Query 018470
Match_columns 355
No_of_seqs 180 out of 707
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 09:17:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018470.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018470hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03064 TRX_Fd_NuoE TRX-like [ 99.7 1.4E-17 3.1E-22 129.9 7.4 71 252-341 1-80 (80)
2 cd03063 TRX_Fd_FDH_beta TRX-li 99.7 2.2E-17 4.7E-22 135.7 8.7 76 254-345 2-81 (92)
3 cd02980 TRX_Fd_family Thioredo 99.7 5.6E-17 1.2E-21 123.8 7.6 72 253-341 1-77 (77)
4 cd03081 TRX_Fd_NuoE_FDH_gamma 99.7 9.9E-17 2.1E-21 126.6 7.0 70 252-340 1-79 (80)
5 cd03083 TRX_Fd_NuoE_hoxF TRX-l 99.6 3.2E-16 7E-21 123.7 6.9 70 252-340 1-79 (80)
6 PRK07539 NADH dehydrogenase su 99.6 5.5E-16 1.2E-20 136.0 7.9 76 247-341 69-153 (154)
7 TIGR01958 nuoE_fam NADH-quinon 99.6 5.6E-16 1.2E-20 135.0 7.8 75 248-341 64-147 (148)
8 PF01257 2Fe-2S_thioredx: Thio 99.6 7.9E-16 1.7E-20 133.6 7.8 76 247-341 60-144 (145)
9 cd03082 TRX_Fd_NuoE_W_FDH_beta 99.6 2.5E-15 5.3E-20 117.5 6.8 69 253-340 2-71 (72)
10 PRK05988 formate dehydrogenase 99.5 2.9E-14 6.3E-19 126.3 8.4 77 247-342 70-155 (156)
11 PRK07571 bidirectional hydroge 99.5 2.5E-14 5.5E-19 128.6 7.9 75 248-341 84-167 (169)
12 cd03062 TRX_Fd_Sucrase TRX-lik 99.5 6.7E-14 1.4E-18 114.6 8.4 78 253-346 2-87 (97)
13 COG1905 NuoE NADH:ubiquinone o 99.5 7.2E-14 1.6E-18 125.3 7.7 79 247-344 72-159 (160)
14 PRK12373 NADH dehydrogenase su 99.3 3.1E-12 6.6E-17 128.4 8.8 80 248-346 85-174 (400)
15 COG3411 Ferredoxin [Energy pro 99.1 7.5E-11 1.6E-15 92.1 4.5 48 282-346 2-49 (64)
16 KOG3196 NADH:ubiquinone oxidor 99.0 4.3E-10 9.2E-15 104.6 6.8 79 248-345 109-196 (233)
17 PF06999 Suc_Fer-like: Sucrase 97.9 4.3E-05 9.3E-10 70.0 8.0 81 250-344 130-218 (230)
18 PF07845 DUF1636: Protein of u 97.6 0.0002 4.4E-09 61.6 6.8 70 255-340 1-85 (116)
19 COG5469 Predicted metal-bindin 96.4 0.012 2.5E-07 52.8 7.3 76 248-339 13-104 (143)
20 PF07293 DUF1450: Protein of u 95.6 0.044 9.6E-07 44.6 6.5 70 253-345 3-75 (78)
21 PRK13669 hypothetical protein; 93.7 0.27 5.8E-06 40.3 6.6 48 253-304 3-53 (78)
22 PF05501 DUF755: Domain of unk 73.4 1.9 4.1E-05 37.7 1.5 51 77-128 9-61 (123)
23 COG5665 NOT5 CCR4-NOT transcri 67.8 15 0.00032 38.6 6.6 36 113-148 116-152 (548)
24 PF13815 Dzip-like_N: Iguana/D 65.4 16 0.00034 31.1 5.4 41 111-151 75-115 (118)
25 PF04889 Cwf_Cwc_15: Cwf15/Cwc 63.2 13 0.00028 36.0 4.9 35 113-147 143-177 (244)
26 PF05812 Herpes_BLRF2: Herpesv 62.8 11 0.00024 33.3 4.0 25 117-141 4-28 (118)
27 PF10147 CR6_interact: Growth 60.4 50 0.0011 31.8 8.2 10 97-106 166-175 (217)
28 PHA03155 hypothetical protein; 58.9 12 0.00026 33.0 3.5 25 117-141 9-33 (115)
29 KOG2985 Uncharacterized conser 58.4 9.9 0.00021 37.8 3.3 22 123-144 132-153 (306)
30 PHA03162 hypothetical protein; 57.7 13 0.00029 33.4 3.7 24 118-141 15-38 (135)
31 cd04785 HTH_CadR-PbrR-like Hel 49.5 47 0.001 28.3 5.6 86 33-143 10-106 (126)
32 PF07795 DUF1635: Protein of u 49.3 49 0.0011 31.9 6.2 26 123-148 15-40 (214)
33 KOG3228 Uncharacterized conser 47.6 35 0.00075 32.9 4.9 38 114-151 124-162 (226)
34 PRK13752 putative transcriptio 47.3 31 0.00068 30.5 4.4 84 33-141 17-109 (144)
35 PF01451 LMWPc: Low molecular 45.6 28 0.0006 29.2 3.6 39 255-293 2-41 (138)
36 PF06658 DUF1168: Protein of u 44.6 59 0.0013 29.4 5.7 21 128-148 77-97 (142)
37 PF14038 YqzE: YqzE-like prote 44.5 22 0.00047 27.6 2.5 28 117-144 9-36 (54)
38 KOG4055 Uncharacterized conser 41.7 72 0.0016 30.6 6.0 29 114-143 108-136 (213)
39 PF11853 DUF3373: Protein of u 41.6 20 0.00044 38.2 2.7 22 121-142 29-50 (489)
40 PHA03308 transcriptional regul 41.3 15 0.00033 41.4 1.8 32 284-323 1383-1414(1463)
41 cd04784 HTH_CadR-PbrR Helix-Tu 41.0 81 0.0017 26.7 5.8 29 113-141 76-104 (127)
42 KOG3116 Predicted C3H1-type Zn 40.2 32 0.0007 31.9 3.4 12 53-64 36-47 (177)
43 PF08496 Peptidase_S49_N: Pept 40.0 48 0.001 30.1 4.5 39 113-151 46-84 (155)
44 COG4759 Uncharacterized protei 39.7 52 0.0011 33.4 5.0 72 251-340 130-209 (316)
45 cd04783 HTH_MerR1 Helix-Turn-H 39.7 89 0.0019 26.5 5.8 45 97-141 53-102 (126)
46 PRK14538 putative bifunctional 39.0 60 0.0013 36.7 5.9 109 27-142 624-751 (838)
47 KOG2385 Uncharacterized conser 38.5 20 0.00044 38.9 2.1 12 53-64 552-563 (633)
48 cd04786 HTH_MerR-like_sg7 Heli 37.7 80 0.0017 27.4 5.4 33 114-146 76-108 (131)
49 KOG4848 Extracellular matrix-a 36.9 94 0.002 30.0 6.0 39 98-143 178-217 (225)
50 PF09403 FadA: Adhesion protei 36.6 1E+02 0.0022 27.4 5.8 49 94-146 9-57 (126)
51 PF15509 DUF4650: Domain of un 36.3 53 0.0011 35.4 4.7 41 78-127 325-372 (520)
52 PF14284 PcfJ: PcfJ-like prote 36.0 91 0.002 28.1 5.6 48 95-142 7-55 (169)
53 TIGR02047 CadR-PbrR Cd(II)/Pb( 36.0 78 0.0017 27.1 5.0 85 33-142 10-105 (127)
54 PF11208 DUF2992: Protein of u 35.8 82 0.0018 28.1 5.2 31 113-143 83-113 (132)
55 KOG0286 G-protein beta subunit 33.9 40 0.00086 34.4 3.2 24 123-146 2-25 (343)
56 cd04790 HTH_Cfa-like_unk Helix 33.8 88 0.0019 28.3 5.2 90 33-148 11-106 (172)
57 PF06936 Selenoprotein_S: Sele 33.8 82 0.0018 29.7 5.1 39 105-143 74-114 (190)
58 cd04782 HTH_BltR Helix-Turn-He 32.6 56 0.0012 26.6 3.4 80 33-137 10-95 (97)
59 PF10500 SR-25: Nuclear RNA-sp 32.2 27 0.00059 33.9 1.7 17 260-276 181-197 (225)
60 COG0394 Wzb Protein-tyrosine-p 31.6 47 0.001 29.2 2.9 36 252-290 3-38 (139)
61 PRK00247 putative inner membra 30.8 1E+02 0.0022 32.5 5.6 50 123-172 338-406 (429)
62 PF06658 DUF1168: Protein of u 29.7 1.5E+02 0.0033 26.8 5.9 28 124-151 77-104 (142)
63 PRK11778 putative inner membra 29.7 76 0.0016 32.2 4.4 39 113-151 44-82 (330)
64 KOG1636 DNA polymerase delta p 29.1 23 0.00049 34.9 0.6 15 51-65 242-256 (260)
65 KOG2138 Predicted RNA binding 28.3 60 0.0013 36.6 3.6 16 158-173 843-858 (883)
66 cd03489 Topoisomer_IB_N_Ldtopo 28.2 73 0.0016 30.8 3.8 35 114-148 84-118 (212)
67 PLN02316 synthase/transferase 27.8 75 0.0016 36.9 4.5 32 120-151 434-465 (1036)
68 PF11598 COMP: Cartilage oligo 27.0 1.7E+02 0.0036 21.9 4.7 34 118-151 3-39 (45)
69 cd00660 Topoisomer_IB_N Topois 26.8 75 0.0016 30.8 3.6 35 114-148 87-121 (215)
70 cd03488 Topoisomer_IB_N_htopoI 25.6 81 0.0018 30.5 3.6 35 114-148 87-121 (215)
71 PF08257 Sulfakinin: Sulfakini 25.6 30 0.00066 18.2 0.4 9 50-58 1-9 (9)
72 PF09278 MerR-DNA-bind: MerR, 25.3 1.3E+02 0.0028 22.1 4.0 44 97-140 10-60 (65)
73 TIGR00993 3a0901s04IAP86 chlor 24.8 1.7E+02 0.0037 33.1 6.3 19 135-153 444-462 (763)
74 KOG0796 Spliceosome subunit [R 24.5 1.2E+02 0.0026 30.9 4.7 57 93-158 134-193 (319)
75 PRK15002 redox-sensitivie tran 24.0 1.2E+02 0.0026 27.3 4.2 52 83-141 56-115 (154)
76 PRK09514 zntR zinc-responsive 23.7 1.3E+02 0.0027 26.4 4.2 29 113-141 78-106 (140)
77 PF08701 GN3L_Grn1: GNL3L/Grn1 23.1 1.9E+02 0.004 23.8 4.8 21 122-142 48-68 (79)
78 cd04766 HTH_HspR Helix-Turn-He 22.9 1.2E+02 0.0026 24.2 3.7 20 121-140 70-89 (91)
79 cd03490 Topoisomer_IB_N_1 Topo 22.7 1.1E+02 0.0023 29.7 3.8 35 114-148 86-120 (217)
80 PF01920 Prefoldin_2: Prefoldi 21.9 2.1E+02 0.0045 22.7 4.9 36 113-148 66-101 (106)
81 cd04768 HTH_BmrR-like Helix-Tu 21.8 1.2E+02 0.0026 24.7 3.4 80 33-138 10-95 (96)
82 PF05501 DUF755: Domain of unk 21.5 59 0.0013 28.6 1.7 15 158-172 106-120 (123)
83 KOG2138 Predicted RNA binding 21.4 81 0.0018 35.6 3.1 17 159-175 841-857 (883)
84 KOG0416 Ubiquitin-protein liga 21.2 1.6E+02 0.0034 28.1 4.4 40 8-51 30-69 (189)
85 PHA00727 hypothetical protein 21.2 1.1E+02 0.0024 29.9 3.6 31 117-147 51-81 (278)
86 PF12999 PRKCSH-like: Glucosid 21.1 2.5E+02 0.0054 26.4 5.8 39 113-151 136-174 (176)
87 COG0359 RplI Ribosomal protein 20.7 1.5E+02 0.0031 27.1 4.1 41 108-148 30-70 (148)
88 PF06991 Prp19_bind: Splicing 20.2 61 0.0013 32.1 1.7 16 162-177 19-34 (276)
No 1
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=99.72 E-value=1.4e-17 Score=129.92 Aligned_cols=71 Identities=32% Similarity=0.597 Sum_probs=64.8
Q ss_pred CcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCC
Q 018470 252 TKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSI 322 (355)
Q Consensus 252 ~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~ 322 (355)
+++|+||+|+.|..+||.+|+++|++.++. .+.+..+||||.|..||+|.|++
T Consensus 1 ~~~v~vC~~~~C~~~Ga~~~~~~l~~~l~~~~~~~~~~~~v~v~~t~ClG~C~~gP~v~v~g------------------ 62 (80)
T cd03064 1 KHVIRVCTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMIND------------------ 62 (80)
T ss_pred CEEEEECCCcHHHhCCHHHHHHHHHHHhCCCCCCcCCCCEEEEEEecCcCcCCCCCEEEECC------------------
Confidence 578999999999999999999999999862 36899999999999999999964
Q ss_pred ceeeecCCcchHHHHHHHH
Q 018470 323 NSLCIGVGLEDVDMILANI 341 (355)
Q Consensus 323 n~lY~~VtpEDVdeIVe~h 341 (355)
.||.+|++++|++||+++
T Consensus 63 -~~y~~vt~~~i~~i~~~~ 80 (80)
T cd03064 63 -DVYGRLTPEKVDAILEAL 80 (80)
T ss_pred -EEECCCCHHHHHHHHHhC
Confidence 899999999999999763
No 2
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=99.72 E-value=2.2e-17 Score=135.69 Aligned_cols=76 Identities=22% Similarity=0.148 Sum_probs=68.7
Q ss_pred EEEEccCCccccccHHHHHHHHHHHhC---CccEEEeecCCCCCCCCCeEEEe-CCCCCChhhhhccCCCCCCceeeecC
Q 018470 254 RIEVCMGGKCKKLGAGALLEEFERKAG---AECDVSMCKCMGKCRDGPNLRVS-NSHDGDSAIRIQGYAKPSINSLCIGV 329 (355)
Q Consensus 254 rI~VC~Gt~C~ksGS~aVLeafee~Lg---~eV~V~~tGCLG~Cg~GPnVrV~-pe~dg~~~~~~~~~v~~p~n~lY~~V 329 (355)
+|+||+||+|.++||.+|+++|++++. .++.|+.+||||+|..||+|.|+ | ++ +++|.+|
T Consensus 2 ~I~Vc~gT~ciAaGA~~V~~al~~ei~~~gl~v~v~~tGC~G~C~~ePlV~V~~p--~g--------------~v~Y~~V 65 (92)
T cd03063 2 RIYVPRDAAALALGADEVAEAIEAEAAARGLAATIVRNGSRGMYWLEPLVEVETP--GG--------------RVAYGPV 65 (92)
T ss_pred EEEEeCChhhhhhCHHHHHHHHHHHHHHcCCeEEEEEecCceecCCCCEEEEEeC--CC--------------cEEEEeC
Confidence 699999999999999999999999985 35799999999999999999996 7 22 2899999
Q ss_pred CcchHHHHHHHHhcCC
Q 018470 330 GLEDVDMILANILGKD 345 (355)
Q Consensus 330 tpEDVdeIVe~hlg~~ 345 (355)
+++||++||+.|+.+.
