Query 023342
Match_columns 283
No_of_seqs 72 out of 74
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 03:18:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023342.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023342hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12046 DUF3529: Protein of u 100.0 2.1E-77 4.5E-82 520.2 20.9 169 101-273 2-173 (173)
2 PRK11198 LysM domain/BON super 92.8 0.16 3.4E-06 43.1 4.1 57 116-178 1-62 (147)
3 PF05140 ResB: ResB-like famil 81.8 17 0.00038 35.7 10.9 25 142-166 106-130 (464)
4 PF11990 DUF3487: Protein of u 75.5 3.4 7.4E-05 34.8 3.5 63 166-234 12-82 (121)
5 COG5375 Uncharacterized protei 74.9 1.8 3.9E-05 40.2 1.8 22 157-178 188-209 (216)
6 PF05915 DUF872: Eukaryotic pr 70.0 9.8 0.00021 31.9 4.9 49 179-228 43-95 (115)
7 TIGR03750 conj_TIGR03750 conju 69.0 7.6 0.00017 32.7 4.0 64 167-235 10-80 (111)
8 PF13567 DUF4131: Domain of un 67.8 18 0.0004 28.1 5.8 8 236-243 80-87 (176)
9 PF09286 Pro-kuma_activ: Pro-k 67.2 8.5 0.00018 31.6 4.0 34 144-177 59-95 (143)
10 PF05818 TraT: Enterobacterial 60.5 25 0.00053 32.7 6.0 70 132-202 21-101 (215)
11 PRK06080 1,4-dihydroxy-2-napht 53.2 32 0.00069 31.4 5.5 36 150-185 55-93 (293)
12 PF10003 DUF2244: Integral mem 52.6 23 0.00051 29.8 4.2 59 179-239 6-69 (140)
13 PF06570 DUF1129: Protein of u 49.0 34 0.00075 30.2 4.9 26 205-230 175-200 (206)
14 PF09186 DUF1949: Domain of un 46.7 37 0.00081 23.1 3.8 34 149-182 8-43 (56)
15 PF07226 DUF1422: Protein of u 44.8 32 0.00069 29.6 3.8 45 189-233 71-115 (117)
16 PF05620 DUF788: Protein of un 44.7 53 0.0012 28.5 5.3 27 105-131 48-74 (170)
17 PF14946 DUF4501: Domain of un 41.9 17 0.00036 33.2 1.8 31 98-128 88-120 (180)
18 PF00474 SSF: Sodium:solute sy 40.9 17 0.00036 34.1 1.8 55 179-233 335-397 (406)
19 PF05211 NLBH: Neuraminyllacto 40.7 12 0.00026 35.7 0.7 21 145-165 88-108 (258)
20 PRK03094 hypothetical protein; 39.5 22 0.00047 28.6 1.9 17 149-165 10-26 (80)
21 PF12191 stn_TNFRSF12A: Tumour 39.3 8.8 0.00019 33.4 -0.3 26 219-244 93-118 (129)
22 TIGR01006 polys_exp_MPA1 polys 39.2 98 0.0021 27.1 6.2 70 130-199 118-193 (226)
23 PF11374 DUF3176: Protein of u 37.5 19 0.00041 29.7 1.4 61 171-232 7-71 (111)
24 COG5488 Integral membrane prot 37.2 58 0.0013 29.5 4.4 55 184-240 30-89 (164)
25 PF10267 Tmemb_cc2: Predicted 37.2 39 0.00085 33.9 3.7 64 167-231 323-393 (395)
26 TIGR03062 pip_yhgE_Cterm YhgE/ 35.3 94 0.002 26.3 5.3 48 179-226 95-144 (208)
27 TIGR01160 SUI1_MOF2 translatio 35.2 53 0.0012 27.6 3.7 33 248-280 77-110 (110)
28 PRK11056 hypothetical protein; 35.1 56 0.0012 28.3 3.8 45 189-233 71-115 (120)
29 TIGR03861 phenyl_ABC_PedC alco 34.4 85 0.0018 27.6 5.0 48 180-227 139-190 (253)
30 PRK06737 acetolactate synthase 32.8 71 0.0015 25.0 3.8 49 217-268 15-65 (76)
31 TIGR00751 menA 1,4-dihydroxy-2 32.1 79 0.0017 29.7 4.7 56 170-227 68-126 (284)
32 PRK10408 putative L-valine exp 31.7 34 0.00074 29.2 2.0 45 183-230 41-90 (111)
33 PF03698 UPF0180: Uncharacteri 31.5 34 0.00074 27.3 1.9 17 149-165 10-26 (80)
34 TIGR02056 ChlG chlorophyll syn 31.5 1.1E+02 0.0024 28.7 5.5 18 210-227 128-145 (306)
35 TIGR01167 LPXTG_anchor LPXTG-m 30.2 61 0.0013 20.6 2.6 26 98-124 6-31 (34)
36 PF11666 DUF2933: Protein of u 29.5 41 0.00088 25.2 1.9 19 208-226 21-39 (55)
37 PF13829 DUF4191: Domain of un 29.2 93 0.002 29.2 4.6 22 185-206 29-50 (224)
38 PF04217 DUF412: Protein of un 28.9 56 0.0012 28.8 2.9 35 193-227 44-83 (143)
39 PRK14447 acylphosphatase; Prov 28.6 1.7E+02 0.0036 23.3 5.3 31 249-280 45-75 (95)
40 PF09911 DUF2140: Uncharacteri 28.4 1.3E+02 0.0028 26.9 5.1 34 143-177 50-89 (187)
41 COG1575 MenA 1,4-dihydroxy-2-n 28.3 89 0.0019 30.5 4.4 45 180-227 94-138 (303)
42 PF13710 ACT_5: ACT domain; PD 28.2 52 0.0011 24.2 2.3 48 218-268 6-55 (63)
43 PRK01002 nickel responsive reg 27.3 82 0.0018 27.0 3.6 44 234-278 84-129 (141)
44 PF02080 TrkA_C: TrkA-C domain 27.3 89 0.0019 22.0 3.3 22 247-268 50-71 (71)
45 PRK05951 ubiA prenyltransferas 27.0 1.4E+02 0.0031 27.8 5.4 18 209-226 115-132 (296)
46 TIGR01291 nodJ ABC-2 type tran 26.8 1.2E+02 0.0026 27.1 4.8 49 179-227 137-189 (253)
47 COG3317 NlpB Uncharacterized l 26.1 90 0.002 31.1 4.1 31 131-165 97-128 (342)
48 PLN02922 prenyltransferase 26.1 1.6E+02 0.0035 28.1 5.7 34 193-227 107-140 (315)
49 PRK14444 acylphosphatase; Prov 25.3 1.1E+02 0.0024 24.2 3.8 24 245-268 39-63 (92)
50 PRK13304 L-aspartate dehydroge 24.7 4.2E+02 0.0091 24.2 7.9 97 117-256 124-223 (265)
51 PF13268 DUF4059: Protein of u 24.2 1.1E+02 0.0024 24.4 3.5 19 110-128 18-36 (72)
52 PRK11152 ilvM acetolactate syn 24.1 53 0.0012 25.6 1.8 22 144-165 12-33 (76)
53 PF00708 Acylphosphatase: Acyl 23.5 1.2E+02 0.0026 23.3 3.6 35 245-280 40-74 (91)
54 KOG2174 Leptin receptor gene-r 23.5 1.4E+02 0.0031 26.2 4.4 46 183-233 7-55 (131)
55 smart00833 CobW_C Cobalamin sy 23.2 94 0.002 22.9 2.9 24 256-282 13-36 (92)
56 PF04133 Vps55: Vacuolar prote 23.1 1.2E+02 0.0027 25.6 3.9 39 184-225 2-43 (120)
57 PF01957 NfeD: NfeD-like C-ter 22.9 19 0.00041 28.6 -1.0 11 269-279 101-111 (144)
58 PF12123 Amidase02_C: N-acetyl 22.6 1E+02 0.0023 22.3 2.9 18 145-162 25-42 (45)
59 PF13194 DUF4010: Domain of un 22.5 73 0.0016 28.9 2.6 46 195-240 69-119 (211)
60 PF14991 MLANA: Protein melan- 22.4 29 0.00063 29.9 0.0 43 91-137 21-63 (118)
61 CHL00177 ccs1 c-type cytochrom 22.3 3.3E+02 0.0072 27.4 7.3 37 146-182 125-162 (426)
62 TIGR02762 TraL_TIGR type IV co 22.1 1.2E+02 0.0026 24.3 3.5 22 214-235 41-66 (95)
63 PF07584 BatA: Aerotolerance r 22.0 61 0.0013 24.4 1.7 26 210-235 7-33 (77)
64 PRK07566 bacteriochlorophyll/c 21.9 1.1E+02 0.0025 28.7 3.8 20 37-56 9-28 (314)
65 PRK14440 acylphosphatase; Prov 21.8 1.9E+02 0.0041 22.8 4.5 35 245-280 39-73 (90)
66 COG0314 MoaE Molybdopterin con 21.5 1.1E+02 0.0024 26.8 3.4 16 165-180 27-42 (149)
67 PRK14425 acylphosphatase; Prov 21.3 2E+02 0.0044 22.8 4.6 35 245-280 42-76 (94)
68 PF08753 NikR_C: NikR C termin 21.2 1.4E+02 0.003 22.9 3.5 32 246-278 42-73 (78)
69 PF04156 IncA: IncA protein; 20.8 59 0.0013 27.7 1.6 26 208-233 41-66 (191)
70 PRK10527 hypothetical protein; 20.4 92 0.002 26.5 2.6 41 189-234 6-47 (125)
71 PRK10614 multidrug efflux syst 20.3 6.1E+02 0.013 28.0 9.3 75 142-222 811-887 (1025)
72 PRK13387 1,4-dihydroxy-2-napht 20.2 1.9E+02 0.0041 27.6 4.9 20 209-228 113-132 (317)
No 1
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=100.00 E-value=2.1e-77 Score=520.16 Aligned_cols=169 Identities=40% Similarity=0.673 Sum_probs=166.7
Q ss_pred hhhhhHHHHHHHHHhhhhhhhhhhccccceeEEEEEeecCCCCChhHHHHHHHHHhhhcCceeec---CceEEEEEEeec
Q 023342 101 LASYYTSLGLFVISVPGLWSLIKRSVKSKIVQKTFVGEGESKKAPNQVAGEIFSFFTRNNFVVTD---RGEVITFEGMMV 177 (283)
Q Consensus 101 ~aSyySTL~LTlLlaiGL~FFIRAS~KDRi~qrT~vv~~~s~~p~~evl~~L~~yF~~R~Y~V~~---~~~vItFEG~V~ 177 (283)
.++|||||+||+|++||||||||||+||||+++|+++++ |+++++++|++||++|||+|++ ++|+|||||+|+
T Consensus 2 ~~~~~STl~LtlLl~iGL~ffiraS~KdRt~~~~~~s~~----p~~~~~~~l~~yf~~r~y~v~~~d~~~~~itFeG~V~ 77 (173)
T PF12046_consen 2 TASLYSTLLLTLLLAIGLFFFIRASVKDRTEQVTFESPQ----PPDEVLEQLKAYFEQRNYRVAEGDAEGEVITFEGFVA 77 (173)
T ss_pred CchhhHHHHHHHHHHhHHHHHHHHhccccEEEEEEEcCC----CHHHHHHHHHHHHHhcCceecccCccccEEEEEEEec
Confidence 479999999999999999999999999999999999988 9999999999999999999999 799999999999
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHHHhhhcchhhhhhcCCcceeEEEEEEECCCCCcceEEEEecH
Q 023342 178 PSRGQAAFLTFCTCISLASVALVLTITYPDIGNNWFWITILSPLAGAYYWKRASRKEQIKVKMMVGEDGDLSEILVQGDD 257 (283)
Q Consensus 178 pS~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~LLSPLAGifYWqkA~R~EqV~lKL~s~dd~~~S~ItV~aHR 257 (283)
||+|||+|||||+++|++|+||||+|++|++|||||+|++|||+||+||||||+|+|+|+|||+++||+++|+|+|+|||
T Consensus 78 pS~~lA~fLt~l~~~Gl~cl~LVL~~l~P~~g~~~~~L~lLsPlAG~~Yw~kA~R~E~v~lkl~~~~~~~~s~i~v~ahr 157 (173)
T PF12046_consen 78 PSWFLAIFLTFLAAIGLACLGLVLSILFPDLGWWPLLLVLLSPLAGIFYWQKAGRPEQVELKLESADDESGSDITVRAHR 157 (173)
T ss_pred CcHhHHHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHhhhhhhhhhhcCCCcceEEEEEEEcCCCCcceEEEEEcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCcCc
Q 023342 258 QQVEQMRKELQLNEKG 273 (283)
Q Consensus 258 DELi~L~~eL~L~ekG 273 (283)
||||+|+++|+|+|+|
T Consensus 158 DEL~~L~~~L~L~~~G 173 (173)
T PF12046_consen 158 DELIELQKELQLKSKG 173 (173)
T ss_pred HHHHHHHHhcCCCCCC
Confidence 9999999999999998
No 2
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=92.75 E-value=0.16 Score=43.12 Aligned_cols=57 Identities=14% Similarity=0.215 Sum_probs=43.1
Q ss_pred hhhhhhhhhccccceeEEEEEeecCCCCChhHHHHHHHHHhhhcCceeec-----CceEEEEEEeecC
Q 023342 116 PGLWSLIKRSVKSKIVQKTFVGEGESKKAPNQVAGEIFSFFTRNNFVVTD-----RGEVITFEGMMVP 178 (283)
Q Consensus 116 iGL~FFIRAS~KDRi~qrT~vv~~~s~~p~~evl~~L~~yF~~R~Y~V~~-----~~~vItFEG~V~p 178 (283)
.|||+|||-+-|. +.....-+...+++.+.|.+.+++.|+...+ .+.++|+.|.|..
