Query 032568
Match_columns 138
No_of_seqs 109 out of 247
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 03:08:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032568.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032568hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2351 RNA polymerase II, fou 100.0 1.7E-44 3.8E-49 258.6 11.1 134 1-138 1-134 (134)
2 COG5250 RPB4 RNA polymerase II 100.0 1.1E-34 2.3E-39 206.8 11.5 133 3-138 4-138 (138)
3 smart00657 RPOL4c DNA-directed 100.0 5E-32 1.1E-36 194.8 12.4 118 16-138 1-118 (118)
4 PRK14981 DNA-directed RNA poly 100.0 1.6E-30 3.4E-35 185.7 11.1 111 14-136 2-112 (112)
5 PF03874 RNA_pol_Rpb4: RNA pol 99.9 2.7E-27 5.9E-32 168.7 10.4 110 23-135 1-117 (117)
6 COG1460 Uncharacterized protei 99.8 9.5E-20 2.1E-24 129.6 10.2 111 14-136 3-113 (114)
7 KOG4168 Predicted RNA polymera 98.9 8.1E-09 1.8E-13 76.3 7.4 113 20-134 7-130 (149)
8 PF06569 DUF1128: Protein of u 78.9 4.8 0.0001 26.6 4.2 41 95-136 31-71 (71)
9 COG4840 Uncharacterized protei 63.4 8.4 0.00018 25.2 2.6 36 100-136 36-71 (71)
10 COG4800 Predicted transcriptio 55.2 24 0.00053 26.5 4.2 54 75-136 19-72 (170)
11 PF02022 Integrase_Zn: Integra 53.0 12 0.00027 21.8 1.9 23 78-100 13-35 (40)
12 PF11829 DUF3349: Protein of u 48.1 72 0.0016 22.2 5.4 79 52-133 2-87 (96)
13 COG4778 PhnL ABC-type phosphon 44.4 66 0.0014 25.4 5.2 48 50-101 86-152 (235)
14 TIGR01878 cas_Csa5 CRISPR-asso 42.6 15 0.00032 25.7 1.3 68 55-132 4-78 (97)
15 PF04282 DUF438: Family of unk 42.4 55 0.0012 21.5 3.9 37 60-97 21-57 (71)
16 COG4545 Glutaredoxin-related p 42.1 8.6 0.00019 25.9 0.0 18 95-113 9-26 (85)
17 PF06207 DUF1002: Protein of u 39.2 45 0.00098 26.5 3.7 45 93-137 165-210 (225)
18 COG1378 Predicted transcriptio 34.9 55 0.0012 26.2 3.6 32 75-106 3-37 (247)
19 KOG4465 Uncharacterized conser 33.1 58 0.0013 28.4 3.6 66 21-86 246-311 (598)
20 PF11459 DUF2893: Protein of u 32.9 54 0.0012 21.4 2.7 39 93-135 9-49 (69)
21 cd08315 Death_TRAILR_DR4_DR5 D 32.6 1.6E+02 0.0035 20.0 6.2 74 53-134 4-77 (96)
22 PF10975 DUF2802: Protein of u 32.5 43 0.00092 21.7 2.2 37 52-97 31-67 (70)
23 PHA00542 putative Cro-like pro 32.2 1.5E+02 0.0031 19.4 4.8 56 76-137 22-77 (82)
24 PF12162 STAT1_TAZ2bind: STAT1 31.8 32 0.00069 17.8 1.2 14 95-108 5-18 (23)
25 smart00341 HRDC Helicase and R 31.0 85 0.0018 19.7 3.5 47 85-135 29-75 (81)
26 PF08328 ASL_C: Adenylosuccina 31.0 1.3E+02 0.0027 21.7 4.5 43 58-101 71-113 (115)
27 PF07299 FBP: Fibronectin-bind 30.5 37 0.0008 26.8 1.9 71 52-134 8-78 (208)
28 PF01381 HTH_3: Helix-turn-hel 30.5 30 0.00065 20.2 1.2 48 77-131 1-48 (55)
29 PF00570 HRDC: HRDC domain Blo 30.1 38 0.00082 20.8 1.6 23 86-108 27-49 (68)
30 PF00619 CARD: Caspase recruit 28.7 1.6E+02 0.0034 18.6 5.1 52 77-133 22-73 (85)
31 PF12763 EF-hand_4: Cytoskelet 28.4 42 0.0009 23.4 1.7 40 60-99 11-53 (104)
32 PF04552 Sigma54_DBD: Sigma-54 27.8 90 0.0019 23.4 3.6 32 104-136 108-148 (160)
