Query 029022
Match_columns 200
No_of_seqs 202 out of 1644
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 06:14:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029022.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029022hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0207 Cation transport ATPas 99.6 2E-14 4.2E-19 135.9 11.5 116 36-176 2-119 (951)
2 KOG0207 Cation transport ATPas 99.5 7E-14 1.5E-18 132.2 12.4 122 30-175 70-195 (951)
3 PRK10671 copA copper exporting 99.4 3.9E-12 8.4E-17 123.0 15.5 138 29-170 3-143 (834)
4 PF00403 HMA: Heavy-metal-asso 99.3 6.6E-12 1.4E-16 83.2 6.8 45 130-174 1-46 (62)
5 PF00403 HMA: Heavy-metal-asso 99.2 8.7E-11 1.9E-15 77.8 8.0 59 32-91 1-62 (62)
6 COG2608 CopZ Copper chaperone 99.1 6.3E-10 1.4E-14 76.2 8.2 65 29-94 2-69 (71)
7 COG2608 CopZ Copper chaperone 99.1 3.5E-10 7.6E-15 77.4 6.5 46 128-173 3-49 (71)
8 KOG1603 Copper chaperone [Inor 98.6 2.5E-07 5.4E-12 63.6 7.6 64 28-93 4-68 (73)
9 KOG4656 Copper chaperone for s 98.5 5.2E-07 1.1E-11 73.0 8.0 69 27-97 5-73 (247)
10 COG2217 ZntA Cation transport 98.5 2.3E-07 5.1E-12 88.2 6.0 45 128-173 3-48 (713)
11 KOG1603 Copper chaperone [Inor 98.0 2E-05 4.3E-10 54.0 5.8 44 127-170 5-48 (73)
12 TIGR00003 copper ion binding p 98.0 4.6E-05 1E-09 47.5 6.7 46 128-173 3-49 (68)
13 PLN02957 copper, zinc superoxi 97.8 0.00012 2.7E-09 61.2 9.2 67 29-97 6-72 (238)
14 KOG4656 Copper chaperone for s 97.8 4.3E-05 9.2E-10 62.1 5.5 44 127-170 7-50 (247)
15 PLN02957 copper, zinc superoxi 97.6 0.00018 3.8E-09 60.3 6.9 45 127-171 6-50 (238)
16 COG2217 ZntA Cation transport 97.6 0.00016 3.4E-09 69.2 7.2 64 29-94 2-69 (713)
17 PRK10671 copA copper exporting 97.5 6.7E-05 1.5E-09 73.0 3.2 41 128-170 4-45 (834)
18 PRK11033 zntA zinc/cadmium/mer 97.3 0.0005 1.1E-08 66.3 7.1 47 127-173 53-100 (741)
19 TIGR00003 copper ion binding p 97.1 0.0066 1.4E-07 37.3 8.1 61 30-91 3-66 (68)
20 PRK11033 zntA zinc/cadmium/mer 95.8 0.036 7.9E-07 53.6 7.8 65 28-93 52-117 (741)
21 PRK14054 methionine sulfoxide 94.4 0.041 8.9E-07 43.9 3.3 38 138-175 10-66 (172)
22 TIGR02052 MerP mercuric transp 93.3 0.49 1.1E-05 31.7 6.8 45 128-172 24-69 (92)
23 PRK05528 methionine sulfoxide 93.3 0.1 2.2E-06 41.0 3.6 38 138-175 8-59 (156)
24 cd00371 HMA Heavy-metal-associ 93.1 0.55 1.2E-05 26.1 5.9 41 132-172 3-44 (63)
25 PRK00058 methionine sulfoxide 92.5 0.14 3E-06 42.2 3.5 38 138-175 52-108 (213)
26 PRK13014 methionine sulfoxide 92.4 0.1 2.2E-06 42.2 2.4 37 139-175 16-71 (186)
27 PF01625 PMSR: Peptide methion 91.5 0.28 6E-06 38.5 3.9 37 139-175 8-63 (155)
28 PRK05550 bifunctional methioni 88.6 0.43 9.4E-06 41.0 3.1 38 138-175 134-190 (283)
29 TIGR00401 msrA methionine-S-su 88.3 0.45 9.8E-06 37.1 2.8 38 138-175 7-63 (149)
30 PRK13748 putative mercuric red 88.3 1.3 2.9E-05 41.0 6.4 43 130-172 3-46 (561)
31 COG0225 MsrA Peptide methionin 87.6 0.63 1.4E-05 37.1 3.2 37 139-175 14-69 (174)
32 KOG1635 Peptide methionine sul 84.6 1.1 2.4E-05 35.8 3.2 38 138-175 31-87 (191)
33 TIGR02052 MerP mercuric transp 79.7 15 0.00032 24.2 8.3 62 30-92 24-88 (92)
34 PRK14018 trifunctional thiored 78.4 2 4.4E-05 40.1 3.1 37 139-175 206-260 (521)
35 PF01883 DUF59: Domain of unkn 78.3 4 8.8E-05 27.1 3.9 32 128-159 35-72 (72)
36 COG2177 FtsX Cell division pro 77.7 28 0.00061 30.2 9.8 86 33-159 65-151 (297)
37 PF11410 Antifungal_pept: Anti 68.3 0.91 2E-05 26.7 -1.1 21 178-198 15-35 (36)
38 COG1888 Uncharacterized protei 65.5 47 0.001 23.7 7.3 66 29-95 6-79 (97)
39 PRK10553 assembly protein for 64.8 46 0.001 23.4 7.1 19 142-160 57-75 (87)
40 COG4669 EscJ Type III secretor 64.3 13 0.00028 31.3 4.5 20 142-161 112-131 (246)
41 PF02680 DUF211: Uncharacteriz 62.6 19 0.00041 25.9 4.5 65 28-93 4-75 (95)
42 COG0841 AcrB Cation/multidrug 62.3 36 0.00079 34.5 8.0 116 44-177 64-194 (1009)
43 PF09580 Spore_YhcN_YlaJ: Spor 61.3 15 0.00034 28.7 4.4 33 141-173 77-109 (177)
44 PF01883 DUF59: Domain of unkn 61.1 17 0.00036 24.0 3.9 32 30-61 35-72 (72)
45 PRK13748 putative mercuric red 59.4 57 0.0012 30.2 8.4 63 32-95 3-67 (561)
46 PF03927 NapD: NapD protein; 54.7 67 0.0014 22.0 6.8 32 129-160 41-72 (79)
47 TIGR02945 SUF_assoc FeS assemb 53.4 15 0.00032 26.0 2.8 21 142-162 58-78 (99)
48 TIGR03406 FeS_long_SufT probab 51.7 22 0.00047 28.4 3.7 34 128-161 114-153 (174)
49 PF01514 YscJ_FliF: Secretory 51.5 15 0.00032 30.0 2.8 20 142-161 118-137 (206)
50 PF11405 Inhibitor_I67: Bromel 48.9 6.9 0.00015 22.8 0.3 16 184-199 6-21 (41)
51 TIGR02898 spore_YhcN_YlaJ spor 48.6 34 0.00074 26.9 4.3 33 141-173 56-88 (158)
52 PF00873 ACR_tran: AcrB/AcrD/A 48.5 44 0.00096 33.7 6.2 121 43-178 62-196 (1021)
53 TIGR02544 III_secr_YscJ type I 47.2 18 0.00039 29.3 2.6 20 142-161 110-129 (193)
54 PF13085 Fer2_3: 2Fe-2S iron-s 45.7 9.1 0.0002 28.2 0.6 17 171-187 43-59 (110)
55 PRK11026 ftsX cell division AB 45.4 1.7E+02 0.0036 25.3 8.6 92 31-160 68-164 (309)
56 PF13193 AMP-binding_C: AMP-bi 45.3 23 0.0005 23.2 2.6 17 143-159 1-17 (73)
57 cd00729 rubredoxin_SM Rubredox 44.1 17 0.00037 20.9 1.5 20 181-200 4-25 (34)
58 PRK15348 type III secretion sy 42.6 23 0.0005 29.9 2.7 22 141-162 109-130 (249)
59 PF09360 zf-CDGSH: Iron-bindin 40.8 14 0.00031 21.8 0.9 15 175-189 17-31 (38)
60 TIGR00489 aEF-1_beta translati 40.5 29 0.00063 24.5 2.5 22 139-160 62-83 (88)
61 PF07649 C1_3: C1-like domain; 40.1 8.5 0.00018 21.2 -0.2 20 181-200 2-22 (30)
62 cd04888 ACT_PheB-BS C-terminal 38.1 37 0.0008 22.0 2.7 32 128-159 42-74 (76)
63 PF04579 Keratin_matx: Keratin 37.7 12 0.00025 26.5 0.1 9 178-186 23-31 (97)
64 smart00362 RRM_2 RNA recogniti 37.1 95 0.0021 18.7 4.9 42 131-172 2-48 (72)
65 PRK11152 ilvM acetolactate syn 37.0 1.4E+02 0.0029 20.4 6.5 60 76-159 16-75 (76)
66 PF13008 zf-Paramyx-P: Zinc-bi 37.0 20 0.00042 22.4 1.1 19 174-199 25-43 (47)
67 TIGR03406 FeS_long_SufT probab 36.6 84 0.0018 25.0 4.9 49 31-85 115-169 (174)
68 COG2151 PaaD Predicted metal-s 36.4 37 0.00081 25.1 2.7 21 141-161 69-89 (111)
69 PRK10555 aminoglycoside/multid 35.9 30 0.00064 35.1 2.7 38 141-178 159-196 (1037)
70 PF04438 zf-HIT: HIT zinc fing 35.6 11 0.00025 21.0 -0.1 16 181-199 4-19 (30)
71 PF02682 AHS1: Allophanate hyd 34.5 80 0.0017 25.6 4.6 36 138-175 24-61 (202)
72 PRK15324 type III secretion sy 34.0 35 0.00077 28.9 2.5 22 142-163 111-132 (252)
73 COG3062 NapD Uncharacterized p 33.9 1.8E+02 0.0039 20.9 6.4 26 44-70 21-46 (94)
74 PF03076 GP3: Equine arteritis 33.6 6.8 0.00015 29.5 -1.6 41 137-177 106-146 (160)
75 PF08777 RRM_3: RNA binding mo 33.4 1.2E+02 0.0026 21.8 5.0 43 130-172 3-46 (105)
76 PTZ00423 glideosome-associated 31.1 26 0.00056 27.4 1.1 19 181-200 164-182 (193)
77 PF01206 TusA: Sulfurtransfera 30.9 88 0.0019 20.2 3.6 23 130-152 2-25 (70)
78 PF14437 MafB19-deam: MafB19-l 30.7 1.3E+02 0.0029 23.3 5.0 39 28-67 99-139 (146)
79 PF11918 DUF3436: Domain of un 30.5 34 0.00074 22.1 1.4 21 152-175 6-26 (55)
80 PRK00435 ef1B elongation facto 30.2 48 0.001 23.4 2.3 23 138-160 61-83 (88)
81 TIGR00915 2A0602 The (Largely 28.5 45 0.00097 33.9 2.6 37 142-178 160-196 (1044)
82 KOG3813 Uncharacterized conser 28.4 7.1 0.00015 36.3 -2.7 44 142-187 275-318 (640)
83 PRK15127 multidrug efflux syst 27.8 48 0.001 33.7 2.7 37 142-178 160-196 (1049)
84 PF09987 DUF2226: Uncharacteri 26.9 87 0.0019 27.2 3.7 35 142-184 226-260 (297)
85 PF12677 DUF3797: Domain of un 26.9 27 0.00059 21.9 0.5 11 179-189 13-23 (49)
86 PF08478 POTRA_1: POTRA domain 26.4 51 0.0011 21.2 1.8 28 142-169 37-65 (69)
87 PRK12575 succinate dehydrogena 25.6 41 0.00089 28.1 1.5 17 171-187 47-63 (235)
88 PF03434 DUF276: DUF276 ; Int 25.5 1E+02 0.0022 26.2 3.7 28 142-169 90-117 (291)
89 TIGR02159 PA_CoA_Oxy4 phenylac 25.3 95 0.0021 24.0 3.4 33 128-161 26-64 (146)
90 PRK10614 multidrug efflux syst 24.8 56 0.0012 33.1 2.5 37 142-178 160-197 (1025)
91 PF00736 EF1_GNE: EF-1 guanine 23.8 98 0.0021 21.8 3.0 22 139-160 62-84 (89)
92 PRK14054 methionine sulfoxide 23.5 1.4E+02 0.003 23.7 4.1 28 40-67 10-37 (172)
93 cd00292 EF1B Elongation factor 23.5 80 0.0017 22.2 2.4 22 139-160 62-83 (88)
94 PF06155 DUF971: Protein of un 23.2 2.5E+02 0.0055 19.2 5.2 33 156-188 2-41 (89)
95 smart00704 ZnF_CDGSH CDGSH-typ 23.1 47 0.001 19.6 1.0 13 177-189 14-26 (38)
96 PRK09577 multidrug efflux prot 22.8 67 0.0015 32.6 2.7 37 142-178 159-195 (1032)
97 PRK10503 multidrug efflux syst 22.8 65 0.0014 32.7 2.5 37 142-178 169-206 (1040)
98 PF06898 YqfD: Putative stage 21.8 4.2E+02 0.009 23.6 7.3 29 142-170 146-175 (385)
99 KOG3456 NADH:ubiquinone oxidor 21.6 31 0.00067 25.4 0.0 9 182-190 107-115 (120)
100 PF13291 ACT_4: ACT domain; PD 21.2 2.4E+02 0.0052 18.5 4.5 33 28-60 47-79 (80)
101 PF05478 Prominin: Prominin; 20.7 43 0.00094 33.0 0.8 25 174-199 113-140 (806)
102 PF05207 zf-CSL: CSL zinc fing 20.5 43 0.00092 21.4 0.5 9 176-184 17-25 (55)
103 COG2092 EFB1 Translation elong 20.4 88 0.0019 22.2 2.1 23 138-160 61-83 (88)
104 KOG3848 Extracellular protein 20.3 56 0.0012 29.8 1.3 32 167-200 310-341 (516)
No 1
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=99.56 E-value=2e-14 Score=135.86 Aligned_cols=116 Identities=22% Similarity=0.376 Sum_probs=103.2
Q ss_pred eccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC-CCChHHHHHHHHhhcCCeeeecCCCCCCCCCCCCchhHHhh
Q 029022 36 DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELISPLPKPPPPDADDQEKKEQ 114 (200)
Q Consensus 36 ~M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~-~~~~~~i~~~i~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~ 114 (200)
+|+|..|+..|+.+++..+||.++.+++..+++.|.++ ..+++.|.+.|+ ++||++.+.+....
