Query 033108
Match_columns 127
No_of_seqs 132 out of 855
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 09:54:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033108.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033108hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03148 Blue copper-like prot 100.0 9.8E-41 2.1E-45 248.9 11.6 103 24-127 13-118 (167)
2 PF02298 Cu_bind_like: Plastoc 100.0 2.6E-32 5.7E-37 183.7 4.3 79 42-120 1-85 (85)
3 PRK02710 plastocyanin; Provisi 98.7 4.7E-07 1E-11 63.9 10.7 93 24-127 21-119 (119)
4 PF00127 Copper-bind: Copper b 98.5 4.6E-07 9.9E-12 61.7 6.3 74 51-126 17-98 (99)
5 TIGR02656 cyanin_plasto plasto 98.3 7.1E-06 1.5E-10 55.9 9.0 89 33-127 2-99 (99)
6 TIGR03102 halo_cynanin halocya 98.1 2.9E-05 6.2E-10 55.0 9.1 88 29-127 21-115 (115)
7 COG3794 PetE Plastocyanin [Ene 98.0 7.4E-05 1.6E-09 53.9 9.4 80 36-127 43-127 (128)
8 TIGR02375 pseudoazurin pseudoa 97.8 0.0002 4.3E-09 50.8 7.8 72 51-127 15-87 (116)
9 TIGR02657 amicyanin amicyanin. 97.1 0.0037 8E-08 41.1 7.5 70 51-127 11-83 (83)
10 PF06525 SoxE: Sulfocyanin (So 96.9 0.004 8.6E-08 47.9 7.1 72 55-126 90-185 (196)
11 TIGR03095 rusti_cyanin rusticy 96.8 0.0058 1.3E-07 44.8 6.5 72 53-127 54-148 (148)
12 KOG3858 Ephrin, ligand for Eph 95.3 0.14 3.1E-06 40.4 8.4 32 54-85 46-86 (233)
13 PF13473 Cupredoxin_1: Cupredo 95.0 0.053 1.2E-06 36.7 4.6 63 51-126 35-104 (104)
14 TIGR03094 sulfo_cyanin sulfocy 94.4 0.038 8.2E-07 42.3 2.8 24 103-126 161-184 (195)
15 COG4454 Uncharacterized copper 91.9 0.29 6.3E-06 36.5 4.2 77 51-127 63-157 (158)
16 PF00812 Ephrin: Ephrin; Inte 90.0 0.62 1.4E-05 34.2 4.4 34 53-86 24-68 (145)
17 TIGR03096 nitroso_cyanin nitro 89.3 0.72 1.6E-05 33.6 4.2 55 51-116 61-122 (135)
18 TIGR02695 azurin azurin. Azuri 87.8 3.1 6.7E-05 30.0 6.6 22 103-125 102-124 (125)
19 PRK02888 nitrous-oxide reducta 77.8 9.8 0.00021 34.3 7.1 65 51-126 555-632 (635)
20 PF07172 GRP: Glycine rich pro 77.8 1.5 3.3E-05 29.9 1.6 12 22-33 16-27 (95)
21 PF00116 COX2: Cytochrome C ox 76.8 3.9 8.4E-05 28.7 3.6 65 51-127 46-120 (120)
22 TIGR02376 Cu_nitrite_red nitri 73.7 8.1 0.00018 31.4 5.1 72 52-126 60-144 (311)
23 TIGR02866 CoxB cytochrome c ox 72.5 13 0.00029 28.0 5.8 80 35-126 95-190 (201)
24 PRK09723 putative fimbrial-lik 72.3 47 0.001 28.6 9.5 49 23-73 19-68 (421)
25 cd02859 AMPKbeta_GBD_like AMP- 64.5 33 0.0007 22.0 5.6 46 60-108 3-50 (79)
26 COG1622 CyoA Heme/copper-type 64.0 29 0.00064 27.5 6.3 64 52-127 138-211 (247)
27 PRK10378 inactive ferrous ion 63.9 31 0.00068 29.1 6.7 15 98-112 91-105 (375)
28 PLN02604 oxidoreductase 61.6 41 0.00089 29.6 7.4 69 51-126 55-142 (566)
29 cd06555 ASCH_PF0470_like ASC-1 60.6 8.9 0.00019 26.8 2.5 14 53-66 30-43 (109)
30 PF09792 But2: Ubiquitin 3 bin 54.0 53 0.0012 23.8 5.8 27 98-126 100-126 (143)
31 COG3241 Azurin [Energy product 53.9 6.4 0.00014 28.6 0.9 28 96-124 114-147 (151)
32 TIGR02228 sigpep_I_arch signal 53.4 44 0.00095 24.6 5.3 26 52-77 58-87 (158)
33 PF05382 Amidase_5: Bacterioph 53.2 51 0.0011 24.1 5.6 36 53-88 74-114 (145)
34 PF10731 Anophelin: Thrombin i 50.7 11 0.00023 24.0 1.4 28 13-41 5-32 (65)
35 PF10377 ATG11: Autophagy-rela 50.6 23 0.00049 25.3 3.3 18 53-70 41-58 (129)
36 PF02839 CBM_5_12: Carbohydrat 47.3 12 0.00026 20.8 1.2 17 47-63 2-18 (41)
37 KOG1546 Metacaspase involved i 46.2 13 0.00028 31.2 1.6 30 54-85 134-168 (362)
38 PF07732 Cu-oxidase_3: Multico 45.6 6.6 0.00014 27.3 -0.1 72 52-126 27-113 (117)
39 PF06462 Hyd_WA: Propeller; I 42.6 54 0.0012 17.6 3.3 24 98-121 3-27 (32)
40 PF12961 DUF3850: Domain of Un 40.9 18 0.00039 23.6 1.4 13 52-64 26-38 (72)
41 PLN02354 copper ion binding / 38.6 2.8E+02 0.006 24.5 9.6 75 48-126 54-144 (552)
42 TIGR01480 copper_res_A copper- 37.9 1.1E+02 0.0023 27.3 6.2 84 42-127 488-587 (587)
43 PF02362 B3: B3 DNA binding do 37.9 22 0.00048 23.0 1.5 19 50-68 69-87 (100)
44 PF11008 DUF2846: Protein of u 37.8 1.3E+02 0.0028 20.5 5.7 58 50-110 40-100 (117)
45 PF14326 DUF4384: Domain of un 37.8 26 0.00056 22.6 1.8 15 54-68 2-16 (83)
46 PF04014 Antitoxin-MazE: Antid 37.4 8.8 0.00019 22.2 -0.4 33 35-68 2-34 (47)
47 KOG3416 Predicted nucleic acid 36.1 35 0.00076 24.8 2.4 31 33-64 40-71 (134)
48 KOG2315 Predicted translation 35.0 99 0.0022 27.6 5.4 63 48-110 208-277 (566)
49 TIGR03388 ascorbase L-ascorbat 34.7 73 0.0016 27.8 4.6 69 52-127 33-120 (541)
50 MTH00047 COX2 cytochrome c oxi 32.9 49 0.0011 25.2 2.9 26 99-126 160-189 (194)
51 PF09451 ATG27: Autophagy-rela 30.3 55 0.0012 25.9 2.9 21 26-46 218-238 (268)
52 COG3627 PhnJ Uncharacterized e 29.7 32 0.0007 27.3 1.5 23 97-119 257-280 (291)
53 COG4446 Uncharacterized protei 28.8 50 0.0011 24.0 2.2 23 53-76 90-112 (141)
54 MTH00140 COX2 cytochrome c oxi 28.7 74 0.0016 24.6 3.3 26 99-126 184-213 (228)
55 PF14478 DUF4430: Domain of un 27.9 21 0.00045 22.2 0.1 25 40-64 39-68 (68)
56 PLN00044 multi-copper oxidase- 27.7 1.4E+02 0.003 26.8 5.2 72 52-127 61-147 (596)
57 PF11604 CusF_Ec: Copper bindi 27.0 37 0.00081 21.4 1.2 21 48-68 36-56 (70)
58 cd04491 SoSSB_OBF SoSSB_OBF: A 25.5 72 0.0016 20.1 2.4 31 33-64 26-58 (82)
59 PF02933 CDC48_2: Cell divisio 25.1 61 0.0013 19.7 1.9 17 51-67 15-31 (64)
60 PTZ00047 cytochrome c oxidase 25.1 97 0.0021 23.2 3.3 25 100-126 118-146 (162)
61 KOG3342 Signal peptidase I [In 24.6 29 0.00064 26.2 0.4 23 53-75 76-102 (180)
62 PRK09495 glnH glutamine ABC tr 24.2 85 0.0018 23.5 2.9 20 25-44 18-37 (247)
63 PF00686 CBM_20: Starch bindin 23.7 1.1E+02 0.0024 19.9 3.1 35 32-66 17-67 (96)
64 PF04945 YHS: YHS domain; Int 23.2 68 0.0015 18.3 1.7 19 94-112 11-30 (47)
65 COG1430 Uncharacterized conser 23.2 52 0.0011 23.6 1.4 21 47-67 103-123 (126)
66 PLN02191 L-ascorbate oxidase 22.7 2.1E+02 0.0044 25.4 5.3 68 52-126 55-141 (574)
67 MTH00117 COX2 cytochrome c oxi 22.6 1.3E+02 0.0028 23.3 3.7 26 99-126 184-213 (227)
68 PRK06461 single-stranded DNA-b 22.2 1.5E+02 0.0033 20.8 3.7 31 33-64 43-74 (129)
69 cd05829 Sortase_E Sortase E (S 22.2 1.7E+02 0.0038 20.8 4.1 23 53-75 71-93 (144)
70 MTH00129 COX2 cytochrome c oxi 22.1 1E+02 0.0022 24.0 3.0 26 99-126 184-213 (230)
71 cd04466 S1_YloQ_GTPase S1_YloQ 21.6 1.3E+02 0.0028 17.9 2.9 21 53-73 36-56 (68)
72 COG4043 Preprotein translocase 21.5 40 0.00087 23.6 0.6 15 51-65 30-44 (111)
73 TIGR03511 GldH_lipo gliding mo 21.5 3.4E+02 0.0073 20.0 6.5 27 59-85 42-74 (156)
74 MTH00154 COX2 cytochrome c oxi 21.4 1.3E+02 0.0027 23.5 3.4 26 99-126 184-213 (227)
75 MTH00168 COX2 cytochrome c oxi 21.4 1.2E+02 0.0026 23.5 3.3 26 99-126 184-213 (225)
76 PF07731 Cu-oxidase_2: Multico 20.8 1.6E+02 0.0034 20.0 3.5 25 103-127 111-135 (138)
77 MTH00139 COX2 cytochrome c oxi 20.2 1.2E+02 0.0027 23.3 3.1 26 99-126 184-213 (226)
78 TIGR01451 B_ant_repeat conserv 20.1 79 0.0017 18.8 1.6 16 50-65 3-18 (53)
79 PF11766 Candida_ALS_N: Cell-w 20.1 58 0.0012 26.0 1.2 36 51-86 5-47 (249)
No 1
>PLN03148 Blue copper-like protein; Provisional
Probab=100.00 E-value=9.8e-41 Score=248.92 Aligned_cols=103 Identities=38% Similarity=0.690 Sum_probs=95.8
Q ss_pred hhccccccEEEEecCCCCCccc--cccccCCCeEEeCCEEEEEeCCCCCeEEEEcccCcCCCCCCCCceeeccCCcEEEe
Q 033108 24 VYIEIVDATTYTVGDSGGWSFN--MASWAKGKRFKAGDTLVFNYDPTLHNVVAVNRAGYRSCTAPGGAKVYSSGKDRIKL 101 (127)
Q Consensus 24 ~~~~~a~a~~~~VG~~~gW~~~--~~~Wa~~~~f~vGD~L~F~y~~~~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~~v~L 101 (127)
++...+.|++|+|||+.||+++ +++|+++++|++||+|+|+|+++.|||+||++++|++|+.++|+..+++|++.|+|
T Consensus 13 ~~~~~~~a~~~~VGd~~GW~~~~~Y~~WA~~k~F~VGD~LvF~Y~~~~hnV~~V~~~~Y~~C~~~~pi~~~tsG~d~v~L 92 (167)
T PLN03148 13 FSASATTATDHIVGANKGWNPGINYTLWANNQTFYVGDLISFRYQKTQYNVFEVNQTGYDNCTTEGAAGNWTSGKDFIPL 92 (167)
T ss_pred HhhhhccceEEEeCCCCCcCCCCChhHhhcCCCCccCCEEEEEecCCCceEEEEChHHcCcccCCCCcceecCCCcEEEe
Confidence 3456778999999999999864 48999999999999999999999999999999999999999999999999999999
Q ss_pred cC-cceEEEcCCCCCCCCCCEEEEEeC
Q 033108 102 VR-GQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 102 ~~-G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
++ |++||||+ ++||+.||||+|+|.
