Query psy1153
Match_columns 195
No_of_seqs 187 out of 1551
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 20:46:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1153.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1153hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2358|consensus 100.0 2E-33 4.3E-38 228.1 6.8 176 18-194 7-198 (213)
2 COG0694 Thioredoxin-like prote 100.0 6.1E-28 1.3E-32 175.6 9.5 78 118-195 6-85 (93)
3 PF01106 NifU: NifU-like domai 99.9 6.1E-26 1.3E-30 157.0 8.5 68 126-194 1-68 (68)
4 TIGR03341 YhgI_GntY IscR-regul 99.9 2.7E-25 5.9E-30 181.8 8.8 108 85-195 72-180 (190)
5 PRK11190 Fe/S biogenesis prote 99.9 1.4E-24 3.1E-29 177.7 8.3 79 116-194 101-181 (192)
6 TIGR02000 NifU_proper Fe-S clu 99.8 1.2E-20 2.7E-25 163.3 9.2 74 119-194 217-290 (290)
7 PF08712 Nfu_N: Scaffold prote 99.8 9.5E-20 2.1E-24 131.7 5.5 71 29-100 17-87 (87)
8 COG0694 Thioredoxin-like prote 99.0 2E-10 4.4E-15 83.7 3.8 67 2-68 14-85 (93)
9 PF01106 NifU: NifU-like domai 99.0 5.8E-11 1.3E-15 82.0 0.5 63 2-65 1-66 (68)
10 TIGR03341 YhgI_GntY IscR-regul 98.8 1.4E-09 3E-14 89.2 2.7 69 2-70 110-182 (190)
11 PRK11190 Fe/S biogenesis prote 98.8 2E-09 4.4E-14 88.3 2.8 68 2-69 111-183 (192)
12 KOG2358|consensus 98.6 2.3E-08 5E-13 82.0 2.3 68 1-68 127-199 (213)
13 TIGR02000 NifU_proper Fe-S clu 98.5 7.7E-08 1.7E-12 83.7 2.6 62 2-65 224-288 (290)
14 PF01883 DUF59: Domain of unkn 97.6 0.00059 1.3E-08 46.8 7.9 68 123-192 1-71 (72)
15 COG2151 PaaD Predicted metal-s 96.8 0.0089 1.9E-07 45.1 8.1 72 119-192 10-86 (111)
16 TIGR02945 SUF_assoc FeS assemb 95.3 0.14 3.1E-06 37.0 8.0 69 122-192 2-74 (99)
17 TIGR03406 FeS_long_SufT probab 95.1 0.19 4E-06 40.8 8.7 72 119-192 71-150 (174)
18 PRK11670 antiporter inner memb 85.4 4.5 9.7E-05 36.4 8.0 69 122-192 13-84 (369)
19 TIGR02159 PA_CoA_Oxy4 phenylac 84.8 3.9 8.5E-05 32.2 6.4 48 141-191 13-60 (146)
20 PF02061 Lambda_CIII: Lambda P 81.3 1.9 4.2E-05 26.8 2.7 25 160-184 7-31 (45)
21 PRK10862 SoxR reducing system 75.1 4.1 8.9E-05 32.2 3.7 25 145-169 6-32 (154)
22 PF04246 RseC_MucC: Positive r 71.7 3.9 8.4E-05 31.2 2.7 22 147-168 1-24 (135)
23 PF07315 DUF1462: Protein of u 63.4 7.7 0.00017 28.2 2.6 26 162-188 11-36 (93)
24 PF11718 CPSF73-100_C: Pre-mRN 62.1 92 0.002 25.9 12.3 117 66-184 74-209 (216)
25 PRK12463 chorismate synthase; 60.6 11 0.00024 34.3 3.8 62 10-76 209-270 (390)
26 COG0082 AroC Chorismate syntha 59.8 11 0.00024 34.0 3.6 66 3-76 191-256 (369)
27 PF10646 Germane: Sporulation 59.8 55 0.0012 23.6 6.9 74 118-192 22-105 (117)
28 PRK11023 outer membrane lipopr 57.8 43 0.00093 27.2 6.5 65 117-193 45-109 (191)
29 PF01883 DUF59: Domain of unkn 57.1 33 0.00071 22.9 4.9 47 51-98 16-62 (72)
30 cd07304 Chorismate_synthase Ch 53.8 18 0.00039 32.5 3.9 60 9-75 192-251 (344)
31 PF00403 HMA: Heavy-metal-asso 53.6 34 0.00074 21.8 4.4 41 50-90 15-57 (62)
32 COG4837 Uncharacterized protei 51.4 13 0.00029 27.3 2.2 27 162-189 18-44 (106)
33 PF09012 FeoC: FeoC like trans 50.8 19 0.0004 24.1 2.8 26 142-172 41-66 (69)
34 COG3086 RseC Positive regulato 50.3 20 0.00043 28.4 3.2 35 146-181 7-43 (150)
35 PF01545 Cation_efflux: Cation 50.3 91 0.002 26.1 7.6 67 119-191 203-274 (284)
36 PRK05382 chorismate synthase; 50.2 23 0.00051 32.0 4.1 60 10-76 191-250 (359)
37 PF13192 Thioredoxin_3: Thiore 49.3 18 0.00039 24.5 2.6 25 155-184 3-27 (76)
38 PF01264 Chorismate_synt: Chor 48.8 15 0.00034 32.9 2.7 55 10-71 191-245 (346)
39 PLN02754 chorismate synthase 46.0 28 0.0006 32.1 3.9 32 45-76 254-285 (413)
40 PF08821 CGGC: CGGC domain; I 43.1 35 0.00075 25.4 3.4 23 162-186 45-67 (107)
41 TIGR00033 aroC chorismate synt 40.5 17 0.00037 32.7 1.7 32 45-76 220-251 (351)
42 PF13793 Pribosyltran_N: N-ter 39.5 27 0.00059 26.2 2.4 40 119-166 9-48 (116)
43 PF05258 DUF721: Protein of un 35.2 1.4E+02 0.003 20.0 7.3 62 122-191 21-87 (89)
44 PHA02782 hypothetical protein; 35.1 88 0.0019 29.2 5.3 58 119-183 368-428 (503)
45 PRK09509 fieF ferrous iron eff 34.2 2.2E+02 0.0048 24.4 7.6 67 119-189 211-279 (299)
46 TIGR01297 CDF cation diffusion 33.8 1.7E+02 0.0036 24.3 6.7 67 120-192 191-262 (268)
47 PRK15431 ferrous iron transpor 31.6 21 0.00046 25.2 0.7 26 142-171 43-69 (78)
48 PRK10614 multidrug efflux syst 30.6 4.2E+02 0.0091 27.2 9.9 20 46-65 62-81 (1025)
49 PRK11688 hypothetical protein; 30.2 1.3E+02 0.0028 23.2 5.0 42 119-163 6-47 (154)
50 TIGR03820 lys_2_3_AblA lysine- 29.0 1.9E+02 0.004 26.8 6.5 24 83-106 228-251 (417)
51 PRK09437 bcp thioredoxin-depen 28.5 39 0.00085 25.6 1.8 34 141-174 19-54 (154)
52 PF04865 Baseplate_J: Baseplat 27.3 1.6E+02 0.0035 24.1 5.4 66 118-188 161-228 (243)
53 PRK09579 multidrug efflux prot 27.2 3.7E+02 0.0081 27.6 8.9 22 46-67 62-83 (1017)
54 COG5429 Uncharacterized secret 24.8 57 0.0012 28.0 2.2 23 153-175 43-65 (261)
55 PRK00446 cyaY frataxin-like pr 24.1 1.8E+02 0.0038 21.5 4.5 34 120-161 11-44 (105)
56 PRK10503 multidrug efflux syst 23.9 4.8E+02 0.01 26.8 9.0 112 46-160 71-199 (1040)
57 COG1509 KamA Lysine 2,3-aminom 23.4 3.3E+02 0.0071 24.8 6.8 25 49-73 178-202 (369)
58 TIGR02554 PrgH type III secret 23.0 3.4E+02 0.0073 24.9 6.9 59 121-192 224-287 (389)
59 TIGR03421 FeS_CyaY iron donor 22.9 1.8E+02 0.004 21.3 4.4 31 121-160 11-41 (102)
60 cd04888 ACT_PheB-BS C-terminal 22.8 2.2E+02 0.0048 18.3 5.4 51 137-193 20-74 (76)
61 cd03018 PRX_AhpE_like Peroxire 22.7 61 0.0013 24.1 1.9 35 140-174 15-52 (149)
62 COG1579 Zn-ribbon protein, pos 22.4 50 0.0011 28.2 1.5 17 153-169 189-206 (239)
63 PRK11198 LysM domain/BON super 21.6 1.2E+02 0.0026 23.5 3.4 62 118-193 23-84 (147)
64 PF00873 ACR_tran: AcrB/AcrD/A 21.2 2.3E+02 0.005 28.8 6.1 109 45-192 59-175 (1021)
65 PF08777 RRM_3: RNA binding mo 20.8 1.1E+02 0.0023 22.5 2.7 31 123-162 15-47 (105)
66 TIGR02174 CXXU_selWTH selT/sel 20.7 1.4E+02 0.0029 20.2 3.1 24 163-188 6-29 (72)
No 1
>KOG2358|consensus
Probab=100.00 E-value=2e-33 Score=228.05 Aligned_cols=176 Identities=43% Similarity=0.689 Sum_probs=152.2
Q ss_pred CCceEEEEecC-----------CcccCC-CccccCCCcccccCChHHhhhccc-CCeeEEEeecceEEEEecCCCCCccc
Q psy1153 18 GGDIQFISFQD-----------GVLEEP-GQTIDFPTGQAAYCSPLGKLLFRI-EGVKSVFFGHDFITVTKQDDDVDWKL 84 (195)
Q Consensus 18 ~g~~~fi~~e~-----------~~~vl~-gg~~~f~~~~~a~~~~La~~Lf~i-~gV~~V~~~~dfVtVtk~~~~~~W~~ 84 (195)
..| |||++.. +..+++ -+...|++.-.+..+||+..+|.+ ++|+++|+++|||||+|..++..|.-
T Consensus 7 a~r-~~i~t~~tPn~~Sl~f~p~~~i~~~~~~~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~ 85 (213)
T KOG2358|consen 7 AAR-MFIQTQITPNPSSLLFLPGKQILSERGLGDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSV 85 (213)
T ss_pred hhh-hcccccCCCCcccccccCCCcccccccccccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccchhhhHhh
Confidence 445 8888754 555553 456778887778899999999965 49999999999999999974599999
Q ss_pred hhHHHHHHHHHhhhcCCCcccCCCCCCC-CCCCCCchHHHHHHHHHHHhcCchhhhccCCcEEEEEEeC--CEEEEEEcc
Q psy1153 85 LKPEIFATIMDFFSSGLPVLTDAQPSSD-TVIHEDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQG--GVVKLKMQG 161 (195)
Q Consensus 85 l~~~i~~~I~d~l~s~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~--g~v~v~l~G 161 (195)
|+|.+...++|+++.++|.+........ ....+++++....|+++|+++|||.|+.|||+++++++++ |.|+++|+|
T Consensus 86 L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqg 165 (213)
T KOG2358|consen 86 LDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQG 165 (213)
T ss_pred hchhhHHHHhccccccchhhccchhhhhhcccccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhh
Confidence 9999999999999999998876644211 1224678999999999999999999999999999999997 599999999
Q ss_pred cCCCCcchHHHHHHHHHHHHHhhCCCccceeeC
Q psy1153 162 SCTSCPSSVVTLKNGVQNMLQFYIPETTPGLNM 194 (195)
