Query 047402
Match_columns 178
No_of_seqs 136 out of 1063
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 10:45:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047402.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047402hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02386 superoxide dismutase 100.0 4.1E-45 8.8E-50 289.5 15.9 128 45-178 14-152 (152)
2 PLN02642 copper, zinc superoxi 100.0 6.3E-45 1.4E-49 291.3 15.5 127 45-177 20-157 (164)
3 PRK15388 Cu/Zn superoxide dism 100.0 2.2E-41 4.8E-46 273.5 16.7 121 45-176 39-177 (177)
4 PRK10290 superoxide dismutase; 100.0 1.5E-40 3.3E-45 268.1 15.0 119 45-175 37-173 (173)
5 COG2032 SodC Cu/Zn superoxide 100.0 1.3E-37 2.8E-42 250.7 14.8 119 46-175 43-179 (179)
6 KOG0441 Cu2+/Zn2+ superoxide d 100.0 2.8E-37 6.1E-42 243.2 11.9 128 45-178 15-154 (154)
7 cd00305 Cu-Zn_Superoxide_Dismu 100.0 1.3E-36 2.8E-41 238.3 14.7 118 45-175 14-142 (144)
8 PF00080 Sod_Cu: Copper/zinc s 100.0 4.3E-35 9.3E-40 227.7 11.8 118 45-174 12-142 (142)
9 PLN02957 copper, zinc superoxi 100.0 3.8E-31 8.3E-36 222.4 13.0 108 45-177 92-207 (238)
10 KOG4656 Copper chaperone for s 100.0 6.1E-29 1.3E-33 204.4 10.8 112 45-177 94-216 (247)
11 PF07452 CHRD: CHRD domain; I 70.6 13 0.00029 27.2 5.4 34 46-79 21-55 (119)
12 smart00754 CHRD A domain in th 64.5 18 0.00039 26.7 5.0 42 46-87 21-62 (118)
13 TIGR02567 YscW type III secret 59.6 28 0.00061 26.9 5.4 45 16-68 3-47 (124)
14 cd00305 Cu-Zn_Superoxide_Dismu 53.3 5.9 0.00013 30.8 0.7 13 159-171 132-144 (144)
15 PF11008 DUF2846: Protein of u 51.3 38 0.00083 25.0 4.8 22 46-67 25-49 (117)
16 PF07731 Cu-oxidase_2: Multico 36.8 38 0.00082 25.0 2.9 22 59-80 42-63 (138)
17 PF07495 Y_Y_Y: Y_Y_Y domain; 28.0 52 0.0011 21.1 2.1 19 62-80 30-48 (66)
18 PRK15396 murein lipoprotein; P 22.8 63 0.0014 23.0 1.8 20 8-27 5-24 (78)
19 PF09912 DUF2141: Uncharacteri 20.4 1E+02 0.0022 22.8 2.7 21 59-79 41-61 (112)
20 COG3056 Uncharacterized lipopr 20.2 1E+02 0.0022 25.8 2.7 28 4-31 11-38 (204)
21 PRK09967 putative outer membra 20.1 90 0.002 24.6 2.4 22 8-29 3-24 (160)
No 1
>PLN02386 superoxide dismutase [Cu-Zn]
Probab=100.00 E-value=4.1e-45 Score=289.49 Aligned_cols=128 Identities=64% Similarity=0.981 Sum_probs=118.9
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-----CCCccCCCCCCCCCCCCCCCCcccccceEeCCCC-
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-----NDPTLTVLDKNTVLQMMKNCHDCDLGNANVRDDV- 118 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-----aGgH~np~~~~hg~p~~~~~h~GDLgni~~~~~G- 118 (178)
+.|+|+|+|..++.++|+++|+||+||+|+|||||+|||+ +|+||||.++.|+.|++..+|+||||||+++++|
T Consensus 14 v~G~v~f~q~~~g~v~i~~~~~GL~pG~hg~HIHe~Gd~~~g~~SaGgHfnP~~~~Hg~~~~~~~H~GDLgNi~~~~~G~ 93 (152)
T PLN02386 14 VKGTIFFTQEGDGPTTVTGSLSGLKPGLHGFHVHALGDTTNGCMSTGPHFNPAGKEHGAPEDENRHAGDLGNVTVGDDGT 93 (152)
T ss_pred CEEEEEEEEcCCCCEEEEEEEeCCCCCceeEEEeCCCCCCCCcccccCccCCCCCCCCCCCcccCccccccCEEECCCCe
Confidence 4699999998766799999999999999999999999985 4799999999999999889999999999999999
Q ss_pred -----ccceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEeecC
Q 047402 119 -----VDNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIGIQG 178 (178)
Q Consensus 119 -----~~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~~~~ 178 (178)
++++++|.++++|+|||||||+++|||++ ++++.|+++|+||+|||||||+++.
