Query 046960
Match_columns 165
No_of_seqs 24 out of 26
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 06:14:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02879 L-ascorbate peroxidas 97.2 0.00051 1.1E-08 58.2 4.5 41 96-137 18-63 (251)
2 cd00314 plant_peroxidase_like 96.3 0.0088 1.9E-07 48.6 5.5 42 97-138 2-49 (255)
3 PLN02364 L-ascorbate peroxidas 96.2 0.0063 1.4E-07 51.4 4.3 43 94-137 15-62 (250)
4 PLN02608 L-ascorbate peroxidas 94.9 0.036 7.9E-07 48.2 4.4 41 92-134 12-52 (289)
5 cd00649 catalase_peroxidase_1 94.9 0.033 7.3E-07 50.9 4.2 61 96-156 45-128 (409)
6 cd00691 ascorbate_peroxidase A 94.1 0.061 1.3E-06 45.3 3.7 38 95-133 13-50 (253)
7 TIGR00198 cat_per_HPI catalase 92.8 0.25 5.4E-06 48.1 6.0 58 96-154 432-506 (716)
8 PF00141 peroxidase: Peroxidas 92.0 0.097 2.1E-06 43.0 2.0 30 98-127 1-30 (230)
9 cd08200 catalase_peroxidase_2 91.2 0.21 4.6E-06 44.1 3.3 55 100-154 17-88 (297)
10 PRK15061 catalase/hydroperoxid 90.0 0.37 8E-06 47.1 4.0 68 91-158 48-142 (726)
11 TIGR00198 cat_per_HPI catalase 89.3 0.48 1E-05 46.2 4.3 70 91-161 46-142 (716)
12 PRK15061 catalase/hydroperoxid 88.6 1.1 2.5E-05 43.9 6.2 55 100-154 442-513 (726)
13 cd08201 plant_peroxidase_like_ 87.7 0.38 8.2E-06 41.8 2.2 36 103-138 32-72 (264)
14 cd00692 ligninase Ligninase an 84.5 2.1 4.5E-05 38.0 5.2 20 110-129 35-54 (328)
15 cd00693 secretory_peroxidase H 79.7 1.5 3.3E-05 37.9 2.5 33 95-127 15-47 (298)
16 PHA02800 hypothetical protein; 78.1 1 2.2E-05 37.3 1.0 36 121-157 13-50 (161)
17 PF10518 TAT_signal: TAT (twin 74.9 2.3 5E-05 25.1 1.6 22 53-74 2-23 (26)
18 PF10491 Nrf1_DNA-bind: NLS-bi 74.7 4.1 8.9E-05 35.1 3.7 33 75-107 1-50 (214)
19 PF10784 Plasmid_stab_B: Plasm 73.3 5.1 0.00011 29.1 3.4 43 86-129 25-67 (72)
20 PF13259 DUF4050: Protein of u 62.5 4.7 0.0001 30.6 1.5 32 125-156 86-120 (122)
21 PLN00064 photosystem II protei 45.5 70 0.0015 26.9 5.8 24 53-76 34-57 (166)
22 PLN00019 photosystem I reactio 42.6 50 0.0011 28.8 4.7 89 29-126 19-111 (223)
23 PF09280 XPC-binding: XPC-bind 40.4 25 0.00054 24.2 2.1 20 99-118 10-29 (59)
24 PRK15352 type III secretion sy 40.2 32 0.00069 27.4 2.9 26 91-125 97-122 (125)
25 TIGR02811 formate_TAT formate 40.2 15 0.00033 25.8 1.0 12 53-64 9-20 (66)
26 TIGR01409 TAT_signal_seq Tat ( 39.7 18 0.00039 21.3 1.1 19 54-72 2-20 (29)
27 PF02197 RIIa: Regulatory subu 38.4 28 0.00061 21.8 2.0 23 93-115 2-24 (38)
28 PF11090 DUF2833: Protein of u 35.4 33 0.00071 25.8 2.2 28 85-112 32-59 (86)
29 PF10036 RLL: Putative carniti 33.3 64 0.0014 27.3 3.9 29 77-105 203-231 (249)
30 PLN03030 cationic peroxidase; 32.9 38 0.00083 30.3 2.6 33 95-127 38-70 (324)
31 PF10399 UCR_Fe-S_N: Ubiquitin 31.5 24 0.00052 23.0 0.8 10 51-60 7-16 (41)
32 TIGR03808 RR_plus_rpt_1 twin-a 29.7 15 0.00033 34.5 -0.4 37 53-92 3-39 (455)
33 PLN00042 photosystem II oxygen 28.9 60 0.0013 28.7 3.1 31 34-67 34-66 (260)
34 cd08529 STKc_FA2-like Catalyti 28.5 82 0.0018 23.2 3.4 70 54-125 180-256 (256)
35 COG5173 SEC6 Exocyst complex s 27.8 74 0.0016 31.8 3.8 46 79-125 450-500 (742)
36 smart00549 TAFH TAF homology. 27.6 38 0.00083 25.9 1.5 24 91-116 42-65 (92)
37 TIGR00013 taut 4-oxalocrotonat 27.1 94 0.002 19.7 3.1 26 88-113 14-39 (63)
38 KOG0486 Transcription factor P 26.3 56 0.0012 30.2 2.5 41 69-109 89-134 (351)
39 PF01429 MBD: Methyl-CpG bindi 25.8 53 0.0011 22.8 1.8 17 131-147 37-53 (77)
40 COG0481 LepA Membrane GTPase L 25.4 38 0.00083 33.1 1.4 31 100-140 313-346 (603)
41 PRK15376 pathogenicity island 25.2 82 0.0018 31.1 3.5 12 99-110 588-599 (670)
42 PF13431 TPR_17: Tetratricopep 25.2 77 0.0017 18.7 2.2 29 102-130 2-32 (34)
43 PF12318 FAD-SLDH: Membrane bo 24.9 1E+02 0.0022 24.7 3.5 7 53-59 2-8 (168)
44 PF13428 TPR_14: Tetratricopep 24.8 1.2E+02 0.0026 18.1 3.1 26 95-120 17-42 (44)
45 COG0337 AroB 3-dehydroquinate 23.5 66 0.0014 29.4 2.5 102 36-140 217-333 (360)
46 cd01396 MeCP2_MBD MeCP2, MBD1, 23.5 70 0.0015 22.8 2.1 18 131-148 32-49 (77)
47 PF11002 RDM: RFPL defining mo 23.5 27 0.00058 23.6 0.0 31 81-111 4-37 (42)
48 PF08986 DUF1889: Domain of un 23.3 76 0.0016 25.3 2.5 41 80-121 64-115 (119)
49 cd02334 ZZ_dystrophin Zinc fin 22.3 29 0.00063 23.1 -0.0 10 132-141 11-20 (49)
50 PF07531 TAFH: NHR1 homology t 20.9 45 0.00098 25.4 0.8 24 91-116 43-66 (96)
51 PF06324 Pigment_DH: Pigment-d 20.6 34 0.00075 19.6 0.1 16 109-124 1-18 (18)
52 cd00122 MBD MeCP2, MBD1, MBD2, 20.1 85 0.0019 20.9 1.9 18 131-148 31-48 (62)
No 1
>PLN02879 L-ascorbate peroxidase
Probab=97.17 E-value=0.00051 Score=58.16 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhhcCCCchhHHHHHHhccccccccccCCC-----cee
Q 046960 96 SNIKETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTKP-----LRF 137 (165)
Q Consensus 96 s~ik~~L~~ai~~~peliPslltLaLNDA~TYDKaTKtg-----~~~ 137 (165)
..++..|.+.|+ .....|.++|||..||+|||+.+++| |||
T Consensus 18 ~~~~~~~~~~~~-~~~~~p~~vRla~Hdagt~~~~~~~GG~~Gsirf 63 (251)
T PLN02879 18 QRCKRKLRGLIA-EKHCAPIVLRLAWHSAGTFDVKTKTGGPFGTIRH 63 (251)
T ss_pred HHHHHHHHHHHh-CCCchhHhHHHHHhhhccccCCCCCCCCCeeecC
Confidence 345667777776 46999999999999999999999999 888
No 2
>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=96.32 E-value=0.0088 Score=48.60 Aligned_cols=42 Identities=38% Similarity=0.486 Sum_probs=36.3
Q ss_pred HHHHHHHHHhhcCCCchhHHHHHHhcccccccccc-CCC-----ceee
Q 046960 97 NIKETLQTALKGNPDLIPSLLTLALNDAMTYDKVR-TKP-----LRFK 138 (165)
Q Consensus 97 ~ik~~L~~ai~~~peliPslltLaLNDA~TYDKaT-Ktg-----~~~~ 138 (165)
.|+..|...++.+|.++|++|||+..|+.|||..+ +.| |+|.