Q Consensus 162 aC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~~ 194 (195)
+|.+||++..||++|||++|+.|+|+||.|+.+
T Consensus 166 act~cpss~vtlk~Gie~mL~~y~~eVK~v~qv 198 (213)
T KOG2358|consen 166 ACTECPSSLVTLKNGIENMLEIYVPEVKGVIQV 198 (213)
T ss_pred hhccCCcccchhhhhHHHHHHhhcceeeEEEec
Confidence 999999999999999999999999999998753
No 2
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=6.1e-28 Score=175.57 Aligned_cols=78 Identities=41% Similarity=0.778 Sum_probs=74.8
Q ss_pred CchHHHHHHHHHHHhcCchhhhccCCcEEEEEEe--CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccceeeCC
Q psy1153 118 DDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQ--GGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGLNME 195 (195)
Q Consensus 118 ~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~--~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~~~ 195 (195)
.++++.++++++|+++|||+|++||||++|++|+ +|+|+|||+|||+|||||+.|||++||++|++++|++++|..++
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 4778999999999999999999999999999998 78999999999999999999999999999999999999998764
No 3
>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=99.93 E-value=6.1e-26 Score=156.98 Aligned_cols=68 Identities=38% Similarity=0.810 Sum_probs=64.6
Q ss_pred HHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccceeeC
Q psy1153 126 IKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGLNM 194 (195)
Q Consensus 126 i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~~ 194 (195)
|+++|++ |||+|++||||++|+++++++|+|||+|+|+|||+|..||+++||++|++++|++++|..+
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-IRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVVPV 68 (68)
T ss_dssp HHHHHHH-CHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEEEC
T ss_pred CHHHHHH-hChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEEEC
Confidence 6889996 9999999999999999999999999999999999999999999999999999999999864
No 4
>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=2.7e-25 Score=181.76 Aligned_cols=108 Identities=24% Similarity=0.407 Sum_probs=86.1
Q ss_pred hhHHHHHHHHHhhhcCCCcccCCCCCCCCCCCCCchHHHHHHHHHHHhcCchhhhccCCcEEEEEEe-CCEEEEEEcccC
Q psy1153 85 LKPEIFATIMDFFSSGLPVLTDAQPSSDTVIHEDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQ-GGVVKLKMQGSC 163 (195)
Q Consensus 85 l~~~i~~~I~d~l~s~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~-~g~v~v~l~GaC 163 (195)
|.-...++..+-++++..+-++++ + .....+++++.++|+++|+++|||+|++|||||+|++|+ +++|+|||+|+|
T Consensus 72 L~g~~IDyve~~~g~gF~f~NPna--~-~~~~~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC 148 (190)
T TIGR03341 72 LEDAVIDFVTDRMGGQLTLKAPNA--K-MPKVADDAPLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGC 148 (190)
T ss_pred hCCCEEEEeecCCCceeEEeCCcc--C-CCcCccchHHHHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecC
Confidence 444444444444455543333332 1 123345778999999999999999999999999999997 579999999999
Q ss_pred CCCcchHHHHHHHHHHHHHhhCCCccceeeCC
Q psy1153 164 TSCPSSVVTLKNGVQNMLQFYIPETTPGLNME 195 (195)
Q Consensus 164 ~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~~~ 195 (195)
+|||||.+||+++||++||+++|++++|.++.
T Consensus 149 ~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~~ 180 (190)
T TIGR03341 149 NGCSMVDVTLKDGVEKTLLERFPELKGVRDAT 180 (190)
T ss_pred CCCcchHHHHHHHHHHHHHHhCCCcceEEEec
Confidence 99999999999999999999999999998763
No 5
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=99.91 E-value=1.4e-24 Score=177.72 Aligned_cols=79 Identities=25% Similarity=0.506 Sum_probs=74.4
Q ss_pred CCCchHHHHHHHHHHHhcCchhhhccCCcEEEEEEe-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCC-Cccceee
Q psy1153 116 HEDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQ-GGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIP-ETTPGLN 193 (195)
Q Consensus 116 ~~~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~-~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~p-ev~~V~~ 193 (195)
..+++++.++|+++|+++|||+|++|||||+|++|+ +|+|+|||+|||+|||||++||+++||++|++++| +|++|.+
T Consensus 101 ~~~~~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~ 180 (192)
T PRK11190 101 VADDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRD 180 (192)
T ss_pred CcccHHHHHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEE
Confidence 345778999999999999999999999999999997 68999999999999999999999999999999999 9999987
Q ss_pred C
Q psy1153 194 M 194 (195)
Q Consensus 194 ~ 194 (195)
+
T Consensus 181 v 181 (192)
T PRK11190 181 L 181 (192)
T ss_pred e
Confidence 6
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=1.2e-20 Score=163.26 Aligned_cols=74 Identities=30% Similarity=0.592 Sum_probs=69.7
Q ss_pred chHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccceeeC
Q psy1153 119 DDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGLNM 194 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~~ 194 (195)
..+..++|+++| ++|||+|++|||||+|++|++++|+|||+|+|+|||+|.+||+. ||++|++++|++..|..+
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-EEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVEAV 290 (290)
T ss_pred hHHHHHHHHHHH-HHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEEeC
Confidence 456778999999 59999999999999999999999999999999999999999998 999999999999999864
No 7
>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=99.79 E-value=9.5e-20 Score=131.74 Aligned_cols=71 Identities=52% Similarity=0.820 Sum_probs=55.4
Q ss_pred CcccCCCccccCCCcccccCChHHhhhcccCCeeEEEeecceEEEEecCCCCCccchhHHHHHHHHHhhhcC
Q psy1153 29 GVLEEPGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQDDDVDWKLLKPEIFATIMDFFSSG 100 (195)
Q Consensus 29 ~~~vl~gg~~~f~~~~~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk~~~~~~W~~l~~~i~~~I~d~l~s~ 100 (195)
++.++++++.+|.+..+|..+|||+.||+++||++||+++|||||||.+ +++|++|+++|+++|++||.+|
T Consensus 17 ~~~~~~~~s~~f~~~~~a~~spLA~~Lf~i~gV~~Vf~~~dfItVtK~~-~~~W~~l~~~I~~~I~~~l~sG 87 (87)
T PF08712_consen 17 DEPLLPGGSFEFKSAEEASDSPLAQALFAIPGVKSVFIGDDFITVTKNP-DADWEDLKPEIREVIMEFLESG 87 (87)
T ss_dssp SS-SSTS---EEESSS-TTS-HHHHHHHTSTTEEEEEEETTEEEEEE-T-TS-HHHHHHHHHHHTH------
T ss_pred CceeecCccEEeCChHHcccCHHHHHhcCCCCEeEEEEECCEEEEeeCC-CCCHHHHHHHHHHHHhhhccCC
Confidence 7889998899999999999999999999999999999999999999996 9999999999999999999876
No 8
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.03 E-value=2e-10 Score=83.73 Aligned_cols=67 Identities=28% Similarity=0.483 Sum_probs=59.9
Q ss_pred HHHHHhhccCCccccCCCceEEEEecC--CcccCC--CccccCCCcccccCChHHhhhc-ccCCeeEEEeec
Q psy1153 2 IKELLDTRIRPTVQEDGGDIQFISFQD--GVLEEP--GQTIDFPTGQAAYCSPLGKLLF-RIEGVKSVFFGH 68 (195)
Q Consensus 2 ~~~~l~~~irp~~~~d~g~~~fi~~e~--~~~vl~--gg~~~f~~~~~a~~~~La~~Lf-~i~gV~~V~~~~ 68 (195)
|+++|+++|||+|..||||+.|+.+++ |.+++. |+|.+|+++..|.+..+.++|. .+|.|..|.-..
T Consensus 14 v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v~ 85 (93)
T COG0694 14 VEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQVT 85 (93)
T ss_pred HHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEcc
Confidence 678999999999999999999999984 677775 8999999999999999999999 589998887554
No 9
>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=99.02 E-value=5.8e-11 Score=82.00 Aligned_cols=63 Identities=30% Similarity=0.551 Sum_probs=57.1
Q ss_pred HHHHHhhccCCccccCCCceEEEEecCCcccCC--CccccCCCcccccCChHHhhhc-ccCCeeEEE
Q psy1153 2 IKELLDTRIRPTVQEDGGDIQFISFQDGVLEEP--GQTIDFPTGQAAYCSPLGKLLF-RIEGVKSVF 65 (195)
Q Consensus 2 ~~~~l~~~irp~~~~d~g~~~fi~~e~~~~vl~--gg~~~f~~~~~a~~~~La~~Lf-~i~gV~~V~ 65 (195)
|+++|+. |||+|+.|||+++|+.++++..++. |+|.+|+++..+.+..+.++|. ++|.+..|.