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~~-------------- 66 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSEI-------------- 66 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCcc--------------
Confidence 49999999999999999999999999999999999873 578999999999 89999987643211
Q ss_pred hhhcccCCCCcceEEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeee
Q 029022 115 QKVEKKEEPPAAITVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMC 176 (200)
Q Consensus 115 ~~~~~~~~~~~~~~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~ 176 (200)
...+..|.| ||+|++|++.||+.|++..||.++.|.+...++.|.|||..+-
T Consensus 67 ----------~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s 119 (951)
T KOG0207|consen 67 ----------TASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTS 119 (951)
T ss_pred ----------ccceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccC
Confidence 123678999 8999999999999999999999999999999999999998764
No 2
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=99.53 E-value=7e-14 Score=132.19 Aligned_cols=122 Identities=23% Similarity=0.402 Sum_probs=106.9
Q ss_pred eEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC--CCChHHHHHHHHhhcCCeeeecCCCCCCCCCCC
Q 029022 30 EIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRKVELISPLPKPPPPDA 106 (200)
Q Consensus 30 ~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~--~~~~~~i~~~i~~~~G~~a~~~~~~~~~~~~~~ 106 (200)
+..++++ |+|.+|++.|++.|++++|+.++.+.+...++.+.++ .+.++.+.+.++ ++||.+.++......
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie-~~gf~a~~i~~~~~~----- 143 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIE-DLGFSAELIESVNGN----- 143 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHH-hcCccceehhcccCC-----
Confidence 5679998 9999999999999999999999999999999999762 468899999999 899998866421110
Q ss_pred CchhHHhhhhhcccCCCCcceEEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCCee
Q 029022 107 DDQEKKEQQKVEKKEEPPAAITVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLM 175 (200)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~ 175 (200)
...++.|.| ||+|++|+.+||+.|.+++||.+++|+++++++.|.|||..+
T Consensus 144 ------------------~~~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~ 195 (951)
T KOG0207|consen 144 ------------------SNQKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEIT 195 (951)
T ss_pred ------------------CCCcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEeccccc
Confidence 013689999 899999999999999999999999999999999999999865
No 3
>PRK10671 copA copper exporting ATPase; Provisional
Probab=99.42 E-value=3.9e-12 Score=122.97 Aligned_cols=138 Identities=16% Similarity=0.273 Sum_probs=98.5
Q ss_pred ceEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcCCeeeecCCCCCCC-CCCC
Q 029022 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELISPLPKPP-PPDA 106 (200)
Q Consensus 29 ~~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G~~a~~~~~~~~~~-~~~~ 106 (200)
.+.+|.|+ |+|++|+.+|+++|++++||..+.+++. +..+.+ ..+.+.+...++ ++||.+.+..+..... ....
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~-~~~~~~i~~~i~-~~Gy~~~~~~~~~~~~~~~~~ 78 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTG-TASAEALIETIK-QAGYDASVSHPKAKPLTESSI 78 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEe-cCCHHHHHHHHH-hcCCccccccccccccccccc
Confidence 45789998 9999999999999999999999999994 455655 568899999998 8999988653211100 0000
Q ss_pred CchhHHhhhhhcccCCCCcceEEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEE
Q 029022 107 DDQEKKEQQKVEKKEEPPAAITVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYY 170 (200)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~y 170 (200)
..+.....+............++.|.| ||+|++|+..|++.|.+++||.++.+|+.++++.|.+
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~ 143 (834)
T PRK10671 79 PSEALTAASEELPAATADDDDSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMG 143 (834)
T ss_pred CchhhhhhhhhccccccCcCceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEc
Confidence 000000000000000011123577889 8999999999999999999999999999999988874
No 4
>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=99.31 E-value=6.6e-12 Score=83.23 Aligned_cols=45 Identities=22% Similarity=0.378 Sum_probs=42.9
Q ss_pred EEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCCe
Q 029022 130 VLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNL 174 (200)
Q Consensus 130 ~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~ 174 (200)
+|.| ||+|++|+.+|+++|.++|||.++.|||.+++++|.|++..
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~ 46 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDK 46 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTT
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCC
Confidence 5889 89999999999999999999999999999999999998764
No 5
>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=99.21 E-value=8.7e-11 Score=77.79 Aligned_cols=59 Identities=34% Similarity=0.574 Sum_probs=53.3
Q ss_pred EEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC--CCChHHHHHHHHhhcCCe
Q 029022 32 VLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRK 91 (200)
Q Consensus 32 ~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~--~~~~~~i~~~i~~~~G~~ 91 (200)
+|.|. |+|++|+.+|+++|.+++||.++.+|+.+++++|.++ .+++++|.++|+ ++||+
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 58896 9999999999999999999999999999999999872 346799999999 79984
No 6
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.09 E-value=6.3e-10 Score=76.19 Aligned_cols=65 Identities=29% Similarity=0.484 Sum_probs=57.2
Q ss_pred ceEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC--CCChHHHHHHHHhhcCCeeee
Q 029022 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRKVEL 94 (200)
Q Consensus 29 ~~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~--~~~~~~i~~~i~~~~G~~a~~ 94 (200)
....|++. |+|++|+.+|+++|.+++||.+++++|..+++.|.++ .++.++|.++|+ .+||.+..
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~ 69 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEE 69 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeee
Confidence 35689997 9999999999999999999999999999988887652 468999999999 79998753
No 7
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.08 E-value=3.5e-10 Score=77.44 Aligned_cols=46 Identities=17% Similarity=0.279 Sum_probs=43.7
Q ss_pred EEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCC
Q 029022 128 TVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLN 173 (200)
Q Consensus 128 ~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~ 173 (200)
+..|.| ||+|.+|+.+|+++|.+++||.++.|||..+++.|+||+.
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~ 49 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSN 49 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCC
Confidence 478999 9999999999999999999999999999999999999874
No 8
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.60 E-value=2.5e-07 Score=63.56 Aligned_cols=64 Identities=48% Similarity=0.893 Sum_probs=56.5
Q ss_pred cceEEEEEeccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcC-Ceee
Q 029022 28 TPEIVLKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSG-RKVE 93 (200)
Q Consensus 28 ~~~~~~~V~M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G-~~a~ 93 (200)
.....+.++|+|.+|..+|.+.|..+.||.++.++...++++|.+ .+++..++..+.+ .| ....
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g-~~~p~~vl~~l~k-~~~k~~~ 68 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKG-NVDPVKLLKKLKK-TGGKRAE 68 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEE-ecCHHHHHHHHHh-cCCCceE
Confidence 456788889999999999999999999999999999999999999 6899999999984 54 4443
No 9
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.50 E-value=5.2e-07 Score=73.00 Aligned_cols=69 Identities=29% Similarity=0.530 Sum_probs=62.6
Q ss_pred CcceEEEEEeccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcCCeeeecCC
Q 029022 27 ETPEIVLKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELISP 97 (200)
Q Consensus 27 ~~~~~~~~V~M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G~~a~~~~~ 97 (200)
++.++.|.|.|+|.+|+..|+..|..++||.++.+++..+.+.|.+ ...+..|...|+ ..|.++.+...
T Consensus 5 ~~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~t-s~p~s~i~~~le-~tGr~Avl~G~ 73 (247)
T KOG4656|consen 5 DTYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVET-SVPPSEIQNTLE-NTGRDAVLRGA 73 (247)
T ss_pred CceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEc-cCChHHHHHHHH-hhChheEEecC
Confidence 4567899999999999999999999999999999999999999988 778999999999 79999877644
No 10
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.46 E-value=2.3e-07 Score=88.20 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=42.9
Q ss_pred EEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCC
Q 029022 128 TVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLN 173 (200)
Q Consensus 128 ~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~ 173 (200)
+..|.| ||+|++|+++|| +|.+++||.++.|||+++++.|.||+.
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~ 48 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPE 48 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEeccc
Confidence 578999 999999999999 999999999999999999999999975
No 11
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=97.98 E-value=2e-05 Score=54.01 Aligned_cols=44 Identities=30% Similarity=0.434 Sum_probs=40.9
Q ss_pred eEEEEEeeccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEE
Q 029022 127 ITVVLNVRMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYY 170 (200)
Q Consensus 127 ~~~~l~IgM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~y 170 (200)
...++.+.|||.+|+.+|.+.|..+.||.++.+++..++++|.-
T Consensus 5 ~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g 48 (73)
T KOG1603|consen 5 KTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKG 48 (73)
T ss_pred cEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEE
Confidence 35778889999999999999999999999999999999999974
No 12
>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=97.95 E-value=4.6e-05 Score=47.52 Aligned_cols=46 Identities=13% Similarity=0.294 Sum_probs=42.4
Q ss_pred EEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCC
Q 029022 128 TVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLN 173 (200)
Q Consensus 128 ~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~ 173 (200)
+..+.| ||+|.+|+..|++.+.+.+++..+.+++....+.|.|++.
