Query 037303
Match_columns 69
No_of_seqs 159 out of 1044
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 10:53:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037303.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037303hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03030 cationic peroxidase; 99.9 2.8E-27 6.1E-32 173.9 6.0 64 1-68 71-148 (324)
2 cd00693 secretory_peroxidase H 99.9 1.6E-24 3.4E-29 157.2 6.0 67 1-68 48-128 (298)
3 PF00141 peroxidase: Peroxidas 99.8 7.3E-22 1.6E-26 138.3 -0.2 63 1-69 32-109 (230)
4 PLN02608 L-ascorbate peroxidas 99.6 1.2E-16 2.6E-21 116.3 4.1 56 1-68 53-123 (289)
5 cd00692 ligninase Ligninase an 99.6 4E-16 8.6E-21 115.2 4.7 58 1-68 65-137 (328)
6 PLN02364 L-ascorbate peroxidas 99.6 4.6E-16 9.9E-21 111.1 3.2 57 1-69 55-126 (250)
7 cd00691 ascorbate_peroxidase A 99.6 2.1E-15 4.5E-20 107.6 3.1 62 1-68 43-122 (253)
8 cd00314 plant_peroxidase_like 99.5 4.9E-15 1.1E-19 103.9 3.2 60 1-68 41-116 (255)
9 PLN02879 L-ascorbate peroxidas 99.4 3.3E-13 7.1E-18 96.7 3.8 56 1-68 56-126 (251)
10 cd08201 plant_peroxidase_like_ 99.3 1.5E-12 3.3E-17 94.1 1.5 60 1-68 64-132 (264)
11 TIGR00198 cat_per_HPI catalase 97.4 8.5E-05 1.8E-09 60.1 2.5 46 17-66 113-172 (716)
12 cd00649 catalase_peroxidase_1 91.7 0.092 2E-06 40.5 1.4 47 16-66 102-162 (409)
13 PRK15061 catalase/hydroperoxid 83.6 0.75 1.6E-05 37.9 1.9 47 16-66 114-174 (726)
14 cd08200 catalase_peroxidase_2 75.1 2.2 4.8E-05 31.8 2.0 52 16-67 62-136 (297)
15 PF01756 ACOX: Acyl-CoA oxidas 69.5 1.1 2.4E-05 29.9 -0.6 37 31-67 109-154 (187)
16 COG4027 Uncharacterized protei 68.6 5 0.00011 28.2 2.4 31 34-64 13-64 (194)
17 PTZ00248 eukaryotic translatio 66.6 6.1 0.00013 29.6 2.7 31 29-59 195-232 (319)
18 PF07541 EIF_2_alpha: Eukaryot 61.6 12 0.00025 23.8 3.0 31 29-59 71-108 (114)
19 TIGR00198 cat_per_HPI catalase 56.3 6.9 0.00015 32.4 1.5 49 16-67 480-549 (716)
20 PRK03987 translation initiatio 54.9 13 0.00029 26.8 2.7 31 29-59 186-224 (262)
21 TIGR01868 casD_Cas5e CRISPR sy 54.8 9.5 0.00021 27.1 1.9 21 32-63 129-149 (230)
22 PRK15061 catalase/hydroperoxid 50.8 19 0.00041 30.0 3.2 52 16-67 487-561 (726)
23 PF09704 Cas_Cas5d: CRISPR-ass 43.9 23 0.0005 23.5 2.4 26 31-67 124-149 (218)
24 TIGR01895 cas_Cas5t CRISPR-ass 37.4 28 0.00062 24.1 2.0 25 31-66 106-130 (215)
25 KOG2916 Translation initiation 34.6 39 0.00084 25.4 2.5 31 29-59 193-230 (304)
26 KOG0136 Acyl-CoA oxidase [Lipi 30.5 56 0.0012 27.1 2.9 36 32-67 593-633 (670)
27 PF05184 SapB_1: Saposin-like 30.5 31 0.00068 17.0 1.1 14 32-45 23-36 (39)
28 PF08134 cIII: cIII protein fa 28.4 48 0.001 18.2 1.6 17 29-45 26-42 (44)
29 cd04894 ACT_ACR-like_1 ACT dom 27.3 43 0.00094 20.1 1.4 12 34-45 58-69 (69)
30 COG1093 SUI2 Translation initi 26.0 72 0.0016 23.7 2.6 30 30-59 190-226 (269)
31 PF01221 Dynein_light: Dynein 24.1 52 0.0011 19.5 1.4 25 30-62 36-60 (89)
32 PF07710 P53_tetramer: P53 tet 23.0 77 0.0017 17.2 1.8 14 29-42 20-33 (42)
33 PLN02443 acyl-coenzyme A oxida 23.0 25 0.00054 28.5 -0.3 34 34-67 583-625 (664)
34 COG1709 Predicted transcriptio 21.3 30 0.00066 25.3 -0.1 17 26-42 140-156 (241)
35 PHA02634 hypothetical protein; 21.2 19 0.00041 20.3 -0.9 9 2-10 25-33 (49)
36 PRK02090 phosphoadenosine phos 21.0 1E+02 0.0023 21.3 2.6 28 27-54 23-51 (241)
37 COG0049 RpsG Ribosomal protein 21.0 1.1E+02 0.0025 20.7 2.6 28 33-60 58-88 (148)
38 PF11933 DUF3451: Domain of un 20.3 69 0.0015 22.8 1.6 16 42-57 150-165 (225)
No 1
>PLN03030 cationic peroxidase; Provisional
Probab=99.94 E-value=2.8e-27 Score=173.94 Aligned_cols=64 Identities=48% Similarity=0.851 Sum_probs=60.1
Q ss_pred CCceeeecccCCCCccccccCCCCCCCcchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDGL 66 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg~ 66 (69)
|||||||||++ ..||++.+|. ++||||+||.||++||++||++|| ++|||.|+|++|||||+
T Consensus 71 GCDaSvLl~~~---~~Ek~a~~N~-~l~Gf~~i~~iK~~~e~~CPg~VSCADilalAarDaV~~~gGP~~~v~~GRrDg~ 146 (324)
T PLN03030 71 GCDASILIDGS---NTEKTALPNL-LLRGYDVIDDAKTQLEAACPGVVSCADILALAARDSVVLTNGLTWPVPTGRRDGR 146 (324)
T ss_pred CCceEEeeCCC---cccccCCCCc-CcchHHHHHHHHHHHHhhCCCcccHHHHHHHHhhccccccCCCceeeeccccCCC