T Consensus 2 ~v~~~l~~~~~~~~~~~~~llRl~fHD~~~~~~~~~~~gg~dgsi~~~ 49 (255)
T cd00314 2 AIKAILEDLITQAGALAGSLLRLAFHDAGTYDIADGKGGGADGSIRFE 49 (255)
T ss_pred hHHHHHHHHHHhCcchHHHHHHHHHHHhccccccCCCCCCCCceEecc
Confidence 47788888888899999999999999999999998 333 8885
No 3
>PLN02364 L-ascorbate peroxidase 1
Probab=96.21 E-value=0.0063 Score=51.35 Aligned_cols=43 Identities=21% Similarity=0.371 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHhhcCCCchhHHHHHHhccccccccccCCC-----cee
Q 046960 94 FISNIKETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTKP-----LRF 137 (165)
Q Consensus 94 Fqs~ik~~L~~ai~~~peliPslltLaLNDA~TYDKaTKtg-----~~~ 137 (165)
=..+|++.|.+.| .+|...|.+|||+..||+|||...++| |+|
T Consensus 15 ~~~~~~~~~~~~~-~~~~~a~~~lRl~FHd~~t~dc~~~~GG~dgSi~~ 62 (250)
T PLN02364 15 AVEKCRRKLRGLI-AEKNCAPIMVRLAWHSAGTFDCQSRTGGPFGTMRF 62 (250)
T ss_pred HHHHHHHHHHHHH-hCCCcHHHHHHHHHccccCcCcCCCCCCCCccccc
Confidence 3567888999988 579999999999999999999999875 666
No 4
>PLN02608 L-ascorbate peroxidase
Probab=94.92 E-value=0.036 Score=48.18 Aligned_cols=41 Identities=32% Similarity=0.400 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHhhcCCCchhHHHHHHhccccccccccCCC
Q 046960 92 SEFISNIKETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTKP 134 (165)
Q Consensus 92 seFqs~ik~~L~~ai~~~peliPslltLaLNDA~TYDKaTKtg 134 (165)
.||+. ++..|. ++..+|.+.|.+|||+..|++|||+.++.|
T Consensus 12 ~~~~~-~~~~~~-~~~~d~~~a~~llRLaFHDc~t~d~~~~~g 52 (289)
T PLN02608 12 KEIEK-ARRDLR-ALIASKNCAPIMLRLAWHDAGTYDAKTKTG 52 (289)
T ss_pred HHHHH-HHHHHH-HHHHCCCcHHHHHHHhhhhcCCcCCCCCCC
Confidence 34443 444443 355689999999999999999999999887
No 5
>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=94.88 E-value=0.033 Score=50.87 Aligned_cols=61 Identities=25% Similarity=0.364 Sum_probs=46.3
Q ss_pred HHHHHHHHHHhhcCC--------CchhHHHHHHhccccccccccCCC------ceee---------hhHHHHHHHHHHHH
Q 046960 96 SNIKETLQTALKGNP--------DLIPSLLTLALNDAMTYDKVRTKP------LRFK---------CLVDVIKFLYLLWR 152 (165)
Q Consensus 96 s~ik~~L~~ai~~~p--------eliPslltLaLNDA~TYDKaTKtg------~~~~---------~~~~~~~~~~~~~~ 152 (165)
..+|..|++.|+..- -..|.+||||--||.|||+.+++| |||. -|--++++|--+-.
T Consensus 45 ~~~~~di~~ll~~s~~~wp~D~g~~gp~lvRlAWh~AgTy~~~d~~GG~ngg~iRf~pe~~~~~N~gL~~a~~~L~pik~ 124 (409)
T cd00649 45 EALKEDLKALMTDSQDWWPADYGHYGPLFIRMAWHSAGTYRIADGRGGAGTGQQRFAPLNSWPDNVNLDKARRLLWPIKQ 124 (409)
T ss_pred HHHHHHHHHHHhcccccCccccCCcccceeeeeccccccccCcCCCCCCCCCccccccccCcHhhhhHHHHHHHHHHHHH
Confidence 456778888888653 489999999999999999999999 9996 24445666655555
Q ss_pred HhCC
Q 046960 153 KEGN 156 (165)
Q Consensus 153 ~~~~ 156 (165)
|-++
T Consensus 125 k~~~ 128 (409)
T cd00649 125 KYGN 128 (409)
T ss_pred HcCC
Confidence 5553
No 6
>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=94.07 E-value=0.061 Score=45.32 Aligned_cols=38 Identities=24% Similarity=0.428 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHhhcCCCchhHHHHHHhccccccccccCC
Q 046960 95 ISNIKETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTK 133 (165)
Q Consensus 95 qs~ik~~L~~ai~~~peliPslltLaLNDA~TYDKaTKt 133 (165)
++.|++.++.+++ +|.+.|++|||+..|.++||.....
