Query 024167
Match_columns 271
No_of_seqs 311 out of 1908
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 02:34:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024167hhsearch_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 5.9E-13 1.3E-17 95.3 7.7 58 85-143 1-62 (62)
2 KOG1603 Copper chaperone [Inor 99.3 6.8E-12 1.5E-16 93.7 8.6 67 81-147 4-70 (73)
3 COG2608 CopZ Copper chaperone 99.3 1.8E-11 3.8E-16 91.1 8.1 65 82-147 2-70 (71)
4 KOG4656 Copper chaperone for s 98.9 5.1E-09 1.1E-13 92.2 8.3 70 82-152 7-76 (247)
5 PRK10671 copA copper exporting 98.6 3.3E-07 7.2E-12 96.1 13.7 139 1-147 25-164 (834)
6 KOG0207 Cation transport ATPas 98.6 2.4E-07 5.2E-12 96.1 11.2 121 1-152 16-142 (951)
7 KOG0207 Cation transport ATPas 98.5 8.2E-07 1.8E-11 92.2 11.0 118 1-148 91-215 (951)
8 PLN02957 copper, zinc superoxi 98.4 1.5E-06 3.2E-11 78.7 10.1 71 81-152 5-75 (238)
9 PRK10671 copA copper exporting 98.3 1.9E-06 4E-11 90.5 8.4 64 82-148 3-67 (834)
10 COG2217 ZntA Cation transport 98.1 8.9E-06 1.9E-10 84.1 7.4 62 83-146 3-69 (713)
11 TIGR00003 copper ion binding p 97.8 0.00025 5.5E-09 46.9 8.2 61 83-144 3-67 (68)
12 PF00403 HMA: Heavy-metal-asso 97.3 0.00035 7.7E-09 49.5 3.9 40 1-41 20-62 (62)
13 KOG1603 Copper chaperone [Inor 96.8 0.0021 4.5E-08 47.7 4.6 45 1-45 26-70 (73)
14 PRK11033 zntA zinc/cadmium/mer 96.6 0.0055 1.2E-07 64.0 7.4 64 82-146 53-118 (741)
15 COG2608 CopZ Copper chaperone 95.6 0.022 4.9E-07 42.0 4.6 42 1-43 24-68 (71)
16 TIGR02052 MerP mercuric transp 93.6 0.97 2.1E-05 32.5 9.1 63 83-146 24-90 (92)
17 cd00371 HMA Heavy-metal-associ 89.6 2.7 5.9E-05 24.5 7.4 49 89-137 6-56 (63)
18 PRK13748 putative mercuric red 86.9 3 6.5E-05 41.7 8.5 64 85-149 3-69 (561)
19 KOG4656 Copper chaperone for s 83.8 1.5 3.3E-05 39.4 4.1 44 1-45 28-71 (247)
20 PLN02957 copper, zinc superoxi 82.4 2.6 5.7E-05 38.1 5.3 45 1-46 27-71 (238)
21 PF01883 DUF59: Domain of unkn 77.9 3.7 8E-05 29.7 3.9 33 82-114 34-72 (72)
22 PF01206 TusA: Sulfurtransfera 75.3 7.2 0.00016 27.9 4.8 53 85-147 2-57 (70)
23 COG1888 Uncharacterized protei 68.8 32 0.00069 27.1 7.2 66 81-147 5-79 (97)
24 PF05663 DUF809: Protein of un 65.7 14 0.00031 29.5 4.8 44 93-137 47-90 (138)
25 PF02680 DUF211: Uncharacteriz 63.6 39 0.00084 26.7 6.8 64 81-146 4-76 (95)
26 cd03421 SirA_like_N SirA_like_ 60.7 24 0.00053 25.0 5.0 51 86-147 2-55 (67)
27 PRK11018 hypothetical protein; 59.0 39 0.00085 25.1 6.0 57 83-147 8-65 (78)
28 COG2217 ZntA Cation transport 57.6 14 0.0003 38.9 4.5 42 1-43 23-68 (713)
29 PF02162 XYPPX: XYPPX repeat ( 54.0 11 0.00024 19.8 1.6 7 240-246 4-10 (15)
30 PRK11023 outer membrane lipopr 47.9 1.9E+02 0.0041 25.2 10.9 42 92-133 125-168 (191)
31 TIGR03406 FeS_long_SufT probab 47.8 23 0.0005 30.8 3.6 54 83-141 114-173 (174)
32 TIGR02945 SUF_assoc FeS assemb 46.3 26 0.00057 26.8 3.4 40 97-141 58-97 (99)
33 PRK10553 assembly protein for 42.6 88 0.0019 24.1 5.7 44 94-137 17-61 (87)
34 PRK06418 transcription elongat 42.6 68 0.0015 27.8 5.7 67 86-152 10-101 (166)
35 PF04972 BON: BON domain; Int 39.9 20 0.00044 24.9 1.7 32 98-130 3-37 (64)
36 COG1888 Uncharacterized protei 39.5 47 0.001 26.2 3.7 40 1-41 28-75 (97)
37 PF14492 EFG_II: Elongation Fa 39.0 1.5E+02 0.0033 21.7 6.4 54 93-146 15-73 (75)
38 cd00652 TBP_TLF TATA box bindi 39.0 2.5E+02 0.0055 24.1 9.7 55 83-137 97-166 (174)
39 PF03927 NapD: NapD protein; 37.8 1.3E+02 0.0028 22.5 5.9 42 95-137 16-58 (79)
40 PF14437 MafB19-deam: MafB19-l 37.8 75 0.0016 27.0 5.0 41 82-123 100-142 (146)
41 PF13732 DUF4162: Domain of un 37.2 87 0.0019 22.8 4.9 43 103-147 26-69 (84)
42 cd04888 ACT_PheB-BS C-terminal 35.4 89 0.0019 21.9 4.6 33 82-114 41-74 (76)
43 cd03420 SirA_RHOD_Pry_redox Si 32.6 1.2E+02 0.0027 21.6 5.0 52 86-147 2-56 (69)
44 PF09580 Spore_YhcN_YlaJ: Spor 32.5 1.1E+02 0.0024 25.8 5.4 33 92-124 73-105 (177)
45 cd00291 SirA_YedF_YeeD SirA, Y 32.5 1.5E+02 0.0032 20.7 5.3 52 86-147 2-56 (69)
46 PF02680 DUF211: Uncharacteriz 31.9 53 0.0012 25.9 3.0 38 2-40 27-72 (95)
47 cd04518 TBP_archaea archaeal T 30.7 3.5E+02 0.0077 23.3 10.2 23 115-137 143-165 (174)
48 cd03423 SirA SirA (also known 30.6 1.7E+02 0.0037 20.9 5.4 54 86-147 2-56 (69)
49 COG2151 PaaD Predicted metal-s 30.2 78 0.0017 25.6 3.8 53 84-141 51-109 (111)
50 COG0841 AcrB Cation/multidrug 29.2 4.1E+02 0.0089 29.4 10.2 44 94-137 155-207 (1009)
51 cd03422 YedF YedF is a bacteri 29.1 1.7E+02 0.0036 21.0 5.1 53 87-147 3-56 (69)
52 PF13192 Thioredoxin_3: Thiore 28.1 67 0.0014 23.3 2.9 13 84-97 3-15 (76)
53 PRK11670 antiporter inner memb 27.6 1.6E+02 0.0035 28.4 6.2 68 83-151 48-146 (369)
54 PF06495 Transformer: Fruit fl 26.5 1E+02 0.0022 27.0 4.1 11 229-239 141-151 (182)
55 COG2177 FtsX Cell division pro 26.2 1.8E+02 0.0038 27.5 6.0 48 82-142 61-108 (297)
56 PRK00299 sulfur transfer prote 25.3 2.9E+02 0.0062 20.5 6.2 56 83-146 9-65 (81)
57 PRK00394 transcription factor; 24.8 4.6E+02 0.01 22.7 9.8 22 116-137 145-166 (179)