Confidence 89999999964 3699999998 789999999999999999999999 78999999999999998
Q ss_pred CC
Q 037303 67 IN 68 (69)
Q Consensus 67 ~s 68 (69)
+|
T Consensus 147 ~s 148 (324)
T PLN03030 147 VS 148 (324)
T ss_pred CC
Confidence 86
No 2
>cd00693 secretory_peroxidase Horseradish peroxidase and related secretory plant peroxidases. Secretory peroxidases belong to class III of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class III peroxidases are found in the extracellular space or in the vacuole in plants where they have been implicated in hydrogen peroxide detoxification, auxin catabolism and lignin biosynthesis, and stress response. Class III peroxidases contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=99.90 E-value=1.6e-24 Score=157.23 Aligned_cols=67 Identities=49% Similarity=0.808 Sum_probs=63.0
Q ss_pred CCceeeecccCCCCccccccCCCCCCCcchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDGL 66 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg~ 66 (69)
||||||||+++++...|+++++|. +++||++|+.||++||+.||++|| ++|||.|+|++||||++
T Consensus 48 GcDaSill~~~~~~~~E~~~~~N~-~l~g~~~i~~iK~~~e~~cp~~VScADiialAar~av~~~GGP~~~v~~GR~D~~ 126 (298)
T cd00693 48 GCDASVLLDSTANNTSEKDAPPNL-SLRGFDVIDDIKAALEAACPGVVSCADILALAARDAVVLAGGPSYEVPLGRRDGR 126 (298)
T ss_pred CcceeEEecCCCCCchhccCCCCC-CcchhHHHHHHHHHHHhhCCCcccHHHHHHHhhhhceeccCCCcccccCCCcCCc
Confidence 899999999987778999999998 689999999999999999999999 68999999999999998
Q ss_pred CC
Q 037303 67 IN 68 (69)
Q Consensus 67 ~s 68 (69)
+|
T Consensus 127 ~s 128 (298)
T cd00693 127 VS 128 (298)
T ss_pred cc
Confidence 65
No 3
>PF00141 peroxidase: Peroxidase; InterPro: IPR002016 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme: Fe3+ + H2O2 --> [Fe4+=O]R' (Compound I) + H2O [Fe4+=O]R' + substrate --> [Fe4+=O]R (Compound II) + oxidised substrate [Fe4+=O]R + substrate --> Fe3+ + H2O + oxidised substrate In this mechanism, the enzyme reacts with one equivalent of H2O2 to give [Fe4+=O]R' (compound I). This is a two-electron oxidation/reduction reaction where H2O2 is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl [] intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical []. Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The first one can be viewed as consisting of 3 major classes []. Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants; and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress []. Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn2+ serves as the reducing substrate []. Class II proteins contain four conserved disulphide bridges and two conserved calcium-binding sites. Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole-3-acetic acid (IAA) catabolism; ethylene biosynthesis; and so on. Class III proteins are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes. The crystal structures of a number of these proteins show that they share the same architecture - two all-alpha domains between which the haem group is embedded. ; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1QPA_B 2DV2_A 2B2R_B 1MWV_B 2FXJ_A 2FXG_A 2B2O_B 1X7U_B 2B2Q_A 2FXH_A ....
Probab=99.82 E-value=7.3e-22 Score=138.35 Aligned_cols=63 Identities=56% Similarity=0.911 Sum_probs=55.1
Q ss_pred CCceeeecccCCCCccccccCCCCCCCc-chhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSAQ-GYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDG 65 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~lr-g~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg 65 (69)
|||||||| ...|+++++|. +|+ +|++|+.||+++|.+||++|| +.|||.|+|++||+|+
T Consensus 32 GcDgSil~-----~~~e~~~~~N~-gl~~~~~~i~~ik~~~~~~cp~~VS~ADiialAa~~av~~~GGP~~~v~~GR~D~ 105 (230)
T PF00141_consen 32 GCDGSILL-----FSAEKDAPPNR-GLRDGFDVIDPIKAKLEAACPGVVSCADIIALAARDAVELCGGPRIPVPLGRRDG 105 (230)
T ss_dssp SSSSGGGG-----STTGGGSGGGT-THHHHHHHHHHHHHHHCHHSTTTS-HHHHHHHHHHHHHHHTTGGHSHBEB-EBB-
T ss_pred ccccceec-----ccccccccccc-CcceeeechhhHHhhhcccccCCCCHHHHHHHHhhhccccccccccccccccccc
Confidence 89999999 35799999998 577 999999999999999999999 7899999999999999
Q ss_pred CCCC
Q 037303 66 LINS 69 (69)
Q Consensus 66 ~~s~ 69 (69)
++|.