T Consensus 13 ~~~V~~~v~~~~~-~~~~~~~llRl~FHDc~~~d~s~~~ 50 (253)
T cd00691 13 LEAARNDIAKLID-DKNCAPILVRLAWHDSGTYDKETKT 50 (253)
T ss_pred HHHHHHHHHHHHH-cCCcHHHHHHHHHHHHhccccccCC
Confidence 3578899999999 9999999999999999999877665
No 7
>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=92.80 E-value=0.25 Score=48.09 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=45.3
Q ss_pred HHHHHHHHHHhhcCCCchhHHHHHHhccccccccccCCC------cee-----------ehhHHHHHHHHHHHHHh
Q 046960 96 SNIKETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTKP------LRF-----------KCLVDVIKFLYLLWRKE 154 (165)
Q Consensus 96 s~ik~~L~~ai~~~peliPslltLaLNDA~TYDKaTKtg------~~~-----------~~~~~~~~~~~~~~~~~ 154 (165)
+.|++ |++.|-..---+|-||++|--+|.|||+.+|+| ||| .-|-.|+++|.-+-.|-
T Consensus 432 ~di~~-lk~~i~~sgl~~~~lVr~AWhsA~Tyr~sd~rGGaNGariRl~pe~~w~~N~p~gL~~vl~~Le~Ik~~f 506 (716)
T TIGR00198 432 GDIKE-LKQQILASGLSVSELVCTAWASASTFRSSDYRGGANGARIRLEPQKNWPVNEPTRLAKVLAVLEKIQAEF 506 (716)
T ss_pred HHHHH-HHHHHHhcCCcHHHHHHHhhhhcccccCCCCCCCCCcceeecchhcCcccCCHHHHHHHHHHHHHHHHHc
Confidence 45665 555555555678999999999999999999999 999 46777888887665554
No 8
>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=92.03 E-value=0.097 Score=43.01 Aligned_cols=30 Identities=37% Similarity=0.771 Sum_probs=27.3
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHhcccccc
Q 046960 98 IKETLQTALKGNPDLIPSLLTLALNDAMTY 127 (165)
Q Consensus 98 ik~~L~~ai~~~peliPslltLaLNDA~TY 127 (165)
+++.++++++.+|.+.|.+|||+..|+++|
T Consensus 1 Vr~~v~~~~~~~~~~~~~~lRl~FHDc~~~ 30 (230)
T PF00141_consen 1 VRSDVRAAFKKDPTLAPGLLRLAFHDCFVY 30 (230)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHTTH
T ss_pred CHHHHHHHHHHCcCccHHHHHHHccccccc
Confidence 367788899999999999999999999996
No 9
>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=91.23 E-value=0.21 Score=44.12 Aligned_cols=55 Identities=16% Similarity=0.218 Sum_probs=43.3
Q ss_pred HHHHHHhhcCCCchhHHHHHHhccccccccccCCC------ceee---------h--hHHHHHHHHHHHHHh
Q 046960 100 ETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTKP------LRFK---------C--LVDVIKFLYLLWRKE 154 (165)
Q Consensus 100 ~~L~~ai~~~peliPslltLaLNDA~TYDKaTKtg------~~~~---------~--~~~~~~~~~~~~~~~ 154 (165)
+.|+..|...---+|-++|||--+|.|||+.+|+| |||. . |-.|+++|.-+-.|-
T Consensus 17 ~~lk~~i~~~gl~~~~lvrlAWhsAgTyr~sd~rGGaNGariRl~pe~~w~~N~~~~L~~~~~~Le~ik~~~ 88 (297)
T cd08200 17 AALKAKILASGLTVSELVSTAWASASTFRNSDKRGGANGARIRLAPQKDWEVNEPEELAKVLAVLEGIQKEF 88 (297)
T ss_pred HHHHHHHHhcCCcHHHHHHHhhhccccccCCCCCCCCCcccccCccccCcCccCcHHHHHHHHHHHHHHHHh
Confidence 45666666555668999999999999999999999 9994 3 667888877665554
No 10
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=89.98 E-value=0.37 Score=47.13 Aligned_cols=68 Identities=25% Similarity=0.360 Sum_probs=49.4
Q ss_pred HHHHHH----HHHHHHHHHhhcCC--------CchhHHHHHHhccccccccccCCC------ceeeh---------hHHH
Q 046960 91 RSEFIS----NIKETLQTALKGNP--------DLIPSLLTLALNDAMTYDKVRTKP------LRFKC---------LVDV 143 (165)
Q Consensus 91 rseFqs----~ik~~L~~ai~~~p--------eliPslltLaLNDA~TYDKaTKtg------~~~~~---------~~~~ 143 (165)
+.||++ .+|.-|.+.++..- -..|.++|||--+|.|||+.+++| |||.- |-.+
T Consensus 48 ~~~~~~ld~~a~k~di~~l~~~sqdwwpaD~g~ygp~~vRlAWH~AgTYr~~d~rGGangg~iRf~pe~~w~~N~gL~ka 127 (726)
T PRK15061 48 AEEFKKLDLEALKKDLKALMTDSQDWWPADYGHYGPLFIRMAWHSAGTYRIGDGRGGAGGGQQRFAPLNSWPDNVNLDKA 127 (726)
T ss_pred HHHhchhhHHHHHHHHHHHHhcccccccccCCCccceeeeeeecccccccCcCCCCCCCCCcccCcccccchhhhhHHHH
Confidence 445544 47778888887543 488999999999999999999999 99973 3345
Q ss_pred HHHHHHHHHHhCCce
Q 046960 144 IKFLYLLWRKEGNKL 158 (165)
Q Consensus 144 ~~~~~~~~~~~~~~~ 158 (165)
+++|.-+-.|-|+++
T Consensus 128 ~~~L~pik~ky~~~i 142 (726)
T PRK15061 128 RRLLWPIKQKYGNKI 142 (726)
T ss_pred HHHHHHHHHHhCCCc
Confidence 555555555666543
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=89.35 E-value=0.48 Score=46.19 Aligned_cols=70 Identities=24% Similarity=0.331 Sum_probs=50.7
Q ss_pred HHHHHH----HHHHHHHHHhhcCC--------CchhHHHHHHhccccccccccCCC------ceeehh---------HHH
Q 046960 91 RSEFIS----NIKETLQTALKGNP--------DLIPSLLTLALNDAMTYDKVRTKP------LRFKCL---------VDV 143 (165)
Q Consensus 91 rseFqs----~ik~~L~~ai~~~p--------eliPslltLaLNDA~TYDKaTKtg------~~~~~~---------~~~ 143 (165)
+.||++ .+|.-|++.++..- ...|.++|+|--+|.|||+.+++| |||.=+ -.+
T Consensus 46 ~~~~~~ld~~a~~~dl~~l~~~s~~wwpad~g~ygp~~vRlAWHsAgTYr~~d~rGGa~gg~iRf~P~~sw~~N~~Ldka 125 (716)
T TIGR00198 46 AEEFQQLDLAAVKQDLKHLMTDSQSWWPADWGHYGGLFIRMAWHAAGTYRIADGRGGAATGNQRFAPLNSWPDNVNLDKA 125 (716)
T ss_pred HHHhhhccHHHHHHHHHHHHhcCcccCccccCCcceeeeeeeccccccccCCCCCCCCCCCceecccccCchhhhhHHHH
Confidence 556665 46788888888643 389999999999999999999999 999633 334
Q ss_pred HHHHHHHHHHhCCceeee
Q 046960 144 IKFLYLLWRKEGNKLMSC 161 (165)
Q Consensus 144 ~~~~~~~~~~~~~~~~~~ 161 (165)
+++|.-+-.|-|++ +||
T Consensus 126 ~~lL~pIk~kyp~~-VS~ 142 (716)
T TIGR00198 126 RRLLWPIKKKYGNK-LSW 142 (716)
T ss_pred HHHHHHHHHHCCCc-eeH
Confidence 55554444555554 455
No 12
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=88.61 E-value=1.1 Score=43.86 Aligned_cols=55 Identities=16% Similarity=0.186 Sum_probs=44.1
Q ss_pred HHHHHHhhcCCCchhHHHHHHhccccccccccCCC------ceee-----------hhHHHHHHHHHHHHHh
Q 046960 100 ETLQTALKGNPDLIPSLLTLALNDAMTYDKVRTKP------LRFK-----------CLVDVIKFLYLLWRKE 154 (165)
Q Consensus 100 ~~L~~ai~~~peliPslltLaLNDA~TYDKaTKtg------~~~~-----------~~~~~~~~~~~~~~~~ 154 (165)
..|+..|.+.-=-+|-||++|--+|.|||+.+|+| |||. -|-.|+++|.-+-.+-
T Consensus 442 ~~lk~~i~~~gl~~~~LVr~AWhsA~Tyr~sd~rGGaNGarIRl~Pq~~w~~N~p~~L~~vl~~LE~Ik~~f 513 (726)
T PRK15061 442 AALKAKILASGLSVSELVSTAWASASTFRGSDKRGGANGARIRLAPQKDWEVNEPAQLAKVLAVLEGIQAEF 513 (726)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHhhcccccCCCCCCCCCccceecccccCccccCHHHHHHHHHHHHHHHHHH
Confidence 45666666554559999999999999999999999 9985 5777888888776653
No 13
>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=87.72 E-value=0.38 Score=41.80 Aligned_cols=36 Identities=14% Similarity=0.123 Sum_probs=31.0
Q ss_pred HHHhhcCCCchhHHHHHHhccccccccccCCC-----ceee
Q 046960 103 QTALKGNPDLIPSLLTLALNDAMTYDKVRTKP-----LRFK 138 (165)
Q Consensus 103 ~~ai~~~peliPslltLaLNDA~TYDKaTKtg-----~~~~ 138 (165)
..+...++...+.+|||+.-|+.|||+++|.| |+|.