T Consensus 1 ~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s 62 (147)
T PRK11198 1 MGLFSFVKEAGEK------LFDAVTAQADNEDAADALKEHISKQGLGDADVNVQVEDGKATVSGDAAS 62 (147)
T ss_pred CcHHHHHHHHHHH------hcCCCCcccchHHHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCC
Confidence 3999999999885 1111111234688889999999999998765 5899999999984
No 3
>PF05140 ResB: ResB-like family ; InterPro: IPR007816 This domain is found in a number of known and suspected cytochrome c biogenesis proteins, including ResB []. Mutations in ResB indicate that they are essential for growth []. ResB is predicted to be a transmembrane protein.
Probab=81.82 E-value=17 Score=35.67 Aligned_cols=25 Identities=8% Similarity=0.319 Sum_probs=22.5
Q ss_pred CCChhHHHHHHHHHhhhcCceeecC
Q 023342 142 KKAPNQVAGEIFSFFTRNNFVVTDR 166 (283)
Q Consensus 142 ~~p~~evl~~L~~yF~~R~Y~V~~~ 166 (283)
+.+++++++.+.+.|++++|+|...
T Consensus 106 ~~~~~~~~~~~~~~L~~~gyrv~~~ 130 (464)
T PF05140_consen 106 PGDPEEALERLAALLKKKGYRVRRQ 130 (464)
T ss_pred CCChHHHHHHHHHHHHhCCcEEEEe
Confidence 3599999999999999999999774
No 4
>PF11990 DUF3487: Protein of unknown function (DUF3487); InterPro: IPR021877 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.
Probab=75.53 E-value=3.4 Score=34.83 Aligned_cols=63 Identities=24% Similarity=0.282 Sum_probs=45.6
Q ss_pred CceEEEEEEeecCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHH--HHHHHhhhcchhhhhh------cCCcce
Q 023342 166 RGEVITFEGMMVPSRGQAAFLTFCTCISLASVALVLTITYPDIGNNW--FWITILSPLAGAYYWK------RASRKE 234 (283)
Q Consensus 166 ~~~vItFEG~V~pS~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~--l~L~LLSPLAGifYWq------kA~R~E 234 (283)
++|-+.|.|.=.+..+.++.+++.+. +.+|+.++++ .|||. ...++++|+.+++... |.+|+|
T Consensus 12 N~ePvV~rGlT~~El~~~a~~~~~~g---~~~gl~la~~---~g~~a~~pt~~ll~~~~~v~~gg~~l~rlKRGKP~ 82 (121)
T PF11990_consen 12 NREPVVFRGLTADELGLAAGVGFVAG---LVVGLPLALL---TGWWAMIPTGALLGPILGVFVGGKLLARLKRGKPE 82 (121)
T ss_pred cCCCCeecCCCHHHHHHHHHHHHHHH---HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHcCCch
Confidence 35667899999999999888766443 5667777776 46664 3455888999988754 456666
No 5
>COG5375 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.85 E-value=1.8 Score=40.24 Aligned_cols=22 Identities=41% Similarity=0.788 Sum_probs=19.1
Q ss_pred hhcCceeecCceEEEEEEeecC
Q 023342 157 TRNNFVVTDRGEVITFEGMMVP 178 (283)
Q Consensus 157 ~~R~Y~V~~~~~vItFEG~V~p 178 (283)
..-+|+|.|.|++|+|||+|+.
T Consensus 188 ~ads~~v~D~G~iivF~g~Vr~ 209 (216)
T COG5375 188 TADSYSVTDKGKIIVFEGNVRT 209 (216)
T ss_pred EeeeeEeecCCcEEEEecceEE
Confidence 3568999999999999999974
No 6
>PF05915 DUF872: Eukaryotic protein of unknown function (DUF872); InterPro: IPR008590 This entry represents several uncharacterised eukaryotic transmembrane proteins. The function of this currently unknown.
Probab=70.03 E-value=9.8 Score=31.86 Aligned_cols=49 Identities=27% Similarity=0.306 Sum_probs=33.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHc----CCCchHHHHHHHhhhcchhhhhh
Q 023342 179 SRGQAAFLTFCTCISLASVALVLTITY----PDIGNNWFWITILSPLAGAYYWK 228 (283)
Q Consensus 179 S~~LAiFLTfLaaiGl~CLgLVLsil~----P~lG~~~l~L~LLSPLAGifYWq 228 (283)
+..+|+||.++|++ +.++|+++..-. .+-++.++.+.+|.=+.|.||-+
T Consensus 43 ~I~la~~Lli~G~~-li~~g~l~~~~~i~~~~~~~~~llilG~L~fIPG~Y~~~ 95 (115)
T PF05915_consen 43 SIALAVFLLIFGTV-LIIIGLLLFFGHIDGDRDRGWALLILGILCFIPGFYHTR 95 (115)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHhcccCCCCcccchHHHHHHHHHhccHHHHH
Confidence 45788888887777 555666655544 34456666677888888998754
No 7
>TIGR03750 conj_TIGR03750 conjugative transfer region protein, TIGR03750 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=68.97 E-value=7.6 Score=32.68 Aligned_cols=64 Identities=17% Similarity=0.180 Sum_probs=42.9
Q ss_pred ceEEEEEEeecCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHHH-HHHHhhhcchhhhhhc------CCccee
Q 023342 167 GEVITFEGMMVPSRGQAAFLTFCTCISLASVALVLTITYPDIGNNWF-WITILSPLAGAYYWKR------ASRKEQ 235 (283)
Q Consensus 167 ~~vItFEG~V~pS~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~l-~L~LLSPLAGifYWqk------A~R~Eq 235 (283)
.|-+.|+|.=.+..+.|+.+++.+. +-+|+.++.++- +|... ..++++|++++++..+ .+|+|.
T Consensus 10 ~ePvV~rGlT~~El~~~~~~~~~~g---l~~g~~l~~~~~--~w~~~p~~~lig~~l~v~~gg~~l~rlKRGrPe~ 80 (111)
T TIGR03750 10 REPVVFRGLTADELGVAAGVGLAAG---LVLGLLLALLAG--PWALIPTGALLGPILVVLIGGKLLARLKRGKPEG 80 (111)
T ss_pred CCCceecccCHHHHHHHHHHHHHHH---HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHhHHHHHHHHcCCCch
Confidence 5667899999999999998877654 334444433332 22222 3558899999988654 577774
No 8
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=67.78 E-value=18 Score=28.15 Aligned_cols=8 Identities=0% Similarity=-0.134 Sum_probs=4.0
Q ss_pred EEEEEEEC
Q 023342 236 IKVKMMVG 243 (283)
Q Consensus 236 V~lKL~s~ 243 (283)
++.++++.
T Consensus 80 v~g~V~~~ 87 (176)
T PF13567_consen 80 VQGTVESV 87 (176)
T ss_pred EEEEEccc
Confidence 55555444
No 9
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=67.23 E-value=8.5 Score=31.64 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=28.2
Q ss_pred ChhHHHHHHHHHhhhcCceeec---CceEEEEEEeec
Q 023342 144 APNQVAGEIFSFFTRNNFVVTD---RGEVITFEGMMV 177 (283)
Q Consensus 144 p~~evl~~L~~yF~~R~Y~V~~---~~~vItFEG~V~ 177 (283)
|.++-.+.+.+||+++|..+.. .+..|+++|.|.
T Consensus 59 p~~~~v~~V~~wL~~~G~~~~~~~~~~~~i~~~~tv~ 95 (143)
T PF09286_consen 59 PSPEDVAAVKSWLKSHGLTVVEVSANGDWITVSGTVA 95 (143)
T ss_dssp --HHHHHHHHHHHHHCT-EEEEEETTTTEEEEEEEHH
T ss_pred CCHHHHHHHHHHHHHcCCceeEEeCCCCEEEEEEeHH
Confidence 6677889999999999999887 699999999875
No 10
>PF05818 TraT: Enterobacterial TraT complement resistance protein; InterPro: IPR008874 The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between Escherichia coli and its surroundings []. The protein plays a role in preventing unproductive conjugation between bacteria carrying like plasmids.; GO: 0046999 regulation of conjugation, 0019867 outer membrane
Probab=60.46 E-value=25 Score=32.74 Aligned_cols=70 Identities=20% Similarity=0.276 Sum_probs=48.9
Q ss_pred EEEEEeec--CCCCChhHHHHHHHHHhhhcCceeecC--------ceEEEEEEeecCChHHHHHH-HHHHHHHHHHHHHH
Q 023342 132 QKTFVGEG--ESKKAPNQVAGEIFSFFTRNNFVVTDR--------GEVITFEGMMVPSRGQAAFL-TFCTCISLASVALV 200 (283)
Q Consensus 132 qrT~vv~~--~s~~p~~evl~~L~~yF~~R~Y~V~~~--------~~vItFEG~V~pS~~LAiFL-TfLaaiGl~CLgLV 200 (283)
+||..+.. .|+++. .+-.+|.+.++.+||+|.+. +--|.+-|.+.+.-....+= .+=++++.+.+|-.
