Query 037040
Match_columns 198
No_of_seqs 140 out of 1087
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 08:00:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037040.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037040hhsearch_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 1.6E-51 3.5E-56 330.3 19.4 150 46-197 2-151 (152)
2 PLN02642 copper, zinc superoxi 100.0 3E-51 6.4E-56 331.6 19.8 153 43-197 5-157 (164)
3 PRK15388 Cu/Zn superoxide dism 100.0 4.4E-45 9.4E-50 298.6 19.3 143 44-195 24-176 (177)
4 PRK10290 superoxide dismutase; 100.0 3.1E-44 6.8E-49 293.0 19.2 131 55-195 34-173 (173)
5 KOG0441 Cu2+/Zn2+ superoxide d 100.0 2.6E-44 5.7E-49 285.8 15.0 149 47-197 3-153 (154)
6 cd00305 Cu-Zn_Superoxide_Dismu 100.0 6.2E-42 1.4E-46 272.2 18.7 140 47-195 2-142 (144)
7 PF00080 Sod_Cu: Copper/zinc s 100.0 5.8E-42 1.3E-46 270.4 14.6 139 48-194 1-142 (142)
8 COG2032 SodC Cu/Zn superoxide 100.0 2E-41 4.3E-46 275.6 17.6 144 45-195 28-179 (179)
9 PLN02957 copper, zinc superoxi 100.0 1.5E-36 3.3E-41 259.0 16.9 129 45-198 80-208 (238)
10 KOG4656 Copper chaperone for s 100.0 9.6E-36 2.1E-40 246.5 8.4 136 46-198 82-217 (247)
11 COG4704 Uncharacterized protei 74.7 5.4 0.00012 31.8 4.2 21 72-92 75-95 (151)
12 PF07452 CHRD: CHRD domain; I 74.6 17 0.00036 27.0 6.8 36 57-92 19-55 (119)
13 smart00754 CHRD A domain in th 73.5 18 0.00038 27.1 6.7 38 56-93 18-55 (118)
14 PF08139 LPAM_1: Prokaryotic m 54.2 14 0.00031 21.0 2.2 19 16-34 6-24 (25)
15 cd00305 Cu-Zn_Superoxide_Dismu 38.9 13 0.00029 29.2 0.7 36 45-80 13-49 (144)
16 PRK10301 hypothetical protein; 35.2 2.1E+02 0.0045 22.0 7.4 23 72-94 86-109 (124)
17 PRK10081 entericidin B membran 32.0 59 0.0013 21.3 2.8 14 16-29 2-15 (48)
18 PF07731 Cu-oxidase_2: Multico 30.9 69 0.0015 24.0 3.5 23 72-94 42-64 (138)
19 PRK09810 entericidin A; Provis 29.7 57 0.0012 20.7 2.3 19 16-34 2-20 (41)
20 COG2834 LolA Outer membrane li 29.1 91 0.002 25.8 4.2 33 57-89 41-74 (211)
21 PF09559 Cas6: Cas6 Crispr; I 28.7 41 0.00089 28.3 2.0 34 155-195 152-189 (195)
22 PF08896 DUF1842: Domain of un 27.3 1.4E+02 0.0031 22.8 4.7 28 53-80 28-55 (114)
23 PF15240 Pro-rich: Proline-ric 27.1 41 0.0009 27.9 1.7 20 22-41 2-21 (179)
24 PF07172 GRP: Glycine rich pro 26.3 44 0.00096 24.8 1.6 20 16-35 1-21 (95)
25 COG5510 Predicted small secret 26.1 89 0.0019 20.1 2.7 7 16-22 2-8 (44)
26 PF15284 PAGK: Phage-encoded v 24.0 82 0.0018 21.7 2.4 20 16-35 1-20 (61)
27 PRK15222 putative pilin struct 22.9 2.1E+02 0.0045 23.3 4.9 24 69-94 51-75 (156)
28 PF07495 Y_Y_Y: Y_Y_Y domain; 22.4 83 0.0018 20.4 2.3 20 75-94 30-49 (66)
29 PHA02291 hypothetical protein 22.0 1.2E+02 0.0025 23.5 3.2 21 16-36 1-21 (132)
30 TIGR02807 cas6_var CRISPR-asso 21.8 51 0.0011 27.6 1.4 33 155-194 152-188 (190)
31 PRK10455 periplasmic protein; 20.7 1.1E+02 0.0024 24.7 3.0 19 16-34 1-19 (161)
No 1
>PLN02386 superoxide dismutase [Cu-Zn]
Probab=100.00 E-value=1.6e-51 Score=330.26 Aligned_cols=150 Identities=61% Similarity=0.977 Sum_probs=144.3
Q ss_pred ccEEEEEcCCCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCCCccccCCcccCCCCCCCCCCCCCCCCC
Q 037040 46 VKAVAYVISKWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAHFCQSTGDHFNPFRKHHGGPEDWIRHAG 125 (198)
Q Consensus 46 ~~Ava~l~g~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~~c~saGgHfnP~~~~h~~p~~~~~~~G 125 (198)
.+|+|+|+++..++|+|+|+|..++.++|+++|+||+||.|+|||||+|||+++|.|+|+||||.++.|+.|++..+|+|
T Consensus 2 ~~a~a~~~~~~~v~G~v~f~q~~~g~v~i~~~~~GL~pG~hg~HIHe~Gd~~~g~~SaGgHfnP~~~~Hg~~~~~~~H~G 81 (152)
T PLN02386 2 VKAVAVLNSSEGVKGTIFFTQEGDGPTTVTGSLSGLKPGLHGFHVHALGDTTNGCMSTGPHFNPAGKEHGAPEDENRHAG 81 (152)
T ss_pred ceEEEEEcCCCCCEEEEEEEEcCCCCEEEEEEEeCCCCCceeEEEeCCCCCCCCcccccCccCCCCCCCCCCCcccCccc
Confidence 47999999988899999999987767999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEEec
Q 037040 126 DLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIGLQ 197 (198)
Q Consensus 126 DLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~~s 197 (198)
|||||.++++|+++++++++ +++|.++++|+|||||||+++|||++++++.|+++||+|+|||||||+++
T Consensus 82 DLgNi~~~~~G~a~~~~~~~--~~~L~g~~~i~GrslVIHa~~DD~~~~~~~~s~~~G~aG~RiACgvI~~~ 151 (152)