T Consensus 32 ~~~~~~~~~~aa~~LRL~FHDc~t~~~~~g~gGcDgSIlle 72 (264)
T cd08201 32 DCAPGPGRQAAAEWLRTAFHDMATHNVDDGTGGLDASIQYE 72 (264)
T ss_pred ccCcCCCccHHHHHHHHHHHhhcCcccCCCCCCCCcceeec
Confidence 44555678899999999999999999999998 7764
No 14
>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=84.48 E-value=2.1 Score=37.99 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=17.7
Q ss_pred CCchhHHHHHHhcccccccc
Q 046960 110 PDLIPSLLTLALNDAMTYDK 129 (165)
Q Consensus 110 peliPslltLaLNDA~TYDK 129 (165)
-+++|.+|||+..|++|||+
T Consensus 35 ~~~a~~~lRL~FHD~~~~~~ 54 (328)
T cd00692 35 GEEAHESLRLTFHDAIGFSP 54 (328)
T ss_pred chHHHHhHHHhhhccccccc
Confidence 45778899999999999996
No 15
>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=79.66 E-value=1.5 Score=37.86 Aligned_cols=33 Identities=27% Similarity=0.484 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhcCCCchhHHHHHHhcccccc
Q 046960 95 ISNIKETLQTALKGNPDLIPSLLTLALNDAMTY 127 (165)
Q Consensus 95 qs~ik~~L~~ai~~~peliPslltLaLNDA~TY 127 (165)
.+.|+..++++++.+|.+.|.+|||+..|+.++
T Consensus 15 e~iV~~~v~~~~~~~~~~a~~~lRl~FHDc~v~ 47 (298)
T cd00693 15 ESIVRSVVRAAVKADPRLAAALLRLHFHDCFVR 47 (298)
T ss_pred HHHHHHHHHHHHHhCCCcCchhhhhhhHhhhcc
Confidence 467889999999999999999999999999863
No 16
>PHA02800 hypothetical protein; Provisional
Probab=78.10 E-value=1 Score=37.34 Aligned_cols=36 Identities=28% Similarity=0.564 Sum_probs=25.9
Q ss_pred hccccccccccCCCcee--ehhHHHHHHHHHHHHHhCCc
Q 046960 121 LNDAMTYDKVRTKPLRF--KCLVDVIKFLYLLWRKEGNK 157 (165)
Q Consensus 121 LNDA~TYDKaTKtg~~~--~~~~~~~~~~~~~~~~~~~~ 157 (165)
..|--+||++.|.. || .--.|-|=+.|++||+.||+
T Consensus 13 ~~~~~~~~~~~~~~-~~~~~~si~dII~~Yi~WR~ng~~ 50 (161)
T PHA02800 13 IHDFTDYDNFEKKN-SFSMSYQLTGFLQYYFIWRFNGGK 50 (161)
T ss_pred ccccchhhhHhhhh-hhhhhhhHHHHHHHHhhhhcCCCh
Confidence 45777899999876 22 22334455689999999987
No 17
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=74.91 E-value=2.3 Score=25.08 Aligned_cols=22 Identities=23% Similarity=0.302 Sum_probs=16.6
Q ss_pred ccchhhhhhhhhhhhhhhhccC
Q 046960 53 FGRRDILKCIGATIGMEIISSS 74 (165)
Q Consensus 53 frRRDlL~c~GaAvGmeLI~ss 74 (165)
..||++||-.+++.++-++.+.
T Consensus 2 ~sRR~fLk~~~a~~a~~~~~~~ 23 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAAAALGGC 23 (26)
T ss_pred CcHHHHHHHHHHHHHHHHhccc
Confidence 5799999888887777666543
No 18
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=74.68 E-value=4.1 Score=35.09 Aligned_cols=33 Identities=27% Similarity=0.552 Sum_probs=26.0
Q ss_pred Cchhhhhhhhh-----------------HHHHHHHHHHHHHHHHHHHHhh
Q 046960 75 GSVEMARAADL-----------------IQRRQRSEFISNIKETLQTALK 107 (165)
Q Consensus 75 ~~~~~A~AAdL-----------------iqrrQrseFqs~ik~~L~~ai~ 107 (165)
|+||||+||-+ |.+||++.++-+.+.+|.+--+
T Consensus 1 gpvg~aaaaa~~~~kkrkr~h~fe~npsirkrq~~rllrkl~~~~de~~t 50 (214)
T PF10491_consen 1 GPVGVAAAAAIATGKKRKRPHVFETNPSIRKRQQTRLLRKLRQTIDEYTT 50 (214)
T ss_pred CchhHHHHHHHHhcccccCCceeecChhHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788888766 8889999999999988876544
No 19
>PF10784 Plasmid_stab_B: Plasmid stability protein; InterPro: IPR019720 This family is conserved in the Enterobacteriales. It is a putative plasmid stability protein in that it is expressed from the operon involved in stability, but its actual function has not yet been characterised but it may be involved in the control of plasmid partition.; PDB: 2JD3_A.
Probab=73.26 E-value=5.1 Score=29.06 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCchhHHHHHHhcccccccc
Q 046960 86 IQRRQRSEFISNIKETLQTALKGNPDLIPSLLTLALNDAMTYDK 129 (165)
Q Consensus 86 iqrrQrseFqs~ik~~L~~ai~~~peliPslltLaLNDA~TYDK 129 (165)
+++++|++|+-.+--+=-...|.+|+ .|.+|.-.++|-+|-|.