T Consensus 66 ~~edv~~Iv~~~~~~~ 81 (92)
T cd03063 66 TPADVASLLDAGALEG 81 (92)
T ss_pred CHHHHHHHHHHHhhcC
Confidence 9999999999998754
No 3
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=99.69 E-value=5.6e-17 Score=123.77 Aligned_cols=72 Identities=35% Similarity=0.565 Sum_probs=66.1
Q ss_pred cEEEEccCCccccccHHHHHHHHHHHhCC-----ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCCceeee
Q 018470 253 KRIEVCMGGKCKKLGAGALLEEFERKAGA-----ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSINSLCI 327 (355)
Q Consensus 253 ~rI~VC~Gt~C~ksGS~aVLeafee~Lg~-----eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~n~lY~ 327 (355)
++|+||+++.|..+|+.+|+++|++.+.. ++.+..++|||.|..||+|.|+| ++ .||.
T Consensus 1 ~~I~VC~~~~C~~~G~~~l~~~l~~~~~~~~~~~~v~v~~~~Clg~C~~~P~v~i~~--~~---------------~~y~ 63 (77)
T cd02980 1 HHILVCTGTACGLRGAEELLEALEKELGIRGGDGRVTVERVGCLGACGLAPVVVVYP--DG---------------VWYG 63 (77)
T ss_pred CEEEEccCCCcccCCHHHHHHHHHHHHhhhcCCCeEEEEEcCCcCcccCCCEEEEeC--CC---------------eEEc
Confidence 57999999999999999999999999863 57999999999999999999998 22 7999
Q ss_pred cCCcchHHHHHHHH
Q 018470 328 GVGLEDVDMILANI 341 (355)
Q Consensus 328 ~VtpEDVdeIVe~h 341 (355)
+|+++++++||++|
T Consensus 64 ~v~~~~~~~il~~~ 77 (77)
T cd02980 64 RVTPEDVEEIVEEL 77 (77)
T ss_pred cCCHHHHHHHHHhC
Confidence 99999999999875
No 4
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=99.67 E-value=9.9e-17 Score=126.61 Aligned_cols=70 Identities=23% Similarity=0.473 Sum_probs=64.2
Q ss_pred CcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCC
Q 018470 252 TKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSI 322 (355)
Q Consensus 252 ~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~ 322 (355)
+++|.||+|++|+.+||.+|+++|++.++. .++|..++|||.|+.||+|+|+.
T Consensus 1 ~~~i~vC~~~~C~~~G~~~ll~~l~~~l~~~~g~~~~dg~~~l~~~~ClG~C~~gP~~~v~~------------------ 62 (80)
T cd03081 1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMIDG------------------ 62 (80)
T ss_pred CeEEEEcCChHHHhCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEeeecCccCCCCEEEECC------------------
Confidence 579999999999999999999999999863 26899999999999999999954
Q ss_pred ceeeecCCcchHHHHHHH
Q 018470 323 NSLCIGVGLEDVDMILAN 340 (355)
Q Consensus 323 n~lY~~VtpEDVdeIVe~ 340 (355)
.||.++++++|++||++
T Consensus 63 -~~~~~~~~e~i~~il~~ 79 (80)
T cd03081 63 -EVHGRVDPEKFDALLAE 79 (80)
T ss_pred -EEECCCCHHHHHHHHHc
Confidence 78999999999999975
No 5
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=99.64 E-value=3.2e-16 Score=123.70 Aligned_cols=70 Identities=23% Similarity=0.335 Sum_probs=63.9
Q ss_pred CcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCC
Q 018470 252 TKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSI 322 (355)
Q Consensus 252 ~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~ 322 (355)
+++|.||.|++|+.+||.+|+++|++.++. .+.+..++|||.|..||+|+|++
T Consensus 1 ~~~i~vC~~~~C~~~Ga~~v~~~l~~~l~~~~~~~t~d~~v~l~~~gClG~C~~~P~v~V~~------------------ 62 (80)
T cd03083 1 KYRIYLSDSITDRMNGYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCTGLCDQGPALLINN------------------ 62 (80)
T ss_pred CEEEEEcCChHHHhCCHHHHHHHHHHHHCCCCCCcCCCCeEEEEEeceecCcCCCCeEEECC------------------
Confidence 578999999999999999999999999962 25899999999999999999954
Q ss_pred ceeeecCCcchHHHHHHH
Q 018470 323 NSLCIGVGLEDVDMILAN 340 (355)
Q Consensus 323 n~lY~~VtpEDVdeIVe~ 340 (355)
.+|.+|+++||++||+.
T Consensus 63 -~~y~~v~~~~v~~iv~~ 79 (80)
T cd03083 63 -RVFTRLTPGRIDQIAEL 79 (80)
T ss_pred -EEECCCCHHHHHHHHhc
Confidence 78999999999999975
No 6
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=99.63 E-value=5.5e-16 Score=135.97 Aligned_cols=76 Identities=21% Similarity=0.475 Sum_probs=68.7
Q ss_pred cccCCCcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccC
Q 018470 247 TTTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGY 317 (355)
Q Consensus 247 ~~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~ 317 (355)
....++++|+||+|+.|+.+||.+|+++|++.+++ .+++..++|||.|+.||+|+|++
T Consensus 69 ~~p~gk~~I~VC~g~~C~~~Ga~~l~~~l~~~L~i~~g~tt~dg~~~l~~~~ClG~C~~gPvv~V~~------------- 135 (154)
T PRK07539 69 RQPVGRHVIQVCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECLGACDNAPVVMIND------------- 135 (154)
T ss_pred cCCCCCEEEEEcCCchHHHCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEccccCccCCCCEEEECC-------------
Confidence 34567899999999999999999999999999872 25889999999999999999986
Q ss_pred CCCCCceeeecCCcchHHHHHHHH
Q 018470 318 AKPSINSLCIGVGLEDVDMILANI 341 (355)
Q Consensus 318 v~~p~n~lY~~VtpEDVdeIVe~h 341 (355)
.||.+|++++|++||+++
T Consensus 136 ------~~y~~vt~e~v~~il~~~ 153 (154)
T PRK07539 136 ------DTYEDLTPEKIDELLDEL 153 (154)
T ss_pred ------EEeCCCCHHHHHHHHHhc
Confidence 689999999999999875
No 7
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=99.63 E-value=5.6e-16 Score=134.96 Aligned_cols=75 Identities=23% Similarity=0.447 Sum_probs=68.5
Q ss_pred ccCCCcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCC
Q 018470 248 TTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYA 318 (355)
Q Consensus 248 ~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v 318 (355)
.+.++++|.||+|++|+.+||.+|+++|++.+++ .+++..++|||.|+.||+|+|++
T Consensus 64 ~p~gk~~I~VC~g~~C~~~Ga~~v~~~l~~~L~i~~g~~t~dg~~~l~~~~ClG~C~~aP~v~V~~-------------- 129 (148)
T TIGR01958 64 EPVGRYHLQVCTNVPCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGACGNAPVMMIND-------------- 129 (148)
T ss_pred CCCCCEEEEEcCCchhhhcCHHHHHHHHHHHhCCCCCCCCCCCeEEEEEcCccCccCCCCEEEECC--------------
Confidence 4567899999999999999999999999999974 25899999999999999999986
Q ss_pred CCCCceeeecCCcchHHHHHHHH
Q 018470 319 KPSINSLCIGVGLEDVDMILANI 341 (355)
Q Consensus 319 ~~p~n~lY~~VtpEDVdeIVe~h 341 (355)
.+|.+|+++++++||+++
T Consensus 130 -----~~y~~vt~e~v~~il~~~ 147 (148)
T TIGR01958 130 -----DYYEFLTPEKLDELLERY 147 (148)
T ss_pred -----EEeCCCCHHHHHHHHHhc
Confidence 689999999999999864
No 8
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=99.62 E-value=7.9e-16 Score=133.65 Aligned_cols=76 Identities=30% Similarity=0.533 Sum_probs=66.5
Q ss_pred cccCCCcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccC
Q 018470 247 TTTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGY 317 (355)
Q Consensus 247 ~~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~ 317 (355)
..+.++++|.||+|+.|+.+||.+|+++|++.+++ .+++..++|||.|..||+|+|++
T Consensus 60 ~~p~gk~~I~VC~g~~C~~~Ga~~l~~~l~~~l~i~~g~~~~dg~~~l~~~~ClG~C~~aP~v~V~~------------- 126 (145)
T PF01257_consen 60 LEPKGKHHIRVCTGTSCHLRGAEELLEALEEELGIKPGETTEDGKFTLEETGCLGACDQAPVVMVDG------------- 126 (145)
T ss_dssp SSS--SEEEEEE-SHHHHTTTHHHHHHHHHHHHCTSCCCCSTTTTEEEEEESSSSSGGGSSEEEECC-------------
T ss_pred cCCCCCcEEEeCCCchHHhCCCHHHHHHHHHHhCCcccccCCCceEEEEECCCccccCCCCEEEECC-------------
Confidence 35667899999999999999999999999999962 35899999999999999999965
Q ss_pred CCCCCceeeecCCcchHHHHHHHH
Q 018470 318 AKPSINSLCIGVGLEDVDMILANI 341 (355)
Q Consensus 318 v~~p~n~lY~~VtpEDVdeIVe~h 341 (355)
.||.+|++++|++||+++
T Consensus 127 ------~~y~~vt~e~v~~il~~l 144 (145)
T PF01257_consen 127 ------EWYGNVTPEKVDEILEEL 144 (145)
T ss_dssp ------CEEESSSCCHHHHHHHHH
T ss_pred ------EEECCCCHHHHHHHHHhc
Confidence 689999999999999876
No 9
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=99.59 E-value=2.5e-15 Score=117.53 Aligned_cols=69 Identities=25% Similarity=0.415 Sum_probs=64.2
Q ss_pred cEEEEccCCccccccHHHHHHHHHHHhCC-ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCCceeeecCCc
Q 018470 253 KRIEVCMGGKCKKLGAGALLEEFERKAGA-ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSINSLCIGVGL 331 (355)
Q Consensus 253 ~rI~VC~Gt~C~ksGS~aVLeafee~Lg~-eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~n~lY~~Vtp 331 (355)
++|.||+|+.|+.+||.+|+++|++.++. .+++..++|||.|+.||+|+|++ .+|.++++
T Consensus 2 ~~I~vC~~~~C~~~Ga~~l~~~l~~~L~~~~v~l~~~~ClG~C~~gP~v~V~~-------------------~~~~~~t~ 62 (72)
T cd03082 2 LTVRVCDSLSCAMAGAEELLAALEAGLGPEGVRVVRAPCVGRCERAPAALVGQ-------------------RPVDGATP 62 (72)
T ss_pred eEEEEcCChHHHHCCHHHHHHHHHHHhCCCeEEEEecCcCCccCCCCeEEECC-------------------EEeCCcCH
Confidence 58999999999999999999999999986 58999999999999999999987 57999999
Q ss_pred chHHHHHHH
Q 018470 332 EDVDMILAN 340 (355)
Q Consensus 332 EDVdeIVe~ 340 (355)
++++++++.
