Query 024597
Match_columns 265
No_of_seqs 193 out of 1329
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:54:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024597.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024597hhsearch_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 6.5E-50 1.4E-54 340.3 19.4 150 83-257 2-151 (152)
2 PLN02642 copper, zinc superoxi 100.0 2.5E-49 5.5E-54 341.0 19.2 152 82-258 7-158 (164)
3 KOG0441 Cu2+/Zn2+ superoxide d 100.0 1.7E-44 3.6E-49 307.6 15.0 150 84-257 3-153 (154)
4 PRK15388 Cu/Zn superoxide dism 100.0 7.9E-41 1.7E-45 291.4 18.5 135 90-256 34-177 (177)
5 cd00305 Cu-Zn_Superoxide_Dismu 100.0 1.2E-40 2.5E-45 279.3 17.7 141 83-255 1-142 (144)
6 PRK10290 superoxide dismutase; 100.0 1.4E-40 3E-45 288.9 17.4 133 90-255 32-173 (173)
7 PF00080 Sod_Cu: Copper/zinc s 100.0 2.7E-40 5.8E-45 273.5 15.4 140 85-254 1-142 (142)
8 COG2032 SodC Cu/Zn superoxide 100.0 2.5E-36 5.3E-41 263.1 16.0 142 84-255 30-179 (179)
9 PLN02957 copper, zinc superoxi 100.0 7.2E-35 1.6E-39 261.8 16.7 129 82-258 80-208 (238)
10 KOG4656 Copper chaperone for s 100.0 7.6E-34 1.6E-38 253.1 10.4 135 85-259 84-218 (247)
11 cd00305 Cu-Zn_Superoxide_Dismu 67.5 4.3 9.4E-05 34.2 2.4 13 239-251 132-144 (144)
12 smart00754 CHRD A domain in th 60.2 41 0.0009 26.8 6.7 23 132-154 32-54 (118)
13 PF07452 CHRD: CHRD domain; I 54.5 72 0.0016 25.2 7.2 22 133-154 34-55 (119)
14 PF07731 Cu-oxidase_2: Multico 22.4 92 0.002 24.7 2.9 22 134-155 42-63 (138)
15 PF09559 Cas6: Cas6 Crispr; I 20.8 72 0.0016 28.9 2.2 37 215-256 152-190 (195)
No 1
>PLN02386 superoxide dismutase [Cu-Zn]
Probab=100.00 E-value=6.5e-50 Score=340.25 Aligned_cols=150 Identities=62% Similarity=1.002 Sum_probs=144.2
Q ss_pred eeeEEEEecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCCCC
Q 024597 83 KKAVAVLKGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTNGC 162 (265)
Q Consensus 83 ~~AvAvLkg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~gC 162 (265)
++|+|+|++++.|+|+|+|+|..+ +.+.|+++++||+||.|+|||||+|||+++|
T Consensus 2 ~~a~a~~~~~~~v~G~v~f~q~~~-------------------------g~v~i~~~~~GL~pG~hg~HIHe~Gd~~~g~ 56 (152)
T PLN02386 2 VKAVAVLNSSEGVKGTIFFTQEGD-------------------------GPTTVTGSLSGLKPGLHGFHVHALGDTTNGC 56 (152)
T ss_pred ceEEEEEcCCCCCEEEEEEEEcCC-------------------------CCEEEEEEEeCCCCCceeEEEeCCCCCCCCc
Confidence 579999999888999999999865 5699999999999999999999999999999
Q ss_pred CCCCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCcccC
Q 024597 163 MSTGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLTT 242 (265)
Q Consensus 163 ~SaGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~t 242 (265)
.|+||||||+++.|+.|+++.||+||||||+++++|++++.+++++++|.++++|+|||||||+++|||++++++.|+++
T Consensus 57 ~SaGgHfnP~~~~Hg~~~~~~~H~GDLgNi~~~~~G~a~~~~~~~~~~L~g~~~i~GrslVIHa~~DD~~~~~~~~s~~~ 136 (152)
T PLN02386 57 MSTGPHFNPAGKEHGAPEDENRHAGDLGNVTVGDDGTATFTIVDKQIPLTGPNSIVGRAVVVHADPDDLGKGGHELSKST 136 (152)
T ss_pred ccccCccCCCCCCCCCCCcccCccccccCEEECCCCeEEEEEECCceEeCCCCccCCcEEEEEccCCCcCCCcccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeEEEEEecc
Q 024597 243 GNAGGRLACGMHKKY 257 (265)
Q Consensus 243 GnaG~RiACGvI~~~ 257 (265)
||+|+|||||||++.