T PLN02386 82 DLGNVTVGDDGTATFTIVDK--QIPLTGPNSIVGRAVVVHADPDDLGKGGHELSKSTGNAGGRVACGIIGLQ 151 (152)
T ss_pred cccCEEECCCCeEEEEEECC--ceEeCCCCccCCcEEEEEccCCCcCCCcccccccCCCCCceEEEEEEEec
Confidence 99999999999999999998 99999999999999999999999999999999999999999999999986
No 2
>PLN02642 copper, zinc superoxide dismutase
Probab=100.00 E-value=3e-51 Score=331.64 Aligned_cols=153 Identities=51% Similarity=0.824 Sum_probs=146.3
Q ss_pred CccccEEEEEcCCCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCCCccccCCcccCCCCCCCCCCCCCC
Q 037040 43 VPTVKAVAYVISKWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAHFCQSTGDHFNPFRKHHGGPEDWIR 122 (198)
Q Consensus 43 ~~~~~Ava~l~g~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~~c~saGgHfnP~~~~h~~p~~~~~ 122 (198)
....+|+|++++++.++|+|+|+|..++.++|+++|+||+||.|+|||||+|||+++|.|+|+||||.++.|+.|++..+
T Consensus 5 ~~~~~A~a~~~g~~~v~G~v~f~q~~~g~v~I~~~v~GL~pG~HG~HIHe~Gd~~~g~~SaGgHfNP~~~~HG~~~~~~r 84 (164)
T PLN02642 5 RGNLRAVALIAGDNNVRGCLQFVQDIFGTTHVTGKISGLSPGFHGFHIHSFGDTTNGCISTGPHFNPLNRVHGPPNEEER 84 (164)
T ss_pred CCCeeEEEEEcCCCCcEEEEEEEECCCCcEEEEEEEcCCCCCceeEEEcCCCcCCCCcccccCcccCCCCcCCCCCcCCC
Confidence 35678999999988899999999987766999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEEec
Q 037040 123 HAGDLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIGLQ 197 (198)
Q Consensus 123 ~~GDLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~~s 197 (198)
|+||||||+++++|+++++++++ .++|.++++|+|||||||+.+|||++++++.|+++||+|+|||||||+++
T Consensus 85 H~GDLgNi~a~~~G~a~~~~~~~--~i~L~g~~~iiGRalVVHa~~DD~~~~~~~~s~~tGnaG~RiACGVI~~~ 157 (164)
T PLN02642 85 HAGDLGNILAGSDGVAEILIKDK--HIPLSGQYSILGRAVVVHADPDDLGKGGHKLSKSTGNAGSRVGCGIIGLQ 157 (164)
T ss_pred cccccCCEEECCCCeEEEEEEcC--ceecCCCCCcCCcEEEEeccCCccCcCcccccccCCCCCceEEEEEEEec
Confidence 99999999999999999999999 99999999999999999999999999999999999999999999999975
No 3
>PRK15388 Cu/Zn superoxide dismutase; Provisional
Probab=100.00 E-value=4.4e-45 Score=298.56 Aligned_cols=143 Identities=27% Similarity=0.406 Sum_probs=125.0
Q ss_pred ccccEEEEE-cCCCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCC--------CccccCCcccCCCC-C
Q 037040 44 PTVKAVAYV-ISKWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAH--------FCQSTGDHFNPFRK-H 113 (198)
Q Consensus 44 ~~~~Ava~l-~g~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~--------~c~saGgHfnP~~~-~ 113 (198)
+...+...+ ++++++.|+++|+|..++ ++|+++++||+||.|+|||||+|||++ +|.|||+||||+++ .
T Consensus 24 ~~~~~~~~~~~~~g~~~G~v~f~~~~~g-v~I~~~l~GL~pG~HGfHIHe~GdC~~~~~~G~~~~~~SAGgHfNP~~~~~ 102 (177)
T PRK15388 24 LTVKMNDALSSGTGENIGEITVSETPYG-LLFTPHLNGLTPGIHGFHVHTNPSCMPGMKDGKEVPALMAGGHLDPEKTGK 102 (177)
T ss_pred ccEEEEEeecCCCCceEEEEEEEEcCCc-EEEEEEEcCCCCcceEEEEccCCCccCcccCCCcccccccCCCcCCCCCCC
Confidence 344443333 356889999999999887 999999999999999999999999973 28999999999997 7
Q ss_pred CCCCCCCCCCCCCCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEE
Q 037040 114 HGGPEDWIRHAGDLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGV 193 (198)
Q Consensus 114 h~~p~~~~~~~GDLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgv 193 (198)
|+.|++..+|+||||||+++++|++++.++++ .+. ++++|+|||||||+++|||++ .|+++||+|+||||||
T Consensus 103 Hg~p~~~~~H~GDLpNi~a~~dG~a~~~~~~~--~~~--~~~~i~GralVIHa~~DD~~~----~p~~~GnaG~RiACGV 174 (177)
T PRK15388 103 HLGPYNDKGHLGDLPGLVVNADGTATYPLLAP--RLK--SLSELKGHSLMIHKGGDNYSD----KPAPLGGGGARFACGV 174 (177)
T ss_pred CCCCCCCCCCcCcCcCEEECCCccEEEEEEeC--Ccc--cCcccCCcEEEEECCCCCCCC----CCCcCCCCCceEEEEe
Confidence 99998888999999999999999999999988 653 347999999999999999964 5778999999999999
Q ss_pred EE
Q 037040 194 IG 195 (198)
Q Consensus 194 I~ 195 (198)
|+
T Consensus 175 I~ 176 (177)
T PRK15388 175 IE 176 (177)
T ss_pred ec
Confidence 97
No 4
>PRK10290 superoxide dismutase; Provisional
Probab=100.00 E-value=3.1e-44 Score=292.98 Aligned_cols=131 Identities=29% Similarity=0.525 Sum_probs=118.8
Q ss_pred CCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCC----C----ccccCCcccCCCC-CCCCCCCCCCCCC
Q 037040 55 KWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAH----F----CQSTGDHFNPFRK-HHGGPEDWIRHAG 125 (198)