58 TIGR03527 selenium_YedF seleni 24.8 1.5E+02 0.0032 26.1 5.0 51 89-147 5-55 (194)
59 PF13740 ACT_6: ACT domain; PD 24.1 2.6E+02 0.0057 20.1 5.5 55 83-137 2-63 (76)
60 cd06167 LabA_like LabA_like pr 22.5 1.1E+02 0.0024 24.6 3.5 30 120-150 103-132 (149)
61 KOG2236 Uncharacterized conser 22.4 1.6E+02 0.0034 29.7 5.0 10 139-148 278-287 (483)
62 PF08777 RRM_3: RNA binding mo 21.9 3.3E+02 0.0071 21.4 6.0 53 85-137 3-58 (105)
63 COG0425 SirA Predicted redox p 21.7 3.5E+02 0.0075 20.2 5.8 52 83-143 5-59 (78)
64 cd02410 archeal_CPSF_KH The ar 21.7 2.7E+02 0.006 23.6 5.7 59 93-151 52-116 (145)
65 PF13291 ACT_4: ACT domain; PD 21.3 2.2E+02 0.0047 20.4 4.6 33 81-113 47-79 (80)
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=99.42 E-value=5.9e-13 Score=95.27 Aligned_cols=58 Identities=28% Similarity=0.513 Sum_probs=53.8
Q ss_pred EEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEec---CCHHHHHHHHHhhcCCc
Q 024167 85 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MDVKELVPYLKEKLKRN 143 (271)
Q Consensus 85 ~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~---~d~~~L~~~l~kk~G~~ 143 (271)
+|+| +|+|++|+++|+++|.+++||.++.+|+.+++|+|.+. +++.+|+++|+ ++||+
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 99999999999999999999999999999999999976 45699999999 89984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.33 E-value=6.8e-12 Score=93.69 Aligned_cols=67 Identities=45% Similarity=0.684 Sum_probs=60.8
Q ss_pred ceeEEEEeeccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 81 ESTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 81 ~~~v~l~VgM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
..+.+|++.|||.+|+.+|++.|+.+.||.++.+|...++|||.|.+++..|++.|++..+.++.+|
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 3568899999999999999999999999999999999999999999999999999994333777766
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.28 E-value=1.8e-11 Score=91.09 Aligned_cols=65 Identities=23% Similarity=0.470 Sum_probs=58.1
Q ss_pred eeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEE--e-cCCHHHHHHHHHhhcCCceEEc
Q 024167 82 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--G-TMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 82 ~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~--g-~~d~~~L~~~l~kk~G~~ae~v 147 (271)
.+..|.| +|+|.+|+.+|+++|.+++||.++.||+..++++|+ + .++.++|+++|. .+||.+..+
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 999999999999999999999999999999666665 4 579999999999 999998764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.90 E-value=5.1e-09 Score=92.24 Aligned_cols=70 Identities=20% Similarity=0.406 Sum_probs=65.1
Q ss_pred eeEEEEeeccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEccCCCC
Q 024167 82 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 152 (271)
Q Consensus 82 ~~v~l~VgM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v~~~~~ 152 (271)
-+++|.|.|||.+|++.|+..|..++||.+|+||+..+.|.|.+.+.+.+|...|+ .+|++|.+......
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 46799999999999999999999999999999999999999999999999999999 99999999755443
No 5
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.65 E-value=3.3e-07 Score=96.08 Aligned_cols=139 Identities=14% Similarity=0.289 Sum_probs=95.9
Q ss_pred CCCCCCceEEEEeccCcEEEEEeecChHHHHHHHHHhhcccccccCCCCCCCCCCCCCcccccccCCCCCccccccCCCC
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLVSPQPKKDAGGGEKKSEEKSEKKPDDKKSEEKKPPK 80 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~vd~~~lv~~I~~k~Gy~aelvs~~p~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~ 80 (271)
|++++||.++.||+ ++.+|.+..+...+.+.|+ .+||.+.+.++......... ...+.........+.. ....
T Consensus 25 l~~~~gv~~v~v~~--~~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~~~ 97 (834)
T PRK10671 25 LEQRPDVEQADVSI--TEAHVTGTASAEALIETIK-QAGYDASVSHPKAKPLTESS---IPSEALTAASEELPAA-TADD 97 (834)
T ss_pred HhcCCCcceEEEee--eEEEEEecCCHHHHHHHHH-hcCCcccccccccccccccc---cCchhhhhhhhhcccc-ccCc
Confidence 56789999999998 4566766678889999999 79999886542111110000 0000000000000000 0001
Q ss_pred ceeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 81 ESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 81 ~~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
..++.|.| +|+|.+|+.+|++.|.+++||.++.+++.++++.|.+..++..+...+. ++||.+.++
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 9999999999999999999999999999999999886678888888888 899987644
No 6
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.61 E-value=2.4e-07 Score=96.13 Aligned_cols=121 Identities=17% Similarity=0.319 Sum_probs=102.6
Q ss_pred CCCCCCceEEEEeccCcEEEEEee--cChHHHHHHHHHhhcccccccCCCCCCCCCCCCCcccccccCCCCCccccccCC
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGK--VEPAKLKERLEAKTKKKVDLVSPQPKKDAGGGEKKSEEKSEKKPDDKKSEEKKP 78 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~--vd~~~lv~~I~~k~Gy~aelvs~~p~~~~~~~~~~~~~~~~~k~~~~~~~~~~~ 78 (271)
++..+||.++.|++.++.++|.++ ++++.+.++|+ ..|+.+.+++.. .