33 PRK11239 hypothetical protein; 27.3 3.2E+02 0.0069 21.7 7.7 48 83-133 92-142 (215)
34 PRK12402 replication factor C 27.1 1.9E+02 0.0041 23.0 5.6 58 72-129 188-247 (337)
35 cd07921 PCA_45_Doxase_A_like S 26.8 1.1E+02 0.0023 21.7 3.5 28 69-96 24-55 (106)
36 PRK09726 antitoxin HipB; Provi 26.7 73 0.0016 20.9 2.6 54 71-131 11-64 (88)
37 TIGR01128 holA DNA polymerase 26.6 2.5E+02 0.0054 21.9 6.2 68 65-132 108-179 (302)
38 TIGR02498 type_III_ssaH type I 26.0 2.1E+02 0.0046 19.2 5.0 56 54-109 21-78 (79)
39 PF12844 HTH_19: Helix-turn-he 25.8 1.5E+02 0.0034 17.6 4.6 49 76-131 3-51 (64)
40 cd07321 Extradiol_Dioxygenase_ 25.4 1.6E+02 0.0034 19.2 4.0 18 79-96 28-45 (77)
41 PRK07168 bifunctional uroporph 25.4 60 0.0013 28.5 2.5 57 67-131 412-469 (474)
42 PF15076 DUF4543: Domain of un 25.0 1.2E+02 0.0025 19.9 3.2 30 23-52 8-37 (75)
43 PF13443 HTH_26: Cro/C1-type H 24.4 1.6E+02 0.0035 17.4 3.8 49 77-131 2-50 (63)
44 cd07923 Gallate_dioxygenase_C 24.3 1.4E+02 0.0031 20.6 3.7 27 70-96 17-47 (94)
45 cd08325 CARD_CASP1-like Caspas 24.2 2.2E+02 0.0047 18.7 4.8 40 77-116 22-61 (83)
46 PF03701 UPF0181: Uncharacteri 24.2 1.3E+02 0.0029 18.5 3.2 24 71-95 14-37 (51)
47 PF07746 LigA: Aromatic-ring-o 24.1 1E+02 0.0023 20.9 3.0 17 79-95 23-39 (88)
48 PF12125 Beta-TrCP_D: D domain 24.1 91 0.002 18.3 2.3 31 62-94 1-31 (40)
49 COG3612 Uncharacterized protei 24.0 1.7E+02 0.0037 22.0 4.4 42 53-94 91-132 (157)
50 KOG4646 Uncharacterized conser 23.6 74 0.0016 24.1 2.4 17 85-101 73-89 (173)
51 PF06287 DUF1039: Protein of u 23.1 2E+02 0.0043 18.7 4.0 56 54-109 8-65 (66)
52 cd08784 Death_DRs Death Domain 23.1 2.2E+02 0.0048 18.4 4.6 55 77-133 14-68 (79)
53 PF10041 DUF2277: Uncharacteri 22.7 1.3E+02 0.0028 20.2 3.2 27 46-72 12-38 (78)
54 PF09868 DUF2095: Uncharacteri 22.0 96 0.0021 22.6 2.6 6 59-64 68-73 (128)
55 cd04777 HTH_MerR-like_sg1 Heli 21.9 1.3E+02 0.0028 20.4 3.2 47 89-136 4-53 (107)
56 PF13812 PPR_3: Pentatricopept 21.7 1.3E+02 0.0027 15.1 2.7 26 62-87 8-33 (34)
57 cd07925 LigA_like_1 The A subu 21.3 1.6E+02 0.0035 20.9 3.6 16 79-94 38-53 (106)
58 PF09999 DUF2240: Uncharacteri 21.2 2.6E+02 0.0057 20.7 4.9 73 20-92 30-126 (144)
59 PRK10945 gene expression modul 21.0 2.6E+02 0.0056 18.5 4.3 35 57-92 7-41 (72)
60 PF06603 UpxZ: UpxZ family of 21.0 1.2E+02 0.0025 21.6 2.8 32 61-93 23-54 (106)
61 PF08920 SF3b1: Splicing facto 21.0 42 0.0009 25.0 0.6 15 115-129 83-97 (144)
62 PRK04081 hypothetical protein; 21.0 58 0.0013 25.7 1.4 36 93-130 62-97 (207)
63 COG0789 SoxR Predicted transcr 20.9 1.1E+02 0.0023 20.9 2.7 46 89-135 4-54 (124)
64 PF02845 CUE: CUE domain; Int 20.3 1.6E+02 0.0035 16.5 3.0 20 102-128 5-24 (42)
65 PRK06424 transcription factor; 20.1 3.3E+02 0.0072 20.0 5.3 50 75-131 87-136 (144)
66 COG4003 Uncharacterized protei 20.1 1.1E+02 0.0024 21.1 2.4 46 58-110 37-85 (98)