T Consensus 63 ~~i~~~~~~ 71 (72)
T cd03082 63 AAVAAAVEA 71 (72)
T ss_pred HHHHHHHhc
Confidence 999998863
No 10
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=99.52 E-value=2.9e-14 Score=126.32 Aligned_cols=77 Identities=18% Similarity=0.399 Sum_probs=69.6
Q ss_pred cccCCCcEEEEccCCccccccHHHHHHHHHHHhCC-------c--cEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccC
Q 018470 247 TTTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGA-------E--CDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGY 317 (355)
Q Consensus 247 ~~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~-------e--V~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~ 317 (355)
....++++|.||+|+.|+.+||.+|+++|++.|++ + +++..+.|+|.|+.||+|+|+.
T Consensus 70 ~~p~Gk~~I~VC~~~~C~~~G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~ClG~C~~aP~~~in~------------- 136 (156)
T PRK05988 70 THPPGRHVLKLCRAEACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAMLDG------------- 136 (156)
T ss_pred CCCCCCEEEEEeCCchhhcCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECC-------------
Confidence 35678999999999999999999999999999973 2 4899999999999999999976
Q ss_pred CCCCCceeeecCCcchHHHHHHHHh
Q 018470 318 AKPSINSLCIGVGLEDVDMILANIL 342 (355)
Q Consensus 318 v~~p~n~lY~~VtpEDVdeIVe~hl 342 (355)
.+|.+++++++++|++++.
T Consensus 137 ------~~~~~lt~~~~~~il~~~~ 155 (156)
T PRK05988 137 ------EVHGRLDPQRLDALLAEAR 155 (156)
T ss_pred ------EEeCCCCHHHHHHHHHHhh
Confidence 6799999999999998764
No 11
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=99.52 E-value=2.5e-14 Score=128.62 Aligned_cols=75 Identities=21% Similarity=0.400 Sum_probs=68.9
Q ss_pred ccCCCcEEEEccCCccccccHHHHHHHHHHHhCC-------c--cEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCC
Q 018470 248 TTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGA-------E--CDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYA 318 (355)
Q Consensus 248 ~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~-------e--V~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v 318 (355)
...++++|.||+|++|+.+||.+|+++|++.|++ + +++..+.|+|.|+.||+|+|++
T Consensus 84 ~P~Gk~~I~VC~g~aC~~~G~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~ClG~C~~AP~~~Vn~-------------- 149 (169)
T PRK07571 84 KPSGEHTCVVCTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDG-------------- 149 (169)
T ss_pred CCCCCEEEEEcCChHHHHCCcHHHHHHHHHHhCCCCCCcCCCCeEEEEEecccCccCCCCeEEECC--------------
Confidence 4568999999999999999999999999999973 2 4899999999999999999976
Q ss_pred CCCCceeeecCCcchHHHHHHHH
Q 018470 319 KPSINSLCIGVGLEDVDMILANI 341 (355)
Q Consensus 319 ~~p~n~lY~~VtpEDVdeIVe~h 341 (355)
.+|++++++++++||++|
T Consensus 150 -----~~~~~lt~e~v~~il~~~ 167 (169)
T PRK07571 150 -----KVAGKQTPESVLEKVQGW 167 (169)
T ss_pred -----EEeCCCCHHHHHHHHHHH
Confidence 679999999999999987
No 12
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=99.50 E-value=6.7e-14 Score=114.61 Aligned_cols=78 Identities=18% Similarity=0.163 Sum_probs=67.8
Q ss_pred cEEEEccC----CccccccHHHHHHHHHHHhC----CccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCCce
Q 018470 253 KRIEVCMG----GKCKKLGAGALLEEFERKAG----AECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSINS 324 (355)
Q Consensus 253 ~rI~VC~G----t~C~ksGS~aVLeafee~Lg----~eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~n~ 324 (355)
.+|+||++ ..|...| ..|+++|++.+. .++.+..++|+|.|..||||+|||-.+ ++
T Consensus 2 ~~ilVCth~rrd~~C~~~g-~~l~~~l~~~l~~~~~~~v~v~~~~clG~c~~gp~vvvyP~~~---------------g~ 65 (97)
T cd03062 2 PLVLVCTHGKRDKRCGICG-PPLAAELRAELPEHGPGGVRVWEVSHVGGHKFAGNVIIYPKGD---------------GI 65 (97)
T ss_pred CEEEEeCCCCCCcChhhcC-HHHHHHHHHHHHHhCCCceEEEeCCcCCccCcCCEEEEEeCCC---------------ee
Confidence 58999996 5698888 699999999985 358999999999999999999999211 39
Q ss_pred eeecCCcchHHHHHHHHhcCCC
Q 018470 325 LCIGVGLEDVDMILANILGKDM 346 (355)
Q Consensus 325 lY~~VtpEDVdeIVe~hlg~~~ 346 (355)
||+.|+|+||++||++|+..+.
T Consensus 66 wy~~v~p~~v~~Iv~~hl~~g~ 87 (97)
T cd03062 66 WYGRVTPEHVPPIVDRLILGGK 87 (97)
T ss_pred EEeecCHHHHHHHHHHHhcCCc
Confidence 9999999999999999997754
No 13
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=99.48 E-value=7.2e-14 Score=125.26 Aligned_cols=79 Identities=25% Similarity=0.528 Sum_probs=70.1
Q ss_pred cccCCCcEEEEccCCccccccHHHHHHHHHHHhCC---------ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccC
Q 018470 247 TTTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGA---------ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGY 317 (355)
Q Consensus 247 ~~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~---------eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~ 317 (355)
....++++|.||+|+.|+.+||.+|+++|++.+++ .+++.++.|+|.|+.||+|+|++
T Consensus 72 ~~P~Gr~~i~VC~~t~C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~ClGaC~~AP~vmind------------- 138 (160)
T COG1905 72 LKPVGRHHIRVCTGTACHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECLGACGQAPVVMIND------------- 138 (160)
T ss_pred cCcCCCeEEEEeCCcHHhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeeecccccCCEEEECC-------------
Confidence 34567999999999999999999999999999983 24899999999999999999987
Q ss_pred CCCCCceeeecCCcchHHHHHHHHhcC
Q 018470 318 AKPSINSLCIGVGLEDVDMILANILGK 344 (355)
Q Consensus 318 v~~p~n~lY~~VtpEDVdeIVe~hlg~ 344 (355)
.+|+++|+|.|++||+++..+
T Consensus 139 ------~~~~~lt~e~l~eil~~~~~~ 159 (160)
T COG1905 139 ------DVYGRLTPEKLEEILEKLKAK 159 (160)
T ss_pred ------chhccCCHHHHHHHHHHHhcC
Confidence 358889999999999987643
No 14
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=99.33 E-value=3.1e-12 Score=128.38 Aligned_cols=80 Identities=20% Similarity=0.368 Sum_probs=71.0
Q ss_pred ccCCC-cEEEEccCCccccccHHHHHHHHHHHhCC-------c--cEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccC
Q 018470 248 TTTRT-KRIEVCMGGKCKKLGAGALLEEFERKAGA-------E--CDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGY 317 (355)
Q Consensus 248 ~~~~~-~rI~VC~Gt~C~ksGS~aVLeafee~Lg~-------e--V~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~ 317 (355)
...++ ++|.||+|+.|+.+||.+|+++|++.|++ + +++..+.|||.|..||+|+|+.
T Consensus 85 ~P~Gk~~~I~VC~~t~C~l~Ga~~ll~~le~~Lgik~GeTT~DG~FTLe~veCLGaC~~APv~~Ind------------- 151 (400)
T PRK12373 85 QPVGTRAHIQVCGTTPCMLRGSEALMAVCKSKIHAHPHELNADGTLSWEEVECLGACVNAPMVQIGK------------- 151 (400)
T ss_pred cCCCCceEEEEcCChHHHhCChHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEECC-------------
Confidence 34565 79999999999999999999999999974 2 4899999999999999999976
Q ss_pred CCCCCceeeecCCcchHHHHHHHHhcCCC
Q 018470 318 AKPSINSLCIGVGLEDVDMILANILGKDM 346 (355)
Q Consensus 318 v~~p~n~lY~~VtpEDVdeIVe~hlg~~~ 346 (355)
.+|.+++++++++||+++..+..
T Consensus 152 ------~~y~~LTpe~v~~IL~~l~ag~~ 174 (400)
T PRK12373 152 ------DYYEDLTPERLEEIIDAFAAGKG 174 (400)
T ss_pred ------EEeCCCCHHHHHHHHHHHhCCCC
Confidence 67999999999999999976543
No 15
>COG3411 Ferredoxin [Energy production and conversion]
Probab=99.11 E-value=7.5e-11 Score=92.07 Aligned_cols=48 Identities=31% Similarity=0.461 Sum_probs=42.9
Q ss_pred ccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCCceeeecCCcchHHHHHHHHhcCCC
Q 018470 282 ECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSINSLCIGVGLEDVDMILANILGKDM 346 (355)
Q Consensus 282 eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~n~lY~~VtpEDVdeIVe~hlg~~~ 346 (355)
.+.+..+||||.|..||+|.||| ++ +||.+|+++|+++||+.|+.++.
T Consensus 2 ~i~~t~tgCl~~C~~gPvl~vYp--eg---------------vWY~~V~p~~a~rIv~~hl~~Gr 49 (64)
T COG3411 2 SIRVTRTGCLGVCQDGPVLVVYP--EG---------------VWYTRVDPEDARRIVQSHLLGGR 49 (64)
T ss_pred ceEEeecchhhhhccCCEEEEec--CC---------------eeEeccCHHHHHHHHHHHHhCCC
Confidence 35789999999999999999999 33 99999999999999999987543
No 16
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=99.03 E-value=4.3e-10 Score=104.64 Aligned_cols=79 Identities=16% Similarity=0.424 Sum_probs=70.5
Q ss_pred ccCCCcEEEEccCCccccccHHHHHHHHHHHhCCc---------cEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCC
Q 018470 248 TTTRTKRIEVCMGGKCKKLGAGALLEEFERKAGAE---------CDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYA 318 (355)
Q Consensus 248 ~~~~~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~e---------V~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v 318 (355)
...++++|.||+.+.|..+|++.+++++++.++++ .+|..++|||.|-+||+|.|++
T Consensus 109 ~p~gKy~v~VC~ttpC~lrg~d~i~ea~~k~lgi~~Gett~d~~Ftl~e~eClGaCvnaPmi~IND-------------- 174 (233)
T KOG3196|consen 109 KPVGKYHVQVCTTTPCMLRGSDDILEACKKQLGIKVGETTKDGLFTLEEVECLGACVNAPMIAIND-------------- 174 (233)
T ss_pred cCCCCceEEEecCcHHhhhccHHHHHHHHHHhCccccccccccceeeecchhhhhhccCceeeecc--------------
Confidence 34678999999999999999999999999999853 2899999999999999999986
Q ss_pred CCCCceeeecCCcchHHHHHHHHhcCC
Q 018470 319 KPSINSLCIGVGLEDVDMILANILGKD 345 (355)
Q Consensus 319 ~~p~n~lY~~VtpEDVdeIVe~hlg~~ 345 (355)
.+|..+|++++.+|++.+-.+.