T Consensus 93 ~~~G~~YFIcg-~ghC~~GmKl~I~V~ 118 (167)
T PLN03148 93 NKAKRYYFICG-NGQCFNGMKVTILVH 118 (167)
T ss_pred cCCccEEEEcC-CCccccCCEEEEEEc
Confidence 95 99999999 689999999999983
No 2
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=99.97 E-value=2.6e-32 Score=183.74 Aligned_cols=79 Identities=46% Similarity=0.995 Sum_probs=64.6
Q ss_pred Ccccc-----ccccCCCeEEeCCEEEEEeCCCCCeEEEEcccCcCCCCCCCCceeeccCCcEEEecC-cceEEEcCCCCC
Q 033108 42 WSFNM-----ASWAKGKRFKAGDTLVFNYDPTLHNVVAVNRAGYRSCTAPGGAKVYSSGKDRIKLVR-GQNFFICNSAGH 115 (127)
Q Consensus 42 W~~~~-----~~Wa~~~~f~vGD~L~F~y~~~~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~~v~L~~-G~~yFic~~~~h 115 (127)
|++++ ++||++++|++||+|+|+|+++.|+|++|++++|++|+.++|+..+++|++.|+|++ |++||||++++|
T Consensus 1 W~~~~~~~~Y~~Wa~~~~F~vGD~LvF~y~~~~h~V~~V~~~~y~~C~~~~~~~~~~~G~~~v~L~~~G~~YFic~~~~H 80 (85)
T PF02298_consen 1 WTIPTNASNYTDWASGKTFRVGDTLVFNYDSGQHSVVEVSKADYDSCNSSNPISTYSTGNDTVTLTKPGPHYFICGVPGH 80 (85)
T ss_dssp SSSSSSTTHHHHHHCTS-BETTEEEEEE--TTTB-EEEESHHHHHHT--STTSEEE-SSEEEEEE-SSEEEEEE--STTT
T ss_pred CccCCCccchhHhhcCCcEeCCCEEEEEecCCCCeEEecChhhCccCCCCCceecccCCCEEEEeCCCcCeEEEeCCCCc
Confidence 66665 799999999999999999999999999999999999999999999999999999995 999999999999
Q ss_pred CCCCC
Q 033108 116 CGSGM 120 (127)
Q Consensus 116 C~~Gm 120 (127)
|+.||
T Consensus 81 C~~Gq 85 (85)
T PF02298_consen 81 CQKGQ 85 (85)
T ss_dssp TTTT-
T ss_pred ccccC
Confidence 99998
No 3
>PRK02710 plastocyanin; Provisional
Probab=98.67 E-value=4.7e-07 Score=63.90 Aligned_cols=93 Identities=23% Similarity=0.329 Sum_probs=58.7
Q ss_pred hhccccccEEE--EecCCCCC-ccccccccCCCeEEeCCEEEEEeC-CCCCeEEEEcccCcCCCCCCCCceeeccC-CcE
Q 033108 24 VYIEIVDATTY--TVGDSGGW-SFNMASWAKGKRFKAGDTLVFNYD-PTLHNVVAVNRAGYRSCTAPGGAKVYSSG-KDR 98 (127)
Q Consensus 24 ~~~~~a~a~~~--~VG~~~gW-~~~~~~Wa~~~~f~vGD~L~F~y~-~~~h~V~~v~~~~Y~~C~~~~~~~~~~~G-~~~ 98 (127)
+.+..+.++++ .+|.+.|+ .+.| +..++++||++.|... ...|++.--.. +....++ .....| ..+
T Consensus 21 ~~~~~a~a~~~~V~~~~~~~~~~F~P----~~i~v~~Gd~V~~~N~~~~~H~v~~~~~---~~~~~~~--~~~~pg~t~~ 91 (119)
T PRK02710 21 LGVSSASAETVEVKMGSDAGMLAFEP----STLTIKAGDTVKWVNNKLAPHNAVFDGA---KELSHKD--LAFAPGESWE 91 (119)
T ss_pred hcccccccceEEEEEccCCCeeEEeC----CEEEEcCCCEEEEEECCCCCceEEecCC---ccccccc--cccCCCCEEE
Confidence 34445556554 45554443 4444 4589999999999874 46899874211 1111111 112333 346
Q ss_pred EEec-CcceEEEcCCCCCCCCCCEEEEEeC
Q 033108 99 IKLV-RGQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
++++ +|.|-|+|. .|=+.|||..|+|.
T Consensus 92 ~tF~~~G~y~y~C~--~H~~~gM~G~I~V~ 119 (119)
T PRK02710 92 ETFSEAGTYTYYCE--PHRGAGMVGKITVE 119 (119)
T ss_pred EEecCCEEEEEEcC--CCccCCcEEEEEEC
Confidence 7777 599999999 69889999999984
No 4
>PF00127 Copper-bind: Copper binding proteins, plastocyanin/azurin family; InterPro: IPR000923 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. This pollen protein is evolutionary related to the above proteins, but seems to have lost the ability to bind copper. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1UAT_A 1CUO_A 1PLC_A 4PCY_A 3PCY_A 1PND_A 1PNC_A 1JXG_A 6PCY_A 1TKW_A ....
Probab=98.48 E-value=4.6e-07 Score=61.72 Aligned_cols=74 Identities=26% Similarity=0.348 Sum_probs=51.5
Q ss_pred CCCeEEeCCEEEEEe-CCCCCeEEEEccc--CcCCCCCCCC---ceeeccCCc-EEEec-CcceEEEcCCCCCCCCCCEE
Q 033108 51 KGKRFKAGDTLVFNY-DPTLHNVVAVNRA--GYRSCTAPGG---AKVYSSGKD-RIKLV-RGQNFFICNSAGHCGSGMKI 122 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y-~~~~h~V~~v~~~--~Y~~C~~~~~---~~~~~~G~~-~v~L~-~G~~yFic~~~~hC~~GmKl 122 (127)
+..++++||++.|.. +...|++...+.. .-.......+ ......|.+ .++++ +|.|.|+|. | |...||+-
T Consensus 17 ~~i~V~~G~tV~~~n~~~~~Hnv~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~tF~~~G~y~y~C~-P-H~~~GM~G 94 (99)
T PF00127_consen 17 SEITVKAGDTVTFVNNDSMPHNVVFVADGMPAGADSDYVPPGDSSPLLAPGETYSVTFTKPGTYEYYCT-P-HYEAGMVG 94 (99)
T ss_dssp SEEEEETTEEEEEEEESSSSBEEEEETTSSHTTGGHCHHSTTCEEEEBSTTEEEEEEEESSEEEEEEET-T-TGGTTSEE
T ss_pred CEEEECCCCEEEEEECCCCCceEEEecccccccccccccCccccceecCCCCEEEEEeCCCeEEEEEcC-C-CcccCCEE
Confidence 458899999999999 5679999998521 0011111111 122334443 56666 599999999 8 99999999
Q ss_pred EEEe
Q 033108 123 AINA 126 (127)
Q Consensus 123 ~I~V 126 (127)
.|.|
T Consensus 95 ~i~V 98 (99)
T PF00127_consen 95 TIIV 98 (99)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 9987
No 5
>TIGR02656 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts.
Probab=98.31 E-value=7.1e-06 Score=55.93 Aligned_cols=89 Identities=26% Similarity=0.323 Sum_probs=56.1
Q ss_pred EEEecC-CCCCccccccccCCCeEEeCCEEEEEeCC-CCCeEEEEccc--C---cCCCCCCCCceeeccCC-cEEEec-C
Q 033108 33 TYTVGD-SGGWSFNMASWAKGKRFKAGDTLVFNYDP-TLHNVVAVNRA--G---YRSCTAPGGAKVYSSGK-DRIKLV-R 103 (127)
Q Consensus 33 ~~~VG~-~~gW~~~~~~Wa~~~~f~vGD~L~F~y~~-~~h~V~~v~~~--~---Y~~C~~~~~~~~~~~G~-~~v~L~-~ 103 (127)
+..+|. +.+-.+.| +..++++||+++|..+. ..|++...+.. + .......+.......|. ..++++ +
T Consensus 2 ~v~~g~~~g~~~F~P----~~i~v~~G~~V~~~N~~~~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~pG~t~~~tF~~~ 77 (99)
T TIGR02656 2 TVKMGADKGALVFEP----AKISIAAGDTVEWVNNKGGPHNVVFDEDAVPAGVKELAKSLSHKDLLNSPGESYEVTFSTP 77 (99)
T ss_pred EEEEecCCCceeEeC----CEEEECCCCEEEEEECCCCCceEEECCCCCccchhhhcccccccccccCCCCEEEEEeCCC
Confidence 345664 34456655 45899999999999753 58999864321 0 00001100001123343 356777 5
Q ss_pred cceEEEcCCCCCCCCCCEEEEEeC
Q 033108 104 GQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 104 G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
|.|-|+|. +|++.||+-.|.|.
T Consensus 78 G~y~y~C~--~H~~aGM~G~I~V~ 99 (99)
T TIGR02656 78 GTYTFYCE--PHRGAGMVGKITVE 99 (99)
T ss_pred EEEEEEcC--CccccCCEEEEEEC
Confidence 99999999 79999999999884
No 6
>TIGR03102 halo_cynanin halocyanin domain. Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronobacterium pharaonis. This model represents a domain duplicated in some halocyanins, while appearing once in others. This domain includes the characteristic copper ligand residues. This family does not include plastocyanins, and does not include certain divergent paralogs of halocyanin.
Probab=98.14 E-value=2.9e-05 Score=54.99 Aligned_cols=88 Identities=27% Similarity=0.439 Sum_probs=60.1
Q ss_pred cccEEEEec--CC-CCCccccccccCCCeEEeCCEEEEEeCC--CCCeEEEEcccCcCCCCCCCCceeeccC-CcEEEec
Q 033108 29 VDATTYTVG--DS-GGWSFNMASWAKGKRFKAGDTLVFNYDP--TLHNVVAVNRAGYRSCTAPGGAKVYSSG-KDRIKLV 102 (127)
Q Consensus 29 a~a~~~~VG--~~-~gW~~~~~~Wa~~~~f~vGD~L~F~y~~--~~h~V~~v~~~~Y~~C~~~~~~~~~~~G-~~~v~L~ 102 (127)
++..+..|| ++ .+..+.| +..++++||++.|.++. ..|+|...+...|+. .. .....| ...++++
T Consensus 21 ~~~~~v~~G~~~~~g~~~F~P----~~ltV~~GdTVtw~~~~d~~~HnV~s~~~~~f~s----~~-~~~~~G~t~s~Tf~ 91 (115)
T TIGR03102 21 QDEVTVDVGAEANGGGFAFDP----PAIRVDPGTTVVWEWTGEGGGHNVVSDGDGDLDE----SE-RVSEEGTTYEHTFE 91 (115)
T ss_pred CceEEEEecccCCCCceeEeC----CEEEECCCCEEEEEECCCCCCEEEEECCCCCccc----cc-cccCCCCEEEEEec
Confidence 355678888 32 3455655 45899999999999863 589998643333431 11 112233 3478888
Q ss_pred -CcceEEEcCCCCCCCCCCEEEEEeC
Q 033108 103 -RGQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 103 -~G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
+|.|-|+|.. |=..|||-.|.|.
T Consensus 92 ~~G~Y~Y~C~p--H~~~gM~G~I~V~ 115 (115)
T TIGR03102 92 EPGIYLYVCVP--HEALGMKGAVVVE 115 (115)
T ss_pred CCcEEEEEccC--CCCCCCEEEEEEC
Confidence 5999999994 8777999999984
No 7
>COG3794 PetE Plastocyanin [Energy production and conversion]
Probab=98.01 E-value=7.4e-05 Score=53.93 Aligned_cols=80 Identities=28% Similarity=0.338 Sum_probs=56.9
Q ss_pred ecCCCCCccccccccCCCeEEeCCEEEEEeCCC-CCeEEEEcccCcCCCCCCCCceeeccC---CcEEEec-CcceEEEc
Q 033108 36 VGDSGGWSFNMASWAKGKRFKAGDTLVFNYDPT-LHNVVAVNRAGYRSCTAPGGAKVYSSG---KDRIKLV-RGQNFFIC 110 (127)
Q Consensus 36 VG~~~gW~~~~~~Wa~~~~f~vGD~L~F~y~~~-~h~V~~v~~~~Y~~C~~~~~~~~~~~G---~~~v~L~-~G~~yFic 110 (127)
+++...-.+.| +..++.+||++.|.+... .|||...... ++ .....+..+ ..+++++ +|.|.|+|
T Consensus 43 ~~~~~~~vF~P----A~v~v~pGDTVtw~~~d~~~Hnv~~~~~~-----~~-~g~~~~~~~~~~s~~~Tfe~~G~Y~Y~C 112 (128)
T COG3794 43 GVDIGAMVFEP----AEVTVKPGDTVTWVNTDSVGHNVTAVGGM-----DP-EGSGTLKAGINESFTHTFETPGEYTYYC 112 (128)
T ss_pred eccCcceeEcC----cEEEECCCCEEEEEECCCCCceEEEeCCC-----Cc-ccccccccCCCcceEEEecccceEEEEe
Confidence 33444566666 468999999999999877 9999987544 11 111122222 2367777 69999999
Q ss_pred CCCCCCCCCCEEEEEeC
Q 033108 111 NSAGHCGSGMKIAINAM 127 (127)
Q Consensus 111 ~~~~hC~~GmKl~I~V~ 127 (127)
.- |=..|||-+|.|.
T Consensus 113 ~P--H~~~gM~G~IvV~ 127 (128)
T COG3794 113 TP--HPGMGMKGKIVVG 127 (128)
T ss_pred cc--CCCCCcEEEEEeC
Confidence 94 8899999999883
No 8
>TIGR02375 pseudoazurin pseudoazurin. Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related plastocyanins. Several examples of pseudoazurin are encoded by a neighboring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (TIGR02376) of the same species.
Probab=97.76 E-value=0.0002 Score=50.77 Aligned_cols=72 Identities=22% Similarity=0.191 Sum_probs=48.9
Q ss_pred CCCeEEeCCEEEEEeCCCCCeEEEEcccCcCCCCCCCCceeeccCCcEEEec-CcceEEEcCCCCCCCCCCEEEEEeC
Q 033108 51 KGKRFKAGDTLVFNYDPTLHNVVAVNRAGYRSCTAPGGAKVYSSGKDRIKLV-RGQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~~~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~~v~L~-~G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
+..++++||++.|.+....|+|.......- +..++...-.+..-.++++ +|.|-|.|. .|=..||+-.|+|.
T Consensus 15 ~~v~V~~GdTV~f~n~d~~Hnv~~~~~~~p---~g~~~~~s~~g~~~~~tF~~~G~Y~Y~C~--pH~~~GM~G~V~Vg 87 (116)
T TIGR02375 15 AYIRAAPGDTVTFVPTDKGHNVETIKGMIP---EGAEAFKSKINEEYTVTVTEEGVYGVKCT--PHYGMGMVALIQVG 87 (116)
T ss_pred CEEEECCCCEEEEEECCCCeeEEEccCCCc---CCcccccCCCCCEEEEEeCCCEEEEEEcC--CCccCCCEEEEEEC
Confidence 458999999999999877899987532110 0011111001122367777 599999999 59999999999983
No 9
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=97.14 E-value=0.0037 Score=41.12 Aligned_cols=70 Identities=17% Similarity=0.169 Sum_probs=45.8
Q ss_pred CCCeEEeCCEEEEEeCC-CCCeEEEEcccCcCCCCCCCCceeeccCC-cEEEec-CcceEEEcCCCCCCCCCCEEEEEeC
Q 033108 51 KGKRFKAGDTLVFNYDP-TLHNVVAVNRAGYRSCTAPGGAKVYSSGK-DRIKLV-RGQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~-~~h~V~~v~~~~Y~~C~~~~~~~~~~~G~-~~v~L~-~G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
+..++.+||+|.|..+. ..|||...+..+ ..=+...+ ....|. .+++++ ||+|-|.|.... .||-.|.|.
