Query 024092
Match_columns 272
No_of_seqs 306 out of 1847
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 08:54:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024092hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 4.1E-13 8.8E-18 96.2 7.9 58 86-144 1-62 (62)
2 KOG1603 Copper chaperone [Inor 99.3 9.5E-12 2.1E-16 93.0 9.0 68 82-149 4-71 (73)
3 COG2608 CopZ Copper chaperone 99.3 1.2E-11 2.6E-16 92.1 8.2 65 83-148 2-70 (71)
4 KOG4656 Copper chaperone for s 98.9 3.2E-09 7E-14 93.7 8.3 70 83-153 7-76 (247)
5 PRK10671 copA copper exporting 98.7 1.7E-07 3.7E-12 98.3 14.2 139 2-148 25-164 (834)
6 KOG0207 Cation transport ATPas 98.6 2.6E-07 5.6E-12 96.0 11.5 122 2-154 16-143 (951)
7 KOG0207 Cation transport ATPas 98.5 7.7E-07 1.7E-11 92.6 11.2 118 2-149 91-215 (951)
8 PLN02957 copper, zinc superoxi 98.5 1E-06 2.2E-11 79.8 10.3 71 82-153 5-75 (238)
9 PRK10671 copA copper exporting 98.3 1.2E-06 2.7E-11 91.9 8.4 64 83-149 3-67 (834)
10 COG2217 ZntA Cation transport 98.1 5.4E-06 1.2E-10 85.8 7.6 62 84-147 3-69 (713)
11 TIGR00003 copper ion binding p 97.8 0.0002 4.4E-09 47.3 8.7 61 84-145 3-67 (68)
12 PF00403 HMA: Heavy-metal-asso 97.2 0.00043 9.2E-09 49.1 4.1 40 2-42 20-62 (62)
13 KOG1603 Copper chaperone [Inor 96.8 0.0019 4.1E-08 48.1 4.5 45 1-46 25-70 (73)
14 PRK11033 zntA zinc/cadmium/mer 96.7 0.0047 1E-07 64.6 7.5 64 83-147 53-118 (741)
15 COG2608 CopZ Copper chaperone 95.6 0.024 5.2E-07 41.9 4.7 42 2-44 24-68 (71)
16 TIGR02052 MerP mercuric transp 94.0 0.82 1.8E-05 32.9 9.3 63 84-147 24-90 (92)
17 cd00371 HMA Heavy-metal-associ 90.9 2.1 4.5E-05 25.1 7.3 49 90-138 6-56 (63)
18 PRK13748 putative mercuric red 87.9 2.5 5.5E-05 42.3 8.6 64 86-150 3-69 (561)
19 KOG4656 Copper chaperone for s 87.7 0.74 1.6E-05 41.4 4.1 44 2-46 28-71 (247)
20 PLN02957 copper, zinc superoxi 80.5 3.3 7.2E-05 37.5 5.2 45 2-47 27-71 (238)
21 PF01883 DUF59: Domain of unkn 80.1 2.9 6.3E-05 30.3 3.9 33 83-115 34-72 (72)
22 COG1888 Uncharacterized protei 78.7 15 0.00033 28.9 7.5 66 82-148 5-79 (97)
23 PF01206 TusA: Sulfurtransfera 70.1 11 0.00023 27.0 4.7 53 86-148 2-57 (70)
24 PF05663 DUF809: Protein of un 67.8 13 0.00028 29.8 5.0 44 94-138 47-90 (138)
25 PF02680 DUF211: Uncharacteriz 65.1 16 0.00035 28.9 4.9 64 82-147 4-76 (95)
26 PF02162 XYPPX: XYPPX repeat ( 56.7 9.5 0.00021 20.1 1.6 7 241-247 4-10 (15)
27 COG1888 Uncharacterized protei 54.0 21 0.00045 28.2 3.8 41 2-43 28-76 (97)
28 TIGR02945 SUF_assoc FeS assemb 53.5 38 0.00081 26.0 5.3 40 98-142 58-97 (99)
29 COG2217 ZntA Cation transport 52.8 19 0.00042 38.0 4.6 42 2-44 23-68 (713)
30 PRK11023 outer membrane lipopr 50.4 1.7E+02 0.0037 25.5 10.6 43 94-136 126-170 (191)
31 TIGR03406 FeS_long_SufT probab 49.8 21 0.00046 31.1 3.7 54 84-142 114-173 (174)
32 PRK11018 hypothetical protein; 47.4 75 0.0016 23.6 5.9 55 84-148 8-65 (78)
33 cd03421 SirA_like_N SirA_like_ 46.1 57 0.0012 23.1 4.9 51 87-148 2-55 (67)
34 PF02680 DUF211: Uncharacteriz 44.3 28 0.00061 27.5 3.2 40 2-42 26-73 (95)
35 PRK06418 transcription elongat 43.4 75 0.0016 27.6 6.0 68 86-153 9-101 (166)
36 PF14437 MafB19-deam: MafB19-l 43.1 56 0.0012 27.8 5.1 41 83-124 100-142 (146)
37 PF04972 BON: BON domain; Int 39.5 22 0.00048 24.7 1.9 34 98-132 2-38 (64)
38 cd00652 TBP_TLF TATA box bindi 39.2 2.5E+02 0.0055 24.2 10.1 54 85-138 98-166 (174)
39 PRK10553 assembly protein for 38.7 1.2E+02 0.0026 23.4 5.9 43 96-138 18-61 (87)
40 cd04888 ACT_PheB-BS C-terminal 37.8 82 0.0018 22.1 4.7 33 83-115 41-74 (76)
41 PF13732 DUF4162: Domain of un 36.6 87 0.0019 22.8 4.8 43 104-148 26-69 (84)
42 PF09580 Spore_YhcN_YlaJ: Spor 36.2 93 0.002 26.3 5.6 35 93-127 73-107 (177)
43 PRK11670 antiporter inner memb 34.6 1.1E+02 0.0023 29.6 6.3 68 84-152 48-146 (369)
44 PF14492 EFG_II: Elongation Fa 34.1 1.1E+02 0.0024 22.4 5.0 54 94-147 15-73 (75)
45 COG2151 PaaD Predicted metal-s 32.0 70 0.0015 25.9 3.8 54 85-143 51-110 (111)
46 PF08002 DUF1697: Protein of u 32.0 2.1E+02 0.0046 23.6 6.9 50 98-148 22-75 (137)
47 PF03927 NapD: NapD protein; 28.3 2.3E+02 0.0051 21.1 6.0 42 96-138 16-58 (79)
48 PF13740 ACT_6: ACT domain; PD 28.0 2.3E+02 0.005 20.4 5.8 55 84-138 2-63 (76)
49 PF13192 Thioredoxin_3: Thiore 27.7 80 0.0017 22.9 3.3 13 85-98 3-15 (76)
50 PF06495 Transformer: Fruit fl 27.3 97 0.0021 27.2 4.1 12 230-241 141-152 (182)
51 PF04312 DUF460: Protein of un 25.1 2.2E+02 0.0048 24.1 5.7 42 112-154 45-88 (138)
52 cd04518 TBP_archaea archaeal T 24.4 4.7E+02 0.01 22.6 9.7 24 115-138 142-165 (174)
53 PRK05412 putative nucleotide-b 23.9 4.8E+02 0.01 22.6 10.0 51 85-138 94-146 (161)
54 COG4004 Uncharacterized protei 23.8 98 0.0021 24.4 3.2 24 1-24 35-58 (96)
55 PF13291 ACT_4: ACT domain; PD 22.5 2.1E+02 0.0045 20.5 4.7 33 82-114 47-79 (80)
56 PF04461 DUF520: Protein of un 22.4 5.1E+02 0.011 22.4 7.8 52 84-138 93-146 (160)
57 COG4004 Uncharacterized protei 22.4 86 0.0019 24.7 2.6 22 105-126 37-58 (96)
58 KOG2236 Uncharacterized conser 22.4 1.6E+02 0.0034 29.8 5.0 7 259-265 473-479 (483)
59 cd03420 SirA_RHOD_Pry_redox Si 21.8 2.6E+02 0.0057 19.9 5.0 52 87-148 2-56 (69)
60 PRK14054 methionine sulfoxide 21.4 1.7E+02 0.0036 25.5 4.5 45 94-138 10-76 (172)
61 cd00291 SirA_YedF_YeeD SirA, Y 21.4 2.9E+02 0.0063 19.1 5.2 52 87-148 2-56 (69)
62 PF04459 DUF512: Protein of un 20.4 5E+02 0.011 23.1 7.5 56 84-139 99-158 (204)
63 TIGR03028 EpsE polysaccharide 20.2 2.6E+02 0.0057 25.0 5.8 55 86-142 39-109 (239)
64 cd03422 YedF YedF is a bacteri 20.2 3.1E+02 0.0066 19.6 5.1 52 87-148 2-56 (69)
65 PF14535 AMP-binding_C_2: AMP- 20.2 3.8E+02 0.0083 20.3 5.9 55 98-152 7-81 (96)
No 1
>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=99.44 E-value=4.1e-13 Score=96.22 Aligned_cols=58 Identities=28% Similarity=0.513 Sum_probs=53.9
Q ss_pred EEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec---CCHHHHHHHHHHhcCCC
Q 024092 86 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MDVKELVPYLKEKLKRN 144 (272)