T Consensus 175 -----~yyedlt~k~l~eIle~L~~~k 196 (233)
T KOG3196|consen 175 -----DYYEDLTPKKLVEILEDLKAGK 196 (233)
T ss_pred -----hhhccCCHHHHHHHHHHHhcCC
Confidence 4699999999999999986543
No 17
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=97.89 E-value=4.3e-05 Score=69.98 Aligned_cols=81 Identities=21% Similarity=0.208 Sum_probs=64.9
Q ss_pred CCCcEEEEccCC----ccccccHHHHHHHHHHHhCCc----cEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCC
Q 018470 250 TRTKRIEVCMGG----KCKKLGAGALLEEFERKAGAE----CDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPS 321 (355)
Q Consensus 250 ~~~~rI~VC~Gt----~C~ksGS~aVLeafee~Lg~e----V~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p 321 (355)
..+..|+||+.+ .|... +..|.++|++.+... ..|-.+..+|-+.-+|||+||. . ..|
T Consensus 130 ~~~~~iLVCtHg~RD~rCg~~-Gp~l~~~l~~~~~~~~l~~~~V~~iSHiGGHkfAgNvIiy~--~-----------~~p 195 (230)
T PF06999_consen 130 PDKPLILVCTHGKRDKRCGIL-GPPLARELEKELRERGLSRDRVWEISHIGGHKFAGNVIIYS--K-----------PKP 195 (230)
T ss_pred CCCCEEEEcCCCCcCCchhcc-cHHHHHHHHHHhhhcCCccceEEEecccccceecCeEEEEe--c-----------CCC
Confidence 467889999996 57777 578999999998632 2399999999999999999991 0 012
Q ss_pred CceeeecCCcchHHHHHHHHhcC
Q 018470 322 INSLCIGVGLEDVDMILANILGK 344 (355)
Q Consensus 322 ~n~lY~~VtpEDVdeIVe~hlg~ 344 (355)
...||+.|+|++|..||+++..+
T Consensus 196 ~g~wyGrv~p~~v~~iv~~t~~~ 218 (230)
T PF06999_consen 196 DGIWYGRVTPEDVEGIVDATILD 218 (230)
T ss_pred cEEEEEeeCHHHHHHHHHHHHhC
Confidence 34999999999999999995443
No 18
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=97.58 E-value=0.0002 Score=61.62 Aligned_cols=70 Identities=21% Similarity=0.366 Sum_probs=57.6
Q ss_pred EEEccCCccccc---------cHHHHHHHHHHHhC-----CccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCC
Q 018470 255 IEVCMGGKCKKL---------GAGALLEEFERKAG-----AECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKP 320 (355)
Q Consensus 255 I~VC~Gt~C~ks---------GS~aVLeafee~Lg-----~eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~ 320 (355)
|+||+ .|+.. +++.|+++|++.+. .+++|.++.||..|..|=+|.+... +. +
T Consensus 1 l~VC~--tCr~~~~~~~~~~~~G~~L~~aL~~~~~~~~~~~~v~v~~v~CL~~C~r~CtVA~~~~-gK-------~---- 66 (116)
T PF07845_consen 1 LFVCT--TCRRSGEDPEDGPRPGAALLDALRAALADAPLPDGVEVRPVECLSACDRPCTVALQAP-GK-------W---- 66 (116)
T ss_pred CEEeC--CCCCCCCCCCCCCChHHHHHHHHHHHHhcCCCCCceEEEeccHHhcCCCceEEEEEcC-CC-------c----
Confidence 56785 66665 89999999999863 4689999999999999999999851 32 2
Q ss_pred CCceeeecCCc-chHHHHHHH
Q 018470 321 SINSLCIGVGL-EDVDMILAN 340 (355)
Q Consensus 321 p~n~lY~~Vtp-EDVdeIVe~ 340 (355)
+.+|+++++ ++++.||+-
T Consensus 67 --tYlfGdl~p~~~a~~il~~ 85 (116)
T PF07845_consen 67 --TYLFGDLDPDEDAEDILAF 85 (116)
T ss_pred --EEEEecCCcccCHHHHHHH
Confidence 478999999 999999963
No 19
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=96.42 E-value=0.012 Score=52.78 Aligned_cols=76 Identities=18% Similarity=0.372 Sum_probs=60.3
Q ss_pred ccCCCcEEEEccCCcccc----------ccHHHHHHHHHHHhC-----CccEEEeecCCCCCCCCCeEEEeCCCCCChhh
Q 018470 248 TTTRTKRIEVCMGGKCKK----------LGAGALLEEFERKAG-----AECDVSMCKCMGKCRDGPNLRVSNSHDGDSAI 312 (355)
Q Consensus 248 ~~~~~~rI~VC~Gt~C~k----------sGS~aVLeafee~Lg-----~eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~ 312 (355)
....+|+++||. .|+. +++..|++.+++... .+.++.++.||..|..|=+|.+... ++
T Consensus 13 ~~~~~htlfVCk--sC~~~~~~~~~~~p~~G~~Ll~kl~~l~qe~~~~~e~~I~~VeCl~~C~r~c~vA~~~~-~k---- 85 (143)
T COG5469 13 NGMPKHTLFVCK--SCRDVSQEGKENGPSDGSILLDKLQELAQEWEIAHEFEIQTVECLAACNRGCVVAFSGP-GK---- 85 (143)
T ss_pred cccCceEEEEec--cccccccCCccCCCCcHHHHHHHHHHHHhhhhhhccceeeeeHhhhhcCCCeEEEEecC-CC----
Confidence 467889999997 5543 467889999997653 4668999999999999998888752 22
Q ss_pred hhccCCCCCCceeeecCCcch-HHHHHH
Q 018470 313 RIQGYAKPSINSLCIGVGLED-VDMILA 339 (355)
Q Consensus 313 ~~~~~v~~p~n~lY~~VtpED-VdeIVe 339 (355)
+ ..+|++++|+| ...||+
T Consensus 86 ---~------sYLFgdL~p~d~a~dLl~ 104 (143)
T COG5469 86 ---P------SYLFGDLTPDDSASDLLE 104 (143)
T ss_pred ---c------eEEEccCCccccHHHHHH
Confidence 1 37899999999 888886
No 20
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=95.60 E-value=0.044 Score=44.60 Aligned_cols=70 Identities=17% Similarity=0.346 Sum_probs=50.6
Q ss_pred cEEEEccCCccccccHHHHHHHHHHHhCCccEEEeecCCCCCCC---CCeEEEeCCCCCChhhhhccCCCCCCceeeecC
Q 018470 253 KRIEVCMGGKCKKLGAGALLEEFERKAGAECDVSMCKCMGKCRD---GPNLRVSNSHDGDSAIRIQGYAKPSINSLCIGV 329 (355)
Q Consensus 253 ~rI~VC~Gt~C~ksGS~aVLeafee~Lg~eV~V~~tGCLG~Cg~---GPnVrV~pe~dg~~~~~~~~~v~~p~n~lY~~V 329 (355)
..|++|.+. ...|+..+++.|++. .++.|...||+|.|+. .|=..|++ .+-..-
T Consensus 3 piVefC~~N--l~~g~~~~~~~Le~~--p~~~Vie~gCl~~Cg~C~~~pFAlVnG-------------------~~V~A~ 59 (78)
T PF07293_consen 3 PIVEFCVSN--LASGTDQVYEKLEKD--PDIDVIEYGCLSYCGPCAKKPFALVNG-------------------EIVAAE 59 (78)
T ss_pred ceEEEcccC--chhhhHHHHHHHhcC--CCccEEEcChhhhCcCCCCCccEEECC-------------------EEEecC
Confidence 468899854 567999999999864 6778999999988764 78888876 223345
Q ss_pred CcchHHHHHHHHhcCC
Q 018470 330 GLEDVDMILANILGKD 345 (355)
Q Consensus 330 tpEDVdeIVe~hlg~~ 345 (355)
|+|+.-+-|.+++.+.
T Consensus 60 t~eeL~~kI~~~i~e~ 75 (78)
T PF07293_consen 60 TAEELLEKIKEKIEEN 75 (78)
T ss_pred CHHHHHHHHHHHHhcc
Confidence 6666666666666553
No 21
>PRK13669 hypothetical protein; Provisional
Probab=93.66 E-value=0.27 Score=40.32 Aligned_cols=48 Identities=27% Similarity=0.506 Sum_probs=37.8
Q ss_pred cEEEEccCCccccccHHHHHHHHHHHhCCccEEEeecCCCCCC---CCCeEEEeC
Q 018470 253 KRIEVCMGGKCKKLGAGALLEEFERKAGAECDVSMCKCMGKCR---DGPNLRVSN 304 (355)
Q Consensus 253 ~rI~VC~Gt~C~ksGS~aVLeafee~Lg~eV~V~~tGCLG~Cg---~GPnVrV~p 304 (355)
..|++|.+. ..+|+..+++.|++ ..++.|...||++.|+ .+|=..|++
T Consensus 3 piVEfC~sN--l~~G~~~~~~~Le~--dP~~dVie~gCls~CG~C~~~~FAlVng 53 (78)
T PRK13669 3 PIVEFCVSN--LASGSQAAFEKLEK--DPNLDVLEYGCLGYCGICSEGLFALVNG 53 (78)
T ss_pred ceeeehhcc--hhhhHHHHHHHHHh--CCCceEEEcchhhhCcCcccCceEEECC
Confidence 358889876 46789988888854 4678899999998775 578888876
No 22
>PF05501 DUF755: Domain of unknown function (DUF755) ; InterPro: IPR008474 This family is predominated by ORFs from Anelloviridae. The function of this family remains to be determined.
Probab=73.40 E-value=1.9 Score=37.74 Aligned_cols=51 Identities=24% Similarity=0.105 Sum_probs=31.0
Q ss_pred hHhHHHHHHHHHHHhcCcccccccCCcCCccccchhhhhHHHH--HHHHHHHHh
Q 018470 77 IKSVRKKLKFMKRLSSDLLPLEAFGNEDASSLRNEERISEAVQ--VLQAQLLQL 128 (355)
Q Consensus 77 ~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~~l~~~~~~sea~e--~L~~qL~q~ 128 (355)
++.-.+-.|++=+-..+...++.-|-. |..++-.+++-|-.. -||.=|+||
T Consensus 9 PI~S~~~YK~~tr~~~~~~~~St~GTs-d~~~L~~qLlKEC~kt~~L~~l~~ql 61 (123)
T PF05501_consen 9 PIDSLKQYKSRTRNSSDPNQSSTPGTS-DVDSLQKQLLKECQKTSQLMQLLQQL 61 (123)
T ss_pred CccCHHHHHHHHhCCCCCCCCCcCCcc-hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456677777777777666665554 333344666666544 566666666
No 23
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=67.78 E-value=15 Score=38.64 Aligned_cols=36 Identities=25% Similarity=0.264 Sum_probs=27.1
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHH-HHHHHH
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEK-KAQIKT 148 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~e-ka~lKa 148 (355)
-|++|++.|.+||||..|+|-|-.-.|-+= -|+|..
T Consensus 116 ~i~~~~~el~~q~e~~ea~e~e~~~erh~~h~~~le~ 152 (548)
T COG5665 116 FIHDCLDELQKQLEQYEAQENEEQTERHEFHIANLEN 152 (548)
T ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 799999999999999999987765444332 344443
No 24
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=65.39 E-value=16 Score=31.12 Aligned_cols=41 Identities=32% Similarity=0.491 Sum_probs=36.8
Q ss_pred hhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Q 018470 111 EERISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKTTMK 151 (355)
Q Consensus 111 ~~~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa~~~ 151 (355)
++.+++-.+.|..+++++..+-++++++.++.++++|..++
T Consensus 75 q~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~ 115 (118)
T PF13815_consen 75 QEYLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKK 115 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66788888999999999999999999999999999999876
No 25
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=63.16 E-value=13 Score=35.98 Aligned_cols=35 Identities=23% Similarity=0.261 Sum_probs=26.6
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIK 147 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lK 147 (355)
-=.|=++.||+||+..|.|+.+.+++..+++++..
T Consensus 143 ddeDd~~~Ll~ELekIKkER~ee~~~~e~~~~~~~ 177 (244)
T PF04889_consen 143 DDEDDTAALLRELEKIKKERAEEKARKEEEKAEEE 177 (244)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556789999999999998888877776644433
No 26
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=62.85 E-value=11 Score=33.27 Aligned_cols=25 Identities=36% Similarity=0.555 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 117 AVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 117 a~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
.+|-|.+||++|+-|-|.||||.++
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~ 28 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQ 28 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4688999999999999999998764
No 27
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=60.40 E-value=50 Score=31.85 Aligned_cols=10 Identities=30% Similarity=0.375 Sum_probs=8.6
Q ss_pred ccccCCcCCc
Q 018470 97 LEAFGNEDAS 106 (355)
Q Consensus 97 ~~~~g~~~d~ 106 (355)
-..|||..||
T Consensus 166 re~fGy~vDp 175 (217)
T PF10147_consen 166 REHFGYKVDP 175 (217)
T ss_pred HHHhCCcCCC
Confidence 5679999999
No 28
>PHA03155 hypothetical protein; Provisional
Probab=58.93 E-value=12 Score=32.97 Aligned_cols=25 Identities=36% Similarity=0.502 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 117 AVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 117 a~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
.+|-|.+||++|+-|-|.||||.++
T Consensus 9 tvEeLaaeL~kL~~ENK~LKkkl~~ 33 (115)
T PHA03155 9 DVEELEKELQKLKIENKALKKKLLQ 33 (115)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3688999999999999999998765
No 29
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.44 E-value=9.9 Score=37.80 Aligned_cols=22 Identities=32% Similarity=0.371 Sum_probs=15.4
Q ss_pred HHHHHhhHHHHHHHHHHHHHHH
Q 018470 123 AQLLQLRSEQKELKKMMKEKKA 144 (355)
Q Consensus 123 ~qL~q~r~eekelKk~~K~eka 144 (355)
-+++....+||++|+.-+-+|.