T Consensus 25 v~~~~Rgdf~R~aliaG~aL~~~dpr-LP~lLa~~~~~~~t~~~ 67 (72)
T PF10784_consen 25 VPQRERGDFQRAALIAGLALHQLDPR-LPYLLAALFTGETTADQ 67 (72)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHH-TH-HHHHHHHH-STT--HHH
T ss_pred cCHhHhhHHHHHHHHHHHHHHhcChH-HHHHHHHHhCCCCCHHH
Confidence 57899999999877666666777888 69999999998887664
No 20
>PF13259 DUF4050: Protein of unknown function (DUF4050)
Probab=62.53 E-value=4.7 Score=30.58 Aligned_cols=32 Identities=34% Similarity=0.548 Sum_probs=26.9
Q ss_pred cccccccCCCceeeh---hHHHHHHHHHHHHHhCC
Q 046960 125 MTYDKVRTKPLRFKC---LVDVIKFLYLLWRKEGN 156 (165)
Q Consensus 125 ~TYDKaTKtg~~~~~---~~~~~~~~~~~~~~~~~ 156 (165)
.+|++---++-.|++ |-|+|+||.-.|-.||-
T Consensus 86 ~iY~~Lv~~~~pf~~PI~L~dmv~~Lv~gW~~eg~ 120 (122)
T PF13259_consen 86 AIYEKLVGSNKPFKQPIPLSDMVDFLVDGWEEEGL 120 (122)
T ss_pred HHHHHHhcCCCCCCCCcCHHHHHHHHHHHhhcCCc
Confidence 468888777888887 67999999999999984
No 21
>PLN00064 photosystem II protein Psb27; Provisional
Probab=45.51 E-value=70 Score=26.87 Aligned_cols=24 Identities=13% Similarity=0.167 Sum_probs=18.5
Q ss_pred ccchhhhhhhhhhhhhhhhccCCc
Q 046960 53 FGRRDILKCIGATIGMEIISSSGS 76 (165)
Q Consensus 53 frRRDlL~c~GaAvGmeLI~ss~~ 76 (165)
-.||++|...++++...++....+
T Consensus 34 ~~rr~~~~~~~~~~~~~~~~~~~~ 57 (166)
T PLN00064 34 LLRREFLSLATTILTSAALLPVAP 57 (166)
T ss_pred hHHHHHHHHHHHHHHHHHhccCcc
Confidence 378999988777777777777765
No 22
>PLN00019 photosystem I reaction center subunit III; Provisional
Probab=42.64 E-value=50 Score=28.82 Aligned_cols=89 Identities=19% Similarity=0.335 Sum_probs=50.5
Q ss_pred cccCCcceeeeeeccccchhhcccccchhhhhhhhhhhhhhhhccCCchhhhhhhhhHHHHHHHHHHHHHHHHHHH---H
Q 046960 29 TRCSAHAGAIRCHKIETQITVEAGFGRRDILKCIGATIGMEIISSSGSVEMARAADLIQRRQRSEFISNIKETLQT---A 105 (165)
Q Consensus 29 ~~~~~~~~~I~C~k~~~~va~e~~frRRDlL~c~GaAvGmeLI~ss~~~~~A~AAdLiqrrQrseFqs~ik~~L~~---a 105 (165)
...++.+..|.|++.. .+....++ .++..+.....+..+... ...|..+-|.+=.+-..||.+.+..+++ -
T Consensus 19 ~~~~~~~~~~~csa~~--~~~~~~m~--~~~al~~~~~~~~~~~~~--~a~Ad~agLtPCses~aF~kR~~~~~k~Le~r 92 (223)
T PLN00019 19 VAAPRRSARVVCSASK--ASAAGKFA--AALALAAILLAAPMVAPP--EALADIAGLTPCKESKAFAKREKQEIKKLESR 92 (223)
T ss_pred cccCcceEEEEeeccc--hhHHHHHH--HHHHHHHHHHHHhhcCCc--cccccccCCccCccCHHHHHHHHHHHHHHHHh
Confidence 3455566778888753 11112132 334444443433333322 3346667788888888999999877755 3
Q ss_pred hh-cCCCchhHHHHHHhccccc
Q 046960 106 LK-GNPDLIPSLLTLALNDAMT 126 (165)
Q Consensus 106 i~-~~peliPslltLaLNDA~T 126 (165)
+| -+|+-.|. |||+.-+.
T Consensus 93 lkkY~~~s~pa---lAl~~~i~ 111 (223)
T PLN00019 93 LKLYAPDSAPA---LALNATIE 111 (223)
T ss_pred hhccCCCCchh---hhhhhchH
Confidence 33 34554554 67877654
No 23
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=40.43 E-value=25 Score=24.23 Aligned_cols=20 Identities=35% Similarity=0.669 Sum_probs=16.1
Q ss_pred HHHHHHHhhcCCCchhHHHH
Q 046960 99 KETLQTALKGNPDLIPSLLT 118 (165)
Q Consensus 99 k~~L~~ai~~~peliPsllt 118 (165)
...|+.+|+.||+++|.+|.
T Consensus 10 f~~lR~~vq~NP~lL~~lLq 29 (59)
T PF09280_consen 10 FQQLRQLVQQNPQLLPPLLQ 29 (59)
T ss_dssp HHHHHHHHHC-GGGHHHHHH
T ss_pred HHHHHHHHHHCHHHHHHHHH
Confidence 45688999999999998875
No 24
>PRK15352 type III secretion system protein SsaO; Provisional
Probab=40.24 E-value=32 Score=27.40 Aligned_cols=26 Identities=35% Similarity=0.506 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHhhcCCCchhHHHHHHhcccc
Q 046960 91 RSEFISNIKETLQTALKGNPDLIPSLLTLALNDAM 125 (165)
Q Consensus 91 rseFqs~ik~~L~~ai~~~peliPslltLaLNDA~ 125 (165)
|||+|.+.....++-=| ++++||||-
T Consensus 97 ~s~lq~n~nalmk~kek---------itmvl~day 122 (125)
T PRK15352 97 RSELQKNFNALMKKKEK---------ITMVLSDAY 122 (125)
T ss_pred HHHHHHHHHHHHhhhhh---------hheehhhhh
Confidence 67777666554444322 578999984
No 25
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=40.19 E-value=15 Score=25.79 Aligned_cols=12 Identities=50% Similarity=0.783 Sum_probs=9.3
Q ss_pred ccchhhhhhhhh
Q 046960 53 FGRRDILKCIGA 64 (165)
Q Consensus 53 frRRDlL~c~Ga 64 (165)
..|||+||.+|+
T Consensus 9 ~sRR~Flk~lg~ 20 (66)
T TIGR02811 9 PSRRDLLKGLGV 20 (66)
T ss_pred ccHHHHHHHHHH
Confidence 689999976555
No 26
>TIGR01409 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence. Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors.
Probab=39.65 E-value=18 Score=21.34 Aligned_cols=19 Identities=32% Similarity=0.307 Sum_probs=12.9
Q ss_pred cchhhhhhhhhhhhhhhhc
Q 046960 54 GRRDILKCIGATIGMEIIS 72 (165)
Q Consensus 54 rRRDlL~c~GaAvGmeLI~ 72 (165)
.|||.||-.|++.++-.+.
T Consensus 2 sRR~Flk~~~~~~a~~~~~ 20 (29)
T TIGR01409 2 SRRDFLKGAAAAGAAAGLG 20 (29)
T ss_pred chhhhHHHHHHHHHHHhcc
Confidence 6999997776655554443
No 27
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=38.42 E-value=28 Score=21.84 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHhhcCCCchhH
Q 046960 93 EFISNIKETLQTALKGNPDLIPS 115 (165)
Q Consensus 93 eFqs~ik~~L~~ai~~~peliPs 115 (165)
+|+.-+++..++++..+|+++-.
T Consensus 2 ~l~~lL~~~~~~vl~~qP~Di~~ 24 (38)
T PF02197_consen 2 GLQELLKEFTREVLREQPDDILQ 24 (38)
T ss_dssp THHHHHHHHHHHHHHH--S-HHH
T ss_pred cHHHHHHHHHHHHHHHCCCcHHH
Confidence 56778889999999999998754
No 28
>PF11090 DUF2833: Protein of unknown function (DUF2833); InterPro: IPR020335 This entry contains proteins with no known function.
Probab=35.45 E-value=33 Score=25.84 Aligned_cols=28 Identities=39% Similarity=0.528 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCc
Q 046960 85 LIQRRQRSEFISNIKETLQTALKGNPDL 112 (165)
Q Consensus 85 LiqrrQrseFqs~ik~~L~~ai~~~pel 112 (165)
-+.++||-||...|++.+..+++..|.+
T Consensus 32 ~~~~~~~~eF~k~i~~~~d~~l~~Y~~l 59 (86)
T PF11090_consen 32 SLTKKERREFRKLIKEYLDKMLKQYPVL 59 (86)
T ss_pred hcCHhhhHHHHHHHHHHHHHHHHHhhhe
Confidence 4567899999999999999999966554
No 29
>PF10036 RLL: Putative carnitine deficiency-associated protein; InterPro: IPR019265 This family of proteins conserved from nematodes to humans is of approximately 250 amino acids. It is purported to be carnitine deficiency-associated protein but this could not be confirmed. It carries a characteristic RLL sequence-motif. The function is unknown.