T Consensus 106 ~~s~ 109 (230)
T PF00141_consen 106 TVSS 109 (230)
T ss_dssp SSGG
T ss_pred cccc
Confidence 8863
No 4
>PLN02608 L-ascorbate peroxidase
Probab=99.64 E-value=1.2e-16 Score=116.30 Aligned_cols=56 Identities=21% Similarity=0.191 Sum_probs=50.1
Q ss_pred CCceeeecccCCCCccccccCCCCCCC-cchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSA-QGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDG 65 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~l-rg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg 65 (69)
|||||||+. .|+++++|. +| +||++|+.||+++ ++|| +.|||.|+|++||||+
T Consensus 53 GcDgSIll~------~E~~~~~N~-gL~~g~~vid~iK~~~-----~~VScADilalAardAV~~~GGP~~~v~~GR~D~ 120 (289)
T PLN02608 53 GPNGSIRNE------EEYSHGANN-GLKIAIDLCEPVKAKH-----PKITYADLYQLAGVVAVEVTGGPTIDFVPGRKDS 120 (289)
T ss_pred CCCeeeecc------cccCCcccc-chHHHHHHHHHHHHHc-----CCcCHHHHHHHHHHHHHHhcCCCccCCCCCCCCC
Confidence 899999983 689999998 67 6999999999997 4788 7899999999999999
Q ss_pred CCC
Q 037303 66 LIN 68 (69)
Q Consensus 66 ~~s 68 (69)
+++
T Consensus 121 ~~s 123 (289)
T PLN02608 121 NAC 123 (289)
T ss_pred CcC
Confidence 875
No 5
>cd00692 ligninase Ligninase and other manganese-dependent fungal peroxidases. Ligninases and related extracellular fungal peroxidases belong to class II of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class II peroxidases are fungal glycoproteins that have been implicated in the oxidative breakdown of lignin, the main cell wall component of woody plants. They contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=99.62 E-value=4e-16 Score=115.16 Aligned_cols=58 Identities=22% Similarity=0.261 Sum_probs=51.8
Q ss_pred CCceeeecccCCCCccccccCCCCCCCcchhHHHHHHHHhhhhCCCeee---------------ccCCCceeecCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS---------------YSEGPYWPVRLGRRDG 65 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS---------------~~gGp~~~V~~GRrDg 65 (69)
||||||||+.+ .|+++.+|. +|+ ++|+.||..+|+.| || ..|||+|+|++||||+
T Consensus 65 GcDgSill~~~----~E~~~~~N~-gL~--~vvd~lk~~~e~~c---VScADiialAa~~AV~~~~GGP~i~v~~GR~D~ 134 (328)
T cd00692 65 GADGSIVLFDD----IETAFHANI-GLD--EIVEALRPFHQKHN---VSMADFIQFAGAVAVSNCPGAPRLEFYAGRKDA 134 (328)
T ss_pred CcCceeecCCc----ccccCCCCC-CHH--HHHHHHHHHHHhcC---cCHHHHHHHHHHHHHHhcCCCCcccccCCCCCC
Confidence 89999999843 699999997 567 89999999999999 99 3599999999999999
Q ss_pred CCC
Q 037303 66 LIN 68 (69)
Q Consensus 66 ~~s 68 (69)
+++
T Consensus 135 ~~s 137 (328)
T cd00692 135 TQP 137 (328)
T ss_pred CCC
Confidence 875
No 6
>PLN02364 L-ascorbate peroxidase 1
Probab=99.60 E-value=4.6e-16 Score=111.07 Aligned_cols=57 Identities=25% Similarity=0.364 Sum_probs=49.7
Q ss_pred CCceeeecccCCCCccccccCCCCCCC-cchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSA-QGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDG 65 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~l-rg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg 65 (69)
||||||. ...|+++++|. ++ +||++|+.||+++ ++|| ++|||.|+|++||||+
T Consensus 55 G~dgSi~------~~~E~~~~~N~-gl~~~~~~i~~ik~~~-----~~VScADilalAardAV~~~GGP~~~v~~GR~D~ 122 (250)
T PLN02364 55 GPFGTMR------FDAEQAHGANS-GIHIALRLLDPIREQF-----PTISFADFHQLAGVVAVEVTGGPDIPFHPGREDK 122 (250)
T ss_pred CCCcccc------ccccccCCCcc-CHHHHHHHHHHHHHHc-----CCcCHHHHHHHHHHHHHHhcCCCeeCCCCCCCCc
Confidence 8999993 34699999997 56 8999999999998 5788 7899999999999999
Q ss_pred CCCC
Q 037303 66 LINS 69 (69)
Q Consensus 66 ~~s~ 69 (69)
++|.
T Consensus 123 ~~s~ 126 (250)
T PLN02364 123 PQPP 126 (250)
T ss_pred cccc
Confidence 8763
No 7
>cd00691 ascorbate_peroxidase Ascorbate peroxidases and cytochrome C peroxidases. Ascorbate peroxidases are a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Along with related catalase-peroxidases, ascorbate peroxidases belong to class I of the plant superfamily. Ascorbate peroxidases are found in the chloroplasts and/or cytosol of algae and plants, where they have been shown to control the concentration of lethal hydrogen peroxide molecules. The yeast cytochrome c peroxidase is a divergent member of the family; it forms a complex with cytochrome c to catalyze the reduction of hydrogen peroxide to water.
Probab=99.55 E-value=2.1e-15 Score=107.61 Aligned_cols=62 Identities=24% Similarity=0.226 Sum_probs=52.5
Q ss_pred CCceeeecccCCC---CccccccCCCCCCC-cchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCC
Q 037303 1 GCYASILLDDIDD---FKWGKNAWPNRNSA-QGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGR 62 (69)
Q Consensus 1 GCDaSiLL~~~~~---~~~e~~a~~n~~~l-rg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GR 62 (69)
+||+|++++...+ ..+|+++++|. +| +||++|+.||+++ | +|| ++|||.|+|++||
T Consensus 43 ~~d~s~~~~G~d~s~~~~~E~~~~~N~-~L~~~~~~i~~iK~~~----~-~VScADilalAar~Av~~~GGP~~~v~~GR 116 (253)
T cd00691 43 TYDKETKTGGSNGTIRFDPELNHGANA-GLDIARKLLEPIKKKY----P-DISYADLWQLAGVVAIEEMGGPKIPFRPGR 116 (253)
T ss_pred ccccccCCCCCCccccchhhcCCcccc-chHHHHHHHHHHHHHc----C-CCCHHHHHHHHHHHHHHHcCCCccCcccCC
Confidence 5899998865432 34799999998 56 8999999999986 4 788 7899999999999
Q ss_pred CCCCCC
Q 037303 63 RDGLIN 68 (69)
Q Consensus 63 rDg~~s 68 (69)
||+++|
T Consensus 117 ~D~~~s 122 (253)
T cd00691 117 VDASDP 122 (253)
T ss_pred CCCCcc
Confidence 999876
No 8
>cd00314 plant_peroxidase_like Heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX), which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions. Several sub-families can be identified. Class I includes intracellular peroxidases present in fungi, plants, archaea and bacteria, called catalase-peroxidases, that can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. Catalase-peroxidases are typically comprised of two homologous domains that probably arose via a single gene duplication event. Class II includes ligninase and other extracellular fungal peroxidases, while class III is comprised