Q Consensus 86 ~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~---vd~~~L~~~l~kk~G~~ 144 (272)
+|.| +|+|++|+++|+++|.+++||.++.+|+.+++|+|.+. +++.+|.++|+ ++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 5888 99999999999999999999999999999999999986 45599999999 89984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.32 E-value=9.5e-12 Score=93.01 Aligned_cols=68 Identities=44% Similarity=0.671 Sum_probs=61.1
Q ss_pred ceEEEEEeeccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcCCCeEEcc
Q 024092 82 ESTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVP 149 (272)
Q Consensus 82 ~~~v~l~VgM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G~~aelv~ 149 (272)
..+.+|.+.|||.+|..+|++.|+.++||.++.+|...++|||.|.+++..|++.|++..+.++.++.
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 35678999999999999999999999999999999999999999999999999999943337777663
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.30 E-value=1.2e-11 Score=92.12 Aligned_cols=65 Identities=23% Similarity=0.470 Sum_probs=58.1
Q ss_pred eEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEE--e-cCCHHHHHHHHHHhcCCCeEEc
Q 024092 83 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--G-TMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 83 ~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~--g-~vd~~~L~~~l~kk~G~~aelv 148 (272)
.+.+|.| +|+|.+|+.+|+++|.+++||.++.||+..++++|+ + .++.+.|+++|. .+||.+..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 3578999 999999999999999999999999999999666666 4 579999999999 999998764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.93 E-value=3.2e-09 Score=93.68 Aligned_cols=70 Identities=20% Similarity=0.406 Sum_probs=65.2
Q ss_pred eEEEEEeeccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcCCCeEEccCCCC
Q 024092 83 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 153 (272)
Q Consensus 83 ~~v~l~VgM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G~~aelv~~~~~ 153 (272)
-+++|.|.|||++|++.|+..|..++||.+|+||+..+.|.|.+.+.+.+|...|+ .+|++|.|....+.
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAGKP 76 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCCch
Confidence 56789999999999999999999999999999999999999999999999999999 99999999855443
No 5
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.72 E-value=1.7e-07 Score=98.32 Aligned_cols=139 Identities=15% Similarity=0.268 Sum_probs=97.1
Q ss_pred CCCCCCceEEEeeccCcEEEEEeecCHHHHHHHHHHhhccccccCCCCCCCCCCCCCCcccccccCCCCCcccccCCCCC
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLVSPQPKKDAGGGEKKSEEKSEKKPDDKKSEEKKPPK 81 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~vd~~~li~~I~~k~Gy~velvs~~pk~~~~~~e~~~~~~~~~k~~~k~~~~~~~~~ 81 (272)
|++++||.++.||+ ++.+|.+..+...+.+.|+ .+||.+++.++............ +.........+.. ....
T Consensus 25 l~~~~gv~~v~v~~--~~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~-~~~~ 97 (834)
T PRK10671 25 LEQRPDVEQADVSI--TEAHVTGTASAEALIETIK-QAGYDASVSHPKAKPLTESSIPS---EALTAASEELPAA-TADD 97 (834)
T ss_pred HhcCCCcceEEEee--eEEEEEecCCHHHHHHHHH-hcCCcccccccccccccccccCc---hhhhhhhhhcccc-ccCc
Confidence 67889999999998 4566767778899999999 99999886542211111100000 0000000000000 0011
Q ss_pred ceEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcCCCeEEc
Q 024092 82 ESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 82 ~~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G~~aelv 148 (272)
..++.|.+ +|+|.+|+.+|++.|..++||.++.+++.++++.|.+..++..+...++ .+||.+.++
T Consensus 98 ~~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 98 DDSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred CceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 23567888 9999999999999999999999999999999999886678888988898 899987654
No 6
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.61 E-value=2.6e-07 Score=96.00 Aligned_cols=122 Identities=17% Similarity=0.303 Sum_probs=104.2
Q ss_pred CCCCCCceEEEeeccCcEEEEEee--cCHHHHHHHHHHhhccccccCCCCCCCCCCCCCCcccccccCCCCCcccccCCC
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGK--VEPAKLKERLEAKTKKKVDLVSPQPKKDAGGGEKKSEEKSEKKPDDKKSEEKKP 79 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~--vd~~~li~~I~~k~Gy~velvs~~pk~~~~~~e~~~~~~~~~k~~~k~~~~~~~ 79 (272)
++..+||.++.|++..+..+|.+. ++++.|.++|+ ..|+.+++++...
T Consensus 16 ~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~----------------------------- 65 (951)
T KOG0207|consen 16 ISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSE----------------------------- 65 (951)
T ss_pred HhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCc-----------------------------
Confidence 567899999999999999999884 68899999999 8999887654321
Q ss_pred CCceEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe---cCCHHHHHHHHHHhcCCCeEEccCCCCc
Q 024092 80 PKESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEVVPAKKDD 154 (272)
Q Consensus 80 ~~~~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g---~vd~~~L~~~l~kk~G~~aelv~~~~~~ 154 (272)
....+..|.| ||+|.+|++.|++.|+++.||.++.|-+...+..|.- ...++.+.+.++ ++|+.++++......
T Consensus 66 ~~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie-~~gf~a~~i~~~~~~ 143 (951)
T KOG0207|consen 66 ITASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIE-DLGFSAELIESVNGN 143 (951)
T ss_pred cccceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHH-hcCccceehhcccCC
Confidence 1123678899 9999999999999999999999999999999999983 467899999999 999999998765543
No 7
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.49 E-value=7.7e-07 Score=92.56 Aligned_cols=118 Identities=19% Similarity=0.324 Sum_probs=99.8
Q ss_pred CCCCCCceEEEeeccCcEEEEEee---cCHHHHHHHHHHhhccccccCCCCCCCCCCCCCCcccccccCCCCCcccccCC
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGK---VEPAKLKERLEAKTKKKVDLVSPQPKKDAGGGEKKSEEKSEKKPDDKKSEEKK 78 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~---vd~~~li~~I~~k~Gy~velvs~~pk~~~~~~e~~~~~~~~~k~~~k~~~~~~ 78 (272)
|++++||.++.|.+.+.+.+|..+ ..+..+.+.++ +.|+.+++++...