T Consensus 94 a~~~~~~~~~~L~g~~~i~GrslVIHa~~DD~~~------~~~~~s~~~G~aG~RiACgvI~~~~ 152 (152)
T PLN02386 94 ATFTIVDKQIPLTGPNSIVGRAVVVHADPDDLGK------GGHELSKSTGNAGGRVACGIIGLQG 152 (152)
T ss_pred EEEEEECCceEeCCCCccCCcEEEEEccCCCcCC------CcccccccCCCCCceEEEEEEEecC
Confidence 46778888899999999999999999987 8899999999999999999999863
No 2
>PLN02642 copper, zinc superoxide dismutase
Probab=100.00 E-value=6.3e-45 Score=291.30 Aligned_cols=127 Identities=51% Similarity=0.823 Sum_probs=117.8
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-----CCCccCCCCCCCCCCCCCCCCcccccceEeCCCC-
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-----NDPTLTVLDKNTVLQMMKNCHDCDLGNANVRDDV- 118 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-----aGgH~np~~~~hg~p~~~~~h~GDLgni~~~~~G- 118 (178)
++|+|+|+|..++.|+|+++|+||+||+|+|||||+|||+ +|+||||.++.||.|++..||+||||||+++++|
T Consensus 20 v~G~v~f~q~~~g~v~I~~~v~GL~pG~HG~HIHe~Gd~~~g~~SaGgHfNP~~~~HG~~~~~~rH~GDLgNi~a~~~G~ 99 (164)
T PLN02642 20 VRGCLQFVQDIFGTTHVTGKISGLSPGFHGFHIHSFGDTTNGCISTGPHFNPLNRVHGPPNEEERHAGDLGNILAGSDGV 99 (164)
T ss_pred cEEEEEEEECCCCcEEEEEEEcCCCCCceeEEEcCCCcCCCCcccccCcccCCCCcCCCCCcCCCcccccCCEEECCCCe
Confidence 4699999998766799999999999999999999999985 5899999999999999999999999999999999
Q ss_pred -----ccceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEeec
Q 047402 119 -----VDNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIGIQ 177 (178)
Q Consensus 119 -----~~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~~~ 177 (178)
+++.++|.+.++|+|||||||+++|||++ +++|.|+++||||+|||||||+++
T Consensus 100 a~~~~~~~~i~L~g~~~iiGRalVVHa~~DD~~~------~~~~~s~~tGnaG~RiACGVI~~~ 157 (164)
T PLN02642 100 AEILIKDKHIPLSGQYSILGRAVVVHADPDDLGK------GGHKLSKSTGNAGSRVGCGIIGLQ 157 (164)
T ss_pred EEEEEEcCceecCCCCCcCCcEEEEeccCCccCc------CcccccccCCCCCceEEEEEEEec
Confidence 35667888889999999999999999987 889999999999999999999975
No 3
>PRK15388 Cu/Zn superoxide dismutase; Provisional
Probab=100.00 E-value=2.2e-41 Score=273.53 Aligned_cols=121 Identities=24% Similarity=0.312 Sum_probs=105.0
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-------------CCCccCCCCC-CCCCCCCCCCCccccc
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-------------NDPTLTVLDK-NTVLQMMKNCHDCDLG 110 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-------------aGgH~np~~~-~hg~p~~~~~h~GDLg 110 (178)
+.|+++|+|..+ +++|+++++||+||+|||||||+|||+ +|+||||+++ .|+.|++..+|+||||
T Consensus 39 ~~G~v~f~~~~~-gv~I~~~l~GL~pG~HGfHIHe~GdC~~~~~~G~~~~~~SAGgHfNP~~~~~Hg~p~~~~~H~GDLp 117 (177)
T PRK15388 39 NIGEITVSETPY-GLLFTPHLNGLTPGIHGFHVHTNPSCMPGMKDGKEVPALMAGGHLDPEKTGKHLGPYNDKGHLGDLP 117 (177)
T ss_pred eEEEEEEEEcCC-cEEEEEEEcCCCCcceEEEEccCCCccCcccCCCcccccccCCCcCCCCCCCCCCCCCCCCCcCcCc
Confidence 459999999874 599999999999999999999999984 6899999987 7998988889999999
Q ss_pred ceEeCCCCccceee----eCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEee
Q 047402 111 NANVRDDVVDNQIS----LSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIGI 176 (178)
Q Consensus 111 ni~~~~~G~~~~i~----L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~~ 176 (178)
||+++++|+..... +...++|+|||||||+++|||++ .++++||||+|||||||+.