Probab=99.53 E-value=4.9e-15 Score=103.88 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=53.8
Q ss_pred CCceeeecccCCCCccccccCCCCCCCcchhHHHHHHHHhhhhCCCeee--------------cc--CCCceeecCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS--------------YS--EGPYWPVRLGRRD 64 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~--gGp~~~V~~GRrD 64 (69)
||||||+++. |++.++|.+..++|++|+.||+++|. |++|| .. |||.|++++||+|
T Consensus 41 g~dgsi~~~~------e~~~~~N~~l~~~~~~l~~ik~~~~~--~~~vS~ADlialAa~~Av~~~~~ggp~~~~~~GR~D 112 (255)
T cd00314 41 GADGSIRFEP------ELDRPENGGLDKALRALEPIKSAYDG--GNPVSRADLIALAGAVAVESTFGGGPLIPFRFGRLD 112 (255)
T ss_pred CCCceEeccc------cccCcccccHHHHHHHHHHHHHHcCC--CCcccHHHHHHHHHHHHHHHhccCCCeeeeCCCCCC
Confidence 8999999974 99999998545999999999999999 99999 45 9999999999999
Q ss_pred CCCC
Q 037303 65 GLIN 68 (69)
Q Consensus 65 g~~s 68 (69)
+..+
T Consensus 113 ~~~~ 116 (255)
T cd00314 113 ATEP 116 (255)
T ss_pred Cchh
Confidence 9854
No 9
>PLN02879 L-ascorbate peroxidase
Probab=99.38 E-value=3.3e-13 Score=96.66 Aligned_cols=56 Identities=23% Similarity=0.263 Sum_probs=49.1
Q ss_pred CCceeeecccCCCCccccccCCCCCCCc-chhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKNAWPNRNSAQ-GYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDG 65 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~a~~n~~~lr-g~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg 65 (69)
||||||.. ..|++.++|. +|+ +|++|+.||+++ ++|| +.|||.|+|++||+|+
T Consensus 56 G~~Gsirf------~~E~~~~~N~-gL~~~~~~i~~iK~~~-----~~VScADilalAa~~AV~~~GGP~~~~~~GR~D~ 123 (251)
T PLN02879 56 GPFGTIRH------PQELAHDANN-GLDIAVRLLDPIKELF-----PILSYADFYQLAGVVAVEITGGPEIPFHPGRLDK 123 (251)
T ss_pred CCCeeecC------hhhccCCCcC-ChHHHHHHHHHHHHHc-----CCcCHHHHHHHHHHHHHHhcCCCccCCCCCCCCC
Confidence 89999975 2588999998 577 999999999998 5788 7899999999999999
Q ss_pred CCC
Q 037303 66 LIN 68 (69)
Q Consensus 66 ~~s 68 (69)
+.+
T Consensus 124 ~~~ 126 (251)
T PLN02879 124 VEP 126 (251)
T ss_pred CCC
Confidence 865
No 10
>cd08201 plant_peroxidase_like_1 Uncharacterized family of plant peroxidase-like proteins. This is a subgroup of heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX) which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions.
Probab=99.26 E-value=1.5e-12 Score=94.13 Aligned_cols=60 Identities=22% Similarity=0.117 Sum_probs=43.7
Q ss_pred CCceeeecccCCCCccccc-cCCCCCCCcchhHHHHHHHHhhhhCCCee--------eccCCCceeecCCCCCCCCC
Q 037303 1 GCYASILLDDIDDFKWGKN-AWPNRNSAQGYEVIDNIKAEVEKACPLTI--------SYSEGPYWPVRLGRRDGLIN 68 (69)
Q Consensus 1 GCDaSiLL~~~~~~~~e~~-a~~n~~~lrg~~~Id~iKa~le~~Cpg~V--------S~~gGp~~~V~~GRrDg~~s 68 (69)
||||||||+. ..+|+. ..+|. ++++|++|+.+| -.|...+ ++.|||.|+|++||+|++++
T Consensus 64 GcDgSIlle~---~~~En~G~~~n~-~l~~~~~i~~~~----VScADiialAa~~AV~~~GGP~i~v~~GR~Da~~s 132 (264)
T cd08201 64 GLDASIQYEL---DRPENIGSGFNT-TLNFFVNFYSPR----SSMADLIAMGVVTSVASCGGPVVPFRAGRIDATEA 132 (264)
T ss_pred CCCcceeecC---CChhhccCchhh-ccccceeeccCc----cCHHHHHHHHHHHHHHHcCCCeecccccCCCcccc
Confidence 8999999984 246777 44454 689999987763 1121111 17899999999999999875
No 11
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=97.43 E-value=8.5e-05 Score=60.10 Aligned_cols=46 Identities=20% Similarity=-0.009 Sum_probs=32.2
Q ss_pred ccccCCCCCCCcchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCCC
Q 037303 17 GKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDGL 66 (69)
Q Consensus 17 e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg~ 66 (69)
|++-+.|.+.-+.+.+++.|| +.||++|| .+|||.|.+.+||+|+.
T Consensus 113 ~~sw~~N~~Ldka~~lL~pIk----~kyp~~VS~ADLivLAG~vAVE~~Ggp~i~f~~GR~D~~ 172 (716)
T TIGR00198 113 LNSWPDNVNLDKARRLLWPIK----KKYGNKLSWADLIILAGTVAYESMGLKVFGFAGGREDIW 172 (716)
T ss_pred ccCchhhhhHHHHHHHHHHHH----HHCCCceeHHHHHHHHHHHHHHHhCCCccCCCCCCCCCC
Confidence 444444542123455555555 46999999 68999999999999983
No 12
>cd00649 catalase_peroxidase_1 N-terminal catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms, where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to class I of the plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C
Probab=91.71 E-value=0.092 Score=40.51 Aligned_cols=47 Identities=19% Similarity=-0.055 Sum_probs=33.8
Q ss_pred cccccCCCCCCCcchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCCC
Q 037303 16 WGKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDGL 66 (69)
Q Consensus 16 ~e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg~ 66 (69)
.|..-+.|.+.-+...+++.||++. |..|| ..|||.++...||.|..
T Consensus 102 pe~~~~~N~gL~~a~~~L~pik~k~----~~~iS~ADL~~LaG~~AiE~~Ggp~ipf~~GR~Da~ 162 (409)
T cd00649 102 PLNSWPDNVNLDKARRLLWPIKQKY----GNKISWADLMILAGNVALESMGFKTFGFAGGREDVW 162 (409)
T ss_pred cccCcHhhhhHHHHHHHHHHHHHHc----CCCccHHHHHHHHHHHHHHHcCCCcccccCCCCccC
Confidence 4555566653225677777788765 44577 57999999999999985
No 13
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=83.57 E-value=0.75 Score=37.93 Aligned_cols=47 Identities=19% Similarity=-0.055 Sum_probs=33.8
Q ss_pred cccccCCCCCCCcchhHHHHHHHHhhhhCCCeee--------------ccCCCceeecCCCCCCC
Q 037303 16 WGKNAWPNRNSAQGYEVIDNIKAEVEKACPLTIS--------------YSEGPYWPVRLGRRDGL 66 (69)
Q Consensus 16 ~e~~a~~n~~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~gGp~~~V~~GRrDg~ 66 (69)
.|..-+.|.+.-+...+++.||++- |..|| ..|||.++...||.|..