T Consensus 137 G~aG~RiACgvI~~~ 151 (152)
T PLN02386 137 GNAGGRVACGIIGLQ 151 (152)
T ss_pred CCCCceEEEEEEEec
Confidence 999999999999864
No 2
>PLN02642 copper, zinc superoxide dismutase
Probab=100.00 E-value=2.5e-49 Score=341.02 Aligned_cols=152 Identities=53% Similarity=0.909 Sum_probs=145.5
Q ss_pred ceeeEEEEecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCCC
Q 024597 82 AKKAVAVLKGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTNG 161 (265)
Q Consensus 82 ~~~AvAvLkg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~g 161 (265)
-++|+|++++.+.++|+|+|+|... +.++|+++|+||+||.|+|||||+|||+++
T Consensus 7 ~~~A~a~~~g~~~v~G~v~f~q~~~-------------------------g~v~I~~~v~GL~pG~HG~HIHe~Gd~~~g 61 (164)
T PLN02642 7 NLRAVALIAGDNNVRGCLQFVQDIF-------------------------GTTHVTGKISGLSPGFHGFHIHSFGDTTNG 61 (164)
T ss_pred CeeEEEEEcCCCCcEEEEEEEECCC-------------------------CcEEEEEEEcCCCCCceeEEEcCCCcCCCC
Confidence 4679999999888999999999865 458999999999999999999999999999
Q ss_pred CCCCCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCccc
Q 024597 162 CMSTGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLT 241 (265)
Q Consensus 162 C~SaGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~ 241 (265)
|.|+|+||||.++.||.|+++.||+||||||+++++|++++.++++.++|.++++|+|||||||+.+|||++++++.|++
T Consensus 62 ~~SaGgHfNP~~~~HG~~~~~~rH~GDLgNi~a~~~G~a~~~~~~~~i~L~g~~~iiGRalVVHa~~DD~~~~~~~~s~~ 141 (164)
T PLN02642 62 CISTGPHFNPLNRVHGPPNEEERHAGDLGNILAGSDGVAEILIKDKHIPLSGQYSILGRAVVVHADPDDLGKGGHKLSKS 141 (164)
T ss_pred cccccCcccCCCCcCCCCCcCCCcccccCCEEECCCCeEEEEEEcCceecCCCCCcCCcEEEEeccCCccCcCccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeEEEEEeccc
Q 024597 242 TGNAGGRLACGMHKKYL 258 (265)
Q Consensus 242 tGnaG~RiACGvI~~~~ 258 (265)
+||+|.|||||||++..