T Consensus 1 V~~~l~~-IrP~L~~dGGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V~ 66 (68)
T PF01106_consen 1 VEEVLEE-IRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVV 66 (68)
T ss_dssp HHHHHHH-CHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEE
T ss_pred CHHHHHH-hChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEE
Confidence 6899996 9999999999999999999977775 9999999999999999999999 799998885
No 10
>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=98.84 E-value=1.4e-09 Score=89.24 Aligned_cols=69 Identities=23% Similarity=0.347 Sum_probs=61.4
Q ss_pred HHHHHhhccCCccccCCCceEEEEecC-CcccCC--CccccCCCcccccCChHHhhhc-ccCCeeEEEeecce
Q psy1153 2 IKELLDTRIRPTVQEDGGDIQFISFQD-GVLEEP--GQTIDFPTGQAAYCSPLGKLLF-RIEGVKSVFFGHDF 70 (195)
Q Consensus 2 ~~~~l~~~irp~~~~d~g~~~fi~~e~-~~~vl~--gg~~~f~~~~~a~~~~La~~Lf-~i~gV~~V~~~~df 70 (195)
|+++|+.+|||+|+.|||+++|+.+++ +.++|. |+|.+|+++..|.+..+.++|. .+|+|++|.-..|+
T Consensus 110 i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~~~~~ 182 (190)
T TIGR03341 110 INYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDATDH 182 (190)
T ss_pred HHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEEecCc
Confidence 788998899999999999999999975 565665 9999999999999999999998 69999999877654
No 11
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=98.82 E-value=2e-09 Score=88.35 Aligned_cols=68 Identities=16% Similarity=0.256 Sum_probs=59.9
Q ss_pred HHHHHhhccCCccccCCCceEEEEecC-CcccCC--CccccCCCcccccCChHHhhhc-ccC-CeeEEEeecc
Q psy1153 2 IKELLDTRIRPTVQEDGGDIQFISFQD-GVLEEP--GQTIDFPTGQAAYCSPLGKLLF-RIE-GVKSVFFGHD 69 (195)
Q Consensus 2 ~~~~l~~~irp~~~~d~g~~~fi~~e~-~~~vl~--gg~~~f~~~~~a~~~~La~~Lf-~i~-gV~~V~~~~d 69 (195)
|+++|+++|||+|+.||||++|+.+++ |..+|. |+|.+|+++..|++..+.++|. .+| +|++|.-..+
T Consensus 111 i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v~~ 183 (192)
T PRK11190 111 VEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDLTE 183 (192)
T ss_pred HHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEecc
Confidence 789999999999999999999999975 665554 9999999999999999999998 588 9999876554
No 12
>KOG2358|consensus
Probab=98.58 E-value=2.3e-08 Score=81.99 Aligned_cols=68 Identities=34% Similarity=0.592 Sum_probs=59.5
Q ss_pred CHHHHHhhccCCccccCCCceEEEEecCC--cccC--CCccccCCCcccccCChHHhhhc-ccCCeeEEEeec
Q psy1153 1 MIKELLDTRIRPTVQEDGGDIQFISFQDG--VLEE--PGQTIDFPTGQAAYCSPLGKLLF-RIEGVKSVFFGH 68 (195)
Q Consensus 1 ~~~~~l~~~irp~~~~d~g~~~fi~~e~~--~~vl--~gg~~~f~~~~~a~~~~La~~Lf-~i~gV~~V~~~~ 68 (195)
|||++|++||||+++.|||++.|+.+++| ...+ .|.|.+|+++..+.++.+.++|. .++.||.|.=+.
T Consensus 127 ~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~eVK~v~qv~ 199 (213)
T KOG2358|consen 127 TIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVPEVKGVIQVP 199 (213)
T ss_pred HHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcceeeEEEecc
Confidence 68999999999999999999999999994 3333 48999999999999999999998 688888876543
No 13
>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=98.47 E-value=7.7e-08 Score=83.68 Aligned_cols=62 Identities=21% Similarity=0.357 Sum_probs=56.0
Q ss_pred HHHHHhhccCCccccCCCceEEEEecCCcccCC--CccccCCCcccccCChHHhhhc-ccCCeeEEE
Q psy1153 2 IKELLDTRIRPTVQEDGGDIQFISFQDGVLEEP--GQTIDFPTGQAAYCSPLGKLLF-RIEGVKSVF 65 (195)
Q Consensus 2 ~~~~l~~~irp~~~~d~g~~~fi~~e~~~~vl~--gg~~~f~~~~~a~~~~La~~Lf-~i~gV~~V~ 65 (195)
|+++| ++|||+|+.|||+++|+.+++|..++. |+|.+|+++..|.+. +.+.|. .+|.+..|.
T Consensus 224 v~~~l-~~irP~l~~dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p~~~~V~ 288 (290)
T TIGR02000 224 IQKVL-EEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLGEFVVVE 288 (290)
T ss_pred HHHHH-HHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCCCceEEE
Confidence 67889 599999999999999999998877776 899999999999998 999998 699998886
No 14
>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=97.57 E-value=0.00059 Score=46.82 Aligned_cols=68 Identities=21% Similarity=0.414 Sum_probs=56.5
Q ss_pred HHHHHHHHHhcCchhhhc---cCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcccee
Q psy1153 123 VQMIKELLDTRIRPTVQE---DGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGL 192 (195)
Q Consensus 123 ~~~i~~~l~~~irP~l~~---dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~ 192 (195)
+++|.++|.+..-|.+.. +-|-|+=+.+++|.|+|.|.-...+|| ....|+..|++.|+ .+|++++|.
T Consensus 1 k~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~gv~~V~ 71 (72)
T PF01883_consen 1 KQAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALPGVKSVK 71 (72)
T ss_dssp HHHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT-SEEE
T ss_pred CHHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCCCceEe
Confidence 367889999899998886 458899999999999999999999999 55889999999999 799998875
No 15
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=96.83 E-value=0.0089 Score=45.08 Aligned_cols=72 Identities=28% Similarity=0.350 Sum_probs=59.4
Q ss_pred chHHHHHHHHHHHhcCchhhhc---cCCcEEEEEEe--CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcccee
Q psy1153 119 DDETVQMIKELLDTRIRPTVQE---DGGDIQFISFQ--GGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGL 192 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~---dGG~ie~v~~~--~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~ 192 (195)
...+.++|.++|.+.+.|.|.- +-|-|+=+.++ +|.++|+|+..-.|||++. -+..-++++|++ +|+++.|.
T Consensus 10 ~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~-~i~~~v~~al~~-~~~v~~v~ 86 (111)
T COG2151 10 IKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAE-VIADQVEAALEE-IPGVEDVE 86 (111)
T ss_pred hhhhHHHHHHHhhcCCCcccceeeEeeccEEEEEEecCCceEEEEEecCCCCCCccH-HHHHHHHHHHHh-cCCcceEE
Confidence 4567889999999999999985 67888888886 4599999999999999994 455789999888 77776654
No 16
>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=95.32 E-value=0.14 Score=37.02 Aligned_cols=69 Identities=22% Similarity=0.321 Sum_probs=54.3
Q ss_pred HHHHHHHHHHhcCchhhhc---cCCcEEEEEEeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcccee
Q psy1153 122 TVQMIKELLDTRIRPTVQE---DGGDIQFISFQG-GVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGL 192 (195)
Q Consensus 122 ~~~~i~~~l~~~irP~l~~---dGG~ie~v~~~~-g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~ 192 (195)
+.++|.++|.+..-|.+.. .-|-|.=+.+++ |.|++.+.-...+||.. ..|+..++..|.. +|++.+|.
T Consensus 2 ~~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~-~~l~~~i~~al~~-l~gv~~v~ 74 (99)
T TIGR02945 2 LKDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVA-GSMPGEVENAVRA-VPGVGSVT 74 (99)
T ss_pred HHHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChH-HHHHHHHHHHHHh-CCCCceEE
Confidence 4578999999888898876 445566667775 89999999988899977 5588899999976 78877664
No 17
>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=95.09 E-value=0.19 Score=40.81 Aligned_cols=72 Identities=18% Similarity=0.233 Sum_probs=59.0
Q ss_pred chHHHHHHHHHHHhcCchhhhc---cCCcEEEEEEeC---C--EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccc
Q psy1153 119 DDETVQMIKELLDTRIRPTVQE---DGGDIQFISFQG---G--VVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTP 190 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~---dGG~ie~v~~~~---g--~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~ 190 (195)
++...++|.++|.+..-|.+.. +-|-|+=+.+++ + .|+|.|.-...+|++. ..|+..|+.+|.. +|++++
T Consensus 71 ~~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~Id~~~~~~~~V~I~mtLt~p~c~~~-~~L~~dV~~aL~~-l~gV~~ 148 (174)
T TIGR03406 71 GEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMG-PVLVEDVEDKVLA-VPNVDE 148 (174)
T ss_pred ccccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEEecccCCCCEEEEEEEeCCCCCcHH-HHHHHHHHHHHHh-CCCcee
Confidence 3445688999999999999886 567787778876 6 8999999999999987 6677889999975 788877
Q ss_pred ee
Q psy1153 191 GL 192 (195)
Q Consensus 191 V~ 192 (195)
|.
T Consensus 149 V~ 150 (174)
T TIGR03406 149 VE 150 (174)
T ss_pred EE
Confidence 64
No 18
>PRK11670 antiporter inner membrane protein; Provisional
Probab=85.37 E-value=4.5 Score=36.37 Aligned_cols=69 Identities=12% Similarity=0.066 Sum_probs=55.9
Q ss_pred HHHHHHHHHHhcCchhhhc---cCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcccee
Q psy1153 122 TVQMIKELLDTRIRPTVQE---DGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGL 192 (195)
Q Consensus 122 ~~~~i~~~l~~~irP~l~~---dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~ 192 (195)
..++|.++|....-|.+.. .-|-|.=+.++++.+++.+.-.-.+||.. ..++..+++.|+. +|++++|.
T Consensus 13 ~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~ 84 (369)
T PRK11670 13 LRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAF-EELKEQCSAELLR-ITGAKAID 84 (369)
T ss_pred hHHHHHHHHhcCCCCCCCCChhhhCCeeEEEEeCCEEEEEEEECCCCchHH-HHHHHHHHHHHHh-cCCCceEE
Confidence 4588999999888898886 45666667788899999998888889977 5588899999987 78887654
No 19
>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=84.78 E-value=3.9 Score=32.16 Aligned_cols=48 Identities=17% Similarity=0.365 Sum_probs=39.7
Q ss_pred cCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccce
Q psy1153 141 DGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPG 191 (195)
Q Consensus 141 dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V 191 (195)
+-|-|.=+.++++.|.|.|.-.-++||+. ..|++.|+++|+.. ++.+|
T Consensus 13 dLG~Vr~V~v~gd~V~VtIt~Ty~gcpa~-e~L~~~I~~aL~~~--Gv~~V 60 (146)
T TIGR02159 13 DLGMVREVDVDGGGVVVKFTPTYSGCPAL-EVIRQDIRDAVRAL--GVEVV 60 (146)
T ss_pred hcCCeeEEEEECCEEEEEEEeCCCCCchH-HHHHHHHHHHHHhc--CCCeE
Confidence 45778888888999999999999999987 67889999999883 55544
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=81.32 E-value=1.9 Score=26.76 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=21.7
Q ss_pred cccCCCCcchHHHHHHHHHHHHHhh
Q psy1153 160 QGSCTSCPSSVVTLKNGVQNMLQFY 184 (195)
Q Consensus 160 ~GaC~gCp~s~~tl~~~Ie~~l~~~ 184 (195)
+++|.|||.-+..|.+.|-..||.-
T Consensus 7 G~~~~G~~ql~ESLLdrItRklr~g 31 (45)
T PF02061_consen 7 GWPRMGCPQLSESLLDRITRKLRDG 31 (45)
T ss_pred CccccCCchhhHHHHHHHHHHHHHH
Confidence 5799999988888999999999874
No 21
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=75.10 E-value=4.1 Score=32.22 Aligned_cols=25 Identities=32% Similarity=0.752 Sum_probs=19.9
Q ss_pred EEEEEEeCCEEEEEEc--ccCCCCcch
Q psy1153 145 IQFISFQGGVVKLKMQ--GSCTSCPSS 169 (195)
Q Consensus 145 ie~v~~~~g~v~v~l~--GaC~gCp~s 169 (195)
-.+++++++.++|+.. .+|++|.+.