Probab=33.28 E-value=64 Score=27.27 Aligned_cols=29 Identities=28% Similarity=0.334 Sum_probs=22.6
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 046960 77 VEMARAADLIQRRQRSEFISNIKETLQTA 105 (165)
Q Consensus 77 ~~~A~AAdLiqrrQrseFqs~ik~~L~~a 105 (165)
...|..--|+.-++..|.|+.|.++|-.+
T Consensus 203 ~~aa~iLRlL~i~~LR~lQt~Ine~iv~v 231 (249)
T PF10036_consen 203 NEAARILRLLHIEDLRELQTKINETIVAV 231 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566789999999999999998643
No 30
>PLN03030 cationic peroxidase; Provisional
Probab=32.89 E-value=38 Score=30.27 Aligned_cols=33 Identities=27% Similarity=0.550 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhhcCCCchhHHHHHHhcccccc
Q 046960 95 ISNIKETLQTALKGNPDLIPSLLTLALNDAMTY 127 (165)
Q Consensus 95 qs~ik~~L~~ai~~~peliPslltLaLNDA~TY 127 (165)
.+.|+..++.+++.+|.+.|.+|||..-|....
T Consensus 38 E~iV~~~v~~~~~~d~~~aa~llRL~FHDCfv~ 70 (324)
T PLN03030 38 ESIVRKTVQSHFQSNPAIAPGLLRMHFHDCFVR 70 (324)
T ss_pred HHHHHHHHHHHHhhCcccchhhhhhhhhhheec
Confidence 345899999999999999999999999998654
No 31
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=31.50 E-value=24 Score=23.02 Aligned_cols=10 Identities=40% Similarity=0.484 Sum_probs=5.6
Q ss_pred ccccchhhhh
Q 046960 51 AGFGRRDILK 60 (165)
Q Consensus 51 ~~frRRDlL~ 60 (165)
..-.|||+|.
T Consensus 7 ~~~~RRdFL~ 16 (41)
T PF10399_consen 7 VDPTRRDFLT 16 (41)
T ss_dssp ---HHHHHHH
T ss_pred CCchHHHHHH
Confidence 3367899883
No 32
>TIGR03808 RR_plus_rpt_1 twin-arg-translocated uncharacterized repeat protein. Members of this protein family have a Sec-independent twin-arginine tranlocation (TAT) signal sequence, which enables tranfer of proteins folded around prosthetic groups to cross the plasma membrane. These proteins have four copies of a repeat of about 23 amino acids that resembles the beta-helix repeat. Beta-helix refers to a structural motif in which successive beta strands wind around to stack parallel in a right-handed helix, as in AlgG and related enzymes of carbohydrate metabolism. The twin-arginine motif suggests that members of this protein family bind some unknown cofactor.
Probab=29.72 E-value=15 Score=34.49 Aligned_cols=37 Identities=30% Similarity=0.313 Sum_probs=24.6
Q ss_pred ccchhhhhhhhhhhhhhhhccCCchhhhhhhhhHHHHHHH
Q 046960 53 FGRRDILKCIGATIGMEIISSSGSVEMARAADLIQRRQRS 92 (165)
Q Consensus 53 frRRDlL~c~GaAvGmeLI~ss~~~~~A~AAdLiqrrQrs 92 (165)
.+||++|+...++++-.+..-+.+ +.||.+++.|++.
T Consensus 3 ~~rr~~~~~~~~~~~~~~~~~~~~---~~~~p~~p~r~~d 39 (455)
T TIGR03808 3 LNRRRLLGASAAGAAGALALPSAA---ARAAPLTSTLGRD 39 (455)
T ss_pred ccHHHHhhhhhhhhcchhccccch---hhccCCCCccCCC
Confidence 479999966555444344444444 8889999988853
No 33
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=28.92 E-value=60 Score=28.66 Aligned_cols=31 Identities=26% Similarity=0.419 Sum_probs=17.4
Q ss_pred cceeeeeeccccchhhcccccchhhh-hhhhh-hhh
Q 046960 34 HAGAIRCHKIETQITVEAGFGRRDIL-KCIGA-TIG 67 (165)
Q Consensus 34 ~~~~I~C~k~~~~va~e~~frRRDlL-~c~Ga-AvG 67 (165)
++-+|-|.+... +++...||..| ..+|+ |+|
T Consensus 34 ~~~~~~~~~~~~---~~~~~srr~~l~~~~ga~a~~ 66 (260)
T PLN00042 34 RPSQVVCRAQEE---DNSAVSRRAALALLAGAAAAG 66 (260)
T ss_pred CCcceeeecccc---ccccccHHHHHHHHHHHHHhh
Confidence 335567776432 33446666665 66776 444
No 34
>cd08529 STKc_FA2-like Catalytic domain of the Protein Serine/Threonine Kinase, Chlamydomonas reinhardtii FA2 and similar domains. Serine/Threonine Kinases (STKs), Chlamydomonas reinhardtii FA2-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Chlamydomonas reinhardtii FA2-like subfamily belongs to the (NIMA)-related kinase (Nek) family. The Nek family includes seven different Chlamydomonas Neks (CNKs 1-6 and Fa2). This subfamily includes FA2 and CNK4. The Nek family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Chlamydomonas reinhardtii FA2 was discovered in a genetic screen for deflagellation-defective mutants. It is essential for basal-body/centriole-associated microtubule severing, and plays a role in cell cyc
Probab=28.47 E-value=82 Score=23.23 Aligned_cols=70 Identities=14% Similarity=0.260 Sum_probs=43.9
Q ss_pred cchhhhhhhhhhhhhhhhccCCchhhhhhhhhHHHHHHH-------HHHHHHHHHHHHHhhcCCCchhHHHHHHhcccc
Q 046960 54 GRRDILKCIGATIGMEIISSSGSVEMARAADLIQRRQRS-------EFISNIKETLQTALKGNPDLIPSLLTLALNDAM 125 (165)
Q Consensus 54 rRRDlL~c~GaAvGmeLI~ss~~~~~A~AAdLiqrrQrs-------eFqs~ik~~L~~ai~~~peliPslltLaLNDA~ 125 (165)
.+-|+=. +|. +-.||+.+..+.......++++.-.+. .+-..++..+...++-+|+.-|+...+.-++++
T Consensus 180 ~~~Di~s-lG~-il~~l~~g~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~p~~Rp~~~~ll~~~~~ 256 (256)
T cd08529 180 EKSDVWA-LGV-VLYECCTGKHPFDANNQGALILKIIRGVFPPVSQMYSQQLAQLIDQCLTKDYRQRPDTFQLLRNPSL 256 (256)
T ss_pred CccchHH-HHH-HHHHHHhCCCCCCCCCHHHHHHHHHcCCCCCCccccCHHHHHHHHHHccCCcccCcCHHHHhhCCCC
Confidence 4456653 355 667888877663323333333322211 334567888888999999999998888877653
No 35
>COG5173 SEC6 Exocyst complex subunit SEC6 [Intracellular trafficking and secretion]
Probab=27.78 E-value=74 Score=31.79 Aligned_cols=46 Identities=28% Similarity=0.392 Sum_probs=36.5
Q ss_pred hhhhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCchhH--H---HHHHhcccc
Q 046960 79 MARAADLIQRRQRSEFISNIKETLQTALKGNPDLIPS--L---LTLALNDAM 125 (165)
Q Consensus 79 ~A~AAdLiqrrQrseFqs~ik~~L~~ai~~~peliPs--l---ltLaLNDA~ 125 (165)