T Consensus 142 tGnaG~RiACGVI~~~~ 158 (164)
T PLN02642 142 TGNAGSRVGCGIIGLQS 158 (164)
T ss_pred CCCCCceEEEEEEEecc
Confidence 99999999999999754
No 3
>KOG0441 consensus Cu2+/Zn2+ superoxide dismutase SOD1 [Inorganic ion transport and metabolism]
Probab=100.00 E-value=1.7e-44 Score=307.59 Aligned_cols=150 Identities=58% Similarity=0.940 Sum_probs=143.5
Q ss_pred eeEEEEecCC-ceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCCCC
Q 024597 84 KAVAVLKGTS-NVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTNGC 162 (265)
Q Consensus 84 ~AvAvLkg~~-~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~gC 162 (265)
+|+|+++++. .|.|+|.|+|..+. .++.|++.++||+||.|+||||+|||.++||
T Consensus 3 ~~~avl~g~~~~V~G~i~F~Q~~~~------------------------~~~~v~~~i~GL~pg~hgfHvHqfGD~t~GC 58 (154)
T KOG0441|consen 3 QAVAVLEGDEIQVIGVITFEQFLPG------------------------EPLRVSGEVTGLPPGKHGFHVHQFGDNTNGC 58 (154)
T ss_pred ceEEEEecCCCCceeEEEEEEcCCC------------------------CcEEEEEEEecCCCceeeEEEEeccCCCCCh
Confidence 7899999975 79999999996552 4799999999999999999999999999999
Q ss_pred CCCCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCcccC
Q 024597 163 MSTGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLTT 242 (265)
Q Consensus 163 ~SaGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~t 242 (265)
.|+|+||||.++.||.|.++.||.||||||.++++|.....+.|.+++|+|+++|+||++|||+.+||+|+|++++++.+
T Consensus 59 ~SaGphFNp~~~~hg~p~~~~rH~gdlGnv~~~~~G~~~~~~~d~~i~l~g~~sivgrs~vvHa~~ddLg~G~~~~s~kt 138 (154)
T KOG0441|consen 59 KSAGPHFNPNKKTHGGPVDEVRHVGDLGNVDAKDDGVISRVFGDSVITLSGPNSIVGRSVVVHAGEDDLGKGGHELSKKT 138 (154)
T ss_pred hcCCCCCCCcccCCCCccccccccccccccccCCCceEEEEEccceEEEeeccccceeEEEEeccCccccCCchhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeEEEEEecc
Q 024597 243 GNAGGRLACGMHKKY 257 (265)
Q Consensus 243 GnaG~RiACGvI~~~ 257 (265)
||+|+|+|||+|++.
T Consensus 139 gnag~r~aCgvi~~~ 153 (154)
T KOG0441|consen 139 GNAGARPACGVIGIA 153 (154)
T ss_pred cccCCCccceeeecc
Confidence 999999999999864
No 4
>PRK15388 Cu/Zn superoxide dismutase; Provisional
Probab=100.00 E-value=7.9e-41 Score=291.38 Aligned_cols=135 Identities=29% Similarity=0.563 Sum_probs=121.1
Q ss_pred ecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCC----C----
Q 024597 90 KGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTN----G---- 161 (265)
Q Consensus 90 kg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~----g---- 161 (265)
++.+++.|+|+|+|... + ++|+++++||+||.|+|||||+|||+. |
T Consensus 34 ~~~g~~~G~v~f~~~~~-------------------------g-v~I~~~l~GL~pG~HGfHIHe~GdC~~~~~~G~~~~ 87 (177)
T PRK15388 34 SGTGENIGEITVSETPY-------------------------G-LLFTPHLNGLTPGIHGFHVHTNPSCMPGMKDGKEVP 87 (177)
T ss_pred CCCCceEEEEEEEEcCC-------------------------c-EEEEEEEcCCCCcceEEEEccCCCccCcccCCCccc
Confidence 55678999999999865 4 889999999999999999999999972 3
Q ss_pred CCCCCccccCCCC-CCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCcc
Q 024597 162 CMSTGAHFNPNNM-THGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSL 240 (265)
Q Consensus 162 C~SaGgHfNP~~~-~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~ 240 (265)
|.|+||||||+++ .|+.|++..+|+||||||+++++|++++.++++.+. +.++|+|||||||+++|||++ .++
T Consensus 88 ~~SAGgHfNP~~~~~Hg~p~~~~~H~GDLpNi~a~~dG~a~~~~~~~~~~--~~~~i~GralVIHa~~DD~~~----~p~ 161 (177)
T PRK15388 88 ALMAGGHLDPEKTGKHLGPYNDKGHLGDLPGLVVNADGTATYPLLAPRLK--SLSELKGHSLMIHKGGDNYSD----KPA 161 (177)
T ss_pred ccccCCCcCCCCCCCCCCCCCCCCCcCcCcCEEECCCccEEEEEEeCCcc--cCcccCCcEEEEECCCCCCCC----CCC
Confidence 8999999999997 799998888999999999999999999999998764 346899999999999999975 367
Q ss_pred cCCCCCCeeEEEEEec
Q 024597 241 TTGNAGGRLACGMHKK 256 (265)
Q Consensus 241 ~tGnaG~RiACGvI~~ 256 (265)
++||+|+|||||||+.