67 TIGR03070 couple_hipB transcri 20.1 1E+02 0.0022 17.6 2.1 50 75-131 5-54 (58)
No 1
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=100.00 E-value=1.7e-44 Score=258.65 Aligned_cols=134 Identities=51% Similarity=0.844 Sum_probs=127.4
Q ss_pred CChhhhhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q 032568 1 MSGEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREI 80 (138)
Q Consensus 1 ~~~~~~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~l 80 (138)
|++++||||++|+||++|..+.||++|||+.+|+++..++++ +.|+..+++.||.+|+.|+++||+|++++++.+||.+
T Consensus 1 ~~g~~EEdAa~lk~g~EFe~~~~L~~sEa~lllE~~~~q~~r-s~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~i 79 (134)
T KOG2351|consen 1 PRGEEEEDAAELKLGKEFETADALMLSEARLLLEHRLEQRRR-SEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRTI 79 (134)
T ss_pred CcchhhccHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHhh-cccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 578999999999999999999999999999999999987754 5677889999999999999999999999999999999
Q ss_pred HHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568 81 LSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 138 (138)
Q Consensus 81 l~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~ 138 (138)
|+..|||+||+|||+||||+|++|||+|||||++| + +|+.|++||+.|+..|+|+
T Consensus 80 Ls~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nk--i-dD~~le~iL~dls~lr~fq 134 (134)
T KOG2351|consen 80 LSGKGLHKFEVAQLGNLCPETAEEAKALVPSLENK--I-DDDELEQILKDLSTLRTFQ 134 (134)
T ss_pred HhhCCcchhhHHHHhccCcccHHHHHHhccccccc--c-CHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999964 5 9999999999999999996
No 2
>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]
Probab=100.00 E-value=1.1e-34 Score=206.79 Aligned_cols=133 Identities=32% Similarity=0.563 Sum_probs=119.0
Q ss_pred hhhhhhhhccccCccccccccccHHHHHHHHHHHHHHhhhcCCCCCc--chhHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q 032568 3 GEEEENAAELKIGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMN--QVSQVFEKSLQYVKRFSRYKNPDAVRQVREI 80 (138)
Q Consensus 3 ~~~~e~~~~l~lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~--~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~l 80 (138)
++.||||++||+|++|+|..+|++||++.+++....++++.....+. +...++++|+.|++.||+|++.+.+.+++.+
T Consensus 4 ~~~ee~aa~lklg~efe~ed~l~lsEAr~lie~~l~~rrretn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~~~~ 83 (138)
T COG5250 4 AIFEEDAAQLKLGPEFENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALRTT 83 (138)
T ss_pred hHhhhhHHHhhcCccccchHHHHHHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 57899999999999999999999999999999988776432222122 3344699999999999999999999999999
Q ss_pred HHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568 81 LSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 138 (138)
Q Consensus 81 l~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~ 138 (138)