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAP 49 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCC
Confidence 356889 8999999999999999999999999999999999999764
No 13
>PLN02957 copper, zinc superoxide dismutase
Probab=97.83 E-value=0.00012 Score=61.20 Aligned_cols=67 Identities=31% Similarity=0.490 Sum_probs=58.5
Q ss_pred ceEEEEEeccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcCCeeeecCC
Q 029022 29 PEIVLKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELISP 97 (200)
Q Consensus 29 ~~~~~~V~M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G~~a~~~~~ 97 (200)
.++.|.+.|+|.+|+.+|++.|.+++||..+.+++..+++.|.+ ..+...+...++ ++||.+.++..
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~-~~~~~~I~~aIe-~~Gy~a~~~~~ 72 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLG-SSPVKAMTAALE-QTGRKARLIGQ 72 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEe-cCCHHHHHHHHH-HcCCcEEEecC
Confidence 44567778999999999999999999999999999999999987 567888889998 79999876654
No 14
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=97.79 E-value=4.3e-05 Score=62.07 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=41.2
Q ss_pred eEEEEEeeccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEE
Q 029022 127 ITVVLNVRMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYY 170 (200)
Q Consensus 127 ~~~~l~IgM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~y 170 (200)
-+++|.|.|||.+|+..|.+.|..++||.++.|++..+.+.|.-
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~t 50 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVET 50 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEc
Confidence 36789999999999999999999999999999999999999874
No 15
>PLN02957 copper, zinc superoxide dismutase
Probab=97.62 E-value=0.00018 Score=60.25 Aligned_cols=45 Identities=16% Similarity=0.362 Sum_probs=41.8
Q ss_pred eEEEEEeeccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEc
Q 029022 127 ITVVLNVRMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYS 171 (200)
Q Consensus 127 ~~~~l~IgM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~yd 171 (200)
+.+.|.++|+|.+|+.+|+++|.+++||..+.+|+..+++.|.|+
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~ 50 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS 50 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec
Confidence 467788899999999999999999999999999999999999983
No 16
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.61 E-value=0.00016 Score=69.22 Aligned_cols=64 Identities=28% Similarity=0.542 Sum_probs=55.2
Q ss_pred ceEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC--CCC-hHHHHHHHHhhcCCeeee
Q 029022 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TAD-PIKVCERLQKKSGRKVEL 94 (200)
Q Consensus 29 ~~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~--~~~-~~~i~~~i~~~~G~~a~~ 94 (200)
.+..|.+. |+|++|+.+|+ +|.+++||..+.+|+.++++.|.++ ..+ .+.+...++ ..||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 35679998 99999999999 9999999999999999999999873 234 678888998 79998753
No 17
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.50 E-value=6.7e-05 Score=73.05 Aligned_cols=41 Identities=12% Similarity=0.184 Sum_probs=36.6
Q ss_pred EEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEE
Q 029022 128 TVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYY 170 (200)
Q Consensus 128 ~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~y 170 (200)
+++|.| ||+|++|+.+|+++|.+++||.++.|||. +++|++
T Consensus 4 ~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~ 45 (834)
T PRK10671 4 TIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTG 45 (834)
T ss_pred EEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEe
Confidence 578999 89999999999999999999999999995 455554
No 18
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.35 E-value=0.0005 Score=66.25 Aligned_cols=47 Identities=17% Similarity=0.250 Sum_probs=44.1
Q ss_pred eEEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCC
Q 029022 127 ITVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLN 173 (200)
Q Consensus 127 ~~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~ 173 (200)
.+..|.| ||+|++|+..|++.|.+++||.++.+|+.++++.|.|++.
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~ 100 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADND 100 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEeccc
Confidence 4678999 8999999999999999999999999999999999999875
No 19
>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=97.07 E-value=0.0066 Score=37.31 Aligned_cols=61 Identities=23% Similarity=0.441 Sum_probs=48.4
Q ss_pred eEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC--CCChHHHHHHHHhhcCCe
Q 029022 30 EIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRK 91 (200)
Q Consensus 30 ~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~--~~~~~~i~~~i~~~~G~~ 91 (200)
+..+.+. |+|.+|+..++..+...+++....+++....+.+.++ ..+...+...+. ..||.
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~ 66 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYE 66 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCC
Confidence 4568897 9999999999999999999999999999998888752 235556656565 56764
No 20
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=95.75 E-value=0.036 Score=53.59 Aligned_cols=65 Identities=29% Similarity=0.453 Sum_probs=51.7
Q ss_pred cceEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcCCeee
Q 029022 28 TPEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVE 93 (200)
Q Consensus 28 ~~~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G~~a~ 93 (200)
..+..+.+. |+|++|+..++..+.+++||..+.+++.+.++.+.++......+...++ ..||.+.
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~ 117 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLR 117 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcccccc
Confidence 446678897 9999999999999999999999999999999888752112255666676 6888754
No 21
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=94.44 E-value=0.041 Score=43.92 Aligned_cols=38 Identities=13% Similarity=0.251 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHhccCCeeEEEeecCCcE-------------------EEEEEcCCee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHSHFPLI-------------------LQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vnlat~~-------------------a~V~ydp~~~ 175 (200)
++|=+-+|..+.+++||.++.|-++.+. +.|+|||..|
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~i 66 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVI 66 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcC
Confidence 3677889999999999999999877665 8899999865
No 22
>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=93.35 E-value=0.49 Score=31.73 Aligned_cols=45 Identities=22% Similarity=0.354 Sum_probs=39.2
Q ss_pred EEEEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcC
Q 029022 128 TVVLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSL 172 (200)
Q Consensus 128 ~~~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp 172 (200)
+..+.+ +|.|..|...++..+...+|+..+.+++......+.|++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDD 69 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECC
Confidence 456778 899999999999999999999999999999887777654
No 23
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=93.34 E-value=0.1 Score=41.01 Aligned_cols=38 Identities=8% Similarity=0.215 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHhccCCeeEEEeecCCc--------------EEEEEEcCCee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHSHFPL--------------ILQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vnlat~--------------~a~V~ydp~~~ 175 (200)
++|=+-+|..+.+++||.++.|-++.+ .+.|+|||..|
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~i 59 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMV 59 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcC
Confidence 467888999999999999999976543 37899999865
No 24
>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=93.06 E-value=0.55 Score=26.06 Aligned_cols=41 Identities=20% Similarity=0.280 Sum_probs=35.0
Q ss_pred Ee-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcC
Q 029022 132 NV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSL 172 (200)
Q Consensus 132 ~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp 172 (200)
.+ +|.|..|...++..+...+|+....+++......+.|++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDP 44 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECC
Confidence 35 789999999999999999999888888888877777754
No 25
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=92.51 E-value=0.14 Score=42.21 Aligned_cols=38 Identities=13% Similarity=0.295 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHhccCCeeEEEeecCC-------------------cEEEEEEcCCee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHSHFP-------------------LILQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vnlat-------------------~~a~V~ydp~~~ 175 (200)
++|=+-+|..+.+++||.++.|-++. +.+.|+|||..|
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~I 108 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVI 108 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccC
Confidence 35678889999999999999998873 458899999854
No 26
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=92.36 E-value=0.1 Score=42.22 Aligned_cols=37 Identities=16% Similarity=0.185 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhccCCeeEEEeecCCcE-------------------EEEEEcCCee
Q 029022 139 ACAQGLRKRIRKIQGIYFHWHSHFPLI-------------------LQIYYSLNLM 175 (200)
Q Consensus 139 sCa~~IE~aL~~~~GV~~a~Vnlat~~-------------------a~V~ydp~~~ 175 (200)
+|=+-+|..+.+++||.++.|-++.+. +.|+|||..|
T Consensus 16 GCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~i 71 (186)
T PRK13014 16 GCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQV 71 (186)
T ss_pred CCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcC
Confidence 466778999999999999999876654 7899999854
No 27
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=91.47 E-value=0.28 Score=38.50 Aligned_cols=37 Identities=14% Similarity=0.298 Sum_probs=31.4
Q ss_pred hHHHHHHHHHhccCCeeEEEeecCCc-------------------EEEEEEcCCee
Q 029022 139 ACAQGLRKRIRKIQGIYFHWHSHFPL-------------------ILQIYYSLNLM 175 (200)
Q Consensus 139 sCa~~IE~aL~~~~GV~~a~Vnlat~-------------------~a~V~ydp~~~ 175 (200)
+|=+.+|..+.+++||.++.|-++.+ .+.|+|||..|
T Consensus 8 GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~i 63 (155)
T PF01625_consen 8 GCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVI 63 (155)
T ss_dssp SSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS
T ss_pred CCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcc
Confidence 57788999999999999999987554 56899999865
No 28
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=88.56 E-value=0.43 Score=41.02 Aligned_cols=38 Identities=11% Similarity=0.154 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHhccCCeeEEEeecCCc-------------------EEEEEEcCCee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHSHFPL-------------------ILQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vnlat~-------------------~a~V~ydp~~~ 175 (200)
.+|=+-+|..+.+++||.++.|-++.+ .+.|+|||..|
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~i 190 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKI 190 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccC
Confidence 356788999999999999999976544 47899999865
No 29
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=88.35 E-value=0.45 Score=37.08 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHhccCCeeEEEeecC-------------------CcEEEEEEcCCee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHSHF-------------------PLILQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vnla-------------------t~~a~V~ydp~~~ 175 (200)
.+|=+-+|..+.+++||.++.+-++ .+.+.|+|||..|
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~i 63 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVI 63 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcC
Confidence 3677889999999999999998643 3456788999865
No 30
>PRK13748 putative mercuric reductase; Provisional
Probab=88.29 E-value=1.3 Score=41.01 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=38.7
Q ss_pred EEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcC
Q 029022 130 VLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSL 172 (200)
Q Consensus 130 ~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp 172 (200)
.+.+ +|+|++|...++..+..++|+..+.+++..+...+.|++
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~ 46 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEV 46 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECC
Confidence 4668 899999999999999999999999999999998888754
No 31
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=87.57 E-value=0.63 Score=37.11 Aligned_cols=37 Identities=14% Similarity=0.263 Sum_probs=29.6
Q ss_pred hHHHHHHHHHhccCCeeEEEeecCCc-------------------EEEEEEcCCee
Q 029022 139 ACAQGLRKRIRKIQGIYFHWHSHFPL-------------------ILQIYYSLNLM 175 (200)
Q Consensus 139 sCa~~IE~aL~~~~GV~~a~Vnlat~-------------------~a~V~ydp~~~ 175 (200)
+|=|-+|+.+.++|||.++.+-++.+ .+.|+|||.+|
T Consensus 14 GCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~i 69 (174)
T COG0225 14 GCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVI 69 (174)
T ss_pred cCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccc
Confidence 56677899999999999998875544 46788998765
No 32
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=84.60 E-value=1.1 Score=35.76 Aligned_cols=38 Identities=11% Similarity=0.251 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHhccCCeeEEEeecCC-------------------cEEEEEEcCCee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHSHFP-------------------LILQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vnlat-------------------~~a~V~ydp~~~ 175 (200)
++|-+.+|.+..++|||..-+|-++. +.++|.|||..+
T Consensus 31 ~GCFWg~E~a~~~l~gV~~T~vGYagG~~~nPtYk~vc~~tT~HaEvvrV~ydpk~~ 87 (191)
T KOG1635|consen 31 AGCFWGVELAYQRLPGVVRTEVGYAGGITDNPTYKDVCSGTTNHAEVVRVQYDPKVI 87 (191)
T ss_pred ccchhhHHHHHhhcCCeEEEeecccCCccCCcchhhhccCCCCcceEEEEEeCcccc
Confidence 36789999999999999999997654 356788888754
No 33
>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=79.67 E-value=15 Score=24.19 Aligned_cols=62 Identities=26% Similarity=0.362 Sum_probs=43.0
Q ss_pred eEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC--CCChHHHHHHHHhhcCCee
Q 029022 30 EIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRKV 92 (200)
Q Consensus 30 ~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~--~~~~~~i~~~i~~~~G~~a 92 (200)
++.+.+. +.|..|...++..+...+++....+++......+... ..+...+...+. ..||..