T Consensus 6 ~~Vv~v~~~~a~Ve~~r~saCg~C~a~ 32 (154)
T PRK10862 6 ATVVSWQNGIALLRCEVKAGCSSCASR 32 (154)
T ss_pred EEEEEEECCEEEEEEecCCCCcCcCCC
Confidence 3678889999888874 799988864
No 22
>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=71.66 E-value=3.9 Score=31.21 Aligned_cols=22 Identities=23% Similarity=0.771 Sum_probs=17.3
Q ss_pred EEEEeCCEEEEEE--cccCCCCcc
Q psy1153 147 FISFQGGVVKLKM--QGSCTSCPS 168 (195)
Q Consensus 147 ~v~~~~g~v~v~l--~GaC~gCp~ 168 (195)
+++++++.++|+. +.+|++|.+
T Consensus 1 Vv~v~~~~~~V~~~r~saC~~C~~ 24 (135)
T PF04246_consen 1 VVAVEGGIAWVEVQRSSACGSCSA 24 (135)
T ss_pred CEEEeCCEEEEEEccCCcCcccCC
Confidence 4678899988888 478888873
No 23
>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=63.39 E-value=7.7 Score=28.24 Aligned_cols=26 Identities=31% Similarity=0.452 Sum_probs=18.4
Q ss_pred cCCCCcchHHHHHHHHHHHHHhhCCCc
Q psy1153 162 SCTSCPSSVVTLKNGVQNMLQFYIPET 188 (195)
Q Consensus 162 aC~gCp~s~~tl~~~Ie~~l~~~~pev 188 (195)
+|.+=|||-.|. .+++.+|++++|+.
T Consensus 11 SCVn~PsSkeTy-eWL~aal~RKyp~~ 36 (93)
T PF07315_consen 11 SCVNAPSSKETY-EWLEAALKRKYPDQ 36 (93)
T ss_dssp GGSSS--HHHHH-HHHHHHHHHH-TTS
T ss_pred hhcCCCCchhHH-HHHHHHHhCcCCCC
Confidence 455558887776 69999999999986
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=62.07 E-value=92 Score=25.90 Aligned_cols=117 Identities=18% Similarity=0.278 Sum_probs=76.7
Q ss_pred eecceEEEEecCCC---CCccc------hhHHHHHHHHHhhhcCCCcccCCCCC-------CCCCCCCCchHHHHHHHHH
Q psy1153 66 FGHDFITVTKQDDD---VDWKL------LKPEIFATIMDFFSSGLPVLTDAQPS-------SDTVIHEDDDETVQMIKEL 129 (195)
Q Consensus 66 ~~~dfVtVtk~~~~---~~W~~------l~~~i~~~I~d~l~s~~~~~~~~~~~-------~~~~~~~~~~~~~~~i~~~ 129 (195)
...+-|+|+..++. .+|.. +...|...|.+.-.++.++....... .......+.....+++..+
T Consensus 74 ~V~~~V~v~~~~~~~v~lEW~s~~~nDmiADsv~a~il~~~ssp~svk~~~~~~~h~h~~~~~~~~~~~~~~~~~~l~~~ 153 (216)
T PF11718_consen 74 RVMGCVTVTYDPNEEVVLEWESSPVNDMIADSVVAVILQIDSSPASVKLSSKSCSHSHSHDPNPHEKSDEEERLERLIEL 153 (216)
T ss_pred EEeeeEEEEEeCCcEEEEEEcCCcchhHHHHHHHHHHHHHhhCCccccccccccccccccccccccccCHHHHHHHHHHH
Confidence 33466888887521 25643 44455555566555555544322221 0001123567888999999
Q ss_pred HHhcCchhhhc--cCCcE-EEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhh
Q psy1153 130 LDTRIRPTVQE--DGGDI-QFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFY 184 (195)
Q Consensus 130 l~~~irP~l~~--dGG~i-e~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~ 184 (195)
|+....+.... .+|.. -.+.+++..+.|.|..-..-|. +..|++.||..|++-
T Consensus 154 L~~qFG~~~~~~~~~~~~~~~v~vd~~~A~I~~~t~~Vec~--d~~Lk~rve~~l~r~ 209 (216)
T PF11718_consen 154 LEAQFGDVEVPDIEKPKEPLSVTVDGKVAHIDLSTLEVECE--DEPLKQRVETALKRL 209 (216)
T ss_pred HHHHcCCCccccccccceeEEEEeCCcEEEEecCCCceecC--CHHHHHHHHHHHHHH
Confidence 99998888543 45555 5677788899999988888888 688999999999874
No 25
>PRK12463 chorismate synthase; Reviewed
Probab=60.64 E-value=11 Score=34.35 Aligned_cols=62 Identities=16% Similarity=0.194 Sum_probs=39.9
Q ss_pred cCCccccCCCceEEEEecCCcccCCCccccCCCcccccCChHHhhhcccCCeeEEEeecceEEEEec
Q psy1153 10 IRPTVQEDGGDIQFISFQDGVLEEPGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQ 76 (195)
Q Consensus 10 irp~~~~d~g~~~fi~~e~~~~vl~gg~~~f~~~~~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk~ 76 (195)
.|-.--.-||-++.+-+ | +|.|--++...++-..+.|++++|.||.||+|.|+..|=.-.+.
T Consensus 209 ak~~gDSlGGivev~~~--g---vP~GLGspv~fd~kLda~LA~A~msIpAVKgVE~G~Gf~~a~~~ 270 (390)
T PRK12463 209 AKSSGDSIGGIVEVIAE--G---MPIGVGSYVHYDRKLDAKLAGAIMSINAFKGAEIGVGFEAARQP 270 (390)
T ss_pred HHHhCCCCceEEEEEEE--C---CCCCCCCCccccccchHHHHHHhcCcCceeEEEEccchhhhhCC
Confidence 33333345666666654 2 34232232223345667899999999999999999998666554
No 26
>COG0082 AroC Chorismate synthase [Amino acid transport and metabolism]
Probab=59.80 E-value=11 Score=33.98 Aligned_cols=66 Identities=23% Similarity=0.295 Sum_probs=45.5
Q ss_pred HHHHhhccCCccccCCCceEEEEecCCcccCCCccccCCCcccccCChHHhhhcccCCeeEEEeecceEEEEec
Q psy1153 3 KELLDTRIRPTVQEDGGDIQFISFQDGVLEEPGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQ 76 (195)
Q Consensus 3 ~~~l~~~irp~~~~d~g~~~fi~~e~~~~vl~gg~~~f~~~~~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk~ 76 (195)
++.|+ ++|..-..-||.+++|-. | +|.|--++. .. -..+.||++||.||-||+|.|+.+|=...+.
T Consensus 191 ~~~i~-~~k~~GDSiGgvvevva~--g---vP~GLG~pv-fd-kLda~lA~AlmsI~AvKGVEiG~GF~~a~~~ 256 (369)
T COG0082 191 EELID-KAKKEGDSIGGVVEVVAE--G---VPAGLGEPV-FD-KLDAKLAHALMSIPAVKGVEIGDGFEAARMR 256 (369)
T ss_pred HHHHH-HHHhcCCCcccEEEEEEe--C---CCCCCCCcc-cc-cchHHHHHHhhCCccceeEEeccchhhhhcc
Confidence 34454 566666667888888855 3 342322222 22 5567899999999999999999999766654
No 27
>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=59.77 E-value=55 Score=23.56 Aligned_cols=74 Identities=15% Similarity=0.254 Sum_probs=44.9
Q ss_pred CchHHHHHHHHHHHhc-------CchhhhccCCcEEEEEEe-CCEEEEEEcccCC--CCcchHHHHHHHHHHHHHhhCCC
Q psy1153 118 DDDETVQMIKELLDTR-------IRPTVQEDGGDIQFISFQ-GGVVKLKMQGSCT--SCPSSVVTLKNGVQNMLQFYIPE 187 (195)
Q Consensus 118 ~~~~~~~~i~~~l~~~-------irP~l~~dGG~ie~v~~~-~g~v~v~l~GaC~--gCp~s~~tl~~~Ie~~l~~~~pe 187 (195)
.++.....++.++... .+|.+. .|-.+.=+.++ +++++|.|..+=. .=.+...-+...|-..|.+.+++
T Consensus 22 ~~~~~~~~v~~L~~gp~~~~~~~~~~~~p-~~~~l~~v~~~~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~ 100 (117)
T PF10646_consen 22 EEDDAEAAVNALLKGPSDSEGPGLRSALP-PGTKLNSVTVDDGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPG 100 (117)
T ss_pred CchHHHHHHHHHHhCCCccccceeeecCC-CccceeeEEECCCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCC
Confidence 3456677777777753 233332 33333334445 4499999987432 12222345667888888878999
Q ss_pred cccee
Q psy1153 188 TTPGL 192 (195)
Q Consensus 188 v~~V~ 192 (195)
+++|.