T Consensus 118 Ni~a~~dG~a~~~~~~~~~~~~~~i~GralVIHa~~DD~~~----------~p~~~GnaG~RiACGVI~~ 177 (177)
T PRK15388 118 GLVVNADGTATYPLLAPRLKSLSELKGHSLMIHKGGDNYSD----------KPAPLGGGGARFACGVIEK 177 (177)
T ss_pred CEEECCCccEEEEEEeCCcccCcccCCcEEEEECCCCCCCC----------CCCcCCCCCceEEEEeecC
Confidence 99999999543221 22457999999999999999975 4677999999999999973
No 4
>PRK10290 superoxide dismutase; Provisional
Probab=100.00 E-value=1.5e-40 Score=268.07 Aligned_cols=119 Identities=27% Similarity=0.374 Sum_probs=103.1
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-------------CCCccCCCCC-CCCCCCCCCCCccccc
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-------------NDPTLTVLDK-NTVLQMMKNCHDCDLG 110 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-------------aGgH~np~~~-~hg~p~~~~~h~GDLg 110 (178)
..|+++|+|.++ +|+|+++++||+||+|+|||||+|||+ +|+||||.++ .|+.|+. .+|+||||
T Consensus 37 ~~G~v~f~~~~~-gv~i~~~l~GL~pG~HGfHIHe~Gdc~~~~~~G~~~~~~sAGgHfNP~~~~~hg~p~~-~~H~GDL~ 114 (173)
T PRK10290 37 SIGSVTITETDK-GLEFSPDLKALPPGEHGFHIHAKGSCQPATKDGKASAAEAAGGHLDPQNTGKHEGPEG-AGHLGDLP 114 (173)
T ss_pred eEEEEEEEEcCC-cEEEEEEEcCCCCCceEEEEeCCCccCCcccCCCcccccccCCccCCCCCcCCCCCCC-CCCcCccc
Confidence 359999999974 699999999999999999999999985 5799999998 7888864 68999999
Q ss_pred ceEeCCCCccce-ee---eCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEe
Q 047402 111 NANVRDDVVDNQ-IS---LSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIG 175 (178)
Q Consensus 111 ni~~~~~G~~~~-i~---L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~ 175 (178)
||+++++|+.+. +. +.+.+||+|||||||+++|||++ .++++||||+|||||||+
T Consensus 115 ni~a~~dG~a~~~~~~~~~~~~~~i~GralVIH~~~DD~~~----------~~~~~GnaG~RiACGVI~ 173 (173)
T PRK10290 115 ALVVNNDGKATDPVIAPRLKSLDEVKDKALMVHVGGDNMSD----------QPKPLGGGGERYACGVIK 173 (173)
T ss_pred CEEECCCeeEEEEEEeCCccCccccCCcEEEEECCCCCCCC----------CCCcCCCCcceEEEEeEC
Confidence 999999995432 11 23468999999999999999975 367899999999999995
No 5
>COG2032 SodC Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=1.3e-37 Score=250.73 Aligned_cols=119 Identities=30% Similarity=0.425 Sum_probs=106.6
Q ss_pred eeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-----------CCCccCCC-CCCCCCCCCCCCCcccccceE
Q 047402 46 NRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-----------NDPTLTVL-DKNTVLQMMKNCHDCDLGNAN 113 (178)
Q Consensus 46 ~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-----------aGgH~np~-~~~hg~p~~~~~h~GDLgni~ 113 (178)
-|+|+|++.+. ++.++..+.+|+||+|||||||+|+|+ +||||||. .++|+.|+++.+|.|||+||+
T Consensus 43 vG~vt~~e~~~-g~~~~~~~~~L~pg~hGfHIHe~G~C~pkdgk~~~~~sAGGHfdP~~~~~Hg~p~~~~~H~GDLP~L~ 121 (179)
T COG2032 43 VGTVTITETGY-GLLFTPALGGLPPGEHGFHIHEKGSCTPKDGKPVDFLSAGGHFDPQNTKKHGGPNADGGHAGDLPNLF 121 (179)
T ss_pred eEEEEEeecCC-ceEEeecccCCCCcceeEEecccCCCcCCCCCCcccccccCCcCCccCCCCCCCCCCCCCcCcCcceE
Confidence 48999999986 599999999999999999999999996 47999999 789999999889999999999
Q ss_pred eCCCCc------cceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEe
Q 047402 114 VRDDVV------DNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIG 175 (178)
Q Consensus 114 ~~~~G~------~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~ 175 (178)
++++|+ ++.+++.+..+++|||||||+++|||.+ ...|+|++|+|+|||||+
T Consensus 122 v~~dG~a~~~v~~~~~~l~~l~~v~G~alvIHag~Dd~~~----------~P~p~G~aG~R~ACGVI~ 179 (179)
T COG2032 122 VNADGKATLPVLAPRLKLKGLLEVKGRALVIHAGGDDYST----------QPEPLGGAGARVACGVIK 179 (179)
T ss_pred ECCCCcEEEEEecccceeccccccCCeEEEEEcCCccccC----------CCccCCCCccceeeeeeC
Confidence 999993 4567777889999999999999999975 123399999999999995
No 6
>KOG0441 consensus Cu2+/Zn2+ superoxide dismutase SOD1 [Inorganic ion transport and metabolism]
Probab=100.00 E-value=2.8e-37 Score=243.24 Aligned_cols=128 Identities=48% Similarity=0.729 Sum_probs=118.1
Q ss_pred eeeEEEEEEcCC-CcEEEEEEEeCCCCCceeeEEecCCCCC-----CCCccCCCCCCCCCCCCCCCCcccccceEeCCCC
Q 047402 45 TNRSDDLIMGDG-GQTTVTGSFSGLKPGLHGFHVHALGNTT-----NDPTLTVLDKNTVLQMMKNCHDCDLGNANVRDDV 118 (178)