T Consensus 132 ~~~ek~~~~ek~~kk~s~k~kk 153 (306)
T KOG2985|consen 132 GEVEKVSSEEKEEKKSSDKDKK 153 (306)
T ss_pred hhhHHHHHHHHhhhhhhhhhhh
Confidence 4677777888888877665543
No 30
>PHA03162 hypothetical protein; Provisional
Probab=57.69 E-value=13 Score=33.43 Aligned_cols=24 Identities=42% Similarity=0.564 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 118 VQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 118 ~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
+|-|.+||++|+-|-|.||||.++
T Consensus 15 mEeLaaeL~kLqmENK~LKkkl~~ 38 (135)
T PHA03162 15 MEDLAAEIAKLQLENKALKKKIKE 38 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 688999999999999999998764
No 31
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.47 E-value=47 Score=28.29 Aligned_cols=86 Identities=21% Similarity=0.355 Sum_probs=48.5
Q ss_pred eeeeccc-cchhhcc---cccccccccceeccccccchhhhhhhhhhhhHhHHHHHHHHHHHhcCcccccccCCcCCc--
Q 018470 33 FRVSERT-RNSFRRL---SSRFSDCGHQQYYVSPRKETKKKEKEKSSEIKSVRKKLKFMKRLSSDLLPLEAFGNEDAS-- 106 (355)
Q Consensus 33 ~~v~~~~-r~~~~~~---~~~F~D~ghl~yy~~~~k~~~~k~k~k~~~~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~-- 106 (355)
++||-++ |+ +-+. .....++|-.|||...-- ..+++++. |..+||..+-
T Consensus 10 ~gvs~~tlR~-Ye~~Gll~~~~r~~~g~R~Y~~~~l-----------------~~l~~I~~-------lr~~G~sL~eI~ 64 (126)
T cd04785 10 TGVNVETIRY-YESIGLLPEPARTAGGYRLYGAAHV-----------------ERLRFIRR-------ARDLGFSLEEIR 64 (126)
T ss_pred HCcCHHHHHH-HHHCCCCCCCCcCCCCccccCHHHH-----------------HHHHHHHH-------HHHCCCCHHHHH
Confidence 4566666 54 3333 222345556688865422 23445554 5566665331
Q ss_pred cccc-----hhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 018470 107 SLRN-----EERISEAVQVLQAQLLQLRSEQKELKKMMKEKK 143 (355)
Q Consensus 107 ~l~~-----~~~~sea~e~L~~qL~q~r~eekelKk~~K~ek 143 (355)
.+++ .....++.++|.++++++..+-.+|++.++.=+
T Consensus 65 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~ 106 (126)
T cd04785 65 ALLALSDRPDRSCAEADAIARAHLADVRARIADLRRLEAELK 106 (126)
T ss_pred HHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1222 123456677888888888888888876665433
No 32
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=49.29 E-value=49 Score=31.92 Aligned_cols=26 Identities=23% Similarity=0.230 Sum_probs=19.0
Q ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 123 AQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 123 ~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
-||+++|.+-+|--|+++++-+.|+.
T Consensus 15 lELE~~k~~A~EElRk~eeqi~~L~~ 40 (214)
T PF07795_consen 15 LELEATKMEANEELRKREEQIAHLKD 40 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48899888888777777777555544
No 33
>KOG3228 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.65 E-value=35 Score=32.93 Aligned_cols=38 Identities=24% Similarity=0.239 Sum_probs=25.8
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHH-HHHHHHhhh
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEK-KAQIKTTMK 151 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~e-ka~lKa~~~ 151 (355)
=.|-|+.||.+|++.+.|+.|.+-.+.+| |+.-...+|
T Consensus 124 DeDdt~aLlaele~ikkERaee~~~~e~e~k~~e~r~r~ 162 (226)
T KOG3228|consen 124 DEDDTQALLAELENIKKERAEEQARKEEEQKAEEERIRM 162 (226)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 36789999999999999988765433333 333333444
No 34
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=47.31 E-value=31 Score=30.48 Aligned_cols=84 Identities=19% Similarity=0.248 Sum_probs=46.8
Q ss_pred eeeeccc-cchhhccc---ccccccccceeccccccchhhhhhhhhhhhHhHHHHHHHHHHHhcCcccccccCCcCCc--
Q 018470 33 FRVSERT-RNSFRRLS---SRFSDCGHQQYYVSPRKETKKKEKEKSSEIKSVRKKLKFMKRLSSDLLPLEAFGNEDAS-- 106 (355)
Q Consensus 33 ~~v~~~~-r~~~~~~~---~~F~D~ghl~yy~~~~k~~~~k~k~k~~~~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~-- 106 (355)
++||.+| |+ +-++| .--.++|..|||...-= .++++++. |..+||..+-
T Consensus 17 ~Gvs~~TLRy-YE~~GLl~p~~r~~~gyR~Y~~~~l-----------------~rl~~I~~-------lr~~G~sL~eI~ 71 (144)
T PRK13752 17 AGVNVETIRF-YQRKGLLPEPDKPYGSIRRYGEADV-----------------TRVRFVKS-------AQRLGFSLDEIA 71 (144)
T ss_pred HCcCHHHHHH-HHHCCCCCCCccCCCCCeecCHHHH-----------------HHHHHHHH-------HHHcCCCHHHHH
Confidence 5677788 75 33332 12345677899976432 23445554 5566665331
Q ss_pred cccc---hhhhhHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 107 SLRN---EERISEAVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 107 ~l~~---~~~~sea~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
.+++ ...-.++.++|.+++++++.+..++.+.+..
T Consensus 72 ~ll~~~~~~~~~~~~~ll~~k~~~l~~~i~~L~~~~~~ 109 (144)
T PRK13752 72 ELLRLEDGTHCEEASSLAEHKLKDVREKMADLARMEAV 109 (144)
T ss_pred HHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1221 2222456667777778877777776655444
No 35
>PF01451 LMWPc: Low molecular weight phosphotyrosine protein phosphatase; InterPro: IPR023485 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [, ]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 alpha-helices and 4 beta-strands forming a 3-layer alpha-beta-alpha sandwich architecture.; PDB: 3RH0_B 1JL3_B 2IPA_B 1Z2D_A 1Z2E_A 2CWD_D 2L18_A 2L17_A 2L19_A 1BVH_A ....
Probab=45.60 E-value=28 Score=29.21 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=32.4
Q ss_pred EEEccCCccccccHHHHHHHHHHH-hCCccEEEeecCCCC
Q 018470 255 IEVCMGGKCKKLGAGALLEEFERK-AGAECDVSMCKCMGK 293 (355)
Q Consensus 255 I~VC~Gt~C~ksGS~aVLeafee~-Lg~eV~V~~tGCLG~ 293 (355)
++||+|+.|++-=|+++++.+-+. .+.++.|...|=.+.
T Consensus 2 LFvC~~N~cRS~mAEai~~~~~~~~~~~~~~v~SAG~~~~ 41 (138)
T PF01451_consen 2 LFVCTGNICRSPMAEAILRHLLKQRLGDRFEVESAGTEAW 41 (138)
T ss_dssp EEEESSSSSHHHHHHHHHHHHHHHTHTTTEEEEEEESSST
T ss_pred EEEeCCCcchHHHHHHHHHHhccccccCCcEEEEEeeccc
Confidence 689999999999999999999776 577777877776633
No 36
>PF06658 DUF1168: Protein of unknown function (DUF1168); InterPro: IPR009548 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=44.59 E-value=59 Score=29.43 Aligned_cols=21 Identities=33% Similarity=0.341 Sum_probs=11.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 018470 128 LRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 128 ~r~eekelKk~~K~eka~lKa 148 (355)
..+|+|-.|+..|-+|+|.+.
T Consensus 77 ~~~eekTaKkR~KR~KkK~kk 97 (142)
T PF06658_consen 77 KEAEEKTAKKRAKRQKKKQKK 97 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 345566666666666554444
No 37
>PF14038 YqzE: YqzE-like protein
Probab=44.53 E-value=22 Score=27.55 Aligned_cols=28 Identities=29% Similarity=0.239 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 018470 117 AVQVLQAQLLQLRSEQKELKKMMKEKKA 144 (355)
Q Consensus 117 a~e~L~~qL~q~r~eekelKk~~K~eka 144 (355)
.||-+++=+++=|+|+|+.|.++|++|.
T Consensus 9 ~Tqq~V~YmdtPkeERk~~k~~rK~~k~ 36 (54)
T PF14038_consen 9 MTQQFVKYMDTPKEERKERKEERKEEKE 36 (54)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHHhcCC
Confidence 4677888889999999999988888763
No 38
>KOG4055 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.65 E-value=72 Score=30.58 Aligned_cols=29 Identities=28% Similarity=0.283 Sum_probs=13.4
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEKK 143 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~ek 143 (355)
+-+|.++=+..+ |--||||--||..|.+|
T Consensus 108 ~daefq~r~ek~-~kaaEeKTaKKRaKRqk 136 (213)
T KOG4055|consen 108 LDAEFQIRLEKN-QKAAEEKTAKKRAKRQK 136 (213)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 333444333333 33456665555555553
No 39
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=41.56 E-value=20 Score=38.15 Aligned_cols=22 Identities=23% Similarity=0.321 Sum_probs=12.0
Q ss_pred HHHHHHHhhHHHHHHHHHHHHH
Q 018470 121 LQAQLLQLRSEQKELKKMMKEK 142 (355)
Q Consensus 121 L~~qL~q~r~eekelKk~~K~e 142 (355)
|++|+|+|+.|-.|||+|+++-
T Consensus 29 ~~qkie~L~kql~~Lk~q~~~l 50 (489)
T PF11853_consen 29 LLQKIEALKKQLEELKAQQDDL 50 (489)
T ss_pred HHHHHHHHHHHHHHHHHhhccc
Confidence 3445666665555555554443
No 40
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=41.29 E-value=15 Score=41.37 Aligned_cols=32 Identities=16% Similarity=0.011 Sum_probs=21.7
Q ss_pred EEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCCc
Q 018470 284 DVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSIN 323 (355)
Q Consensus 284 ~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~n 323 (355)
.|.+-.=|..=.-+|...+.+ |+ +.++.+|.|
T Consensus 1383 hveglalmrarnpaplalllg--dd------yshyhtprn 1414 (1463)
T PHA03308 1383 HVEGLALMRARNPAPLALLLG--DD------YSHYHTPRN 1414 (1463)
T ss_pred hhhhHHHHhccCCcceeeeec--cc------cccccCCCC
Confidence 455556666777888887776 32 566777876
No 41
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=40.97 E-value=81 Score=26.71 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=21.5
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
...+..++|..+++++..+-.++++.++.
T Consensus 76 ~~~~~~~~l~~~~~~l~~~i~~L~~~~~~ 104 (127)
T cd04784 76 SCAEVNALIDEHLAHVRARIAELQALEKQ 104 (127)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566788888999888888887766543
No 42
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=40.22 E-value=32 Score=31.95 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=7.2
Q ss_pred cccceecccccc
Q 018470 53 CGHQQYYVSPRK 64 (355)
Q Consensus 53 ~ghl~yy~~~~k 64 (355)
-||.-|-+..+|
T Consensus 36 ~GHWtYECk~kR 47 (177)
T KOG3116|consen 36 AGHWTYECKNKR 47 (177)
T ss_pred hccceeeecCce
Confidence 367777655544
No 43
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=40.00 E-value=48 Score=30.10 Aligned_cols=39 Identities=31% Similarity=0.323 Sum_probs=25.0
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKTTMK 151 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa~~~ 151 (355)
-|+|-.+-+-++|++.....+++|+..|++|++.|+..+
T Consensus 46 ~Lne~Y~~~k~~L~~all~k~e~K~~~K~~KK~~K~~~K 84 (155)
T PF08496_consen 46 DLNERYEDMKEQLKQALLDKKELKAWEKAEKKEEKAKAK 84 (155)
T ss_pred eHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhh
Confidence 466666777777777666666776666666555555433
No 44
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=39.71 E-value=52 Score=33.41 Aligned_cols=72 Identities=21% Similarity=0.304 Sum_probs=56.0
Q ss_pred CCcEEEEccCC----ccccccHHHHHHHHHHHhC----CccEEEeecCCCCCCCCCeEEEeCCCCCChhhhhccCCCCCC
Q 018470 251 RTKRIEVCMGG----KCKKLGAGALLEEFERKAG----AECDVSMCKCMGKCRDGPNLRVSNSHDGDSAIRIQGYAKPSI 322 (355)
Q Consensus 251 ~~~rI~VC~Gt----~C~ksGS~aVLeafee~Lg----~eV~V~~tGCLG~Cg~GPnVrV~pe~dg~~~~~~~~~v~~p~ 322 (355)
-.+.|+||+.+ +|.+.| .-+++.++.... ..+.|-.|.=+|.-.-+|.+.-.| .
T Consensus 130 h~RdiLVCTHgn~D~cCarfG-~P~Y~~~r~~~a~l~~~~lRvWq~SHfgGHrFAPTlidlP-----------------~ 191 (316)
T COG4759 130 HTRDILVCTHGNVDVCCARFG-YPFYQQLRAQYADLNLENLRVWQSSHFGGHRFAPTLIDLP-----------------Q 191 (316)
T ss_pred hhceEEEecCCChhhhhhhcC-cHHHHHHHHhhhhccccceEEEEecccCccccCchhhcCC-----------------C
Confidence 34689999986 465555 567777777764 347899999999999999887766 2
Q ss_pred ceeeecCCcchHHHHHHH
Q 018470 323 NSLCIGVGLEDVDMILAN 340 (355)
Q Consensus 323 n~lY~~VtpEDVdeIVe~ 340 (355)
+.+|+++.++-.+.||.+
T Consensus 192 GqyyG~Ld~~~~~~l~~r 209 (316)
T COG4759 192 GQYYGHLDPESLDSLLTR 209 (316)
T ss_pred CceeeecCHHHHHHHHhc
Confidence 478999999999888864
No 45
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.68 E-value=89 Score=26.47 Aligned_cols=45 Identities=18% Similarity=0.241 Sum_probs=27.0
Q ss_pred ccccCCcCCc--cccc---hhhhhHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 97 LEAFGNEDAS--SLRN---EERISEAVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 97 ~~~~g~~~d~--~l~~---~~~~sea~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
|..+||..+- .+++ .....+..++|..+++++..+-.+|.+.+..
