Score=22.92 Aligned_cols=38 Identities=16% Similarity=0.330 Sum_probs=24.4
Q ss_pred CcEEEEEee-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccc
Q 030084 98 GNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGD 142 (183)
Q Consensus 98 GDVELVdVe-dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~ 142 (183)
++.++..+. ++.+.||+.. .+....+.+.+.|++.+++
T Consensus 68 ~~~~v~~~~~~~~~~i~~~~-------~~~~~~~~~~~~l~~~~~~ 106 (289)
T PRK13022 68 EDAQVQNFGSSRDVLIRLPP-------ASEELSEKVKKALNKAYGP 106 (289)
T ss_pred CCceEEEcCCCCEEEEEeCC-------CChHHHHHHHHHHHhhcCC
Confidence 466666664 5678899764 1233446778888887764
No 62
>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=21.12 E-value=1.2e+02 Score=21.34 Aligned_cols=23 Identities=35% Similarity=0.647 Sum_probs=18.3
Q ss_pred CCCCcchHHHHHHHHHHHHHHHccc
Q 030084 118 CGSCPSSTTTMSMGIERVLKEKFGD 142 (183)
Q Consensus 118 CsGCpsS~~TLk~~IE~~Lre~~P~ 142 (183)
|.+|....... .+.++|++.||+
T Consensus 6 C~~C~y~~Ra~--~l~q~L~~~Fp~ 28 (72)
T TIGR02174 6 CGSCGYKPRAA--WLKQELLEEFPD 28 (72)
T ss_pred CCCCCChHHHH--HHHHHHHHHCCC
Confidence 78888666555 788999999996
No 63
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=21.09 E-value=37 Score=25.42 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=24.2
Q ss_pred hCCCcEEEEEeeCCEEEEEEccc--CCCCcchHHHH
Q 030084 95 ADGGNIDVVSVEDGVVSVKLQGA--CGSCPSSTTTM 128 (183)
Q Consensus 95 sdGGDVELVdVedg~V~VrL~GA--CsGCpsS~~TL 128 (183)
.+|..+.+-++.+..+.|-+-+. |..|-.....+
T Consensus 16 ~~g~~~~l~~~~gk~~vv~f~~~~~Cp~C~~~~p~l 51 (146)
T PF08534_consen 16 LDGKPVSLSDFKGKPVVVNFWASAWCPPCRKELPYL 51 (146)
T ss_dssp TTSEEEEGGGGTTSEEEEEEESTTTSHHHHHHHHHH
T ss_pred CCCCEecHHHhCCCeEEEEEEccCCCCcchhhhhhH
Confidence 46677777777778877777755 77777766655
No 64
>PF02741 FTR_C: FTR, proximal lobe; InterPro: IPR002770 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure []. In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].; GO: 0016740 transferase activity, 0006730 one-carbon metabolic process; PDB: 1M5S_B 1M5H_E 1FTR_C 2FHJ_B 2FHK_D.
Probab=20.53 E-value=99 Score=25.84 Aligned_cols=55 Identities=13% Similarity=0.225 Sum_probs=28.7
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHHhhhhhh-----------ccCCcc
Q 030084 117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRY-----------YYTTAV 181 (183)
Q Consensus 117 ACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~Lr~a~~-----------~~~~~~ 181 (183)
+-..|| ||+..++ ...+|+++..|-.+. =+.++.|.|++|++.==.|.. ||||-+
T Consensus 75 N~~yCP----TLr~~~~---~S~lp~~v~~V~EIV---IdGl~~~av~~Amr~Gi~Aa~~~~Gv~~IsAGNYGGkL 140 (150)
T PF02741_consen 75 NDAYCP----TLRGKVE---DSELPEGVNAVYEIV---IDGLSEEAVAEAMRAGIEAACAVPGVVRISAGNYGGKL 140 (150)
T ss_dssp -GGG-G----GGGCCCT---T-S--TT--EEEEEE---EEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS
T ss_pred CcCcCc----ccccccc---cccCCCCCCeEEEEE---EcCCCHHHHHHHHHHHHHHHhcCCCeEEEecCCcCCcc
Confidence 345677 5654441 233566777774432 247999999999876444433 788753
No 65
>PRK14965 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.49 E-value=4.9e+02 Score=25.29 Aligned_cols=66 Identities=12% Similarity=0.138 Sum_probs=44.9
Q ss_pred HHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcc--hHHHHHHHHHHHHHHHcccccc
Q 030084 79 AKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPS--STTTMSMGIERVLKEKFGDAIK 145 (183)
Q Consensus 79 ~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCps--S~~TLk~~IE~~Lre~~P~eV~ 145 (183)
+..+-..+.+.+|.+++-=.+.+++..+++.+.|.|... ..|-. ........++..|.+.++..++
T Consensus 450 W~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 517 (576)
T PRK14965 450 WRAFVAFVKGKKPALGASLEQGSPLGVSAGLLEIGFPEG-SFELSAMQDPDSRAELKALAEQFFGRPTR 517 (576)
T ss_pred HHHHHHHHHhccHHHHHHHhcCceeeecCCeEEEEeCch-HHHHHHhcChHHHHHHHHHHHHHhCCCeE
Confidence 444444444556888776667889999999999988753 22222 2344557899999999986554
No 66
>PLN02536 diaminopimelate epimerase
Probab=20.30 E-value=1.4e+02 Score=26.09 Aligned_cols=40 Identities=23% Similarity=0.398 Sum_probs=28.8
Q ss_pred HHhhcchhhhC-----CCcEEEEEe-eCCEEEEEE-------cccCCCCcchH
Q 030084 86 LEDVRPYLIAD-----GGNIDVVSV-EDGVVSVKL-------QGACGSCPSST 125 (183)
Q Consensus 86 Le~IRP~Lqsd-----GGDVELVdV-edg~V~VrL-------~GACsGCpsS~ 125 (183)
+.++-|.|+.| |=+|+++.+ +.+.++||- +-||+++..|.
T Consensus 165 ~~~~g~~i~~~~~FP~~~NV~f~~v~~~~~i~~rt~ERGvg~TlACGTGacA~ 217 (267)
T PLN02536 165 LEKIGPKFEHHEMFPARTNTEFVQVVSRSHLKMRVWERGAGATLACGTGACAL 217 (267)
T ss_pred hHHhChhccccCCCCCCcEEEEEEEcCCCEEEEEEeccCCchhhccCccHHHH
Confidence 35667777766 889999999 567888875 45777655554
Done!