Q Consensus 55 ~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~----~----c~saGgHfnP~~~-~h~~p~~~~~~~G 125 (198)
++.+.|+++|+|..++ ++|+++++||+||.|+|||||+|||+. + |.|+|+||||.++ .|+.|+. .+|+|
T Consensus 34 ~g~~~G~v~f~~~~~g-v~i~~~l~GL~pG~HGfHIHe~Gdc~~~~~~G~~~~~~sAGgHfNP~~~~~hg~p~~-~~H~G 111 (173)
T PRK10290 34 VGQSIGSVTITETDKG-LEFSPDLKALPPGEHGFHIHAKGSCQPATKDGKASAAEAAGGHLDPQNTGKHEGPEG-AGHLG 111 (173)
T ss_pred CCceEEEEEEEEcCCc-EEEEEEEcCCCCCceEEEEeCCCccCCcccCCCcccccccCCccCCCCCcCCCCCCC-CCCcC
Confidence 5789999999999887 999999999999999999999999983 2 8999999999998 7888874 68999
Q ss_pred CCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEE
Q 037040 126 DLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIG 195 (198)
Q Consensus 126 DLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~ 195 (198)
|||||+++++|+++++++++ .++ +.++|+|||||||+++|||++ .++|+||+|+|||||||+
T Consensus 112 DL~ni~a~~dG~a~~~~~~~--~~~--~~~~i~GralVIH~~~DD~~~----~~~~~GnaG~RiACGVI~ 173 (173)
T PRK10290 112 DLPALVVNNDGKATDPVIAP--RLK--SLDEVKDKALMVHVGGDNMSD----QPKPLGGGGERYACGVIK 173 (173)
T ss_pred cccCEEECCCeeEEEEEEeC--Ccc--CccccCCcEEEEECCCCCCCC----CCCcCCCCcceEEEEeEC
Confidence 99999999999999999988 654 458999999999999999964 477899999999999995
No 5
>KOG0441 consensus Cu2+/Zn2+ superoxide dismutase SOD1 [Inorganic ion transport and metabolism]
Probab=100.00 E-value=2.6e-44 Score=285.81 Aligned_cols=149 Identities=49% Similarity=0.793 Sum_probs=143.2
Q ss_pred cEEEEEcCCC-CeEEEEEEEEeCCC-cEEEEEEEeecCCCceeeEEeecCCCCCCccccCCcccCCCCCCCCCCCCCCCC
Q 037040 47 KAVAYVISKW-GPKGILHFKQEGDG-PTTIKGTLYYLSQGAHGFHIHVYGDMAHFCQSTGDHFNPFRKHHGGPEDWIRHA 124 (198)
Q Consensus 47 ~Ava~l~g~~-~V~G~i~f~q~~~g-~v~V~~~i~GL~pg~hg~HIHe~gd~~~~c~saGgHfnP~~~~h~~p~~~~~~~ 124 (198)
+|+|+++++. .|.|+|.|+|..++ ++.|++.|+||+||.|+||||+|||.+++|.|+|+||||.++.|+.|.++.||+
T Consensus 3 ~~~avl~g~~~~V~G~i~F~Q~~~~~~~~v~~~i~GL~pg~hgfHvHqfGD~t~GC~SaGphFNp~~~~hg~p~~~~rH~ 82 (154)
T KOG0441|consen 3 QAVAVLEGDEIQVIGVITFEQFLPGEPLRVSGEVTGLPPGKHGFHVHQFGDNTNGCKSAGPHFNPNKKTHGGPVDEVRHV 82 (154)
T ss_pred ceEEEEecCCCCceeEEEEEEcCCCCcEEEEEEEecCCCceeeEEEEeccCCCCChhcCCCCCCCcccCCCCcccccccc
Confidence 7899999865 89999999995555 899999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEEec
Q 037040 125 GDLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIGLQ 197 (198)
Q Consensus 125 GDLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~~s 197 (198)
|||||+.++++|.+..++.+. .++|+|+++|+|||+|||+.+||+++|..+.+.++||+|+|+|||+|++.
T Consensus 83 gdlGnv~~~~~G~~~~~~~d~--~i~l~g~~sivgrs~vvHa~~ddLg~G~~~~s~ktgnag~r~aCgvi~~~ 153 (154)
T KOG0441|consen 83 GDLGNVDAKDDGVISRVFGDS--VITLSGPNSIVGRSVVVHAGEDDLGKGGHELSKKTGNAGARPACGVIGIA 153 (154)
T ss_pred ccccccccCCCceEEEEEccc--eEEEeeccccceeEEEEeccCccccCCchhhhhhccccCCCccceeeecc
Confidence 999999999999999999999 99999999999999999999999999999999999999999999999976
No 6
>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=6.2e-42 Score=272.21 Aligned_cols=140 Identities=48% Similarity=0.734 Sum_probs=130.8
Q ss_pred cEEEEEcCC-CCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCCCccccCCcccCCCCCCCCCCCCCCCCC
Q 037040 47 KAVAYVISK-WGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAHFCQSTGDHFNPFRKHHGGPEDWIRHAG 125 (198)
Q Consensus 47 ~Ava~l~g~-~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~~c~saGgHfnP~~~~h~~p~~~~~~~G 125 (198)
+|+|+|++. +.++|+|+|+|..++ ++|+++++||+||.|+|||||+|||+++|+|+|+||||.++.|+.|.+..||+|
T Consensus 2 ~a~~~l~~~~g~v~G~v~f~q~~~~-v~v~~~l~GL~pG~hg~HIHe~Gd~~~~~~saGgh~np~~~~hg~~~~~~~h~G 80 (144)
T cd00305 2 SAVAVLKGPDGKVVGTVTFTQQSGG-VTITGELSGLTPGLHGFHIHEFGDCTNGCTSAGGHFNPFGKKHGGPNDEGRHAG 80 (144)
T ss_pred cEEEEEECCCCceEEEEEEEECCCC-EEEEEEEECCCCCceeEEEEecCCCCCccccccCccCCCCCCCCCCCCCCCCCC
Confidence 589999874 579999999999885 999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEE
Q 037040 126 DLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIG 195 (198)
Q Consensus 126 DLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~ 195 (198)
|||||+++++|+++++++++ +++|++.++++|||||||+.+||| .++|.|++|.|++||+|.