T Consensus 16 ~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~-----------------------------~ 65 (951)
T KOG0207|consen 16 ISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDS-----------------------------E 65 (951)
T ss_pred HhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccC-----------------------------c
Confidence 457899999999999999999984 57899999999 799988765432 1
Q ss_pred CCceeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHhhcCCceEEccCCCC
Q 024167 79 PKESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEVVPAKKD 152 (271)
Q Consensus 79 ~~~~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g---~~d~~~L~~~l~kk~G~~ae~v~~~~~ 152 (271)
....+..|.| ||+|.+|++.|++.|+++.||.++.|-+...+..|.- ...+..+.+.|. ++|+.+++++....
T Consensus 66 ~~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie-~~gf~a~~i~~~~~ 142 (951)
T KOG0207|consen 66 ITASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIE-DLGFSAELIESVNG 142 (951)
T ss_pred cccceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHH-hcCccceehhcccC
Confidence 1123678999 9999999999999999999999999999999999973 367899999999 99999998865554
No 7
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.48 E-value=8.2e-07 Score=92.23 Aligned_cols=118 Identities=19% Similarity=0.362 Sum_probs=98.5
Q ss_pred CCCCCCceEEEEeccCcEEEEEee---cChHHHHHHHHHhhcccccccCCCCCCCCCCCCCcccccccCCCCCccccccC
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGK---VEPAKLKERLEAKTKKKVDLVSPQPKKDAGGGEKKSEEKSEKKPDDKKSEEKK 77 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~---vd~~~lv~~I~~k~Gy~aelvs~~p~~~~~~~~~~~~~~~~~k~~~~~~~~~~ 77 (271)
|++++||.++.|.+.+.+.+|.++ ..+..+.+.|+ +.|+.++++....
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 578899999999999999999874 36778999999 7899877553210
Q ss_pred CCCceeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHhhcCCceEEcc
Q 024167 78 PPKESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEVVP 148 (271)
Q Consensus 78 ~~~~~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g---~~d~~~L~~~l~kk~G~~ae~v~ 148 (271)
.....+++|.| +|+|.+|+.+|++.|.+++||.++.+++.++++.|.- ...+..+++.|. .+|+.+.+..
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 01115689999 9999999999999999999999999999999999974 367899999999 8998877654
No 8
>PLN02957 copper, zinc superoxide dismutase
Probab=98.43 E-value=1.5e-06 Score=78.75 Aligned_cols=71 Identities=24% Similarity=0.462 Sum_probs=63.9
Q ss_pred ceeEEEEeeccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEccCCCC
Q 024167 81 ESTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 152 (271)
Q Consensus 81 ~~~v~l~VgM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v~~~~~ 152 (271)
.+++.|.++|+|..|+.+|+++|.+++||.++.+|+..++++|...++...|+..|+ ++||.++++.....
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 356778889999999999999999999999999999999999998778899999999 99999988866444
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.29 E-value=1.9e-06 Score=90.49 Aligned_cols=64 Identities=20% Similarity=0.384 Sum_probs=58.1
Q ss_pred eeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEcc
Q 024167 82 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVP 148 (271)
Q Consensus 82 ~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v~ 148 (271)
.+++|.| +|+|++|+.+|+++|.+++||.++.||+. +++|++..+...|.+.|+ ++||.+++.+
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 566777789999999999 9999999875
No 10
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.05 E-value=8.9e-06 Score=84.10 Aligned_cols=62 Identities=21% Similarity=0.402 Sum_probs=56.3
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEec---CC-HHHHHHHHHhhcCCceEE
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MD-VKELVPYLKEKLKRNVEV 146 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~---~d-~~~L~~~l~kk~G~~ae~ 146 (271)
++.|.| ||||++|+.+|+ +|.+++||.++.||+.+++++|... .+ .+.+...++ .+||.+..
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 468999 999999999999 9999999999999999999999843 45 789999999 99998876
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=97.76 E-value=0.00025 Score=46.86 Aligned_cols=61 Identities=20% Similarity=0.325 Sum_probs=51.1
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHhhcCCce
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNV 144 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g---~~d~~~L~~~l~kk~G~~a 144 (271)
++.|.| +|+|..|+.+|++.+..+.++..+.+++....+.|.. ..+...+...+. ..|+.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCCc
Confidence 356888 9999999999999999999999999999999998874 346777777776 777643
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=97.26 E-value=0.00035 Score=49.48 Aligned_cols=40 Identities=33% Similarity=0.370 Sum_probs=34.6
Q ss_pred CCCCCCceEEEEeccCcEEEEEeecC---hHHHHHHHHHhhccc
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGKVE---PAKLKERLEAKTKKK 41 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~vd---~~~lv~~I~~k~Gy~ 41 (271)
|.+++||.++.+|+.+++++|.++.+ ++.|+++|+ ++||+
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 45789999999999999999999644 589999999 68883
No 13
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=96.82 E-value=0.0021 Score=47.75 Aligned_cols=45 Identities=36% Similarity=0.568 Sum_probs=37.5
Q ss_pred CCCCCCceEEEEeccCcEEEEEeecChHHHHHHHHHhhccccccc
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLV 45 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~vd~~~lv~~I~~k~Gy~aelv 45 (271)
|..+.||.++.+|...+++||.|.+|+..|++.|+...+..+.+|
T Consensus 26 l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 26 LQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred hhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 467899999999999999999999999999999995332554433
No 14
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.58 E-value=0.0055 Score=64.00 Aligned_cols=64 Identities=14% Similarity=0.250 Sum_probs=52.7
Q ss_pred eeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecC-CHHHHHHHHHhhcCCceEE
Q 024167 82 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTM-DVKELVPYLKEKLKRNVEV 146 (271)
Q Consensus 82 ~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~-d~~~L~~~l~kk~G~~ae~ 146 (271)
.++.|.| +|+|.+|+.+|+++|.+++||.++.+++.++++.|.... ....+...++ .+||.+..
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 999999999999999999999999999999998886321 1266777777 88987653
No 15
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=95.63 E-value=0.022 Score=42.03 Aligned_cols=42 Identities=31% Similarity=0.401 Sum_probs=35.4
Q ss_pred CCCCCCceEEEEeccCcEEEEEe---ecChHHHHHHHHHhhccccc
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTG---KVEPAKLKERLEAKTKKKVD 43 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g---~vd~~~lv~~I~~k~Gy~ae 43 (271)
|..++||.++.|||..++++|+. .++.+.|+++|+ .+||.+.