T Consensus 53 lr~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~ 102 (126)
T cd04783 53 AQELGFTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQRMRAS 102 (126)
T ss_pred HHHcCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566666331 1222 1134556677888888888888777666543
No 46
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=39.02 E-value=60 Score=36.70 Aligned_cols=109 Identities=14% Similarity=0.149 Sum_probs=60.9
Q ss_pred ccccceeeeeccccc--hhhcccccccccccceeccccccc-hhh--hhhhhh---hhhHhH--HHHHHHHHHHhcCccc
Q 018470 27 HLGFGDFRVSERTRN--SFRRLSSRFSDCGHQQYYVSPRKE-TKK--KEKEKS---SEIKSV--RKKLKFMKRLSSDLLP 96 (355)
Q Consensus 27 ~~~~~~~~v~~~~r~--~~~~~~~~F~D~ghl~yy~~~~k~-~~~--k~k~k~---~~~~s~--kkk~k~lk~ls~dl~~ 96 (355)
..+-|...||+||+. .+..+...|.-=||.+-=+..-+. +.. ++++++ ++.... .=|+=|++.
T Consensus 624 e~~d~~i~ISaRS~g~inVq~Iae~~GGGGH~~AAGaqi~~~tlee~~~~L~~~I~~~~~~~~~~MkVIL~~d------- 696 (838)
T PRK14538 624 KISDNTIAISARSYNEINVQTIMEQMEGGGHLNSAATQIKGTNIKTVTQTLKHLLKLEYEKGEKNMEIILLTD------- 696 (838)
T ss_pred EEcCCEEEEEEEeCCCCCHHHHHHHhCCCccHhhheEEeCCCCHHHHHHHHHHHHHHHHhhcchhhhHHHHHH-------
Confidence 345677899999964 577776667777998764443222 111 011110 000000 112223332
Q ss_pred ccccCCcCC-----cc----ccchhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 018470 97 LEAFGNEDA-----SS----LRNEERISEAVQVLQAQLLQLRSEQKELKKMMKEK 142 (355)
Q Consensus 97 ~~~~g~~~d-----~~----l~~~~~~sea~e~L~~qL~q~r~eekelKk~~K~e 142 (355)
...+|-.+| |. |+-.++--.||+.-+++|++.|+++.+.+.+.+++
T Consensus 697 v~~lGk~Gdvv~Vk~GYaNfLiP~~~A~~aT~~nlk~~e~~~~~~~~~~~~~~~~ 751 (838)
T PRK14538 697 IKNKGKKHEIIKVNNGYGNFLIQNKKALLADKENLAKIKKKKILEQEKKRNHELL 751 (838)
T ss_pred HHhcCCCCCEEEECCCchhhhccCCchhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 233454444 11 55577888999999999999987665555555444
No 47
>KOG2385 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.45 E-value=20 Score=38.91 Aligned_cols=12 Identities=42% Similarity=0.382 Sum_probs=10.6
Q ss_pred cccceecccccc
Q 018470 53 CGHQQYYVSPRK 64 (355)
Q Consensus 53 ~ghl~yy~~~~k 64 (355)
+||++||-.+++
T Consensus 552 eGHl~Yrw~~~k 563 (633)
T KOG2385|consen 552 EGHLSYRWSMPK 563 (633)
T ss_pred hhHHHHHHHHHH
Confidence 799999988877
No 48
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=37.71 E-value=80 Score=27.43 Aligned_cols=33 Identities=12% Similarity=0.152 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQI 146 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~eka~l 146 (355)
..+..+.|.++++++..+.++|.+.+..=...+
T Consensus 76 ~~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i 108 (131)
T cd04786 76 HDELLAALERKVADIEALEARLAQNKAQLLVLI 108 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356667888889999888888887765544333
No 49
>KOG4848 consensus Extracellular matrix-associated peroxidase [Extracellular structures; Defense mechanisms]
Probab=36.94 E-value=94 Score=30.04 Aligned_cols=39 Identities=26% Similarity=0.230 Sum_probs=19.7
Q ss_pred cccCCcCCccccchhhhhHHHHHHHHHHHHh-hHHHHHHHHHHHHHH
Q 018470 98 EAFGNEDASSLRNEERISEAVQVLQAQLLQL-RSEQKELKKMMKEKK 143 (355)
Q Consensus 98 ~~~g~~~d~~l~~~~~~sea~e~L~~qL~q~-r~eekelKk~~K~ek 143 (355)
..||+-.|| . +.-.+.+|+|+|.- |...||-|+++|+||
T Consensus 178 e~fGy~vDp--r-----d~RF~emLqqkEkeekK~~KeaKrk~k~ek 217 (225)
T KOG4848|consen 178 EYFGYWVDP--R-----DPRFEEMLQQKEKEEKKAVKEAKRKEKQEK 217 (225)
T ss_pred HHhCccCCC--C-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457777776 2 23345666665431 223344555555554
No 50
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=36.58 E-value=1e+02 Score=27.38 Aligned_cols=49 Identities=14% Similarity=0.209 Sum_probs=23.2
Q ss_pred cccccccCCcCCccccchhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 018470 94 LLPLEAFGNEDASSLRNEERISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQI 146 (355)
Q Consensus 94 l~~~~~~g~~~d~~l~~~~~~sea~e~L~~qL~q~r~eekelKk~~K~eka~l 146 (355)
+-.+++++|.... +..+-.-.+-|=.|+++|..+|..++.+.++++.++
T Consensus 9 ~lllss~sfaA~~----~~~v~~~l~~LEae~q~L~~kE~~r~~~~k~~ae~a 57 (126)
T PF09403_consen 9 MLLLSSISFAATA----TASVESELNQLEAEYQQLEQKEEARYNEEKQEAEAA 57 (126)
T ss_dssp ------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4467788887543 222222366777888888888888888777765443
No 51
>PF15509 DUF4650: Domain of unknown function (DUF4650)
Probab=36.31 E-value=53 Score=35.39 Aligned_cols=41 Identities=24% Similarity=0.239 Sum_probs=27.8
Q ss_pred HhHHHHHHHHHHHhcC-------cccccccCCcCCccccchhhhhHHHHHHHHHHHH
Q 018470 78 KSVRKKLKFMKRLSSD-------LLPLEAFGNEDASSLRNEERISEAVQVLQAQLLQ 127 (355)
Q Consensus 78 ~s~kkk~k~lk~ls~d-------l~~~~~~g~~~d~~l~~~~~~sea~e~L~~qL~q 127 (355)
+++||||-.|.++... +...+..| ...=+|+.|-||+|||.
T Consensus 325 KAKKkKLAsL~s~~~~g~~~se~~e~~sq~g---------S~nd~eslqdlL~ELQ~ 372 (520)
T PF15509_consen 325 KAKKKKLASLMSSPQNGKPPSENLEHVSQCG---------SPNDCESLQDLLNELQY 372 (520)
T ss_pred HHhHHHHHHHHhhhhcCCCCccccccCCCCC---------CCCchHHHHHHHHHHHH
Confidence 4778899999887654 33333332 33446888999999985
No 52
>PF14284 PcfJ: PcfJ-like protein
Probab=36.02 E-value=91 Score=28.15 Aligned_cols=48 Identities=17% Similarity=0.147 Sum_probs=35.6
Q ss_pred ccccccCCcCC-ccccchhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 018470 95 LPLEAFGNEDA-SSLRNEERISEAVQVLQAQLLQLRSEQKELKKMMKEK 142 (355)
Q Consensus 95 ~~~~~~g~~~d-~~l~~~~~~sea~e~L~~qL~q~r~eekelKk~~K~e 142 (355)
.|+..||.+.+ +..+-++-|-+|=+.|+.+.+++++++.+.+..++..
T Consensus 7 ~m~~~l~~d~~~~~~~~P~~L~~~HD~~~~~~~~~~~~~~~~~~~~~~~ 55 (169)
T PF14284_consen 7 RMLEKLGKDLNNEIYLCPKDLKAAHDELVEKYNQIKDEERREKMRKRYP 55 (169)
T ss_pred HHHHHhCcccccccccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35556666634 3244588899999999999999999888777666655
No 53
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=36.02 E-value=78 Score=27.09 Aligned_cols=85 Identities=16% Similarity=0.249 Sum_probs=48.2
Q ss_pred eeeeccc-cchhhccc---ccccccccceeccccccchhhhhhhhhhhhHhHHHHHHHHHHHhcCcccccccCCcCCc--
Q 018470 33 FRVSERT-RNSFRRLS---SRFSDCGHQQYYVSPRKETKKKEKEKSSEIKSVRKKLKFMKRLSSDLLPLEAFGNEDAS-- 106 (355)
Q Consensus 33 ~~v~~~~-r~~~~~~~---~~F~D~ghl~yy~~~~k~~~~k~k~k~~~~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~-- 106 (355)
++||.++ |+ +-..| ....+.+-.|||...-= ..+++++. |..+||..+-
T Consensus 10 ~gvs~~tlR~-Ye~~GLl~~~~r~~~gyR~Y~~~~l-----------------~~l~~I~~-------lr~lG~sL~eI~ 64 (127)
T TIGR02047 10 TGVSVETIRF-YEKQGLLPPPARTDNNYRVYTVGHV-----------------ERLAFIRN-------CRTLDMSLAEIR 64 (127)
T ss_pred HCcCHHHHHH-HHHCCCCCCCCcCCCCCCcCCHHHH-----------------HHHHHHHH-------HHHcCCCHHHHH
Confidence 4566677 54 33332 23445666788865421 23445554 5556665331
Q ss_pred cccc-----hhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 018470 107 SLRN-----EERISEAVQVLQAQLLQLRSEQKELKKMMKEK 142 (355)
Q Consensus 107 ~l~~-----~~~~sea~e~L~~qL~q~r~eekelKk~~K~e 142 (355)
.+++ .....+..++|..+++++..+-.+|.+.+..=
T Consensus 65 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L 105 (127)
T TIGR02047 65 QLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQL 105 (127)
T ss_pred HHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1221 22345667788888888888888887766543
No 54
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=35.84 E-value=82 Score=28.07 Aligned_cols=31 Identities=29% Similarity=0.241 Sum_probs=25.6
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEKK 143 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~ek 143 (355)
+-+.|-+.|-.|+|+.+.+.|...|++|++.
T Consensus 83 ~~TkAQ~ALk~q~E~~K~~rk~~~k~~re~~ 113 (132)
T PF11208_consen 83 ISTKAQQALKLQREQRKKERKKRSKEQREAE 113 (132)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4477888999999999999988888777763
No 55
>KOG0286 consensus G-protein beta subunit [General function prediction only]
Probab=33.86 E-value=40 Score=34.41 Aligned_cols=24 Identities=29% Similarity=0.583 Sum_probs=20.2
Q ss_pred HHHHHhhHHHHHHHHHHHHHHHHH
Q 018470 123 AQLLQLRSEQKELKKMMKEKKAQI 146 (355)
Q Consensus 123 ~qL~q~r~eekelKk~~K~eka~l 146 (355)
.+|+|||.|-+.||.|.+++++++
T Consensus 2 ~~~~~l~~Eae~L~~qi~~~r~~~ 25 (343)
T KOG0286|consen 2 EELEQLRQEAEQLKNQIRDARKKL 25 (343)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHh
Confidence 578999999999999998886554
No 56
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=33.84 E-value=88 Score=28.32 Aligned_cols=90 Identities=20% Similarity=0.259 Sum_probs=51.4
Q ss_pred eeeeccc-cchhhcc---cccccccccceeccccccchhhhhhhhhhhhHhHHHHHHHHHHHhcCcccccccCCcCCc--
Q 018470 33 FRVSERT-RNSFRRL---SSRFSDCGHQQYYVSPRKETKKKEKEKSSEIKSVRKKLKFMKRLSSDLLPLEAFGNEDAS-- 106 (355)
Q Consensus 33 ~~v~~~~-r~~~~~~---~~~F~D~ghl~yy~~~~k~~~~k~k~k~~~~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~-- 106 (355)
++||-++ |+ .-+. .....+++..|||...-= .++.+++. |..+||..+-
T Consensus 11 ~gvs~~tLRy-Ye~~GLl~p~~r~~~gyR~Y~~~dl-----------------~rL~~I~~-------lr~~G~sL~eI~ 65 (172)
T cd04790 11 FGLSRSTLLY-YERIGLLSPSARSESNYRLYGERDL-----------------ERLEQICA-------YRSAGVSLEDIR 65 (172)
T ss_pred HCcCHHHHHH-HHHCCCCCCCccCCCCCccCCHHHH-----------------HHHHHHHH-------HHHcCCCHHHHH
Confidence 4566666 54 2223 223456677788875421 22334443 5566766432
Q ss_pred cccchhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 107 SLRNEERISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 107 ~l~~~~~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
.+++.. ..++.++|..++++++.+-.+++.+++.=.+.++.