Q Consensus 45 ~~G~v~F~q~~~-~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-----aGgH~np~~~~hg~p~~~~~h~GDLgni~~~~~G 118 (178)
+.|++.|+|..+ ..+.|++.++||+||+|+||||+|||.+ +|+||||.++.||.|..+.||.||||||.++++|
T Consensus 15 V~G~i~F~Q~~~~~~~~v~~~i~GL~pg~hgfHvHqfGD~t~GC~SaGphFNp~~~~hg~p~~~~rH~gdlGnv~~~~~G 94 (154)
T KOG0441|consen 15 VIGVITFEQFLPGEPLRVSGEVTGLPPGKHGFHVHQFGDNTNGCKSAGPHFNPNKKTHGGPVDEVRHVGDLGNVDAKDDG 94 (154)
T ss_pred ceeEEEEEEcCCCCcEEEEEEEecCCCceeeEEEEeccCCCCChhcCCCCCCCcccCCCCccccccccccccccccCCCc
Confidence 569999999443 4899999999999999999999999965 4699999999999999999999999999999999
Q ss_pred ------ccceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEeecC
Q 047402 119 ------VDNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIGIQG 178 (178)
Q Consensus 119 ------~~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~~~~ 178 (178)
.+..++|++.++|+|||+|||+.+||+++ |..+.|..+||+|+|+|||+|++++
T Consensus 95 ~~~~~~~d~~i~l~g~~sivgrs~vvHa~~ddLg~------G~~~~s~ktgnag~r~aCgvi~~~~ 154 (154)
T KOG0441|consen 95 VISRVFGDSVITLSGPNSIVGRSVVVHAGEDDLGK------GGHELSKKTGNAGARPACGVIGIAG 154 (154)
T ss_pred eEEEEEccceEEEeeccccceeEEEEeccCccccC------CchhhhhhccccCCCccceeeeccC
Confidence 45678899999999999999999999987 9999999999999999999999864
No 7
>cd00305 Cu-Zn_Superoxide_Dismutase Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730].
Probab=100.00 E-value=1.3e-36 Score=238.26 Aligned_cols=118 Identities=37% Similarity=0.559 Sum_probs=107.5
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-----CCCccCCCCCCCCCCCCCCCCcccccceEeCCCC-
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-----NDPTLTVLDKNTVLQMMKNCHDCDLGNANVRDDV- 118 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-----aGgH~np~~~~hg~p~~~~~h~GDLgni~~~~~G- 118 (178)
+.|+|+|+|.++ .++|+++|+||+||+|+|||||+|||+ +|+||||.++.|+.|.+..+|+||||||+++++|
T Consensus 14 v~G~v~f~q~~~-~v~v~~~l~GL~pG~hg~HIHe~Gd~~~~~~saGgh~np~~~~hg~~~~~~~h~GDLgni~~~~~G~ 92 (144)
T cd00305 14 VVGTVTFTQQSG-GVTITGELSGLTPGLHGFHIHEFGDCTNGCTSAGGHFNPFGKKHGGPNDEGRHAGDLGNIVADKDGV 92 (144)
T ss_pred eEEEEEEEECCC-CEEEEEEEECCCCCceeEEEEecCCCCCccccccCccCCCCCCCCCCCCCCCCCCcCCCEEECCCCe
Confidence 469999999986 899999999999999999999999985 5899999999999999899999999999999999
Q ss_pred -----ccceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEe
Q 047402 119 -----VDNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIG 175 (178)
Q Consensus 119 -----~~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~ 175 (178)
.+.+++|++.++++|||||||+.+|||. ++|.|++|.|++||+|-
T Consensus 93 ~~~~~~~~~~~l~~~~~iiGrsivVH~~~Dd~~------------~~p~~~sg~~~~~G~~~ 142 (144)
T cd00305 93 ATVSVLDPLISLKGGNSIIGRSLVVHAGQDDLG------------KGPDELSGGTGNAGVRV 142 (144)
T ss_pred EEEEEEeCcEEcCCCCCcCCcEEEEecCCCCCC------------CCCCcccccceeeEeEE
Confidence 3456778877899999999999999996 47888899999999885
No 8
>PF00080 Sod_Cu: Copper/zinc superoxide dismutase (SODC); InterPro: IPR001424 Superoxide dismutases are ubiquitous metalloproteins that prevent damage by oxygen-mediated free radicals by catalysing the dismutation of superoxide into molecular oxygen and hydrogen peroxide []. Superoxide is a normal by-product of aerobic respiration and is produced by a number of reactions, including oxidative phosphorylation and photosynthesis. The dismutase enzymes have a very high catalytic efficiency due to the attraction of superoxide to the ions bound at the active site [, ]. There are three forms of superoxide dismutase, depending on the metal cofactor: Cu/Zn (which binds both copper and zinc), Fe and Mn types. The Fe and Mn forms are similar in their primary, secondary and tertiary structures, but are distinct from the Cu/Zn form []. Prokaryotes and protists contain Mn, Fe or both types, while most eukaryotic organisms utilise the Cu/Zn type.; GO: 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 2K4W_A 2APS_B 2WWN_B 2WWO_B 1ESO_A 2AQM_A 3F7L_A 3F7K_A 2E47_A 2E46_A ....