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 56889999999999997777766 358889999999 6999764
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=93.56 E-value=0.97 Score=32.53 Aligned_cols=63 Identities=21% Similarity=0.305 Sum_probs=48.3
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHhhcCCceEE
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEV 146 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g---~~d~~~L~~~l~kk~G~~ae~ 146 (271)
++.+.+ +++|..|..+++..+....++....+++....+.+.- ..+...+...+. ..|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 445667 9999999999999999999999899998888766652 245666656666 67777554
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=89.64 E-value=2.7 Score=24.47 Aligned_cols=49 Identities=33% Similarity=0.556 Sum_probs=36.5
Q ss_pred eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEec--CCHHHHHHHHH
Q 024167 89 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 137 (271)
Q Consensus 89 gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~--~d~~~L~~~l~ 137 (271)
++.|..|...++..+....++....+++....+.+... .+...+...+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH
Confidence 78899999999999999999888888887777666532 24454444444
No 18
>PRK13748 putative mercuric reductase; Provisional
Probab=86.92 E-value=3 Score=41.68 Aligned_cols=64 Identities=20% Similarity=0.321 Sum_probs=50.4
Q ss_pred EEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHhhcCCceEEccC
Q 024167 85 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVVPA 149 (271)
Q Consensus 85 ~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g--~~d~~~L~~~l~kk~G~~ae~v~~ 149 (271)
.+.+ +|+|.+|..+++..+..++++....+++....+.+.. ..+...+...+. ..++.+++...
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 78877665544
No 19
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=83.76 E-value=1.5 Score=39.38 Aligned_cols=44 Identities=27% Similarity=0.421 Sum_probs=38.6
Q ss_pred CCCCCCceEEEEeccCcEEEEEeecChHHHHHHHHHhhccccccc
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLV 45 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~vd~~~lv~~I~~k~Gy~aelv 45 (271)
|..++||.+|.||+..+.+.|.+.+-+.+|...|+ -+|+++-|.
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 56789999999999999999999888899999999 599987653
No 20
>PLN02957 copper, zinc superoxide dismutase
Probab=82.37 E-value=2.6 Score=38.10 Aligned_cols=45 Identities=29% Similarity=0.423 Sum_probs=37.9
Q ss_pred CCCCCCceEEEEeccCcEEEEEeecChHHHHHHHHHhhcccccccC
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGKVEPAKLKERLEAKTKKKVDLVS 46 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~vd~~~lv~~I~~k~Gy~aelvs 46 (271)
|.+++||..+.+|+..++++|.+..+...++..|+ .+||.+++++
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 35789999999999999999998777788888888 7899876553
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=77.86 E-value=3.7 Score=29.72 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=22.6
Q ss_pred eeEEEEeeccchhhH------HHHHHHhhcCCCccEEEE
Q 024167 82 STVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTI 114 (271)
Q Consensus 82 ~~v~l~VgM~C~~Ca------~kIekaL~ki~GV~~v~V 114 (271)
.++.|.+.+.+.+|. ..|+++|..++||.+|+|
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 788899999999999876
No 22
>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=75.27 E-value=7.2 Score=27.93 Aligned_cols=53 Identities=19% Similarity=0.203 Sum_probs=37.7
Q ss_pred EEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHhhcCCceEEc
Q 024167 85 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 85 ~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g--~~d~~~L~~~l~kk~G~~ae~v 147 (271)
+|.+ |+.|+...-++.++|.+++.=+ .+.|.. ......|...++ ..|+.+..+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G~---------~l~v~~d~~~~~~di~~~~~-~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPGE---------VLEVLVDDPAAVEDIPRWCE-ENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCCC---------EEEEEECCccHHHHHHHHHH-HCCCEEEEE
Confidence 5777 9999999999999999975432 333433 234577888888 999975544
No 23
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=68.82 E-value=32 Score=27.07 Aligned_cols=66 Identities=23% Similarity=0.363 Sum_probs=43.1
Q ss_pred ceeEEEEe-eccchhhHHHHHHHhhcCCCccEEEE-----ecCC--CEEEEEe-cCCHHHHHHHHHhhcCCceEEc
Q 024167 81 ESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTI-----DGGK--DLVTVKG-TMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 81 ~~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~V-----d~~~--~~VtV~g-~~d~~~L~~~l~kk~G~~ae~v 147 (271)
...++|.| --|-.--.--+-+.|++++||+.|.+ |..+ =++||.| .+|.++|.+.|. ++|--+.-+
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 45677777 22323333445577888999887754 3333 3455566 589999999999 888765544
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=65.71 E-value=14 Score=29.52 Aligned_cols=44 Identities=14% Similarity=0.124 Sum_probs=23.6
Q ss_pred hhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHH
Q 024167 93 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 137 (271)
Q Consensus 93 ~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~ 137 (271)
..|.+.+ +.|.++.=--....-.-.-++||.+.+..+++...+.
T Consensus 47 qhclrtm-rhleklkipyefqygwlgvkitiksnvpndevtkkvs 90 (138)
T PF05663_consen 47 QHCLRTM-RHLEKLKIPYEFQYGWLGVKITIKSNVPNDEVTKKVS 90 (138)
T ss_pred HHHHHHH-HHHHhcCCCeeeeecceeEEEEEecCCCchHhhhccC
Confidence 4455444 3444443222333333445677778787777766654
No 25
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=63.64 E-value=39 Score=26.71 Aligned_cols=64 Identities=23% Similarity=0.404 Sum_probs=41.8
Q ss_pred ceeEEEEe-eccchhhHHHHHHHhhcCCCccEEEE-----ecCCCEEE--EEec-CCHHHHHHHHHhhcCCceEE
Q 024167 81 ESTVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTI-----DGGKDLVT--VKGT-MDVKELVPYLKEKLKRNVEV 146 (271)
Q Consensus 81 ~~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~V-----d~~~~~Vt--V~g~-~d~~~L~~~l~kk~G~~ae~ 146 (271)
.++++|.| --|-.+ .-.+-++|.+++||..|.+ |..+..+. |.|. +|.+.|.++|+ ++|--+.-
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 45678877 224443 4456688999999988754 44444444 4574 89999999999 88865543
No 26
>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=60.69 E-value=24 Score=25.01 Aligned_cols=51 Identities=16% Similarity=0.210 Sum_probs=35.7
Q ss_pred EEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEE--ecCCHHHHHHHHHhhcCCceEEc
Q 024167 86 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--GTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 86 l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~--g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
|.+ |+.|..-.-+++++| ++..=+ .+.|. .......|...++ +.|+.+.+.
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g~---------~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~ 55 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAGG---------EIEVLVDNEVAKENVSRFAE-SRGYEVSVE 55 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCCC---------EEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence 455 899999999999999 654322 33333 2334578888888 999988543
No 27
>PRK11018 hypothetical protein; Provisional
Probab=58.99 E-value=39 Score=25.12 Aligned_cols=57 Identities=9% Similarity=-0.005 Sum_probs=41.0
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
..+|.+ |+.|+.-.-+.+++|.+++.-+.+. |.++.......|...++ +.|+.+...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L~-------V~~d~~~a~~di~~~~~-~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKGEILE-------VVSDCPQSINNIPLDAR-NHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCCCEEE-------EEeCCccHHHHHHHHHH-HcCCEEEEE
Confidence 468888 9999999999999999886433232 22222345677888888 999987543
No 28
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=57.62 E-value=14 Score=38.93 Aligned_cols=42 Identities=21% Similarity=0.385 Sum_probs=35.4
Q ss_pred CCCCCCceEEEEeccCcEEEEEee---cC-hHHHHHHHHHhhccccc
Q 024167 1 MKNYEGVVDVKTDCGANKVTVTGK---VE-PAKLKERLEAKTKKKVD 43 (271)
Q Consensus 1 L~kl~GV~sv~Vn~a~~kltV~g~---vd-~~~lv~~I~~k~Gy~ae 43 (271)
|++++||..+.|||.+++++|.++ .+ .+.+...++ ..||.+.