T Consensus 91 l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie-~~gf~a~~i~~~~---------------------------- 141 (951)
T KOG0207|consen 91 LRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIE-DLGFSAELIESVN---------------------------- 141 (951)
T ss_pred hhccCCcceEEEEeeccceeEEECCcccCchhHHHHHH-hcCccceehhccc----------------------------
Confidence 678899999999999999999874 46789999999 8999877543210
Q ss_pred CCCceEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe---cCCHHHHHHHHHHhcCCCeEEcc
Q 024092 79 PPKESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEVVP 149 (272)
Q Consensus 79 ~~~~~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g---~vd~~~L~~~l~kk~G~~aelv~ 149 (272)
.....+++|.| +|+|.+|+.+|++.|.+++||.++++++.++++.|.. ...+-.+++.|. .+|+.+.+..
T Consensus 142 ~~~~~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~ 215 (951)
T KOG0207|consen 142 GNSNQKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRP 215 (951)
T ss_pred CCCCCcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeee
Confidence 01115789999 9999999999999999999999999999999999985 367889999998 8999887764
No 8
>PLN02957 copper, zinc superoxide dismutase
Probab=98.47 E-value=1e-06 Score=79.84 Aligned_cols=71 Identities=24% Similarity=0.462 Sum_probs=64.0
Q ss_pred ceEEEEEeeccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcCCCeEEccCCCC
Q 024092 82 ESTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 153 (272)
Q Consensus 82 ~~~v~l~VgM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G~~aelv~~~~~ 153 (272)
++++.|.++|+|.+|+.+|+++|.+++||.++.+|+..++++|...++...|+..|+ ++||.+++++....
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~~ 75 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGDP 75 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCCc
Confidence 356788889999999999999999999999999999999999998778899999999 99999998866443
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.34 E-value=1.2e-06 Score=91.90 Aligned_cols=64 Identities=20% Similarity=0.384 Sum_probs=58.3
Q ss_pred eEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcCCCeEEcc
Q 024092 83 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVP 149 (272)
Q Consensus 83 ~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G~~aelv~ 149 (272)
++++|.| +|+|++|+.+|+++|.+++||..+.||+. +++|++..+...|.++|+ ++||.+++.+
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIK-QAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence 4689999 99999999999999999999999999994 667777789999999999 9999999875
No 10
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.13 E-value=5.4e-06 Score=85.78 Aligned_cols=62 Identities=21% Similarity=0.402 Sum_probs=56.6
Q ss_pred EEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec---CC-HHHHHHHHHHhcCCCeEE
Q 024092 84 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MD-VKELVPYLKEKLKRNVEV 147 (272)
Q Consensus 84 ~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~---vd-~~~L~~~l~kk~G~~ael 147 (272)
++.|.| ||||++|+.+|| +|.+++||.++.||+.+++++|... .+ ++.+...++ .+||.+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 568999 999999999999 9999999999999999999999853 45 788999998 99998877
No 11
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.83 E-value=0.0002 Score=47.32 Aligned_cols=61 Identities=20% Similarity=0.325 Sum_probs=51.4
Q ss_pred EEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe---cCCHHHHHHHHHHhcCCCe
Q 024092 84 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNV 145 (272)
Q Consensus 84 ~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g---~vd~~~L~~~l~kk~G~~a 145 (272)
++.|.| +|+|..|+.+|++.+..+.++..+.+++....+.|.. ..+...+...+. ..|+.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCCc
Confidence 456888 9999999999999999999999999999999998874 346777777776 777653
No 12
>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=97.24 E-value=0.00043 Score=49.12 Aligned_cols=40 Identities=35% Similarity=0.289 Sum_probs=35.5
Q ss_pred CCCCCCceEEEeeccCcEEEEEeec---CHHHHHHHHHHhhccc
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGKV---EPAKLKERLEAKTKKK 42 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~v---d~~~li~~I~~k~Gy~ 42 (272)
|.+++||.++.+|+.+++++|.+.. ++++|+++|+ ++||+
T Consensus 20 l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 20 LSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp HHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred HhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 6788999999999999999999964 4589999999 89984
No 13
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=96.84 E-value=0.0019 Score=48.06 Aligned_cols=45 Identities=40% Similarity=0.535 Sum_probs=38.5
Q ss_pred CCCCCCCceEEEeeccCcEEEEEeecCHHHHHHHHHHhhc-cccccC
Q 024092 1 MLLICLGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTK-KKVDLV 46 (272)
Q Consensus 1 iL~kl~GV~~v~Vd~~~~kvtV~g~vd~~~li~~I~~k~G-y~velv 46 (272)
.|..+.||.++.+|...++|||.|.+++..|++.|++ .+ +.+.+|
T Consensus 25 ~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k-~~~k~~~~~ 70 (73)
T KOG1603|consen 25 VLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK-TGGKRAELW 70 (73)
T ss_pred HhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh-cCCCceEEe
Confidence 3678999999999999999999999999999999994 54 555443
No 14
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.66 E-value=0.0047 Score=64.60 Aligned_cols=64 Identities=14% Similarity=0.250 Sum_probs=52.9
Q ss_pred eEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecC-CHHHHHHHHHHhcCCCeEE
Q 024092 83 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTM-DVKELVPYLKEKLKRNVEV 147 (272)
Q Consensus 83 ~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~v-d~~~L~~~l~kk~G~~ael 147 (272)
.++.|.+ +|+|.+|+.+|+++|.+++||.++.+++.+.++.|.... ....+...++ .+||.+..
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~ 118 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRD 118 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hccccccc
Confidence 4667889 999999999999999999999999999999998887321 1256777777 78987653
No 15
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=95.59 E-value=0.024 Score=41.93 Aligned_cols=42 Identities=33% Similarity=0.306 Sum_probs=36.0
Q ss_pred CCCCCCceEEEeeccCcEEEEEe---ecCHHHHHHHHHHhhccccc
Q 024092 2 LLICLGVVDVKTDCGANKVTVTG---KVEPAKLKERLEAKTKKKVD 44 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g---~vd~~~li~~I~~k~Gy~ve 44 (272)
|..++||.++.|||..++++|+. .++.+.|+++|+ .+||.+.
T Consensus 24 l~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~ 68 (71)
T COG2608 24 LEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVE 68 (71)
T ss_pred HhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCee
Confidence 67899999999999997777665 468899999999 8999864
No 16
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=93.95 E-value=0.82 Score=32.95 Aligned_cols=63 Identities=21% Similarity=0.305 Sum_probs=48.5
Q ss_pred EEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe---cCCHHHHHHHHHHhcCCCeEE
Q 024092 84 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEV 147 (272)
Q Consensus 84 ~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g---~vd~~~L~~~l~kk~G~~ael 147 (272)
++.+.+ +++|..|..+++..+....++..+.+++....+.+.. ..+...+...+. ..|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 455667 9999999999999999999999999999888766652 245566656665 67777654
No 17
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=90.91 E-value=2.1 Score=25.05 Aligned_cols=49 Identities=33% Similarity=0.556 Sum_probs=36.7
Q ss_pred eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec--CCHHHHHHHHH
Q 024092 90 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 138 (272)
Q Consensus 90 gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~--vd~~~L~~~l~ 138 (272)
++.|..|...++..+....++....+++....+.+... .+...+...+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH
Confidence 78899999999999999999888888887777666532 24444444444
No 18
>PRK13748 putative mercuric reductase; Provisional
Probab=87.90 E-value=2.5 Score=42.26 Aligned_cols=64 Identities=20% Similarity=0.321 Sum_probs=50.9
Q ss_pred EEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe--cCCHHHHHHHHHHhcCCCeEEccC
Q 024092 86 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVVPA 150 (272)
Q Consensus 86 ~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g--~vd~~~L~~~l~kk~G~~aelv~~ 150 (272)
.+.+ +|+|.+|..+++..+..++++..+.+++....+.+.. ..+...+...+. ..|+.+++...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 3556 9999999999999999999999999999998877763 245566666676 78887666544
No 19
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=87.67 E-value=0.74 Score=41.43 Aligned_cols=44 Identities=27% Similarity=0.348 Sum_probs=39.9
Q ss_pred CCCCCCceEEEeeccCcEEEEEeecCHHHHHHHHHHhhccccccC
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLV 46 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~vd~~~li~~I~~k~Gy~velv 46 (272)
|..++||.+|.||+..+.|.|.+.+-+.+|...|+ .+|+++-|.