Probab=100.00 E-value=4.3e-35 Score=227.69 Aligned_cols=118 Identities=42% Similarity=0.703 Sum_probs=106.9
Q ss_pred eeeEEEEEEcCCC-cEEEEEEEeCCCCCceeeEEecCCCC-C-----CCCccCCCCCCCCCCCCCCCCcccccceEeCCC
Q 047402 45 TNRSDDLIMGDGG-QTTVTGSFSGLKPGLHGFHVHALGNT-T-----NDPTLTVLDKNTVLQMMKNCHDCDLGNANVRDD 117 (178)
Q Consensus 45 ~~G~v~F~q~~~~-~v~V~~~l~GL~pG~hg~HIHe~Gdc-s-----aGgH~np~~~~hg~p~~~~~h~GDLgni~~~~~ 117 (178)
++|+|+|+|..+. .+.|+++++||+||.|+|||||+|+| + +|+||||.++.|+.|....|+.|||++++++++
T Consensus 12 v~G~v~f~q~~~~~~~~v~~~~~GL~~g~~~~hIH~~g~~~~~~c~s~G~h~np~~~~~~~~~~~~~~~GDL~~~~~~~~ 91 (142)
T PF00080_consen 12 VKGTVTFTQVSDGDGVQVTVSLNGLPPGQHGYHIHENGDCSSNNCSSAGGHYNPTNVPHGGPSADNCHAGDLGNKYVDAD 91 (142)
T ss_dssp EEEEEEEEEETTTTEEEEEEEEESSSSEEEEEEEESSSTCSTTTTGGG-SBCETTTSSSSSTTSSSSCTTEEEEEEESTT
T ss_pred eEEEEEEEEeCCCCCEEEEEEEECCCCCCceEEEEeccccccccccccceecCccccccCCccccccccccccccccccC
Confidence 5799999999864 69999999999999999999999998 3 479999999999999877899999999999999
Q ss_pred C------ccceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEE
Q 047402 118 V------VDNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGII 174 (178)
Q Consensus 118 G------~~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI 174 (178)
| ++..++|++.++|+|||||||+.+||+. ++++|++|+|||||+|
T Consensus 92 G~~~~~~~~~~l~l~g~~siiGRSiVIH~~~~d~~------------~~~~g~~g~RlACg~I 142 (142)
T PF00080_consen 92 GSASFTFTDSNLSLSGPNSIIGRSIVIHSGPDDFT------------SQPTGNAGARLACGVI 142 (142)
T ss_dssp SEEEEEEEESSSBSSSTTBHTTSEEEEESSSSTTT------------HHHHTTTTSEEEEEEE
T ss_pred CceEEEEEeeeEeccCCccccCCEEEEEeCCCCcc------------cccCCCCCCcEEEEeC
Confidence 9 3556788888899999999999999994 7899999999999998
No 9
>PLN02957 copper, zinc superoxide dismutase
Probab=99.97 E-value=3.8e-31 Score=222.40 Aligned_cols=108 Identities=21% Similarity=0.279 Sum_probs=91.8
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCC-----CCCccCCCCCCCCCCCCCCCCcccccceEeCCCCc
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTT-----NDPTLTVLDKNTVLQMMKNCHDCDLGNANVRDDVV 119 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcs-----aGgH~np~~~~hg~p~~~~~h~GDLgni~~~~~G~ 119 (178)
++|+|+|+|.+++.++|+++|+||+||.|+|||||+|||+ +|+||||+++.|+ .+|.||||||+++++|+
T Consensus 92 v~G~v~~~~~~~~~v~i~~~~~GL~pg~hg~hiHe~Gd~~~~~~saG~hfnp~~~~h~-----~~h~GDLgni~~~~~G~ 166 (238)
T PLN02957 92 IFGVVRFAQVSMELARIEAAFSGLSPGTHGWSINEYGDLTRGAASTGKVYNPSDDDTD-----EEPLGDLGTLEADENGE 166 (238)
T ss_pred eEEEEEEEEcCCCCEEEEEEEcCCCCCcEEEEEcCCCCCCCCccccCCCCCCccCCCC-----CCCCCccCCEEeCCCce
Confidence 5799999998766799999999999999999999999985 5799999999997 58999999999999995