T Consensus 162 ~~GnaG~RiACGVI~~ 177 (177)
T PRK15388 162 PLGGGGARFACGVIEK 177 (177)
T ss_pred cCCCCCceEEEEeecC
Confidence 8899999999999963
No 5
>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=1.2e-40 Score=279.25 Aligned_cols=141 Identities=54% Similarity=0.891 Sum_probs=129.7
Q ss_pred eeeEEEEecC-CceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCCC
Q 024597 83 KKAVAVLKGT-SNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTNG 161 (265)
Q Consensus 83 ~~AvAvLkg~-~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~g 161 (265)
++|+|.|++. +.++|+|+|+|..+ .++|+++++||+||.|+|||||+|||+++
T Consensus 1 ~~a~~~l~~~~g~v~G~v~f~q~~~--------------------------~v~v~~~l~GL~pG~hg~HIHe~Gd~~~~ 54 (144)
T cd00305 1 VSAVAVLKGPDGKVVGTVTFTQQSG--------------------------GVTITGELSGLTPGLHGFHIHEFGDCTNG 54 (144)
T ss_pred CcEEEEEECCCCceEEEEEEEECCC--------------------------CEEEEEEEECCCCCceeEEEEecCCCCCc
Confidence 4689999986 47999999999875 48999999999999999999999999999
Q ss_pred CCCCCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCccc
Q 024597 162 CMSTGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLT 241 (265)
Q Consensus 162 C~SaGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~ 241 (265)
|.|+|+||||.++.|+.|.++.||.||||||+++++|++++++.+++++|++.++++|||||||+.+||+++ ++
T Consensus 55 ~~saGgh~np~~~~hg~~~~~~~h~GDLgni~~~~~G~~~~~~~~~~~~l~~~~~iiGrsivVH~~~Dd~~~------~p 128 (144)
T cd00305 55 CTSAGGHFNPFGKKHGGPNDEGRHAGDLGNIVADKDGVATVSVLDPLISLKGGNSIIGRSLVVHAGQDDLGK------GP 128 (144)
T ss_pred cccccCccCCCCCCCCCCCCCCCCCCcCCCEEECCCCeEEEEEEeCcEEcCCCCCcCCcEEEEecCCCCCCC------CC
Confidence 999999999999999999999999999999999999999999999999999889999999999999999974 56
Q ss_pred CCCCCCeeEEEEEe
Q 024597 242 TGNAGGRLACGMHK 255 (265)
Q Consensus 242 tGnaG~RiACGvI~ 255 (265)
.|++|.|++||+|-
T Consensus 129 ~~~sg~~~~~G~~~ 142 (144)
T cd00305 129 DELSGGTGNAGVRV 142 (144)
T ss_pred CcccccceeeEeEE
Confidence 67777888888763
No 6
>PRK10290 superoxide dismutase; Provisional
Probab=100.00 E-value=1.4e-40 Score=288.87 Aligned_cols=133 Identities=32% Similarity=0.611 Sum_probs=118.8
Q ss_pred ecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCC----CC----
Q 024597 90 KGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTT----NG---- 161 (265)
Q Consensus 90 kg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s----~g---- 161 (265)
++.+.+.|+|+|+|..+ + ++|+++++||+||+|+|||||+|||+ +|
T Consensus 32 ~~~g~~~G~v~f~~~~~-------------------------g-v~i~~~l~GL~pG~HGfHIHe~Gdc~~~~~~G~~~~ 85 (173)
T PRK10290 32 QGVGQSIGSVTITETDK-------------------------G-LEFSPDLKALPPGEHGFHIHAKGSCQPATKDGKASA 85 (173)
T ss_pred CCCCceEEEEEEEEcCC-------------------------c-EEEEEEEcCCCCCceEEEEeCCCccCCcccCCCccc
Confidence 33578999999999865 3 89999999999999999999999997 33
Q ss_pred CCCCCccccCCCC-CCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCcc
Q 024597 162 CMSTGAHFNPNNM-THGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSL 240 (265)