|+..|+|+||+||+++|||+|++|||+|||||.+| + +|..+|.||++++.+|+|+
T Consensus 84 L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk--i-dD~~lq~ilkels~l~~~~ 138 (138)
T COG5250 84 LSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK--I-DDAILQAILKELSLLRKFQ 138 (138)
T ss_pred HccCCcchhhHHHhhccccccHHHHHhhccccccc--c-cHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999964 6 9999999999999999996
No 3
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=99.98 E-value=5e-32 Score=194.79 Aligned_cols=118 Identities=42% Similarity=0.715 Sum_probs=106.2
Q ss_pred ccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHh
Q 032568 16 DEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLG 95 (138)
Q Consensus 16 ~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~ 95 (138)
++|.|++||||+||+.||+.++... .+.++..+++.++++|++|+++|+++++++++.++++.|+.++|++||++||+
T Consensus 1 ~~f~~a~~L~n~Ev~~ll~~k~~~~--~~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~ 78 (118)
T smart00657 1 PEFKNATCLTNSEVQLLLELKRQSK--ESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQLG 78 (118)
T ss_pred CCccchhHhHHHHHHHHHHHHHHhh--ccccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 3699999999999999999754322 23344557899999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhcC
Q 032568 96 NLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 138 (138)
Q Consensus 96 NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f~ 138 (138)
||||+|++||++||||++. |+ +++++++||++|+++|.|+
T Consensus 79 Nl~P~s~~E~~~lI~sl~~--r~-~ee~l~~iL~~i~~~~~~~ 118 (118)
T smart00657 79 NLRPETAEEAQLLIPSLEE--RI-DEEELEELLDDLSSLLPFY 118 (118)
T ss_pred CCCCCCHHHHHHHhhhhhc--cC-CHHHHHHHHHHHHHhcCCC
Confidence 9999999999999999984 56 9999999999999999985
No 4
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=99.97 E-value=1.6e-30 Score=185.74 Aligned_cols=111 Identities=23% Similarity=0.369 Sum_probs=101.5
Q ss_pred cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568 14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV 93 (138)
Q Consensus 14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~ 93 (138)
+|++..+.+|||++||+.||+++..++ ++++++++|++|+++|+++++.++.+.+++++...+|++|++++
T Consensus 2 i~k~i~~e~~lt~sEa~~iL~~~~~~~---------els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~ 72 (112)
T PRK14981 2 IGKKILEEEYITIAEAKEILSEIEEER---------ELSYELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVK 72 (112)
T ss_pred chhhhhhcccccHHHHHHHHHHHHhcc---------chhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHH
Confidence 477788999999999999999987532 78999999999999999999888999999999988899999999
Q ss_pred HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568 94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 136 (138)
Q Consensus 94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~ 136 (138)
|+||||+|+||||+||||++. ++ ++++|++||++|++||.