T Consensus 114 pe~~w~~N~gL~ka~~~L~pik~ky----~~~iS~ADLi~LaG~vAiE~~Ggp~i~f~~GR~D~~ 174 (726)
T PRK15061 114 PLNSWPDNVNLDKARRLLWPIKQKY----GNKISWADLMILAGNVALESMGFKTFGFAGGREDVW 174 (726)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHh----CCCccHHHHHHHHHHHHHHHcCCCccCcCCCCCCCc
Confidence 3555556653235777788888765 45577 57999999999999974
No 14
>cd08200 catalase_peroxidase_2 C-terminal non-catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C-terminal do
Probab=75.11 E-value=2.2 Score=31.80 Aligned_cols=52 Identities=21% Similarity=0.123 Sum_probs=35.1
Q ss_pred cccccCCCCC--CCcchhHHHHHHHHhh-hhCCC-eee--------------ccCC-----CceeecCCCCCCCC
Q 037303 16 WGKNAWPNRN--SAQGYEVIDNIKAEVE-KACPL-TIS--------------YSEG-----PYWPVRLGRRDGLI 67 (69)
Q Consensus 16 ~e~~a~~n~~--~lrg~~~Id~iKa~le-~~Cpg-~VS--------------~~gG-----p~~~V~~GRrDg~~ 67 (69)
+|++-..|.. .-+.+.+++.||++.- ..-++ .|| .+|| |.++...||.|...
T Consensus 62 pe~~w~~N~~~~L~~~~~~Le~ik~~~~~~~~~~~~vS~ADLivLaG~vAiE~agg~ag~~p~Ipf~pGR~Da~~ 136 (297)
T cd08200 62 PQKDWEVNEPEELAKVLAVLEGIQKEFNESQSGGKKVSLADLIVLGGCAAVEKAAKDAGVDIKVPFTPGRTDATQ 136 (297)
T ss_pred cccCcCccCcHHHHHHHHHHHHHHHHhcccccCCccccHHHHHHHHhHHHHHHHHhccCCCceeccCCCCCCccc
Confidence 4555566663 2256778888888763 22222 577 4677 99999999999754
No 15
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=69.45 E-value=1.1 Score=29.89 Aligned_cols=37 Identities=27% Similarity=0.539 Sum_probs=21.0
Q ss_pred hHHHHHHHHhhhhC----CCeee---ccCCCceee--cCCCCCCCC
Q 037303 31 EVIDNIKAEVEKAC----PLTIS---YSEGPYWPV--RLGRRDGLI 67 (69)
Q Consensus 31 ~~Id~iKa~le~~C----pg~VS---~~gGp~~~V--~~GRrDg~~ 67 (69)
+-++.|+.+++..| |..|+ ..+=|.|.+ ++||+||.+
T Consensus 109 ~~~~~l~~~i~~l~~~lrp~av~LVDAF~~~D~~L~S~iG~~DG~v 154 (187)
T PF01756_consen 109 EQIKALRKAIEELCAELRPNAVALVDAFDFPDFFLNSPIGRYDGDV 154 (187)
T ss_dssp HHHHHHHHHHHHHHHHHGGGHHHHHHTT---HHHHT-STT-TT--H
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCHHHHcChhccccchH
Confidence 44566777777777 55666 455566644 999999974
No 16
>COG4027 Uncharacterized protein conserved in archaea [Function unknown]
Probab=68.57 E-value=5 Score=28.23 Aligned_cols=31 Identities=39% Similarity=0.706 Sum_probs=21.9
Q ss_pred HHHHHHhhhhCCCe---ee-----------------ccCCCceee-cCCCCC
Q 037303 34 DNIKAEVEKACPLT---IS-----------------YSEGPYWPV-RLGRRD 64 (69)
Q Consensus 34 d~iKa~le~~Cpg~---VS-----------------~~gGp~~~V-~~GRrD 64 (69)
..||+++|.--|+- |+ ..-||+|+| .+||+|
T Consensus 13 kAiq~a~Er~yggw~~kVesLGG~R~~s~ve~~lrea~e~~~~~vlLlGrk~ 64 (194)
T COG4027 13 KAIQYANERNYGGWELKVESLGGGRDPSEVEDNLREALEGPYWPVLLLGRKE 64 (194)
T ss_pred HHHHHHHHhccCCceEEEEecCCCCCcHHHHHHHHHhccCCcceEEEecccc
Confidence 45677777777763 55 345788998 678887
No 17
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=66.62 E-value=6.1 Score=29.63 Aligned_cols=31 Identities=29% Similarity=0.520 Sum_probs=25.1
Q ss_pred chhHHHHHHHHhhhh-------CCCeeeccCCCceeec
Q 037303 29 GYEVIDNIKAEVEKA-------CPLTISYSEGPYWPVR 59 (69)
Q Consensus 29 g~~~Id~iKa~le~~-------Cpg~VS~~gGp~~~V~ 59 (69)
+++=|+.||.+|.++ ||-.|.+.|-|.|.+-
T Consensus 195 ~~dGIe~IK~aL~~~~~~~~~~~~i~i~~igaP~Y~i~ 232 (319)
T PTZ00248 195 DYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIV 232 (319)
T ss_pred CCchHHHHHHHHHHHHhcCCCcCcEEEEEEcCCeEEEE
Confidence 578899999998664 7777779999999774
No 18
>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....
Probab=61.58 E-value=12 Score=23.76 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=21.4
Q ss_pred chhHHHHHHHHhhh---h----CCCeeeccCCCceeec
Q 037303 29 GYEVIDNIKAEVEK---A----CPLTISYSEGPYWPVR 59 (69)
Q Consensus 29 g~~~Id~iKa~le~---~----Cpg~VS~~gGp~~~V~ 59 (69)
.+|=|+.||++|.+ . |+-.+.+.|-|.|.+-
T Consensus 71 ~~dGIe~IK~aL~~~~~~~~~~~~v~I~~igaP~Y~i~ 108 (114)
T PF07541_consen 71 APDGIEAIKKALRAAEEASTEDVPVKIKLIGAPRYRIT 108 (114)
T ss_dssp STTHHHHHHHHHHHHHHCCCTTCCEEEEEECTTEEEEE
T ss_pred CCCHHHHHHHHHHHHHhcCCCCCeEEEEEECCCeEEEE
Confidence 46778888888755 2 3334448999999774
No 19
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=56.25 E-value=6.9 Score=32.39 Aligned_cols=49 Identities=31% Similarity=0.220 Sum_probs=31.2
Q ss_pred cccccCCCC--CCCcchhHHHHHHHHhhhhCCCeee--------------cc---CCCc--eeecCCCCCCCC
Q 037303 16 WGKNAWPNR--NSAQGYEVIDNIKAEVEKACPLTIS--------------YS---EGPY--WPVRLGRRDGLI 67 (69)
Q Consensus 16 ~e~~a~~n~--~~lrg~~~Id~iKa~le~~Cpg~VS--------------~~---gGp~--~~V~~GRrDg~~ 67 (69)
.|++-..|. ..-+.+.+++.||++.-. ..|| .+ |||. .+...||.|...