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 578999999999999999999974 34 578888888 6899764
No 29
>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=54.04 E-value=11 Score=19.84 Aligned_cols=7 Identities=86% Similarity=1.621 Sum_probs=3.3
Q ss_pred CCCCCCC
Q 024167 240 NQGYPPQ 246 (271)
Q Consensus 240 ~~~~~~~ 246 (271)
.+||||+
T Consensus 4 pqG~pPQ 10 (15)
T PF02162_consen 4 PQGYPPQ 10 (15)
T ss_pred CcCCCCC
Confidence 3455544
No 30
>PRK11023 outer membrane lipoprotein; Provisional
Probab=47.89 E-value=1.9e+02 Score=25.17 Aligned_cols=42 Identities=12% Similarity=0.147 Sum_probs=30.9
Q ss_pred chhhHHHHHHHhhcCCCccEEE--EecCCCEEEEEecCCHHHHH
Q 024167 92 CEGCISKIKKIIYKTKGVDNVT--IDGGKDLVTVKGTMDVKELV 133 (271)
Q Consensus 92 C~~Ca~kIekaL~ki~GV~~v~--Vd~~~~~VtV~g~~d~~~L~ 133 (271)
-..=..+|+.+|..-+.|.... |....+.|++.|.++..+.-
T Consensus 125 D~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~ 168 (191)
T PRK11023 125 DTWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAK 168 (191)
T ss_pred cHHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHH
Confidence 3446778999998877776554 44569999999998875543
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=47.78 E-value=23 Score=30.77 Aligned_cols=54 Identities=17% Similarity=0.218 Sum_probs=34.5
Q ss_pred eEEEEeeccchhhH------HHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcC
Q 024167 83 TVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 141 (271)
Q Consensus 83 ~v~l~VgM~C~~Ca------~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G 141 (271)
++.+.+-++..+|. ..|+.+|..++||.+|.|++.. .-..+++.+-+..+.++|
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 45566656655554 4589999999999999886532 223555666555554444
No 32
>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=46.26 E-value=26 Score=26.82 Aligned_cols=40 Identities=13% Similarity=0.143 Sum_probs=25.7
Q ss_pred HHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcC
Q 024167 97 SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 141 (271)
Q Consensus 97 ~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G 141 (271)
..|+.+|..++|+.++.|++.. .-...++.+-+.-++++|
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~~-----~~~~~~~~~~~~~~~~~~ 97 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELVW-----DPPWTPERMSEEARLELG 97 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEEe-----eCCCChHHCCHHHHHHcC
Confidence 4588899999999999888642 222344555444444443
No 33
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=42.60 E-value=88 Score=24.13 Aligned_cols=44 Identities=18% Similarity=0.172 Sum_probs=31.4
Q ss_pred hhHHHHHHHhhcCCCccEEEEecCCCEEEEEe-cCCHHHHHHHHH
Q 024167 94 GCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG-TMDVKELVPYLK 137 (271)
Q Consensus 94 ~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g-~~d~~~L~~~l~ 137 (271)
.=...|.++|..++|++=...|...+++.|+- .-+...+++.|.
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 33678999999999997777777788888872 234555555554
No 34
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=42.59 E-value=68 Score=27.77 Aligned_cols=67 Identities=30% Similarity=0.404 Sum_probs=42.9
Q ss_pred EEeeccchhhHHHHH------------HHhhcC------CCccEEEEecCCCEEEEE---ec--C--CHHHHHHHHHhhc
Q 024167 86 LKIRLHCEGCISKIK------------KIIYKT------KGVDNVTIDGGKDLVTVK---GT--M--DVKELVPYLKEKL 140 (271)
Q Consensus 86 l~VgM~C~~Ca~kIe------------kaL~ki------~GV~~v~Vd~~~~~VtV~---g~--~--d~~~L~~~l~kk~ 140 (271)
++-++-|.+|.++|. ++|.++ .++.-...=...++|++. |. + ..-..+++|++.+
T Consensus 10 ~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~~l 89 (166)
T PRK06418 10 VKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSRKL 89 (166)
T ss_pred eccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHHHh
Confidence 344899999999865 567665 344433322234666653 32 0 1236888998899
Q ss_pred CCceEEccCCCC
Q 024167 141 KRNVEVVPAKKD 152 (271)
Q Consensus 141 G~~ae~v~~~~~ 152 (271)
|++++++.-...
T Consensus 90 gk~VevVE~s~d 101 (166)
T PRK06418 90 GKKVRVVEKTND 101 (166)
T ss_pred CCcEEEEEcCCC
Confidence 999999965443
No 35
>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=39.90 E-value=20 Score=24.87 Aligned_cols=32 Identities=16% Similarity=0.334 Sum_probs=15.1
Q ss_pred HHHHHhhc---CCCccEEEEecCCCEEEEEecCCHH
Q 024167 98 KIKKIIYK---TKGVDNVTIDGGKDLVTVKGTMDVK 130 (271)
Q Consensus 98 kIekaL~k---i~GV~~v~Vd~~~~~VtV~g~~d~~ 130 (271)
+|+.+|.. +++- .+.|....+.|+++|.++..
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s~ 37 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEVPSQ 37 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEESSC
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeCcHH
Confidence 45666665 3444 56777778888888876443
No 36
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.45 E-value=47 Score=26.17 Aligned_cols=40 Identities=23% Similarity=0.383 Sum_probs=26.6
Q ss_pred CCCCCCceEEEEec-------cCcEEEEEe-ecChHHHHHHHHHhhccc
Q 024167 1 MKNYEGVVDVKTDC-------GANKVTVTG-KVEPAKLKERLEAKTKKK 41 (271)
Q Consensus 1 L~kl~GV~sv~Vn~-------a~~kltV~g-~vd~~~lv~~I~~k~Gy~ 41 (271)
|++++||+.|++.+ ..-++||.| +.|...|.+.|+ ..|-.