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~ 88 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPS 88 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCe
Confidence 3456676 9999999999999999999888888887777655421 124444444444 466654
No 34
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=78.38 E-value=2 Score=40.06 Aligned_cols=37 Identities=16% Similarity=0.280 Sum_probs=30.3
Q ss_pred hHHHHHHHHHhccCCeeEEEeecCCc------------------EEEEEEcCCee
Q 029022 139 ACAQGLRKRIRKIQGIYFHWHSHFPL------------------ILQIYYSLNLM 175 (200)
Q Consensus 139 sCa~~IE~aL~~~~GV~~a~Vnlat~------------------~a~V~ydp~~~ 175 (200)
+|=+-+|..+.+++||.++.|-++.+ .+.|+|||..|
T Consensus 206 GCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~i 260 (521)
T PRK14018 206 GCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKL 260 (521)
T ss_pred CCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcC
Confidence 56788899999999999999976544 47889999865
No 35
>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=78.26 E-value=4 Score=27.08 Aligned_cols=32 Identities=16% Similarity=0.370 Sum_probs=21.6
Q ss_pred EEEEEeeccChhH------HHHHHHHHhccCCeeEEEe
Q 029022 128 TVVLNVRMHCEAC------AQGLRKRIRKIQGIYFHWH 159 (200)
Q Consensus 128 ~~~l~IgM~CasC------a~~IE~aL~~~~GV~~a~V 159 (200)
++.|.+.++.++| ...|+.+|..++||.+|.|
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 4556564444444 4789999999999999876
No 36
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=77.65 E-value=28 Score=30.17 Aligned_cols=86 Identities=16% Similarity=0.188 Sum_probs=54.3
Q ss_pred EEEeccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcCCeee-ecCCCCCCCCCCCCchhH
Q 029022 33 LKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVE-LISPLPKPPPPDADDQEK 111 (200)
Q Consensus 33 ~~V~M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G~~a~-~~~~~~~~~~~~~~~~~~ 111 (200)
++++.+ ..|...++..+.+++||.+++. .+.++-.+.+++.+|+... ..+..|-
T Consensus 65 L~~~~~-~~~~~~v~~~i~~~~gV~~v~~-------------~sre~~l~~L~~~lg~~~~~~l~~nPL----------- 119 (297)
T COG2177 65 LQIDAD-QDDAALVREKIEGIPGVKSVRF-------------ISREEALKELQPWLGFGALLMLDENPL----------- 119 (297)
T ss_pred EecCCC-hHHHHHHHHHHhcCCCcceEEE-------------eCHHHHHHHHHHHcCchhhhcCCCCCC-----------
Confidence 333344 8899999999999999988765 2555555555546776511 1111111
Q ss_pred HhhhhhcccCCCCcceEEEEEeeccChhHHHHHHHHHhccCCeeEEEe
Q 029022 112 KEQQKVEKKEEPPAAITVVLNVRMHCEACAQGLRKRIRKIQGIYFHWH 159 (200)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~~l~IgM~CasCa~~IE~aL~~~~GV~~a~V 159 (200)
.+.+.+++ +=+.=...+.++|+.++||.+|+-
T Consensus 120 --------------P~~~vV~~--~~p~~~~~i~~~l~~l~gV~~V~~ 151 (297)
T COG2177 120 --------------PDVFVVTP--DDPPQVKAIAAALRDLPGVAEVDD 151 (297)
T ss_pred --------------CceEEEEe--CCCccHHHHHHHHHcCccceehhc
Confidence 11233333 115556899999999999998764
No 37
>PF11410 Antifungal_pept: Antifungal peptide; InterPro: IPR024206 This peptide has six cysteines involved in three disulphide bonds. The presence of a 'disulphide through disulphide knot' structurally defines this protein as a knottin: the peptide contains a global fold which involves a cysteine-knotted three-stranded antiparallel beta-sheet along with a flexible loop and four beta-reverse turns. It also has an amphiphilic character which is the main structural basis of its biological function []. The peptides in this entry belong to the AMP family. ; PDB: 1DKC_A 1Q3J_A.
Probab=68.28 E-value=0.91 Score=26.71 Aligned_cols=21 Identities=33% Similarity=0.611 Sum_probs=15.5
Q ss_pred eeccccccCCCCCCCCCCCcc
Q 029022 178 YYCRCGVCGNQPSQWPGNCKR 198 (200)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~ 198 (200)
-+|-||||-.+|-+=+|.|++
T Consensus 15 g~CcSg~C~q~~g~~~G~Ck~ 35 (36)
T PF11410_consen 15 GNCCSGFCLQEPGWSYGVCKN 35 (36)
T ss_dssp ---TTSEEEEETTTTCEEEE-
T ss_pred cccccceeEecCCCcCCeeec
Confidence 478899999999888998874
No 38
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=65.47 E-value=47 Score=23.75 Aligned_cols=66 Identities=23% Similarity=0.340 Sum_probs=41.7
Q ss_pred ceEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeec-----CCc--eeEeeCCCCChHHHHHHHHhhcCCeeeec
Q 029022 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADS-----KAS--KVVVKGKTADPIKVCERLQKKSGRKVELI 95 (200)
Q Consensus 29 ~~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l-----~~~--~~~V~~~~~~~~~i~~~i~~~~G~~a~~~ 95 (200)
.++++.+. -+=..-.--+-..|++++||..|.+.+ .+. +++|.+..++.+.|...|+ ..|..+..+
T Consensus 6 RRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSi 79 (97)
T COG1888 6 RRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSI 79 (97)
T ss_pred eeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeeh
Confidence 34455553 222233345567788889887776553 333 4445565789999999999 788766533
No 39
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=64.81 E-value=46 Score=23.41 Aligned_cols=19 Identities=11% Similarity=0.130 Sum_probs=11.8
Q ss_pred HHHHHHHhccCCeeEEEee
Q 029022 142 QGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vn 160 (200)
...-+.|..+|||.++..-
T Consensus 57 ~~~i~~I~~l~GVlsa~lV 75 (87)
T PRK10553 57 LQTIESVRNVEGVLAVSLV 75 (87)
T ss_pred HHHHHHHHcCCCceEEEEE
Confidence 3444556777788777653
No 40
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=64.32 E-value=13 Score=31.28 Aligned_cols=20 Identities=20% Similarity=0.268 Sum_probs=17.9
Q ss_pred HHHHHHHhccCCeeEEEeec
Q 029022 142 QGLRKRIRKIQGIYFHWHSH 161 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnl 161 (200)
..||+.|++++||.+++|..
T Consensus 112 Q~le~tLs~mDGVi~ArV~I 131 (246)
T COG4669 112 QQLEQTLSKMDGVISARVHI 131 (246)
T ss_pred HHHHHHHHhcCceEEEEEEE
Confidence 78999999999999998863
No 41
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=62.58 E-value=19 Score=25.89 Aligned_cols=65 Identities=23% Similarity=0.361 Sum_probs=42.0
Q ss_pred cceEEEEEeccCHhHHHHHHHHHhcCCCccEEEeec-----CCcee--EeeCCCCChHHHHHHHHhhcCCeee
Q 029022 28 TPEIVLKVDMHCEACARKVARALKGFEGVDDITADS-----KASKV--VVKGKTADPIKVCERLQKKSGRKVE 93 (200)
Q Consensus 28 ~~~~~~~V~M~C~~Ca~~Ie~~L~~l~GV~~v~v~l-----~~~~~--~V~~~~~~~~~i~~~i~~~~G~~a~ 93 (200)
..+++|.+-.--..-.-.+...|.+++||..+.+.+ .+..+ +|.|..++.+.|.++|+ ..|-.+.
T Consensus 4 irRlVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IH 75 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIH 75 (95)
T ss_dssp EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEE
T ss_pred eeEEEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEE
Confidence 345666665223334456778899999998887664 34433 34565689999999999 7886654
No 42
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=62.29 E-value=36 Score=34.51 Aligned_cols=116 Identities=14% Similarity=0.268 Sum_probs=63.5
Q ss_pred HHHHHHHhcCCCccEEEeecCCceeEe--eCC-CCChH----HHHHHHHhhcCCeeeecCCCCCCCCCCCCchhHHhhhh
Q 029022 44 RKVARALKGFEGVDDITADSKASKVVV--KGK-TADPI----KVCERLQKKSGRKVELISPLPKPPPPDADDQEKKEQQK 116 (200)
Q Consensus 44 ~~Ie~~L~~l~GV~~v~v~l~~~~~~V--~~~-~~~~~----~i~~~i~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~ 116 (200)
..||++|..++|+..++-.-..+...| +.+ ..|++ ++.+++. ++... ++.+...+.-
T Consensus 64 ~piE~~l~~i~gi~~i~S~S~~G~s~itv~F~~~~d~d~A~~~V~~kv~-~~~~~---LP~~~~~p~v------------ 127 (1009)
T COG0841 64 QPIEQQLNGLDGLDYMSSTSSSGSSSITVTFELGTDPDTAAVQVQNKIQ-QAESR---LPSGVQQPGV------------ 127 (1009)
T ss_pred HHHHHHHhcCCCccEEEEEEcCCcEEEEEEEeCCCChHHHHHHHHHHHH-HHHhc---CCCccCCCce------------
Confidence 568999999999988766554454444 431 34555 4555554 22111 1111000000
Q ss_pred hcccCCCCcceEEEEEe-e--ccC----hhHHHHHHHHHhccCCeeEEEeecC-CcEEEEEEcCCeeee
Q 029022 117 VEKKEEPPAAITVVLNV-R--MHC----EACAQGLRKRIRKIQGIYFHWHSHF-PLILQIYYSLNLMCC 177 (200)
Q Consensus 117 ~~~~~~~~~~~~~~l~I-g--M~C----asCa~~IE~aL~~~~GV~~a~Vnla-t~~a~V~ydp~~~~~ 177 (200)
.+.......-..|.+ + +.= ..=...|...|++++||.++.+.=. ...++|..||..+..
T Consensus 128 --~~~~~~~~~i~~~al~s~~~~~~~l~~~~~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~ 194 (1009)
T COG0841 128 --TVEKSSSNPLLILALTSTTDSSSDLTDYAASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAA 194 (1009)
T ss_pred --EeccCCCceEEEEEEEcCCCChHHHHHHHHHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHH
Confidence 000001111233444 2 330 1224569999999999999998754 677889999976543
No 43
>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=61.27 E-value=15 Score=28.67 Aligned_cols=33 Identities=15% Similarity=0.093 Sum_probs=30.0
Q ss_pred HHHHHHHHhccCCeeEEEeecCCcEEEEEEcCC
Q 029022 141 AQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLN 173 (200)
Q Consensus 141 a~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~ 173 (200)
+..|.+.+.+++||.+|.|=.....|.|.|++.
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~ 109 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYVAVDLD 109 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEEEEEec
Confidence 579999999999999999999999999998765
No 44
>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=61.13 E-value=17 Score=24.00 Aligned_cols=32 Identities=22% Similarity=0.574 Sum_probs=20.9
Q ss_pred eEEEEEeccCHhHH------HHHHHHHhcCCCccEEEe
Q 029022 30 EIVLKVDMHCEACA------RKVARALKGFEGVDDITA 61 (200)
Q Consensus 30 ~~~~~V~M~C~~Ca------~~Ie~~L~~l~GV~~v~v 61 (200)
++.|.+.+..++|. ..|+.+|+.++||.+++|
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 44555555555554 568889999999998875
No 45
>PRK13748 putative mercuric reductase; Provisional
Probab=59.42 E-value=57 Score=30.21 Aligned_cols=63 Identities=22% Similarity=0.377 Sum_probs=46.0
Q ss_pred EEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCC-CCChHHHHHHHHhhcCCeeeec
Q 029022 32 VLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELI 95 (200)
Q Consensus 32 ~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~-~~~~~~i~~~i~~~~G~~a~~~ 95 (200)
.+.+. |+|.+|...++..+...+++....+++......+.+. ..+...+...+. ..||.....