T Consensus 21 ~rtVyv~vrNTSd~~~-~l~~~i~~~L~~kGY~vv~~P~~A~Y~lq~NVL~~~k~~~~~~~~~l~~G~gga~~Ga~~G~~ 99 (215)
T PF05818_consen 21 QRTVYVQVRNTSDKDI-NLESQIISALQAKGYQVVDDPDEAHYWLQANVLYVGKMDPNAAQSALAGGYGGALAGAATGAA 99 (215)
T ss_pred cceEEEEEecCCCCcc-chHHHHHHHHHHCCCEEecChhhCeEEEEeeehhccCCChhHHHHHhhccchhHHHHhHHhhh
Confidence 46666665 466666 79999999999999999872 44466888888888555332 23355555666666
Q ss_pred HH
Q 023342 201 LT 202 (283)
Q Consensus 201 Ls 202 (283)
+.
T Consensus 100 ~g 101 (215)
T PF05818_consen 100 IG 101 (215)
T ss_pred hc
Confidence 66
No 11
>PRK06080 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated
Probab=53.19 E-value=32 Score=31.44 Aligned_cols=36 Identities=11% Similarity=-0.109 Sum_probs=18.8
Q ss_pred HHHHHHhhhc-Cceeec--CceEEEEEEeecCChHHHHH
Q 023342 150 GEIFSFFTRN-NFVVTD--RGEVITFEGMMVPSRGQAAF 185 (283)
Q Consensus 150 ~~L~~yF~~R-~Y~V~~--~~~vItFEG~V~pS~~LAiF 185 (283)
+-+.+|++.+ +.+... +++...-+|.+.+.....+.
T Consensus 55 n~~Ndy~D~~~g~D~~~~~~~~r~l~~G~is~~~~~~~~ 93 (293)
T PRK06080 55 NLANDYGDYVKGTDTEDRVGPLRAIGRGGISPKQVKRAA 93 (293)
T ss_pred HHHHhHHHhccCCCcccccCCcccccCCCCCHHHHHHHH
Confidence 4455566653 343322 23334468888777654433
No 12
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=52.58 E-value=23 Score=29.79 Aligned_cols=59 Identities=17% Similarity=0.122 Sum_probs=31.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHHH-----hhhcchhhhhhcCCcceeEEEE
Q 023342 179 SRGQAAFLTFCTCISLASVALVLTITYPDIGNNWFWITI-----LSPLAGAYYWKRASRKEQIKVK 239 (283)
Q Consensus 179 S~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~L-----LSPLAGifYWqkA~R~EqV~lK 239 (283)
|..-.-|+.+++++++.|+..-+..+ -.|.|+..... +-=+|-..|++.+.+.|.|.+.
T Consensus 6 SLs~~g~~~~~~~~~~~~~~~a~~f~--~~GaW~Vl~F~glev~~l~~a~~~~~r~~~~~E~I~l~ 69 (140)
T PF10003_consen 6 SLSPRGFLIFIAILAAVSLIIAIAFL--LMGAWPVLPFAGLEVLALWYAFRRNYRHARDYERITLS 69 (140)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH--HhchHHHHHHHHHHHHHHHHHHHHHHhhCcCcEEEEEe
Confidence 34445566666666555554433333 23444333221 1234455678889998988764
No 13
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=48.97 E-value=34 Score=30.18 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=20.6
Q ss_pred cCCCchHHHHHHHhhhcchhhhhhcC
Q 023342 205 YPDIGNNWFWITILSPLAGAYYWKRA 230 (283)
Q Consensus 205 ~P~lG~~~l~L~LLSPLAGifYWqkA 230 (283)
.|.+++|.+.+..+.=+++.|||||-
T Consensus 175 np~l~~~~~iiig~i~~~~~~~lkkk 200 (206)
T PF06570_consen 175 NPVLPPWVYIIIGVIAFALRFYLKKK 200 (206)
T ss_pred CcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44577888888888888899999874
No 14
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=46.65 E-value=37 Score=23.06 Aligned_cols=34 Identities=12% Similarity=0.218 Sum_probs=28.7
Q ss_pred HHHHHHHhhhcCceeecC--ceEEEEEEeecCChHH
Q 023342 149 AGEIFSFFTRNNFVVTDR--GEVITFEGMMVPSRGQ 182 (283)
Q Consensus 149 l~~L~~yF~~R~Y~V~~~--~~vItFEG~V~pS~~L 182 (283)
.+.++.|++++++.+.+. ++.|+|...|.++.--
T Consensus 8 ~~~v~~~l~~~~~~i~~~~y~~~V~~~v~v~~~~~~ 43 (56)
T PF09186_consen 8 YGKVERLLEQNGIEIVDEDYTDDVTLTVAVPEEEVE 43 (56)
T ss_dssp HHHHHHHHHHTTTEEEEEEECTTEEEEEEEECCCHH
T ss_pred HHHHHHHHHHCCCEEEcceecceEEEEEEECHHHHH
Confidence 578999999999999884 5559999999998543
No 15
>PF07226 DUF1422: Protein of unknown function (DUF1422); InterPro: IPR009867 This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=44.79 E-value=32 Score=29.60 Aligned_cols=45 Identities=27% Similarity=0.357 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHcCCCchHHHHHHHhhhcchhhhhhcCCcc
Q 023342 189 CTCISLASVALVLTITYPDIGNNWFWITILSPLAGAYYWKRASRK 233 (283)
Q Consensus 189 LaaiGl~CLgLVLsil~P~lG~~~l~L~LLSPLAGifYWqkA~R~ 233 (283)
|-.+|+..=+-.+...+|++|.|++-.++.-=|.=|.|.|=..|+
T Consensus 71 cFflG~f~ySA~vraqyPeiGSNFfp~il~l~L~~Wi~~kl~~~k 115 (117)
T PF07226_consen 71 CFFLGLFGYSAFVRAQYPEIGSNFFPSILCLILVFWIGYKLGFRK 115 (117)
T ss_pred HHHHHHHHHHHHHHHhchhhhhhHHHHHHHHHHHHHHHHHHhhhc
Confidence 335777888889999999999999998877777777776655444
No 16
>PF05620 DUF788: Protein of unknown function (DUF788); InterPro: IPR008506 This family consists of several eukaryotic proteins of unknown function.
Probab=44.69 E-value=53 Score=28.53 Aligned_cols=27 Identities=11% Similarity=0.177 Sum_probs=21.1
Q ss_pred hHHHHHHHHHhhhhhhhhhhcccccee
Q 023342 105 YTSLGLFVISVPGLWSLIKRSVKSKIV 131 (283)
Q Consensus 105 ySTL~LTlLlaiGL~FFIRAS~KDRi~ 131 (283)
+.-++++.+...+.++++.+..+.+..
T Consensus 48 ~~~~~~~~~~~~~~~~~l~~~~rp~~~ 74 (170)
T PF05620_consen 48 WFGYLLFSLPAIFCYYFLEKMARPKYD 74 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCcC
Confidence 344677788888889999999988655
No 17
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=41.92 E-value=17 Score=33.20 Aligned_cols=31 Identities=16% Similarity=0.133 Sum_probs=24.1
Q ss_pred CcchhhhhHHHHHH--HHHhhhhhhhhhhcccc
Q 023342 98 GYSLASYYTSLGLF--VISVPGLWSLIKRSVKS 128 (283)
Q Consensus 98 g~s~aSyySTL~LT--lLlaiGL~FFIRAS~KD 128 (283)
+...+=+--|||++ |+|-+-.||.+|||.|-
T Consensus 88 ~vAASL~LgTffIS~~LilSvA~FFYLKrs~kL 120 (180)
T PF14946_consen 88 QVAASLFLGTFFISLGLILSVASFFYLKRSSKL 120 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhheeecccccC
Confidence 44444456788877 88889999999999885
No 18
>PF00474 SSF: Sodium:solute symporter family; InterPro: IPR001734 Sodium/substrate symport (or co-transport) is a widespread mechanism of solute transport across cytoplasmic membranes of pro- and eukaryotic cells. Thereby the energy stored in an inwardly directed electrochemical sodium gradient (sodium motive force, SMF) is used to drive solute accumulation against a concentration gradient. The SMF is generated by primary sodium pumps (e.g. sodium/potassium ATPases, sodium translocating respiratory chain complexes) or via the action of sodium/proton antiporters. Sodium/substrate transporters are grouped in different families based on sequence similarities [, ]. One of these families, known as the sodium:solute symporter family (SSSF), contains over a hundred members of pro- and eukaryotic origin []. The average hydropathy plot for SSSF proteins predicts 11 to 15 putative transmembrane domains (TMs) in alpha-helical conformation. A secondary structure model of PutP from Escherichia coli suggests the protein contains 13 TMs with the N terminus located on the periplasmic side of the membrane and the C terminus facing the cytoplasm. The results support the idea of a common topological motif for members of the SSSF. Transporters with a C-terminal extension are proposed to have an additional 14th TM. An ordered binding model of sodium/substrate transport suggests that sodium binds to the empty transporter first, thereby inducing a conformational alteration which increases the affinity of the transporter for the solute. The formation of the ternary complex induces another structural change that exposes sodium and substrate to the other site of the membrane. Substrate and sodium are released and the empty transporter re-orientates in the membrane allowing the cycle to start again.; GO: 0005215 transporter activity, 0006810 transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 3DH4_D 2XQ2_A.
Probab=40.94 E-value=17 Score=34.14 Aligned_cols=55 Identities=27% Similarity=0.507 Sum_probs=34.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHcCCCc---hHHHH-----HHHhhhcchhhhhhcCCcc
Q 023342 179 SRGQAAFLTFCTCISLASVALVLTITYPDIG---NNWFW-----ITILSPLAGAYYWKRASRK 233 (283)
Q Consensus 179 S~~LAiFLTfLaaiGl~CLgLVLsil~P~lG---~~~l~-----L~LLSPLAGifYWqkA~R~ 233 (283)
|--+-+..+-+..+..+++++++++..|+.+ ...+. -.++.|+-+-.||||+.|.
T Consensus 335 s~~~~~~~~ri~~~v~~~i~~~la~~~~~~~i~~~~~~~~~~~~~~~~~~~~~gl~wkr~t~~ 397 (406)
T PF00474_consen 335 SEKQLLRVSRIAIVVIGIIAILLALFFPDSGIIDLILFAFGILAAPFFPPLLLGLYWKRATKR 397 (406)
T ss_dssp -SSHHHHHHHHHHHHHHHHHHHHGGGGGGSSHHHHHHHHHTTTHHHHHHHHHHHHH-TT--HH
T ss_pred chhhhhhccceeEEeeHHhHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHhhccCCCCHH
Confidence 4445567788888889999999999998852 11111 1134466777899998763
No 19
>PF05211 NLBH: Neuraminyllactose-binding hemagglutinin precursor (NLBH); InterPro: IPR007876 This family is comprised of several flagellar sheath adhesin proteins also called neuraminyllactose-binding haemagglutinin precursor (NLBH or HpaA) or N-acetylneuraminyllactose-binding fibrillar haemagglutinin receptor-binding subunits. NLBH is found exclusively in Helicobacter which are gut colonising bacteria and bind to sialic acid rich macromolecules present on the gastric epithelium []. The sialic acid-sensitive agglutination of erythrocytes by certain strains of Helicobacter pylori has been attributed to the NLBH protein [].; GO: 0009279 cell outer membrane, 0019861 flagellum; PDB: 2I9I_A 3BGH_B.
Probab=40.71 E-value=12 Score=35.68 Aligned_cols=21 Identities=14% Similarity=0.322 Sum_probs=18.1
Q ss_pred hhHHHHHHHHHhhhcCceeec
Q 023342 145 PNQVAGEIFSFFTRNNFVVTD 165 (283)
Q Consensus 145 ~~evl~~L~~yF~~R~Y~V~~ 165 (283)
.++++.+|++-|++|||+|..