Q ss_pred cceeee---CCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEeec
Q 047402 120 DNQISL---SGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIGIQ 177 (178)
Q Consensus 120 ~~~i~L---~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~~~ 177 (178)
...... ..+++++|||||||+++|+.. .++|||||.|+
T Consensus 167 a~~~~~~~~~~l~~iiGrs~vih~~~D~~~--------------------~~~~~gvi~rs 207 (238)
T PLN02957 167 ATFSGTKEKLKVWDLIGRSLAVYATADKSG--------------------PGIAAAVIARS 207 (238)
T ss_pred EEEEEECCCcCccccCCcEEEEEeCCCCCC--------------------CCeEEEEEecc
Confidence 432111 124799999999999999642 24999999986
No 10
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.96 E-value=6.1e-29 Score=204.37 Aligned_cols=112 Identities=30% Similarity=0.575 Sum_probs=99.5
Q ss_pred eeeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCCC-----CCccCCCCCCCCCCCCCCCCcccccceEeCCCCc
Q 047402 45 TNRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTTN-----DPTLTVLDKNTVLQMMKNCHDCDLGNANVRDDVV 119 (178)
Q Consensus 45 ~~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~Gdcsa-----GgH~np~~~~hg~p~~~~~h~GDLgni~~~~~G~ 119 (178)
++|.|+|.|.....++|+++++||+||.|++|||||||.|+ |-||||+..+||+|. .|||||+.++++|.
T Consensus 94 v~GvvRf~qvt~ek~lid~tvdGlspG~h~~~Ihe~GDlsng~~StG~~ynpf~~p~g~~~-----~gDLGn~~ad~nGr 168 (247)
T KOG4656|consen 94 VQGVVRFVQVTEEKTLIDGTVDGLSPGLHGLHIHEYGDLSNGCESTGKHYNPFQEPHGCPN-----EGDLGNNRADKNGR 168 (247)
T ss_pred ceeEEEEEEeccccEEEEEEecCCCCcccceeEeeccccccchhhcccccCCCcCCCCCCC-----cccccccccccCCc
Confidence 46889999999888999999999999999999999999876 589999999999875 49999999999993
Q ss_pred ------cceeeeCCCCCCcccEEEEecCCCCCCCCCCCCCCCCCCcccCCCCCceeeEEEEeec
Q 047402 120 ------DNQISLSGPNSIIGRAVVVHSDPDNLGKECSSPSGGHELSKTTGNAGGRVACGIIGIQ 177 (178)
Q Consensus 120 ------~~~i~L~g~~siiGRSiVIH~~~Dd~~~~~~~~~g~~~~s~~~G~aG~RiACgvI~~~ 177 (178)
+..++. +++||||+||.+..||++. ++ |++|+|++||||.|+
T Consensus 169 af~s~~de~Lkv---wdlIGRsvVi~k~~ddlgg--------~p-----~nsge~la~gvIARS 216 (247)
T KOG4656|consen 169 AFFSAPDEKLKV---WDLIGRSVVISKSLDDLGG--------EP-----GNSGERLACGVIARS 216 (247)
T ss_pred EEEecccccccH---hhhhceeEEEeccccccCC--------CC-----CCcCcceeEEEeeec
Confidence 345566 5999999999999999853 22 899999999999986
No 11
>PF07452 CHRD: CHRD domain; InterPro: IPR010895 CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made [].
Probab=70.64 E-value=13 Score=27.17 Aligned_cols=34 Identities=21% Similarity=0.311 Sum_probs=27.7
Q ss_pred eeEEEEEEcCCC-cEEEEEEEeCCCCCceeeEEec
Q 047402 46 NRSDDLIMGDGG-QTTVTGSFSGLKPGLHGFHVHA 79 (178)
Q Consensus 46 ~G~v~F~q~~~~-~v~V~~~l~GL~pG~hg~HIHe 79 (178)
.|++.|+-..++ .+.+++.++||....-.+|||.