Q Consensus 162 C~SaGgHfNP~~~-~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~ 240 (265)
|.|+||||||.++ .|+.|++ .+|+||||||+++++|++++.++++.+. +.++|+|||||||+++|||+++ ++
T Consensus 86 ~~sAGgHfNP~~~~~hg~p~~-~~H~GDL~ni~a~~dG~a~~~~~~~~~~--~~~~i~GralVIH~~~DD~~~~----~~ 158 (173)
T PRK10290 86 AEAAGGHLDPQNTGKHEGPEG-AGHLGDLPALVVNNDGKATDPVIAPRLK--SLDEVKDKALMVHVGGDNMSDQ----PK 158 (173)
T ss_pred ccccCCccCCCCCcCCCCCCC-CCCcCcccCEEECCCeeEEEEEEeCCcc--CccccCCcEEEEECCCCCCCCC----CC
Confidence 8999999999998 7888874 6899999999999999999999998754 4578999999999999999763 67
Q ss_pred cCCCCCCeeEEEEEe
Q 024597 241 TTGNAGGRLACGMHK 255 (265)
Q Consensus 241 ~tGnaG~RiACGvI~ 255 (265)
++||+|.|||||||+
T Consensus 159 ~~GnaG~RiACGVI~ 173 (173)
T PRK10290 159 PLGGGGERYACGVIK 173 (173)
T ss_pred cCCCCcceEEEEeEC
Confidence 899999999999995
No 7
>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=2.7e-40 Score=273.50 Aligned_cols=140 Identities=51% Similarity=0.889 Sum_probs=130.3
Q ss_pred eEEEEecC-CceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCC-CCCC
Q 024597 85 AVAVLKGT-SNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDT-TNGC 162 (265)
Q Consensus 85 AvAvLkg~-~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~-s~gC 162 (265)
|+|+|++. +.|+|+|+|+|..+. ..+.|+++++||++|.|+|||||+|++ +++|
T Consensus 1 a~a~l~~~~~~v~G~v~f~q~~~~------------------------~~~~v~~~~~GL~~g~~~~hIH~~g~~~~~~c 56 (142)
T PF00080_consen 1 AVAVLKGAGGKVKGTVTFTQVSDG------------------------DGVQVTVSLNGLPPGQHGYHIHENGDCSSNNC 56 (142)
T ss_dssp EEEEEBETSSSEEEEEEEEEETTT------------------------TEEEEEEEEESSSSEEEEEEEESSSTCSTTTT
T ss_pred CEEEEeCCCCCeEEEEEEEEeCCC------------------------CCEEEEEEEECCCCCCceEEEEeccccccccc
Confidence 79999974 579999999999973 359999999999999999999999999 7789
Q ss_pred CCCCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCcccC
Q 024597 163 MSTGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLTT 242 (265)
Q Consensus 163 ~SaGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~t 242 (265)
.++|+||||.++.|+.|....|+.|||++++++.+|.++..|+|.+++|+|+++|+|||||||+.+||+ .++++
T Consensus 57 ~s~G~h~np~~~~~~~~~~~~~~~GDL~~~~~~~~G~~~~~~~~~~l~l~g~~siiGRSiVIH~~~~d~------~~~~~ 130 (142)
T PF00080_consen 57 SSAGGHYNPTNVPHGGPSADNCHAGDLGNKYVDADGSASFTFTDSNLSLSGPNSIIGRSIVIHSGPDDF------TSQPT 130 (142)
T ss_dssp GGG-SBCETTTSSSSSTTSSSSCTTEEEEEEESTTSEEEEEEEESSSBSSSTTBHTTSEEEEESSSSTT------THHHH
T ss_pred cccceecCccccccCCccccccccccccccccccCCceEEEEEeeeEeccCCccccCCEEEEEeCCCCc------ccccC
Confidence 999999999999999998888999999999999999999999999999999999999999999999987 47899
Q ss_pred CCCCCeeEEEEE
Q 024597 243 GNAGGRLACGMH 254 (265)
Q Consensus 243 GnaG~RiACGvI 254 (265)
|++|.|||||+|
T Consensus 131 g~~g~RlACg~I 142 (142)
T PF00080_consen 131 GNAGARLACGVI 142 (142)
T ss_dssp TTTTSEEEEEEE
T ss_pred CCCCCcEEEEeC
Confidence 999999999998
No 8
>COG2032 SodC Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=2.5e-36 Score=263.07 Aligned_cols=142 Identities=42% Similarity=0.670 Sum_probs=126.8