T Consensus 88 ~~aL~~qIq~IlekrGY~V~~ 108 (258)
T PF05211_consen 88 QKALVNQIQSILEKRGYSVLR 108 (258)
T ss_dssp HHHHHHHHHHHHHCTT-EEEE
T ss_pred HHHHHHHHHHHHHhCCcEEEe
Confidence 478999999999999999975
No 20
>PRK03094 hypothetical protein; Provisional
Probab=39.53 E-value=22 Score=28.58 Aligned_cols=17 Identities=6% Similarity=0.219 Sum_probs=15.2
Q ss_pred HHHHHHHhhhcCceeec
Q 023342 149 AGEIFSFFTRNNFVVTD 165 (283)
Q Consensus 149 l~~L~~yF~~R~Y~V~~ 165 (283)
|..|++||++|||.|.+
T Consensus 10 Ls~i~~~L~~~GYeVv~ 26 (80)
T PRK03094 10 LTDVQQALKQKGYEVVQ 26 (80)
T ss_pred cHHHHHHHHHCCCEEEe
Confidence 67799999999999965
No 21
>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins. Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.
Probab=39.33 E-value=8.8 Score=33.39 Aligned_cols=26 Identities=23% Similarity=0.497 Sum_probs=0.0
Q ss_pred hhcchhhhhhcCCcceeEEEEEEECC
Q 023342 219 SPLAGAYYWKRASRKEQIKVKMMVGE 244 (283)
Q Consensus 219 SPLAGifYWqkA~R~EqV~lKL~s~d 244 (283)
+=+||+.||+|-.|.|++.=-+|+.+
T Consensus 93 ~llsg~lv~rrcrrr~~~ttPIeeTg 118 (129)
T PF12191_consen 93 ALLSGFLVWRRCRRREKFTTPIEETG 118 (129)
T ss_dssp --------------------------
T ss_pred HHHHHHHHHhhhhccccCCCcccccC
Confidence 34569999999999999988776543
No 22
>TIGR01006 polys_exp_MPA1 polysaccharide export protein, MPA1 family, Gram-positive type. This family contains members from Low GC Gram-positive bacteria; they are proposed to have a function in the export of complex polysaccharides.
Probab=39.18 E-value=98 Score=27.15 Aligned_cols=70 Identities=11% Similarity=0.163 Sum_probs=39.6
Q ss_pred eeEEEEEeecCCCCChhHHHHHHHHHhhhcCceeecCceEEEEE------EeecCChHHHHHHHHHHHHHHHHHHH
Q 023342 130 IVQKTFVGEGESKKAPNQVAGEIFSFFTRNNFVVTDRGEVITFE------GMMVPSRGQAAFLTFCTCISLASVAL 199 (283)
Q Consensus 130 i~qrT~vv~~~s~~p~~evl~~L~~yF~~R~Y~V~~~~~vItFE------G~V~pS~~LAiFLTfLaaiGl~CLgL 199 (283)
+.--+..+...++....++++.+.+-|.+...++.+.+++-..+ --+.|+..+-+.+.++++++++|...
T Consensus 118 t~ii~Isv~~~dp~~A~~ian~~~~~~~~~~~~~~~~~~~~vl~~a~~p~~p~~P~~~~~~~~g~~~G~~~~~~~~ 193 (226)
T TIGR01006 118 TRLISISVKDKTPQDASKIANSLREVASKKIPKITNVSDVTTLEEAKPATTPSSPNPKRNLLIGFLLGLVVALIIV 193 (226)
T ss_pred cEEEEEEEeCCCHHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeecCCCCCCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 33344444455666667888888877776655444333322222 23456677767776666666555433
No 23
>PF11374 DUF3176: Protein of unknown function (DUF3176); InterPro: IPR021514 This eukaryotic family of proteins has no known function.
Probab=37.53 E-value=19 Score=29.68 Aligned_cols=61 Identities=25% Similarity=0.432 Sum_probs=47.5
Q ss_pred EEEEeecCChHH----HHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHHHhhhcchhhhhhcCCc
Q 023342 171 TFEGMMVPSRGQ----AAFLTFCTCISLASVALVLTITYPDIGNNWFWITILSPLAGAYYWKRASR 232 (283)
Q Consensus 171 tFEG~V~pS~~L----AiFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~LLSPLAGifYWqkA~R 232 (283)
.|+|+-.|+|.. ...+++++.++=+|+..+++.-.-++-|.||. --=-||+=..|..+|+|
T Consensus 7 ~~dgk~~~~W~~~isln~~isilsti~~a~l~~~v~~~l~QlkW~~f~-~~~r~L~Dl~~~d~ASR 71 (111)
T PF11374_consen 7 VYDGKPVPSWPFGISLNTLISILSTIAKAALLFPVSEGLSQLKWNWFS-RRPRPLSDLHYFDEASR 71 (111)
T ss_pred hhCCcccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCccHHHHHHHHhhcc
Confidence 477888888755 67899999999999999999988887777774 12237777777777776
No 24
>COG5488 Integral membrane protein [Function unknown]
Probab=37.18 E-value=58 Score=29.46 Aligned_cols=55 Identities=24% Similarity=0.258 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCchHH----HHH-HHhhhcchhhhhhcCCcceeEEEEE
Q 023342 184 AFLTFCTCISLASVALVLTITYPDIGNNW----FWI-TILSPLAGAYYWKRASRKEQIKVKM 240 (283)
Q Consensus 184 iFLTfLaaiGl~CLgLVLsil~P~lG~~~----l~L-~LLSPLAGifYWqkA~R~EqV~lKL 240 (283)
.|..++.++|.+|+ +..++|=..|-|| ++| +++-=+|=.+|-+-|.+.|+|+|.=
T Consensus 30 gf~~lm~~~~~~~~--~v~~ff~~igAwpV~~FfGLDvlal~~Afr~nyraArarEeIsvsr 89 (164)
T COG5488 30 GFGVLMLALGILSL--VVAIFFLVIGAWPVLPFFGLDVLALYLAFRANYRAARAREEISVSR 89 (164)
T ss_pred hHHHHHHHHHHHHH--HHHHHHHHhccCceeccchHHHHHHHHHHHHHHHHhhhhhheeech
Confidence 34555566666554 3333333334333 333 3445688889999999999999853
No 25
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=37.18 E-value=39 Score=33.88 Aligned_cols=64 Identities=22% Similarity=0.199 Sum_probs=43.3
Q ss_pred ceEEEEEEeecC--ChHH----HHHHHHHHHHHHHHHHHHHHHHcCCCch-HHHHHHHhhhcchhhhhhcCC
Q 023342 167 GEVITFEGMMVP--SRGQ----AAFLTFCTCISLASVALVLTITYPDIGN-NWFWITILSPLAGAYYWKRAS 231 (283)
Q Consensus 167 ~~vItFEG~V~p--S~~L----AiFLTfLaaiGl~CLgLVLsil~P~lG~-~~l~L~LLSPLAGifYWqkA~ 231 (283)
++++..||.=.+ ..++ -++|+++ ++-|.|++-|+.+..|-++. +-.+.+++.=+.|+|.||+-.
T Consensus 323 Qq~~q~e~~~n~~~r~~l~k~inllL~l~-~vlLv~vSt~~~~~~Pl~~tR~r~~~t~~~v~l~~~~~~~w~ 393 (395)
T PF10267_consen 323 QQVVQLEGTENSRARALLGKLINLLLTLL-TVLLVFVSTVANCPLPLTRTRLRTLTTLLLVGLGAILWQNWD 393 (395)
T ss_pred hhhhhhcccccccHHHHHHHHHHHHHHHH-HHHHHHHHHHhcCCcHHhhccHHHHHHHHHHHHHHHHHhccC
Confidence 567777876522 2233 3334443 67788888888888888764 345566777889999999753
No 26
>TIGR03062 pip_yhgE_Cterm YhgE/Pip C-terminal domain. This family contains the C-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03061, represents the conserved N-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=35.32 E-value=94 Score=26.30 Aligned_cols=48 Identities=8% Similarity=0.177 Sum_probs=32.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHHHhh--hcchhhh
Q 023342 179 SRGQAAFLTFCTCISLASVALVLTITYPDIGNNWFWITILS--PLAGAYY 226 (283)
Q Consensus 179 S~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~LLS--PLAGifY 226 (283)
+....+...+++++...++|+.++.++++.+.....+.+.- ..+|.+|
T Consensus 95 ~~~~~~l~~~l~~~~~~~lg~~l~~~~~~~~~~~~~~~~~~~~~~sG~~~ 144 (208)
T TIGR03062 95 HPPATFGFAILTSLTFMAIIQFLVALFGNVGRFLALVLLVLQLGSSGGTF 144 (208)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHHHHHHHHHccCCCcc
Confidence 56666666788888999999999999998664433322221 2567653
No 27
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=35.19 E-value=53 Score=27.58 Aligned_cols=33 Identities=21% Similarity=0.244 Sum_probs=27.0
Q ss_pred cceEEEEe-cHHHHHHHHHHcCCCcCccEEeeec
Q 023342 248 LSEILVQG-DDQQVEQMRKELQLNEKGMVYVKGI 280 (283)
Q Consensus 248 ~S~ItV~a-HRDELi~L~~eL~L~ekGmv~vkgi 280 (283)
+..|.|+| |||++.++=.+.|+..+-+|.|.|.
T Consensus 77 ~~~IelQGD~re~v~~~L~~~g~~~~~~i~vhg~ 110 (110)
T TIGR01160 77 GEVIQLQGDQRKNVCEFLISQGLLKKDQIKIHGF 110 (110)
T ss_pred CCEEEEeCcHHHHHHHHHHHcCCCCHHHeeecCC
Confidence 46789999 5888999888889888888888773
No 28
>PRK11056 hypothetical protein; Provisional
Probab=35.14 E-value=56 Score=28.26 Aligned_cols=45 Identities=24% Similarity=0.314 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHcCCCchHHHHHHHhhhcchhhhhhcCCcc
Q 023342 189 CTCISLASVALVLTITYPDIGNNWFWITILSPLAGAYYWKRASRK 233 (283)
Q Consensus 189 LaaiGl~CLgLVLsil~P~lG~~~l~L~LLSPLAGifYWqkA~R~ 233 (283)
|-.+|+..=+-++...+|++|.|++-.++.-=|.=|.|.|=..|.
T Consensus 71 cFflG~f~ySA~vraeyPeiGSNF~p~il~~~L~~Wi~~kl~~~~ 115 (120)
T PRK11056 71 CFFLGVFLYSAFVRAEYPEIGSNFFPAVLSVILVFWIGRKLRNRK 115 (120)
T ss_pred HHHHHHHHHHHHHHhcCcccccchHHHHHHHHHHHHHHHHHhccc
Confidence 335677778888999999999999998877777777776544443
No 29
>TIGR03861 phenyl_ABC_PedC alcohol ABC transporter, permease protein. Members of this protein family, part of a larger class of efflux-type ABC transport permease proteins, are found exclusively in genomic contexts with pyrroloquinoline-quinone (PQQ) biosynthesis enzymes and/or PQQ-dependent alcohol dehydrogenases, such as the phenylethanol dehydrogenase PedE of Pseudomonas putida U. Members include PedC, an apparent phenylethanol transport protein whose suggested role is efflux to limit intracellular concentrations of toxic metabolites during phenylethanol catalysis.