T Consensus 11 ~~i~v~~GdtVt~~N~d~~~Hnv~~~~g~~-~~~~~~~~--~~~~g~~~~~tf~~~G~y~y~C~~Hp----~M~G~v~V~ 83 (83)
T TIGR02657 11 PELHVKVGDTVTWINREAMPHNVHFVAGVL-GEAALKGP--MMKKEQAYSLTFTEAGTYDYHCTPHP----FMRGKVVVE 83 (83)
T ss_pred CEEEECCCCEEEEEECCCCCccEEecCCCC-cccccccc--ccCCCCEEEEECCCCEEEEEEcCCCC----CCeEEEEEC
Confidence 34789999999999875 489998653221 11001111 123333 367787 599999999843 599999884
No 10
>PF06525 SoxE: Sulfocyanin (SoxE); InterPro: IPR010532 Members of this family are blue-copper redox proteins designated sulfocyanin, from the archaeal genera Sulfolobus, Ferroplasma, and Picrophilus. The most closely related proteins characterised as functionally different are the rusticyanins.
Probab=96.94 E-value=0.004 Score=47.94 Aligned_cols=72 Identities=26% Similarity=0.348 Sum_probs=45.1
Q ss_pred EEeCCEEEEEeCCC---CCeEEEE-cccCcCCCCCC---CCcee---------ec----cCCc-EE---EecCcceEEEc
Q 033108 55 FKAGDTLVFNYDPT---LHNVVAV-NRAGYRSCTAP---GGAKV---------YS----SGKD-RI---KLVRGQNFFIC 110 (127)
Q Consensus 55 f~vGD~L~F~y~~~---~h~V~~v-~~~~Y~~C~~~---~~~~~---------~~----~G~~-~v---~L~~G~~yFic 110 (127)
.-+|-++.|+|.+. .|++..+ +...+.++..- +.+.. .. .|.. .. .|.+|.||+.|
T Consensus 90 VPAGw~V~i~f~N~~~l~Hnl~iv~~~~~~p~~~~i~~DgkIl~~~G~s~~~~~~~GI~~G~s~~~~~~~l~aG~YwlvC 169 (196)
T PF06525_consen 90 VPAGWNVQITFTNQESLPHNLVIVQNDTPTPNNPPISSDGKILLYVGASPGNYTSNGISSGQSASGVYNDLPAGYYWLVC 169 (196)
T ss_pred EcCCCEEEEEEEcCCCCCeeEEEEeCCCCCCCccccCCCCceeeeccCCCCccccCCccCCceeeEEEccCCCceEEEEc
Confidence 34688888888643 8999998 33333443221 11110 01 2222 22 23359999999
Q ss_pred CCCCCCCCCCEEEEEe
Q 033108 111 NSAGHCGSGMKIAINA 126 (127)
Q Consensus 111 ~~~~hC~~GmKl~I~V 126 (127)
+.+||=+.||-..+.|
T Consensus 170 ~ipGHA~sGMw~~LiV 185 (196)
T PF06525_consen 170 GIPGHAESGMWGVLIV 185 (196)
T ss_pred cCCChhhcCCEEEEEE
Confidence 9999999999887776
No 11
>TIGR03095 rusti_cyanin rusticyanin. Rusticyanin is a blue copper protein, described in an obligate acidophilic chemolithoautroph, Acidithiobacillus ferrooxidans, as an electron transfer protein. It can constitute up to 5 percent of protein in cells grown on Fe(II) and is thought to be part of an electron chain for Fe(II) oxidation, with two c-type cytochromes, an aa3-type cytochrome oxidase, and 02 as terminal electron acceptor. It is rather closely related to sulfocyanin (TIGR03094).
Probab=96.76 E-value=0.0058 Score=44.81 Aligned_cols=72 Identities=24% Similarity=0.262 Sum_probs=46.6
Q ss_pred CeEEeCCEEEEEeCCC----CCeEEEEccc-CcC------------CCCCCCCceeeccC-----CcEEEec-CcceEEE
Q 033108 53 KRFKAGDTLVFNYDPT----LHNVVAVNRA-GYR------------SCTAPGGAKVYSSG-----KDRIKLV-RGQNFFI 109 (127)
Q Consensus 53 ~~f~vGD~L~F~y~~~----~h~V~~v~~~-~Y~------------~C~~~~~~~~~~~G-----~~~v~L~-~G~~yFi 109 (127)
.+++.||++.|...+. .|........ .+. +|....+ -.+| +.+++++ +|+|||.
T Consensus 54 I~v~~Gd~V~v~v~N~~~~~~H~~~I~~~g~~~~~~p~mdG~~~~~~~~i~p~---~~~g~~~~~~~tf~f~~aGtywyh 130 (148)
T TIGR03095 54 IVIPEGVTVHFTVINTDTDSGHNFDISKRGPPYPYMPGMDGLGFVAGTGFLPP---PKSGKFGYTDFTYHFSTAGTYWYL 130 (148)
T ss_pred EEEcCCCEEEEEEEeCCCCccccEEeecCCCccccccccCCCCccccCcccCC---CCCCccceeEEEEECCCCeEEEEE
Confidence 5678999999988643 6777765311 110 1211100 1122 2245555 4999999
Q ss_pred cCCCCCCCCCCEEEEEeC
Q 033108 110 CNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 110 c~~~~hC~~GmKl~I~V~ 127 (127)
|..++|=+.||.-.|.|+
T Consensus 131 C~~pgH~~~GM~G~iiV~ 148 (148)
T TIGR03095 131 CTYPGHAENGMYGKIVVK 148 (148)
T ss_pred cCChhHHHCCCEEEEEEC
Confidence 999999999999998874
No 12
>KOG3858 consensus Ephrin, ligand for Eph receptor tyrosine kinase [Signal transduction mechanisms]
Probab=95.33 E-value=0.14 Score=40.39 Aligned_cols=32 Identities=22% Similarity=0.325 Sum_probs=21.6
Q ss_pred eEEeCCEEEEE---eCCC------CCeEEEEcccCcCCCCC
Q 033108 54 RFKAGDTLVFN---YDPT------LHNVVAVNRAGYRSCTA 85 (127)
Q Consensus 54 ~f~vGD~L~F~---y~~~------~h~V~~v~~~~Y~~C~~ 85 (127)
..++||.|-+- |+.+ ..=++.|++++|+.|+.
T Consensus 46 ~v~igD~ldIiCP~~e~~~~~~~E~yilYmV~~~~y~~C~~ 86 (233)
T KOG3858|consen 46 YVQIGDYLDIICPHYEEGGPEGYEYYILYMVSEEEYDLCEL 86 (233)
T ss_pred EeccCCEEEEECCCCCCCCCCcceEEEEEEeChHHhhhhhc
Confidence 34568888775 3322 22356789999999996
No 13
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=94.99 E-value=0.053 Score=36.72 Aligned_cols=63 Identities=27% Similarity=0.414 Sum_probs=29.8
Q ss_pred CCCeEEeCC--EEEEEeC-CCCCeEEEEcccCcCCCCCCCCceeeccCCc-EEEe--c-CcceEEEcCCCCCCCCCCEEE
Q 033108 51 KGKRFKAGD--TLVFNYD-PTLHNVVAVNRAGYRSCTAPGGAKVYSSGKD-RIKL--V-RGQNFFICNSAGHCGSGMKIA 123 (127)
Q Consensus 51 ~~~~f~vGD--~L~F~y~-~~~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~-~v~L--~-~G~~yFic~~~~hC~~GmKl~ 123 (127)
+..+++.|+ +|+|... ...|++..-+ . +.......|.+ ++++ . ||.|=|+|+.+.+ ||-.
T Consensus 35 ~~i~v~~G~~v~l~~~N~~~~~h~~~i~~--------~-~~~~~l~~g~~~~~~f~~~~~G~y~~~C~~~~~----m~G~ 101 (104)
T PF13473_consen 35 STITVKAGQPVTLTFTNNDSRPHEFVIPD--------L-GISKVLPPGETATVTFTPLKPGEYEFYCTMHPN----MKGT 101 (104)
T ss_dssp -EEEEETTCEEEEEEEE-SSS-EEEEEGG--------G-TEEEEE-TT-EEEEEEEE-S-EEEEEB-SSS-T----TB--
T ss_pred CEEEEcCCCeEEEEEEECCCCcEEEEECC--------C-ceEEEECCCCEEEEEEcCCCCEEEEEEcCCCCc----ceec
Confidence 458999999 5555554 3467665422 1 11123344443 5555 3 5999999998663 6655
Q ss_pred EEe
Q 033108 124 INA 126 (127)
Q Consensus 124 I~V 126 (127)
|.|
T Consensus 102 liV 104 (104)
T PF13473_consen 102 LIV 104 (104)
T ss_dssp ---
T ss_pred ccC
Confidence 554
No 14
>TIGR03094 sulfo_cyanin sulfocyanin. Members of this family are blue-copper redox proteins designated sulfocyanin, from the archaeal genera Sulfolobus, Ferroplasma, and Picrophilus. The most closely related proteins characterized as functionally different are the rustacyanins.
Probab=94.38 E-value=0.038 Score=42.34 Aligned_cols=24 Identities=29% Similarity=0.655 Sum_probs=20.9
Q ss_pred CcceEEEcCCCCCCCCCCEEEEEe
Q 033108 103 RGQNFFICNSAGHCGSGMKIAINA 126 (127)
Q Consensus 103 ~G~~yFic~~~~hC~~GmKl~I~V 126 (127)
+|.||+.|+.+||-+.||=..+.|
T Consensus 161 ~G~YwlvCgipGHAesGMw~~lIV 184 (195)
T TIGR03094 161 AGKYWLVCGITGHAESGMWAVVIV 184 (195)
T ss_pred CeeEEEEcccCChhhcCcEEEEEE
Confidence 599999999999999999665554
No 15
>COG4454 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]
Probab=91.91 E-value=0.29 Score=36.54 Aligned_cols=77 Identities=22% Similarity=0.292 Sum_probs=46.8
Q ss_pred CCCeEEeCCEEEEEeCCC---CCeEEEEcc----cCcCCC----CC--CCC-ceeeccCCc---EEEec-CcceEEEcCC
Q 033108 51 KGKRFKAGDTLVFNYDPT---LHNVVAVNR----AGYRSC----TA--PGG-AKVYSSGKD---RIKLV-RGQNFFICNS 112 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~~---~h~V~~v~~----~~Y~~C----~~--~~~-~~~~~~G~~---~v~L~-~G~~yFic~~ 112 (127)
+...++.|-+++|.-... .|....-.+ +.+..= +. ..+ ......|.. ++.++ +|.|=|+|..
T Consensus 63 ~~~~v~aG~tv~~v~~n~~el~hef~~~~~~~~~~~~~~~~~~~Dme~d~~~~v~L~PG~s~elvv~ft~~g~ye~~C~i 142 (158)
T COG4454 63 SSFEVKAGETVRFVLKNEGELKHEFTMDAPDKNLEHVTHMILADDMEHDDPNTVTLAPGKSGELVVVFTGAGKYEFACNI 142 (158)
T ss_pred CcccccCCcEEeeeecCcccceEEEeccCccccchhHHHhhhCCccccCCcceeEeCCCCcEEEEEEecCCccEEEEecC
Confidence 557888999988876543 455443200 001000 00 111 122344433 45555 6999999999
Q ss_pred CCCCCCCCEEEEEeC
Q 033108 113 AGHCGSGMKIAINAM 127 (127)
Q Consensus 113 ~~hC~~GmKl~I~V~ 127 (127)
|||=+.||.-.|+|.
T Consensus 143 PGHy~AGM~g~itV~ 157 (158)
T COG4454 143 PGHYEAGMVGEITVS 157 (158)
T ss_pred CCcccCCcEEEEEeC
Confidence 999999999999884
No 16
>PF00812 Ephrin: Ephrin; InterPro: IPR001799 Ephrins are a family of proteins [] that are ligands of class V (EPH-related) receptor protein-tyrosine kinases (see IPR001426 from INTERPRO). These receptors and their ligands have been implicated in regulating neuronal axon guidance and in patterning of the developing nervous system and may also serve a patterning and compartmentalisation role outside of the nervous system as well. Ephrins are membrane-attached proteins of 205 to 340 residues. Attachment appears to be crucial for their normal function. Type-A ephrins are linked to the membrane via a glycosylphosphatidylinositol (GPI)-linkage, while type-B ephrins are type-I membrane proteins.; GO: 0016020 membrane; PDB: 3HEI_P 3CZU_B 3MBW_B 1KGY_E 1IKO_P 2WO3_B 2I85_A 2VSK_B 3GXU_B 2VSM_B ....
Probab=90.00 E-value=0.62 Score=34.22 Aligned_cols=34 Identities=26% Similarity=0.422 Sum_probs=24.0
Q ss_pred CeEEeCCEEEEEeC---CC--------CCeEEEEcccCcCCCCCC
Q 033108 53 KRFKAGDTLVFNYD---PT--------LHNVVAVNRAGYRSCTAP 86 (127)
Q Consensus 53 ~~f~vGD~L~F~y~---~~--------~h~V~~v~~~~Y~~C~~~ 86 (127)
...++||.|-+-=+ .. ...++.|++++|+.|+..