T Consensus 101 v~~V~ 105 (117)
T PF10646_consen 101 VKKVQ 105 (117)
T ss_pred ccEEE
Confidence 98885
No 28
>PRK11023 outer membrane lipoprotein; Provisional
Probab=57.79 E-value=43 Score=27.20 Aligned_cols=65 Identities=14% Similarity=0.211 Sum_probs=43.5
Q ss_pred CCchHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccceee
Q psy1153 117 EDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGLN 193 (195)
Q Consensus 117 ~~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~ 193 (195)
-+|..+..+|+..|.. .|.+.. +.+|.+.-+ +|.|+ |.|.- .+...+...++..+. +|+|++|.+
T Consensus 45 ~dD~~i~~~V~~aL~~--~~~l~~-~~~I~V~v~-~G~V~--L~G~V-----~~~~~k~~A~~ia~~-v~GV~~V~N 109 (191)
T PRK11023 45 VDDGTLELRVNNALSK--DEQIKK-EARINVTAY-QGKVL--LTGQS-----PNAELSERAKQIAMG-VEGVNEVYN 109 (191)
T ss_pred ehhHHHHHHHHHHHhh--CcccCc-CceEEEEEE-CCEEE--EEEEe-----CCHHHHHHHHHHHhc-CCCceeecc
Confidence 4688899999999974 666653 446766655 45444 45642 245677777666555 888888875
No 29
>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=57.11 E-value=33 Score=22.87 Aligned_cols=47 Identities=13% Similarity=0.079 Sum_probs=37.7
Q ss_pred HHhhhcccCCeeEEEeecceEEEEecCCCCCccchhHHHHHHHHHhhh
Q psy1153 51 LGKLLFRIEGVKSVFFGHDFITVTKQDDDVDWKLLKPEIFATIMDFFS 98 (195)
Q Consensus 51 La~~Lf~i~gV~~V~~~~dfVtVtk~~~~~~W~~l~~~i~~~I~d~l~ 98 (195)
+...|.....|+++.+.++-|+++-.. ...|......+.+.+.+.+.
T Consensus 16 ~~~~iv~~g~V~~i~i~~~~V~v~l~l-~~~~~~~~~~l~~~i~~~l~ 62 (72)
T PF01883_consen 16 LGKDIVELGMVRDISIEGGKVSVSLEL-PTPACPAAEPLREEIREALK 62 (72)
T ss_dssp TSSBTTTTTSEEEEEECTCEEEEEE---SSTTHTTHHHHHHHHHHHHH
T ss_pred CCCCHHHcCCeeEEEEECCEEEEEEEE-CCCCchHHHHHHHHHHHHHH
Confidence 556666788999999999999999996 77888877888888887776
No 30
>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=53.81 E-value=18 Score=32.50 Aligned_cols=60 Identities=20% Similarity=0.209 Sum_probs=38.5
Q ss_pred ccCCccccCCCceEEEEecCCcccCCCccccCCCcccccCChHHhhhcccCCeeEEEeecceEEEEe
Q psy1153 9 RIRPTVQEDGGDIQFISFQDGVLEEPGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTK 75 (195)
Q Consensus 9 ~irp~~~~d~g~~~fi~~e~~~~vl~gg~~~f~~~~~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk 75 (195)
+.|-.--.-||-++.+-+ | +|.|--++. . +...+.|++.+|.||.||+|.|+.+|=.-..
T Consensus 192 ~ak~~gDSlGG~ve~~~~--g---vP~GLG~p~-f-~klda~la~a~~sIpAvKgve~G~Gf~~a~~ 251 (344)
T cd07304 192 EAKKEGDSVGGVVEVVAT--G---VPAGLGSPV-F-DKLDARLAQALMSIPAVKGVEIGSGFEAARM 251 (344)
T ss_pred HHHHcCCCCceEEEEEEE--C---CCCCCCccc-c-ccchHHHHHHhcCcCceeEEEECcchhhhhc
Confidence 344444445666666655 2 232211111 1 5677899999999999999999998855543
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=53.59 E-value=34 Score=21.79 Aligned_cols=41 Identities=29% Similarity=0.288 Sum_probs=29.2
Q ss_pred hHHhhhcccCCeeEEEee--cceEEEEecCCCCCccchhHHHH
Q psy1153 50 PLGKLLFRIEGVKSVFFG--HDFITVTKQDDDVDWKLLKPEIF 90 (195)
Q Consensus 50 ~La~~Lf~i~gV~~V~~~--~dfVtVtk~~~~~~W~~l~~~i~ 90 (195)
.+.+.|.++|||.++.+. .+-++|+-.++..+.++|...|.
T Consensus 15 ~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~ 57 (62)
T PF00403_consen 15 KVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE 57 (62)
T ss_dssp HHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH
T ss_pred HHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH
Confidence 467788899999888877 58899988863345655544443
No 32
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.37 E-value=13 Score=27.28 Aligned_cols=27 Identities=26% Similarity=0.394 Sum_probs=21.0
Q ss_pred cCCCCcchHHHHHHHHHHHHHhhCCCcc
Q psy1153 162 SCTSCPSSVVTLKNGVQNMLQFYIPETT 189 (195)
Q Consensus 162 aC~gCp~s~~tl~~~Ie~~l~~~~pev~ 189 (195)
+|.+-|+|-.|. .++|.+|++++|+.-
T Consensus 18 SCV~aPtsKdt~-eWLeaalkRKyp~~~ 44 (106)
T COG4837 18 SCVNAPTSKDTY-EWLEAALKRKYPNQP 44 (106)
T ss_pred HhcCCCcchhHH-HHHHHHHhccCCCCC
Confidence 355557786666 699999999999864
No 33
>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=50.75 E-value=19 Score=24.13 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=15.5
Q ss_pred CCcEEEEEEeCCEEEEEEcccCCCCcchHHH
Q psy1153 142 GGDIQFISFQGGVVKLKMQGSCTSCPSSVVT 172 (195)
Q Consensus 142 GG~ie~v~~~~g~v~v~l~GaC~gCp~s~~t 172 (195)
-|.|+-+.-...- .|.|.+|+.+...
T Consensus 41 kG~I~~~~~~~~~-----~~~C~~C~~~~~~ 66 (69)
T PF09012_consen 41 KGYIRKVDMSSCC-----GGSCSSCGPASKE 66 (69)
T ss_dssp CTSCEEEEEE--S-----SSSSSS-SS----
T ss_pred CCcEEEecCCCCC-----CCCCCCCCCcccc
Confidence 7888877765433 8999999988653
No 34
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=50.31 E-value=20 Score=28.41 Aligned_cols=35 Identities=29% Similarity=0.508 Sum_probs=25.6
Q ss_pred EEEEEeCCEEEEEE--cccCCCCcchHHHHHHHHHHHH
Q psy1153 146 QFISFQGGVVKLKM--QGSCTSCPSSVVTLKNGVQNML 181 (195)
Q Consensus 146 e~v~~~~g~v~v~l--~GaC~gCp~s~~tl~~~Ie~~l 181 (195)
.++++++|.++|+= +-+|+.|++...--. ++.+.|
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 45788899888876 579999999866553 555555
No 35
>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=50.29 E-value=91 Score=26.05 Aligned_cols=67 Identities=13% Similarity=0.249 Sum_probs=39.1
Q ss_pred chHHHHHHHHHHHhcCchhhh-ccCCcEEEEEEeCC----EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccce
Q psy1153 119 DDETVQMIKELLDTRIRPTVQ-EDGGDIQFISFQGG----VVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPG 191 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~-~dGG~ie~v~~~~g----~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V 191 (195)
+++..+++++.+++ .|.+. -| ++.+..+..+ .++|++.+.+ .......+.+.|++.|++++|++.+|
T Consensus 203 ~~~~~~~i~~~i~~--~~~v~~v~--~~~~~~~g~~~~~v~i~v~v~~~~--~v~~~~~i~~~i~~~l~~~~~~i~~v 274 (284)
T PF01545_consen 203 DPELVEKIRRIIES--VPGVIEVH--DLRVWQVGRNKYVVEIHVQVDPDM--SVEEAHEIRERIEKRLREKFPGIYDV 274 (284)
T ss_dssp HHHHHHHHHHHHHH--TSS-SEEE--EEEEEEETT-EEEEEEEEEETTTS--BHHHHHHHHHHHHHHHHHHSTTCEEE
T ss_pred cccchhHHHHhhcc--CCceEecc--ceEEEEecCCcEEEEEEEEeCCCC--CHHHHHHHHHHHHHHHHHhCCCcEEE
Confidence 45667888888874 22222 11 2233333222 3445555554 22334568899999999999999864
No 36
>PRK05382 chorismate synthase; Validated
Probab=50.17 E-value=23 Score=31.95 Aligned_cols=60 Identities=20% Similarity=0.242 Sum_probs=39.1
Q ss_pred cCCccccCCCceEEEEecCCcccCCCccccCCCcccccCChHHhhhcccCCeeEEEeecceEEEEec
Q psy1153 10 IRPTVQEDGGDIQFISFQDGVLEEPGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQ 76 (195)
Q Consensus 10 irp~~~~d~g~~~fi~~e~~~~vl~gg~~~f~~~~~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk~ 76 (195)
.|-.--.-||-++.+-+ | ||.|--++.- +-..+.|++++|.||.||+|.|+..|=.-...
T Consensus 191 ak~~gDSlGG~ve~~~~--g---vP~GLG~p~f--~kLda~la~a~msIpAvKgvE~G~Gf~~a~~~ 250 (359)
T PRK05382 191 AKKEGDSLGGVVEVVAE--G---VPAGLGEPVF--DKLDADLAHALMSINAVKGVEIGDGFAAARLR 250 (359)
T ss_pred HHHcCCCCceEEEEEEE--C---CCCCCCcccc--ccchHHHHHHhcCcCceeEEEECcchhhcccc
Confidence 33334445666666655 2 3422112111 56778999999999999999999998666654
No 37
>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=49.34 E-value=18 Score=24.51 Aligned_cols=25 Identities=20% Similarity=0.486 Sum_probs=15.5
Q ss_pred EEEEEcccCCCCcchHHHHHHHHHHHHHhh
Q psy1153 155 VKLKMQGSCTSCPSSVVTLKNGVQNMLQFY 184 (195)
Q Consensus 155 v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~ 184 (195)
+.+ ++-.|..||. +.+.++..+...