Probab=34.39 E-value=85 Score=27.63 Aligned_cols=48 Identities=19% Similarity=0.063 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHH----HHHHHhhhcchhhhh
Q 023342 180 RGQAAFLTFCTCISLASVALVLTITYPDIGNNW----FWITILSPLAGAYYW 227 (283)
Q Consensus 180 ~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~----l~L~LLSPLAGifYW 227 (283)
+.+.+...++.++...++|++++.+.++..... +.+..+.-++|+||=
T Consensus 139 ~l~~~~~~~l~~~~~~~lgl~la~l~~~~~~~~~i~~~~~~~l~flSgi~~p 190 (253)
T TIGR03861 139 YVSVLPALVLVAFMLGALGLALSNLIRQLENFAGVMNFVIFPMFFLSSALYP 190 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhhHhhh
Confidence 344445556777788899999999988754322 233345566788884
No 30
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=32.84 E-value=71 Score=25.01 Aligned_cols=49 Identities=12% Similarity=0.294 Sum_probs=33.3
Q ss_pred HhhhcchhhhhhcCCcceeEEEEEEECCCCCcce--EEEEecHHHHHHHHHHcC
Q 023342 217 ILSPLAGAYYWKRASRKEQIKVKMMVGEDGDLSE--ILVQGDDQQVEQMRKELQ 268 (283)
Q Consensus 217 LLSPLAGifYWqkA~R~EqV~lKL~s~dd~~~S~--ItV~aHRDELi~L~~eL~ 268 (283)
.|.=++|+|- +|+--.|.+.+- ..+++..|. |++.|++++++++.+.|.
T Consensus 15 VL~Ri~~lf~-rRgfNI~Sl~vg--~te~~~~sriti~~~~~~~~i~qi~kQL~ 65 (76)
T PRK06737 15 VLLRISGIFA-RRGYYISSLNLN--ERDTSGVSEMKLTAVCTENEATLLVSQLK 65 (76)
T ss_pred HHHHHHHHHh-ccCcceEEEEec--ccCCCCeeEEEEEEECCHHHHHHHHHHHh
Confidence 3455667664 566667765543 345566665 555699999999999885
No 31
>TIGR00751 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase. This membrane-associated enzyme converts 1,4-dihydroxy-2-naphthoic acid (DHNA) to demethylmenaquinone, a step in menaquinone biosynthesis.
Probab=32.06 E-value=79 Score=29.67 Aligned_cols=56 Identities=21% Similarity=0.286 Sum_probs=26.0
Q ss_pred EEEEEeecCChHHHHHHHHHHHHHHHHHHHHHHHHc-CCC-chHH-HHHHHhhhcchhhhh
Q 023342 170 ITFEGMMVPSRGQAAFLTFCTCISLASVALVLTITY-PDI-GNNW-FWITILSPLAGAYYW 227 (283)
Q Consensus 170 ItFEG~V~pS~~LAiFLTfLaaiGl~CLgLVLsil~-P~l-G~~~-l~L~LLSPLAGifYW 227 (283)
.+-+|.+.|..-..+...+++... .+|+.+...- |.+ +.|+ +++.+++=+.|++|-
T Consensus 68 ~i~~g~is~~~v~~~~~~~~~~a~--~~Gi~l~~~~~~~~~~~~~~l~lg~~~~~~~~~Yt 126 (284)
T TIGR00751 68 GVQKGLITPREVKTALITSVALGA--LSGLVLALLAAPNLSDLFWFIALGALCIAAAITYT 126 (284)
T ss_pred hhcCCCCCHHHHHHHHHHHHHHHH--HHHHHHHHhcccchhhhHHHHHHHHHHHHHhHhhc
Confidence 456777776555444332222222 2233332211 111 1123 456677777888885
No 32
>PRK10408 putative L-valine exporter; Provisional
Probab=31.68 E-value=34 Score=29.20 Aligned_cols=45 Identities=18% Similarity=0.254 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHH--HHHHHHHHHcCCCc-hHHHH--HHHhhhcchhhhhhcC
Q 023342 183 AAFLTFCTCISLA--SVALVLTITYPDIG-NNWFW--ITILSPLAGAYYWKRA 230 (283)
Q Consensus 183 AiFLTfLaaiGl~--CLgLVLsil~P~lG-~~~l~--L~LLSPLAGifYWqkA 230 (283)
+++| ..+|.+ |-=||.|.+=+-+. +.+++ |+...=+.+.|||.|.
T Consensus 41 ~i~L---dsIGIAsIcaLLVVS~~P~v~~~~~k~~ptlvGf~~l~~~fyktrs 90 (111)
T PRK10408 41 GILL---DSIGIASICALLVVSTAPEVMHDPRKLLPTLVGFLVLGACFYKTRS 90 (111)
T ss_pred HHHH---hhccHHHHHHHHHHhcChHHHhChHHHHHHHHHHHHHHHHHHHhcc
Confidence 5554 455544 44467765433322 34444 4444578999999885
No 33
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=31.52 E-value=34 Score=27.29 Aligned_cols=17 Identities=12% Similarity=0.247 Sum_probs=15.6
Q ss_pred HHHHHHHhhhcCceeec
Q 023342 149 AGEIFSFFTRNNFVVTD 165 (283)
Q Consensus 149 l~~L~~yF~~R~Y~V~~ 165 (283)
|..+++||+++||.|.+
T Consensus 10 Ls~v~~~L~~~GyeVv~ 26 (80)
T PF03698_consen 10 LSNVKEALREKGYEVVD 26 (80)
T ss_pred chHHHHHHHHCCCEEEe
Confidence 67899999999999987
No 34
>TIGR02056 ChlG chlorophyll synthase, ChlG. This model represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP).
Probab=31.49 E-value=1.1e+02 Score=28.74 Aligned_cols=18 Identities=17% Similarity=0.314 Sum_probs=8.9
Q ss_pred hHHHHHHHhhhcchhhhh
Q 023342 210 NNWFWITILSPLAGAYYW 227 (283)
Q Consensus 210 ~~~l~L~LLSPLAGifYW 227 (283)
++.+++.+++=+.|++|-
T Consensus 128 ~~~~~l~~~~~~~~~~Yt 145 (306)
T TIGR02056 128 PNVFVLALFGSFIAFIYS 145 (306)
T ss_pred hHHHHHHHHHHHHHHHHc
Confidence 344444455544555553
No 35
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=30.21 E-value=61 Score=20.56 Aligned_cols=26 Identities=38% Similarity=0.266 Sum_probs=15.5
Q ss_pred CcchhhhhHHHHHHHHHhhhhhhhhhh
Q 023342 98 GYSLASYYTSLGLFVISVPGLWSLIKR 124 (283)
Q Consensus 98 g~s~aSyySTL~LTlLlaiGL~FFIRA 124 (283)
|-.....+...++ ++++.|.+++.|+
T Consensus 6 G~~~~~~~~~~G~-~l~~~~~~~~~~r 31 (34)
T TIGR01167 6 GESGNSLLLLLGL-LLLGLGGLLLRKR 31 (34)
T ss_pred CCcccHHHHHHHH-HHHHHHHHHheec
Confidence 4355566666677 4444466666665
No 36
>PF11666 DUF2933: Protein of unknown function (DUF2933); InterPro: IPR021682 This bacterial family of proteins has no known function.
Probab=29.48 E-value=41 Score=25.24 Aligned_cols=19 Identities=16% Similarity=0.385 Sum_probs=17.1
Q ss_pred CchHHHHHHHhhhcchhhh
Q 023342 208 IGNNWFWITILSPLAGAYY 226 (283)
Q Consensus 208 lG~~~l~L~LLSPLAGifY 226 (283)
+|+++|++.++.|+.=+|-
T Consensus 21 ~~~lp~l~lL~CPLmhlFM 39 (55)
T PF11666_consen 21 LGALPYLLLLACPLMHLFM 39 (55)
T ss_pred HHHHHHHHHHHhHHHHHHH
Confidence 6899999999999998887
No 37
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=29.21 E-value=93 Score=29.23 Aligned_cols=22 Identities=9% Similarity=0.295 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHcC
Q 023342 185 FLTFCTCISLASVALVLTITYP 206 (283)
Q Consensus 185 FLTfLaaiGl~CLgLVLsil~P 206 (283)
.+.+++++|.+.++++|.+++.
T Consensus 29 ~~ml~a~l~~~~v~v~ig~l~~ 50 (224)
T PF13829_consen 29 WLMLGAFLGPIAVFVLIGLLFG 50 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc
Confidence 3444555666677888888887
No 38
>PF04217 DUF412: Protein of unknown function, DUF412; InterPro: IPR007334 This family consists of bacterial uncharacterised proteins.
Probab=28.90 E-value=56 Score=28.84 Aligned_cols=35 Identities=29% Similarity=0.345 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHcCCCchHH----HHHHHhh-hcchhhhh
Q 023342 193 SLASVALVLTITYPDIGNNW----FWITILS-PLAGAYYW 227 (283)
Q Consensus 193 Gl~CLgLVLsil~P~lG~~~----l~L~LLS-PLAGifYW 227 (283)
.++|++++.++.+.+...++ .+|.++| |+=|+|.-
T Consensus 44 ~lAv~s~~~Q~~~~~~~~lp~ai~~aLFalSLPlQGl~WL 83 (143)
T PF04217_consen 44 ALAVFSLLWQIAFNGGQALPQAIATALFALSLPLQGLYWL 83 (143)
T ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 46788889999997766666 3344566 99997653
No 39
>PRK14447 acylphosphatase; Provisional
Probab=28.57 E-value=1.7e+02 Score=23.34 Aligned_cols=31 Identities=13% Similarity=0.102 Sum_probs=24.5
Q ss_pred ceEEEEecHHHHHHHHHHcCCCcCccEEeeec
Q 023342 249 SEILVQGDDQQVEQMRKELQLNEKGMVYVKGI 280 (283)
Q Consensus 249 S~ItV~aHRDELi~L~~eL~L~ekGmv~vkgi 280 (283)
-+|.++|++|.|++|.+.|. +.....+|+.+
T Consensus 45 Vei~~qG~~~~l~~f~~~l~-~gp~~a~V~~v 75 (95)
T PRK14447 45 VEAVLEGPRDAVLKVIEWAR-VGPPGARVEDV 75 (95)
T ss_pred EEEEEEeCHHHHHHHHHHHh-hCCCCeEEEEE
Confidence 57999999999999999997 33346666654
No 40
>PF09911 DUF2140: Uncharacterized protein conserved in bacteria (DUF2140); InterPro: IPR018672 This family of conserved hypothetical proteins has no known function.
Probab=28.44 E-value=1.3e+02 Score=26.87 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=24.7
Q ss_pred CChhHHHHHHHHHhhhcC------ceeecCceEEEEEEeec
Q 023342 143 KAPNQVAGEIFSFFTRNN------FVVTDRGEVITFEGMMV 177 (283)
Q Consensus 143 ~p~~evl~~L~~yF~~R~------Y~V~~~~~vItFEG~V~ 177 (283)
...+++=.-+..|+++.. |++.- ++.+.|+|.+.