T Consensus 24 i~V~i~D~ldIiCP~~~~~~~~~~~~E~~~lY~Vs~~~y~~C~~~ 68 (145)
T PF00812_consen 24 IEVRIGDYLDIICPHYEPGGPPPEEYEYYILYMVSEEGYESCSLT 68 (145)
T ss_dssp EEE-TTEEEEEEE--SSSSSSSCSSS-BEEEEEE-HHHHHHTBSS
T ss_pred EEecCCCEEEEECCCCCCCCCCCCCceEEEEEEEcHHHhcccCCC
Confidence 46778999998643 22 456888999999999963
No 17
>TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
Probab=89.26 E-value=0.72 Score=33.58 Aligned_cols=55 Identities=16% Similarity=0.234 Sum_probs=33.5
Q ss_pred CCCeEEeCCEEEEEeCC---CCCeEEEEcccCcCCCCCCCCceeeccCCc-EEEe--c-CcceEEEcCCCCCC
Q 033108 51 KGKRFKAGDTLVFNYDP---TLHNVVAVNRAGYRSCTAPGGAKVYSSGKD-RIKL--V-RGQNFFICNSAGHC 116 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~---~~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~-~v~L--~-~G~~yFic~~~~hC 116 (127)
+..+++.||.+.+.+.+ -.|.+..- +|. . ......|.. ++++ + ||.|.|+|+. ||
T Consensus 61 ~~I~VkaGD~Vtl~vtN~d~~~H~f~i~---~~g---i---s~~I~pGet~TitF~adKpG~Y~y~C~~--HP 122 (135)
T TIGR03096 61 EALVVKKGTPVKVTVENKSPISEGFSID---AYG---I---SEVIKAGETKTISFKADKAGAFTIWCQL--HP 122 (135)
T ss_pred CEEEECCCCEEEEEEEeCCCCccceEEC---CCC---c---ceEECCCCeEEEEEECCCCEEEEEeCCC--CC
Confidence 56889999999887753 24554432 221 1 122333443 3444 4 5999999997 55
No 18
>TIGR02695 azurin azurin. Azurin is a blue copper-binding protein in the plastocyanin/azurin family (see Pfam model pfam00127). It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The most closely related copper-binding proteins to this family are auracyanins, as in Chloroflexus aurantiacus, which have similar redox activities.
Probab=87.79 E-value=3.1 Score=29.98 Aligned_cols=22 Identities=27% Similarity=0.570 Sum_probs=17.2
Q ss_pred Ccc-eEEEcCCCCCCCCCCEEEEE
Q 033108 103 RGQ-NFFICNSAGHCGSGMKIAIN 125 (127)
Q Consensus 103 ~G~-~yFic~~~~hC~~GmKl~I~ 125 (127)
+|. |=|+|++|||=. .||-.+.
T Consensus 102 ~g~~Y~f~CSFPGH~~-~MkG~l~ 124 (125)
T TIGR02695 102 AGEDYTFFCSFPGHWA-MMRGTVK 124 (125)
T ss_pred CCCcceEEEcCCCcHH-hceEEEe
Confidence 465 669999999985 6887654
No 19
>PRK02888 nitrous-oxide reductase; Validated
Probab=77.83 E-value=9.8 Score=34.27 Aligned_cols=65 Identities=14% Similarity=0.200 Sum_probs=39.2
Q ss_pred CCCeEEeCCEEEEEeCCC------CCeEEEEcccCcCCCCCCCCceeeccCCc-E--EEec-CcceEEEcCCCCCCCC--
Q 033108 51 KGKRFKAGDTLVFNYDPT------LHNVVAVNRAGYRSCTAPGGAKVYSSGKD-R--IKLV-RGQNFFICNSAGHCGS-- 118 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~~------~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~-~--v~L~-~G~~yFic~~~~hC~~-- 118 (127)
...++++||.+.|..++- .|+.... +|. .......|.+ + |+.+ ||.||++|+. .|-.
T Consensus 555 ~~i~Vk~GDeVt~~lTN~d~~~DViHGF~Ip---~~n------I~~dv~PG~t~svtF~adkPGvy~~~Cte--fCGa~H 623 (635)
T PRK02888 555 REFTVKQGDEVTVIVTNLDKVEDLTHGFAIP---NYG------VNMEVAPQATASVTFTADKPGVYWYYCTW--FCHALH 623 (635)
T ss_pred ceEEecCCCEEEEEEEeCCcccccccceeec---ccC------ccEEEcCCceEEEEEEcCCCEEEEEECCc--ccccCc
Confidence 347899999999999751 3444431 121 1111223332 3 4445 5999999997 4544
Q ss_pred -CCEEEEEe
Q 033108 119 -GMKIAINA 126 (127)
Q Consensus 119 -GmKl~I~V 126 (127)
+|+-.|.|
T Consensus 624 ~~M~G~~iV 632 (635)
T PRK02888 624 MEMRGRMLV 632 (635)
T ss_pred ccceEEEEE
Confidence 58777766
No 20
>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=77.75 E-value=1.5 Score=29.92 Aligned_cols=12 Identities=33% Similarity=0.279 Sum_probs=5.4
Q ss_pred HHhhccccccEE
Q 033108 22 LLVYIEIVDATT 33 (127)
Q Consensus 22 ~~~~~~~a~a~~ 33 (127)
+||.++.++|++
T Consensus 16 lLlisSevaa~~ 27 (95)
T PF07172_consen 16 LLLISSEVAARE 27 (95)
T ss_pred HHHHHhhhhhHH
Confidence 444444444443
No 21
>PF00116 COX2: Cytochrome C oxidase subunit II, periplasmic domain This family corresponds to chains b and o.; InterPro: IPR002429 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c.; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0016020 membrane; PDB: 3OMN_D 3OMA_B 3OMI_D 3OM3_B 3EHB_B 1AR1_B 1QLE_B 3HB3_B 2IWK_B 2IWF_A ....
Probab=76.84 E-value=3.9 Score=28.70 Aligned_cols=65 Identities=20% Similarity=0.366 Sum_probs=39.8
Q ss_pred CCCeEEeCCEEEEEeCCC--CCeEEEEcccCcCCCCCCCCcee-eccCCc---EEEec-CcceEEEcCCCCCCCCC---C
Q 033108 51 KGKRFKAGDTLVFNYDPT--LHNVVAVNRAGYRSCTAPGGAKV-YSSGKD---RIKLV-RGQNFFICNSAGHCGSG---M 120 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~~--~h~V~~v~~~~Y~~C~~~~~~~~-~~~G~~---~v~L~-~G~~yFic~~~~hC~~G---m 120 (127)
+...+..|+.+.|.-++. .|+...-+ + .++. --.|.. .++.+ ||.|++.|+. .|..| |
T Consensus 46 ~~l~lp~g~~v~~~ltS~DViHsf~ip~---~-------~~k~d~~PG~~~~~~~~~~~~G~y~~~C~e--~CG~gH~~M 113 (120)
T PF00116_consen 46 NELVLPAGQPVRFHLTSEDVIHSFWIPE---L-------GIKMDAIPGRTNSVTFTPDKPGTYYGQCAE--YCGAGHSFM 113 (120)
T ss_dssp SEEEEETTSEEEEEEEESSS-EEEEETT---C-------TEEEEEBTTCEEEEEEEESSSEEEEEEE-S--SSSTTGGG-
T ss_pred ceecccccceEeEEEEcCCccccccccc---c-------CcccccccccceeeeeeeccCCcEEEcCcc--ccCcCcCCC
Confidence 446678999999988753 67766521 1 1111 112332 34555 5999999997 79888 8
Q ss_pred EEEEEeC
Q 033108 121 KIAINAM 127 (127)
Q Consensus 121 Kl~I~V~ 127 (127)
+..|.|+
T Consensus 114 ~~~v~VV 120 (120)
T PF00116_consen 114 PGKVIVV 120 (120)
T ss_dssp EEEEEEE
T ss_pred eEEEEEC
Confidence 8888773
No 22
>TIGR02376 Cu_nitrite_red nitrite reductase, copper-containing. This family consists of copper-type nitrite reductase. It reduces nitrite to nitric oxide, the first step in denitrification.
Probab=73.73 E-value=8.1 Score=31.36 Aligned_cols=72 Identities=25% Similarity=0.258 Sum_probs=42.8
Q ss_pred CCeEEeCCEEEEEeCCC-----CCeEEEEcccCcCCCCCCCCceeeccCCc---EEEec-CcceEEEcCC----CCCCCC
Q 033108 52 GKRFKAGDTLVFNYDPT-----LHNVVAVNRAGYRSCTAPGGAKVYSSGKD---RIKLV-RGQNFFICNS----AGHCGS 118 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~-----~h~V~~v~~~~Y~~C~~~~~~~~~~~G~~---~v~L~-~G~~yFic~~----~~hC~~ 118 (127)
..+++.||+++..+.+. .|++..=-.... +...+......|.+ .|+++ +|++||-|.. ..|=..
T Consensus 60 ~irv~~Gd~v~v~v~N~~~~~~~h~~h~H~~~~~---dg~~~~~~I~PG~t~ty~F~~~~~Gty~YH~H~~~~~~~q~~~ 136 (311)
T TIGR02376 60 LIRVHEGDYVELTLINPPTNTMPHNVDFHAATGA---LGGAALTQVNPGETATLRFKATRPGAFVYHCAPPGMVPWHVVS 136 (311)
T ss_pred eEEEECCCEEEEEEEeCCCCCCceeeeecCCCcc---CCCCcceeECCCCeEEEEEEcCCCEEEEEEcCCCCchhHHhhc
Confidence 37899999999887653 466554111000 11011122334432 45556 4999999995 347788
Q ss_pred CCEEEEEe
Q 033108 119 GMKIAINA 126 (127)
Q Consensus 119 GmKl~I~V 126 (127)
||.-.+.|
T Consensus 137 Gl~G~liV 144 (311)
T TIGR02376 137 GMNGAIMV 144 (311)
T ss_pred CcceEEEe
Confidence 99877765
No 23
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=72.50 E-value=13 Score=28.04 Aligned_cols=80 Identities=19% Similarity=0.319 Sum_probs=45.1
Q ss_pred EecCCCCCccccccc------cCCCeEEeCCEEEEEeCCC--CCeEEEEcccCcCCCCCCCCceee-ccCC-c--EEEec
Q 033108 35 TVGDSGGWSFNMASW------AKGKRFKAGDTLVFNYDPT--LHNVVAVNRAGYRSCTAPGGAKVY-SSGK-D--RIKLV 102 (127)
Q Consensus 35 ~VG~~~gW~~~~~~W------a~~~~f~vGD~L~F~y~~~--~h~V~~v~~~~Y~~C~~~~~~~~~-~~G~-~--~v~L~ 102 (127)
++|-.=.|.+.+.+. .+...+.+|+.++|.-++. .|+-...+. ..+.. -.|. . .++.+
T Consensus 95 v~~~qw~W~f~Y~~~~~~~~~~~~l~vp~g~~v~~~~ts~DV~Hsf~ip~~----------~~k~da~PG~~~~~~~~~~ 164 (201)
T TIGR02866 95 VEGHQWYWSFDYPESRRGFTTVNELVVPAGTPVRLQVTSKDVIHSFWVPEL----------GGKIDAIPGQYNALWFNAD 164 (201)
T ss_pred EEEEEeEEEEEcCCcCCCccccCEEEEEcCCEEEEEEEeCchhhccccccc----------CceEEecCCcEEEEEEEeC
Confidence 445445566655332 1335678899999987752 344333211 11111 1232 2 34455
Q ss_pred -CcceEEEcCCCCCCCC---CCEEEEEe
Q 033108 103 -RGQNFFICNSAGHCGS---GMKIAINA 126 (127)
Q Consensus 103 -~G~~yFic~~~~hC~~---GmKl~I~V 126 (127)
+|.|+..|++ .|.. .|++.|.|
T Consensus 165 ~~G~y~~~c~e--~cG~~h~~M~~~v~v 190 (201)
T TIGR02866 165 EPGVYYGYCAE--LCGAGHSLMLFKVVV 190 (201)
T ss_pred CCEEEEEEehh--hCCcCccCCeEEEEE
Confidence 5999999998 4554 48888876
No 24
>PRK09723 putative fimbrial-like adhesin protein; Provisional
Probab=72.33 E-value=47 Score=28.59 Aligned_cols=49 Identities=24% Similarity=0.395 Sum_probs=27.7
Q ss_pred HhhccccccEEEEecCCCCCccccccccCCCeEEeCCE-EEEEeCCCCCeEE
Q 033108 23 LVYIEIVDATTYTVGDSGGWSFNMASWAKGKRFKAGDT-LVFNYDPTLHNVV 73 (127)
Q Consensus 23 ~~~~~~a~a~~~~VG~~~gW~~~~~~Wa~~~~f~vGD~-L~F~y~~~~h~V~ 73 (127)
.+++.......|.||+..|=.++.+.|... =..||. +.|+|.....+++
T Consensus 19 ~~~~~~~~~~~~~vg~~~~~~~~~~~~~~~--g~~~d~~~~f~~~~~~~~~~ 68 (421)
T PRK09723 19 TASAGTDDNVSYIVGNYYGVGPSDQKWNET--GPSGDATVTFRYATSTNNLV 68 (421)
T ss_pred hhhccccCceEEEEccccccCCcccccccc--CCCcceEEEeccccCCcceE
Confidence 344455668899999977655555555322 234453 3466654444443
No 25
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=64.54 E-value=33 Score=21.98 Aligned_cols=46 Identities=11% Similarity=0.153 Sum_probs=24.6
Q ss_pred EEEEEeCCCCCeEEEE-cccCcCCCCCCCCceeeccC-CcEEEecCcceEE
Q 033108 60 TLVFNYDPTLHNVVAV-NRAGYRSCTAPGGAKVYSSG-KDRIKLVRGQNFF 108 (127)
Q Consensus 60 ~L~F~y~~~~h~V~~v-~~~~Y~~C~~~~~~~~~~~G-~~~v~L~~G~~yF 108 (127)
.+.|.|..+..+|..+ +..+.+. ..|...-.++ ...+.|.+|.|.|
T Consensus 3 ~v~f~~~~~a~~V~v~G~F~~W~~---~~pm~~~~~~~~~~~~L~~g~y~Y 50 (79)
T cd02859 3 PTTFVWPGGGKEVYVTGSFDNWKK---KIPLEKSGKGFSATLRLPPGKYQY 50 (79)
T ss_pred EEEEEEcCCCcEEEEEEEcCCCCc---cccceECCCCcEEEEEcCCCCEEE
Confidence 3678888888888877 4444443 1232222222 1244555676543
No 26
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=63.98 E-value=29 Score=27.52 Aligned_cols=64 Identities=19% Similarity=0.318 Sum_probs=37.7
Q ss_pred CCeEEeCCEEEEEeCCC--CCeEEEEcccCcCCCCCCCCceee-ccCC---cEEEec-CcceEEEcCCCCCCCCC---CE
Q 033108 52 GKRFKAGDTLVFNYDPT--LHNVVAVNRAGYRSCTAPGGAKVY-SSGK---DRIKLV-RGQNFFICNSAGHCGSG---MK 121 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~--~h~V~~v~~~~Y~~C~~~~~~~~~-~~G~---~~v~L~-~G~~yFic~~~~hC~~G---mK 121 (127)
...+.+|..+.|+-++. .|+-...+.. .+.. -.|. ..++.+ +|.|+.+|+. .|..| |+
T Consensus 138 ~l~lPv~~~V~f~ltS~DViHsF~IP~l~----------~k~d~iPG~~~~~~~~~~~~G~Y~g~Cae--~CG~gH~~M~ 205 (247)
T COG1622 138 ELVLPVGRPVRFKLTSADVIHSFWIPQLG----------GKIDAIPGMTTELWLTANKPGTYRGICAE--YCGPGHSFMR 205 (247)
T ss_pred eEEEeCCCeEEEEEEechhceeEEecCCC----------ceeeecCCceEEEEEecCCCeEEEEEcHh--hcCCCcccce
Confidence 36677777777777653 4444432111 0111 1122 134445 4999999996 77776 99
Q ss_pred EEEEeC
Q 033108 122 IAINAM 127 (127)
Q Consensus 122 l~I~V~ 127 (127)
+.|.|.