T Consensus 81 DLgni~~~~~G~~~~~~~~~--~~~l~~~~~iiGrsivVH~~~Dd~------~~~p~~~sg~~~~~G~~~ 142 (144)
T cd00305 81 DLGNIVADKDGVATVSVLDP--LISLKGGNSIIGRSLVVHAGQDDL------GKGPDELSGGTGNAGVRV 142 (144)
T ss_pred cCCCEEECCCCeEEEEEEeC--cEEcCCCCCcCCcEEEEecCCCCC------CCCCCcccccceeeEeEE
Confidence 99999999999999999999 999988889999999999999998 467888889999999874
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=5.8e-42 Score=270.45 Aligned_cols=139 Identities=48% Similarity=0.775 Sum_probs=130.3
Q ss_pred EEEEEcC-CCCeEEEEEEEEeCCC-cEEEEEEEeecCCCceeeEEeecCCC-CCCccccCCcccCCCCCCCCCCCCCCCC
Q 037040 48 AVAYVIS-KWGPKGILHFKQEGDG-PTTIKGTLYYLSQGAHGFHIHVYGDM-AHFCQSTGDHFNPFRKHHGGPEDWIRHA 124 (198)
Q Consensus 48 Ava~l~g-~~~V~G~i~f~q~~~g-~v~V~~~i~GL~pg~hg~HIHe~gd~-~~~c~saGgHfnP~~~~h~~p~~~~~~~ 124 (198)
|+|+|++ .+.|+|+|+|+|..+. .+.|+++++||+||.|+||||++|+| +++|.++|+||||.++.|+.|+...|++
T Consensus 1 a~a~l~~~~~~v~G~v~f~q~~~~~~~~v~~~~~GL~~g~~~~hIH~~g~~~~~~c~s~G~h~np~~~~~~~~~~~~~~~ 80 (142)
T PF00080_consen 1 AVAVLKGAGGKVKGTVTFTQVSDGDGVQVTVSLNGLPPGQHGYHIHENGDCSSNNCSSAGGHYNPTNVPHGGPSADNCHA 80 (142)
T ss_dssp EEEEEBETSSSEEEEEEEEEETTTTEEEEEEEEESSSSEEEEEEEESSSTCSTTTTGGG-SBCETTTSSSSSTTSSSSCT
T ss_pred CEEEEeCCCCCeEEEEEEEEeCCCCCEEEEEEEECCCCCCceEEEEeccccccccccccceecCccccccCCcccccccc
Confidence 7999996 4789999999999965 59999999999999999999999999 7789999999999999999998788999
Q ss_pred CCCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEE
Q 037040 125 GDLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVI 194 (198)
Q Consensus 125 GDLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI 194 (198)
|||++++++.+|.++.+|++. +++|+|+++|+|||||||+++||+ .++++|++|+|||||+|
T Consensus 81 GDL~~~~~~~~G~~~~~~~~~--~l~l~g~~siiGRSiVIH~~~~d~------~~~~~g~~g~RlACg~I 142 (142)
T PF00080_consen 81 GDLGNKYVDADGSASFTFTDS--NLSLSGPNSIIGRSIVIHSGPDDF------TSQPTGNAGARLACGVI 142 (142)
T ss_dssp TEEEEEEESTTSEEEEEEEES--SSBSSSTTBHTTSEEEEESSSSTT------THHHHTTTTSEEEEEEE
T ss_pred ccccccccccCCceEEEEEee--eEeccCCccccCCEEEEEeCCCCc------ccccCCCCCCcEEEEeC
Confidence 999999999999999999998 999999999999999999999998 78899999999999998
No 8
>COG2032 SodC Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=2e-41 Score=275.61 Aligned_cols=144 Identities=38% Similarity=0.594 Sum_probs=130.1
Q ss_pred cccEEEEEc-CCCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCC------CccccCCcccCC-CCCCCC
Q 037040 45 TVKAVAYVI-SKWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAH------FCQSTGDHFNPF-RKHHGG 116 (198)
Q Consensus 45 ~~~Ava~l~-g~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~------~c~saGgHfnP~-~~~h~~ 116 (198)
...+.+.+. .+++..|+|++++.+.+ +.++..+.+|+||.|||||||+|+|++ +|.||||||||. .+.|+.