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~ 67 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLA 67 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeecc
Confidence 35576 9999999999999999999988888888887666531 234455555555 577765443
No 46
>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=54.69 E-value=67 Score=21.98 Aligned_cols=32 Identities=13% Similarity=0.167 Sum_probs=17.6
Q ss_pred EEEEeeccChhHHHHHHHHHhccCCeeEEEee
Q 029022 129 VVLNVRMHCEACAQGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 129 ~~l~IgM~CasCa~~IE~aL~~~~GV~~a~Vn 160 (200)
+.+.|.-....-....-++|..+|||.++..-
T Consensus 41 iVVtiE~~~~~~~~~~~~~i~~l~GVlsa~lv 72 (79)
T PF03927_consen 41 IVVTIEAESSEEEVDLIDAINALPGVLSASLV 72 (79)
T ss_dssp EEEEEEESSHHHHHHHHHHHCCSTTEEEEEES
T ss_pred EEEEEEeCChHHHHHHHHHHHcCCCceEEEEE
Confidence 34444222333344455567788888877653
No 47
>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=53.40 E-value=15 Score=25.99 Aligned_cols=21 Identities=10% Similarity=0.077 Sum_probs=18.2
Q ss_pred HHHHHHHhccCCeeEEEeecC
Q 029022 142 QGLRKRIRKIQGIYFHWHSHF 162 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnla 162 (200)
..|+.+|..++|+.++.|++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 458889999999999999875
No 48
>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=51.72 E-value=22 Score=28.40 Aligned_cols=34 Identities=6% Similarity=0.177 Sum_probs=23.9
Q ss_pred EEEEEeeccChhHH------HHHHHHHhccCCeeEEEeec
Q 029022 128 TVVLNVRMHCEACA------QGLRKRIRKIQGIYFHWHSH 161 (200)
Q Consensus 128 ~~~l~IgM~CasCa------~~IE~aL~~~~GV~~a~Vnl 161 (200)
++.+.+.++-++|. ..|+.+|..++||.++.|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 34555544544443 55899999999999998864
No 49
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=51.50 E-value=15 Score=30.02 Aligned_cols=20 Identities=20% Similarity=0.205 Sum_probs=18.6
Q ss_pred HHHHHHHhccCCeeEEEeec
Q 029022 142 QGLRKRIRKIQGIYFHWHSH 161 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnl 161 (200)
..|++.|..++||.+|+|++
T Consensus 118 ~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 118 GELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHcCCCeeEEEEEE
Confidence 68999999999999999985
No 50
>PF11405 Inhibitor_I67: Bromelain inhibitor VI; InterPro: IPR022713 Bromelain inhibitor VI is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain. ; PDB: 2BI6_H 1BI6_H.
Probab=48.87 E-value=6.9 Score=22.79 Aligned_cols=16 Identities=44% Similarity=0.991 Sum_probs=7.4
Q ss_pred ccCCCCCCCCCCCccC
Q 029022 184 VCGNQPSQWPGNCKRC 199 (200)
Q Consensus 184 ~~~~~~~~~~~~~~~~ 199 (200)
||...-|.-||.||.|
T Consensus 6 yctdtysdcpgfcktc 21 (41)
T PF11405_consen 6 YCTDTYSDCPGFCKTC 21 (41)
T ss_dssp EE----SS--TT-SSE
T ss_pred EeecccccCchHHHHH
Confidence 4567778999999988
No 51
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ 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 that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=48.64 E-value=34 Score=26.87 Aligned_cols=33 Identities=12% Similarity=-0.020 Sum_probs=29.6
Q ss_pred HHHHHHHHhccCCeeEEEeecCCcEEEEEEcCC
Q 029022 141 AQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLN 173 (200)
Q Consensus 141 a~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~ 173 (200)
+.+|.+.+.++|||.+|.+=.....|.|-|+..
T Consensus 56 A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv~~~ 88 (158)
T TIGR02898 56 ADEIASEAAKVKGVKDATVVITGNYAYVGVDLT 88 (158)
T ss_pred HHHHHHHHhcCCCCceEEEEEECCEEEEEEEcC
Confidence 578999999999999999988999999999754
No 52
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=48.45 E-value=44 Score=33.65 Aligned_cols=121 Identities=19% Similarity=0.247 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCccEEEeecCCceeEee----CCCCChHHHHHHHHhhcCCeeeecCCCCCCCCCCCCchhHHhhhhhc
Q 029022 43 ARKVARALKGFEGVDDITADSKASKVVVK----GKTADPIKVCERLQKKSGRKVELISPLPKPPPPDADDQEKKEQQKVE 118 (200)
Q Consensus 43 a~~Ie~~L~~l~GV~~v~v~l~~~~~~V~----~~~~~~~~i~~~i~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (200)
...+|++|+.++||.+++-.-..+...+. . ..|.+.....++.+. ..+.+.-| .+-..+.-
T Consensus 62 t~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f~~-~~d~~~a~~~v~~~i---~~~~~~LP-----------~~~~~p~i 126 (1021)
T PF00873_consen 62 TKPLEEALSSVEGVKEIRSTSREGSSSITVEFDD-GTDIDEALQEVREKI---DQIRSDLP-----------PGVEEPQI 126 (1021)
T ss_dssp HHHHHHTHCSSTTEEEEEEEETTSEEEEEEEEST-TS-HHHHHHHHHHHH---HHHGGGS------------HHHHHHEE
T ss_pred HHHHHHHHcCCCCeEEEEEEecCCcEEEEEEecc-ccCHHHHHHHHHHHH---HhhhhhCc-----------ccccCCce
Q ss_pred ccCCCCcceEEEEEeecc---------ChhHHHHHHHHHhccCCeeEEEee-cCCcEEEEEEcCCeeeee
Q 029022 119 KKEEPPAAITVVLNVRMH---------CEACAQGLRKRIRKIQGIYFHWHS-HFPLILQIYYSLNLMCCY 178 (200)
Q Consensus 119 ~~~~~~~~~~~~l~IgM~---------CasCa~~IE~aL~~~~GV~~a~Vn-lat~~a~V~ydp~~~~~~ 178 (200)
.........-..|.+.-. -..-...|+..|.++|||..+++. .....+.|.+||+.+-.|
T Consensus 127 ~~~~~~~~~i~~~~l~~~~~~~~~~~l~~~~~~~l~~~L~~i~gV~~v~~~G~~~~ei~i~~d~~kl~~~ 196 (1021)
T PF00873_consen 127 FKFDPSDSPIMILALTSDDGTLDLKELRDYAEEQLKPRLERIPGVARVDISGGREREIQIELDPEKLAAY 196 (1021)
T ss_dssp EEEEEECCEEEEEEEEESSSSS-HHHHHHHHHHCTHHHHHTSTTEEEEEESSS--EEEEEEE-HHHHHHT
T ss_pred eeccCCCceeEEEEeccCCCCCCHHHHHHHHHHHHHHhccceeEEEEEEeccchhhhhhheechhhhhhh
No 53
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=47.21 E-value=18 Score=29.28 Aligned_cols=20 Identities=20% Similarity=0.268 Sum_probs=18.3
Q ss_pred HHHHHHHhccCCeeEEEeec
Q 029022 142 QGLRKRIRKIQGIYFHWHSH 161 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnl 161 (200)
..+++.|..++||.+|+|++
T Consensus 110 ~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 110 QRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHhcCCeeeeEEEE
Confidence 68899999999999999986
No 54
>PF13085 Fer2_3: 2Fe-2S iron-sulfur cluster binding domain; PDB: 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N 1KF6_B 3P4P_N 3P4S_B 1L0V_B 1ZOY_B ....
Probab=45.67 E-value=9.1 Score=28.25 Aligned_cols=17 Identities=41% Similarity=0.985 Sum_probs=10.8
Q ss_pred cCCeeeeeeccccccCC
Q 029022 171 SLNLMCCYYCRCGVCGN 187 (200)
Q Consensus 171 dp~~~~~~~~~~~~~~~ 187 (200)
||.+.--+-||.|+||.
T Consensus 43 D~sLafr~sCr~giCGs 59 (110)
T PF13085_consen 43 DPSLAFRYSCRSGICGS 59 (110)
T ss_dssp -TT--B--SSSSSSSST
T ss_pred CCCeEEEecCCCCCCCC
Confidence 78888889999999984
No 55
>PRK11026 ftsX cell division ABC transporter subunit FtsX; Provisional
Probab=45.35 E-value=1.7e+02 Score=25.33 Aligned_cols=92 Identities=16% Similarity=0.226 Sum_probs=53.3
Q ss_pred EEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHHhhcCCee--eecCCCCCCCCCCCC
Q 029022 31 IVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKV--ELISPLPKPPPPDAD 107 (200)
Q Consensus 31 ~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~~~~G~~a--~~~~~~~~~~~~~~~ 107 (200)
+.+.+. -.-..=...+.+.|++.+||.+++. ++.++..+.+++..|++. +.....|-
T Consensus 68 i~vyl~~~~~~~~~~~l~~~L~~~~~V~~v~~-------------vskeeal~~l~~~~g~~~~l~~l~~nPL------- 127 (309)
T PRK11026 68 LTVYLDKTLDDDAANAVVEQLKAEDGVEKVNY-------------LSREEALGEFRNWSGFGGALDMLEENPL------- 127 (309)
T ss_pred EEEEECCCCCHHHHHHHHHHHhCCCCcceEEE-------------ECHHHHHHHHHHhhCchHHHhhCcCCCC-------
Confidence 333343 3334455688899999999987764 355665555543334321 11111111
Q ss_pred chhHHhhhhhcccCCCCcceEEEEEe--eccChhHHHHHHHHHhccCCeeEEEee
Q 029022 108 DQEKKEQQKVEKKEEPPAAITVVLNV--RMHCEACAQGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~~~~~l~I--gM~CasCa~~IE~aL~~~~GV~~a~Vn 160 (200)
...+.+.+ +.+=+.=...|.+.|.++|||.+++.+
T Consensus 128 ------------------P~si~V~~~~~~~~~~~~~~i~~~l~~~~~V~~v~~~ 164 (309)
T PRK11026 128 ------------------PAVAIIIPKLDFQSSEKLNTLRDRLAQIKGVDEVRMD 164 (309)
T ss_pred ------------------CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCceeecC
Confidence 11234444 344556678999999999999987654
No 56
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=45.28 E-value=23 Score=23.23 Aligned_cols=17 Identities=12% Similarity=0.087 Sum_probs=15.1
Q ss_pred HHHHHHhccCCeeEEEe
Q 029022 143 GLRKRIRKIQGIYFHWH 159 (200)
Q Consensus 143 ~IE~aL~~~~GV~~a~V 159 (200)
.||.+|.++|||.++.|
T Consensus 1 EIE~~l~~~~~V~~~~V 17 (73)
T PF13193_consen 1 EIESVLRQHPGVAEAAV 17 (73)
T ss_dssp HHHHHHHTSTTEEEEEE
T ss_pred CHHHHHhcCCCccEEEE
Confidence 38999999999999876
No 57
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=44.11 E-value=17 Score=20.85 Aligned_cols=20 Identities=35% Similarity=0.846 Sum_probs=14.2
Q ss_pred cccccCCC--CCCCCCCCccCC
Q 029022 181 RCGVCGNQ--PSQWPGNCKRCS 200 (200)
Q Consensus 181 ~~~~~~~~--~~~~~~~~~~~~ 200 (200)
+|.+||.. -...|..|..|.