T Consensus 206 ~~v~vv 211 (247)
T COG1622 206 FKVIVV 211 (247)
T ss_pred EEEEEE
Confidence 998873
No 27
>PRK10378 inactive ferrous ion transporter periplasmic protein EfeO; Provisional
Probab=63.89 E-value=31 Score=29.12 Aligned_cols=15 Identities=20% Similarity=0.326 Sum_probs=12.4
Q ss_pred EEEecCcceEEEcCC
Q 033108 98 RIKLVRGQNFFICNS 112 (127)
Q Consensus 98 ~v~L~~G~~yFic~~ 112 (127)
+++|.||+|-|+|+.
T Consensus 91 ~~~L~pGtY~~~C~~ 105 (375)
T PRK10378 91 TANLQPGEYDMTCGL 105 (375)
T ss_pred EEecCCceEEeecCc
Confidence 566778999999976
No 28
>PLN02604 oxidoreductase
Probab=61.61 E-value=41 Score=29.60 Aligned_cols=69 Identities=12% Similarity=0.194 Sum_probs=42.5
Q ss_pred CCCeEEeCCEEEEEeCCC----CCeEEE-----EcccCcC------CCCCCCCceeeccCCc---EEEec-CcceEEEcC
Q 033108 51 KGKRFKAGDTLVFNYDPT----LHNVVA-----VNRAGYR------SCTAPGGAKVYSSGKD---RIKLV-RGQNFFICN 111 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~~----~h~V~~-----v~~~~Y~------~C~~~~~~~~~~~G~~---~v~L~-~G~~yFic~ 111 (127)
...+++.||+++++..+. .|++.. .....+| .|.. ..|.+ .|+++ +|++||=|-
T Consensus 55 P~i~~~~Gd~v~v~v~N~l~~~~~~iH~HG~~~~~~~~~DG~~~~tq~~i-------~pg~s~~y~f~~~~~Gt~wyH~H 127 (566)
T PLN02604 55 PTILAQQGDTVIVELKNSLLTENVAIHWHGIRQIGTPWFDGTEGVTQCPI-------LPGETFTYEFVVDRPGTYLYHAH 127 (566)
T ss_pred CcEEEECCCEEEEEEEeCCCCCCCCEEeCCCCCCCCccccCCCccccCcc-------CCCCeEEEEEEcCCCEEEEEeeC
Confidence 458899999999988643 123221 1000011 1221 22322 45566 499999999
Q ss_pred CCCCCCCCCEEEEEe
Q 033108 112 SAGHCGSGMKIAINA 126 (127)
Q Consensus 112 ~~~hC~~GmKl~I~V 126 (127)
...|=..||.-.|.|
T Consensus 128 ~~~q~~~Gl~G~liV 142 (566)
T PLN02604 128 YGMQREAGLYGSIRV 142 (566)
T ss_pred cHHHHhCCCeEEEEE
Confidence 988888999877765
No 29
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=60.60 E-value=8.9 Score=26.82 Aligned_cols=14 Identities=36% Similarity=0.650 Sum_probs=11.9
Q ss_pred CeEEeCCEEEEEeC
Q 033108 53 KRFKAGDTLVFNYD 66 (127)
Q Consensus 53 ~~f~vGD~L~F~y~ 66 (127)
+.|++||.|+|+=-
T Consensus 30 ~~ikvGD~I~f~~~ 43 (109)
T cd06555 30 QQIKVGDKILFNDL 43 (109)
T ss_pred hcCCCCCEEEEEEc
Confidence 68999999999653
No 30
>PF09792 But2: Ubiquitin 3 binding protein But2 C-terminal domain; InterPro: IPR018620 This entry represents a presumed C-terminal domain of ubiquitin 3 binding proteins (But2). But2 is conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway [].
Probab=53.97 E-value=53 Score=23.81 Aligned_cols=27 Identities=15% Similarity=0.378 Sum_probs=22.4
Q ss_pred EEEecCcceEEEcCCCCCCCCCCEEEEEe
Q 033108 98 RIKLVRGQNFFICNSAGHCGSGMKIAINA 126 (127)
Q Consensus 98 ~v~L~~G~~yFic~~~~hC~~GmKl~I~V 126 (127)
.+++.+|..|-|.. ..|..|+++...+
T Consensus 100 ~~~~~pG~~y~i~~--f~Cp~g~~v~ye~ 126 (143)
T PF09792_consen 100 TFTVSPGNSYVINT--FPCPAGQAVSYEM 126 (143)
T ss_pred ceEECCCCceEeCc--EeCCCCCEEEEEE
Confidence 57888899999996 5899999887654
No 31
>COG3241 Azurin [Energy production and conversion]
Probab=53.88 E-value=6.4 Score=28.64 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=17.9
Q ss_pred CcEEEec-----CcceE-EEcCCCCCCCCCCEEEE
Q 033108 96 KDRIKLV-----RGQNF-FICNSAGHCGSGMKIAI 124 (127)
Q Consensus 96 ~~~v~L~-----~G~~y-Fic~~~~hC~~GmKl~I 124 (127)
.++++++ +|..| |+|++|||=.. ||-.+
T Consensus 114 ~~S~Tfd~~kL~~g~~Y~FfCtFPGH~AL-MkGtl 147 (151)
T COG3241 114 ETSLTFDPAKLADGVEYKFFCTFPGHGAL-MKGTL 147 (151)
T ss_pred cceEecCHHHhcCCceEEEEEecCCcHHh-hccee
Confidence 3567664 37556 99999999432 44433
No 32
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=53.43 E-value=44 Score=24.57 Aligned_cols=26 Identities=19% Similarity=0.434 Sum_probs=19.8
Q ss_pred CCeEEeCCEEEEEeCCC----CCeEEEEcc
Q 033108 52 GKRFKAGDTLVFNYDPT----LHNVVAVNR 77 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~----~h~V~~v~~ 77 (127)
...++.||.++|+.+.+ .|.|..+.+
T Consensus 58 ~~~~~~GDIVvf~~~~~~~~iihRVi~v~~ 87 (158)
T TIGR02228 58 PNDIQVGDVITYKSPGFNTPVTHRVIEINN 87 (158)
T ss_pred cCCCCCCCEEEEEECCCCccEEEEEEEEEC
Confidence 35789999999998753 577777743
No 33
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=53.16 E-value=51 Score=24.13 Aligned_cols=36 Identities=11% Similarity=0.230 Sum_probs=28.5
Q ss_pred CeEEeCCEEEEEeC-----CCCCeEEEEcccCcCCCCCCCC
Q 033108 53 KRFKAGDTLVFNYD-----PTLHNVVAVNRAGYRSCTAPGG 88 (127)
Q Consensus 53 ~~f~vGD~L~F~y~-----~~~h~V~~v~~~~Y~~C~~~~~ 88 (127)
...+.||.+++.-. +.-|..+.++....-.|+...+
T Consensus 74 ~~~q~GDI~I~g~~g~S~G~~GHtgif~~~~~iIhc~y~~~ 114 (145)
T PF05382_consen 74 WNLQRGDIFIWGRRGNSAGAGGHTGIFMDNDTIIHCNYGAN 114 (145)
T ss_pred ccccCCCEEEEcCCCCCCCCCCeEEEEeCCCcEEEecCCCC
Confidence 47899999998664 2359999998888889998644
No 34
>PF10731 Anophelin: Thrombin inhibitor from mosquito; InterPro: IPR018932 Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen. The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite. The inhibitor acts by blocking the exosite, rather than by interacting with the active site. The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.
Probab=50.70 E-value=11 Score=23.98 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHhhccccccEEEEecCCCC
Q 033108 13 IMAALLICLLLVYIEIVDATTYTVGDSGG 41 (127)
Q Consensus 13 ~~~~~~~~~~~~~~~~a~a~~~~VG~~~g 41 (127)
++++.|+|+ +|.+-+.+|-+|.-|+.--
T Consensus 5 l~vialLC~-aLva~vQ~APQYa~GeeP~ 32 (65)
T PF10731_consen 5 LIVIALLCV-ALVAIVQSAPQYAPGEEPS 32 (65)
T ss_pred hhHHHHHHH-HHHHHHhcCcccCCCCCCC
Confidence 345667774 3334456777898887543
No 35
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=50.55 E-value=23 Score=25.31 Aligned_cols=18 Identities=22% Similarity=0.464 Sum_probs=15.5
Q ss_pred CeEEeCCEEEEEeCCCCC
Q 033108 53 KRFKAGDTLVFNYDPTLH 70 (127)
Q Consensus 53 ~~f~vGD~L~F~y~~~~h 70 (127)
+.|++||.+.|-+++..|
T Consensus 41 ~~f~~GDlvLflpt~~~~ 58 (129)
T PF10377_consen 41 RNFQVGDLVLFLPTRNHN 58 (129)
T ss_pred ecCCCCCEEEEEecCCCC
Confidence 679999999999997655
No 36
>PF02839 CBM_5_12: Carbohydrate binding domain; InterPro: IPR003610 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM5 from CAZY and CBM12 from CAZY. These modules have a core structure consisting of a 3-stranded meander beta-sheet, which contain six aromatic groups that may be important for binding. CBM5/12 is found in proteins such as chitinase A1, chitinase B [], and endoglucanase Z []. The overall topology of the CBM is structurally similar to the C-terminal chitin-binding domains (ChBD) of chitinase A1 and chitinase B, however the binding mechanism for the ChBD may be different from that of the CBM [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1ED7_A 1W1V_A 1E15_B 1UR8_A 1E6Z_B 1E6P_A 1W1T_A 1W1P_B 1UR9_A 1E6R_A ....
Probab=47.25 E-value=12 Score=20.85 Aligned_cols=17 Identities=29% Similarity=0.911 Sum_probs=10.2
Q ss_pred ccccCCCeEEeCCEEEE
Q 033108 47 ASWAKGKRFKAGDTLVF 63 (127)
Q Consensus 47 ~~Wa~~~~f~vGD~L~F 63 (127)
..|..+++...||.+.|
T Consensus 2 p~W~~~~~Y~~Gd~V~~ 18 (41)
T PF02839_consen 2 PAWDPGTTYNAGDRVSY 18 (41)
T ss_dssp -B--TTCEE-TT-EEEE
T ss_pred CCcCCCCEEcCCCEEEE
Confidence 36888999999998875
No 37
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=46.17 E-value=13 Score=31.16 Aligned_cols=30 Identities=30% Similarity=0.562 Sum_probs=19.1
Q ss_pred eEEeCCEEEEEeCCCCCeEEE--E---cccCcCCCCC
Q 033108 54 RFKAGDTLVFNYDPTLHNVVA--V---NRAGYRSCTA 85 (127)
Q Consensus 54 ~f~vGD~L~F~y~~~~h~V~~--v---~~~~Y~~C~~ 85 (127)
..+.||+|+|+|+. |.--+ . +..+||.|-.
T Consensus 134 ~aq~gD~LvfHYSG--HGtr~~~~~gDe~dG~DE~I~ 168 (362)
T KOG1546|consen 134 SAQPGDSLVFHYSG--HGTRQPDTNGDEVDGYDETIV 168 (362)
T ss_pred cCCCCCEEEEEecC--CCCcCCCCCCCCCCCCcceee
Confidence 46789999999984 22221 2 2356887654
No 38
>PF07732 Cu-oxidase_3: Multicopper oxidase; InterPro: IPR011707 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 3 (or coupled binuclear) domains. ; GO: 0005507 copper ion binding; PDB: 2QT6_B 3KW7_B 2R7E_A 3CDZ_A 1SDD_A 3G5W_D 3UAC_A 2YXV_A 3OD3_A 3NSY_A ....