+|.-.++|+.+| ..|.|++.+++.+-|+.|||-+|- + |-..=||-|
T Consensus 450 ~~~i~~~~tk~q-~~wks~l~ee~~kq~~~npEs~~p~Gl~eyliav~Nd~l 500 (742)
T COG5173 450 FAHITRTITKYQ-EIWKSNLVEEMDKQFKSNPESSSPAGLEEYLIAVGNDGL 500 (742)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHhcCCCccCCcchHHHHHHHHcCCcc
Confidence 466788999998 479999999999999999999986 2 223447754
No 36
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=27.64 E-value=38 Score=25.93 Aligned_cols=24 Identities=46% Similarity=0.753 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHhhcCCCchhHH
Q 046960 91 RSEFISNIKETLQTALKGNPDLIPSL 116 (165)
Q Consensus 91 rseFqs~ik~~L~~ai~~~peliPsl 116 (165)
-.||.++.++.|+--.+ |.++|.|
T Consensus 42 ~EeF~~~Lq~~lns~~q--P~lvPFL 65 (92)
T smart00549 42 AEEFTSRLQEALNSPLQ--PYLIPFL 65 (92)
T ss_pred HHHHHHHHHHHHcCCCC--chhHHHH
Confidence 46999999999999888 9999976
No 37
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=27.05 E-value=94 Score=19.67 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCch
Q 046960 88 RRQRSEFISNIKETLQTALKGNPDLI 113 (165)
Q Consensus 88 rrQrseFqs~ik~~L~~ai~~~peli 113 (165)
.+|+.+|...|-+.|.+.+...||.+
T Consensus 14 ~eqK~~l~~~it~~l~~~lg~~~~~v 39 (63)
T TIGR00013 14 DEQKRQLIEGVTEAMAETLGANLESI 39 (63)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcccE
Confidence 57899999999999999998777754
No 38
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=26.29 E-value=56 Score=30.18 Aligned_cols=41 Identities=32% Similarity=0.412 Sum_probs=29.1
Q ss_pred hhhccCCchhhhhhhhh-----HHHHHHHHHHHHHHHHHHHHhhcC
Q 046960 69 EIISSSGSVEMARAADL-----IQRRQRSEFISNIKETLQTALKGN 109 (165)
Q Consensus 69 eLI~ss~~~~~A~AAdL-----iqrrQrseFqs~ik~~L~~ai~~~ 109 (165)
|=+.++++..+.++-++ =|||||.-|-|..-++|+..++.|
T Consensus 89 ed~ss~~~~~~gn~~~~~kki~KqrrQrthFtSqqlqele~tF~rN 134 (351)
T KOG0486|consen 89 EDLSSLSPIKMGNEDPNKKKISKQRRQRTHFTSQQLQELEATFQRN 134 (351)
T ss_pred hhcccCCCcccCCCCcccchhhhhhhhhhhhHHHHHHHHHHHHhhc
Confidence 33333433335555554 489999999999999999999864
No 39
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=25.80 E-value=53 Score=22.84 Aligned_cols=17 Identities=24% Similarity=0.493 Sum_probs=15.2
Q ss_pred cCCCceeehhHHHHHHH
Q 046960 131 RTKPLRFKCLVDVIKFL 147 (165)
Q Consensus 131 TKtg~~~~~~~~~~~~~ 147 (165)
+.+|-+||...||.+||
T Consensus 37 sP~Gk~~RS~~eV~~yL 53 (77)
T PF01429_consen 37 SPCGKRFRSKKEVVRYL 53 (77)
T ss_dssp ETTSEEESSHHHHHHHH
T ss_pred CCCCCEEeCHHHHHHHH
Confidence 35899999999999997
No 40
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=25.42 E-value=38 Score=33.11 Aligned_cols=31 Identities=42% Similarity=0.729 Sum_probs=24.1
Q ss_pred HHHHHHhhcCCCchhHHHHHHhccc-cccccccCC--Cceeehh
Q 046960 100 ETLQTALKGNPDLIPSLLTLALNDA-MTYDKVRTK--PLRFKCL 140 (165)
Q Consensus 100 ~~L~~ai~~~peliPslltLaLNDA-~TYDKaTKt--g~~~~~~ 140 (165)
+.|+.|+. +|.|||| ++|.+.|-. |.-|||-
T Consensus 313 e~LrdAle----------KL~LNDasl~~E~EtS~ALGfGfRcG 346 (603)
T COG0481 313 EDLRDALE----------KLQLNDASLTYEPETSQALGFGFRCG 346 (603)
T ss_pred HHHHHHHH----------hcccccceeeeccccchhccCceeeh
Confidence 45666665 8999996 799999976 5778994
No 41
>PRK15376 pathogenicity island 1 effector protein SipA; Provisional
Probab=25.25 E-value=82 Score=31.06 Aligned_cols=12 Identities=33% Similarity=0.570 Sum_probs=9.7
Q ss_pred HHHHHHHhhcCC
Q 046960 99 KETLQTALKGNP 110 (165)
Q Consensus 99 k~~L~~ai~~~p 110 (165)
.++|++||+.+|
T Consensus 588 ~~tLke~it~HP 599 (670)
T PRK15376 588 METLKEVITHHP 599 (670)
T ss_pred HHHHHHHHhcCc
Confidence 357888999888
No 42
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=25.20 E-value=77 Score=18.67 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=20.8
Q ss_pred HHHHhhcCCCchhHHHHHH--hccccccccc
Q 046960 102 LQTALKGNPDLIPSLLTLA--LNDAMTYDKV 130 (165)
Q Consensus 102 L~~ai~~~peliPslltLa--LNDA~TYDKa 130 (165)
.++||+.+|+.......|| |-+...||+|
T Consensus 2 y~kAie~~P~n~~a~~nla~~~~~~g~~~~A 32 (34)
T PF13431_consen 2 YKKAIELNPNNAEAYNNLANLYLNQGDYEEA 32 (34)
T ss_pred hHHHHHHCCCCHHHHHHHHHHHHHCcCHHhh
Confidence 4689999999999987775 3444455544
No 43
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=24.94 E-value=1e+02 Score=24.69 Aligned_cols=7 Identities=43% Similarity=0.871 Sum_probs=6.0
Q ss_pred ccchhhh
Q 046960 53 FGRRDIL 59 (165)
Q Consensus 53 frRRDlL 59 (165)
++||++|
T Consensus 2 ~sRR~~L 8 (168)
T PF12318_consen 2 LSRRRLL 8 (168)
T ss_pred CcHHHHH
Confidence 5799999
No 44
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=24.77 E-value=1.2e+02 Score=18.06 Aligned_cols=26 Identities=27% Similarity=0.230 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHhhcCCCchhHHHHHH
Q 046960 95 ISNIKETLQTALKGNPDLIPSLLTLA 120 (165)
Q Consensus 95 qs~ik~~L~~ai~~~peliPslltLa 120 (165)
.......+.++++.+|+...-...|+
T Consensus 17 ~~~A~~~~~~~l~~~P~~~~a~~~La 42 (44)
T PF13428_consen 17 PDEAERLLRRALALDPDDPEAWRALA 42 (44)
T ss_pred HHHHHHHHHHHHHHCcCCHHHHHHhh
Confidence 34577889999999999987666654
No 45
>COG0337 AroB 3-dehydroquinate synthetase [Amino acid transport and metabolism]
Probab=23.53 E-value=66 Score=29.37 Aligned_cols=102 Identities=28% Similarity=0.335 Sum_probs=56.9
Q ss_pred eeeeeeccccchhhcc-cccchhhhhhhhhhhh--hhhhccCC--------chhhhhhhhhHHHHH--HHHHHHHHHHHH
Q 046960 36 GAIRCHKIETQITVEA-GFGRRDILKCIGATIG--MEIISSSG--------SVEMARAADLIQRRQ--RSEFISNIKETL 102 (165)
Q Consensus 36 ~~I~C~k~~~~va~e~-~frRRDlL~c~GaAvG--meLI~ss~--------~~~~A~AAdLiqrrQ--rseFqs~ik~~L 102 (165)