T Consensus 21 ~G~a~~~l~~~~~~l~y~i~~~gl~~~~~~~hih~ 55 (119)
T PF07452_consen 21 SGTAWFTLDDDGNTLHYSITLSGLSSPPTAAHIHQ 55 (119)
T ss_pred EEEEEEEEECCCCEEEEEEEEeCCCCCcEEEEEEc
Confidence 477777776654 6889999999976778999999
No 12
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=64.46 E-value=18 Score=26.67 Aligned_cols=42 Identities=24% Similarity=0.239 Sum_probs=29.1
Q ss_pred eeEEEEEEcCCCcEEEEEEEeCCCCCceeeEEecCCCCCCCC
Q 047402 46 NRSDDLIMGDGGQTTVTGSFSGLKPGLHGFHVHALGNTTNDP 87 (178)
Q Consensus 46 ~G~v~F~q~~~~~v~V~~~l~GL~pG~hg~HIHe~GdcsaGg 87 (178)
.|.+.|+-..+..+..++.++||..-.-+.|||+-..-.+|+
T Consensus 21 ~G~a~~~l~~~~~l~y~i~~~gl~~~~~~~hih~~~~g~~G~ 62 (118)
T smart00754 21 VGGAWFTLDDDGSLHYQVTLSGLSGPETAAHIHEGEIGTNGP 62 (118)
T ss_pred EEEEEEEECCCCEEEEEEEEcccCCCceeeeEecccCCCCCC
Confidence 366677766456788999999998643389999832334554
No 13
>TIGR02567 YscW type III secretion system chaperone YscW. This family of proteins is found within type III secretion operons. The protein has been characterized as a chaperone for the outer membrane pore component YscC (TIGR02516). YscW is a lipoprotein which is itself localized to the outer membrane and, it is believed, facilitates the oligomerization and localization of YscC.
Probab=59.65 E-value=28 Score=26.91 Aligned_cols=45 Identities=9% Similarity=-0.017 Sum_probs=30.0
Q ss_pred hhhhhhccCccccCCCCcccCCCCCeeeEeeeEEEEEEcCCCcEEEEEEEeCC
Q 047402 16 TNATIGDGCHRQEGSSPFSLPSSGVTEIATNRSDDLIMGDGGQTTVTGSFSGL 68 (178)
Q Consensus 16 ~~~~~~~~c~~~~~~~~~~~~~~g~~~~~~~G~v~F~q~~~~~v~V~~~l~GL 68 (178)
..+++++||.. .|......+..+|.|.|.-.-+....|++++-..
T Consensus 3 ~~~~lLsGCvt--------~~~~~~~~~~i~G~V~~~~~LP~~a~i~V~i~~V 47 (124)
T TIGR02567 3 ILLLLLTGCAS--------QPFPVQSQANVYGWVSMEYHLPRSAYIEVSMCQV 47 (124)
T ss_pred hHhhhhcccCC--------CCCCCCCcEEEEEEEEEEEcCCCCCEEEEEEEEe
Confidence 34667899995 2233333445789999985544677888888764
No 14
>cd00305 Cu-Zn_Superoxide_Dismutase Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730].
Probab=53.29 E-value=5.9 Score=30.76 Aligned_cols=13 Identities=77% Similarity=1.040 Sum_probs=12.1
Q ss_pred cccCCCCCceeeE
Q 047402 159 SKTTGNAGGRVAC 171 (178)
Q Consensus 159 s~~~G~aG~RiAC 171 (178)
|.+.|++|.|+||
T Consensus 132 sg~~~~~G~~~ac 144 (144)
T cd00305 132 SGGTGNAGVRVAC 144 (144)
T ss_pred cccceeeEeEEeC
Confidence 7889999999999
No 15
>PF11008 DUF2846: Protein of unknown function (DUF2846); InterPro: IPR022548 Some members in this group of proteins with unknown function are annotated as lipoproteins. However this cannot be confirmed.
Probab=51.26 E-value=38 Score=25.00 Aligned_cols=22 Identities=5% Similarity=-0.109 Sum_probs=11.4
Q ss_pred eeEEEEEEcCC---CcEEEEEEEeC
Q 047402 46 NRSDDLIMGDG---GQTTVTGSFSG 67 (178)
Q Consensus 46 ~G~v~F~q~~~---~~v~V~~~l~G 67 (178)
++.|.|.+... ..+...+-++|
T Consensus 25 ~a~IYvYR~~~~~g~~~~~~v~vdg 49 (117)
T PF11008_consen 25 KARIYVYRPSSFFGSAVKPDVYVDG 49 (117)
T ss_pred cEEEEEEEECCccCccccceEEECC
Confidence 35678887433 13444444443
No 16
>PF07731 Cu-oxidase_2: Multicopper oxidase; InterPro: IPR011706 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 2 domains.; GO: 0005507 copper ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GDC_C 3ZX1_A 2YAH_A 2YAR_A 2YAQ_A 2YAO_A 2YAM_A 2YAF_A 2YAP_A 2XU9_A ....