T Consensus 480 pe~~w~~N~p~gL~~vl~~Le~Ik~~f~~---~~vS~ADLivLaG~vAVE~aa~~gG~~~~Vpf~pGR~Da~~ 549 (716)
T TIGR00198 480 PQKNWPVNEPTRLAKVLAVLEKIQAEFAK---GPVSLADLIVLGGGAAVEKAALDAGISVNVPFLPGRVDATQ 549 (716)
T ss_pred hhcCcccCCHHHHHHHHHHHHHHHHHcCC---CcccHHHHHHHHHHHHHHHHHHhCCCCcccCcCCCCCcccc
Confidence 466666673 122467777888877642 2577 23 8985 455699999764
No 20
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=54.89 E-value=13 Score=26.78 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=23.2
Q ss_pred chhHHHHHHHHhhhh--------CCCeeeccCCCceeec
Q 037303 29 GYEVIDNIKAEVEKA--------CPLTISYSEGPYWPVR 59 (69)
Q Consensus 29 g~~~Id~iKa~le~~--------Cpg~VS~~gGp~~~V~ 59 (69)
.+|=|+.||.+|.++ |+-.|.+.|-|.|.+-
T Consensus 186 ~~dGi~~Ik~aL~~~~~~~~~~~~~v~i~~ig~P~Y~i~ 224 (262)
T PRK03987 186 EPDGVEIIKKALKAAEKANKYEDVEVEIYYVGAPRYRID 224 (262)
T ss_pred CCChHHHHHHHHHHHHhhcCCCCCcEEEEEECCCeEEEE
Confidence 467788888888664 5545568999999764
No 21
>TIGR01868 casD_Cas5e CRISPR system CASCADE complex protein CasD/Cas5e. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is part of the ECOLI subtype CRISPR/Cas locus, and now characterized as part of the CASCADE complex of that system. It shares a small N-terminal homology region with members of several other CRISPR/Cas subtypes, and we view the families that share this region as being Cas5.
Probab=54.76 E-value=9.5 Score=27.07 Aligned_cols=21 Identities=43% Similarity=1.042 Sum_probs=14.9
Q ss_pred HHHHHHHHhhhhCCCeeeccCCCceeecCCCC
Q 037303 32 VIDNIKAEVEKACPLTISYSEGPYWPVRLGRR 63 (69)
Q Consensus 32 ~Id~iKa~le~~Cpg~VS~~gGp~~~V~~GRr 63 (69)
.+++|+++|.. |.|++++||+
T Consensus 129 ~le~l~~AL~~-----------P~f~lyLGRk 149 (230)
T TIGR01868 129 ALDEIAAALRR-----------PVWPLYLGRK 149 (230)
T ss_pred HHHHHHHHHhC-----------CCCCCccccc
Confidence 45778877763 6777777776
No 22
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=50.81 E-value=19 Score=30.01 Aligned_cols=52 Identities=27% Similarity=0.237 Sum_probs=35.0
Q ss_pred cccccCCCC--CCCcchhHHHHHHHHhhhh-CC-Ceee--------------cc---CC--CceeecCCCCCCCC
Q 037303 16 WGKNAWPNR--NSAQGYEVIDNIKAEVEKA-CP-LTIS--------------YS---EG--PYWPVRLGRRDGLI 67 (69)
Q Consensus 16 ~e~~a~~n~--~~lrg~~~Id~iKa~le~~-Cp-g~VS--------------~~---gG--p~~~V~~GRrDg~~ 67 (69)
.|++-..|. ..-+.+.+++.||++...+ -. ..|| .+ || |..+...||.|...
T Consensus 487 Pq~~w~~N~p~~L~~vl~~LE~Ik~~f~~~~~~~~~vS~ADLivLaG~vAIE~aa~~aG~~~~VPf~pGR~Da~~ 561 (726)
T PRK15061 487 PQKDWEVNEPAQLAKVLAVLEGIQAEFNAAQSGGKKVSLADLIVLGGNAAVEQAAKAAGHDVTVPFTPGRTDATQ 561 (726)
T ss_pred cccCccccCHHHHHHHHHHHHHHHHHHhhccCCCCceeHHHHHHHHHHHHHHHHHHhCCCCcccCcCCCCCCccc
Confidence 466666665 2225678899999987432 22 2588 22 67 88888999999854
No 23
>PF09704 Cas_Cas5d: CRISPR-associated protein (Cas_Cas5); InterPro: IPR021124 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the Cas5 family of proteins. This family belongs to a set of several Cas protein families, one each for a number of different CRISPR/Cas subtypes, that share a region of N-terminal sequence similarity. ; PDB: 3KG4_A.
Probab=43.89 E-value=23 Score=23.47 Aligned_cols=26 Identities=27% Similarity=0.759 Sum_probs=17.4
Q ss_pred hHHHHHHHHhhhhCCCeeeccCCCceeecCCCCCCCC
Q 037303 31 EVIDNIKAEVEKACPLTISYSEGPYWPVRLGRRDGLI 67 (69)
Q Consensus 31 ~~Id~iKa~le~~Cpg~VS~~gGp~~~V~~GRrDg~~ 67 (69)
..+++|+.+|++ |.|.+.|||+..+.
T Consensus 124 ~~le~l~~~L~~-----------p~~~~~LGrke~l~ 149 (218)
T PF09704_consen 124 KLLEELEEALKK-----------PVFPLYLGRKECLA 149 (218)
T ss_dssp HHHHHHHHHHHT-----------T--SS-SSSTTSB-
T ss_pred HHHHHHHHHHhC-----------CCcCceeeCcccCC
Confidence 478889999876 56788899987643
No 24
>TIGR01895 cas_Cas5t CRISPR-associated protein Cas5, Tneap subtype. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family is represented by TM1800 from Thermotoga maritima. It is related to TIGR01868 (CRISPR-associated protein, CT1976 family).