Probab=45.56 E-value=6.6 Score=27.27 Aligned_cols=72 Identities=14% Similarity=0.111 Sum_probs=41.2
Q ss_pred CCeEEeCCEEEEEeCCC---CCeEEEE----ccc-CcCC--CCCCCCceeeccCC---cEEEec--CcceEEEcCCCCCC
Q 033108 52 GKRFKAGDTLVFNYDPT---LHNVVAV----NRA-GYRS--CTAPGGAKVYSSGK---DRIKLV--RGQNFFICNSAGHC 116 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~---~h~V~~v----~~~-~Y~~--C~~~~~~~~~~~G~---~~v~L~--~G~~yFic~~~~hC 116 (127)
..+++.||+|.+++.+. .+++-.= +.. ..|- -....+ ...|. -.++++ +|++||-|...++=
T Consensus 27 tI~v~~Gd~v~i~~~N~l~~~~siH~HG~~~~~~~~~DG~~~~~~~~---i~pG~~~~Y~~~~~~~~Gt~wYH~H~~~~~ 103 (117)
T PF07732_consen 27 TIRVREGDTVRITVTNNLDEPTSIHWHGLHQPPSPWMDGVPGVTQCP---IAPGESFTYEFTANQQAGTYWYHSHVHGQQ 103 (117)
T ss_dssp EEEEETTEEEEEEEEEESSSGBSEEEETSBSTTGGGGSGGTTTSGSS---BSTTEEEEEEEEESSCSEEEEEEECSTTHH
T ss_pred EEEEEcCCeeEEEEEeccccccccccceeeeeeeeecCCccccccee---EEeecceeeeEeeeccccceeEeeCCCchh
Confidence 37899999999998742 3444431 110 0111 000011 12232 256666 39999999988753
Q ss_pred CCCCEEEEEe
Q 033108 117 GSGMKIAINA 126 (127)
Q Consensus 117 ~~GmKl~I~V 126 (127)
..||--++.|
T Consensus 104 ~~GL~G~~iV 113 (117)
T PF07732_consen 104 VMGLYGAIIV 113 (117)
T ss_dssp HTTEEEEEEE
T ss_pred cCcCEEEEEE
Confidence 4888777765
No 39
>PF06462 Hyd_WA: Propeller; InterPro: IPR006624 Tectonins I and II are two dominant proteins in the nuclei and nuclear matrix from plasmodia of Physarum polycephalum (Slime mold) which encode 217 and 353 amino acids, respectively. Tectonin I is homologous to the C-terminal two-thirds of tectonin II. Both proteins contain six tandem repeats that are each 33-37 amino acids in length and define a new consensus sequence. Homologous repeats are found in L-6, a bacterial lipopolysaccharide-binding lectin from horseshoe crab hemocytes. The repetitive sequences of the tectonins and L-6 are reminiscent of the WD repeats of the beta-subunit of G proteins, suggesting that they form beta-propeller domains. The tectonins may be lectins that function as part of a transmembrane signalling complex during phagocytosis [].
Probab=42.63 E-value=54 Score=17.62 Aligned_cols=24 Identities=13% Similarity=0.169 Sum_probs=19.2
Q ss_pred EEEecC-cceEEEcCCCCCCCCCCE
Q 033108 98 RIKLVR-GQNFFICNSAGHCGSGMK 121 (127)
Q Consensus 98 ~v~L~~-G~~yFic~~~~hC~~GmK 121 (127)
...++. |.-||-.++...|..|+.
T Consensus 3 VWav~~~G~v~~R~Gis~~~P~G~~ 27 (32)
T PF06462_consen 3 VWAVTSDGSVYFRTGISPSNPEGTS 27 (32)
T ss_pred EEEEcCCCCEEEECcCCCCCCCCCC
Confidence 345664 999999999999999964
No 40
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=40.89 E-value=18 Score=23.61 Aligned_cols=13 Identities=38% Similarity=0.807 Sum_probs=10.9
Q ss_pred CCeEEeCCEEEEE
Q 033108 52 GKRFKAGDTLVFN 64 (127)
Q Consensus 52 ~~~f~vGD~L~F~ 64 (127)
...|+|||.|.++
T Consensus 26 DRdf~VGD~L~L~ 38 (72)
T PF12961_consen 26 DRDFQVGDILVLR 38 (72)
T ss_pred CCCCCCCCEEEEE
Confidence 3689999999885
No 41
>PLN02354 copper ion binding / oxidoreductase
Probab=38.63 E-value=2.8e+02 Score=24.50 Aligned_cols=75 Identities=11% Similarity=0.146 Sum_probs=45.0
Q ss_pred ccc-CCCeEEeCCEEEEEeCCC--------CCeEEEEcccC-----cCCCCCCCCceeeccCCcEEEec-C-cceEEEcC
Q 033108 48 SWA-KGKRFKAGDTLVFNYDPT--------LHNVVAVNRAG-----YRSCTAPGGAKVYSSGKDRIKLV-R-GQNFFICN 111 (127)
Q Consensus 48 ~Wa-~~~~f~vGD~L~F~y~~~--------~h~V~~v~~~~-----Y~~C~~~~~~~~~~~G~~~v~L~-~-G~~yFic~ 111 (127)
+|. -.+++..||+|+.+-.+. -|.+.+-.... ..+|-.. |- .+=.-.|+++ . |++||=+.
T Consensus 54 q~PGP~I~~~~GD~v~V~v~N~l~~~ttiHWHGi~q~~~~~~DGv~~TQcpI~-PG---~sf~Y~F~~~~q~GT~WYHsH 129 (552)
T PLN02354 54 QFPGPNINSTSNNNIVINVFNNLDEPFLLTWSGIQQRKNSWQDGVPGTNCPIP-PG---TNFTYHFQPKDQIGSYFYYPS 129 (552)
T ss_pred CCcCCcEEEeCCCEEEEEEEECCCCCcccccccccCCCCcccCCCcCCcCCCC-CC---CcEEEEEEeCCCCcceEEecC
Confidence 454 348899999999887543 35555532111 2335332 11 1111257774 4 99999998
Q ss_pred CCCCCCCCCEEEEEe
Q 033108 112 SAGHCGSGMKIAINA 126 (127)
Q Consensus 112 ~~~hC~~GmKl~I~V 126 (127)
...+=..||.-.+.|
T Consensus 130 ~~~Q~~~Gl~G~lII 144 (552)
T PLN02354 130 TGMHRAAGGFGGLRV 144 (552)
T ss_pred ccceecCCccceEEE
Confidence 877777888766655
No 42
>TIGR01480 copper_res_A copper-resistance protein, CopA family. This model represents the CopA copper resistance protein family. CopA is related to laccase (benzenediol:oxygen oxidoreductase) and L-ascorbate oxidase, both copper-containing enzymes. Most members have a typical TAT (twin-arginine translocation) signal sequence with an Arg-Arg pair. Twin-arginine translocation is observed for a large number of periplasmic proteins that cross the inner membrane with metal-containing cofactors already bound. The combination of copper-binding sites and TAT translocation motif suggests a mechansism of resistance by packaging and export.
Probab=37.95 E-value=1.1e+02 Score=27.33 Aligned_cols=84 Identities=20% Similarity=0.346 Sum_probs=50.5
Q ss_pred Ccccccccc--CCCeEEeCCEEEEEeCCC---CCeEE------EE-cccC-cCCCCCCCCceeeccCCcE--EEec-Ccc
Q 033108 42 WSFNMASWA--KGKRFKAGDTLVFNYDPT---LHNVV------AV-NRAG-YRSCTAPGGAKVYSSGKDR--IKLV-RGQ 105 (127)
Q Consensus 42 W~~~~~~Wa--~~~~f~vGD~L~F~y~~~---~h~V~------~v-~~~~-Y~~C~~~~~~~~~~~G~~~--v~L~-~G~ 105 (127)
|+++-..|. ...+++.||.+++.+.+. .|.+. ++ +..+ |.. ..+.+.+...+..+ |..+ ||.
T Consensus 488 wtiNG~~~~~~~pl~v~~Gervri~l~N~t~~~HpmHlHG~~f~v~~~~G~~~~--~~dTv~V~Pg~t~~~~f~ad~pG~ 565 (587)
T TIGR01480 488 WSFDGEAFGLKTPLRFNYGERLRVVLVNDTMMAHPIHLHGMWSELEDGQGEFQV--RKHTVDVPPGGKRSFRVTADALGR 565 (587)
T ss_pred EEECCccCCCCCceEecCCCEEEEEEECCCCCCcceeEcCceeeeecCCCcccc--cCCceeeCCCCEEEEEEECCCCeE
Confidence 887655565 358899999999999643 33332 23 1111 110 00111222222333 4444 699
Q ss_pred eEEEcCCCCCCCCCCEEEEEeC
Q 033108 106 NFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 106 ~yFic~~~~hC~~GmKl~I~V~ 127 (127)
++|=|-...|=+.||--.+.|+
T Consensus 566 w~~HCH~l~H~~~GM~~~~~v~ 587 (587)
T TIGR01480 566 WAYHCHMLLHMEAGMFREVTVR 587 (587)
T ss_pred EEEcCCCHHHHhCcCcEEEEeC
Confidence 9999999889999998877764
No 43
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=37.90 E-value=22 Score=23.02 Aligned_cols=19 Identities=26% Similarity=0.424 Sum_probs=12.1
Q ss_pred cCCCeEEeCCEEEEEeCCC
Q 033108 50 AKGKRFKAGDTLVFNYDPT 68 (127)
Q Consensus 50 a~~~~f~vGD~L~F~y~~~ 68 (127)
+..+.+++||.++|.+...
T Consensus 69 v~~n~L~~GD~~~F~~~~~ 87 (100)
T PF02362_consen 69 VRDNGLKEGDVCVFELIGN 87 (100)
T ss_dssp HHHCT--TT-EEEEEE-SS
T ss_pred HHHcCCCCCCEEEEEEecC
Confidence 3568899999999999853
No 44
>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=37.84 E-value=1.3e+02 Score=20.46 Aligned_cols=58 Identities=12% Similarity=0.090 Sum_probs=31.5
Q ss_pred cCCCeEEeCCEEEEEeCCCCCeEEEEcccCcCCCCCCCCc-eeeccCCc--EEEecCcceEEEc
Q 033108 50 AKGKRFKAGDTLVFNYDPTLHNVVAVNRAGYRSCTAPGGA-KVYSSGKD--RIKLVRGQNFFIC 110 (127)
Q Consensus 50 a~~~~f~vGD~L~F~y~~~~h~V~~v~~~~Y~~C~~~~~~-~~~~~G~~--~v~L~~G~~yFic 110 (127)
+.+..+++.|..+.+-.++..-+.+++...|. .....+. ... +.. .|++.+|..||+-
T Consensus 40 ~~~~~v~vdg~~ig~l~~g~y~~~~v~pG~h~-i~~~~~~~~~~--~~~~l~~~~~~G~~yy~r 100 (117)
T PF11008_consen 40 AVKPDVYVDGELIGELKNGGYFYVEVPPGKHT-ISAKSEFSSSP--GANSLDVTVEAGKTYYVR 100 (117)
T ss_pred cccceEEECCEEEEEeCCCeEEEEEECCCcEE-EEEecCccCCC--CccEEEEEEcCCCEEEEE
Confidence 35577888888888876666666666444332 1111111 101 223 4455577777764
No 45
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=37.82 E-value=26 Score=22.59 Aligned_cols=15 Identities=13% Similarity=0.488 Sum_probs=12.9
Q ss_pred eEEeCCEEEEEeCCC
Q 033108 54 RFKAGDTLVFNYDPT 68 (127)
Q Consensus 54 ~f~vGD~L~F~y~~~ 68 (127)
+|+.||.|.|.+..+
T Consensus 2 ~~~~Ge~v~~~~~~~ 16 (83)
T PF14326_consen 2 VYRVGERVRFRVTSN 16 (83)
T ss_pred cccCCCEEEEEEEeC
Confidence 688999999999764
No 46
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=37.38 E-value=8.8 Score=22.24 Aligned_cols=33 Identities=21% Similarity=0.325 Sum_probs=22.3
Q ss_pred EecCCCCCccccccccCCCeEEeCCEEEEEeCCC
Q 033108 35 TVGDSGGWSFNMASWAKGKRFKAGDTLVFNYDPT 68 (127)
Q Consensus 35 ~VG~~~gW~~~~~~Wa~~~~f~vGD~L~F~y~~~ 68 (127)
.+|.+.+=+.| ..|.....++.||.|.+.+..+
T Consensus 2 kvg~s~~v~iP-k~~~~~l~l~~Gd~v~i~~~~~ 34 (47)
T PF04014_consen 2 KVGNSGQVTIP-KEIREKLGLKPGDEVEIEVEGD 34 (47)
T ss_dssp EETTCSEEEE--HHHHHHTTSSTTTEEEEEEETT
T ss_pred EECCCceEECC-HHHHHHcCCCCCCEEEEEEeCC
Confidence 34544443333 5677677888999999999864
No 47
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=36.09 E-value=35 Score=24.79 Aligned_cols=31 Identities=29% Similarity=0.630 Sum_probs=21.9
Q ss_pred EEEecCCCCCcccccccc-CCCeEEeCCEEEEE
Q 033108 33 TYTVGDSGGWSFNMASWA-KGKRFKAGDTLVFN 64 (127)
Q Consensus 33 ~~~VG~~~gW~~~~~~Wa-~~~~f~vGD~L~F~ 64 (127)
...|||+.| +++.+-|- .+..|+.||.|.|.
T Consensus 40 ~~kVaD~Tg-sI~isvW~e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 40 SCKVADETG-SINISVWDEEGCLIQPGDIIRLT 71 (134)
T ss_pred EEEEecccc-eEEEEEecCcCcccCCccEEEec
Confidence 357999876 33334554 45899999999876
No 48
>KOG2315 consensus Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis]
Probab=34.97 E-value=99 Score=27.59 Aligned_cols=63 Identities=11% Similarity=0.159 Sum_probs=42.6
Q ss_pred cccCCCeEEeCCEEEEEeCCCCCeEEEEcccCcCCCCCCCC----ceee-ccCCc-EEEecC-cceEEEc
Q 033108 48 SWAKGKRFKAGDTLVFNYDPTLHNVVAVNRAGYRSCTAPGG----AKVY-SSGKD-RIKLVR-GQNFFIC 110 (127)
Q Consensus 48 ~Wa~~~~f~vGD~L~F~y~~~~h~V~~v~~~~Y~~C~~~~~----~~~~-~~G~~-~v~L~~-G~~yFic 110 (127)
+=.+.++|..=|.+.|+|++..-.++.+...+.|.-+.+-- .-.+ .+|++ +|+|.+ ||-|=++
T Consensus 208 ~~~a~ksFFkadkvqm~WN~~gt~LLvLastdVDktn~SYYGEq~Lyll~t~g~s~~V~L~k~GPVhdv~ 277 (566)
T KOG2315|consen 208 QPVANKSFFKADKVQMKWNKLGTALLVLASTDVDKTNASYYGEQTLYLLATQGESVSVPLLKEGPVHDVT 277 (566)
T ss_pred chhhhccccccceeEEEeccCCceEEEEEEEeecCCCccccccceEEEEEecCceEEEecCCCCCceEEE
Confidence 33467999999999999998878888776777666554411 1111 23544 688884 8877444
No 49
>TIGR03388 ascorbase L-ascorbate oxidase, plant type. Members of this protein family are the copper-containing enzyme L-ascorbate oxidase (EC 1.10.3.3), also called ascorbase. This family is found in flowering plants, and shows greater sequence similarity to a family of laccases (EC 1.10.3.2) from plants than to other known ascorbate oxidases.