T Consensus 73 I~nL~P~~~dElrai~~~~~~--~~-~~e~l~~ILd~l~k~~~ 112 (112)
T PRK14981 73 IADILPETRDELRAIFAKERY--TL-SPEELDEILDIVKKYRE 112 (112)
T ss_pred HHhcCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhhC
Confidence 999999999999999999952 44 99999999999999973
No 5
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=99.95 E-value=2.7e-27 Score=168.70 Aligned_cols=110 Identities=33% Similarity=0.600 Sum_probs=93.4
Q ss_pred cccHHHHHHHHHHHHHHhhhcC-------CCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHh
Q 032568 23 CLMNCEVAIILDHKYEQLQQTS-------DDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLG 95 (138)
Q Consensus 23 ~Ls~~EV~~iL~~~~~~~~~~~-------~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~ 95 (138)
||||+||..+|+++.+..+..+ .++..+.+.++++|++|+++|+++++++++..+++.|..+||+++|++||+
T Consensus 1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~ 80 (117)
T PF03874_consen 1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQII 80 (117)
T ss_dssp EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHh
Confidence 7999999999997665443221 134568899999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhh
Q 032568 96 NLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 135 (138)
Q Consensus 96 NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r 135 (138)
|+||+|++|+++|||+++. |+ ++++|++||++|++||
T Consensus 81 Nl~P~~~~El~~ii~~~~~--r~-~ee~l~~iL~~v~~~~ 117 (117)
T PF03874_consen 81 NLRPTTAVELRAIIESLES--RF-SEEDLEEILDLVSKYR 117 (117)
T ss_dssp HH--SSHHHHHHHSTTGTT--TS-THHHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhC
Confidence 9999999999999999984 66 9999999999999997
No 6
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.82 E-value=9.5e-20 Score=129.59 Aligned_cols=111 Identities=21% Similarity=0.347 Sum_probs=98.7
Q ss_pred cCccccccccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568 14 IGDEFLKAKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCV 93 (138)
Q Consensus 14 lG~~f~~~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~ 93 (138)
+|+..-+.+++|++||+.||.++.. +.++++.++.||+|+++|+++.+.++.+.+.++++-.++.+.-++.
T Consensus 3 i~k~~le~~yiti~Eak~il~~~~~---------~~eL~y~~~~al~y~~kFakldpe~a~e~veEL~~i~~~~e~~avk 73 (114)
T COG1460 3 IGKKILEEKYITISEAKKILSKVER---------EEELTYEQREALEYAEKFAKLDPEKARELVEELLSIVKMSEKIAVK 73 (114)
T ss_pred hHHHHhhccCccHHHHHHHHHHhcc---------cccchHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhccccHHHHHH
Confidence 4566668899999999999999721 4478999999999999999999888888999999988899999999
Q ss_pred HhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568 94 LGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 136 (138)
Q Consensus 94 l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~ 136 (138)
|+++||+|.+|+|+++.+-.- .+ ++++++.||+.+.+||.
T Consensus 74 IadI~P~t~~ElRsIla~e~~--~~-s~E~l~~Ildiv~Ky~~ 113 (114)
T COG1460 74 IADIMPRTPDELRSILAKERV--ML-SDEELDKILDIVDKYRE 113 (114)
T ss_pred HHHhCCCCHHHHHHHHHHccC--CC-CHHHHHHHHHHHHHHhc
Confidence 999999999999999997762 45 99999999999999984
No 7
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=98.88 E-value=8.1e-09 Score=76.28 Aligned_cols=113 Identities=19% Similarity=0.278 Sum_probs=88.2
Q ss_pred ccccccHHHHHHHHHHHHHHhh-----hcCCC----CCcchhHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHhcCCCH
Q 032568 20 KAKCLMNCEVAIILDHKYEQLQ-----QTSDD----PMNQVSQVFEKSLQYVKRFS--RYKNPDAVRQVREILSRYQLAE 88 (138)