T Consensus 66 ~ll~~~-~~~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~ 106 (172)
T cd04790 66 SLLQQP-GDDATDVLRRRLAELNREIQRLRQQQRAIATLLKQ 106 (172)
T ss_pred HHHhcC-ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 122211 13667789999999998888888777665554443
No 57
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=33.84 E-value=82 Score=29.66 Aligned_cols=39 Identities=26% Similarity=0.237 Sum_probs=18.7
Q ss_pred Cccccc--hhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 018470 105 ASSLRN--EERISEAVQVLQAQLLQLRSEQKELKKMMKEKK 143 (355)
Q Consensus 105 d~~l~~--~~~~sea~e~L~~qL~q~r~eekelKk~~K~ek 143 (355)
||..+. +.-+..|..-+..||++.=++.+|.++++.|||
T Consensus 74 dpd~v~~rqEa~eaAR~RmQEE~dakA~~~kEKq~q~EEEK 114 (190)
T PF06936_consen 74 DPDVVVRRQEAMEAARRRMQEELDAKAEEYKEKQKQEEEEK 114 (190)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 554333 445555666655555544333444444444444
No 58
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.64 E-value=56 Score=26.65 Aligned_cols=80 Identities=18% Similarity=0.298 Sum_probs=46.6
Q ss_pred eeeeccc-cchhhcccc---cccccccceeccccccchhhhhhhhhhhhHhHHHHHHHHHHHhcCcccccccCCcCCc--
Q 018470 33 FRVSERT-RNSFRRLSS---RFSDCGHQQYYVSPRKETKKKEKEKSSEIKSVRKKLKFMKRLSSDLLPLEAFGNEDAS-- 106 (355)
Q Consensus 33 ~~v~~~~-r~~~~~~~~---~F~D~ghl~yy~~~~k~~~~k~k~k~~~~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~-- 106 (355)
++||.++ |+ +-..|- .-.++|..+||...-= ..+.+++. |..+||..+-
T Consensus 10 ~gvs~~tlR~-ye~~Gll~p~~~~~~gyR~Y~~~~~-----------------~~l~~I~~-------lr~~G~~l~eI~ 64 (97)
T cd04782 10 CGISKQTLFH-YDKIGLFKPEIVKENGYRYYTLEQF-----------------EQLDIILL-------LKELGISLKEIK 64 (97)
T ss_pred HCcCHHHHHH-HHHCCCCCCCccCCCCCccCCHHHH-----------------HHHHHHHH-------HHHcCCCHHHHH
Confidence 4567777 65 333322 2245677888865421 12334443 5667776432
Q ss_pred cccchhhhhHHHHHHHHHHHHhhHHHHHHHH
Q 018470 107 SLRNEERISEAVQVLQAQLLQLRSEQKELKK 137 (355)
Q Consensus 107 ~l~~~~~~sea~e~L~~qL~q~r~eekelKk 137 (355)
++++...+.+..++|.++++++.++-+++++
T Consensus 65 ~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 65 DYLDNRNPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2333334567778888888888888777765
No 59
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=32.16 E-value=27 Score=33.85 Aligned_cols=17 Identities=35% Similarity=0.456 Sum_probs=10.2
Q ss_pred CCccccccHHHHHHHHH
Q 018470 260 GGKCKKLGAGALLEEFE 276 (355)
Q Consensus 260 Gt~C~ksGS~aVLeafe 276 (355)
|..=...|..+||+++-
T Consensus 181 GRtRLIkGdGEilEEIV 197 (225)
T PF10500_consen 181 GRTRLIKGDGEILEEIV 197 (225)
T ss_pred CceeeecccchHHHHHh
Confidence 33335567777777663
No 60
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=31.59 E-value=47 Score=29.23 Aligned_cols=36 Identities=28% Similarity=0.425 Sum_probs=26.7
Q ss_pred CcEEEEccCCccccccHHHHHHHHHHHhCCccEEEeecC
Q 018470 252 TKRIEVCMGGKCKKLGAGALLEEFERKAGAECDVSMCKC 290 (355)
Q Consensus 252 ~~rI~VC~Gt~C~ksGS~aVLeafee~Lg~eV~V~~tGC 290 (355)
.+.++||+|+.|++-=|++++..+-. .++.|...|=
T Consensus 3 ~kVLFVC~gN~cRSpmAE~l~~~~~~---~~~~v~SAGt 38 (139)
T COG0394 3 MKVLFVCTGNICRSPMAEALLRHLAP---DNVEVDSAGT 38 (139)
T ss_pred ceEEEEcCCCcccCHHHHHHHHHhcc---CCeEEECCcc
Confidence 45678999999999999988776654 4555555553
No 61
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=30.80 E-value=1e+02 Score=32.52 Aligned_cols=50 Identities=18% Similarity=0.283 Sum_probs=0.0
Q ss_pred HHHHHhhHHHHHHHHHHHHHH-------------------HHHHHhhhhccCCCCCCCCCCCCCCCCCC
Q 018470 123 AQLLQLRSEQKELKKMMKEKK-------------------AQIKTTMKERKGNRKSGSSSSSSSESSDS 172 (355)
Q Consensus 123 ~qL~q~r~eekelKk~~K~ek-------------------a~lKa~~~~~~~~~esssssSsssessds 172 (355)
++.++.|++.|+++++|++.. ++-++.+++..+--|-+..+++++|.+.+
T Consensus 338 ~~~~~~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~e~e~s 406 (429)
T PRK00247 338 AEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENEES 406 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhhhcccccccCCCCcccccccc
No 62
>PF06658 DUF1168: Protein of unknown function (DUF1168); InterPro: IPR009548 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=29.70 E-value=1.5e+02 Score=26.83 Aligned_cols=28 Identities=21% Similarity=0.255 Sum_probs=18.0
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHhhh
Q 018470 124 QLLQLRSEQKELKKMMKEKKAQIKTTMK 151 (355)
Q Consensus 124 qL~q~r~eekelKk~~K~eka~lKa~~~ 151 (355)
+..+-|...+-.||++|-++++.+....
T Consensus 77 ~~~eekTaKkR~KR~KkK~kk~~~k~~~ 104 (142)
T PF06658_consen 77 KEAEEKTAKKRAKRQKKKQKKKKKKKKK 104 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4556677777777777777655555444
No 63
>PRK11778 putative inner membrane peptidase; Provisional
Probab=29.68 E-value=76 Score=32.17 Aligned_cols=39 Identities=26% Similarity=0.305 Sum_probs=28.6
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKTTMK 151 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa~~~ 151 (355)
-|+|-.+-+-++|++...-++++|+..|++|++-|+.++
T Consensus 44 ~l~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~~k~~~~ 82 (330)
T PRK11778 44 NLNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAK 82 (330)
T ss_pred EhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhh
Confidence 466667777778888777788888888887766666555
No 64
>KOG1636 consensus DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair]
Probab=29.06 E-value=23 Score=34.87 Aligned_cols=15 Identities=47% Similarity=1.039 Sum_probs=12.2
Q ss_pred cccccceeccccccc
Q 018470 51 SDCGHQQYYVSPRKE 65 (355)
Q Consensus 51 ~D~ghl~yy~~~~k~ 65 (355)
.|-||+|||-+||=+
T Consensus 242 ~~~g~lr~YLAPKie 256 (260)
T KOG1636|consen 242 EDMGHLRYYLAPKIE 256 (260)
T ss_pred ccCceEEEEEccccC
Confidence 466999999999753
No 65
>KOG2138 consensus Predicted RNA binding protein, contains G-patch domain [RNA processing and modification]
Probab=28.32 E-value=60 Score=36.56 Aligned_cols=16 Identities=56% Similarity=0.513 Sum_probs=7.7
Q ss_pred CCCCCCCCCCCCCCCC
Q 018470 158 KSGSSSSSSSESSDSD 173 (355)
Q Consensus 158 esssssSsssessds~ 173 (355)
..+|||+.||.+||..
T Consensus 843 ~kkSss~~Ssd~sdk~ 858 (883)
T KOG2138|consen 843 PKKSSSSESSDSSDKQ 858 (883)
T ss_pred ccccccccccccchhh
Confidence 3444444555555443
No 66
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=28.25 E-value=73 Score=30.79 Aligned_cols=35 Identities=23% Similarity=0.176 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
.+..-+-+.+|-++-|+--+|.|++.|+||+++..
T Consensus 84 F~~i~~~~~~~~e~kK~~tkeEKk~~K~ek~~~e~ 118 (212)
T cd03489 84 FTPIYEWHLREKEKKKSRTKEEKKALKEEKDKEAE 118 (212)
T ss_pred CHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhc
Confidence 45667788888888888888888888888887776
No 67
>PLN02316 synthase/transferase
Probab=27.81 E-value=75 Score=36.88 Aligned_cols=32 Identities=28% Similarity=0.326 Sum_probs=22.8
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Q 018470 120 VLQAQLLQLRSEQKELKKMMKEKKAQIKTTMK 151 (355)
Q Consensus 120 ~L~~qL~q~r~eekelKk~~K~eka~lKa~~~ 151 (355)
..+++|++.|+++.|.-|++.+++|++||.++
T Consensus 434 ~~~~~l~~~~~~~~~~~r~k~~~~a~~~ae~k 465 (1036)
T PLN02316 434 QIYRKLQEERRLREEAIRAKAEKTARMKAEMK 465 (1036)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 45677887777777766666666788888555
No 68
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=27.01 E-value=1.7e+02 Score=21.88 Aligned_cols=34 Identities=24% Similarity=0.356 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHH---HHHHHHhhh
Q 018470 118 VQVLQAQLLQLRSEQKELKKMMKEK---KAQIKTTMK 151 (355)
Q Consensus 118 ~e~L~~qL~q~r~eekelKk~~K~e---ka~lKa~~~ 151 (355)
+..|++||.++..-=+|+|.-.+++ -+-|+-+-+
T Consensus 3 ~~~l~~ql~~l~~~l~elk~~l~~Q~kE~~~LRntI~ 39 (45)
T PF11598_consen 3 DSQLIKQLSELNQMLQELKELLRQQIKETRFLRNTIM 39 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567778887777777777777776 355665555
No 69
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=26.82 E-value=75 Score=30.77 Aligned_cols=35 Identities=23% Similarity=0.310 Sum_probs=27.4
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
.+..-+-+.+|-|+-|+--+|.|++.|+||.++..
T Consensus 87 F~~i~~~~~~~~e~kK~~s~eEKk~~K~ek~~~e~ 121 (215)
T cd00660 87 FTPIYQYFEEEKEKKKAMSKEEKKAIKEEKEKLEE 121 (215)
T ss_pred CHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhc
Confidence 46677788888888887788888888888877776
No 70
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=25.59 E-value=81 Score=30.52 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=27.4
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
.+..-+-+.+|-|+-|+--+|.|++.|+||.++..
T Consensus 87 F~~i~~~~~~~~e~kK~~tkeEKk~~K~ek~~~e~ 121 (215)
T cd03488 87 FTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEE 121 (215)
T ss_pred CHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhc
Confidence 45667778888888888788888888888877776
No 71
>PF08257 Sulfakinin: Sulfakinin family; InterPro: IPR013259 The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects. For most species there is the potential for producing two sulfakinin peptides, one has a short sulfakinin sequence. The function of the sulfakinins is difficult to assess. For the Periplaneta americana (American cockroach), various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart. In Calliphora vomitoria (Blue blowfly) the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia. In adults of Penaeus monodon (Penoeid shrimp) they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia [].
Probab=25.58 E-value=30 Score=18.16 Aligned_cols=9 Identities=44% Similarity=1.106 Sum_probs=7.1
Q ss_pred cccccccee
Q 018470 50 FSDCGHQQY 58 (355)
Q Consensus 50 F~D~ghl~y 58 (355)
|-|-||.||
T Consensus 1 f~dyghmrf 9 (9)
T PF08257_consen 1 FDDYGHMRF 9 (9)
T ss_pred CCccccccC
Confidence 678899875
No 72
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=25.31 E-value=1.3e+02 Score=22.13 Aligned_cols=44 Identities=16% Similarity=0.259 Sum_probs=28.4
Q ss_pred ccccCCcCCc--ccc-----chhhhhHHHHHHHHHHHHhhHHHHHHHHHHH
Q 018470 97 LEAFGNEDAS--SLR-----NEERISEAVQVLQAQLLQLRSEQKELKKMMK 140 (355)
Q Consensus 97 ~~~~g~~~d~--~l~-----~~~~~sea~e~L~~qL~q~r~eekelKk~~K 140 (355)
+.++||..+- .++ ++....+..++|..+++++...-.++.+.++
T Consensus 10 ~r~lGfsL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~~~~ 60 (65)
T PF09278_consen 10 LRELGFSLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQALRA 60 (65)
T ss_dssp HHHTT--HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6677777542 122 2556677777888888888888887776554
No 73
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=24.80 E-value=1.7e+02 Score=33.08 Aligned_cols=19 Identities=26% Similarity=0.190 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHhhhhc
Q 018470 135 LKKMMKEKKAQIKTTMKER 153 (355)
Q Consensus 135 lKk~~K~eka~lKa~~~~~ 153 (355)
+|||.|||...+|.+|++.