T Consensus 28 L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~ 71 (247)
T KOG4656|consen 28 LKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLR 71 (247)
T ss_pred hccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEe
Confidence 67789999999999999999999999999999999 899987653
No 20
>PLN02957 copper, zinc superoxide dismutase
Probab=80.52 E-value=3.3 Score=37.51 Aligned_cols=45 Identities=29% Similarity=0.336 Sum_probs=38.9
Q ss_pred CCCCCCceEEEeeccCcEEEEEeecCHHHHHHHHHHhhccccccCC
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLVS 47 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~vd~~~li~~I~~k~Gy~velvs 47 (272)
|..++||..+.+|+..++++|.+..+...++..|+ .+||.++++.
T Consensus 27 L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~ 71 (238)
T PLN02957 27 LETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIG 71 (238)
T ss_pred HhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEec
Confidence 56789999999999999999988777888999999 8999876553
No 21
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=80.14 E-value=2.9 Score=30.32 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=22.7
Q ss_pred eEEEEEeeccchhhH------HHHHHHHhcCCCceEEEE
Q 024092 83 STVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTI 115 (272)
Q Consensus 83 ~~v~l~VgM~C~~Ca------~kIekaL~~i~GV~~v~V 115 (272)
.++.|.+.+.+.+|. ..|+.+|..++||.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 356666666655554 788999999999999886
No 22
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=78.74 E-value=15 Score=28.93 Aligned_cols=66 Identities=21% Similarity=0.343 Sum_probs=43.5
Q ss_pred ceEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeC-----C--CCEEEEEe-cCCHHHHHHHHHHhcCCCeEEc
Q 024092 82 ESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDG-----G--KDLVTVKG-TMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 82 ~~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl-----~--~~kVtV~g-~vd~~~L~~~l~kk~G~~aelv 148 (272)
.+.++|.+ --|-.--.--+-+.|++++||+.|++.+ . +=++||.| .+|-++|.+.|+ .+|--+.-+
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSi 79 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSI 79 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeeh
Confidence 35667766 2232223334557888999988776533 3 33566777 589999999999 888665443
No 23
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=70.08 E-value=11 Score=27.03 Aligned_cols=53 Identities=19% Similarity=0.202 Sum_probs=38.0
Q ss_pred EEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec--CCHHHHHHHHHHhcCCCeEEc
Q 024092 86 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 86 ~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~--vd~~~L~~~l~kk~G~~aelv 148 (272)
+|.+ |+.|+...-++.++|.+++.= +.+.|..+ .....|...++ ..|+.+..+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~-~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCE-ENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHH-HCCCEEEEE
Confidence 5777 999999999999999997532 34445432 34577888888 899875444
No 24
>PF05663 DUF809: Protein of unknown function (DUF809); InterPro: IPR008527 This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape).
Probab=67.78 E-value=13 Score=29.84 Aligned_cols=44 Identities=14% Similarity=0.124 Sum_probs=25.3
Q ss_pred hhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHH
Q 024092 94 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 138 (272)
Q Consensus 94 ~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~ 138 (272)
.+|.+.+ +.|.+++=--..+.---.-++||.+.+..+++...+.
T Consensus 47 qhclrtm-rhleklkipyefqygwlgvkitiksnvpndevtkkvs 90 (138)
T PF05663_consen 47 QHCLRTM-RHLEKLKIPYEFQYGWLGVKITIKSNVPNDEVTKKVS 90 (138)
T ss_pred HHHHHHH-HHHHhcCCCeeeeecceeEEEEEecCCCchHhhhccC
Confidence 5666555 4555554333333333445678888887777766554
No 25
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=65.09 E-value=16 Score=28.90 Aligned_cols=64 Identities=23% Similarity=0.404 Sum_probs=42.3
Q ss_pred ceEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeC-----CCC--EEEEEec-CCHHHHHHHHHHhcCCCeEE
Q 024092 82 ESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDG-----GKD--LVTVKGT-MDVKELVPYLKEKLKRNVEV 147 (272)
Q Consensus 82 ~~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl-----~~~--kVtV~g~-vd~~~L~~~l~kk~G~~ael 147 (272)
.++++|.| --|-.+ .-.+-++|.+++||..|++.+ .+. ++||+|. +|.+.|.++|+ ++|--+.-
T Consensus 4 irRlVLDVlKP~~p~-i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHS 76 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPS-IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHS 76 (95)
T ss_dssp EEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEE
T ss_pred eeEEEEEeecCCCCC-HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEe
Confidence 35677777 224443 345668899999998887644 333 4556674 89999999999 88865533
No 26
>PF02162 XYPPX: XYPPX repeat (two copies); InterPro: IPR006031 This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII ANX7_DICDI, the carboxy tail of certain rhodopsins OPSD_LOLSU. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in FP1_MYTED. The molecular function of this repeat is unknown. It is also not clear is all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition.
Probab=56.66 E-value=9.5 Score=20.15 Aligned_cols=7 Identities=86% Similarity=1.621 Sum_probs=3.4
Q ss_pred CCCCCCC
Q 024092 241 NQGYPPQ 247 (272)
Q Consensus 241 ~~~~~~~ 247 (272)
.+||||+
T Consensus 4 pqG~pPQ 10 (15)
T PF02162_consen 4 PQGYPPQ 10 (15)
T ss_pred CcCCCCC
Confidence 3455544
No 27
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=54.05 E-value=21 Score=28.16 Aligned_cols=41 Identities=22% Similarity=0.303 Sum_probs=28.2
Q ss_pred CCCCCCceEEEeec-------cCcEEEEEe-ecCHHHHHHHHHHhhcccc
Q 024092 2 LLICLGVVDVKTDC-------GANKVTVTG-KVEPAKLKERLEAKTKKKV 43 (272)
Q Consensus 2 L~kl~GV~~v~Vd~-------~~~kvtV~g-~vd~~~li~~I~~k~Gy~v 43 (272)
|++++||+.|++.+ ..-++||.| .+|..+|.+.|+ .+|-.+
T Consensus 28 lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~I 76 (97)
T COG1888 28 LSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAI 76 (97)
T ss_pred HhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCee
Confidence 46677777665433 234566667 579999999999 777643
No 28
>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=53.49 E-value=38 Score=26.00 Aligned_cols=40 Identities=13% Similarity=0.150 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcC
Q 024092 98 SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 142 (272)
Q Consensus 98 ~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G 142 (272)
..|+.+|..++|++++.|++. ..-...++.|-+.-++++|
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~-----~~~~~~~~~~~~~~~~~~~ 97 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV-----WDPPWTPERMSEEARLELG 97 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE-----eeCCCChHHCCHHHHHHcC
Confidence 458889999999999999874 2222445555555555554
No 29
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=52.83 E-value=19 Score=37.99 Aligned_cols=42 Identities=24% Similarity=0.316 Sum_probs=36.3
Q ss_pred CCCCCCceEEEeeccCcEEEEEee---cC-HHHHHHHHHHhhccccc
Q 024092 2 LLICLGVVDVKTDCGANKVTVTGK---VE-PAKLKERLEAKTKKKVD 44 (272)
Q Consensus 2 L~kl~GV~~v~Vd~~~~kvtV~g~---vd-~~~li~~I~~k~Gy~ve 44 (272)
|++++||..+.|||.+++++|... .+ .+.+...++ .+||.+.