Q Consensus 20 ~~~~Ls~~EV~~iL~~~~~~~~-----~~~~~----~~~~~~~~~~kTl~Yl~~Fs--~~~~~e~~~~v~~ll~~~~l~~ 88 (138)
....||++||...|.+..+... .-+.. +-.+++.+.+.|++|++.-. .-.+++.+-.+.--+..+||++
T Consensus 7 r~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~~fkLtK 86 (149)
T KOG4168|consen 7 RNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLKSFKLTK 86 (149)
T ss_pred hHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhccccchH
Confidence 4568999999999988762211 00000 01237889999999999864 3456677777777778899999
Q ss_pred hHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhh
Q 032568 89 FELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI 134 (138)
Q Consensus 89 ~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~ 134 (138)
.|+.+|.|+.|.++-|...+|...++ |+.++++|.+++..++++
T Consensus 87 AE~LqiiN~rPss~vel~~~iE~~ee--Rf~~ee~i~elv~~i~~~ 130 (149)
T KOG4168|consen 87 AEILQIINLRPSSSVELYLIIEEVEE--RFQDEEDIEELVETISKT 130 (149)
T ss_pred HHHHHHhccCcchHHHHHHHHHHHHH--hccchhcHHHHHHhcccc
Confidence 99999999999999999999999984 676999999999988764
No 8
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=78.90 E-value=4.8 Score=26.59 Aligned_cols=41 Identities=10% Similarity=0.258 Sum_probs=33.8
Q ss_pred hcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568 95 GNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 136 (138)
Q Consensus 95 ~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~ 136 (138)
-++-....++++-|..-...|++| |..+++.|.++|-++|+
T Consensus 31 ~~f~~~~yedl~diy~~V~~K~~f-S~sEm~aI~~ELG~LRK 71 (71)
T PF06569_consen 31 EDFSEEKYEDLKDIYEMVMSKDSF-SPSEMQAIAEELGQLRK 71 (71)
T ss_pred HhCChhhHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHhhcC
Confidence 345566788888888877777666 99999999999999996
No 9
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.38 E-value=8.4 Score=25.21 Aligned_cols=36 Identities=11% Similarity=0.280 Sum_probs=29.9
Q ss_pred CCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568 100 ETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 136 (138)
Q Consensus 100 ~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~ 136 (138)
...+++.-|.-..++|+++ |..+++.|-+.|..+|+
T Consensus 36 ~~~edLtdiy~mvkkkenf-SpsEmqaiA~eL~rlRk 71 (71)
T COG4840 36 ANYEDLTDIYDMVKKKENF-SPSEMQAIADELGRLRK 71 (71)
T ss_pred ccHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhhC
Confidence 3466777788877777777 99999999999999986
No 10
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=55.25 E-value=24 Score=26.50 Aligned_cols=54 Identities=11% Similarity=0.204 Sum_probs=38.4
Q ss_pred HHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568 75 RQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 136 (138)
Q Consensus 75 ~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~ 136 (138)
+-+..+|...|||..|.+..+|+-|.|.- -++.. +-+--+.|-+|+..|.+|.+
T Consensus 19 ~~l~~~l~Elglt~~eFak~anIP~StLY---Kil~G-----~dpr~~tl~~I~ktir~~ek 72 (170)
T COG4800 19 SCLQKLLDELGLTPSEFAKRANIPLSTLY---KILKG-----SDPRYDTLTRIFKTIRSYEK 72 (170)
T ss_pred HHHHHHHHHcCCCHHHHHHHcCCCHHHHH---HHHhC-----CCccHHHHHHHHHHHHHHHh
Confidence 44566777799999999999999987743 23332 22355778888888877754
No 11
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=52.98 E-value=12 Score=21.78 Aligned_cols=23 Identities=13% Similarity=0.436 Sum_probs=17.0
Q ss_pred HHHHHhcCCCHhHHHHHhcCCCC
Q 032568 78 REILSRYQLAEFELCVLGNLCPE 100 (138)
Q Consensus 78 ~~ll~~~~l~~~E~a~l~NL~P~ 100 (138)
+.|-..||++..++-+|+|-||.