T Consensus 28 lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~ 75 (97)
T COG1888 28 LSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGA 75 (97)
T ss_pred HhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCe
Confidence 45677777665432 344566677 578999999999 46653
No 37
>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=39.01 E-value=1.5e+02 Score=21.66 Aligned_cols=54 Identities=19% Similarity=0.215 Sum_probs=38.5
Q ss_pred hhhHHHHHHHhhcC---CCccEEEEecCCCEEEEE--ecCCHHHHHHHHHhhcCCceEE
Q 024167 93 EGCISKIKKIIYKT---KGVDNVTIDGGKDLVTVK--GTMDVKELVPYLKEKLKRNVEV 146 (271)
Q Consensus 93 ~~Ca~kIekaL~ki---~GV~~v~Vd~~~~~VtV~--g~~d~~~L~~~l~kk~G~~ae~ 146 (271)
.+=..++..+|.++ +---.+..|-.++.+.|. |.+-.+.++++|+++.|..+++
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 34445555555554 444479999999999998 4677889999999777766654
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=38.99 E-value=2.5e+02 Score=24.13 Aligned_cols=55 Identities=9% Similarity=0.034 Sum_probs=35.2
Q ss_pred eEEEEeeccchhhHHHHHHHhh--------cCCCcc------EEE-EecCCCEEEEEecCCHHHHHHHHH
Q 024167 83 TVVLKIRLHCEGCISKIKKIIY--------KTKGVD------NVT-IDGGKDLVTVKGTMDVKELVPYLK 137 (271)
Q Consensus 83 ~v~l~VgM~C~~Ca~kIekaL~--------ki~GV~------~v~-Vd~~~~~VtV~g~~d~~~L~~~l~ 137 (271)
-++-...|.|.=.-..|-..+. ..+|+. .++ .=|.+++|+|+|.-+.+++..+++
T Consensus 97 NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~ 166 (174)
T cd00652 97 NIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVE 166 (174)
T ss_pred EEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHH
Confidence 3444446666666666655554 456643 122 226899999999888888877776
No 39
>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=37.83 E-value=1.3e+02 Score=22.49 Aligned_cols=42 Identities=14% Similarity=0.241 Sum_probs=29.8
Q ss_pred hHHHHHHHhhcCCCccEEEEecCCCEEEEE-ecCCHHHHHHHHH
Q 024167 95 CISKIKKIIYKTKGVDNVTIDGGKDLVTVK-GTMDVKELVPYLK 137 (271)
Q Consensus 95 Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~-g~~d~~~L~~~l~ 137 (271)
=...|.++|..++||+=...+-. +++.|+ -.-+...+.+.|.
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 35688899999999965556665 777776 2346666666666
No 40
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=37.78 E-value=75 Score=27.02 Aligned_cols=41 Identities=22% Similarity=0.312 Sum_probs=31.8
Q ss_pred eeEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecC-CCEEEE
Q 024167 82 STVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGG-KDLVTV 123 (271)
Q Consensus 82 ~~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~-~~~VtV 123 (271)
..++|.| .-.|..|..-|.....+ -|+.+++|... ++++.+
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 77899999888776665 58999988876 665544
No 41
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=37.19 E-value=87 Score=22.76 Aligned_cols=43 Identities=19% Similarity=0.236 Sum_probs=30.6
Q ss_pred hhcCCCccEEEEecCC-CEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 103 IYKTKGVDNVTIDGGK-DLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 103 L~ki~GV~~v~Vd~~~-~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
|..++||.++..+-.. =++.|....+...|++.|. ..|. +.-.
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 8888999999865432 3444555568899999999 7777 5433
No 42
>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=35.36 E-value=89 Score=21.89 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=25.3
Q ss_pred eeEEEEeeccchh-hHHHHHHHhhcCCCccEEEE
Q 024167 82 STVVLKIRLHCEG-CISKIKKIIYKTKGVDNVTI 114 (271)
Q Consensus 82 ~~v~l~VgM~C~~-Ca~kIekaL~ki~GV~~v~V 114 (271)
..+.|.|...-.. -..+|.+.|++++||.+|.+
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 88999999999999999864
No 43
>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=32.59 E-value=1.2e+02 Score=21.64 Aligned_cols=52 Identities=23% Similarity=0.274 Sum_probs=37.3
Q ss_pred EEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHhhcCCceEEc
Q 024167 86 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 86 l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g--~~d~~~L~~~l~kk~G~~ae~v 147 (271)
|.+ |+.|..=.-+++++|.++..=+ .+.|.. ......|....+ ..|+.+..+
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G~---------~l~V~~d~~~a~~di~~~~~-~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDGE---------QLEVKASDPGFARDAQAWCK-STGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCCC---------EEEEEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 455 8999999999999999886322 333332 345678888888 999987644
No 44
>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=32.53 E-value=1.1e+02 Score=25.79 Aligned_cols=33 Identities=21% Similarity=0.221 Sum_probs=28.9
Q ss_pred chhhHHHHHHHhhcCCCccEEEEecCCCEEEEE
Q 024167 92 CEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK 124 (271)
Q Consensus 92 C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~ 124 (271)
=..=+.+|.+.|.+++||.++.|=...+.+.|-
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 456688999999999999999998888888885
No 45
>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=32.48 E-value=1.5e+02 Score=20.66 Aligned_cols=52 Identities=25% Similarity=0.262 Sum_probs=36.3
Q ss_pred EEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEec--CCHHHHHHHHHhhcCCceEEc
Q 024167 86 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 86 l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~--~d~~~L~~~l~kk~G~~ae~v 147 (271)
|.+ |+.|+.=.-++.++|.++..= +.+.|..+ .....|...++ ..|+.+..+
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~g---------~~l~v~~d~~~~~~~i~~~~~-~~g~~~~~~ 56 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKSG---------EVLEVLLDDPGAVEDIPAWAK-ETGHEVLEV 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCCC---------CEEEEEecCCcHHHHHHHHHH-HcCCEEEEE
Confidence 445 889999888999999886533 23344332 34688888888 999986543
No 46
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=31.91 E-value=53 Score=25.94 Aligned_cols=38 Identities=26% Similarity=0.404 Sum_probs=24.1
Q ss_pred CCCCCceEEEEec-----cC--cEEEEEe-ecChHHHHHHHHHhhcc
Q 024167 2 KNYEGVVDVKTDC-----GA--NKVTVTG-KVEPAKLKERLEAKTKK 40 (271)
Q Consensus 2 ~kl~GV~sv~Vn~-----a~--~kltV~g-~vd~~~lv~~I~~k~Gy 40 (271)
.+++||..|++.+ .+ =++||.| +.|...|.++|++ .|=
T Consensus 27 ~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~-~Gg 72 (95)
T PF02680_consen 27 SELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEE-LGG 72 (95)
T ss_dssp HTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHH-TT-
T ss_pred HhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHH-cCC
Confidence 4677877766543 23 3455667 4789999999994 543
No 47
>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=30.67 E-value=3.5e+02 Score=23.33 Aligned_cols=23 Identities=4% Similarity=-0.006 Sum_probs=18.7
Q ss_pred ecCCCEEEEEecCCHHHHHHHHH
Q 024167 115 DGGKDLVTVKGTMDVKELVPYLK 137 (271)
Q Consensus 115 d~~~~~VtV~g~~d~~~L~~~l~ 137 (271)
=|.+++|+|+|.-+.+++..+++
T Consensus 143 IF~SGKvvitGaks~~~~~~a~~ 165 (174)
T cd04518 143 LFSSGKMVITGAKSEEDAKRAVE 165 (174)
T ss_pred EeCCCEEEEEecCCHHHHHHHHH
Confidence 36899999999878877777766
No 48
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of 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 thought 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=30.59 E-value=1.7e+02 Score=20.87 Aligned_cols=54 Identities=19% Similarity=0.260 Sum_probs=37.2
Q ss_pred EEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 86 LKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 86 l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
|.+ |+.|+.=.-+++++|.+++-=+.+ .|.++.......|...++ +.|+.+...