T Consensus 50 ~~k~qlN~li~~YL~~~~k~~~~~y~~~l-~~~v~l~g~~~ 89 (187)
T PF09911_consen 50 TNKEQLNALIASYLKKYQKDEKIKYKFYL-DDQVYLYGTIK 89 (187)
T ss_pred eCHHHHHHHHHHHHHHhcccCCccEEEEe-CCEEEEEEEEE
Confidence 367788888888887754 77776 67777777654
No 41
>COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]
Probab=28.27 E-value=89 Score=30.51 Aligned_cols=45 Identities=18% Similarity=0.141 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHHHhhhcchhhhh
Q 023342 180 RGQAAFLTFCTCISLASVALVLTITYPDIGNNWFWITILSPLAGAYYW 227 (283)
Q Consensus 180 ~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~LLSPLAGifYW 227 (283)
+.+++.+.++...|.+-+|+.+.. ++ +|+.+++.+++=.+|++|-
T Consensus 94 ~~~~l~l~l~~~~g~~llg~~~~~--~s-~~~~l~lG~l~~~~g~~YT 138 (303)
T COG1575 94 PALILSLALFLLAGLALLGVILAA--LS-DWLVLLLGLLCIAAGILYT 138 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--Hh-hhHHHHHHHHHHHheeeec
Confidence 344444444444444444444333 33 5666778888888888884
No 42
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=28.18 E-value=52 Score=24.21 Aligned_cols=48 Identities=35% Similarity=0.610 Sum_probs=30.7
Q ss_pred hhhcchhhhhhcCCcceeEEEEEEECCCCCcce--EEEEecHHHHHHHHHHcC
Q 023342 218 LSPLAGAYYWKRASRKEQIKVKMMVGEDGDLSE--ILVQGDDQQVEQMRKELQ 268 (283)
Q Consensus 218 LSPLAGifYWqkA~R~EqV~lKL~s~dd~~~S~--ItV~aHRDELi~L~~eL~ 268 (283)
|.=++|+|. +|.-..|.+.+.- .+++..+. |+|.|+.++++++.+.|.
T Consensus 6 L~Ri~~vf~-rRg~nI~sl~v~~--~~~~~~~riti~v~~~~~~i~~l~~Ql~ 55 (63)
T PF13710_consen 6 LNRITGVFR-RRGFNIESLSVGP--TEDPGISRITIVVSGDDREIEQLVKQLE 55 (63)
T ss_dssp HHHHHHHHH-TTT-EECEEEEEE---SSTTEEEEEEEEES-CCHHHHHHHHHH
T ss_pred HHHHHHHHh-cCCeEEeeEEeee--cCCCCEEEEEEEEeeCchhHHHHHHHHh
Confidence 344566664 5566777777766 44445454 778888899999988773
No 43
>PRK01002 nickel responsive regulator; Provisional
Probab=27.30 E-value=82 Score=26.97 Aligned_cols=44 Identities=25% Similarity=0.442 Sum_probs=32.6
Q ss_pred eeEEEEEEEC-CCC-CcceEEEEecHHHHHHHHHHcCCCcCccEEee
Q 023342 234 EQIKVKMMVG-EDG-DLSEILVQGDDQQVEQMRKELQLNEKGMVYVK 278 (283)
Q Consensus 234 EqV~lKL~s~-dd~-~~S~ItV~aHRDELi~L~~eL~L~ekGmv~vk 278 (283)
+.|.-.+-.. |.+ ..-.+.|+|..|||.+|-+.|+ ..+|+-++|
T Consensus 84 ~~Iiss~Hvhld~~~ClEvivv~G~~~~I~~l~~kL~-~lkGV~~~k 129 (141)
T PRK01002 84 DLIVASLHIHLDHDHCLEVIVVRGDAKEIRELTEKLM-ALKGVKHVK 129 (141)
T ss_pred CeEEEeeeeecCCCcEEEEEEEEcCHHHHHHHHHHHh-CcCCeeEEE
Confidence 4455555444 333 4556999999999999999999 667988876
No 44
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=27.29 E-value=89 Score=21.99 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=18.5
Q ss_pred CcceEEEEecHHHHHHHHHHcC
Q 023342 247 DLSEILVQGDDQQVEQMRKELQ 268 (283)
Q Consensus 247 ~~S~ItV~aHRDELi~L~~eL~ 268 (283)
.+-.|.|.|++|.+.++.+.+|
T Consensus 50 ~gD~l~v~g~~~~i~~~~~~~g 71 (71)
T PF02080_consen 50 AGDILIVVGDPEDIERFRELFG 71 (71)
T ss_dssp TTEEEEEEEEHHHHHHHHHHT-
T ss_pred CCCEEEEEECHHHHHHHHHhhC
Confidence 3556999999999999999886
No 45
>PRK05951 ubiA prenyltransferase; Reviewed
Probab=27.00 E-value=1.4e+02 Score=27.83 Aligned_cols=18 Identities=17% Similarity=0.200 Sum_probs=10.8
Q ss_pred chHHHHHHHhhhcchhhh
Q 023342 209 GNNWFWITILSPLAGAYY 226 (283)
Q Consensus 209 G~~~l~L~LLSPLAGifY 226 (283)
|++.+++.+++-+.|++|
T Consensus 115 ~~~~l~l~~~~~~~~~~Y 132 (296)
T PRK05951 115 GIGAVTLALLGVFLWTCY 132 (296)
T ss_pred cHHHHHHHHHHHHHHHHH
Confidence 344455556666677777
No 46
>TIGR01291 nodJ ABC-2 type transporter, NodJ family. Nearly all members of this subfamily are NodJ which, together with NodI (TIGR01288), acts to export a variety of modified carbohydrate molecules as signals to plant hosts to establish root nodules. The seed alignment includes a highly divergent member from Azorhizobium caulinodans that is, nonetheless, associated with nodulation. This model is designated as subfamily in part because not all sequences derived from the last common ancestral sequence of Rhizobium sp. and Azorhizobium caulinodans NodJ are necessarily nodulation proteins.
Probab=26.76 E-value=1.2e+02 Score=27.09 Aligned_cols=49 Identities=18% Similarity=0.089 Sum_probs=31.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHcCCCchHH----HHHHHhhhcchhhhh
Q 023342 179 SRGQAAFLTFCTCISLASVALVLTITYPDIGNNW----FWITILSPLAGAYYW 227 (283)
Q Consensus 179 S~~LAiFLTfLaaiGl~CLgLVLsil~P~lG~~~----l~L~LLSPLAGifYW 227 (283)
++...+.+.++.++...++|+.++...++..... +.+..+.-++|+||=
T Consensus 137 ~~l~~~~~~ll~~l~~~~lg~~~a~~~~~~~~~~~i~~~i~~pl~flSg~~~P 189 (253)
T TIGR01291 137 SLIYILPVIALTGLAFASLSMLVAALAPSYAYFAFYQSLVITPMLFLSGVVFP 189 (253)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3444445557777888889999999998864332 223334556777773
No 47
>COG3317 NlpB Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=26.11 E-value=90 Score=31.11 Aligned_cols=31 Identities=19% Similarity=0.309 Sum_probs=26.4
Q ss_pred eEEEEEeecCCCCChh-HHHHHHHHHhhhcCceeec
Q 023342 131 VQKTFVGEGESKKAPN-QVAGEIFSFFTRNNFVVTD 165 (283)
Q Consensus 131 ~qrT~vv~~~s~~p~~-evl~~L~~yF~~R~Y~V~~ 165 (283)
++++++++. ++. .+..++..+|+.|||+++.
T Consensus 97 d~~~lv~~~----~~~~~~Wpqv~~~~qE~gf~i~~ 128 (342)
T COG3317 97 DTRWLVVEN----QPAAYLWPQVRRFLQENGFRIAS 128 (342)
T ss_pred CeeEEEEeC----CchHHhHHHHHHHHHHcCCcccc
Confidence 458888887 444 5999999999999999987
No 48
>PLN02922 prenyltransferase
Probab=26.06 E-value=1.6e+02 Score=28.10 Aligned_cols=34 Identities=18% Similarity=0.114 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHcCCCchHHHHHHHhhhcchhhhh
Q 023342 193 SLASVALVLTITYPDIGNNWFWITILSPLAGAYYW 227 (283)
Q Consensus 193 Gl~CLgLVLsil~P~lG~~~l~L~LLSPLAGifYW 227 (283)
.++|+|+++... ...||+.+++.+++=+.|++|-
T Consensus 107 ~la~~g~~ll~~-~~~~~~~l~iG~~g~~~~~~Yt 140 (315)
T PLN02922 107 ALGAAGLVWASL-VAGNIRVILLLAAAILCGYVYQ 140 (315)
T ss_pred HHHHHHHHHHHH-HccChHHHHHHHHHHHHHHHHh
Confidence 334445555322 2235666667778888888884
No 49
>PRK14444 acylphosphatase; Provisional
Probab=25.26 E-value=1.1e+02 Score=24.23 Aligned_cols=24 Identities=21% Similarity=0.136 Sum_probs=20.3
Q ss_pred CCCc-ceEEEEecHHHHHHHHHHcC
Q 023342 245 DGDL-SEILVQGDDQQVEQMRKELQ 268 (283)
Q Consensus 245 d~~~-S~ItV~aHRDELi~L~~eL~ 268 (283)
.+++ -+|.++|++++|++|.+.|.
T Consensus 39 ~~dG~Vei~~qG~~~~i~~f~~~l~ 63 (92)
T PRK14444 39 LSDGRVEAVFEGSRPAVQKMISWCY 63 (92)
T ss_pred CCCCcEEEEEEcCHHHHHHHHHHHH
Confidence 3444 48999999999999999986
No 50
>PRK13304 L-aspartate dehydrogenase; Reviewed
Probab=24.65 E-value=4.2e+02 Score=24.21 Aligned_cols=97 Identities=20% Similarity=0.220 Sum_probs=63.9
Q ss_pred hhhhhhhhccccceeEEEEEeecCCCCChhHHHHHHHHHhhhcCceeec-CceEEEEEEeecCChHHHHHHHHHHHHHHH
Q 023342 117 GLWSLIKRSVKSKIVQKTFVGEGESKKAPNQVAGEIFSFFTRNNFVVTD-RGEVITFEGMMVPSRGQAAFLTFCTCISLA 195 (283)
Q Consensus 117 GL~FFIRAS~KDRi~qrT~vv~~~s~~p~~evl~~L~~yF~~R~Y~V~~-~~~vItFEG~V~pS~~LAiFLTfLaaiGl~ 195 (283)
+..-.|++..-.++...++.... ||..+. .+...++....+ .+.++.|||..+-
T Consensus 124 ~g~d~i~a~~~G~i~~V~~~~~k----~p~~~~----~~~~~~~~~~~~~~~~~~~f~G~a~e----------------- 178 (265)
T PRK13304 124 VGLDGIKAASLGEIKSVTLTTRK----PPKGLE----GALKELGIDLEEIKEPKVLFEGKAFE----------------- 178 (265)
T ss_pred HhHHHHHHHhcCCccEEEEEEec----ChHHhC----cChhhcCCCccccccceEEEEecHHH-----------------
Confidence 33356777777888777777765 776543 333557777765 5788999998764
Q ss_pred HHHHHHHHHcCCCchHHHHHHHhhhcchhhhhhcCCcceeEEEEEEECC--CCCcceEEEEec
Q 023342 196 SVALVLTITYPDIGNNWFWITILSPLAGAYYWKRASRKEQIKVKMMVGE--DGDLSEILVQGD 256 (283)
Q Consensus 196 CLgLVLsil~P~lG~~~l~L~LLSPLAGifYWqkA~R~EqV~lKL~s~d--d~~~S~ItV~aH 256 (283)
....||.--|---.+.| ||+ |.++|+++... +...=+|.|+|+
T Consensus 179 -----a~~~fP~n~Nva~a~al----a~~---------~~~~v~l~adp~~~~n~h~i~~~g~ 223 (265)
T PRK13304 179 -----AVKKFPANINVAATLSL----ASI---------YPAKVKIIADPNLDRNVHEITVKGS 223 (265)
T ss_pred -----HHHHCCCchhHHHHHHH----hcC---------CCceEEEEECCCCCCceEEEEEEec
Confidence 12679985555544444 454 88999999752 233445888876
No 51
>PF13268 DUF4059: Protein of unknown function (DUF4059)
Probab=24.23 E-value=1.1e+02 Score=24.44 Aligned_cols=19 Identities=32% Similarity=0.667 Sum_probs=14.6
Q ss_pred HHHHHhhhhhhhhhhcccc
Q 023342 110 LFVISVPGLWSLIKRSVKS 128 (283)
Q Consensus 110 LTlLlaiGL~FFIRAS~KD 128 (283)
++++++-|+|.+.||..|-
T Consensus 18 i~V~~~~~~wi~~Ra~~~~ 36 (72)
T PF13268_consen 18 ILVLLVSGIWILWRALRKK 36 (72)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 3567778999999997653
No 52
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=24.11 E-value=53 Score=25.62 Aligned_cols=22 Identities=14% Similarity=0.221 Sum_probs=19.2
Q ss_pred ChhHHHHHHHHHhhhcCceeec
Q 023342 144 APNQVAGEIFSFFTRNNFVVTD 165 (283)
Q Consensus 144 p~~evl~~L~~yF~~R~Y~V~~ 165 (283)
....++.++..-|++|||++.+
T Consensus 12 n~pGVL~Ri~~lf~rRGfnI~s 33 (76)
T PRK11152 12 FRPEVLERVLRVVRHRGFQVCS 33 (76)
T ss_pred CCccHHHHHHHHHhcCCeeeee
Confidence 4567899999999999999977
No 53
>PF00708 Acylphosphatase: Acylphosphatase; InterPro: IPR001792 Acylphosphatase (3.6.1.7 from EC) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates [], its substrates including 1,3-diphosphoglycerate and carbamyl phosphate []. The enzyme has a mainly beta-sheet structure with 2 short alpha-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown []: it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis []. There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. While bacterial and archebacterial hypothetical proteins that are highly similar to that enzyme and that probably possess the same activity. These proteins include: Escherichia coli putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yccX). Bacillus subtilis putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yflL). Archaeoglobus fulgidus putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (O29440 from SWISSPROT). An acylphosphatase-like domain is also found in some prokaryotic hydrogenase maturation HypF carbamoyltransferases [, ].; PDB: 1APS_A 1GXT_A 1GXU_A 2HLT_A 2FHM_A 2HLU_A 3BR8_A 1ULR_A 3TRG_A 2BJD_A ....