T Consensus 28 ~~~~~~~~~~~~G~~vG~vt~~e~~~g-~~~~~~~~~L~pg~hGfHIHe~G~C~pkdgk~~~~~sAGGHfdP~~~~~Hg~ 106 (179)
T COG2032 28 EVKANAVLVDGTGKDVGTVTITETGYG-LLFTPALGGLPPGEHGFHIHEKGSCTPKDGKPVDFLSAGGHFDPQNTKKHGG 106 (179)
T ss_pred cccceeeccCCCCceeEEEEEeecCCc-eEEeecccCCCCcceeEEecccCCCcCCCCCCcccccccCCcCCccCCCCCC
Confidence 345666665 45688999999999998 999999999999999999999999987 599999999999 689999
Q ss_pred CCCCCCCCCCCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEE
Q 037040 117 PEDWIRHAGDLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIG 195 (198)
Q Consensus 117 p~~~~~~~GDLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~ 195 (198)
|+++.+|+|||++|++++||+++..++++ .+++.+..++.|||||||+.+|||.. .+.|+|++|+|+|||||+
T Consensus 107 p~~~~~H~GDLP~L~v~~dG~a~~~v~~~--~~~l~~l~~v~G~alvIHag~Dd~~~----~P~p~G~aG~R~ACGVI~ 179 (179)
T COG2032 107 PNADGGHAGDLPNLFVNADGKATLPVLAP--RLKLKGLLEVKGRALVIHAGGDDYST----QPEPLGGAGARVACGVIK 179 (179)
T ss_pred CCCCCCCcCcCcceEECCCCcEEEEEecc--cceeccccccCCeEEEEEcCCccccC----CCccCCCCccceeeeeeC
Confidence 99989999999999999999999999999 99999999999999999999999942 223499999999999995
No 9
>PLN02957 copper, zinc superoxide dismutase
Probab=100.00 E-value=1.5e-36 Score=259.04 Aligned_cols=129 Identities=29% Similarity=0.408 Sum_probs=116.9
Q ss_pred cccEEEEEcCCCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCCCccccCCcccCCCCCCCCCCCCCCCC
Q 037040 45 TVKAVAYVISKWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAHFCQSTGDHFNPFRKHHGGPEDWIRHA 124 (198)
Q Consensus 45 ~~~Ava~l~g~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~~c~saGgHfnP~~~~h~~p~~~~~~~ 124 (198)
...|+|.++++ .|.|+|+|+|..++.+.|+++|+||+||.|+|||||+|||+++|.|+|+||||.+++|+ .+|+
T Consensus 80 ~~~av~~~~g~-~v~G~v~~~~~~~~~v~i~~~~~GL~pg~hg~hiHe~Gd~~~~~~saG~hfnp~~~~h~-----~~h~ 153 (238)
T PLN02957 80 VSAAVAEFKGP-DIFGVVRFAQVSMELARIEAAFSGLSPGTHGWSINEYGDLTRGAASTGKVYNPSDDDTD-----EEPL 153 (238)
T ss_pred cceEEEEecCC-ceEEEEEEEEcCCCCEEEEEEEcCCCCCcEEEEEcCCCCCCCCccccCCCCCCccCCCC-----CCCC
Confidence 35689999984 69999999999776699999999999999999999999999999999999999999997 6899
Q ss_pred CCCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEEecC
Q 037040 125 GDLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIGLQA 198 (198)
Q Consensus 125 GDLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~~s~ 198 (198)
||||||.++++|+++++++++ .++| ++|+|||||||+++|+. +.++|||||+|||
T Consensus 154 GDLgni~~~~~G~a~~~~~~~--~~~l---~~iiGrs~vih~~~D~~--------------~~~~~~gvi~rsa 208 (238)
T PLN02957 154 GDLGTLEADENGEATFSGTKE--KLKV---WDLIGRSLAVYATADKS--------------GPGIAAAVIARSA 208 (238)
T ss_pred CccCCEEeCCCceEEEEEECC--CcCc---cccCCcEEEEEeCCCCC--------------CCCeEEEEEeccc
Confidence 999999999999999998888 7776 69999999999998852 2359999999986
No 10
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=9.6e-36 Score=246.51 Aligned_cols=136 Identities=44% Similarity=0.749 Sum_probs=124.5
Q ss_pred ccEEEEEcCCCCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeecCCCCCCccccCCcccCCCCCCCCCCCCCCCCC
Q 037040 46 VKAVAYVISKWGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVYGDMAHFCQSTGDHFNPFRKHHGGPEDWIRHAG 125 (198)
Q Consensus 46 ~~Ava~l~g~~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~gd~~~~c~saGgHfnP~~~~h~~p~~~~~~~G 125 (198)
..+++.+.++..|.|.++|.|.....++|++++.||+||.|++||||+||++++|+|+|.||||+..+|++|. .|
T Consensus 82 ~at~a~~~~~~~v~GvvRf~qvt~ek~lid~tvdGlspG~h~~~Ihe~GDlsng~~StG~~ynpf~~p~g~~~-----~g 156 (247)
T KOG4656|consen 82 LATVAKYTGPQAVQGVVRFVQVTEEKTLIDGTVDGLSPGLHGLHIHEYGDLSNGCESTGKHYNPFQEPHGCPN-----EG 156 (247)
T ss_pred HHHHHHhcCCccceeEEEEEEeccccEEEEEEecCCCCcccceeEeeccccccchhhcccccCCCcCCCCCCC-----cc
Confidence 4456667777799999999999987899999999999999999999999999999999999999999999886 39
Q ss_pred CCCCeeeCCCCeEEEEEEEcCceEecCCCCCCCccEEEEecCCCCCCCCCCCCCccCCCCCCeEEEEEEEecC
Q 037040 126 DLGNIYVGFDGKAKINIVDKHKLIPLVGPNSIIGRSVVIHDKHDDLGKVGNYHSKKNGNAGDKIACGVIGLQA 198 (198)
Q Consensus 126 DLgni~~~~~G~a~~~~~~~~~~l~L~g~~sIiGRSIVIH~~~Dd~g~g~~~~s~~~G~aG~RiACgvI~~s~ 198 (198)
||||+.+|++|++.+++.++ .|+. |++||||+||.+..||+| +++ |++|.|+|||||.|||
T Consensus 157 DLGn~~ad~nGraf~s~~de--~Lkv---wdlIGRsvVi~k~~ddlg--g~p-----~nsge~la~gvIARSA 217 (247)
T KOG4656|consen 157 DLGNNRADKNGRAFFSAPDE--KLKV---WDLIGRSVVISKSLDDLG--GEP-----GNSGERLACGVIARSA 217 (247)
T ss_pred cccccccccCCcEEEecccc--cccH---hhhhceeEEEeccccccC--CCC-----CCcCcceeEEEeeecc
Confidence 99999999999999999999 8988 799999999999999983 333 8899999999999986
No 11
>COG4704 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.73 E-value=5.4 Score=31.84 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=16.1
Q ss_pred EEEEEEEeecCCCceeeEEee
Q 037040 72 TTIKGTLYYLSQGAHGFHIHV 92 (198)
Q Consensus 72 v~V~~~i~GL~pg~hg~HIHe 92 (198)
.-+..++.+|+||.|.+-+-+
T Consensus 75 dpv~~~f~~Lk~G~YAvaa~q 95 (151)
T COG4704 75 DPVSKSFYGLKPGKYAVAAFQ 95 (151)
T ss_pred CchhheeecCCCccEEEEEEE
Confidence 346778899999998877643
No 12
>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=74.57 E-value=17 Score=27.05 Aligned_cols=36 Identities=31% Similarity=0.334 Sum_probs=30.5
Q ss_pred CeEEEEEEEEeCCC-cEEEEEEEeecCCCceeeEEee
Q 037040 57 GPKGILHFKQEGDG-PTTIKGTLYYLSQGAHGFHIHV 92 (198)
Q Consensus 57 ~V~G~i~f~q~~~g-~v~V~~~i~GL~pg~hg~HIHe 92 (198)
.-.|.+.|+-..++ .+.+++.++||....-..|||.