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~G~~l-------~V~~dd~~s~~di~~~~~-~~g~~~~~~ 56 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKPGDTL-------LVLATDPSTTRDIPKFCT-FLGHELLAQ 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCCCCEE-------EEEeCCCchHHHHHHHHH-HcCCEEEEE
Confidence 345 889999899999999887522211 222223356678889998 999987654
No 49
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=30.25 E-value=78 Score=25.60 Aligned_cols=53 Identities=19% Similarity=0.369 Sum_probs=33.1
Q ss_pred EEEEeeccchhh------HHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcC
Q 024167 84 VVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 141 (271)
Q Consensus 84 v~l~VgM~C~~C------a~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G 141 (271)
+.+.+.+|-.+| ...|+.+|..++||.++.|++ +..-...+..+....+..+|
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l-----~~~p~Wt~~~ms~ear~~~g 109 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL-----TLSPPWTPDRMSEEARRALG 109 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE-----EEcCCCchhhcCHHHHHhhC
Confidence 444445555555 678999999999999998764 22222445555555443444
No 50
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=29.24 E-value=4.1e+02 Score=29.42 Aligned_cols=44 Identities=11% Similarity=0.196 Sum_probs=35.4
Q ss_pred hhHHHHHHHhhcCCCccEEEEecC-CCEEEEEe--------cCCHHHHHHHHH
Q 024167 94 GCISKIKKIIYKTKGVDNVTIDGG-KDLVTVKG--------TMDVKELVPYLK 137 (271)
Q Consensus 94 ~Ca~kIekaL~ki~GV~~v~Vd~~-~~~VtV~g--------~~d~~~L~~~l~ 137 (271)
--.+.|+..|++++||.+|++--. ...+.|.- .+++.+|..+|+
T Consensus 155 ~~~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~ 207 (1009)
T COG0841 155 YAASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIR 207 (1009)
T ss_pred HHHHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 456679999999999999999886 66677751 367888999998
No 51
>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=29.06 E-value=1.7e+02 Score=21.01 Aligned_cols=53 Identities=8% Similarity=-0.011 Sum_probs=37.1
Q ss_pred Ee-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 87 KI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 87 ~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
.+ |+.|.-=.-+.+++|.++.--+.+. |.++.......|...++ ..|+.+..+
T Consensus 3 D~rG~~CP~Pvi~~kkal~~l~~G~~l~-------V~~d~~~s~~ni~~~~~-~~g~~v~~~ 56 (69)
T cd03422 3 DLRGEPCPYPAIATLEALPSLKPGEILE-------VISDCPQSINNIPIDAR-NHGYKVLAI 56 (69)
T ss_pred ccCCCcCCHHHHHHHHHHHcCCCCCEEE-------EEecCchHHHHHHHHHH-HcCCEEEEE
Confidence 44 8899999999999999886433221 22223345677888888 999988654
No 52
>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=28.13 E-value=67 Score=23.26 Aligned_cols=13 Identities=15% Similarity=0.421 Sum_probs=9.3
Q ss_pred EEEEeeccchhhHH
Q 024167 84 VVLKIRLHCEGCIS 97 (271)
Q Consensus 84 v~l~VgM~C~~Ca~ 97 (271)
+.+ ++..|..|..
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 5777999983
No 53
>PRK11670 antiporter inner membrane protein; Provisional
Probab=27.62 E-value=1.6e+02 Score=28.36 Aligned_cols=68 Identities=12% Similarity=0.147 Sum_probs=43.1
Q ss_pred eEEEEeeccchhh------HHHHHHHhhcCCCccEEEEecCC------------------CEEEEE---e---c-CCHHH
Q 024167 83 TVVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDGGK------------------DLVTVK---G---T-MDVKE 131 (271)
Q Consensus 83 ~v~l~VgM~C~~C------a~kIekaL~ki~GV~~v~Vd~~~------------------~~VtV~---g---~-~d~~~ 131 (271)
.+.|.+.++-..| ...++.+|..++||.++.|.+.. ..+.|. | . .-...
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 3555554443344 35689999999999988776533 223343 1 1 23456
Q ss_pred HHHHHHhhcCCceEEccCCC
Q 024167 132 LVPYLKEKLKRNVEVVPAKK 151 (271)
Q Consensus 132 L~~~l~kk~G~~ae~v~~~~ 151 (271)
|...|. +.|+++-+++-..
T Consensus 128 LA~aLA-~~G~rVlLID~D~ 146 (369)
T PRK11670 128 LALALA-AEGAKVGILDADI 146 (369)
T ss_pred HHHHHH-HCCCcEEEEeCCC
Confidence 777777 8899998885533
No 54
>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=26.46 E-value=1e+02 Score=27.04 Aligned_cols=11 Identities=18% Similarity=0.271 Sum_probs=6.8
Q ss_pred CCCCccccccC
Q 024167 229 PMENQHQVVYA 239 (271)
Q Consensus 229 ~~~~~~g~~~~ 239 (271)
+||+..+|+-.
T Consensus 141 ~m~~~~~y~~~ 151 (182)
T PF06495_consen 141 PMQGAYPYQMP 151 (182)
T ss_pred ccccccccccC
Confidence 46777677643
No 55
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=26.17 E-value=1.8e+02 Score=27.46 Aligned_cols=48 Identities=23% Similarity=0.224 Sum_probs=38.2
Q ss_pred eeEEEEeeccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCC
Q 024167 82 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKR 142 (271)
Q Consensus 82 ~~v~l~VgM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~ 142 (271)
..+.|.++.+ ..|.+.|+..|..++||.+++. ++.++-.+.|++.+|.
T Consensus 61 i~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~------------~sre~~l~~L~~~lg~ 108 (297)
T COG2177 61 ITVYLQIDAD-QDDAALVREKIEGIPGVKSVRF------------ISREEALKELQPWLGF 108 (297)
T ss_pred EEEEEecCCC-hHHHHHHHHHHhcCCCcceEEE------------eCHHHHHHHHHHHcCc
Confidence 4566676666 9999999999999999998754 4667777777778885
No 56
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=25.30 E-value=2.9e+02 Score=20.52 Aligned_cols=56 Identities=9% Similarity=0.266 Sum_probs=38.8
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEE
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEV 146 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~ 146 (271)
..+|.+ |+.|..=.-+++++|.+++.=+.+ +|.++.......|....+ ..|+++..