T Consensus 23 l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~ 68 (713)
T COG2217 23 LNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSAR 68 (713)
T ss_pred HhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCcccc
Confidence 678999999999999999999874 34 678899999 8999764
No 30
>PRK11023 outer membrane lipoprotein; Provisional
Probab=50.38 E-value=1.7e+02 Score=25.45 Aligned_cols=43 Identities=12% Similarity=0.151 Sum_probs=30.8
Q ss_pred hhhHHHHHHHHhcCCCceEE--EEeCCCCEEEEEecCCHHHHHHH
Q 024092 94 EGCISKIKKIIYKTKGVDNV--TIDGGKDLVTVKGTMDVKELVPY 136 (272)
Q Consensus 94 ~~Ca~kIekaL~~i~GV~~v--~Vdl~~~kVtV~g~vd~~~L~~~ 136 (272)
..=..+|+.+|..-+.|... .|....+.|++.|.++..+...+
T Consensus 126 ~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~~a 170 (191)
T PRK11023 126 TWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAKAA 170 (191)
T ss_pred HHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHHHH
Confidence 44677899999877776654 44556899999999887554333
No 31
>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=49.78 E-value=21 Score=31.08 Aligned_cols=54 Identities=17% Similarity=0.218 Sum_probs=34.7
Q ss_pred EEEEEeeccchhhH------HHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcC
Q 024092 84 TVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 142 (272)
Q Consensus 84 ~v~l~VgM~C~~Ca------~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G 142 (272)
++.|.+-++..+|. ..|+.+|..++||.+|.|++.. .-..+++.+-+..+.++|
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~~-----dp~W~~~~~s~~ar~~lg 173 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELVF-----DPPWSREMMSEAAKLELG 173 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEEe-----cCCCChHHCCHHHHHHcC
Confidence 45566666655554 4589999999999999887532 222455666655554444
No 32
>PRK11018 hypothetical protein; Provisional
Probab=47.42 E-value=75 Score=23.61 Aligned_cols=55 Identities=9% Similarity=0.021 Sum_probs=40.5
Q ss_pred EEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEE--ecCCHHHHHHHHHHhcCCCeEEc
Q 024092 84 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--GTMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 84 ~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~--g~vd~~~L~~~l~kk~G~~aelv 148 (272)
..+|.+ |+.|+--.-+.+++|.+++.-+ .+.|. .......|...++ +.|+.+...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G~---------~L~V~~d~~~a~~di~~~~~-~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKGE---------ILEVVSDCPQSINNIPLDAR-NHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCCC---------EEEEEeCCccHHHHHHHHHH-HcCCEEEEE
Confidence 467888 9999999999999999886322 23333 2345577888887 899987543
No 33
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=46.08 E-value=57 Score=23.09 Aligned_cols=51 Identities=16% Similarity=0.186 Sum_probs=36.0
Q ss_pred EEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe--cCCHHHHHHHHHHhcCCCeEEc
Q 024092 87 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 87 l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g--~vd~~~L~~~l~kk~G~~aelv 148 (272)
|.+ |+.|+.-.-+++++| ++..- +.+.|.. ......|...++ +.|+.+.+.
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~ 55 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAE-SRGYEVSVE 55 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence 456 899999999999999 65422 2334433 234478888888 999998554
No 34
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=44.31 E-value=28 Score=27.54 Aligned_cols=40 Identities=25% Similarity=0.299 Sum_probs=26.2
Q ss_pred CCCCCCceEEEeec-----cC--cEEEEEe-ecCHHHHHHHHHHhhccc
Q 024092 2 LLICLGVVDVKTDC-----GA--NKVTVTG-KVEPAKLKERLEAKTKKK 42 (272)
Q Consensus 2 L~kl~GV~~v~Vd~-----~~--~kvtV~g-~vd~~~li~~I~~k~Gy~ 42 (272)
|.+++||..|++.+ .+ =++||.| .+|.+.|.++|+ ..|=.
T Consensus 26 l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~ 73 (95)
T PF02680_consen 26 LSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGV 73 (95)
T ss_dssp HHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-E
T ss_pred HHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCe
Confidence 45678888776544 22 3455667 479999999999 67653
No 35
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=43.42 E-value=75 Score=27.58 Aligned_cols=68 Identities=29% Similarity=0.422 Sum_probs=43.4
Q ss_pred EEEeeccchhhHHHHH------------HHHhcC------CCceEEEEeCCCCEEEEE---ec---C-CHHHHHHHHHHh
Q 024092 86 VLKIRLHCEGCISKIK------------KIIYKT------KGVDNVTIDGGKDLVTVK---GT---M-DVKELVPYLKEK 140 (272)
Q Consensus 86 ~l~VgM~C~~Ca~kIe------------kaL~~i------~GV~~v~Vdl~~~kVtV~---g~---v-d~~~L~~~l~kk 140 (272)
=++-++-|+.|.++|+ ++|.++ .+++-...=...+++.+. |. + -.-.++++|+++
T Consensus 9 c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~~ 88 (166)
T PRK06418 9 CVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSRK 88 (166)
T ss_pred EeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHHH
Confidence 3444999999999864 577766 344333333334666544 32 0 113588889889
Q ss_pred cCCCeEEccCCCC
Q 024092 141 LKRNVEVVPAKKD 153 (272)
Q Consensus 141 ~G~~aelv~~~~~ 153 (272)
+|++++++....+
T Consensus 89 lgk~VevVE~s~d 101 (166)
T PRK06418 89 LGKKVRVVEKTND 101 (166)
T ss_pred hCCcEEEEEcCCC
Confidence 9999999965443
No 36
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=43.08 E-value=56 Score=27.82 Aligned_cols=41 Identities=22% Similarity=0.312 Sum_probs=32.2
Q ss_pred eEEEEEe-eccchhhHHHHHHHHhcCCCceEEEEeCC-CCEEEE
Q 024092 83 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGG-KDLVTV 124 (272)
Q Consensus 83 ~~v~l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~-~~kVtV 124 (272)
..++|.| .-.|..|..-|.....+ -|+.+++|... ++++.+
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~-lGl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEK-LGLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHH-cCCCeEEEEecCCCcEEE
Confidence 4678888 78899999988777666 48999999886 665543
No 37
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=39.48 E-value=22 Score=24.72 Aligned_cols=34 Identities=18% Similarity=0.364 Sum_probs=16.0
Q ss_pred HHHHHHHhc---CCCceEEEEeCCCCEEEEEecCCHHH
Q 024092 98 SKIKKIIYK---TKGVDNVTIDGGKDLVTVKGTMDVKE 132 (272)
Q Consensus 98 ~kIekaL~~---i~GV~~v~Vdl~~~kVtV~g~vd~~~ 132 (272)
.+|+.+|.. +++- .+.|....+.|+++|.++...