Probab=34.69 E-value=73 Score=27.83 Aligned_cols=69 Identities=17% Similarity=0.231 Sum_probs=42.8
Q ss_pred CCeEEeCCEEEEEeCCCC----CeEE-----EEcccCcC------CCCCCCCceeeccCC---cEEEec-CcceEEEcCC
Q 033108 52 GKRFKAGDTLVFNYDPTL----HNVV-----AVNRAGYR------SCTAPGGAKVYSSGK---DRIKLV-RGQNFFICNS 112 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~~----h~V~-----~v~~~~Y~------~C~~~~~~~~~~~G~---~~v~L~-~G~~yFic~~ 112 (127)
..+++.||.+++...+.. +++. +......| .|-. ..|. -.|+++ +|++||-|-.
T Consensus 33 ~i~~~~Gd~v~v~v~N~l~~~~t~iHwHGl~~~~~~~~DG~~~vtq~~I-------~PG~s~~y~f~~~~~Gt~wyH~H~ 105 (541)
T TIGR03388 33 TIRAQAGDTIVVELTNKLHTEGVVIHWHGIRQIGTPWADGTAGVTQCAI-------NPGETFIYNFVVDRPGTYFYHGHY 105 (541)
T ss_pred eEEEEcCCEEEEEEEECCCCCCccEEecCcCCcCCcccCCCCccccCCc-------CCCCEEEEEEEcCCCEEEEEEecc
Confidence 478999999999876532 2222 21110011 1221 2232 246666 4999999998
Q ss_pred CCCCCCCCEEEEEeC
Q 033108 113 AGHCGSGMKIAINAM 127 (127)
Q Consensus 113 ~~hC~~GmKl~I~V~ 127 (127)
..|-..||.-.|.|.
T Consensus 106 ~~q~~~Gl~G~liV~ 120 (541)
T TIGR03388 106 GMQRSAGLYGSLIVD 120 (541)
T ss_pred hHHhhccceEEEEEe
Confidence 888899998887763
No 50
>MTH00047 COX2 cytochrome c oxidase subunit II; Provisional
Probab=32.89 E-value=49 Score=25.22 Aligned_cols=26 Identities=31% Similarity=0.475 Sum_probs=20.2
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
++.+ +|.++..|++ .|..| |++.|.|
T Consensus 160 ~~~~~~G~y~g~C~e--~CG~~H~~M~~~v~v 189 (194)
T MTH00047 160 FCPDRHGVFVGYCSE--LCGVGHSYMPIVIEV 189 (194)
T ss_pred EEcCCCEEEEEEeeh--hhCcCcccCcEEEEE
Confidence 3345 4999999997 78776 8888876
No 51
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=30.33 E-value=55 Score=25.89 Aligned_cols=21 Identities=10% Similarity=0.050 Sum_probs=16.6
Q ss_pred ccccccEEEEecCCCCCcccc
Q 033108 26 IEIVDATTYTVGDSGGWSFNM 46 (127)
Q Consensus 26 ~~~a~a~~~~VG~~~gW~~~~ 46 (127)
....+...|..++.+||.+-|
T Consensus 218 ~i~g~~~n~~~~g~~g~e~iP 238 (268)
T PF09451_consen 218 LIFGSWYNYNRYGARGFELIP 238 (268)
T ss_pred hhhhhheeeccCCCCCceecc
Confidence 345667889999999998765
No 52
>COG3627 PhnJ Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=29.72 E-value=32 Score=27.29 Aligned_cols=23 Identities=26% Similarity=0.743 Sum_probs=18.9
Q ss_pred cEEEec-CcceEEEcCCCCCCCCC
Q 033108 97 DRIKLV-RGQNFFICNSAGHCGSG 119 (127)
Q Consensus 97 ~~v~L~-~G~~yFic~~~~hC~~G 119 (127)
|.+.++ +|.+-|+|+..+||+.-
T Consensus 257 DEvi~DD~G~rmfvCSDTD~C~~r 280 (291)
T COG3627 257 DEVVLDDKGGRMFVCSDTDFCEQR 280 (291)
T ss_pred eeeEEcCCCceEEEecCchHHHhH
Confidence 456776 69999999999999753
No 53
>COG4446 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.85 E-value=50 Score=24.00 Aligned_cols=23 Identities=35% Similarity=0.359 Sum_probs=18.9
Q ss_pred CeEEeCCEEEEEeCCCCCeEEEEc
Q 033108 53 KRFKAGDTLVFNYDPTLHNVVAVN 76 (127)
Q Consensus 53 ~~f~vGD~L~F~y~~~~h~V~~v~ 76 (127)
+-|.-=|.|+|..++ .|+|.+|.
T Consensus 90 rlf~FVDDlEfyl~~-d~~vi~vR 112 (141)
T COG4446 90 RLFGFVDDLEFYLPQ-DHNVIWVR 112 (141)
T ss_pred HHhhcccceEEecCC-CCceEEEe
Confidence 556667999999975 89999994
No 54
>MTH00140 COX2 cytochrome c oxidase subunit II; Provisional
Probab=28.75 E-value=74 Score=24.65 Aligned_cols=26 Identities=27% Similarity=0.533 Sum_probs=20.1
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
++.+ ||.+|..|+. -|..| |++.|.|
T Consensus 184 ~~~~~~g~y~~~C~e--~CG~~H~~M~~~v~v 213 (228)
T MTH00140 184 FEPKRPGVFYGQCSE--ICGANHSFMPIVVEA 213 (228)
T ss_pred EEeCCCEEEEEECcc--ccCcCcCCCeEEEEE
Confidence 3445 5999999997 78777 8888776
No 55
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=27.94 E-value=21 Score=22.25 Aligned_cols=25 Identities=20% Similarity=0.438 Sum_probs=13.2
Q ss_pred CCCccccc-----cccCCCeEEeCCEEEEE
Q 033108 40 GGWSFNMA-----SWAKGKRFKAGDTLVFN 64 (127)
Q Consensus 40 ~gW~~~~~-----~Wa~~~~f~vGD~L~F~ 64 (127)
.+|.+..+ .=+.....+.||.|+|+
T Consensus 39 ~~W~~~vNG~~~~~ga~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 39 SYWMYYVNGESANVGAGSYKLKDGDKITWY 68 (68)
T ss_dssp EEEEEEETTEE-SS-CCC-B--TTEEEEE-
T ss_pred ceeEEEECCEEhhcCcceeEeCCCCEEEeC
Confidence 45665432 22456888999999884
No 56
>PLN00044 multi-copper oxidase-related protein; Provisional
Probab=27.68 E-value=1.4e+02 Score=26.75 Aligned_cols=72 Identities=22% Similarity=0.237 Sum_probs=44.5
Q ss_pred CCeEEeCCEEEEEeCCC--------CCeEEEEccc-----CcCCCCCCCCceeeccCCcEEEec-C-cceEEEcCCCCCC
Q 033108 52 GKRFKAGDTLVFNYDPT--------LHNVVAVNRA-----GYRSCTAPGGAKVYSSGKDRIKLV-R-GQNFFICNSAGHC 116 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~--------~h~V~~v~~~-----~Y~~C~~~~~~~~~~~G~~~v~L~-~-G~~yFic~~~~hC 116 (127)
..+++.||+|+.+-.+. -|.+.+.... .+.+|-.. |-. +=.-.|+++ + |++||=+....+=
T Consensus 61 tI~~~~GD~v~V~V~N~L~~~ttIHWHGl~q~~t~w~DGv~~TQcPI~-PG~---sftY~F~~~dq~GT~WYHsH~~~Q~ 136 (596)
T PLN00044 61 ALNVTTNWNLVVNVRNALDEPLLLTWHGVQQRKSAWQDGVGGTNCAIP-AGW---NWTYQFQVKDQVGSFFYAPSTALHR 136 (596)
T ss_pred cEEEECCCEEEEEEEeCCCCCccEEECCccCCCCccccCCCCCcCCcC-CCC---cEEEEEEeCCCCceeEeeccchhhh
Confidence 37899999999886532 2555543211 22345332 111 111357774 4 9999999888777
Q ss_pred CCCCEEEEEeC
Q 033108 117 GSGMKIAINAM 127 (127)
Q Consensus 117 ~~GmKl~I~V~ 127 (127)
..|+.-.|.|+
T Consensus 137 ~~Gl~GalII~ 147 (596)
T PLN00044 137 AAGGYGAITIN 147 (596)
T ss_pred hCcCeeEEEEc
Confidence 88888777663
No 57
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=26.96 E-value=37 Score=21.43 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=14.3
Q ss_pred cccCCCeEEeCCEEEEEeCCC
Q 033108 48 SWAKGKRFKAGDTLVFNYDPT 68 (127)
Q Consensus 48 ~Wa~~~~f~vGD~L~F~y~~~ 68 (127)
+-+.-..+++||.+.|.+...
T Consensus 36 ~~~~l~~l~~Gd~V~F~~~~~ 56 (70)
T PF11604_consen 36 DPVDLAGLKPGDKVRFTFERT 56 (70)
T ss_dssp TTSEESS-STT-EEEEEEEEE
T ss_pred ChhhhhcCCCCCEEEEEEEEC
Confidence 334457899999999999753
No 58
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=25.51 E-value=72 Score=20.10 Aligned_cols=31 Identities=23% Similarity=0.541 Sum_probs=22.6
Q ss_pred EEEecCCCCCccccccccCC--CeEEeCCEEEEE
Q 033108 33 TYTVGDSGGWSFNMASWAKG--KRFKAGDTLVFN 64 (127)
Q Consensus 33 ~~~VG~~~gW~~~~~~Wa~~--~~f~vGD~L~F~ 64 (127)
+..++|+.| .....-|... ..+..||.+.+.
T Consensus 26 ~~~l~D~TG-~i~~~~W~~~~~~~~~~G~vv~i~ 58 (82)
T cd04491 26 SGLVGDETG-TIRFTLWDEKAADDLEPGDVVRIE 58 (82)
T ss_pred EEEEECCCC-EEEEEEECchhcccCCCCCEEEEE
Confidence 467888877 6666777653 678888888777
No 59
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=25.09 E-value=61 Score=19.74 Aligned_cols=17 Identities=35% Similarity=0.677 Sum_probs=13.6
Q ss_pred CCCeEEeCCEEEEEeCC
Q 033108 51 KGKRFKAGDTLVFNYDP 67 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y~~ 67 (127)
.++.|..||.+.|.+..
T Consensus 15 ~~~pv~~Gd~i~~~~~~ 31 (64)
T PF02933_consen 15 EGRPVTKGDTIVFPFFG 31 (64)
T ss_dssp TTEEEETT-EEEEEETT
T ss_pred cCCCccCCCEEEEEeCC
Confidence 35789999999999974
No 60
>PTZ00047 cytochrome c oxidase subunit II; Provisional
Probab=25.07 E-value=97 Score=23.23 Aligned_cols=25 Identities=28% Similarity=0.566 Sum_probs=18.6
Q ss_pred Eec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 100 KLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 100 ~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
..+ +|.+|..|+. -|..| |.+.|.|
T Consensus 118 ~~~~~G~y~gqCsE--lCG~gHs~M~~~V~v 146 (162)
T PTZ00047 118 FILREGVFYGQCSE--MCGTLHGFMPIVVEA 146 (162)
T ss_pred ecCCCeEEEEEcch--hcCcCccCceEEEEE
Confidence 334 5999999997 56654 8888776
No 61
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.58 E-value=29 Score=26.15 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=18.4
Q ss_pred CeEEeCCEEEEEeCC----CCCeEEEE
Q 033108 53 KRFKAGDTLVFNYDP----TLHNVVAV 75 (127)
Q Consensus 53 ~~f~vGD~L~F~y~~----~~h~V~~v 75 (127)
..+++||.++|+... =.|.|..+
T Consensus 76 ~p~~vGdivVf~vegR~IPiVHRviK~ 102 (180)
T KOG3342|consen 76 DPIRVGDIVVFKVEGREIPIVHRVIKQ 102 (180)
T ss_pred CcceeccEEEEEECCccCchhHHHHHH
Confidence 559999999999983 26877765
No 62
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=24.25 E-value=85 Score=23.46 Aligned_cols=20 Identities=5% Similarity=-0.041 Sum_probs=13.1
Q ss_pred hccccccEEEEecCCCCCcc
Q 033108 25 YIEIVDATTYTVGDSGGWSF 44 (127)
Q Consensus 25 ~~~~a~a~~~~VG~~~gW~~ 44 (127)
.+..+.+.+..||-...|.+
T Consensus 18 ~~~~~~~~~l~v~~~~~~~P 37 (247)
T PRK09495 18 VSSHAADKKLVVATDTAFVP 37 (247)
T ss_pred hHhhccCCeEEEEeCCCCCC
Confidence 34556677888986656653
No 63
>PF00686 CBM_20: Starch binding domain; InterPro: IPR002044 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain binds to starch, and is found often at the C terminus of a variety of glycosyl hydrolases acting on polysaccharides more rapidly than on oligosaccharides. Reations include: the hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose, the degradation of starch to cyclodextrins by formation of a 1,4-alpha-D-glucosidic bond, and hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides to remove successive maltose units from the non-reducing ends of the chains.; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1KUL_A 1ACZ_A 1AC0_A 1KUM_A 2Z0B_C 9CGT_A 3CGT_A 6CGT_A 4CGT_A 1CGT_A ....