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~G~~l-------~V~~dd~~~~~di~~~~~-~~G~~~~~ 65 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQPGETL-------LIIADDPATTRDIPSFCR-FMDHELLA 65 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCCCCEE-------EEEeCCccHHHHHHHHHH-HcCCEEEE
Confidence 467888 999999999999999988532222 122222345577777777 89988754
No 57
>PRK00394 transcription factor; Reviewed
Probab=24.80 E-value=4.6e+02 Score=22.70 Aligned_cols=22 Identities=9% Similarity=0.152 Sum_probs=16.2
Q ss_pred cCCCEEEEEecCCHHHHHHHHH
Q 024167 116 GGKDLVTVKGTMDVKELVPYLK 137 (271)
Q Consensus 116 ~~~~~VtV~g~~d~~~L~~~l~ 137 (271)
|.+++|+|+|.-+.+++..+++
T Consensus 145 F~SGKvvitGaks~~~~~~a~~ 166 (179)
T PRK00394 145 FGSGKLVITGAKSEEDAEKAVE 166 (179)
T ss_pred EcCCEEEEEecCCHHHHHHHHH
Confidence 6899999998766665555554
No 58
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=24.76 E-value=1.5e+02 Score=26.09 Aligned_cols=51 Identities=20% Similarity=0.191 Sum_probs=36.7
Q ss_pred eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHhhcCCceEEc
Q 024167 89 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 147 (271)
Q Consensus 89 gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~~d~~~L~~~l~kk~G~~ae~v 147 (271)
|+.|+.=.-+.+++|.+++.=+.+ +|.+......+.|.+.++ ..|+.+...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~g~~L-------~VlvD~~~a~~nV~~~~~-~~G~~v~~~ 55 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGEEGVL-------TVIVDNEAAKENVSKFAT-SLGYEVEVE 55 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCEE-------EEEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 789999999999999998632112 223333345678888888 999988654
No 59
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=24.12 E-value=2.6e+02 Score=20.12 Aligned_cols=55 Identities=9% Similarity=0.102 Sum_probs=37.3
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCC-ccEEEEecCCCEEEEE----ec-CCHHHHHHHHH
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKG-VDNVTIDGGKDLVTVK----GT-MDVKELVPYLK 137 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~G-V~~v~Vd~~~~~VtV~----g~-~d~~~L~~~l~ 137 (271)
.+++.| |.+..+....|.++|.+..+ |.++....-.+..+.. +. .+.+.|...|.
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 7777777766666543 22 13455666655
No 60
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=22.53 E-value=1.1e+02 Score=24.59 Aligned_cols=30 Identities=37% Similarity=0.444 Sum_probs=26.1
Q ss_pred EEEEEecCCHHHHHHHHHhhcCCceEEccCC
Q 024167 120 LVTVKGTMDVKELVPYLKEKLKRNVEVVPAK 150 (271)
Q Consensus 120 ~VtV~g~~d~~~L~~~l~kk~G~~ae~v~~~ 150 (271)
-|.|+|+-|...+++.|+ +.|+++.++...
T Consensus 103 ivLvSgD~Df~~~i~~lr-~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGDSDFVPLVERLR-ELGKRVIVVGFE 132 (149)
T ss_pred EEEEECCccHHHHHHHHH-HcCCEEEEEccC
Confidence 456788899999999999 889999999776
No 61
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.37 E-value=1.6e+02 Score=29.69 Aligned_cols=10 Identities=20% Similarity=0.248 Sum_probs=4.3
Q ss_pred hcCCceEEcc
Q 024167 139 KLKRNVEVVP 148 (271)
Q Consensus 139 k~G~~ae~v~ 148 (271)
++|..|-++.
T Consensus 278 ~ig~~vy~ap 287 (483)
T KOG2236|consen 278 CIGEKVYYAP 287 (483)
T ss_pred ccCCeeEecC
Confidence 3444444443
No 62
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=21.88 E-value=3.3e+02 Score=21.39 Aligned_cols=53 Identities=21% Similarity=0.142 Sum_probs=31.7
Q ss_pred EEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHH
Q 024167 85 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLK 137 (271)
Q Consensus 85 ~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g--~~d~~~L~~~l~ 137 (271)
+|.| +++=.-+...|+.+|+.+..|.-|.+........|.- .-..+.+++.+.
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~ 58 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLK 58 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHH
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHH
Confidence 5666 6776667999999999999888887777777777763 334778888887
No 63
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=3.5e+02 Score=20.17 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=35.6
Q ss_pred eEEEEe-eccchhhHHHHHHHhhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHhhcCCc
Q 024167 83 TVVLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRN 143 (271)
Q Consensus 83 ~v~l~V-gM~C~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g--~~d~~~L~~~l~kk~G~~ 143 (271)
..+|.+ |++|..=.-.++++|.+++-=+ .+.|.. ......|...+++..|+.
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~Ge---------~LeV~~ddp~~~~dIp~~~~~~~~~~ 59 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKPGE---------ILEVIADDPAAKEDIPAWAKKEGGHE 59 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCCCC---------EEEEEecCcchHHHHHHHHHHcCCcE
Confidence 468888 9999999999999999886433 333432 234467777777334343
No 64
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.66 E-value=2.7e+02 Score=23.61 Aligned_cols=59 Identities=15% Similarity=0.209 Sum_probs=41.8
Q ss_pred hhhHHHHHHHhhcCCCccEEEEecCCCEEEEEec----C--CHHHHHHHHHhhcCCceEEccCCC
Q 024167 93 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT----M--DVKELVPYLKEKLKRNVEVVPAKK 151 (271)
Q Consensus 93 ~~Ca~kIekaL~ki~GV~~v~Vd~~~~~VtV~g~----~--d~~~L~~~l~kk~G~~ae~v~~~~ 151 (271)
..-...|++.+-.-.||.++..|..++.|+|... + -....+..|..++|+...++...+
T Consensus 52 e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 52 EEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 3345566666666679999999999999999732 1 234555666669999999875544
No 65
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=21.28 E-value=2.2e+02 Score=20.40 Aligned_cols=33 Identities=15% Similarity=0.256 Sum_probs=26.0
Q ss_pred ceeEEEEeeccchhhHHHHHHHhhcCCCccEEE
Q 024167 81 ESTVVLKIRLHCEGCISKIKKIIYKTKGVDNVT 113 (271)
Q Consensus 81 ~~~v~l~VgM~C~~Ca~kIekaL~ki~GV~~v~ 113 (271)
...+.|.|...-..=-..|.+.|++++||.+|.
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 345666666777777889999999999998874
Done!