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s~~ 38 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVPSQE 38 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEESSCH
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCcHHH
Confidence 356666665 4444 567777788888888764433
No 38
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=39.23 E-value=2.5e+02 Score=24.18 Aligned_cols=54 Identities=9% Similarity=0.031 Sum_probs=34.7
Q ss_pred EEEEeeccchhhHHHHHHHHh--------cCCCce------EEE-EeCCCCEEEEEecCCHHHHHHHHH
Q 024092 85 VVLKIRLHCEGCISKIKKIIY--------KTKGVD------NVT-IDGGKDLVTVKGTMDVKELVPYLK 138 (272)
Q Consensus 85 v~l~VgM~C~~Ca~kIekaL~--------~i~GV~------~v~-Vdl~~~kVtV~g~vd~~~L~~~l~ 138 (272)
++-...|.|.=.-..|-..+. ..+|+. .++ .=|.+++|+|+|.-+.+++..+++
T Consensus 98 Ivas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~ 166 (174)
T cd00652 98 IVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVE 166 (174)
T ss_pred EEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHH
Confidence 344446666666666655554 445642 222 235899999999888888888776
No 39
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=38.75 E-value=1.2e+02 Score=23.43 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=30.9
Q ss_pred hHHHHHHHHhcCCCceEEEEeCCCCEEEEEe-cCCHHHHHHHHH
Q 024092 96 CISKIKKIIYKTKGVDNVTIDGGKDLVTVKG-TMDVKELVPYLK 138 (272)
Q Consensus 96 Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g-~vd~~~L~~~l~ 138 (272)
=...|.++|..++|++=...|...+++.|+- .-+...+++.|.
T Consensus 18 ~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 18 RISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 3678999999999998777777788887772 224455555554
No 40
>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=37.79 E-value=82 Score=22.12 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=25.5
Q ss_pred eEEEEEeeccchh-hHHHHHHHHhcCCCceEEEE
Q 024092 83 STVVLKIRLHCEG-CISKIKKIIYKTKGVDNVTI 115 (272)
Q Consensus 83 ~~v~l~VgM~C~~-Ca~kIekaL~~i~GV~~v~V 115 (272)
..+.|.+..+-.. -..+|.+.|.+++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 3455666555555 88999999999999999875
No 41
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=36.64 E-value=87 Score=22.78 Aligned_cols=43 Identities=19% Similarity=0.236 Sum_probs=30.8
Q ss_pred HhcCCCceEEEEeCCC-CEEEEEecCCHHHHHHHHHHhcCCCeEEc
Q 024092 104 IYKTKGVDNVTIDGGK-DLVTVKGTMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 104 L~~i~GV~~v~Vdl~~-~kVtV~g~vd~~~L~~~l~kk~G~~aelv 148 (272)
|..++||.++..+-.. -++.|....+...|++.|. ..|. +.-.
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~-~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELI-EKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHH-hCCC-eeEE
Confidence 8888999999875433 3455555667899999998 7777 5433
No 42
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=36.22 E-value=93 Score=26.27 Aligned_cols=35 Identities=20% Similarity=0.177 Sum_probs=29.7
Q ss_pred chhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec
Q 024092 93 CEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT 127 (272)
Q Consensus 93 C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~ 127 (272)
=..=+.+|.+.|.+++||.++.|=...+.|.|--.
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~ 107 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVAVD 107 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEE
Confidence 35567899999999999999999998888887643
No 43
>PRK11670 antiporter inner membrane protein; Provisional
Probab=34.55 E-value=1.1e+02 Score=29.56 Aligned_cols=68 Identities=12% Similarity=0.147 Sum_probs=43.4
Q ss_pred EEEEEeeccchhh------HHHHHHHHhcCCCceEEEEeCCC------------------CEEEEE------ec-CCHHH
Q 024092 84 TVVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDGGK------------------DLVTVK------GT-MDVKE 132 (272)
Q Consensus 84 ~v~l~VgM~C~~C------a~kIekaL~~i~GV~~v~Vdl~~------------------~kVtV~------g~-vd~~~ 132 (272)
.+.|.+.++-..| .+.++.+|..++||.++.|++.. ..+.|. |. .-...
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 3455554443333 35689999999999988876543 233344 11 23455
Q ss_pred HHHHHHHhcCCCeEEccCCC
Q 024092 133 LVPYLKEKLKRNVEVVPAKK 152 (272)
Q Consensus 133 L~~~l~kk~G~~aelv~~~~ 152 (272)
|...|. +.|+++-+++-..
T Consensus 128 LA~aLA-~~G~rVlLID~D~ 146 (369)
T PRK11670 128 LALALA-AEGAKVGILDADI 146 (369)
T ss_pred HHHHHH-HCCCcEEEEeCCC
Confidence 777787 8899998886543
No 44
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=34.12 E-value=1.1e+02 Score=22.43 Aligned_cols=54 Identities=19% Similarity=0.215 Sum_probs=37.7
Q ss_pred hhhHHHHHHHHhcC---CCceEEEEeCCCCEEEEEe--cCCHHHHHHHHHHhcCCCeEE
Q 024092 94 EGCISKIKKIIYKT---KGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEV 147 (272)
Q Consensus 94 ~~Ca~kIekaL~~i---~GV~~v~Vdl~~~kVtV~g--~vd~~~L~~~l~kk~G~~ael 147 (272)
.+=..++..+|.++ +---.+..|-.++.+.|.| .+-.+.++++|+++.|..+++
T Consensus 15 ~~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 15 KEDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp HHHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred HhHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 33445555565544 3344799999999999985 566788999999777766654
No 45
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=32.00 E-value=70 Score=25.91 Aligned_cols=54 Identities=19% Similarity=0.347 Sum_probs=34.2
Q ss_pred EEEEeeccchhh------HHHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHHHHHHHhcCC
Q 024092 85 VVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKR 143 (272)
Q Consensus 85 v~l~VgM~C~~C------a~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~~~l~kk~G~ 143 (272)
+.+.+.++-.+| ...|+.+|..++||.++.|++ +..-...+..+.+..+..+|+
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l-----~~~p~Wt~~~ms~ear~~~g~ 110 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL-----TLSPPWTPDRMSEEARRALGI 110 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE-----EEcCCCchhhcCHHHHHhhCC
Confidence 444445555555 678999999999999998875 222224455555555434443
No 46
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=32.00 E-value=2.1e+02 Score=23.58 Aligned_cols=50 Identities=22% Similarity=0.276 Sum_probs=33.3
Q ss_pred HHHHHHHhcCCCceEEEEeCCCCEEEEEecCCHHHHH----HHHHHhcCCCeEEc
Q 024092 98 SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELV----PYLKEKLKRNVEVV 148 (272)
Q Consensus 98 ~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~vd~~~L~----~~l~kk~G~~aelv 148 (272)
..++.+|..+ |...|..=++++-|.++...++..|. +.|.+..|+.+.++
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 4566777776 89999999999999999777776655 44555678887665
No 47
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=28.35 E-value=2.3e+02 Score=21.13 Aligned_cols=42 Identities=14% Similarity=0.212 Sum_probs=29.8
Q ss_pred hHHHHHHHHhcCCCceEEEEeCCCCEEEEEe-cCCHHHHHHHHH
Q 024092 96 CISKIKKIIYKTKGVDNVTIDGGKDLVTVKG-TMDVKELVPYLK 138 (272)
Q Consensus 96 Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g-~vd~~~L~~~l~ 138 (272)
=...|.++|..++||+=...+-. +++.|+- .-+...+.+.|.