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg 25 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICG 25 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCC
Confidence 57788876 234788888874
No 58
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=42.63 E-value=23 Score=29.92 Aligned_cols=22 Identities=9% Similarity=0.108 Sum_probs=19.6
Q ss_pred HHHHHHHHhccCCeeEEEeecC
Q 029022 141 AQGLRKRIRKIQGIYFHWHSHF 162 (200)
Q Consensus 141 a~~IE~aL~~~~GV~~a~Vnla 162 (200)
...+++.|..++||.+|+|+++
T Consensus 109 egELarTI~~idgV~~ArVhL~ 130 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTIA 130 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEEE
Confidence 3789999999999999999864
No 59
>PF09360 zf-CDGSH: Iron-binding zinc finger CDGSH type; InterPro: IPR018967 This entry represents iron-sulphur domain containing proteins that have a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. The CDGSH-type domain binds a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family []. CDGSH-type domains are found in mitoNEET, an iron-containing integral protein of the outer mitochondrian membrane (OMM). MitoNEET forms a dimeric structure with a NEET fold, and contains two domains: a beta-cap region and a cluster-binding domain that coordinated two acid-labile 2Fe-2S clusters (one bound to each protomer) []. The CDGSH iron-sulphur domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, (IPR019610 from INTERPRO) [, ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM. ; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 3TBO_A 3FNV_B 3TBM_B 3TBN_A 3S2R_A 3S2Q_A 3LPQ_A 2QH7_A 3EW0_A 2R13_A ....
Probab=40.82 E-value=14 Score=21.78 Aligned_cols=15 Identities=40% Similarity=0.840 Sum_probs=9.5
Q ss_pred eeeeeccccccCCCC
Q 029022 175 MCCYYCRCGVCGNQP 189 (200)
Q Consensus 175 ~~~~~~~~~~~~~~~ 189 (200)
.=-++||||.=.|+|
T Consensus 17 ~~~~lC~Cg~S~~~P 31 (38)
T PF09360_consen 17 GTYALCRCGKSKNKP 31 (38)
T ss_dssp SEEEE-SSS--TTTT
T ss_pred CEEEEecCCCCCCCC
Confidence 445789999998887
No 60
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=40.46 E-value=29 Score=24.54 Aligned_cols=22 Identities=9% Similarity=0.095 Sum_probs=19.1
Q ss_pred hHHHHHHHHHhccCCeeEEEee
Q 029022 139 ACAQGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 139 sCa~~IE~aL~~~~GV~~a~Vn 160 (200)
.-...||.+|++++||+++.|-
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 4458999999999999999874
No 61
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=40.14 E-value=8.5 Score=21.21 Aligned_cols=20 Identities=35% Similarity=1.044 Sum_probs=9.3
Q ss_pred cccccCCCCCC-CCCCCccCC
Q 029022 181 RCGVCGNQPSQ-WPGNCKRCS 200 (200)
Q Consensus 181 ~~~~~~~~~~~-~~~~~~~~~ 200 (200)
+|..|+..-+. |.-.|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECD 22 (30)
T ss_dssp --TTTS----S--EEE-TTT-
T ss_pred cCCcCCCcCCCCceEECccCC
Confidence 47789888877 998888873
No 62
>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=38.14 E-value=37 Score=22.01 Aligned_cols=32 Identities=16% Similarity=0.163 Sum_probs=23.4
Q ss_pred EEEEEeeccChh-HHHHHHHHHhccCCeeEEEe
Q 029022 128 TVVLNVRMHCEA-CAQGLRKRIRKIQGIYFHWH 159 (200)
Q Consensus 128 ~~~l~IgM~Cas-Ca~~IE~aL~~~~GV~~a~V 159 (200)
.+.|.|...=.. =...|-++|+++|||.+|.+
T Consensus 42 ~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 42 NVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 455555434443 67899999999999999875
No 63
>PF04579 Keratin_matx: Keratin, high-sulphur matrix protein; InterPro: IPR007659 This is a family of keratins, high-sulphur matrix proteins. The keratin products of mammalian epidermal derivatives such as wool and hair consist of microfibrils embedded in a rigid matrix of other proteins. The matrix proteins include the high-sulphur and high-tyrosine keratins, having molecular weights of 6-20 kDa, whereas microfibrils contain the larger, low-sulphur keratins (40-56 kDa) [].; GO: 0005198 structural molecule activity, 0045095 keratin filament
Probab=37.71 E-value=12 Score=26.49 Aligned_cols=9 Identities=67% Similarity=1.560 Sum_probs=7.5
Q ss_pred eeccccccC
Q 029022 178 YYCRCGVCG 186 (200)
Q Consensus 178 ~~~~~~~~~ 186 (200)
-.||||||-
T Consensus 23 k~CrCGVCL 31 (97)
T PF04579_consen 23 KCCRCGVCL 31 (97)
T ss_pred ccccCceec
Confidence 379999995
No 64
>smart00362 RRM_2 RNA recognition motif.
Probab=37.09 E-value=95 Score=18.67 Aligned_cols=42 Identities=12% Similarity=-0.004 Sum_probs=31.1
Q ss_pred EEe-eccChhHHHHHHHHHhccCCeeEEEeecCC----cEEEEEEcC
Q 029022 131 LNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFP----LILQIYYSL 172 (200)
Q Consensus 131 l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat----~~a~V~ydp 172 (200)
+.| |+....-...|.+.+...-.|..+.+.... +.+.|+|.-
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~ 48 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFES 48 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCC
Confidence 345 565555668889999888888888877665 788888843
No 65
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=37.05 E-value=1.4e+02 Score=20.43 Aligned_cols=60 Identities=15% Similarity=0.089 Sum_probs=41.9
Q ss_pred ChHHHHHHHHhhcCCeeeecCCCCCCCCCCCCchhHHhhhhhcccCCCCcceEEEEEeeccChhHHHHHHHHHhccCCee
Q 029022 76 DPIKVCERLQKKSGRKVELISPLPKPPPPDADDQEKKEQQKVEKKEEPPAAITVVLNVRMHCEACAQGLRKRIRKIQGIY 155 (200)
Q Consensus 76 ~~~~i~~~i~~~~G~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~IgM~CasCa~~IE~aL~~~~GV~ 155 (200)
-...+...++ +-||.++-++.++.. .+...+++|.++ -......|.+.|.|+.+|.
T Consensus 16 VL~Ri~~lf~-rRGfnI~sl~v~~t~---------------------~~~~sriti~v~--~~~~i~ql~kQL~KL~dV~ 71 (76)
T PRK11152 16 VLERVLRVVR-HRGFQVCSMNMTQNT---------------------DAQNINIELTVA--SERPIDLLSSQLNKLVDVA 71 (76)
T ss_pred HHHHHHHHHh-cCCeeeeeEEeeecC---------------------CCCEEEEEEEEC--CCchHHHHHHHHhcCcCeE
Confidence 4566777777 689998766443311 111345666664 4788899999999999999
Q ss_pred EEEe
Q 029022 156 FHWH 159 (200)
Q Consensus 156 ~a~V 159 (200)
.+.+
T Consensus 72 ~V~~ 75 (76)
T PRK11152 72 HVEI 75 (76)
T ss_pred EEEE
Confidence 8876
No 66
>PF13008 zf-Paramyx-P: Zinc-binding domain of Paramyxoviridae V protein; InterPro: IPR024279 The paramyxoviruses, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT []. The P mRNA encodes a variety of proteins beyond P. Protein V consists of PNT fused to a C-terminal zinc-binding region. This conserved region consists of the two-zinc-binding section sandwiched between beta sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction []. In the Henipavirus family, which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation [].; GO: 0046872 metal ion binding; PDB: 2HYE_B 2B5L_D.
Probab=37.01 E-value=20 Score=22.43 Aligned_cols=19 Identities=37% Similarity=0.891 Sum_probs=9.7
Q ss_pred eeeeeeccccccCCCCCCCCCCCccC
Q 029022 174 LMCCYYCRCGVCGNQPSQWPGNCKRC 199 (200)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (200)
..=++-|+||-| |..|.+|
T Consensus 25 ~p~r~~C~CG~C-------P~~C~~C 43 (47)
T PF13008_consen 25 TPRREKCTCGEC-------PRICSLC 43 (47)
T ss_dssp S-EEE--SSTTS--------S--SSS
T ss_pred ccEEeeEECCCC-------cchhhhh
Confidence 344788999988 6667776
No 67
>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=36.63 E-value=84 Score=25.04 Aligned_cols=49 Identities=10% Similarity=0.229 Sum_probs=30.8
Q ss_pred EEEEEeccCHhHH------HHHHHHHhcCCCccEEEeecCCceeEeeCCCCChHHHHHHHH
Q 029022 31 IVLKVDMHCEACA------RKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQ 85 (200)
Q Consensus 31 ~~~~V~M~C~~Ca------~~Ie~~L~~l~GV~~v~v~l~~~~~~V~~~~~~~~~i~~~i~ 85 (200)
+.+.+.++-++|. ..|+.+|.+++||.++.|++. ... .++.+.+.+..+
T Consensus 115 V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~-----~dp-~W~~~~~s~~ar 169 (174)
T TIGR03406 115 VDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELV-----FDP-PWSREMMSEAAK 169 (174)
T ss_pred EEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEE-----ecC-CCChHHCCHHHH
Confidence 4455545555554 458889999999998888652 222 456665555443
No 68
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=36.42 E-value=37 Score=25.08 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=18.7
Q ss_pred HHHHHHHHhccCCeeEEEeec
Q 029022 141 AQGLRKRIRKIQGIYFHWHSH 161 (200)
Q Consensus 141 a~~IE~aL~~~~GV~~a~Vnl 161 (200)
...++.+|..++||.++.|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 578999999999999999864
No 69
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=35.93 E-value=30 Score=35.10 Aligned_cols=38 Identities=8% Similarity=0.136 Sum_probs=31.3
Q ss_pred HHHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeeee
Q 029022 141 AQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCCY 178 (200)
Q Consensus 141 a~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~~ 178 (200)
+..|+..|.+++||.++.++-....++|.+||...-.|
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~ 196 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSF 196 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHc
Confidence 36689999999999999998666678999999765544
No 70
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=35.60 E-value=11 Score=21.04 Aligned_cols=16 Identities=56% Similarity=1.595 Sum_probs=10.0
Q ss_pred cccccCCCCCCCCCCCccC
Q 029022 181 RCGVCGNQPSQWPGNCKRC 199 (200)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~ 199 (200)
.|.+||+ ++.+ .|.+|
T Consensus 4 ~C~vC~~-~~kY--~Cp~C 19 (30)
T PF04438_consen 4 LCSVCGN-PAKY--RCPRC 19 (30)
T ss_dssp EETSSSS-EESE--E-TTT
T ss_pred CCccCcC-CCEE--ECCCc
Confidence 3778888 5543 66666
No 71
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=34.54 E-value=80 Score=25.62 Aligned_cols=36 Identities=17% Similarity=0.122 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHhc--cCCeeEEEeecCCcEEEEEEcCCee
Q 029022 138 EACAQGLRKRIRK--IQGIYFHWHSHFPLILQIYYSLNLM 175 (200)
Q Consensus 138 asCa~~IE~aL~~--~~GV~~a~Vnlat~~a~V~ydp~~~ 175 (200)
..-+..+.++|.+ ++||.++.-.+. ++.|.|||..+
T Consensus 24 ~~~v~al~~~l~~~~~~gi~e~vp~~~--sllV~fdp~~~ 61 (202)
T PF02682_consen 24 NARVLALARALRAAPLPGIVEVVPAYR--SLLVHFDPLRI 61 (202)
T ss_dssp HHHHHHHHHHHHHHT-TTEEEEEEESS--EEEEEESTTTS
T ss_pred HHHHHHHHHHHhcCCCCCeEEeecccc--EEEEEEcCCcC
Confidence 4556788888888 899998876555 89999999865
No 72
>PRK15324 type III secretion system lipoprotein PrgK; Provisional
Probab=34.01 E-value=35 Score=28.86 Aligned_cols=22 Identities=14% Similarity=0.157 Sum_probs=19.2
Q ss_pred HHHHHHHhccCCeeEEEeecCC
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFP 163 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat 163 (200)
..+++.|..++||.+|+|+++-
T Consensus 111 ~ELarTI~~IdgV~~ARVHl~l 132 (252)
T PRK15324 111 QRLEQSLQTMEGVLSARVHISY 132 (252)
T ss_pred HHHHHHHHhcCCcceEEEEEEC
Confidence 6899999999999999997544
No 73
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=33.93 E-value=1.8e+02 Score=20.88 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=13.0
Q ss_pred HHHHHHHhcCCCccEEEeecCCceeEe
Q 029022 44 RKVARALKGFEGVDDITADSKASKVVV 70 (200)
Q Consensus 44 ~~Ie~~L~~l~GV~~v~v~l~~~~~~V 70 (200)
.+|..+|..+||+.-..-+.. +++.|
T Consensus 21 ~av~~~L~~ip~~EV~~~d~~-GKlVV 46 (94)
T COG3062 21 SAVKTALLAIPGCEVYGEDAE-GKLVV 46 (94)
T ss_pred HHHHHHHhcCCCcEeeccCCC-ceEEE
Confidence 456666666666543333322 44444
No 74
>PF03076 GP3: Equine arteritis virus GP3; InterPro: IPR004310 This entry contains proteins encoded by ORF3 of Equine arteritis virus. They are possible envelope glcoproteins.