Q ss_pred eeEEEE-ecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCC--
Q 024597 84 KAVAVL-KGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTN-- 160 (265)
Q Consensus 84 ~AvAvL-kg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~-- 160 (265)
++.+.+ .+++...|+|+++|... + +.++..+.||+||+|||||||+|+|++
T Consensus 30 ~~~~~~~~~~G~~vG~vt~~e~~~-------------------------g-~~~~~~~~~L~pg~hGfHIHe~G~C~pkd 83 (179)
T COG2032 30 KANAVLVDGTGKDVGTVTITETGY-------------------------G-LLFTPALGGLPPGEHGFHIHEKGSCTPKD 83 (179)
T ss_pred cceeeccCCCCceeEEEEEeecCC-------------------------c-eEEeecccCCCCcceeEEecccCCCcCCC
Confidence 344444 33457889999999886 4 889999999999999999999999987
Q ss_pred ----CCCCCCccccCC-CCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCC
Q 024597 161 ----GCMSTGAHFNPN-NMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGG 235 (265)
Q Consensus 161 ----gC~SaGgHfNP~-~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~ 235 (265)
.|.||||||||. ...|+.|+++.+|.|||+||++++||.++..++++.+++.+..+++|||||||+..|||.+..
T Consensus 84 gk~~~~~sAGGHfdP~~~~~Hg~p~~~~~H~GDLP~L~v~~dG~a~~~v~~~~~~l~~l~~v~G~alvIHag~Dd~~~~P 163 (179)
T COG2032 84 GKPVDFLSAGGHFDPQNTKKHGGPNADGGHAGDLPNLFVNADGKATLPVLAPRLKLKGLLEVKGRALVIHAGGDDYSTQP 163 (179)
T ss_pred CCCcccccccCCcCCccCCCCCCCCCCCCCcCcCcceEECCCCcEEEEEecccceeccccccCCeEEEEEcCCccccCCC
Confidence 599999999999 789999999999999999999999999999999999999999999999999999999997532
Q ss_pred CCCcccCCCCCCeeEEEEEe
Q 024597 236 HELSLTTGNAGGRLACGMHK 255 (265)
Q Consensus 236 ~~~s~~tGnaG~RiACGvI~ 255 (265)
.|+||+|+|+|||||+
T Consensus 164 ----~p~G~aG~R~ACGVI~ 179 (179)
T COG2032 164 ----EPLGGAGARVACGVIK 179 (179)
T ss_pred ----ccCCCCccceeeeeeC
Confidence 3399999999999995
No 9
>PLN02957 copper, zinc superoxide dismutase
Probab=100.00 E-value=7.2e-35 Score=261.82 Aligned_cols=129 Identities=31% Similarity=0.522 Sum_probs=116.8
Q ss_pred ceeeEEEEecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCCC
Q 024597 82 AKKAVAVLKGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTNG 161 (265)
Q Consensus 82 ~~~AvAvLkg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~g 161 (265)
...|+|.++|. .|+|+|+|+|..+ +.+.|+++++||+||.|+|||||+|||+++
T Consensus 80 ~~~av~~~~g~-~v~G~v~~~~~~~-------------------------~~v~i~~~~~GL~pg~hg~hiHe~Gd~~~~ 133 (238)
T PLN02957 80 VSAAVAEFKGP-DIFGVVRFAQVSM-------------------------ELARIEAAFSGLSPGTHGWSINEYGDLTRG 133 (238)
T ss_pred cceEEEEecCC-ceEEEEEEEEcCC-------------------------CCEEEEEEEcCCCCCcEEEEEcCCCCCCCC
Confidence 34689999986 5999999999875 459999999999999999999999999999
Q ss_pred CCCCCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCccc
Q 024597 162 CMSTGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLT 241 (265)
Q Consensus 162 C~SaGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~ 241 (265)
|.|+|+||||+++.|+ .+|.||||||+++++|++++.+.++.++|+ +|||||||||+.+|+.