T Consensus 13 ~~L~~~f~ip~~vAk~IV~~C~~ 35 (40)
T PF02022_consen 13 KALRHKFGIPRLVAKQIVNQCPK 35 (40)
T ss_dssp HHHHHHHT--HHHHHHHHHHSCC
T ss_pred HHHHHHHccCHHHHHHHHHHCHH
Confidence 34445899999999999999996
No 12
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=48.13 E-value=72 Score=22.15 Aligned_cols=79 Identities=13% Similarity=0.197 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHHh-hcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcCC------CCCHHHHHhhcccccccCCCCCHHHH
Q 032568 52 SQVFEKSLQYVKR-FSRYKNPDAVRQVREILSRYQLAEFELCVLGNLC------PETVEEAIAMVPSIKTRGRAHDDEAI 124 (138)
Q Consensus 52 ~~~~~kTl~Yl~~-Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~------P~t~eEar~Lipsl~~k~r~~~de~L 124 (138)
+..+.+.+++++. |..-=+...---+..+|.+- |++.|+.+++.-. |.|..++...|-.... ...++++|
T Consensus 2 ~~~l~~iv~WLRaGYP~GvP~~Dy~PLlALL~r~-Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt~--~~P~~~di 78 (96)
T PF11829_consen 2 PSFLASIVDWLRAGYPEGVPPTDYVPLLALLRRR-LTDDEVAEVAAELAARGDPPVDRIDIGVAITRVTD--ELPTPEDI 78 (96)
T ss_dssp HHHHHHHHHHHHHH-TT-B-HHHHHHHHHHHTTT-S-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHHHCS--S-S-HHHH
T ss_pred ChHHHHHHHHHHccCCCCCCCCccHHHHHHhccc-CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHc--CCcCHHHH
Confidence 4556677777776 33322344445566677664 8998888776433 5588899999988874 35689999
Q ss_pred HHHHHHHHh
Q 032568 125 EKMLNDLSL 133 (138)
Q Consensus 125 ~~IL~~l~~ 133 (138)
..+..-|+.
T Consensus 79 ~RV~~~Laa 87 (96)
T PF11829_consen 79 ERVRARLAA 87 (96)
T ss_dssp HHHHHHHHT
T ss_pred HHHHHHHHh
Confidence 998877753
No 13
>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=44.41 E-value=66 Score=25.45 Aligned_cols=48 Identities=31% Similarity=0.425 Sum_probs=30.3
Q ss_pred chhHHHHHHHHHHHhhcCCCC-------------------HHHHHHHHHHHHhcCCCHhHHHHHhcCCCCC
Q 032568 50 QVSQVFEKSLQYVKRFSRYKN-------------------PDAVRQVREILSRYQLAEFELCVLGNLCPET 101 (138)
Q Consensus 50 ~~~~~~~kTl~Yl~~Fs~~~~-------------------~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t 101 (138)
+.-.+-++|+-||+.|-+.-+ ..+....+.+|.+.++.+. |..|.|.|
T Consensus 86 ~vl~vRr~TiGyVSQFLRviPRV~aLdVvaePll~~gv~~~~a~~~a~~Ll~rLnlper----LW~LaPaT 152 (235)
T COG4778 86 EVLEVRRTTIGYVSQFLRVIPRVSALDVVAEPLLARGVPREVARAKAADLLTRLNLPER----LWSLAPAT 152 (235)
T ss_pred HHHHHHHhhhHHHHHHHHhccCcchHHHHHhHHHHcCCCHHHHHHHHHHHHHHcCCCHH----HhcCCCcc
Confidence 344566789999999955322 2344555566666666543 66777766
No 14
>TIGR01878 cas_Csa5 CRISPR-associated protein, Csa5 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents a minor family of Cas protein found in the (all archaeal) APERN subtype of CRISPR/Cas locus, so the family is designated Csa5, for CRISPR/Cas Subtype Protein 5.