Probab=23.70 E-value=1.1e+02 Score=19.89 Aligned_cols=35 Identities=26% Similarity=0.662 Sum_probs=26.2
Q ss_pred EEEEecCC---CCCccc-------------cccccCCCeEEeCCEEEEEeC
Q 033108 32 TTYTVGDS---GGWSFN-------------MASWAKGKRFKAGDTLVFNYD 66 (127)
Q Consensus 32 ~~~~VG~~---~gW~~~-------------~~~Wa~~~~f~vGD~L~F~y~ 66 (127)
.-+++|+. ..|++. +..|.....+..|..++|+|-
T Consensus 17 ~v~i~Gs~~~LG~W~~~~a~~l~~~~~~~~~~~W~~~v~lp~~~~~eYKy~ 67 (96)
T PF00686_consen 17 SVYIVGSCPELGNWDPKKAVPLQWNEGTENYPIWSATVDLPAGTPFEYKYV 67 (96)
T ss_dssp EEEEEESSGGGTTTSGGGSBESEBESSSSTTTSEEEEEEEETTSEEEEEEE
T ss_pred EEEEEECcHHhCCCChHhccccccccCCCCCCeEEEEEECcCCCEEEEEEE
Confidence 35789985 369863 147888788889999999994
No 64
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=23.25 E-value=68 Score=18.35 Aligned_cols=19 Identities=16% Similarity=0.683 Sum_probs=11.5
Q ss_pred cCCcEEEec-CcceEEEcCC
Q 033108 94 SGKDRIKLV-RGQNFFICNS 112 (127)
Q Consensus 94 ~G~~~v~L~-~G~~yFic~~ 112 (127)
.+...+... .|..|++|+.
T Consensus 11 ~~~~~~~~~y~G~~Y~FCS~ 30 (47)
T PF04945_consen 11 PGNAAYSVEYNGRTYYFCSE 30 (47)
T ss_dssp -----EEEEETTEEEEESSH
T ss_pred ccCccEEEEECCEEEEEcCH
Confidence 345566676 6999999985
No 65
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=23.16 E-value=52 Score=23.61 Aligned_cols=21 Identities=33% Similarity=0.458 Sum_probs=18.1
Q ss_pred ccccCCCeEEeCCEEEEEeCC
Q 033108 47 ASWAKGKRFKAGDTLVFNYDP 67 (127)
Q Consensus 47 ~~Wa~~~~f~vGD~L~F~y~~ 67 (127)
..|++...+++||.|.|..-+
T Consensus 103 ~G~~~~~~i~vGd~v~~~~~~ 123 (126)
T COG1430 103 AGWAARLGIKVGDRVEFRPLG 123 (126)
T ss_pred CCchhhcCCccCCEEEecccC
Confidence 578889999999999998754
No 66
>PLN02191 L-ascorbate oxidase
Probab=22.68 E-value=2.1e+02 Score=25.40 Aligned_cols=68 Identities=18% Similarity=0.294 Sum_probs=42.0
Q ss_pred CCeEEeCCEEEEEeCCCC---------CeEEEEcccCcC------CCCCCCCceeeccCC---cEEEecC-cceEEEcCC
Q 033108 52 GKRFKAGDTLVFNYDPTL---------HNVVAVNRAGYR------SCTAPGGAKVYSSGK---DRIKLVR-GQNFFICNS 112 (127)
Q Consensus 52 ~~~f~vGD~L~F~y~~~~---------h~V~~v~~~~Y~------~C~~~~~~~~~~~G~---~~v~L~~-G~~yFic~~ 112 (127)
..+++.||+|+.+..+.. |.+.+-....+| .|-. ..|. -.|++++ |++||=|-.
T Consensus 55 ~i~~~~Gd~v~v~v~N~l~~~~tsiHwHGl~~~~~~~~DGv~gvtq~pI-------~PG~s~~Y~f~~~~~GT~wYHsH~ 127 (574)
T PLN02191 55 TIDAVAGDTIVVHLTNKLTTEGLVIHWHGIRQKGSPWADGAAGVTQCAI-------NPGETFTYKFTVEKPGTHFYHGHY 127 (574)
T ss_pred eEEEEcCCEEEEEEEECCCCCCccEECCCCCCCCCccccCCCccccCCc-------CCCCeEEEEEECCCCeEEEEeeCc
Confidence 478999999998876431 333322111111 1222 1222 2566664 999999998
Q ss_pred CCCCCCCCEEEEEe
Q 033108 113 AGHCGSGMKIAINA 126 (127)
Q Consensus 113 ~~hC~~GmKl~I~V 126 (127)
..+-..||.-.+.|
T Consensus 128 ~~q~~~Gl~G~liV 141 (574)
T PLN02191 128 GMQRSAGLYGSLIV 141 (574)
T ss_pred HHHHhCCCEEEEEE
Confidence 88888898877766
No 67
>MTH00117 COX2 cytochrome c oxidase subunit II; Provisional
Probab=22.57 E-value=1.3e+02 Score=23.34 Aligned_cols=26 Identities=23% Similarity=0.509 Sum_probs=19.6
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
+..+ ||.+|-.|++ -|..| |.+.|.|
T Consensus 184 ~~~~~~G~y~g~CsE--~CG~~Hs~M~~~v~v 213 (227)
T MTH00117 184 FITTRPGVFYGQCSE--ICGANHSFMPIVVES 213 (227)
T ss_pred EEEcccceEEEEecc--ccccCccCCeEEEEE
Confidence 3445 5999999997 67766 8888775
No 68
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=22.24 E-value=1.5e+02 Score=20.75 Aligned_cols=31 Identities=23% Similarity=0.538 Sum_probs=22.6
Q ss_pred EEEecCCCCCccccccccCC-CeEEeCCEEEEE
Q 033108 33 TYTVGDSGGWSFNMASWAKG-KRFKAGDTLVFN 64 (127)
Q Consensus 33 ~~~VG~~~gW~~~~~~Wa~~-~~f~vGD~L~F~ 64 (127)
+.+++|..| .+..+.|-.. ..|..||.+.++
T Consensus 43 ~~~l~D~TG-~I~~tlW~~~a~~l~~GdvV~I~ 74 (129)
T PRK06461 43 EAVVGDETG-RVKLTLWGEQAGSLKEGEVVEIE 74 (129)
T ss_pred EEEEECCCC-EEEEEEeCCccccCCCCCEEEEE
Confidence 357888877 4555677633 468999999988
No 69
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=22.21 E-value=1.7e+02 Score=20.76 Aligned_cols=23 Identities=13% Similarity=0.170 Sum_probs=16.3
Q ss_pred CeEEeCCEEEEEeCCCCCeEEEE
Q 033108 53 KRFKAGDTLVFNYDPTLHNVVAV 75 (127)
Q Consensus 53 ~~f~vGD~L~F~y~~~~h~V~~v 75 (127)
..+++||.|..+...+.--.++|
T Consensus 71 ~~l~~GD~I~v~~~~g~~~~Y~V 93 (144)
T cd05829 71 GDLRKGDKVEVTRADGQTATFRV 93 (144)
T ss_pred hcCCCCCEEEEEECCCCEEEEEE
Confidence 56789999999995554344444
No 70
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional
Probab=22.07 E-value=1e+02 Score=24.04 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=19.0
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
+..+ ||.+|..|+. -|..| |++.|.|
T Consensus 184 ~~~~~~G~~~g~C~e--~CG~~H~~M~~~v~v 213 (230)
T MTH00129 184 FIASRPGVFYGQCSE--ICGANHSFMPIVVEA 213 (230)
T ss_pred EEeCCceEEEEEChh--hccccccCCcEEEEE
Confidence 3344 5999999997 66665 8887765
No 71
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=21.61 E-value=1.3e+02 Score=17.94 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=14.0
Q ss_pred CeEEeCCEEEEEeCCCCCeEE
Q 033108 53 KRFKAGDTLVFNYDPTLHNVV 73 (127)
Q Consensus 53 ~~f~vGD~L~F~y~~~~h~V~ 73 (127)
....+||++.+.-+.+.+.+.
T Consensus 36 ~~~~VGD~V~~~~~~~~~~~I 56 (68)
T cd04466 36 NPPAVGDRVEFEPEDDGEGVI 56 (68)
T ss_pred CCCCCCcEEEEEECCCCcEEE
Confidence 446899999997644444333
No 72
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.52 E-value=40 Score=23.62 Aligned_cols=15 Identities=40% Similarity=0.778 Sum_probs=12.5
Q ss_pred CCCeEEeCCEEEEEe
Q 033108 51 KGKRFKAGDTLVFNY 65 (127)
Q Consensus 51 ~~~~f~vGD~L~F~y 65 (127)
+....++||+++|+=
T Consensus 30 krr~ik~GD~IiF~~ 44 (111)
T COG4043 30 KRRQIKPGDKIIFNG 44 (111)
T ss_pred hhcCCCCCCEEEEcC
Confidence 457889999999984
No 73
>TIGR03511 GldH_lipo gliding motility-associated lipoprotein GldH. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Probab=21.47 E-value=3.4e+02 Score=19.96 Aligned_cols=27 Identities=22% Similarity=0.244 Sum_probs=17.0
Q ss_pred CEEEEEeC----CCCCeEEE-E-cccCcCCCCC
Q 033108 59 DTLVFNYD----PTLHNVVA-V-NRAGYRSCTA 85 (127)
Q Consensus 59 D~L~F~y~----~~~h~V~~-v-~~~~Y~~C~~ 85 (127)
|+|.|.++ .+.+++.. + +-.+|.-.+.
T Consensus 42 d~l~F~~~~~d~~~~y~l~l~lR~n~~Ypy~nl 74 (156)
T TIGR03511 42 DTLDFEIPITDYTASYRLFLLIRNDNRYPYRNL 74 (156)
T ss_pred CcEEEEEeecCCCCcEEEEEEEEcCCCCcccCe
Confidence 77778775 34677754 4 5667766554
No 74
>MTH00154 COX2 cytochrome c oxidase subunit II; Provisional
Probab=21.40 E-value=1.3e+02 Score=23.46 Aligned_cols=26 Identities=31% Similarity=0.567 Sum_probs=19.5
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
++.+ +|.+|..|+. -|..| |++.|.|
T Consensus 184 ~~~~~~G~y~g~Cse--~CG~~H~~M~~~v~v 213 (227)
T MTH00154 184 FLINRPGLFFGQCSE--ICGANHSFMPIVIES 213 (227)
T ss_pred EEEcCceEEEEEeec--hhCcCccCCeEEEEE
Confidence 4445 5999999997 67766 8887765
No 75
>MTH00168 COX2 cytochrome c oxidase subunit II; Provisional
Probab=21.36 E-value=1.2e+02 Score=23.45 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=19.6
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
+..+ +|.+|..|++ -|..| |.+.|.|
T Consensus 184 ~~~~~~G~~~g~CsE--~CG~~Hs~M~~~v~v 213 (225)
T MTH00168 184 FLSSRPGSFYGQCSE--ICGANHSFMPIVVEF 213 (225)
T ss_pred EEcCCCEEEEEEccc--ccCcCcCCCeEEEEE
Confidence 3445 5999999997 67776 8887775
No 76
>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=20.76 E-value=1.6e+02 Score=19.98 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=21.4
Q ss_pred CcceEEEcCCCCCCCCCCEEEEEeC
Q 033108 103 RGQNFFICNSAGHCGSGMKIAINAM 127 (127)
Q Consensus 103 ~G~~yFic~~~~hC~~GmKl~I~V~ 127 (127)
||.+.|=|-.-.|=..||-..+.|.
T Consensus 111 ~G~w~~HCHi~~H~~~GM~~~~~v~ 135 (138)
T PF07731_consen 111 PGPWLFHCHILEHEDNGMMAVFVVG 135 (138)
T ss_dssp TEEEEEEESSHHHHHTT-EEEEEEC
T ss_pred ceEEEEEEchHHHHhCCCeEEEEEc
Confidence 6999999999999999999888874
No 77
>MTH00139 COX2 cytochrome c oxidase subunit II; Provisional
Probab=20.20 E-value=1.2e+02 Score=23.34 Aligned_cols=26 Identities=27% Similarity=0.534 Sum_probs=19.7
Q ss_pred EEec-CcceEEEcCCCCCCCCC---CEEEEEe
Q 033108 99 IKLV-RGQNFFICNSAGHCGSG---MKIAINA 126 (127)
Q Consensus 99 v~L~-~G~~yFic~~~~hC~~G---mKl~I~V 126 (127)
++.+ ||.+|..|++ -|..| |.+.|.|
T Consensus 184 ~~~~~~G~y~g~CsE--~CG~~Hs~M~~~v~v 213 (226)
T MTH00139 184 FFINRPGVFYGQCSE--ICGANHSFMPIVVEA 213 (226)
T ss_pred EEcCCCEEEEEEChh--hcCcCcCCCeEEEEE
Confidence 3445 5999999997 68776 8887775
No 78
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=20.09 E-value=79 Score=18.75 Aligned_cols=16 Identities=19% Similarity=0.337 Sum_probs=12.2
Q ss_pred cCCCeEEeCCEEEEEe
Q 033108 50 AKGKRFKAGDTLVFNY 65 (127)
Q Consensus 50 a~~~~f~vGD~L~F~y 65 (127)
++..+..+||.|.|.-
T Consensus 3 ~d~~~~~~Gd~v~Yti 18 (53)
T TIGR01451 3 VDKTVATIGDTITYTI 18 (53)
T ss_pred cCccccCCCCEEEEEE
Confidence 3557889999988765
No 79
>PF11766 Candida_ALS_N: Cell-wall agglutinin N-terminal ligand-sugar binding ; InterPro: IPR024672 This N-terminal domain is likely to be the sugar or ligand binding domain of yeast alpha-agglutinin [] and agglutinin-like (ALS) proteins.; PDB: 2YLH_A 2Y7M_A 2Y7L_A 2Y7O_A 2Y7N_A.
Probab=20.08 E-value=58 Score=26.00 Aligned_cols=36 Identities=28% Similarity=0.548 Sum_probs=23.2
Q ss_pred CCCeEEeCCEE------EEEeCCCCCeEEEE-cccCcCCCCCC
Q 033108 51 KGKRFKAGDTL------VFNYDPTLHNVVAV-NRAGYRSCTAP 86 (127)
Q Consensus 51 ~~~~f~vGD~L------~F~y~~~~h~V~~v-~~~~Y~~C~~~ 86 (127)
.+..++.||+. |||+...+-+|... +...|..|...
T Consensus 5 dgs~v~~GDtFtL~MPcVfKf~t~~~sv~L~~~~~~yAtC~~~ 47 (249)
T PF11766_consen 5 DGSNVSPGDTFTLTMPCVFKFTTSQTSVDLTAGGTTYATCTFQ 47 (249)
T ss_dssp ETTT--TT-EEEEEEETEEEESSS-SEEEEEETTEEEEEEEEE
T ss_pred cccccCCCCEEEEecceEEEEecCCCEEEEEeCCEEEEEeccc
Confidence 35778899987 67787666677664 77788888863
Done!