T Consensus 134 ~~saG~hfnp~~~~h~-----~~h~GDLgni~~~~~G~a~~~~~~~~~~l~---~iiGrs~vih~~~D~~---------- 195 (238)
T PLN02957 134 AASTGKVYNPSDDDTD-----EEPLGDLGTLEADENGEATFSGTKEKLKVW---DLIGRSLAVYATADKS---------- 195 (238)
T ss_pred ccccCCCCCCccCCCC-----CCCCCccCCEEeCCCceEEEEEECCCcCcc---ccCCcEEEEEeCCCCC----------
Confidence 9999999999999998 689999999999999999999999988875 8999999999998862
Q ss_pred CCCCCCeeEEEEEeccc
Q 024597 242 TGNAGGRLACGMHKKYL 258 (265)
Q Consensus 242 tGnaG~RiACGvI~~~~ 258 (265)
+++++||||.|+.
T Consensus 196 ----~~~~~~gvi~rsa 208 (238)
T PLN02957 196 ----GPGIAAAVIARSA 208 (238)
T ss_pred ----CCCeEEEEEeccc
Confidence 2359999999975
No 10
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=7.6e-34 Score=253.06 Aligned_cols=135 Identities=44% Similarity=0.773 Sum_probs=123.7
Q ss_pred eEEEEecCCceEEEEEEEEecCCCCcccCCCccccceEEEEEEeecCCCeEEEEEEcCCCCCceeEEEeecCCCCCCCCC
Q 024597 85 AVAVLKGTSNVEGVVTLTQEDGDIPYLKKPFATRSYILVYVVLVSMKSPTTVNVRVTGLTPGPHGFHLHEYGDTTNGCMS 164 (265)
Q Consensus 85 AvAvLkg~~~V~G~Vtf~Q~~~~~pyl~~p~~~~s~~~~~~~~v~~~g~t~V~v~vtGL~pG~Hg~HIHE~Gd~s~gC~S 164 (265)
+++.+.+.+.|.|.|+|.|... ..++|+++++||+||.|++|||||||.++||.|
T Consensus 84 t~a~~~~~~~v~GvvRf~qvt~-------------------------ek~lid~tvdGlspG~h~~~Ihe~GDlsng~~S 138 (247)
T KOG4656|consen 84 TVAKYTGPQAVQGVVRFVQVTE-------------------------EKTLIDGTVDGLSPGLHGLHIHEYGDLSNGCES 138 (247)
T ss_pred HHHHhcCCccceeEEEEEEecc-------------------------ccEEEEEEecCCCCcccceeEeeccccccchhh
Confidence 5566666678999999999987 469999999999999999999999999999999
Q ss_pred CCccccCCCCCCCCCCCCCCCCCCCCceEECCCCeEEEEEEeceeeeCCCCCCCccEEEEecCCCCCCCCCCCCcccCCC
Q 024597 165 TGAHFNPNNMTHGAPKDEVRHAGDLGNIVANANGVAEATIVDNQISLDGPNTVVGRAFVVHELEDDLGKGGHELSLTTGN 244 (265)
Q Consensus 165 aGgHfNP~~~~hg~P~~~~~h~GDLGnI~a~~~G~a~~~~~d~~l~L~G~~sIIGRSIVIH~~~DD~g~g~~~~s~~tGn 244 (265)
+|.||||+...||+|.. |||||+.+|++|++.+++.|..|++| ++||||+||....||+| +++ ||
T Consensus 139 tG~~ynpf~~p~g~~~~-----gDLGn~~ad~nGraf~s~~de~Lkvw---dlIGRsvVi~k~~ddlg--g~p-----~n 203 (247)
T KOG4656|consen 139 TGKHYNPFQEPHGCPNE-----GDLGNNRADKNGRAFFSAPDEKLKVW---DLIGRSVVISKSLDDLG--GEP-----GN 203 (247)
T ss_pred cccccCCCcCCCCCCCc-----ccccccccccCCcEEEecccccccHh---hhhceeEEEeccccccC--CCC-----CC
Confidence 99999999999998864 99999999999999999999999998 89999999999999984 333 89
Q ss_pred CCCeeEEEEEecccc
Q 024597 245 AGGRLACGMHKKYLT 259 (265)
Q Consensus 245 aG~RiACGvI~~~~~ 259 (265)
+|.|++||||.|+.-
T Consensus 204 sge~la~gvIARSAG 218 (247)
T KOG4656|consen 204 SGERLACGVIARSAG 218 (247)
T ss_pred cCcceeEEEeeeccc
Confidence 999999999999864
No 11
>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=67.52 E-value=4.3 Score=34.15 Aligned_cols=13 Identities=69% Similarity=0.915 Sum_probs=12.1