T Consensus 444 ~kkq~ke~~~r~k~~k~~~ 462 (763)
T TIGR00993 444 QKKQWREELKRMKMMKKFG 462 (763)
T ss_pred HHHHHHHHHHHHHHHHhhc
Confidence 7999999999999987743
No 74
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=24.48 E-value=1.2e+02 Score=30.94 Aligned_cols=57 Identities=18% Similarity=0.126 Sum_probs=33.9
Q ss_pred CcccccccCCcCCccccchhhhhHHHHHHHHHHHHhhH-HHHHHHHHHHHHH--HHHHHhhhhccCCCC
Q 018470 93 DLLPLEAFGNEDASSLRNEERISEAVQVLQAQLLQLRS-EQKELKKMMKEKK--AQIKTTMKERKGNRK 158 (355)
Q Consensus 93 dl~~~~~~g~~~d~~l~~~~~~sea~e~L~~qL~q~r~-eekelKk~~K~ek--a~lKa~~~~~~~~~e 158 (355)
-|..-.+||..+++ |..+.+|.++|+||+ +..+.+..++.-. +.+--.+|.-|..|.
T Consensus 134 ~l~~~E~LG~eG~V---------eeaq~~~~e~E~lk~~e~e~~~~~~~~~~~~~~~~~qkl~VCeVCG 193 (319)
T KOG0796|consen 134 LLEKAEELGEEGNV---------EEAQKAMKEVEELKAKEKEEAEESYNTTMPGASAQQQKLRVCEVCG 193 (319)
T ss_pred HHHHHHHHhhcCCH---------HHHHHHHHHHHHHHHHHHHHHHHHHccCcchhhhhhhhhhHHHhhh
Confidence 34445556666666 566788999999998 4444444444331 222334566677773
No 75
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=24.02 E-value=1.2e+02 Score=27.30 Aligned_cols=52 Identities=15% Similarity=0.043 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCcccccccCCcCCc--cccc----h-h-hhhHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 83 KLKFMKRLSSDLLPLEAFGNEDAS--SLRN----E-E-RISEAVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 83 k~k~lk~ls~dl~~~~~~g~~~d~--~l~~----~-~-~~sea~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
.+++++. |..+||..+- .+++ + . ...+-.++|.++++++..+-.+|++.++.
T Consensus 56 ~L~~I~~-------lr~lG~sL~eIk~ll~~~~~~~~~~~~~~~~ll~~k~~~l~~~I~~L~~~~~~ 115 (154)
T PRK15002 56 YVAIIKI-------AQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDE 115 (154)
T ss_pred HHHHHHH-------HHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556664 6777776442 1222 1 1 22344556666677777776666655544
No 76
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.69 E-value=1.3e+02 Score=26.38 Aligned_cols=29 Identities=17% Similarity=0.336 Sum_probs=21.6
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKE 141 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~ 141 (355)
...+..++|.++++++..+-.+|.+.+..
T Consensus 78 ~~~~~~~~l~~~~~~l~~~i~~L~~~~~~ 106 (140)
T PRK09514 78 TCQEVKGIVDEKLAEVEAKIAELQHMRRS 106 (140)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667788888888888888887766543
No 77
>PF08701 GN3L_Grn1: GNL3L/Grn1 putative GTPase; InterPro: IPR014813 Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA []. This family contains a potential nuclear localisation signal.
Probab=23.05 E-value=1.9e+02 Score=23.83 Aligned_cols=21 Identities=19% Similarity=0.205 Sum_probs=9.6
Q ss_pred HHHHHHhhHHHHHHHHHHHHH
Q 018470 122 QAQLLQLRSEQKELKKMMKEK 142 (355)
Q Consensus 122 ~~qL~q~r~eekelKk~~K~e 142 (355)
|.|+++.+....|.+.++++.
T Consensus 48 L~eie~~k~~~ee~k~~~ke~ 68 (79)
T PF08701_consen 48 LKEIEEKKERAEEEKEKQKEA 68 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444
No 78
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.88 E-value=1.2e+02 Score=24.21 Aligned_cols=20 Identities=35% Similarity=0.632 Sum_probs=15.4
Q ss_pred HHHHHHHhhHHHHHHHHHHH
Q 018470 121 LQAQLLQLRSEQKELKKMMK 140 (355)
Q Consensus 121 L~~qL~q~r~eekelKk~~K 140 (355)
|+.|+++++++=.+++++..
T Consensus 70 l~~~~~~l~~~l~~l~~~~~ 89 (91)
T cd04766 70 LEEELAELRAELDELRARLR 89 (91)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 88888888888888776543
No 79
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=22.71 E-value=1.1e+02 Score=29.75 Aligned_cols=35 Identities=20% Similarity=0.149 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 114 ISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 114 ~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
.+..-+-+.+|-|+-|+--+|.|++.|+||.++..
T Consensus 86 F~~i~~~~~~~ke~kK~~tkeEKk~~K~ek~~~e~ 120 (217)
T cd03490 86 FSLIKNHLEEEKEKKKNLNKEEKEAKKKERAKREY 120 (217)
T ss_pred CHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhc
Confidence 45667777777777777777778888888777766
No 80
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=21.92 E-value=2.1e+02 Score=22.73 Aligned_cols=36 Identities=25% Similarity=0.401 Sum_probs=19.8
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
.|.+-.+.|-.++..++.+.+.+.++.++-+++|++
T Consensus 66 ~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~ 101 (106)
T PF01920_consen 66 ELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYE 101 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444555555555555555555555555555554
No 81
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.75 E-value=1.2e+02 Score=24.68 Aligned_cols=80 Identities=21% Similarity=0.272 Sum_probs=43.6
Q ss_pred eeeeccc-cchhhcc---cccccccccceeccccccchhhhhhhhhhhhHhHHHHHHHHHHHhcCcccccccCCcCCc--
Q 018470 33 FRVSERT-RNSFRRL---SSRFSDCGHQQYYVSPRKETKKKEKEKSSEIKSVRKKLKFMKRLSSDLLPLEAFGNEDAS-- 106 (355)
Q Consensus 33 ~~v~~~~-r~~~~~~---~~~F~D~ghl~yy~~~~k~~~~k~k~k~~~~~s~kkk~k~lk~ls~dl~~~~~~g~~~d~-- 106 (355)
++|+-++ |+ +-+. ...-.+.+..+||...-= ..+++++. |..+||..+-
T Consensus 10 ~gvs~~tLRy-ye~~Gll~p~~~~~~gyR~Y~~~~l-----------------~~l~~I~~-------lr~~G~~l~~I~ 64 (96)
T cd04768 10 AGVSIRTLRH-YDDIGLFKPAKIAENGYRYYSYAQL-----------------YQLQFILF-------LRELGFSLAEIK 64 (96)
T ss_pred HCcCHHHHHH-HHHCCCCCCCccCCCCeeeCCHHHH-----------------HHHHHHHH-------HHHcCCCHHHHH
Confidence 4566666 54 2222 222346778888876422 23345553 5566666332
Q ss_pred cccchhhhhHHHHHHHHHHHHhhHHHHHHHHH
Q 018470 107 SLRNEERISEAVQVLQAQLLQLRSEQKELKKM 138 (355)
Q Consensus 107 ~l~~~~~~sea~e~L~~qL~q~r~eekelKk~ 138 (355)
.+++... .+..++|..++++++++-.+++..
T Consensus 65 ~~l~~~~-~~~~~~l~~~~~~l~~~i~~l~~~ 95 (96)
T cd04768 65 ELLDTEM-EELTAMLLEKKQAIQQKIDRLQQL 95 (96)
T ss_pred HHHhcCc-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 1222111 266777888888887777777653
No 82
>PF05501 DUF755: Domain of unknown function (DUF755) ; InterPro: IPR008474 This family is predominated by ORFs from Anelloviridae. The function of this family remains to be determined.
Probab=21.53 E-value=59 Score=28.58 Aligned_cols=15 Identities=73% Similarity=0.565 Sum_probs=6.3
Q ss_pred CCCCCCCCCCCCCCC
Q 018470 158 KSGSSSSSSSESSDS 172 (355)
Q Consensus 158 esssssSsssessds 172 (355)
.||||||++++||++
T Consensus 106 ~SSSSSSssssSSss 120 (123)
T PF05501_consen 106 SSSSSSSSSSSSSSS 120 (123)
T ss_pred CCCCCCCCCCCCCCC
Confidence 344444444444443
No 83
>KOG2138 consensus Predicted RNA binding protein, contains G-patch domain [RNA processing and modification]
Probab=21.45 E-value=81 Score=35.57 Aligned_cols=17 Identities=53% Similarity=0.483 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCCCCCCc
Q 018470 159 SGSSSSSSSESSDSDNG 175 (355)
Q Consensus 159 sssssSsssessds~c~ 175 (355)
.--++|||++|||++=.
T Consensus 841 rk~kkSss~~Ssd~sdk 857 (883)
T KOG2138|consen 841 RKPKKSSSSESSDSSDK 857 (883)
T ss_pred cCccccccccccccchh
Confidence 33466888888877643
No 84
>KOG0416 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=1.6e+02 Score=28.06 Aligned_cols=40 Identities=23% Similarity=0.242 Sum_probs=19.2
Q ss_pred ccccccccCCCcccceeecccccceeeeeccccchhhccccccc
Q 018470 8 QRFLPCIPSDTGDRFPIKYHLGFGDFRVSERTRNSFRRLSSRFS 51 (355)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~r~~~~~~~~~F~ 51 (355)
+-|.-||-|-... +|+=|+=+.+|-+=.-+-|.-=+-||-
T Consensus 30 ~ef~V~f~GP~ds----~YegGvWkv~V~lPd~YP~KSPSIGFv 69 (189)
T KOG0416|consen 30 QEFYVKFHGPKDS----PYEGGVWKVRVELPDNYPFKSPSIGFV 69 (189)
T ss_pred cEEEEEeeCCCCC----cccCceEEEEEECCCCCCCCCCcccce
Confidence 3455555443331 344455555555555554444444554
No 85
>PHA00727 hypothetical protein
Probab=21.15 E-value=1.1e+02 Score=29.86 Aligned_cols=31 Identities=26% Similarity=0.416 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 018470 117 AVQVLQAQLLQLRSEQKELKKMMKEKKAQIK 147 (355)
Q Consensus 117 a~e~L~~qL~q~r~eekelKk~~K~eka~lK 147 (355)
-.|+-.+|++|+++|--..||+.|.||+-.+
T Consensus 51 efelk~~qf~qlkael~kkkkk~kkekvdv~ 81 (278)
T PHA00727 51 EFELKKQQFEQLKAELSKKKKKFKKEKVDVR 81 (278)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhccee
Confidence 3578889999999998888887777765443
No 86
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=21.10 E-value=2.5e+02 Score=26.37 Aligned_cols=39 Identities=18% Similarity=0.335 Sum_probs=20.9
Q ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Q 018470 113 RISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKTTMK 151 (355)
Q Consensus 113 ~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa~~~ 151 (355)
++.++.++..+-+++.+..+++++++.++-+..|++.++
T Consensus 136 ~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei~~~~~ 174 (176)
T PF12999_consen 136 IYKEGLKIRQELIEEAKKKREELEKKLEELEKEIQAAKQ 174 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344444444444455555555555555555666666554
No 87
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=20.73 E-value=1.5e+02 Score=27.14 Aligned_cols=41 Identities=12% Similarity=-0.040 Sum_probs=29.2
Q ss_pred ccchhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 018470 108 LRNEERISEAVQVLQAQLLQLRSEQKELKKMMKEKKAQIKT 148 (355)
Q Consensus 108 l~~~~~~sea~e~L~~qL~q~r~eekelKk~~K~eka~lKa 148 (355)
|+-.+.=-.|++..++++++.|+++......++++-.++|.
T Consensus 30 LiPkglAv~At~~n~~~~e~~r~~~e~~~~~~~~~a~~lk~ 70 (148)
T COG0359 30 LIPKGLAVPATKGNLKLLEARRAKLEKKAAEELAEAEALKE 70 (148)
T ss_pred hccccchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455666789999999999777777666666666555554
No 88
>PF06991 Prp19_bind: Splicing factor, Prp19-binding domain; InterPro: IPR009730 This entry represents the C terminus (approximately 300 residues) of eukaryotic micro-fibrillar-associated protein 1, which is a component of elastin-associated microfibrils in the extracellular matrix [].
Probab=20.23 E-value=61 Score=32.06 Aligned_cols=16 Identities=44% Similarity=0.522 Sum_probs=8.3
Q ss_pred CCCCCCCCCCCCCccc
Q 018470 162 SSSSSSESSDSDNGDV 177 (355)
Q Consensus 162 ssSsssessds~c~~V 177 (355)
+||++++|||||=+.+
T Consensus 19 esse~Ee~SdSEde~~ 34 (276)
T PF06991_consen 19 ESSEEEESSDSEDEEE 34 (276)
T ss_pred cccccccccccccccc
Confidence 3444555666665533
Done!