T Consensus 3 I~v-~~~~C~~C~~----~~~~~~~~~~~~ 27 (76)
T PF13192_consen 3 IKV-FSPGCPYCPE----LVQLLKEAAEEL 27 (76)
T ss_dssp EEE-ECSSCTTHHH----HHHHHHHHHHHT
T ss_pred EEE-eCCCCCCcHH----HHHHHHHHHHhc
Confidence 566 6666888883 334555655553
No 38
>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=48.84 E-value=15 Score=32.93 Aligned_cols=55 Identities=24% Similarity=0.266 Sum_probs=33.7
Q ss_pred cCCccccCCCceEEEEecCCcccCCCccccCCCcccccCChHHhhhcccCCeeEEEeecceE
Q psy1153 10 IRPTVQEDGGDIQFISFQDGVLEEPGQTIDFPTGQAAYCSPLGKLLFRIEGVKSVFFGHDFI 71 (195)
Q Consensus 10 irp~~~~d~g~~~fi~~e~~~~vl~gg~~~f~~~~~a~~~~La~~Lf~i~gV~~V~~~~dfV 71 (195)
.|-.--.-||-++.+-+ | ||.|--++. .+ ...+.|++.||.||.||+|.|+..|=
T Consensus 191 ak~~gDSlGG~ve~~~~--g---vP~GLG~p~-fd-kLda~la~al~sIpAvKgvEfG~Gf~ 245 (346)
T PF01264_consen 191 AKKEGDSLGGIVEVVAT--G---VPAGLGSPV-FD-KLDARLAQALMSIPAVKGVEFGDGFE 245 (346)
T ss_dssp HHHTTGGB-EEEEEEEE--S-----TT-SBSS-CC-SHHHHHHHHHHTSTTEEEEEETTGGG
T ss_pred HHHhCCCCCeEEEEEEE--e---cCCCCCCCC-cC-cHHHHHHHHhhCCCCeeeEEecCcHH
Confidence 33334445666676655 3 342211211 22 55678999999999999999999873
No 39
>PLN02754 chorismate synthase
Probab=46.05 E-value=28 Score=32.06 Aligned_cols=32 Identities=16% Similarity=0.204 Sum_probs=27.4
Q ss_pred cccCChHHhhhcccCCeeEEEeecceEEEEec
Q psy1153 45 AAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQ 76 (195)
Q Consensus 45 ~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk~ 76 (195)
+-..+.|++.+|.||.||+|.|+..|=.-...
T Consensus 254 dkLda~LA~Al~SIpAVKGVEfG~GF~~a~~~ 285 (413)
T PLN02754 254 DKLEAELAKAMMSLPATKGFEIGSGFAGTLLT 285 (413)
T ss_pred ccchHHHHHHhcCcCceeEEEEccchhhhhcc
Confidence 56778999999999999999999998666544
No 40
>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=43.08 E-value=35 Score=25.37 Aligned_cols=23 Identities=17% Similarity=0.443 Sum_probs=15.1
Q ss_pred cCCCCcchHHHHHHHHHHHHHhhCC
Q psy1153 162 SCTSCPSSVVTLKNGVQNMLQFYIP 186 (195)
Q Consensus 162 aC~gCp~s~~tl~~~Ie~~l~~~~p 186 (195)
.|.|||. ..+...++.+++..++
T Consensus 45 ~CgGCpg--~~~~~~~~~l~~~~~d 67 (107)
T PF08821_consen 45 TCGGCPG--RKLVRRIKKLKKNGAD 67 (107)
T ss_pred eCCCCCh--hHHHHHHHHHHHCCCC
Confidence 5999993 4455677777755443
No 41
>TIGR00033 aroC chorismate synthase. Homotetramer (noted in E.coli) suggests reason for good conservation.
Probab=40.54 E-value=17 Score=32.71 Aligned_cols=32 Identities=22% Similarity=0.290 Sum_probs=26.5
Q ss_pred cccCChHHhhhcccCCeeEEEeecceEEEEec
Q psy1153 45 AAYCSPLGKLLFRIEGVKSVFFGHDFITVTKQ 76 (195)
Q Consensus 45 ~a~~~~La~~Lf~i~gV~~V~~~~dfVtVtk~ 76 (195)
+...+.|++++|.||.||+|.|+..|=.-...
T Consensus 220 ~kLda~La~a~msIpAvKgvE~G~Gf~~a~~~ 251 (351)
T TIGR00033 220 DKLDARLAHAMMSIPAVKGVEIGDGFELASMR 251 (351)
T ss_pred ccchHHHHHHhcCcCceeEEEECcchhhcccc
Confidence 46678999999999999999999988554433
No 42
>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=39.54 E-value=27 Score=26.15 Aligned_cols=40 Identities=18% Similarity=0.233 Sum_probs=25.7
Q ss_pred chHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCC
Q psy1153 119 DDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSC 166 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gC 166 (195)
..++.++|.+.|. ..-|.+++..|-||..+||+.+.+.|+
T Consensus 9 ~~~La~~ia~~L~--------~~~~~~~~~~F~dGE~~v~i~~~v~g~ 48 (116)
T PF13793_consen 9 SQDLAERIAEALG--------IPLGKVETKRFPDGETYVRIPESVRGK 48 (116)
T ss_dssp GHHHHHHHHHHTT--------S-EE-EEEEE-TTS-EEEEESS--TTS
T ss_pred CHHHHHHHHHHhC--------CceeeeEEEEcCCCCEEEEecccccCC
Confidence 4566777777775 444568999999999999999876543
No 43
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=35.16 E-value=1.4e+02 Score=20.03 Aligned_cols=62 Identities=11% Similarity=0.251 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHH---HHHHHHHHHHhhC--CCccce
Q psy1153 122 TVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVT---LKNGVQNMLQFYI--PETTPG 191 (195)
Q Consensus 122 ~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~t---l~~~Ie~~l~~~~--pev~~V 191 (195)
...++.+....-+-|.++. ....+++++|+++|...-+ +-.+. .+.-|-..|++++ +.|+++
T Consensus 21 ~~~~l~~~w~~ivg~~l~~---~~~~~~i~~g~L~i~v~~~-----~~~~~L~~~~~~il~~l~~~~g~~~i~~I 87 (89)
T PF05258_consen 21 QLARLQQNWKQIVGPELAQ---HTRPVSIKDGTLVIEVDSS-----AWAQELRYMKPQILKKLNEFLGFPAIKDI 87 (89)
T ss_pred HHHHHHHHHHHHhCHHHHc---cEEEEEEECCEEEEEECCH-----HHHHHHHHHHHHHHHHHHHHcCCCCccEe
Confidence 3556666666566666654 4899999999999954321 11223 3445556666666 345544
No 44
>PHA02782 hypothetical protein; Provisional
Probab=35.09 E-value=88 Score=29.15 Aligned_cols=58 Identities=16% Similarity=0.261 Sum_probs=37.9
Q ss_pred chHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHHH---HHHHHHHHHh
Q psy1153 119 DDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTL---KNGVQNMLQF 183 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl---~~~Ie~~l~~ 183 (195)
.+.+.++|++.|-+.|-.+...+|| .-|++++|.+-.| .||++....| ...|+..+++
T Consensus 368 Tkkl~~rIKEiLP~yVSAFANT~GG-yLfIGVdDdt~~I------iG~~~e~e~L~~Le~aIe~cI~K 428 (503)
T PHA02782 368 AKQLRTRIRQQLPSILSSFANTEGG-YLFIGVDNNTHKV------IGFTVGQDYLKLVENDIEKYIKR 428 (503)
T ss_pred HHHHHHHHHHHhhHHhHhheeCCCC-EEEEEEcCCCCeE------eeeecCHHHHHHHHHHHHHHHHh
Confidence 4458899999999888766666666 4588998762222 2666544444 3666666654
No 45
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=34.20 E-value=2.2e+02 Score=24.38 Aligned_cols=67 Identities=16% Similarity=0.169 Sum_probs=37.2
Q ss_pred chHHHHHHHHHHHhcCchhhhc-cCCcEEEEEEeCC-EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcc
Q psy1153 119 DDETVQMIKELLDTRIRPTVQE-DGGDIQFISFQGG-VVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETT 189 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~-dGG~ie~v~~~~g-~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~ 189 (195)
+++..++|++.+. .+ |.+.. | ++.....-+. .+.+.+.-...-+-.....+.+.+|+.|++.+|++.
T Consensus 211 ~~~~~~~I~~~i~-~~-~~v~~v~--~l~~~~~G~~~~v~v~i~v~~~~~~~e~h~i~~~ie~~l~~~~~~~~ 279 (299)
T PRK09509 211 PDEERQEIIDIVT-SW-PGVSGAH--DLRTRQSGPTRFIQLHLEMEDNLPLVQAHMIADQVEQALLRRFPGSD 279 (299)
T ss_pred CHHHHHHHHHHHH-hC-CCCcCce--eeeeEeeCCeEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHhCCCCE
Confidence 5567888888887 33 33322 2 4444433221 233333322222222335567899999999999764
No 46
>TIGR01297 CDF cation diffusion facilitator family transporter. This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. 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.
Probab=33.80 E-value=1.7e+02 Score=24.28 Aligned_cols=67 Identities=15% Similarity=0.155 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHHhcCchhhh-ccCCcEEEEEEeCC----EEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcccee
Q psy1153 120 DETVQMIKELLDTRIRPTVQ-EDGGDIQFISFQGG----VVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGL 192 (195)
Q Consensus 120 ~~~~~~i~~~l~~~irP~l~-~dGG~ie~v~~~~g----~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~ 192 (195)
++..+++++.+. .+ |.+. -| ++.....-++ .++|.+.+.++-. ....+...+|+.+++.+|++..|.
T Consensus 191 ~~~~~~i~~~i~-~~-~~v~~v~--~~~~~~~G~~~~~v~~~v~v~~~~~~~--~ah~i~~~i~~~i~~~~~~v~~v~ 262 (268)
T TIGR01297 191 EEDLEEIKKAIL-SI-PGVKGVH--DLHIWRIGPGKLFLDVHVVVDPDLDLK--QAHDIALEIEREILKRHPGIEHVT 262 (268)
T ss_pred cccHHHHHHHHh-cC-CCcccce--EeEEEEcCCCCEEEEEEEEECCCCChh--HHHHHHHHHHHHHHHhcCCCCeEE
Confidence 345677777776 33 3332 12 2444444332 4556666654322 224566789999999899997763
No 47
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=31.58 E-value=21 Score=25.19 Aligned_cols=26 Identities=35% Similarity=0.635 Sum_probs=16.2
Q ss_pred CCcEEEEEEe-CCEEEEEEcccCCCCcchHH
Q psy1153 142 GGDIQFISFQ-GGVVKLKMQGSCTSCPSSVV 171 (195)
Q Consensus 142 GG~ie~v~~~-~g~v~v~l~GaC~gCp~s~~ 171 (195)
=|.|+=+.=+ .|-. +|.|.+||-+..