Q ss_pred cccCCCCCCeeEE
Q 024597 239 SLTTGNAGGRLAC 251 (265)
Q Consensus 239 s~~tGnaG~RiAC 251 (265)
+..+|++|.|+||
T Consensus 132 sg~~~~~G~~~ac 144 (144)
T cd00305 132 SGGTGNAGVRVAC 144 (144)
T ss_pred cccceeeEeEEeC
Confidence 6789999999999
No 12
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=60.20 E-value=41 Score=26.82 Aligned_cols=23 Identities=26% Similarity=0.436 Sum_probs=18.2
Q ss_pred CCeEEEEEEcCCCCCceeEEEee
Q 024597 132 SPTTVNVRVTGLTPGPHGFHLHE 154 (265)
Q Consensus 132 g~t~V~v~vtGL~pG~Hg~HIHE 154 (265)
+.+..+++++||..-.-..|||+
T Consensus 32 ~~l~y~i~~~gl~~~~~~~hih~ 54 (118)
T smart00754 32 GSLHYQVTLSGLSGPETAAHIHE 54 (118)
T ss_pred CEEEEEEEEcccCCCceeeeEec
Confidence 45788899999986434899998
No 13
>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=54.55 E-value=72 Score=25.15 Aligned_cols=22 Identities=23% Similarity=0.567 Sum_probs=19.0
Q ss_pred CeEEEEEEcCCCCCceeEEEee
Q 024597 133 PTTVNVRVTGLTPGPHGFHLHE 154 (265)
Q Consensus 133 ~t~V~v~vtGL~pG~Hg~HIHE 154 (265)
.+.+++.++||....-.+|||.
T Consensus 34 ~l~y~i~~~gl~~~~~~~hih~ 55 (119)
T PF07452_consen 34 TLHYSITLSGLSSPPTAAHIHQ 55 (119)
T ss_pred EEEEEEEEeCCCCCcEEEEEEc
Confidence 5778999999977778999998
No 14
>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=22.42 E-value=92 Score=24.74 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=16.7
Q ss_pred eEEEEEEcCCCCCceeEEEeec
Q 024597 134 TTVNVRVTGLTPGPHGFHLHEY 155 (265)
Q Consensus 134 t~V~v~vtGL~pG~Hg~HIHE~ 155 (265)
..+++.+.+.....|.||+|-+
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 4567777776677899999964
No 15
>PF09559 Cas6: Cas6 Crispr; InterPro: IPR014174 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this entry resemble the Cas6 proteins described by IPR010156 from INTERPRO in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR regions in Anabaena variabilis (strain ATCC 29413/PCC 7937), Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus (strain DK 1622). Oddly, an orphan member is found in Thiobacillus denitrificans (strain ATCC 25259), whose genome does not seem to contain other evidence of CRISPR repeats or cas genes.
Probab=20.85 E-value=72 Score=28.95 Aligned_cols=37 Identities=30% Similarity=0.505 Sum_probs=22.9
Q ss_pred CCCCccEEEEecCCCCCCCCCCCCc-ccCCCC-CCeeEEEEEec
Q 024597 215 NTVVGRAFVVHELEDDLGKGGHELS-LTTGNA-GGRLACGMHKK 256 (265)
Q Consensus 215 ~sIIGRSIVIH~~~DD~g~g~~~~s-~~tGna-G~RiACGvI~~ 256 (265)
..|+|||++||+..++- .+. |..|=. ..++.||+.-.
T Consensus 152 ~~v~g~sL~v~~L~~e~-----Sl~LQ~~GLG~~r~mGCGlFiP 190 (195)
T PF09559_consen 152 GTVVGRSLMVAGLSPED-----SLRLQEQGLGGKRHMGCGLFIP 190 (195)
T ss_pred cceEEEEEEecCCChhh-----ceeehhhccCCCcccceeEecc
Confidence 46899999999965431 111 122322 46799998754
Done!