Probab=23.53 E-value=1.2e+02 Score=23.28 Aligned_cols=35 Identities=26% Similarity=0.298 Sum_probs=26.6
Q ss_pred CCCcceEEEEecHHHHHHHHHHcCCCcCccEEeeec
Q 023342 245 DGDLSEILVQGDDQQVEQMRKELQLNEKGMVYVKGI 280 (283)
Q Consensus 245 d~~~S~ItV~aHRDELi~L~~eL~L~ekGmv~vkgi 280 (283)
++..-+|.++|.+++|+++-+.+.-.+.. ..|+-+
T Consensus 40 ~dg~V~i~~~G~~~~l~~f~~~l~~g~p~-a~V~~i 74 (91)
T PF00708_consen 40 PDGSVEIEAEGEEEQLEEFIKWLKKGPPP-ARVDEI 74 (91)
T ss_dssp TTSEEEEEEEEEHHHHHHHHHHHHHSSTT-SEEEEE
T ss_pred CCCEEEEEEEeCHHHHHHHHHHHHhCCCC-cEEEEE
Confidence 33457899999999999999999766555 555543
No 54
>KOG2174 consensus Leptin receptor gene-related protein [Signal transduction mechanisms]
Probab=23.50 E-value=1.4e+02 Score=26.15 Aligned_cols=46 Identities=22% Similarity=0.306 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHH---HhhhcchhhhhhcCCcc
Q 023342 183 AAFLTFCTCISLASVALVLTITYPDIGNNWFWIT---ILSPLAGAYYWKRASRK 233 (283)
Q Consensus 183 AiFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~---LLSPLAGifYWqkA~R~ 233 (283)
-+.|++..++|+.-+ +|+-..|. .|||+..+ +|+|+.-.|. +|+|.
T Consensus 7 i~~Lsf~~a~G~~l~--iL~CAL~~-nwwPlf~~~~yvl~PiP~l~f--~a~~~ 55 (131)
T KOG2174|consen 7 IAGLSFAGAVGLLLL--ILGCALFR-NWWPLFVILFYVLSPIPNLLF--IAGRT 55 (131)
T ss_pred HHHHHHHHHHHHHHH--HHHhhhcc-chHHHHHHHHHHhcCCchHHh--ccccc
Confidence 357788777777654 34444565 67776654 6789987665 34443
No 55
>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.
Probab=23.17 E-value=94 Score=22.93 Aligned_cols=24 Identities=29% Similarity=0.428 Sum_probs=16.3
Q ss_pred cHHHHHHHHHHcCCCcCccEEeeeccc
Q 023342 256 DDQQVEQMRKELQLNEKGMVYVKGIFE 282 (283)
Q Consensus 256 HRDELi~L~~eL~L~ekGmv~vkgi~e 282 (283)
|++++++.=+++. .+..|+||++.
T Consensus 13 ~~~~l~~~l~~l~---~~i~R~KG~v~ 36 (92)
T smart00833 13 HPQRLLAALDELP---EGVLRAKGFFW 36 (92)
T ss_pred CHHHHHHHHHhcc---CCeEEEEEEEE
Confidence 4566666555553 67999999873
No 56
>PF04133 Vps55: Vacuolar protein sorting 55 ; InterPro: IPR007262 Vps55 is involved in the secretion of the Golgi form of the soluble vacuolar carboxypeptidase Y, but not the trafficking of the membrane-bound vacuolar alkaline phosphatase. Both Vps55 and obesity receptor gene-related protein are important for functioning membrane trafficking to the vacuole/lysosome of eukaryotic cells [].
Probab=23.13 E-value=1.2e+02 Score=25.57 Aligned_cols=39 Identities=18% Similarity=0.215 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCchHHHHHH---Hhhhcchhh
Q 023342 184 AFLTFCTCISLASVALVLTITYPDIGNNWFWIT---ILSPLAGAY 225 (283)
Q Consensus 184 iFLTfLaaiGl~CLgLVLsil~P~lG~~~l~L~---LLSPLAGif 225 (283)
|.|++..++|++=+=|-++. .-+|||++.+ +|+|+.=++
T Consensus 2 I~Ls~~~aiG~lL~IL~CAL---~~nw~PL~v~~~y~laPiP~~i 43 (120)
T PF04133_consen 2 IGLSFFLAIGFLLVILSCAL---YKNWWPLFVVLFYVLAPIPNLI 43 (120)
T ss_pred eehHHHHHHHHHHHHHHHHH---hcccHHHHHHHHHHHHhhhHHH
Confidence 45777888887766555555 2235555533 567887666
No 57
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=22.85 E-value=19 Score=28.60 Aligned_cols=11 Identities=55% Similarity=0.721 Sum_probs=5.2
Q ss_pred CCcCccEEeee
Q 023342 269 LNEKGMVYVKG 279 (283)
Q Consensus 269 L~ekGmv~vkg 279 (283)
..+.|+|+++|
T Consensus 101 ~~~~G~V~~~G 111 (144)
T PF01957_consen 101 LNGSGRVKVDG 111 (144)
T ss_dssp SSS-EEEEETT
T ss_pred cCCcEEEEECC
Confidence 44555555554
No 58
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=22.62 E-value=1e+02 Score=22.30 Aligned_cols=18 Identities=0% Similarity=0.154 Sum_probs=13.4
Q ss_pred hhHHHHHHHHHhhhcCce
Q 023342 145 PNQVAGEIFSFFTRNNFV 162 (283)
Q Consensus 145 ~~evl~~L~~yF~~R~Y~ 162 (283)
++.-++.+.+||.+|||-
T Consensus 25 s~~~L~k~~~wld~rgWw 42 (45)
T PF12123_consen 25 SDAELDKFTAWLDERGWW 42 (45)
T ss_dssp -HHHHHHHHHHHHHTT--
T ss_pred CHHHHHHHHHHHHhcCcE
Confidence 346788999999999984
No 59
>PF13194 DUF4010: Domain of unknown function (DUF4010)
Probab=22.51 E-value=73 Score=28.91 Aligned_cols=46 Identities=22% Similarity=0.374 Sum_probs=25.6
Q ss_pred HHHHHHHHHHcCCCc---hHHHHHH-Hhhhcchhhhhhc-CCcceeEEEEE
Q 023342 195 ASVALVLTITYPDIG---NNWFWIT-ILSPLAGAYYWKR-ASRKEQIKVKM 240 (283)
Q Consensus 195 ~CLgLVLsil~P~lG---~~~l~L~-LLSPLAGifYWqk-A~R~EqV~lKL 240 (283)
.=+.+++.++.|++- +.|+.+. +.+=..+.|+||| ....|+.++++
T Consensus 69 ~R~l~iv~i~~~~l~~~l~~p~~~~~~~~~~~a~~~~r~~~~~~~~~~~~~ 119 (211)
T PF13194_consen 69 VRVLLIVAILNPALLRSLALPLLAMALVGLLAALLLWRRREEPEEDEELKL 119 (211)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCCCC
Confidence 335566667777754 3344333 4455677788888 34445444443
No 60
>PF14991 MLANA: Protein melan-A; PDB: 2GTZ_F 2GT9_F 3MRO_P 2GUO_C 3MRQ_P 2GTW_C 3L6F_C 3MRP_P.
Probab=22.45 E-value=29 Score=29.90 Aligned_cols=43 Identities=23% Similarity=0.291 Sum_probs=1.3
Q ss_pred hhhhccCCcchhhhhHHHHHHHHHhhhhhhhhhhccccceeEEEEEe
Q 023342 91 LLAESTAGYSLASYYTSLGLFVISVPGLWSLIKRSVKSKIVQKTFVG 137 (283)
Q Consensus 91 ~~~~~~~g~s~aSyySTL~LTlLlaiGL~FFIRAS~KDRi~qrT~vv 137 (283)
.-||...|-. .-++.|-+||.+|-|++=|||-=.++..++.-+
T Consensus 21 itAEEAaGIG----iL~VILgiLLliGCWYckRRSGYk~L~~k~~~~ 63 (118)
T PF14991_consen 21 ITAEEAAGIG----ILIVILGILLLIGCWYCKRRSGYKTLRDKSLHA 63 (118)
T ss_dssp -------SSS-------------------------------------
T ss_pred eeHHHhccce----eHHHHHHHHHHHhheeeeecchhhhhhhccccc
Confidence 3445443543 457889999999999999999876665555544
No 61
>CHL00177 ccs1 c-type cytochrome biogenensis protein; Validated
Probab=22.26 E-value=3.3e+02 Score=27.43 Aligned_cols=37 Identities=8% Similarity=0.231 Sum_probs=25.5
Q ss_pred hHHHHHHHHHhhhcCceeecCce-EEEEEEeecCChHH
Q 023342 146 NQVAGEIFSFFTRNNFVVTDRGE-VITFEGMMVPSRGQ 182 (283)
Q Consensus 146 ~evl~~L~~yF~~R~Y~V~~~~~-vItFEG~V~pS~~L 182 (283)
.+..+++.+.+++++|+|...++ .--.+|....--.+
T Consensus 125 ~~~~~~~~~~L~~~gy~v~~~~~~l~A~KG~~gr~G~~ 162 (426)
T CHL00177 125 KFSLSKLAYKLKSKNYSIFQQGNKIYAYKGLIGRIAPI 162 (426)
T ss_pred hhHHHHHHHHHHHCCeEEEEeCcEEEEecCcchhhhHH
Confidence 45678999999999999988543 44455555443333
No 62
>TIGR02762 TraL_TIGR type IV conjugative transfer system protein TraL. This protein is part of the type IV secretion system for conjugative plasmid transfer. The function of the TraL protein is unknown.