Probab=37.39 E-value=28 Score=24.06 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=19.2
Q ss_pred hHHHHHHHHhhhhCCCeeeccCCCceeecCCCCCCC
Q 037303 31 EVIDNIKAEVEKACPLTISYSEGPYWPVRLGRRDGL 66 (69)
Q Consensus 31 ~~Id~iKa~le~~Cpg~VS~~gGp~~~V~~GRrDg~ 66 (69)
+++++++.+|+. |.|...|||++-+
T Consensus 106 ~~le~l~~~L~~-----------p~~~~~LGrsedl 130 (215)
T TIGR01895 106 HFLHEFEENFRK-----------PRYYPLLGRSEDL 130 (215)
T ss_pred HHHHHHHHHHhC-----------CCcCcccCCccce
Confidence 567788888876 5788899998754
No 25
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=34.57 E-value=39 Score=25.42 Aligned_cols=31 Identities=39% Similarity=0.747 Sum_probs=24.2
Q ss_pred chhHHHHHHHHhhh-------hCCCeeeccCCCceeec
Q 037303 29 GYEVIDNIKAEVEK-------ACPLTISYSEGPYWPVR 59 (69)
Q Consensus 29 g~~~Id~iKa~le~-------~Cpg~VS~~gGp~~~V~ 59 (69)
+|+=|+.||++|.+ .||-.+-|..-|.|-|-
T Consensus 193 ~yeGI~aIK~alk~a~~~~te~~piki~LIApPlYVlT 230 (304)
T KOG2916|consen 193 GYEGIDAIKAALKAALNLSTEECPIKIKLIAPPLYVLT 230 (304)
T ss_pred cccCHHHHHHHHHHHHhCCcccCceEEEEecCceEEEE
Confidence 79999999999866 46666667788888764
No 26
>KOG0136 consensus Acyl-CoA oxidase [Lipid transport and metabolism]
Probab=30.49 E-value=56 Score=27.15 Aligned_cols=36 Identities=25% Similarity=0.332 Sum_probs=26.4
Q ss_pred HHHHHHHHhhhhCCCeeeccCCCce-----eecCCCCCCCC
Q 037303 32 VIDNIKAEVEKACPLTISYSEGPYW-----PVRLGRRDGLI 67 (69)
Q Consensus 32 ~Id~iKa~le~~Cpg~VS~~gGp~~-----~V~~GRrDg~~ 67 (69)
+=++++.-|...=|+-||+.-+..| .-.+||+||.+
T Consensus 593 v~~~l~~lL~~iRpnAVaLvDsFd~~D~~L~SvLGryDGnV 633 (670)
T KOG0136|consen 593 VRDQLYELLTKIRPNAVALVDSFDFHDRELNSVLGRYDGNV 633 (670)
T ss_pred HHHHHHHHHHHhCcCeEEeecccccchhhhcccccccCCch
Confidence 3345677777788999997766544 23799999976
No 27
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=30.47 E-value=31 Score=16.98 Aligned_cols=14 Identities=43% Similarity=0.698 Sum_probs=11.6
Q ss_pred HHHHHHHHhhhhCC
Q 037303 32 VIDNIKAEVEKACP 45 (69)
Q Consensus 32 ~Id~iKa~le~~Cp 45 (69)
..++|+..|+..|.
T Consensus 23 t~~~I~~~l~~~C~ 36 (39)
T PF05184_consen 23 TEEEIKKALEKACN 36 (39)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred cHHHHHHHHHHHHh
Confidence 56789999999885
No 28
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=28.39 E-value=48 Score=18.15 Aligned_cols=17 Identities=18% Similarity=0.346 Sum_probs=14.1
Q ss_pred chhHHHHHHHHhhhhCC
Q 037303 29 GYEVIDNIKAEVEKACP 45 (69)
Q Consensus 29 g~~~Id~iKa~le~~Cp 45 (69)
=-.+|..++..||..|-
T Consensus 26 ~rrLIRaa~k~lealc~ 42 (44)
T PF08134_consen 26 IRRLIRAARKQLEALCQ 42 (44)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 34589999999999994
No 29
>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.30 E-value=43 Score=20.06 Aligned_cols=12 Identities=42% Similarity=0.811 Sum_probs=10.0
Q ss_pred HHHHHHhhhhCC
Q 037303 34 DNIKAEVEKACP 45 (69)
Q Consensus 34 d~iKa~le~~Cp 45 (69)
+..|..|+.+||
T Consensus 58 ~lLK~RL~~~CP 69 (69)
T cd04894 58 DLLKNRLMSACP 69 (69)
T ss_pred HHHHHHHHhcCC
Confidence 457999999998
No 30
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=25.99 E-value=72 Score=23.69 Aligned_cols=30 Identities=17% Similarity=0.345 Sum_probs=20.6
Q ss_pred hhHHHHHHHHhhhh---CCCeee----ccCCCceeec
Q 037303 30 YEVIDNIKAEVEKA---CPLTIS----YSEGPYWPVR 59 (69)
Q Consensus 30 ~~~Id~iKa~le~~---Cpg~VS----~~gGp~~~V~ 59 (69)
.+=|+.||++|.++ -+.-|. +.|-|.|.+-
T Consensus 190 ~dGVe~IK~aL~~A~~~~~~~v~~kv~~VgaPrYri~ 226 (269)
T COG1093 190 PDGVEKIKKALKAAEDNGEEEVELKVYYVGAPRYRID 226 (269)
T ss_pred CCcHHHHHHHHHHHHhcCccceeEEEEEecCCeEEEE
Confidence 45688888888664 233244 8899999874
No 31
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=24.09 E-value=52 Score=19.50 Aligned_cols=25 Identities=36% Similarity=0.732 Sum_probs=16.3
Q ss_pred hhHHHHHHHHhhhhCCCeeeccCCCceeecCCC
Q 037303 30 YEVIDNIKAEVEKACPLTISYSEGPYWPVRLGR 62 (69)
Q Consensus 30 ~~~Id~iKa~le~~Cpg~VS~~gGp~~~V~~GR 62 (69)
-++-+.||..|+..- ||.|.|-.|+
T Consensus 36 ~eiA~~iK~~lD~~y--------G~~Wh~IVG~ 60 (89)
T PF01221_consen 36 KEIAEFIKQELDKKY--------GPTWHCIVGK 60 (89)
T ss_dssp HHHHHHHHHHHHHHH--------SS-EEEEEES
T ss_pred HHHHHHHHHHHhccc--------CCceEEEECC
Confidence 456677777777754 5677776665
No 32
>PF07710 P53_tetramer: P53 tetramerisation motif; InterPro: IPR010991 The p53 protein is a tetrameric transcription factor that plays a central role in the prevention of neoplastic transformation []. Oligomerization appears to be essential for the tumour suppressing activity of p53. p53 can be divided into different functional domains: an N-terminal transactivation domain, a proline-rich domain, a DNA-binding domain (IPR008967 from INTERPRO), a tetramerisation domain and a C-terminal regulatory region. The tetramerisation domain of human p53 extends from residues 325 to 356, and has a 4-helical bundle fold. The tetramerisation domain is essential for DNA binding, protein-protein interactions, post-translational modifications, and p53 degradation [].; GO: 0051262 protein tetramerization; PDB: 3Q06_B 1SAL_B 1OLH_B 1AIE_A 1PES_D 1SAK_D 1SAE_B 2J11_D 1PET_A 1OLG_A ....