T Consensus 19 ~a~G~a~~~l~~~~~~l~y~i~~~gl~~~~~~~hih~ 55 (119)
T PF07452_consen 19 SASGTAWFTLDDDGNTLHYSITLSGLSSPPTAAHIHQ 55 (119)
T ss_pred CCEEEEEEEEECCCCEEEEEEEEeCCCCCcEEEEEEc
Confidence 56789999888876 6889999999966678999998
No 13
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=73.47 E-value=18 Score=27.12 Aligned_cols=38 Identities=32% Similarity=0.264 Sum_probs=29.7
Q ss_pred CCeEEEEEEEEeCCCcEEEEEEEeecCCCceeeEEeec
Q 037040 56 WGPKGILHFKQEGDGPTTIKGTLYYLSQGAHGFHIHVY 93 (198)
Q Consensus 56 ~~V~G~i~f~q~~~g~v~V~~~i~GL~pg~hg~HIHe~ 93 (198)
....|.+.|+-..++.+..++.++||..-.-..|||+-
T Consensus 18 t~a~G~a~~~l~~~~~l~y~i~~~gl~~~~~~~hih~~ 55 (118)
T smart00754 18 TGAVGGAWFTLDDDGSLHYQVTLSGLSGPETAAHIHEG 55 (118)
T ss_pred CCcEEEEEEEECCCCEEEEEEEEcccCCCceeeeEecc
Confidence 35678888888755568899999999864338999983
No 14
>PF08139 LPAM_1: Prokaryotic membrane lipoprotein lipid attachment site; InterPro: IPR012640 In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [,]. This lipid attachment site is found in homologues of the VirB proteins of type IV secretion systems (T4SS). Conjugal transfer across the cell envelope of Gram-negative bacteria is mediated by a supramolecular structure termed mating pair formation (Mpf) complex. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now known as T4SS. T4SS are involved in the delivery of effector molecules to eukaryotic target cells; each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection [].
Probab=54.20 E-value=14 Score=20.96 Aligned_cols=19 Identities=26% Similarity=0.356 Sum_probs=9.7
Q ss_pred hhhhhHHHHHHHHHHHHHH
Q 037040 16 MERTASIKLVALLAVLFCF 34 (198)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~ 34 (198)
|-|...+.+++++.+++|+
T Consensus 6 mmKkil~~l~a~~~LagCs 24 (25)
T PF08139_consen 6 MMKKILFPLLALFMLAGCS 24 (25)
T ss_pred HHHHHHHHHHHHHHHhhcc
Confidence 4444454555555555554
No 15
>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=38.89 E-value=13 Score=29.16 Aligned_cols=36 Identities=8% Similarity=-0.108 Sum_probs=22.6
Q ss_pred cccEEEEEcCC-CCeEEEEEEEEeCCCcEEEEEEEee
Q 037040 45 TVKAVAYVISK-WGPKGILHFKQEGDGPTTIKGTLYY 80 (198)
Q Consensus 45 ~~~Ava~l~g~-~~V~G~i~f~q~~~g~v~V~~~i~G 80 (198)
....++.|+.. ..+.=+++++....+.--+.+.-.|
T Consensus 13 ~v~G~v~f~q~~~~v~v~~~l~GL~pG~hg~HIHe~G 49 (144)
T cd00305 13 KVVGTVTFTQQSGGVTITGELSGLTPGLHGFHIHEFG 49 (144)
T ss_pred ceEEEEEEEECCCCEEEEEEEECCCCCceeEEEEecC
Confidence 45678888743 3677777777666664445555554
No 16
>PRK10301 hypothetical protein; Provisional
Probab=35.22 E-value=2.1e+02 Score=21.97 Aligned_cols=23 Identities=22% Similarity=0.186 Sum_probs=17.5
Q ss_pred EEEEEEEe-ecCCCceeeEEeecC
Q 037040 72 TTIKGTLY-YLSQGAHGFHIHVYG 94 (198)
Q Consensus 72 v~V~~~i~-GL~pg~hg~HIHe~g 94 (198)
..+++.+. .|++|.|.+..+..+
T Consensus 86 ~~~~v~l~~~L~~G~YtV~Wrvvs 109 (124)
T PRK10301 86 KQLIVPLADSLKPGTYTVDWHVVS 109 (124)
T ss_pred cEEEEECCCCCCCccEEEEEEEEe
Confidence 45677774 799999988888755
No 17
>PRK10081 entericidin B membrane lipoprotein; Provisional
Probab=31.98 E-value=59 Score=21.30 Aligned_cols=14 Identities=14% Similarity=0.266 Sum_probs=7.2
Q ss_pred hhhhhHHHHHHHHH
Q 037040 16 MERTASIKLVALLA 29 (198)
Q Consensus 16 ~~~~~~~~~~~~~~ 29 (198)
|||+..+.++++++
T Consensus 2 mKk~i~~i~~~l~~ 15 (48)
T PRK10081 2 VKKTIAAIFSVLVL 15 (48)
T ss_pred hHHHHHHHHHHHHH
Confidence 77775443433333
No 18
>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=30.91 E-value=69 Score=23.97 Aligned_cols=23 Identities=22% Similarity=0.236 Sum_probs=17.9
Q ss_pred EEEEEEEeecCCCceeeEEeecC
Q 037040 72 TTIKGTLYYLSQGAHGFHIHVYG 94 (198)
Q Consensus 72 v~V~~~i~GL~pg~hg~HIHe~g 94 (198)
..+++.+.+.....|.||+|-..