Probab=36.82 E-value=38 Score=25.02 Aligned_cols=22 Identities=23% Similarity=0.224 Sum_probs=17.8
Q ss_pred EEEEEEEeCCCCCceeeEEecC
Q 047402 59 TTVTGSFSGLKPGLHGFHVHAL 80 (178)
Q Consensus 59 v~V~~~l~GL~pG~hg~HIHe~ 80 (178)
-.+++.|.+.....|.||+|-+
T Consensus 42 ~~v~~~l~N~~~~~Hp~HlHG~ 63 (138)
T PF07731_consen 42 DVVEIVLQNNGSMPHPFHLHGH 63 (138)
T ss_dssp SEEEEEEEECTTSSEEEEETTS
T ss_pred CEEEEEEECCCCCccceEEEee
Confidence 4777788887777899999964
No 17
>PF07495 Y_Y_Y: Y_Y_Y domain; InterPro: IPR011123 This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It is named after the conserved tyrosines found in the alignment. The exact function is not known.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=28.01 E-value=52 Score=21.11 Aligned_cols=19 Identities=32% Similarity=0.441 Sum_probs=14.2
Q ss_pred EEEEeCCCCCceeeEEecC
Q 047402 62 TGSFSGLKPGLHGFHVHAL 80 (178)
Q Consensus 62 ~~~l~GL~pG~hg~HIHe~ 80 (178)
+++++.|+||.|-|+|...
T Consensus 30 ~~~~~~L~~G~Y~l~V~a~ 48 (66)
T PF07495_consen 30 SISYTNLPPGKYTLEVRAK 48 (66)
T ss_dssp EEEEES--SEEEEEEEEEE
T ss_pred EEEEEeCCCEEEEEEEEEE
Confidence 7888899999999988763
No 18
>PRK15396 murein lipoprotein; Provisional
Probab=22.83 E-value=63 Score=22.99 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=16.0
Q ss_pred HHHHHHHhhhhhhhccCccc
Q 047402 8 RLANDKATTNATIGDGCHRQ 27 (178)
Q Consensus 8 ~~~~~~~~~~~~~~~~c~~~ 27 (178)
.++++.+.+..++++||..-
T Consensus 5 kl~l~av~ls~~LLaGCAs~ 24 (78)
T PRK15396 5 KLVLGAVILGSTLLAGCSSN 24 (78)
T ss_pred HHHHHHHHHHHHHHHHcCCc
Confidence 46778888888889999954
No 19
>PF09912 DUF2141: Uncharacterized protein conserved in bacteria (DUF2141); InterPro: IPR018673 This family of conserved hypothetical proteins has no known function.
Probab=20.43 E-value=1e+02 Score=22.81 Aligned_cols=21 Identities=38% Similarity=0.460 Sum_probs=17.8
Q ss_pred EEEEEEEeCCCCCceeeEEec
Q 047402 59 TTVTGSFSGLKPGLHGFHVHA 79 (178)
Q Consensus 59 v~V~~~l~GL~pG~hg~HIHe 79 (178)
-.+++.+..|+||.|++-+..
T Consensus 41 ~~~~~~f~~lp~G~YAi~v~h 61 (112)
T PF09912_consen 41 GTVTITFEDLPPGTYAIAVFH 61 (112)
T ss_pred CcEEEEECCCCCccEEEEEEE
Confidence 467889999999999988763
No 20
>COG3056 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=20.20 E-value=1e+02 Score=25.76 Aligned_cols=28 Identities=11% Similarity=-0.011 Sum_probs=20.0
Q ss_pred cchhHHHHHHHhhhhhhhccCccccCCC
Q 047402 4 LKPLRLANDKATTNATIGDGCHRQEGSS 31 (178)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~c~~~~~~~ 31 (178)
-|.++.-+=+.+..-++++||.++....
T Consensus 11 ~k~~t~k~L~~laa~~lLagC~a~~~tl 38 (204)
T COG3056 11 SKNMTKKILFPLAAIFLLAGCAAPPTTL 38 (204)
T ss_pred hHHHHHHHHHHHHHHHHHHhcCCCCcee
Confidence 3555666666677777889999988653
No 21
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=20.09 E-value=90 Score=24.65 Aligned_cols=22 Identities=18% Similarity=0.298 Sum_probs=18.1
Q ss_pred HHHHHHHhhhhhhhccCccccC
Q 047402 8 RLANDKATTNATIGDGCHRQEG 29 (178)
Q Consensus 8 ~~~~~~~~~~~~~~~~c~~~~~ 29 (178)
.+|.+.+.+.+++++||...-+
T Consensus 3 ~~~~~~~~~~~~~~~g~~~~~~ 24 (160)
T PRK09967 3 KHLVAPLIFTSLILTGCQSPQG 24 (160)
T ss_pred hhHHHHHHHHHHHhhccCCCCC
Confidence 5688899999999999987543
Done!