Probab=22.13 E-value=1.2e+02 Score=24.32 Aligned_cols=22 Identities=14% Similarity=0.080 Sum_probs=10.7
Q ss_pred HHHHhhhcchhhhh---h-cCCccee
Q 023342 214 WITILSPLAGAYYW---K-RASRKEQ 235 (283)
Q Consensus 214 ~L~LLSPLAGifYW---q-kA~R~Eq 235 (283)
..+++++.++..++ | |.+|.|.
T Consensus 41 ~g~~lg~~~~~~~~~lrr~K~g~~~~ 66 (95)
T TIGR02762 41 IGLILGAAVMLIWKRLRRIKGGEGEN 66 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChh
Confidence 44556665552221 2 5666654
No 63
>PF07584 BatA: Aerotolerance regulator N-terminal; InterPro: IPR024163 The Batl operon appears to be important in pathogenicity and aerotolerance. BatA ensures bacterial survival in the early stages of the infection process, when the infected sites are aerobic, and is produced under conditions of oxidative stress []. Proteins produced by the Batl operon share a highly-conserved sequence at their N terminus and the full length proteins carry multiple membrane-spanning domains []. This entry represents the conserved N-terminal domain, which is also found in some uncharacterised proteins.
Probab=22.02 E-value=61 Score=24.42 Aligned_cols=26 Identities=27% Similarity=0.575 Sum_probs=16.0
Q ss_pred hHHHHHHHhhhc-chhhhhhcCCccee
Q 023342 210 NNWFWITILSPL-AGAYYWKRASRKEQ 235 (283)
Q Consensus 210 ~~~l~L~LLSPL-AGifYWqkA~R~Eq 235 (283)
++++++.++-|+ -.++||.+-+|.+.
T Consensus 7 P~~L~~Llllp~~i~~~~~~~~~~~~~ 33 (77)
T PF07584_consen 7 PWYLWLLLLLPLPIIIHYFLRRRRRRV 33 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccCCCc
Confidence 455555555566 66777777666555
No 64
>PRK07566 bacteriochlorophyll/chlorophyll a synthase; Reviewed
Probab=21.86 E-value=1.1e+02 Score=28.75 Aligned_cols=20 Identities=30% Similarity=0.180 Sum_probs=10.0
Q ss_pred cccccCCCCCCCCCcccchh
Q 023342 37 SWLRQAPNPPSSPTTRAKKK 56 (283)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~ 56 (283)
+-|||-.+|.....|++|-|
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~ 28 (314)
T PRK07566 9 SKPRQLLGPKGASPTTSIWK 28 (314)
T ss_pred cccccccccccccccchHHH
Confidence 44555555554444455533
No 65
>PRK14440 acylphosphatase; Provisional
Probab=21.80 E-value=1.9e+02 Score=22.84 Aligned_cols=35 Identities=9% Similarity=0.247 Sum_probs=25.1
Q ss_pred CCCcceEEEEecHHHHHHHHHHcCCCcCccEEeeec
Q 023342 245 DGDLSEILVQGDDQQVEQMRKELQLNEKGMVYVKGI 280 (283)
Q Consensus 245 d~~~S~ItV~aHRDELi~L~~eL~L~ekGmv~vkgi 280 (283)
++..-+|.++|++|.++++.+.+. +......|+.|
T Consensus 39 ~dG~Vei~~~G~~~~v~~f~~~l~-~gp~~a~V~~i 73 (90)
T PRK14440 39 PDGSVEVVAEGYEEALSKLLERIK-QGPPAAEVEKV 73 (90)
T ss_pred CCCCEEEEEEcCHHHHHHHHHHHh-hCCCCcEEEEE
Confidence 333467999999999999999997 33334555543
No 66
>COG0314 MoaE Molybdopterin converting factor, large subunit [Coenzyme metabolism]
Probab=21.53 E-value=1.1e+02 Score=26.78 Aligned_cols=16 Identities=25% Similarity=0.650 Sum_probs=14.1
Q ss_pred cCceEEEEEEeecCCh
Q 023342 165 DRGEVITFEGMMVPSR 180 (283)
Q Consensus 165 ~~~~vItFEG~V~pS~ 180 (283)
+.|-++||.|+||---
T Consensus 27 ~~GAivtF~G~VR~~~ 42 (149)
T COG0314 27 EAGAIVTFVGIVREEN 42 (149)
T ss_pred cCceEEEEEEEEecCC
Confidence 6799999999999765
No 67
>PRK14425 acylphosphatase; Provisional
Probab=21.34 E-value=2e+02 Score=22.85 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=25.5
Q ss_pred CCCcceEEEEecHHHHHHHHHHcCCCcCccEEeeec
Q 023342 245 DGDLSEILVQGDDQQVEQMRKELQLNEKGMVYVKGI 280 (283)
Q Consensus 245 d~~~S~ItV~aHRDELi~L~~eL~L~ekGmv~vkgi 280 (283)
++..-+|.++|+.++|++|.+.|. +....-.|+.+
T Consensus 42 ~dGsVei~~qG~~~~le~f~~~l~-~gp~~a~V~~i 76 (94)
T PRK14425 42 SDGSVTALIAGPDSAISAMIERFR-RGPPGASVSGV 76 (94)
T ss_pred CCCeEEEEEEeCHHHHHHHHHHHh-hCCCceEEEEE
Confidence 334477999999999999999997 33234555544
No 68
>PF08753 NikR_C: NikR C terminal nickel binding domain; InterPro: IPR014864 NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This protein corresponds to the C-terminal regulatory domain which contains four nickel binding sites at the tetramer interface []. ; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 2WVB_B 2WVD_C 3QSI_B 3LGH_A 2CAD_A ....
Probab=21.22 E-value=1.4e+02 Score=22.94 Aligned_cols=32 Identities=28% Similarity=0.454 Sum_probs=25.7
Q ss_pred CCcceEEEEecHHHHHHHHHHcCCCcCccEEee
Q 023342 246 GDLSEILVQGDDQQVEQMRKELQLNEKGMVYVK 278 (283)
Q Consensus 246 ~~~S~ItV~aHRDELi~L~~eL~L~ekGmv~vk 278 (283)
...-.+.|+|..|||.+|-..|.- .+|.-++|
T Consensus 42 ~ClEvivv~G~~~~I~~l~~~l~~-~kGV~~~~ 73 (78)
T PF08753_consen 42 NCLEVIVVRGPADRIKELAEKLRS-LKGVKHVK 73 (78)
T ss_dssp EEEEEEEEEEEHHHHHHHHHHHHT-STTEEEEE
T ss_pred CeEEEEEEEcCHHHHHHHHHHHhc-cCCeeEEE
Confidence 345669999999999999999853 47877765
No 69
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=20.79 E-value=59 Score=27.74 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=13.7
Q ss_pred CchHHHHHHHhhhcchhhhhhcCCcc
Q 023342 208 IGNNWFWITILSPLAGAYYWKRASRK 233 (283)
Q Consensus 208 lG~~~l~L~LLSPLAGifYWqkA~R~ 233 (283)
+|...+++.++.=..|++|-.+-.+.
T Consensus 41 lg~~~lAlg~vL~~~g~~~~~~~~~~ 66 (191)
T PF04156_consen 41 LGIALLALGVVLLSLGLLCLLSKRPV 66 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccc
Confidence 34444444444445677776555443
No 70
>PRK10527 hypothetical protein; Provisional
Probab=20.41 E-value=92 Score=26.52 Aligned_cols=41 Identities=20% Similarity=0.225 Sum_probs=26.8
Q ss_pred HHHHHHHHHHH-HHHHHcCCCchHHHHHHHhhhcchhhhhhcCCcce
Q 023342 189 CTCISLASVAL-VLTITYPDIGNNWFWITILSPLAGAYYWKRASRKE 234 (283)
Q Consensus 189 LaaiGl~CLgL-VLsil~P~lG~~~l~L~LLSPLAGifYWqkA~R~E 234 (283)
+-++|..|+|| ++.+..|-+.--+|+|. |.+.+-|.+.|-|
T Consensus 6 ~~~lG~~~~~LG~iGi~LPlLPTTPFlLL-----Aa~cfaRsSpR~~ 47 (125)
T PRK10527 6 LIIIGWLAVVLGTLGVVLPLLPTTPFILL-----AAWCFARSSPRFH 47 (125)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCcHHHHH-----HHHHHHcCCHHHH
Confidence 44567777777 56778888887777764 4455555555544
No 71
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=20.30 E-value=6.1e+02 Score=27.99 Aligned_cols=75 Identities=20% Similarity=0.111 Sum_probs=43.2
Q ss_pred CCChhHHHHHHHHHhhhcCceeecCceEEEEEEeecCChHHHHH--HHHHHHHHHHHHHHHHHHHcCCCchHHHHHHHhh
Q 023342 142 KKAPNQVAGEIFSFFTRNNFVVTDRGEVITFEGMMVPSRGQAAF--LTFCTCISLASVALVLTITYPDIGNNWFWITILS 219 (283)
Q Consensus 142 ~~p~~evl~~L~~yF~~R~Y~V~~~~~vItFEG~V~pS~~LAiF--LTfLaaiGl~CLgLVLsil~P~lG~~~l~L~LLS 219 (283)
..+..++.+++++.+++-++ ..|-.+.|.|.... ..-.| +....+++++.+=|||..+|-++ ..++.+.+--
T Consensus 811 g~~~~~~~~~i~~~l~~~~l---P~g~~~~~~G~~~~--~~~~~~~l~~~~~~al~li~liL~~~F~S~-~~pliI~~tI 884 (1025)
T PRK10614 811 GKSLSDASAAIERAMTQLGV---PSTVRGSFAGTAQV--FQETMNSQLILILAAIATVYIVLGILYESY-VHPLTILSTL 884 (1025)
T ss_pred CCCHHHHHHHHHHHHHhCCC---CCCeEEEeccHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-HHHHHHHHHH
Confidence 45778888899998876321 23556788887654 22222 22333455555667777777663 2333333334
Q ss_pred hcc
Q 023342 220 PLA 222 (283)
Q Consensus 220 PLA 222 (283)
|+|
T Consensus 885 Pla 887 (1025)
T PRK10614 885 PSA 887 (1025)
T ss_pred HHH
Confidence 665
No 72
>PRK13387 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional
Probab=20.16 E-value=1.9e+02 Score=27.55 Aligned_cols=20 Identities=15% Similarity=0.074 Sum_probs=13.3
Q ss_pred chHHHHHHHhhhcchhhhhh
Q 023342 209 GNNWFWITILSPLAGAYYWK 228 (283)
Q Consensus 209 G~~~l~L~LLSPLAGifYWq 228 (283)
||+.+.+.+++=+.|++|-.
T Consensus 113 g~~~l~igl~g~~~~~~Yt~ 132 (317)
T PRK13387 113 SWLLLVIGLICFAIGILYTG 132 (317)
T ss_pred cHHHHHHHHHHHHHhhhhcC
Confidence 55556666777777777743
Done!