T Consensus 42 ~~v~~~l~N~~~~~Hp~HlHG~~ 64 (138)
T PF07731_consen 42 DVVEIVLQNNGSMPHPFHLHGHS 64 (138)
T ss_dssp SEEEEEEEECTTSSEEEEETTSE
T ss_pred CEEEEEEECCCCCccceEEEeeE
Confidence 46777778877778999999654
No 19
>PRK09810 entericidin A; Provisional
Probab=29.66 E-value=57 Score=20.65 Aligned_cols=19 Identities=26% Similarity=0.274 Sum_probs=8.8
Q ss_pred hhhhhHHHHHHHHHHHHHH
Q 037040 16 MERTASIKLVALLAVLFCF 34 (198)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~ 34 (198)
|+|...+.+++++++.+|.
T Consensus 2 Mkk~~~l~~~~~~~L~aCN 20 (41)
T PRK09810 2 MKRLIVLVLLASTLLTGCN 20 (41)
T ss_pred hHHHHHHHHHHHHHHhhhh
Confidence 6665443344444444443
No 20
>COG2834 LolA Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]
Probab=29.10 E-value=91 Score=25.83 Aligned_cols=33 Identities=12% Similarity=0.135 Sum_probs=17.1
Q ss_pred CeEEEEEEEEeCCC-cEEEEEEEeecCCCceeeE
Q 037040 57 GPKGILHFKQEGDG-PTTIKGTLYYLSQGAHGFH 89 (198)
Q Consensus 57 ~V~G~i~f~q~~~g-~v~V~~~i~GL~pg~hg~H 89 (198)
.+.++...+..... ....++++.=-.|+.+-|+
T Consensus 41 ~~s~~f~q~~~~g~~~~~~~g~~~~kkP~~~R~~ 74 (211)
T COG2834 41 SYSASFTQTVESGSGKQTQEGKLWIKRPNLFRWE 74 (211)
T ss_pred cceeEEEEEEEcCCCceEEEEEEEEecCCeEEEE
Confidence 45555555545443 2333366666666655554
No 21
>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=28.74 E-value=41 Score=28.27 Aligned_cols=34 Identities=21% Similarity=0.548 Sum_probs=23.4
Q ss_pred CCCCccEEEEecCCCCCCCCCCCCC---ccCCCC-CCeEEEEEEE
Q 037040 155 NSIIGRSVVIHDKHDDLGKVGNYHS---KKNGNA-GDKIACGVIG 195 (198)
Q Consensus 155 ~sIiGRSIVIH~~~Dd~g~g~~~~s---~~~G~a-G~RiACgvI~ 195 (198)
..|.|||++||....+ .| |..|=. ..++.||++-
T Consensus 152 ~~v~g~sL~v~~L~~e-------~Sl~LQ~~GLG~~r~mGCGlFi 189 (195)
T PF09559_consen 152 GTVVGRSLMVAGLSPE-------DSLRLQEQGLGGKRHMGCGLFI 189 (195)
T ss_pred cceEEEEEEecCCChh-------hceeehhhccCCCcccceeEec
Confidence 5688999999997653 33 344433 3568999874
No 22
>PF08896 DUF1842: Domain of unknown function (DUF1842); InterPro: IPR014992 This domain is found at the N terminus of proteins that are functionally uncharacterised.
Probab=27.26 E-value=1.4e+02 Score=22.84 Aligned_cols=28 Identities=11% Similarity=0.158 Sum_probs=22.1
Q ss_pred cCCCCeEEEEEEEEeCCCcEEEEEEEee
Q 037040 53 ISKWGPKGILHFKQEGDGPTTIKGTLYY 80 (198)
Q Consensus 53 ~g~~~V~G~i~f~q~~~g~v~V~~~i~G 80 (198)
.+...|.|..+++|...-++.|..+++|
T Consensus 28 ~~~~~VsG~a~ItQat~ppl~~~s~v~G 55 (114)
T PF08896_consen 28 TPDKSVSGRARITQATNPPLNFHSDVWG 55 (114)
T ss_pred CCCCEEEeEEEEEEecCCCcceEEEeEE
Confidence 3568999999999988666777777765
No 23
>PF15240 Pro-rich: Proline-rich
Probab=27.12 E-value=41 Score=27.93 Aligned_cols=20 Identities=10% Similarity=0.092 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHhhccccC
Q 037040 22 IKLVALLAVLFCFVNATKSR 41 (198)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~ 41 (198)
+++|+.+||||++++...++
T Consensus 2 LlVLLSvALLALSSAQ~~dE 21 (179)
T PF15240_consen 2 LLVLLSVALLALSSAQSTDE 21 (179)
T ss_pred hhHHHHHHHHHhhhcccccc
Confidence 34455566666666544433
No 24
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=26.29 E-value=44 Score=24.75 Aligned_cols=20 Identities=35% Similarity=0.290 Sum_probs=8.3
Q ss_pred hhhhhHHHHHHHHH-HHHHHh
Q 037040 16 MERTASIKLVALLA-VLFCFV 35 (198)
Q Consensus 16 ~~~~~~~~~~~~~~-~~~~~~ 35 (198)
|-.++.++|.++|| ++++++
T Consensus 1 MaSK~~llL~l~LA~lLlisS 21 (95)
T PF07172_consen 1 MASKAFLLLGLLLAALLLISS 21 (95)
T ss_pred CchhHHHHHHHHHHHHHHHHh
Confidence 33333344444444 344444
No 25
>COG5510 Predicted small secreted protein [Function unknown]
Probab=26.08 E-value=89 Score=20.09 Aligned_cols=7 Identities=29% Similarity=0.506 Sum_probs=4.4
Q ss_pred hhhhhHH
Q 037040 16 MERTASI 22 (198)
Q Consensus 16 ~~~~~~~ 22 (198)
|+|++.+
T Consensus 2 mk~t~l~ 8 (44)
T COG5510 2 MKKTILL 8 (44)
T ss_pred chHHHHH
Confidence 7777543
No 26
>PF15284 PAGK: Phage-encoded virulence factor
Probab=24.01 E-value=82 Score=21.67 Aligned_cols=20 Identities=20% Similarity=0.122 Sum_probs=14.5
Q ss_pred hhhhhHHHHHHHHHHHHHHh
Q 037040 16 MERTASIKLVALLAVLFCFV 35 (198)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~ 35 (198)
|++.-+++++++|++.+...