T Consensus 43 kGkverv~~~~~gC~----sGsCk~C~e~~~ 69 (78)
T PRK15431 43 MGKAVRIQEEPDGCL----SGSCKSCPEGKA 69 (78)
T ss_pred CCCeEeeccCCCCCC----CCCCCCCCCCcc
Confidence 4666655422 2332 899999998753
No 48
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=30.59 E-value=4.2e+02 Score=27.17 Aligned_cols=20 Identities=35% Similarity=0.522 Sum_probs=17.1
Q ss_pred ccCChHHhhhcccCCeeEEE
Q psy1153 46 AYCSPLGKLLFRIEGVKSVF 65 (195)
Q Consensus 46 a~~~~La~~Lf~i~gV~~V~ 65 (195)
....|+.+.|..++||+.+.
T Consensus 62 ~vt~piE~~l~~i~gv~~i~ 81 (1025)
T PRK10614 62 SVATPLERSLGRIAGVNEMT 81 (1025)
T ss_pred HHHHHHHHHhcCCCCceEEE
Confidence 45679999999999999984
No 49
>PRK11688 hypothetical protein; Provisional
Probab=30.20 E-value=1.3e+02 Score=23.15 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=32.8
Q ss_pred chHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccC
Q psy1153 119 DDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSC 163 (195)
Q Consensus 119 ~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC 163 (195)
.+++.+++++.+. .-.|+.+..| ++++.+++|.+.++|.-.=
T Consensus 6 ~~~~~~~~~~~~~-~~~pf~~~lG--~~~~~~~~g~~~~~l~~~~ 47 (154)
T PRK11688 6 QEEALKLVGEIFV-YHMPFNRLLG--LELERLEPDFVELSFKMQP 47 (154)
T ss_pred HHHHHHHHHHHHH-hcCCHHHHhC--cEEEEEeCCEEEEEeeCCH
Confidence 4678888888887 4578888775 7888888999999986543
No 50
>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=28.98 E-value=1.9e+02 Score=26.76 Aligned_cols=24 Identities=8% Similarity=0.253 Sum_probs=17.6
Q ss_pred cchhHHHHHHHHHhhhcCCCcccC
Q psy1153 83 KLLKPEIFATIMDFFSSGLPVLTD 106 (195)
Q Consensus 83 ~~l~~~i~~~I~d~l~s~~~~~~~ 106 (195)
.++.+++++++.....+|.++...
T Consensus 228 ~Eit~~a~~Al~~L~~aGI~l~nQ 251 (417)
T TIGR03820 228 REITASSKKALAKLADAGIPLGNQ 251 (417)
T ss_pred HhChHHHHHHHHHHHHcCCEEEee
Confidence 578888888888887777654443
No 51
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=28.46 E-value=39 Score=25.57 Aligned_cols=34 Identities=24% Similarity=0.435 Sum_probs=22.4
Q ss_pred cCCcEEEEEEeCCEEEEEEcc--cCCCCcchHHHHH
Q psy1153 141 DGGDIQFISFQGGVVKLKMQG--SCTSCPSSVVTLK 174 (195)
Q Consensus 141 dGG~ie~v~~~~g~v~v~l~G--aC~gCp~s~~tl~ 174 (195)
+|..+.+-++++..+.|-+-. -|..|+.....|.
T Consensus 19 ~G~~~~l~~~~gk~~ll~f~~~~~~p~C~~~~~~l~ 54 (154)
T PRK09437 19 DGEQVSLTDFQGQRVLVYFYPKAMTPGCTVQACGLR 54 (154)
T ss_pred CCCEEeHHHhCCCCEEEEEECCCCCCchHHHHHHHH
Confidence 566677767766666666654 3677887665554
No 52
>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=27.27 E-value=1.6e+02 Score=24.13 Aligned_cols=66 Identities=11% Similarity=0.191 Sum_probs=42.6
Q ss_pred CchHHHHHHHHHH--HhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCc
Q psy1153 118 DDDETVQMIKELL--DTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPET 188 (195)
Q Consensus 118 ~~~~~~~~i~~~l--~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev 188 (195)
.++++.++|++.| + .+||. |-.+.+.....-.+.|.+..-...=+......+..|++.|+.++-+.
T Consensus 161 ~~~~l~~~V~~~i~~~-~~~p~----~~~v~v~~~~~~~v~v~~~l~~~~~~~~~~~~~~~i~~al~~y~~~~ 228 (243)
T PF04865_consen 161 PSQELLAAVQAYINAE-DVRPL----GDRVTVKAPTYVPVDVTATLTVYPGYDTAEVIQAAIKAALRAYFNSL 228 (243)
T ss_pred CCHHHHHHHHHHhhhh-ccCCC----ceEEEEECCEEEEEEEEEEEEECCCCChHHHHHHHHHHHHHHHHHhh
Confidence 4678899999999 5 66665 33666666665556666654444222223455558889998887553
No 53
>PRK09579 multidrug efflux protein; Reviewed
Probab=27.16 E-value=3.7e+02 Score=27.56 Aligned_cols=22 Identities=23% Similarity=0.194 Sum_probs=18.1
Q ss_pred ccCChHHhhhcccCCeeEEEee
Q psy1153 46 AYCSPLGKLLFRIEGVKSVFFG 67 (195)
Q Consensus 46 a~~~~La~~Lf~i~gV~~V~~~ 67 (195)
.-..|+.+.|..++||+.+.-.
T Consensus 62 ~Vt~plE~~L~~v~gi~~i~S~ 83 (1017)
T PRK09579 62 YITQPLQQSLASAEGIDYMTSV 83 (1017)
T ss_pred HHHHHHHHHhcCCCCceEEEEE
Confidence 4567999999999999988743
No 54
>COG5429 Uncharacterized secreted protein [Function unknown]
Probab=24.84 E-value=57 Score=27.98 Aligned_cols=23 Identities=39% Similarity=0.756 Sum_probs=18.4
Q ss_pred CEEEEEEcccCCCCcchHHHHHH
Q psy1153 153 GVVKLKMQGSCTSCPSSVVTLKN 175 (195)
Q Consensus 153 g~v~v~l~GaC~gCp~s~~tl~~ 175 (195)
++|.+--.-.|++||-++.-|..
T Consensus 43 ~VVELfTSQGCsSCPPAd~~l~k 65 (261)
T COG5429 43 GVVELFTSQGCSSCPPADANLAK 65 (261)
T ss_pred eEEEEeecCCcCCCChHHHHHHH
Confidence 56777777889999999877753
No 55
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=24.09 E-value=1.8e+02 Score=21.48 Aligned_cols=34 Identities=35% Similarity=0.507 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcc
Q psy1153 120 DETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQG 161 (195)
Q Consensus 120 ~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~G 161 (195)
+++...|++.|+.. .+.|++ +.+.+|+++|.+..
T Consensus 11 d~~l~~ie~~ld~~-------~~~d~D-~e~~~gVLti~f~~ 44 (105)
T PRK00446 11 DALWQAIEEQLDDD-------GDADID-CERNGGVLTLTFEN 44 (105)
T ss_pred HHHHHHHHHHHHhc-------cCCCee-eeccCCEEEEEECC
Confidence 34555666666621 344543 23357888888753
No 56
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=23.86 E-value=4.8e+02 Score=26.85 Aligned_cols=112 Identities=20% Similarity=0.386 Sum_probs=67.2
Q ss_pred ccCChHHhhhcccCCeeEEEee----cceEEEEecCCCCCccchhHHHHHHHHHh---hhcCC---CcccCCCCCC-C-C
Q psy1153 46 AYCSPLGKLLFRIEGVKSVFFG----HDFITVTKQDDDVDWKLLKPEIFATIMDF---FSSGL---PVLTDAQPSS-D-T 113 (195)
Q Consensus 46 a~~~~La~~Lf~i~gV~~V~~~----~dfVtVtk~~~~~~W~~l~~~i~~~I~d~---l~s~~---~~~~~~~~~~-~-~ 113 (195)
.--.|+.+.|..++||+.+.-. ...|+|+-++ +.+|+....++++.+.+. |..+. |.+....... + .
T Consensus 71 ~Vt~piE~~l~~v~gv~~i~S~S~~G~s~i~v~f~~-g~d~~~a~~ev~~~i~~~~~~LP~~~~~~p~~~~~~~~~~pv~ 149 (1040)
T PRK10503 71 AVTAPLERQFGQMSGLKQMSSQSSGGASVITLQFQL-TLPLDVAEQEVQAAINAATNLLPSDLPNPPVYSKVNPADPPIM 149 (1040)
T ss_pred HHHHHHHHHhcCCCCccEEEEEecCCeEEEEEEEEC-CCChHHHHHHHHHHHHHHHHhCCCccCCCCEEEEeCCCCCceE
Confidence 4567999999999999888763 4457777775 789888888888887654 32221 2221110000 0 0
Q ss_pred --CCCCCchHHHHHHHHHHHhcCchhhhccCCcEEEEEEeC---CEEEEEEc
Q psy1153 114 --VIHEDDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQG---GVVKLKMQ 160 (195)
Q Consensus 114 --~~~~~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~---g~v~v~l~ 160 (195)
....+ ..-...+++..++.++|.|..--| +.-+.+.+ ..+.|.+.
T Consensus 150 ~~~l~~~-~~~~~~L~~~~~~~l~~~L~~i~g-V~~V~~~G~~~~ei~V~vd 199 (1040)
T PRK10503 150 TLAVTST-AMPMTQVEDMVETRVAQKISQVSG-VGLVTLSGGQRPAVRVKLN 199 (1040)
T ss_pred EEEEEcC-CCCHHHHHHHHHHHHHHHhcCCCC-ceEEEecCCCceEEEEEEC
Confidence 00011 112356777787788999988665 33344443 46777774
No 57
>COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism]
Probab=23.43 E-value=3.3e+02 Score=24.82 Aligned_cols=25 Identities=32% Similarity=0.170 Sum_probs=19.0
Q ss_pred ChHHhhhcccCCeeEEEeecceEEE
Q psy1153 49 SPLGKLLFRIEGVKSVFFGHDFITV 73 (195)
Q Consensus 49 ~~La~~Lf~i~gV~~V~~~~dfVtV 73 (195)
..|...|.+||.|+.|-|+..-..|
T Consensus 178 ~~ll~~L~~IpHv~iiRi~TR~pvv 202 (369)
T COG1509 178 EWLLKRLRAIPHVKIIRIGTRLPVV 202 (369)
T ss_pred HHHHHHHhcCCceeEEEeeccccee
Confidence 3577778889999999999765444
No 58
>TIGR02554 PrgH type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex.
Probab=22.97 E-value=3.4e+02 Score=24.88 Aligned_cols=59 Identities=14% Similarity=0.160 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhcCchhhhccCCcEEEEEEe-----CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCcccee
Q psy1153 121 ETVQMIKELLDTRIRPTVQEDGGDIQFISFQ-----GGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGL 192 (195)
Q Consensus 121 ~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~-----~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~ 192 (195)
..+++|.+.|. .++..+.+..++ .-++. +.+. =++.+.+-+..+.+.|+.++|-.++|.