Probab=33.58 E-value=6.8 Score=29.51 Aligned_cols=41 Identities=17% Similarity=0.164 Sum_probs=34.9
Q ss_pred ChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeee
Q 029022 137 CEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCC 177 (200)
Q Consensus 137 CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~ 177 (200)
-|||++-+=..+....|.-.++.+|..+-+++..-|.+||-
T Consensus 106 nascvqvvc~~~ns~~glg~~sfsfidedlrlhirptlicw 146 (160)
T PF03076_consen 106 NASCVQVVCNLSNSTAGLGQLSFSFIDEDLRLHIRPTLICW 146 (160)
T ss_pred ccceeeeeeecccCCCCcceEEEEEecccceeecccHHHHH
Confidence 46788777778889999999999999998888888999873
No 75
>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=33.39 E-value=1.2e+02 Score=21.82 Aligned_cols=43 Identities=5% Similarity=0.042 Sum_probs=27.5
Q ss_pred EEEe-eccChhHHHHHHHHHhccCCeeEEEeecCCcEEEEEEcC
Q 029022 130 VLNV-RMHCEACAQGLRKRIRKIQGIYFHWHSHFPLILQIYYSL 172 (200)
Q Consensus 130 ~l~I-gM~CasCa~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp 172 (200)
.|.| |++=.-.-..|...|+.+..|..|.+......+.|+|.-
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~ 46 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKT 46 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECC
Confidence 4666 665555589999999999999999998888999999953
No 76
>PTZ00423 glideosome-associated protein 45; Provisional
Probab=31.08 E-value=26 Score=27.44 Aligned_cols=19 Identities=37% Similarity=0.858 Sum_probs=16.1
Q ss_pred cccccCCCCCCCCCCCccCC
Q 029022 181 RCGVCGNQPSQWPGNCKRCS 200 (200)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~ 200 (200)
||| |+-++..-|.+|+-|.
T Consensus 164 RCG-cdLg~~Hden~CkICr 182 (193)
T PTZ00423 164 RCG-CDLGERHDENACKICR 182 (193)
T ss_pred hhC-CCCCcccCcccCchhc
Confidence 666 7889999999999883
No 77
>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=30.91 E-value=88 Score=20.24 Aligned_cols=23 Identities=13% Similarity=0.382 Sum_probs=18.7
Q ss_pred EEEe-eccChhHHHHHHHHHhccC
Q 029022 130 VLNV-RMHCEACAQGLRKRIRKIQ 152 (200)
Q Consensus 130 ~l~I-gM~CasCa~~IE~aL~~~~ 152 (200)
+|.+ |+.|+...-.+.++|.+++
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~ 25 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP 25 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC
Confidence 5677 8999999999999999974
No 78
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=30.70 E-value=1.3e+02 Score=23.32 Aligned_cols=39 Identities=18% Similarity=0.399 Sum_probs=31.1
Q ss_pred cceEEEEEe-ccCHhHHHHHHHHHhcCCCccEEEeecC-Cce
Q 029022 28 TPEIVLKVD-MHCEACARKVARALKGFEGVDDITADSK-ASK 67 (200)
Q Consensus 28 ~~~~~~~V~-M~C~~Ca~~Ie~~L~~l~GV~~v~v~l~-~~~ 67 (200)
...+++.|+ -.|..|..-|.....++ |+.++.|... +++
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~ 139 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGK 139 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCc
Confidence 456888998 99999998888888776 7888877765 553
No 79
>PF11918 DUF3436: Domain of unknown function (DUF3436); InterPro: IPR024591 This uncharacterised N-terminal domain is associated with the interphotoreceptor retinol-binding protein family. It is about 50 amino acids in length and has two conserved sequence motifs: DPRL and SYEP.
Probab=30.51 E-value=34 Score=22.07 Aligned_cols=21 Identities=24% Similarity=0.154 Sum_probs=15.9
Q ss_pred CCeeEEEeecCCcEEEEEEcCCee
Q 029022 152 QGIYFHWHSHFPLILQIYYSLNLM 175 (200)
Q Consensus 152 ~GV~~a~Vnlat~~a~V~ydp~~~ 175 (200)
.||++ ++...|+.|+|.|..+
T Consensus 6 ~GVQ~---slnDpRL~ISYEP~~~ 26 (55)
T PF11918_consen 6 AGVQS---SLNDPRLVISYEPSYV 26 (55)
T ss_pred ccccc---cccCCCeEEEeCCCCC
Confidence 45554 5788899999999754
No 80
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=30.22 E-value=48 Score=23.43 Aligned_cols=23 Identities=9% Similarity=0.114 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHhccCCeeEEEee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vn 160 (200)
..-...||.+|.+++||+++.|-
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEE
Confidence 46668999999999999999874
No 81
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=28.54 E-value=45 Score=33.87 Aligned_cols=37 Identities=11% Similarity=0.143 Sum_probs=31.0
Q ss_pred HHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeeee
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCCY 178 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~~ 178 (200)
..|+..|.++|||.++.+.-....+.|.+||...-.|
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~ 196 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSY 196 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHc
Confidence 5699999999999999998777778999999765444
No 82
>KOG3813 consensus Uncharacterized conserved protein (tumor-suppressor AXUD1 in humans) [General function prediction only]
Probab=28.44 E-value=7.1 Score=36.28 Aligned_cols=44 Identities=23% Similarity=0.300 Sum_probs=30.7
Q ss_pred HHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeeeeeccccccCC
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCCYYCRCGVCGN 187 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~~~~~~~~~~~ 187 (200)
.+=.++|.+-.||..+.-+-...--.++ +...-|-|+|| |||.-
T Consensus 275 ~rrRraLLkaSGVrkIDaeEK~elralR-nSReeCGCsCr-~~CdP 318 (640)
T KOG3813|consen 275 QRRRRALLKASGVRKIDAEEKDELRALR-NSREECGCSCR-GVCDP 318 (640)
T ss_pred HHHHHHHHHhccccccchhhHHHHHHHH-hhHHhhCCccc-ceeCh
Confidence 5778999999999887755222111122 34678999999 99963
No 83
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=27.85 E-value=48 Score=33.72 Aligned_cols=37 Identities=11% Similarity=0.120 Sum_probs=30.6
Q ss_pred HHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeeee
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCCY 178 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~~ 178 (200)
..|+..|.++|||.++++.-....+.|..||...-.|
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~ 196 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKF 196 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHc
Confidence 4689999999999999997656678999999865544
No 84
>PF09987 DUF2226: Uncharacterized protein conserved in archaea (DUF2226); InterPro: IPR019249 This entry includes hypothetical proteins of unknown function.
Probab=26.92 E-value=87 Score=27.24 Aligned_cols=35 Identities=26% Similarity=0.536 Sum_probs=26.5
Q ss_pred HHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeeeeeccccc
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCCYYCRCGV 184 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~~~~~~~~ 184 (200)
.+|...|.+++|++++.|+ +.|.|+... |+|.|-+
T Consensus 226 ~~i~~~l~~~~~~~d~~v~-----l~i~~~~~~---~~~~~~i 260 (297)
T PF09987_consen 226 EKIKNSLKNILGIQDVLVD-----LKIEYEEGR---YICFCNI 260 (297)
T ss_pred HHHHHHHhcCCCcceeEEE-----EEeeccccc---ccccccc
Confidence 6777889999999999885 467777543 7777643
No 85
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=26.90 E-value=27 Score=21.95 Aligned_cols=11 Identities=55% Similarity=1.585 Sum_probs=9.6
Q ss_pred eccccccCCCC
Q 029022 179 YCRCGVCGNQP 189 (200)
Q Consensus 179 ~~~~~~~~~~~ 189 (200)
||.|..|||+-
T Consensus 13 Y~~Cp~CGN~~ 23 (49)
T PF12677_consen 13 YCKCPKCGNDK 23 (49)
T ss_pred hccCcccCCcE
Confidence 89999999973
No 86
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=26.37 E-value=51 Score=21.15 Aligned_cols=28 Identities=25% Similarity=0.324 Sum_probs=22.0
Q ss_pred HHHHHHHhccCCeeEEEeec-CCcEEEEE
Q 029022 142 QGLRKRIRKIQGIYFHWHSH-FPLILQIY 169 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnl-at~~a~V~ 169 (200)
..+++.|.++|.|.+|.|.. -.+++.|.
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P~~l~I~ 65 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFPNTLEIK 65 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCCCEEEEE
Confidence 78999999999999999984 33455553
No 87
>PRK12575 succinate dehydrogenase iron-sulfur subunit; Provisional
Probab=25.60 E-value=41 Score=28.07 Aligned_cols=17 Identities=35% Similarity=0.712 Sum_probs=12.8
Q ss_pred cCCeeeeeeccccccCC
Q 029022 171 SLNLMCCYYCRCGVCGN 187 (200)
Q Consensus 171 dp~~~~~~~~~~~~~~~ 187 (200)
||.+.--+-||.|+||.
T Consensus 47 d~~l~fr~sCr~giCGs 63 (235)
T PRK12575 47 DETLSYRRSCREGICGS 63 (235)
T ss_pred CCCeeeeccCCCCCCCC
Confidence 55555567899999984
No 88
>PF03434 DUF276: DUF276 ; InterPro: IPR005096 This family is specific to Borrelia burgdorferi (Lyme disease spirochete). The protein is encoded on extrachromosomal DNA and is of unknown function.
Probab=25.45 E-value=1e+02 Score=26.15 Aligned_cols=28 Identities=11% Similarity=0.229 Sum_probs=25.5
Q ss_pred HHHHHHHhccCCeeEEEeecCCcEEEEE
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFPLILQIY 169 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat~~a~V~ 169 (200)
..|.++|..++||..+.+--..+++.+.