T Consensus 1 Mkk~ksifL~l~~~LsA~~F 20 (61)
T PF15284_consen 1 MKKFKSIFLALVFILSAAGF 20 (61)
T ss_pred ChHHHHHHHHHHHHHHHhhh
Confidence 77777788888777765544
No 27
>PRK15222 putative pilin structural protein SafD; Provisional
Probab=22.88 E-value=2.1e+02 Score=23.33 Aligned_cols=24 Identities=29% Similarity=0.504 Sum_probs=12.6
Q ss_pred CCcEEEEEEEeecCCCce-eeEEeecC
Q 037040 69 DGPTTIKGTLYYLSQGAH-GFHIHVYG 94 (198)
Q Consensus 69 ~g~v~V~~~i~GL~pg~h-g~HIHe~g 94 (198)
+|...-++.|. -++.| ||||=...
T Consensus 51 DG~~latGrI~--~~g~htGF~Vwsna 75 (156)
T PRK15222 51 DGMVLAQGWVT--YHGSHSGFRVWSDE 75 (156)
T ss_pred CCcEEEEEEEE--eCCCceeEEEEecc
Confidence 44455555555 44445 56666554
No 28
>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=22.44 E-value=83 Score=20.40 Aligned_cols=20 Identities=10% Similarity=0.087 Sum_probs=14.2
Q ss_pred EEEEeecCCCceeeEEeecC
Q 037040 75 KGTLYYLSQGAHGFHIHVYG 94 (198)
Q Consensus 75 ~~~i~GL~pg~hg~HIHe~g 94 (198)
+++++.|+||.|-|+|...-
T Consensus 30 ~~~~~~L~~G~Y~l~V~a~~ 49 (66)
T PF07495_consen 30 SISYTNLPPGKYTLEVRAKD 49 (66)
T ss_dssp EEEEES--SEEEEEEEEEEE
T ss_pred EEEEEeCCCEEEEEEEEEEC
Confidence 77778899998888887643
No 29
>PHA02291 hypothetical protein
Probab=21.95 E-value=1.2e+02 Score=23.48 Aligned_cols=21 Identities=33% Similarity=0.395 Sum_probs=12.7
Q ss_pred hhhhhHHHHHHHHHHHHHHhh
Q 037040 16 MERTASIKLVALLAVLFCFVN 36 (198)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~ 36 (198)
|-+.+.++-+++++|++.+..
T Consensus 1 MS~K~~iFYiL~~~VL~~si~ 21 (132)
T PHA02291 1 MSRKASIFYILVVIVLAFSIS 21 (132)
T ss_pred CCcchhhHHHHHHHHHHHHHH
Confidence 555666666666666655543
No 30
>TIGR02807 cas6_var CRISPR-associated protein, Cas6-related. Members of this protein family resemble the Cas6 proteins described by TIGR01877 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 ATCC 29413, Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus DK 1622. Oddly, an orphan member is found in Thiobacillus denitrificans ATCC 25259, whose genome does not seem to contain other evidence of CRISPR repeats or cas genes.
Probab=21.82 E-value=51 Score=27.61 Aligned_cols=33 Identities=21% Similarity=0.545 Sum_probs=22.5
Q ss_pred CCCCccEEEEecCCCCCCCCCCCCC---ccCCCC-CCeEEEEEE
Q 037040 155 NSIIGRSVVIHDKHDDLGKVGNYHS---KKNGNA-GDKIACGVI 194 (198)
Q Consensus 155 ~sIiGRSIVIH~~~Dd~g~g~~~~s---~~~G~a-G~RiACgvI 194 (198)
..|.|||++||...++ .| |..|=. ..++.||++
T Consensus 152 ~~v~g~sL~v~~Ls~e-------dSl~LQ~~GLGg~r~mGCGlF 188 (190)
T TIGR02807 152 FTVVGFALELHGLSAE-------DSLRLQEQGLGGRRKMGCGLF 188 (190)
T ss_pred ceEEEEEEEEcCCChH-------HhHhHHHhcCCCCCceeeeec
Confidence 5788999999997543 33 333433 356899986
No 31
>PRK10455 periplasmic protein; Reviewed
Probab=20.66 E-value=1.1e+02 Score=24.73 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=14.9
Q ss_pred hhhhhHHHHHHHHHHHHHH
Q 037040 16 MERTASIKLVALLAVLFCF 34 (198)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~ 34 (198)
|||.+.+.++++|++.+++
T Consensus 1 mrk~t~~~~as~l~~g~~~ 19 (161)
T PRK10455 1 MRKLTALFVASTLALGAAN 19 (161)
T ss_pred ChhHHHHHHHHHHHHHHHH
Confidence 8888888888888876654
Done!