T Consensus 224 ~~~~~i~~~L~--------~~~P~l~~~kv~l~~P~~Pvl~--l~~q---~~~~~~~~~~~l~~~l~~~~pya~~v~ 287 (389)
T TIGR02554 224 AERQRVSRWLD--------EAGPQLAFYRLRLDAPRHPELW--LSRQ---RNAAPAAARARLIGELRRLMPYARDVR 287 (389)
T ss_pred HHHHHHHHHHH--------hhCCcceEEEEEcCCCCCCEEE--Eecc---cCCCCHHHHHHHHHHHHHhCCccceeE
Confidence 45667888877 444455555553 23443 4442 123445666789999999999988775
No 59
>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=22.86 E-value=1.8e+02 Score=21.25 Aligned_cols=31 Identities=29% Similarity=0.542 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEc
Q psy1153 121 ETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQ 160 (195)
Q Consensus 121 ~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~ 160 (195)
++..+|++.|+ ..+.|+++ .+.+|+++|.+.
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 34445555554 45555432 234788888775
No 60
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.79 E-value=2.2e+02 Score=18.33 Aligned_cols=51 Identities=14% Similarity=0.128 Sum_probs=31.9
Q ss_pred hhhccCCcEEEEEEe---CCEEEEEEcccCCCCcchHH-HHHHHHHHHHHhhCCCccceee
Q psy1153 137 TVQEDGGDIQFISFQ---GGVVKLKMQGSCTSCPSSVV-TLKNGVQNMLQFYIPETTPGLN 193 (195)
Q Consensus 137 ~l~~dGG~ie~v~~~---~g~v~v~l~GaC~gCp~s~~-tl~~~Ie~~l~~~~pev~~V~~ 193 (195)
.|+.+|.+|..+... ++...+++.=.- +... .| +.+-+.|++ +|+|.+|.-
T Consensus 20 ~la~~~inI~~i~~~~~~~~~~~i~~~v~v----~~~~~~l-~~l~~~L~~-i~~V~~v~~ 74 (76)
T cd04888 20 TIAQVRGNVLTINQNIPIHGRANVTISIDT----STMNGDI-DELLEELRE-IDGVEKVEL 74 (76)
T ss_pred HHHHcCCCEEEEEeCCCCCCeEEEEEEEEc----CchHHHH-HHHHHHHhc-CCCeEEEEE
Confidence 445889999888762 455555554322 1122 34 467777777 888888764
No 61
>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=22.65 E-value=61 Score=24.07 Aligned_cols=35 Identities=20% Similarity=0.428 Sum_probs=23.0
Q ss_pred ccCCcEEEEEEeC-CEEEEEEc-c-cCCCCcchHHHHH
Q psy1153 140 EDGGDIQFISFQG-GVVKLKMQ-G-SCTSCPSSVVTLK 174 (195)
Q Consensus 140 ~dGG~ie~v~~~~-g~v~v~l~-G-aC~gCp~s~~tl~ 174 (195)
.+|..+.+-++.+ ..+.|-+- + -|..|+.....|.
T Consensus 15 ~~g~~v~l~~~~g~k~~vl~f~~~~~c~~C~~~~~~l~ 52 (149)
T cd03018 15 QNGQEVRLSEFRGRKPVVLVFFPLAFTPVCTKELCALR 52 (149)
T ss_pred CCCCEEeHHHHcCCCeEEEEEeCCCCCccHHHHHHHHH
Confidence 3577777777766 66556553 3 4899987655664
No 62
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=22.45 E-value=50 Score=28.16 Aligned_cols=17 Identities=24% Similarity=0.562 Sum_probs=12.8
Q ss_pred CEEEEEEc-ccCCCCcch
Q psy1153 153 GVVKLKMQ-GSCTSCPSS 169 (195)
Q Consensus 153 g~v~v~l~-GaC~gCp~s 169 (195)
|++-|.+. ++|+||-+-
T Consensus 189 g~gvvpl~g~~C~GC~m~ 206 (239)
T COG1579 189 GVGVVPLEGRVCGGCHMK 206 (239)
T ss_pred CceEEeecCCcccCCeee
Confidence 56666665 489999986
No 63
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=21.61 E-value=1.2e+02 Score=23.50 Aligned_cols=62 Identities=11% Similarity=0.199 Sum_probs=38.7
Q ss_pred CchHHHHHHHHHHHhcCchhhhccCCcEEEEEEeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHhhCCCccceee
Q psy1153 118 DDDETVQMIKELLDTRIRPTVQEDGGDIQFISFQGGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFYIPETTPGLN 193 (195)
Q Consensus 118 ~~~~~~~~i~~~l~~~irP~l~~dGG~ie~v~~~~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~~pev~~V~~ 193 (195)
+.+.+..+|...|... -+ .-+++ -+.+++|+|+++ |...+...++.+..+... +|.|++|.+
T Consensus 23 ~~~~~~~~i~~~i~~~---~~--~~~~i-~V~v~~G~v~l~-------G~v~s~~~~~~~~~aa~~-v~GV~~V~d 84 (147)
T PRK11198 23 DNEDAADALKEHISKQ---GL--GDADV-NVQVEDGKATVS-------GDAASQEAKEKILLAVGN-IQGIASVDD 84 (147)
T ss_pred chHHHHHHHHHHHHhc---CC--CcCCc-eEEEeCCEEEEE-------EEeCCHHHHHHHHHHhcc-CCCcceecc
Confidence 3566777777777631 22 22234 356679999984 334456666677766666 888888764
No 64
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=21.22 E-value=2.3e+02 Score=28.79 Aligned_cols=109 Identities=22% Similarity=0.259 Sum_probs=60.6
Q ss_pred cccCChHHhhhcccCCeeEEEee--cceEEEEecCCCCCccchhHHHHHHHHHhhhcCCCcccCCCCCCCCCCCCCchHH
Q psy1153 45 AAYCSPLGKLLFRIEGVKSVFFG--HDFITVTKQDDDVDWKLLKPEIFATIMDFFSSGLPVLTDAQPSSDTVIHEDDDET 122 (195)
Q Consensus 45 ~a~~~~La~~Lf~i~gV~~V~~~--~dfVtVtk~~~~~~W~~l~~~i~~~I~d~l~s~~~~~~~~~~~~~~~~~~~~~~~ 122 (195)
.....|+.+.|..++||+.+.-. .+.-+|+-.- +|+ .+-++.
T Consensus 59 ~~vt~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f---~~~---------------------------------~d~~~a 102 (1021)
T PF00873_consen 59 QLVTKPLEEALSSVEGVKEIRSTSREGSSSITVEF---DDG---------------------------------TDIDEA 102 (1021)
T ss_dssp HHTHHHHHHTHCSSTTEEEEEEEETTSEEEEEEEE---STT---------------------------------S-HHHH
T ss_pred HHHHHHHHHHHcCCCCeEEEEEEecCCcEEEEEEe---ccc---------------------------------cCHHHH
Confidence 34577999999999999998855 3333333331 220 123344
Q ss_pred HHHHHHHHHhcCchhhhccCCcEEEEEE--e-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHhh---CCCcccee
Q psy1153 123 VQMIKELLDTRIRPTVQEDGGDIQFISF--Q-GGVVKLKMQGSCTSCPSSVVTLKNGVQNMLQFY---IPETTPGL 192 (195)
Q Consensus 123 ~~~i~~~l~~~irP~l~~dGG~ie~v~~--~-~g~v~v~l~GaC~gCp~s~~tl~~~Ie~~l~~~---~pev~~V~ 192 (195)
...+++.|+ .+++.+..+=..-.+..+ . .....+.+.+. +=..+...|++.++..|+.+ +|+|.+|.
T Consensus 103 ~~~v~~~i~-~~~~~LP~~~~~p~i~~~~~~~~~i~~~~l~~~--~~~~~~~~l~~~~~~~l~~~L~~i~gV~~v~ 175 (1021)
T PF00873_consen 103 LQEVREKID-QIRSDLPPGVEEPQIFKFDPSDSPIMILALTSD--DGTLDLKELRDYAEEQLKPRLERIPGVARVD 175 (1021)
T ss_dssp HHHHHHHHH-HHGGGS-HHHHHHEEEEEEEECCEEEEEEEEES--SSSS-HHHHHHHHHHCTHHHHHTSTTEEEEE
T ss_pred HHHHHHHHH-hhhhhCcccccCCceeeccCCCceeEEEEeccC--CCCCCHHHHHHHHHHHHHHhccceeEEEEEE
Confidence 556666666 566554433223333333 3 34667788776 11244567766666666654 56666654
No 65
>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=20.85 E-value=1.1e+02 Score=22.49 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=18.9
Q ss_pred HHHHHHHHHhcCchhhhccCCcEEEEEEeC--CEEEEEEccc
Q psy1153 123 VQMIKELLDTRIRPTVQEDGGDIQFISFQG--GVVKLKMQGS 162 (195)
Q Consensus 123 ~~~i~~~l~~~irP~l~~dGG~ie~v~~~~--g~v~v~l~Ga 162 (195)
.+.|++++. .+| .|.+|+|.. ..-+|||..+
T Consensus 15 re~iK~~f~--------~~g-~V~yVD~~~G~~~g~VRf~~~ 47 (105)
T PF08777_consen 15 REDIKEAFS--------QFG-EVAYVDFSRGDTEGYVRFKTP 47 (105)
T ss_dssp HHHHHHHT---------SS---EEEEE--TT-SEEEEEESS-
T ss_pred HHHHHHHHH--------hcC-CcceEEecCCCCEEEEEECCc
Confidence 556666665 444 999999964 5899999875
No 66
>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=20.66 E-value=1.4e+02 Score=20.23 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=18.4
Q ss_pred CCCCcchHHHHHHHHHHHHHhhCCCc
Q psy1153 163 CTSCPSSVVTLKNGVQNMLQFYIPET 188 (195)
Q Consensus 163 C~gCp~s~~tl~~~Ie~~l~~~~pev 188 (195)
|.+|...... ..+.+.|...+|+.
T Consensus 6 C~~C~y~~Ra--~~l~q~L~~~Fp~~ 29 (72)
T TIGR02174 6 CGSCGYKPRA--AWLKQELLEEFPDL 29 (72)
T ss_pred CCCCCChHHH--HHHHHHHHHHCCCC
Confidence 7788765444 47889999999984
Done!