+.-||.-...-|++.| .-.-|-+|. +|=|+| .|-..+-+ ++||..|+.+-.+-= ..+=..+++..|
T Consensus 217 I~rs~~~Ka~VV~~De~E~G~R~~LN-~GHT~GHAiE~~~~y~~~~HGeAVaiGmv~aa~ls~~lG~~~~~~~~r~~~~L 295 (360)
T COG0337 217 IARSCQIKAEVVAQDEKESGLRAILN-LGHTFGHAIEALTGYGKWLHGEAVAIGMVMAARLSERLGLLDKADAERILNLL 295 (360)
T ss_pred HHHHHHHhhHHhhcCccchhhHHHHh-cchHHHHHHHHHhCCCccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 3344543333333333 355577884 343343 33333333 288899988855543 222245666666
Q ss_pred HHHhhcCCCchhH-HHHHHhccccccccccCCC-ceeehh
Q 046960 103 QTALKGNPDLIPS-LLTLALNDAMTYDKVRTKP-LRFKCL 140 (165)
Q Consensus 103 ~~ai~~~peliPs-lltLaLNDA~TYDKaTKtg-~~~~~~ 140 (165)
+++== |-..|. +-.-.|=++|++||....| |||--+
T Consensus 296 ~~~gL--P~~~~~~~~~~~l~~~m~~DKK~~~g~i~~vl~ 333 (360)
T COG0337 296 KRYGL--PTSLPDELDAEKLLEAMARDKKVLGGKIRFVLL 333 (360)
T ss_pred HHcCC--CccCCCcCCHHHHHHHHhhcccccCCceEEEee
Confidence 65533 655554 3333455789999999998 777543
No 46
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=23.52 E-value=70 Score=22.79 Aligned_cols=18 Identities=17% Similarity=0.425 Sum_probs=15.5
Q ss_pred cCCCceeehhHHHHHHHH
Q 046960 131 RTKPLRFKCLVDVIKFLY 148 (165)
Q Consensus 131 TKtg~~~~~~~~~~~~~~ 148 (165)
+.+|-+||+..+|.+||-
T Consensus 32 sP~Gkk~RS~~ev~~yL~ 49 (77)
T cd01396 32 SPTGKKFRSKVELARYLE 49 (77)
T ss_pred CCCCCEEECHHHHHHHHH
Confidence 456899999999999984
No 47
>PF11002 RDM: RFPL defining motif (RDM); InterPro: IPR022723 The RFPL defining motif (RDM) is a domain found on RFPL (Ret finger protein like) proteins. In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex []. The RDM domain is thought to have emerged from a neofunctionalisation event. It is found N-terminal to the SPRY domain (PF00622 from PFAM). ; PDB: 2FBE_B.
Probab=23.48 E-value=27 Score=23.57 Aligned_cols=31 Identities=32% Similarity=0.455 Sum_probs=0.0
Q ss_pred hhhhhHHHHHHHHHHHHHHH---HHHHHhhcCCC
Q 046960 81 RAADLIQRRQRSEFISNIKE---TLQTALKGNPD 111 (165)
Q Consensus 81 ~AAdLiqrrQrseFqs~ik~---~L~~ai~~~pe 111 (165)
.-.|+.+..|....-|+||+ .|+.+++-||.
T Consensus 4 qk~Di~p~~qLg~Lvs~iKelEPqL~~iL~MnPr 37 (42)
T PF11002_consen 4 QKNDIRPNFQLGKLVSKIKELEPQLRAILQMNPR 37 (42)
T ss_dssp ----------------------------------
T ss_pred ccccccHHHHHHHHHHHHHHhCHHHHHHHccCcc
Confidence 34689999999999999987 47777877775
No 48
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=23.34 E-value=76 Score=25.34 Aligned_cols=41 Identities=27% Similarity=0.412 Sum_probs=23.4
Q ss_pred hhhhhhHHHHHH----HHHHHHHHHH-------HHHHhhcCCCchhHHHHHHh
Q 046960 80 ARAADLIQRRQR----SEFISNIKET-------LQTALKGNPDLIPSLLTLAL 121 (165)
Q Consensus 80 A~AAdLiqrrQr----seFqs~ik~~-------L~~ai~~~peliPslltLaL 121 (165)
|+|+|++-|-++ .+|-.+.-+- =+-+|| |||...+-++--|
T Consensus 64 asa~dv~aRg~qeGWn~gFT~k~agwaeki~sG~rivIK-nPEyFs~YMreqL 115 (119)
T PF08986_consen 64 ASAADVTARGEQEGWNPGFTEKVAGWAEKIASGERIVIK-NPEYFSSYMREQL 115 (119)
T ss_dssp --HHHHHHHHHHCT--HHHHHHHHHHHHHHHCT-----S-SGGGS-HHHHHHH
T ss_pred CCHHHHHHhcccccCChhHHHHHHHHHHHHhcCCeeeec-ChHHHHHHHHHHH
Confidence 889999998874 4666554332 233455 9999988877544
No 49
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=22.29 E-value=29 Score=23.09 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=8.2
Q ss_pred CCCceeehhH
Q 046960 132 TKPLRFKCLV 141 (165)
Q Consensus 132 Ktg~~~~~~~ 141 (165)
=.|+||||++
T Consensus 11 i~g~RykC~~ 20 (49)
T cd02334 11 ITGFRYRCLK 20 (49)
T ss_pred ceeeeEECCC
Confidence 3689999985
No 50
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=20.94 E-value=45 Score=25.44 Aligned_cols=24 Identities=38% Similarity=0.661 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHhhcCCCchhHH
Q 046960 91 RSEFISNIKETLQTALKGNPDLIPSL 116 (165)
Q Consensus 91 rseFqs~ik~~L~~ai~~~peliPsl 116 (165)
-.||.+++++.|+-..+ |-++|.|
T Consensus 43 ~EeF~~~Lq~~lns~pq--P~lvPFL 66 (96)
T PF07531_consen 43 AEEFTSKLQEELNSSPQ--PYLVPFL 66 (96)
T ss_dssp HHHHHHHHHHHCTSS----TTHHHHH
T ss_pred HHHHHHHHHHHhcCCCC--cchHHHH
Confidence 47899999999999988 9999976
No 51
>PF06324 Pigment_DH: Pigment-dispersing hormone (PDH); InterPro: IPR009396 This family consists of several eukaryotic pigment-dispersing hormone (PDH) proteins. The pigment-dispersing hormone (PDH) is produced in the eyestalks of Crustacea where it induces light-adapting movements of pigment in the compound eye and regulates the pigment dispersion in the chromatophores [].; GO: 0005179 hormone activity, 0009416 response to light stimulus, 0005576 extracellular region
Probab=20.57 E-value=34 Score=19.60 Aligned_cols=16 Identities=63% Similarity=0.852 Sum_probs=10.0
Q ss_pred CCCchhHHHHH--Hhccc
Q 046960 109 NPDLIPSLLTL--ALNDA 124 (165)
Q Consensus 109 ~peliPslltL--aLNDA 124 (165)
|.|+|-|+|-+ .+|||
T Consensus 1 NselINslLglpk~m~dA 18 (18)
T PF06324_consen 1 NSELINSLLGLPKVMNDA 18 (18)
T ss_pred ChHHHHHHHcchhhcccC
Confidence 56777787754 34554
No 52
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=20.12 E-value=85 Score=20.93 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=15.3
Q ss_pred cCCCceeehhHHHHHHHH
Q 046960 131 RTKPLRFKCLVDVIKFLY 148 (165)
Q Consensus 131 TKtg~~~~~~~~~~~~~~ 148 (165)
+.+|-+||...||.+||-
T Consensus 31 sP~Gk~~Rs~~ev~~yL~ 48 (62)
T cd00122 31 SPCGKKLRSKPEVARYLE 48 (62)
T ss_pred CCCCceecCHHHHHHHHH
Confidence 456899999999999874
Done!