T Consensus 90 ~Avk~aLL~~~gv~haNI~SsaGtiniY 117 (291)
T PF03434_consen 90 EAVKSALLNLNGVEHANIKSSAGTINIY 117 (291)
T ss_pred HHHHHHhcCCCCceeeeeecCCCeeEEE
Confidence 7899999999999999998888888875
No 89
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=25.32 E-value=95 Score=23.96 Aligned_cols=33 Identities=24% Similarity=0.391 Sum_probs=21.5
Q ss_pred EEEEEeeccChhHH------HHHHHHHhccCCeeEEEeec
Q 029022 128 TVVLNVRMHCEACA------QGLRKRIRKIQGIYFHWHSH 161 (200)
Q Consensus 128 ~~~l~IgM~CasCa------~~IE~aL~~~~GV~~a~Vnl 161 (200)
.+.+.|-++=.+|. ..|+.+|..+ |+.++.|++
T Consensus 26 ~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i 64 (146)
T TIGR02159 26 GVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVST 64 (146)
T ss_pred EEEEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeE
Confidence 34555544444443 4588899887 998888763
No 90
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=24.82 E-value=56 Score=33.12 Aligned_cols=37 Identities=11% Similarity=-0.036 Sum_probs=30.1
Q ss_pred HHHHHHHhccCCeeEEEeecC-CcEEEEEEcCCeeeee
Q 029022 142 QGLRKRIRKIQGIYFHWHSHF-PLILQIYYSLNLMCCY 178 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnla-t~~a~V~ydp~~~~~~ 178 (200)
..|+..|.++|||.++.++-. ...++|.+||..+-+|
T Consensus 160 ~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~ 197 (1025)
T PRK10614 160 TQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQ 197 (1025)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHc
Confidence 579999999999999998743 4678999999866554
No 91
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=23.81 E-value=98 Score=21.78 Aligned_cols=22 Identities=14% Similarity=0.057 Sum_probs=19.2
Q ss_pred hHHHHHHHHH-hccCCeeEEEee
Q 029022 139 ACAQGLRKRI-RKIQGIYFHWHS 160 (200)
Q Consensus 139 sCa~~IE~aL-~~~~GV~~a~Vn 160 (200)
.-...||.+| +..+||+++.|-
T Consensus 62 ~~~d~lee~i~~~~e~Vqsvei~ 84 (89)
T PF00736_consen 62 GSTDDLEEAIESFEEGVQSVEIE 84 (89)
T ss_dssp CGHHHHHHHHTTCTTTEEEEEEE
T ss_pred cChHHHHHHHHhcCCCccEEEEE
Confidence 4678999999 999999999874
No 92
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=23.52 E-value=1.4e+02 Score=23.74 Aligned_cols=28 Identities=11% Similarity=0.194 Sum_probs=21.6
Q ss_pred HhHHHHHHHHHhcCCCccEEEeecCCce
Q 029022 40 EACARKVARALKGFEGVDDITADSKASK 67 (200)
Q Consensus 40 ~~Ca~~Ie~~L~~l~GV~~v~v~l~~~~ 67 (200)
++|=--++..+.+++||.++.+-.+.+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 3455567788899999999999876664
No 93
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=23.49 E-value=80 Score=22.22 Aligned_cols=22 Identities=14% Similarity=0.057 Sum_probs=19.0
Q ss_pred hHHHHHHHHHhccCCeeEEEee
Q 029022 139 ACAQGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 139 sCa~~IE~aL~~~~GV~~a~Vn 160 (200)
.-...||.+|.+.+||+++.|-
T Consensus 62 ~~td~lee~i~~~d~VqsveI~ 83 (88)
T cd00292 62 GGTDELEEAISEEDGVQSVDVE 83 (88)
T ss_pred cCcHHHHHHHhccCCceEEEEE
Confidence 4458999999999999999874
No 94
>PF06155 DUF971: Protein of unknown function (DUF971); InterPro: IPR010376 This domain is found in gamma-butyrobetaine dioxygenase and trimethyllysine dioxygenase proteins.; PDB: 2L6N_A 3LUU_A 2L6P_A 3MS5_A 3O2G_A 3N6W_A.
Probab=23.21 E-value=2.5e+02 Score=19.18 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=23.2
Q ss_pred EEEeecCCcEEEEEEcCCeeeee-------eccccccCCC
Q 029022 156 FHWHSHFPLILQIYYSLNLMCCY-------YCRCGVCGNQ 188 (200)
Q Consensus 156 ~a~Vnlat~~a~V~ydp~~~~~~-------~~~~~~~~~~ 188 (200)
.++++.....+.|+|+-...-.+ +|+|.-|-+.
T Consensus 2 ~i~l~~~~~~l~i~w~DG~~~~~~~~~LRd~C~Ca~C~~~ 41 (89)
T PF06155_consen 2 EIKLDKDERHLEIEWSDGQESRFPYEWLRDNCPCAECRGE 41 (89)
T ss_dssp EEEEECCTTEEEEEETTSEEEEEEHHHHHHT-SSSSTCST
T ss_pred eEEEecCCCEEEEEECCCCEEEECHHHHhccCCChhhccc
Confidence 46677788889999965554443 5999999853
No 95
>smart00704 ZnF_CDGSH CDGSH-type zinc finger. Function unknown.
Probab=23.13 E-value=47 Score=19.60 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.9
Q ss_pred eeeccccccCCCC
Q 029022 177 CYYCRCGVCGNQP 189 (200)
Q Consensus 177 ~~~~~~~~~~~~~ 189 (200)
-+.||||-=.|+|
T Consensus 14 ~~lC~C~~S~~~P 26 (38)
T smart00704 14 YALCRCGRSKNFP 26 (38)
T ss_pred EEEeeCCCCCCCC
Confidence 4689999988887
No 96
>PRK09577 multidrug efflux protein; Reviewed
Probab=22.81 E-value=67 Score=32.58 Aligned_cols=37 Identities=8% Similarity=0.110 Sum_probs=29.6
Q ss_pred HHHHHHHhccCCeeEEEeecCCcEEEEEEcCCeeeee
Q 029022 142 QGLRKRIRKIQGIYFHWHSHFPLILQIYYSLNLMCCY 178 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnlat~~a~V~ydp~~~~~~ 178 (200)
..|+..|.++|||.++.++-....+.|..||...-.|
T Consensus 159 ~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~ 195 (1032)
T PRK09577 159 ANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAAL 195 (1032)
T ss_pred HHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHc
Confidence 5799999999999999998766667787888754433
No 97
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=22.77 E-value=65 Score=32.75 Aligned_cols=37 Identities=8% Similarity=0.133 Sum_probs=30.1
Q ss_pred HHHHHHHhccCCeeEEEeec-CCcEEEEEEcCCeeeee
Q 029022 142 QGLRKRIRKIQGIYFHWHSH-FPLILQIYYSLNLMCCY 178 (200)
Q Consensus 142 ~~IE~aL~~~~GV~~a~Vnl-at~~a~V~ydp~~~~~~ 178 (200)
..|+..|.++|||.++.+.- ....++|.+||...-.|
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~ 206 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAAL 206 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHc
Confidence 47999999999999998874 34788999999866544
No 98
>PF06898 YqfD: Putative stage IV sporulation protein YqfD; InterPro: IPR010690 This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown [].
Probab=21.80 E-value=4.2e+02 Score=23.65 Aligned_cols=29 Identities=14% Similarity=0.084 Sum_probs=24.9
Q ss_pred HHHHHHH-hccCCeeEEEeecCCcEEEEEE
Q 029022 142 QGLRKRI-RKIQGIYFHWHSHFPLILQIYY 170 (200)
Q Consensus 142 ~~IE~aL-~~~~GV~~a~Vnlat~~a~V~y 170 (200)
..||+.| .++|++..+.|++...++.|..
T Consensus 146 ~~ie~~l~~~~~~i~WV~i~~~GT~l~I~v 175 (385)
T PF06898_consen 146 EEIEKKLRKQFPDISWVGIEIKGTRLIIEV 175 (385)
T ss_pred HHHHHHHHhhCCCeEEEEEEEEeeEEEEEE
Confidence 4677776 4789999999999999999987
No 99
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=21.64 E-value=31 Score=25.43 Aligned_cols=9 Identities=44% Similarity=1.065 Sum_probs=6.7
Q ss_pred ccccCCCCC
Q 029022 182 CGVCGNQPS 190 (200)
Q Consensus 182 ~~~~~~~~~ 190 (200)
|||||++--
T Consensus 107 CgYCGlrf~ 115 (120)
T KOG3456|consen 107 CGYCGLRFV 115 (120)
T ss_pred cccchhhhh
Confidence 789998643
No 100
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=21.22 E-value=2.4e+02 Score=18.46 Aligned_cols=33 Identities=24% Similarity=0.359 Sum_probs=25.1
Q ss_pred cceEEEEEeccCHhHHHHHHHHHhcCCCccEEE
Q 029022 28 TPEIVLKVDMHCEACARKVARALKGFEGVDDIT 60 (200)
Q Consensus 28 ~~~~~~~V~M~C~~Ca~~Ie~~L~~l~GV~~v~ 60 (200)
...+.|.+...-..=...|-..|++++||.+|.
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 445666666666666778889999999998774
No 101
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=20.70 E-value=43 Score=32.98 Aligned_cols=25 Identities=40% Similarity=1.103 Sum_probs=15.0
Q ss_pred eeeeeeccccccCCCCCCC--C-CCCccC
Q 029022 174 LMCCYYCRCGVCGNQPSQW--P-GNCKRC 199 (200)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~--~-~~~~~~ 199 (200)
..|||.| ||-||.--.|- . ..|+|+
T Consensus 113 ~fCcCRC-c~~CGg~~~~~~~~~~~c~R~ 140 (806)
T PF05478_consen 113 CFCCCRC-CGNCGGRMHQRDKKNDACRRG 140 (806)
T ss_pred HHhcccc-CCCcCCccccccccccccchH
Confidence 4567766 78887654333 2 367774
No 102
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=20.49 E-value=43 Score=21.38 Aligned_cols=9 Identities=56% Similarity=1.305 Sum_probs=6.1
Q ss_pred eeeeccccc
Q 029022 176 CCYYCRCGV 184 (200)
Q Consensus 176 ~~~~~~~~~ 184 (200)
=-|-||||-
T Consensus 17 ~~y~CRCG~ 25 (55)
T PF05207_consen 17 YSYPCRCGG 25 (55)
T ss_dssp EEEEETTSS
T ss_pred EEEcCCCCC
Confidence 456788873
No 103
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=20.38 E-value=88 Score=22.18 Aligned_cols=23 Identities=13% Similarity=0.211 Sum_probs=19.4
Q ss_pred hhHHHHHHHHHhccCCeeEEEee
Q 029022 138 EACAQGLRKRIRKIQGIYFHWHS 160 (200)
Q Consensus 138 asCa~~IE~aL~~~~GV~~a~Vn 160 (200)
.+=...+|.+|..+.||.++.|-
T Consensus 61 Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 61 EGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred ccCcHHHHHHHhhccCcceEEEE
Confidence 34578999999999999998863
No 104
>KOG3848 consensus Extracellular protein TEM7, contains PSI domain (tumor endothelial marker in humans) [Extracellular structures]
Probab=20.29 E-value=56 Score=29.80 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=27.3
Q ss_pred EEEEcCCeeeeeeccccccCCCCCCCCCCCccCC
Q 029022 167 QIYYSLNLMCCYYCRCGVCGNQPSQWPGNCKRCS 200 (200)
Q Consensus 167 ~V~ydp~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 (200)
.|.+.|+-+|--|=+|+-|-| |+-+-||--|+
T Consensus 310 aVeltaqPTCLqfn~Cd~C~n--s~ltFnClWC~ 341 (516)
T KOG3848|consen 310 AVELTAQPTCLQFNTCDTCTN--STLTFNCLWCH 341 (516)
T ss_pred eEEeccCCceeccCCcChhhc--cCCCceeehHh
Confidence 477899999999999999988 56779997764
Done!