Probab=23.01 E-value=77 Score=17.17 Aligned_cols=14 Identities=29% Similarity=0.577 Sum_probs=12.5
Q ss_pred chhHHHHHHHHhhh
Q 037303 29 GYEVIDNIKAEVEK 42 (69)
Q Consensus 29 g~~~Id~iKa~le~ 42 (69)
.|+++-+|+.+||.
T Consensus 20 ~yE~l~kine~LEL 33 (42)
T PF07710_consen 20 RYEMLKKINEALEL 33 (42)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 39999999999986
No 33
>PLN02443 acyl-coenzyme A oxidase
Probab=23.00 E-value=25 Score=28.51 Aligned_cols=34 Identities=18% Similarity=0.181 Sum_probs=21.9
Q ss_pred HHHHHHhhhhC----CCeeec---cCCCcee--ecCCCCCCCC
Q 037303 34 DNIKAEVEKAC----PLTISY---SEGPYWP--VRLGRRDGLI 67 (69)
Q Consensus 34 d~iKa~le~~C----pg~VS~---~gGp~~~--V~~GRrDg~~ 67 (69)
+.|+..++..| |..|++ .+=|.+. -++||+||.+
T Consensus 583 ~~i~~~i~~l~~~lrp~av~LvDaf~~~d~~L~S~lG~~DG~v 625 (664)
T PLN02443 583 SLANDQLRSLYSQVRPNAVALVDAFNYTDHYLGSVLGRYDGNV 625 (664)
T ss_pred HHHHHHHHHHHHHHhHhHHHHhhccCCCHHHhCchhhccCChH
Confidence 44566666655 566663 3446553 4899999974
No 34
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=21.25 E-value=30 Score=25.25 Aligned_cols=17 Identities=47% Similarity=0.696 Sum_probs=15.0
Q ss_pred CCcchhHHHHHHHHhhh
Q 037303 26 SAQGYEVIDNIKAEVEK 42 (69)
Q Consensus 26 ~lrg~~~Id~iKa~le~ 42 (69)
.+.||-+||.|||-||-
T Consensus 140 ~v~GyTVvDSikAIL~l 156 (241)
T COG1709 140 DVYGYTVVDSIKAILEL 156 (241)
T ss_pred ceeeeEEehhHHHHHhc
Confidence 36899999999999975
No 35
>PHA02634 hypothetical protein; Provisional
Probab=21.16 E-value=19 Score=20.32 Aligned_cols=9 Identities=67% Similarity=1.036 Sum_probs=8.0
Q ss_pred Cceeeeccc
Q 037303 2 CYASILLDD 10 (69)
Q Consensus 2 CDaSiLL~~ 10 (69)
||.||+|+.
T Consensus 25 Cgi~Ifl~~ 33 (49)
T PHA02634 25 CDASILLNK 33 (49)
T ss_pred cCHhHhHHH
Confidence 899999985
No 36
>PRK02090 phosphoadenosine phosphosulfate reductase; Provisional
Probab=21.03 E-value=1e+02 Score=21.31 Aligned_cols=28 Identities=14% Similarity=0.108 Sum_probs=20.1
Q ss_pred CcchhHHHHHHHHhhhhCCC-eeeccCCC
Q 037303 27 AQGYEVIDNIKAEVEKACPL-TISYSEGP 54 (69)
Q Consensus 27 lrg~~~Id~iKa~le~~Cpg-~VS~~gGp 54 (69)
++..+.++.||.+++..=.. .||.|||.
T Consensus 23 ~~~~~~~e~i~~a~~~~~~~i~vs~SGGK 51 (241)
T PRK02090 23 LEGASAQERLAWALENFGGRLALVSSFGA 51 (241)
T ss_pred hccCCHHHHHHHHHHHcCCCEEEEecCCH
Confidence 57888999999999863222 56666664
No 37
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=20.97 E-value=1.1e+02 Score=20.72 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=21.1
Q ss_pred HHHHHHHhhhhCCC--eee-ccCCCceeecC
Q 037303 33 IDNIKAEVEKACPL--TIS-YSEGPYWPVRL 60 (69)
Q Consensus 33 Id~iKa~le~~Cpg--~VS-~~gGp~~~V~~ 60 (69)
|+-...+||..-|. |.| -.||-.|+||.
T Consensus 58 iqvf~~Ai~N~~P~~Ev~srrvGGa~yqvpV 88 (148)
T COG0049 58 LQVFEKAIENVKPREEVKSRRVGGATYQVPV 88 (148)
T ss_pred HHHHHHHHHhcCchhheeeeeeCCeeeEecC
Confidence 33357888888885 566 78999999975
No 38
>PF11933 DUF3451: Domain of unknown function (DUF3451); InterPro: IPR024583 This presumed domain is functionally uncharacterised. It is found in eukaryotic proteins, is typically between 199 and 238 amino acids in length, and has a conserved ADD sequence motif.
Probab=20.32 E-value=69 Score=22.80 Aligned_cols=16 Identities=19% Similarity=0.287 Sum_probs=12.5
Q ss_pred hhCCCeeeccCCCcee
Q 037303 42 KACPLTISYSEGPYWP 57 (69)
Q Consensus 42 ~~Cpg~VS~~gGp~~~ 57 (69)
..|.|+||+.||+...
T Consensus 150 vdcNGvvsl~g~~~~~ 165 (225)
T PF11933_consen 150 VDCNGVVSLTGGSSLR 165 (225)
T ss_pred eecCceeeccCCCCcc
Confidence 3699999998887543
Done!