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 35678899999999966666666 7776662 345666666665
No 48
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=27.99 E-value=2.3e+02 Score=20.43 Aligned_cols=55 Identities=9% Similarity=0.102 Sum_probs=37.5
Q ss_pred EEEEEe-eccchhhHHHHHHHHhcCCC-ceEEEEeCCCCEEEEE----ec-CCHHHHHHHHH
Q 024092 84 TVVLKI-RLHCEGCISKIKKIIYKTKG-VDNVTIDGGKDLVTVK----GT-MDVKELVPYLK 138 (272)
Q Consensus 84 ~v~l~V-gM~C~~Ca~kIekaL~~i~G-V~~v~Vdl~~~kVtV~----g~-vd~~~L~~~l~ 138 (272)
.+++.| |.+..+....|-++|.+..+ |.++....-.+..+.. +. -+.++|...|.
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~ 63 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALE 63 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHH
Confidence 467777 99999999999999999876 7777777766765544 22 13455666665
No 49
>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=27.66 E-value=80 Score=22.86 Aligned_cols=13 Identities=15% Similarity=0.421 Sum_probs=9.4
Q ss_pred EEEEeeccchhhHH
Q 024092 85 VVLKIRLHCEGCIS 98 (272)
Q Consensus 85 v~l~VgM~C~~Ca~ 98 (272)
+.+ ++..|..|..
T Consensus 3 I~v-~~~~C~~C~~ 15 (76)
T PF13192_consen 3 IKV-FSPGCPYCPE 15 (76)
T ss_dssp EEE-ECSSCTTHHH
T ss_pred EEE-eCCCCCCcHH
Confidence 344 5778999984
No 50
>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus
Probab=27.30 E-value=97 Score=27.25 Aligned_cols=12 Identities=17% Similarity=0.224 Sum_probs=7.4
Q ss_pred CCCCccccccCC
Q 024092 230 PMENQHQVVYAN 241 (272)
Q Consensus 230 ~~~~~~g~~~~~ 241 (272)
+||+..+|+-..
T Consensus 141 ~m~~~~~y~~~~ 152 (182)
T PF06495_consen 141 PMQGAYPYQMPP 152 (182)
T ss_pred ccccccccccCC
Confidence 467777776443
No 51
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=25.09 E-value=2.2e+02 Score=24.05 Aligned_cols=42 Identities=17% Similarity=0.272 Sum_probs=34.3
Q ss_pred EEEEeCCCCEEEEEe--cCCHHHHHHHHHHhcCCCeEEccCCCCc
Q 024092 112 NVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVVPAKKDD 154 (272)
Q Consensus 112 ~v~Vdl~~~kVtV~g--~vd~~~L~~~l~kk~G~~aelv~~~~~~ 154 (272)
=+.+||..+-+.+.+ .++..+|++.|. +.|+.+-+.++....
T Consensus 45 iAildL~G~~l~l~S~R~~~~~evi~~I~-~~G~PviVAtDV~p~ 88 (138)
T PF04312_consen 45 IAILDLDGELLDLKSSRNMSRSEVIEWIS-EYGKPVIVATDVSPP 88 (138)
T ss_pred EEEEecCCcEEEEEeecCCCHHHHHHHHH-HcCCEEEEEecCCCC
Confidence 367899999999886 589999999999 999998887654443
No 52
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=24.42 E-value=4.7e+02 Score=22.63 Aligned_cols=24 Identities=4% Similarity=0.033 Sum_probs=19.2
Q ss_pred EeCCCCEEEEEecCCHHHHHHHHH
Q 024092 115 IDGGKDLVTVKGTMDVKELVPYLK 138 (272)
Q Consensus 115 Vdl~~~kVtV~g~vd~~~L~~~l~ 138 (272)
.=|.+++|+|+|.-+.+++..+++
T Consensus 142 lIF~SGKvvitGaks~~~~~~a~~ 165 (174)
T cd04518 142 LLFSSGKMVITGAKSEEDAKRAVE 165 (174)
T ss_pred EEeCCCEEEEEecCCHHHHHHHHH
Confidence 346899999999878888777776
No 53
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=23.86 E-value=4.8e+02 Score=22.60 Aligned_cols=51 Identities=29% Similarity=0.363 Sum_probs=34.2
Q ss_pred EEEEeeccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec--CCHHHHHHHHH
Q 024092 85 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 138 (272)
Q Consensus 85 v~l~VgM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~--vd~~~L~~~l~ 138 (272)
+.|+-|+.-. .+.+|-+.|... .. .|.+....++|+|+|. =|...+++.|+
T Consensus 94 i~lk~GI~~e-~AKkIvK~IKd~-kl-KVqa~IQGd~vRVtgKkrDDLQ~viallk 146 (161)
T PRK05412 94 VKLKQGIDQE-LAKKIVKLIKDS-KL-KVQAQIQGDQVRVTGKKRDDLQAVIALLR 146 (161)
T ss_pred EehhhccCHH-HHHHHHHHHHhc-CC-ceeEEecCcEEEEecCCHhHHHHHHHHHH
Confidence 3333377654 567888888653 23 3778888999999994 24566667776
No 54
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.84 E-value=98 Score=24.45 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=21.5
Q ss_pred CCCCCCCceEEEeeccCcEEEEEe
Q 024092 1 MLLICLGVVDVKTDCGANKVTVTG 24 (272)
Q Consensus 1 iL~kl~GV~~v~Vd~~~~kvtV~g 24 (272)
|+..++|++.+.++..+.+|.|++
T Consensus 35 ivas~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 35 IVASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EEEecCCceEEEEecccceEEEec
Confidence 456789999999999999999987
No 55
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=22.52 E-value=2.1e+02 Score=20.53 Aligned_cols=33 Identities=15% Similarity=0.256 Sum_probs=25.9
Q ss_pred ceEEEEEeeccchhhHHHHHHHHhcCCCceEEE
Q 024092 82 ESTVVLKIRLHCEGCISKIKKIIYKTKGVDNVT 114 (272)
Q Consensus 82 ~~~v~l~VgM~C~~Ca~kIekaL~~i~GV~~v~ 114 (272)
...+.|.|...-..=...|.+.|.+++||.+|.
T Consensus 47 ~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 47 TARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 345666666677777789999999999998874
No 56
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=22.40 E-value=5.1e+02 Score=22.40 Aligned_cols=52 Identities=29% Similarity=0.379 Sum_probs=30.7
Q ss_pred EEEEEeeccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec--CCHHHHHHHHH
Q 024092 84 TVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 138 (272)
Q Consensus 84 ~v~l~VgM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~--vd~~~L~~~l~ 138 (272)
.+.|+-|+.-+ .+.+|-+.|... ++. |++....++|+|+|. =|...+++.|+
T Consensus 93 ~i~lk~GI~~d-~AKkIvK~IKd~-klK-Vqa~IQgd~vRVtgKkrDDLQ~viallk 146 (160)
T PF04461_consen 93 VIKLKQGIDQD-TAKKIVKLIKDS-KLK-VQAQIQGDQVRVTGKKRDDLQEVIALLK 146 (160)
T ss_dssp EEEE--S--HH-HHHHHHHHHHHH---S-EEEEEETTEEEEEES-HHHHHHHHHHHH
T ss_pred EEEeecccCHH-HHHHHHHHHHhc-CCc-eeEEecCcEEEEecCCHHHHHHHHHHHH
Confidence 34444477654 556777777643 232 777778999999995 24556666666
No 57
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.39 E-value=86 Score=24.75 Aligned_cols=22 Identities=14% Similarity=0.262 Sum_probs=19.7
Q ss_pred hcCCCceEEEEeCCCCEEEEEe
Q 024092 105 YKTKGVDNVTIDGGKDLVTVKG 126 (272)
Q Consensus 105 ~~i~GV~~v~Vdl~~~kVtV~g 126 (272)
..++|++.+.+++.+.++.|++
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 3468999999999999999996
No 58
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.38 E-value=1.6e+02 Score=29.75 Aligned_cols=7 Identities=29% Similarity=0.178 Sum_probs=3.1
Q ss_pred CCCCCCC
Q 024092 259 QMFSDEN 265 (272)
Q Consensus 259 qmfsden 265 (272)
+||--.|
T Consensus 473 ~~~q~q~ 479 (483)
T KOG2236|consen 473 PMNQMQN 479 (483)
T ss_pred hhhcccC
Confidence 4444433
No 59
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=21.76 E-value=2.6e+02 Score=19.95 Aligned_cols=52 Identities=23% Similarity=0.288 Sum_probs=37.7
Q ss_pred EEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEe--cCCHHHHHHHHHHhcCCCeEEc
Q 024092 87 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 87 l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g--~vd~~~L~~~l~kk~G~~aelv 148 (272)
|.+ |+.|+.=.-+.+++|.+++. .+.+.|.. ......|....+ ..|+.+..+
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~-~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCK-STGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 456 89999999999999998862 23344443 234577888887 999987654
No 60
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=21.41 E-value=1.7e+02 Score=25.48 Aligned_cols=45 Identities=18% Similarity=0.265 Sum_probs=33.0
Q ss_pred hhhHHHHHHHHhcCCCceEEEEeCCCCE-------------------EEEEe---cCCHHHHHHHHH
Q 024092 94 EGCISKIKKIIYKTKGVDNVTIDGGKDL-------------------VTVKG---TMDVKELVPYLK 138 (272)
Q Consensus 94 ~~Ca~kIekaL~~i~GV~~v~Vdl~~~k-------------------VtV~g---~vd~~~L~~~l~ 138 (272)
++|--.++..+.+++||.++.+=.+.+. |.|+- .++.++|+...-
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 4566777788889999999999776554 55553 366777877665
No 61
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.41 E-value=2.9e+02 Score=19.13 Aligned_cols=52 Identities=25% Similarity=0.276 Sum_probs=36.8
Q ss_pred EEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEEec--CCHHHHHHHHHHhcCCCeEEc
Q 024092 87 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 87 l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~g~--vd~~~L~~~l~kk~G~~aelv 148 (272)
|.+ |+.|+.=.-++.++|.+++. .+.+.|..+ .....|...++ ..|+.+..+
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~-~~g~~~~~~ 56 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAK-ETGHEVLEV 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHH-HcCCEEEEE
Confidence 445 88999988889999988653 334444432 34678888888 899986554
No 62
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=20.38 E-value=5e+02 Score=23.08 Aligned_cols=56 Identities=14% Similarity=0.175 Sum_probs=36.0
Q ss_pred EEEEEeeccchhhHHHHHHHHhcCCCce----EEEEeCCCCEEEEEecCCHHHHHHHHHH
Q 024092 84 TVVLKIRLHCEGCISKIKKIIYKTKGVD----NVTIDGGKDLVTVKGTMDVKELVPYLKE 139 (272)
Q Consensus 84 ~v~l~VgM~C~~Ca~kIekaL~~i~GV~----~v~Vdl~~~kVtV~g~vd~~~L~~~l~k 139 (272)
.+.+-.|..-......+-+.|++++|.. .|.=++=.++|||.|-+...+|+++|+.
T Consensus 99 ~v~ivTG~la~~~l~~~~~~l~~~~~~~v~V~~V~N~fFG~~ItVaGLLTg~Dii~~L~~ 158 (204)
T PF04459_consen 99 RVTIVTGVLAYPFLKPLVEKLNRIPGLEVEVVPVKNRFFGGTITVAGLLTGQDIIEQLKG 158 (204)
T ss_pred eEEEEeeHHHHHHHHHHHHHHhccCCCeEEEEEeecCCCCCCeEEeeCccHHHHHHHhCc
Confidence 3333335555555555555666667742 2222444678999999999999999983
No 63
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=20.21 E-value=2.6e+02 Score=24.98 Aligned_cols=55 Identities=22% Similarity=0.160 Sum_probs=39.5
Q ss_pred EEEe-eccchhhHHHHHHHHhc---CCCceEEEEe---CCCCEEEEEecCC---------HHHHHHHHHHhcC
Q 024092 86 VLKI-RLHCEGCISKIKKIIYK---TKGVDNVTID---GGKDLVTVKGTMD---------VKELVPYLKEKLK 142 (272)
Q Consensus 86 ~l~V-gM~C~~Ca~kIekaL~~---i~GV~~v~Vd---l~~~kVtV~g~vd---------~~~L~~~l~kk~G 142 (272)
.+++ ||+...=...|++.|.+ +... .|+|+ +...+|+|.|.+. ...|+++|. .+|
T Consensus 39 ~v~v~G~T~~e~~~~I~~~l~~~~~~~~p-~V~V~v~~~~~~~V~V~GeV~~PG~~~l~~~~tl~~ai~-~AG 109 (239)
T TIGR03028 39 EVKLGGETPAAAERKIASRLSKGGFVKQP-QVTINVLQYRGQQVSVLGQVNRPGRYPLETAGRVSDVLA-LAG 109 (239)
T ss_pred eEEECCCCHHHHHHHHHHHHhhcCcccCC-EEEEEEEeccceEEEEEEEecCCceEEcCCCCcHHHHHH-HcC
Confidence 5677 99999999999999985 2221 23443 4577999998532 267999998 555
No 64
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=20.19 E-value=3.1e+02 Score=19.62 Aligned_cols=52 Identities=10% Similarity=0.043 Sum_probs=37.1
Q ss_pred EEe-eccchhhHHHHHHHHhcCCCceEEEEeCCCCEEEEE--ecCCHHHHHHHHHHhcCCCeEEc
Q 024092 87 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--GTMDVKELVPYLKEKLKRNVEVV 148 (272)
Q Consensus 87 l~V-gM~C~~Ca~kIekaL~~i~GV~~v~Vdl~~~kVtV~--g~vd~~~L~~~l~kk~G~~aelv 148 (272)
|.+ |+.|+-=.-+.+++|.+++-- +.+.|. .......|...++ ..|+.+..+
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~-~~g~~v~~~ 56 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDAR-NHGYKVLAI 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHH-HcCCEEEEE
Confidence 345 889999999999999988632 223333 3345677888887 999988654
No 65
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=20.17 E-value=3.8e+02 Score=20.25 Aligned_cols=55 Identities=31% Similarity=0.385 Sum_probs=31.7
Q ss_pred HHHHHHHhcCCCce-EEEEeC----CCCEEEEE--e--cC-C--------HHHHHHHHHHhcCCCeEE--ccCCC
Q 024092 98 SKIKKIIYKTKGVD-NVTIDG----GKDLVTVK--G--TM-D--------VKELVPYLKEKLKRNVEV--VPAKK 152 (272)
Q Consensus 98 ~kIekaL~~i~GV~-~v~Vdl----~~~kVtV~--g--~v-d--------~~~L~~~l~kk~G~~ael--v~~~~ 152 (272)
..|+.+|.+++++. ...+-+ ..+.++|. . .. + ...|.+.|+..+|..+.+ +++..
T Consensus 7 ~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~~~~~~~~~~~~l~~~i~~~lk~~lgv~~~V~lv~~gt 81 (96)
T PF14535_consen 7 SQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRPGFSDDAEDLEALAERIAERLKERLGVRPEVELVPPGT 81 (96)
T ss_dssp HHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEESTTCCTTHHHHHHHHHHHHHHHHHHHSS-EEEEEE-TT-
T ss_pred HHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECCccCcchHHHHHHHHHHHHHHHhhcCceEEEEEECCCC
Confidence 46899999999987 333322 33445544 2 12 1 245777777778877654 55543
Done!