Probab=42.55 E-value=15 Score=25.67 Aligned_cols=68 Identities=19% Similarity=0.231 Sum_probs=37.7
Q ss_pred HHHHHHHHHhhcCCCCHHH-HHHHHHHHHhcCCCHhHHHHHhcCCCCC----H--HHHHhhcccccccCCCCCHHHHHHH
Q 032568 55 FEKSLQYVKRFSRYKNPDA-VRQVREILSRYQLAEFELCVLGNLCPET----V--EEAIAMVPSIKTRGRAHDDEAIEKM 127 (138)
Q Consensus 55 ~~kTl~Yl~~Fs~~~~~e~-~~~v~~ll~~~~l~~~E~a~l~NL~P~t----~--eEar~Lipsl~~k~r~~~de~L~~I 127 (138)
..++.-||.||+..-+++. ...+.+++..+.. +...+++.-+. . ..++.++|++ .++++++.+
T Consensus 4 ~~es~tyvDr~gnals~e~v~~aL~ea~R~~~s----~~~~a~~~~~gk~~~~kegk~~~~~~~l------ptdeeVe~f 73 (97)
T TIGR01878 4 YSESPTYVDRFGNALSKEAVEVALYEAQRILRS----IREGADIDIEGKRYMEKEGKNRILVGYL------PTDKEVEDF 73 (97)
T ss_pred ccCCchHHHHHHhhcCHHHHHHHHHHHHHHHHH----HHhhhhHHHHhHHHhhhcCcceeecCCC------CcHHHHHHH
Confidence 3567889999986555553 3355566654321 00022222111 1 1334666755 389999999
Q ss_pred HHHHH
Q 032568 128 LNDLS 132 (138)
Q Consensus 128 L~~l~ 132 (138)
+..+.
T Consensus 74 ~r~~~ 78 (97)
T TIGR01878 74 LRDVR 78 (97)
T ss_pred HHHhH
Confidence 98553
No 15
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=42.35 E-value=55 Score=21.47 Aligned_cols=37 Identities=16% Similarity=0.188 Sum_probs=25.4
Q ss_pred HHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcC
Q 032568 60 QYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNL 97 (138)
Q Consensus 60 ~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL 97 (138)
++.+.|+...+.+- ..++..|-..|++..|+-.|+|+
T Consensus 21 ~F~~~~~~Vs~~EI-~~~Eq~Li~eG~~~eeiq~LCdv 57 (71)
T PF04282_consen 21 EFKKLFSDVSASEI-SAAEQELIQEGMPVEEIQKLCDV 57 (71)
T ss_pred HHHHHHCCCCHHHH-HHHHHHHHHcCCCHHHHHHHhHH
Confidence 46667888865554 44444444478999999888875
No 16
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=42.06 E-value=8.6 Score=25.94 Aligned_cols=18 Identities=28% Similarity=0.724 Sum_probs=12.3
Q ss_pred hcCCCCCHHHHHhhccccc
Q 032568 95 GNLCPETVEEAIAMVPSIK 113 (138)
Q Consensus 95 ~NL~P~t~eEar~Lipsl~ 113 (138)
+|+||.++. |..-+.++.
T Consensus 9 sn~Cpdca~-a~eyl~rl~ 26 (85)
T COG4545 9 SNLCPDCAP-AVEYLERLN 26 (85)
T ss_pred cccCcchHH-HHHHHHHcC
Confidence 689998864 555555554
No 17
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=39.17 E-value=45 Score=26.52 Aligned_cols=45 Identities=22% Similarity=0.292 Sum_probs=36.1
Q ss_pred HHhcCCCCCHHHHHhhcccccccCCC-CCHHHHHHHHHHHHhhhhc
Q 032568 93 VLGNLCPETVEEAIAMVPSIKTRGRA-HDDEAIEKMLNDLSLIKKF 137 (138)
Q Consensus 93 ~l~NL~P~t~eEar~Lipsl~~k~r~-~~de~L~~IL~~l~~~r~f 137 (138)
+|+.-.|.|.++++.+|-..-....+ +++++++.|.+.+.++++-
T Consensus 165 ~va~~~~~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~~~~~~ 210 (225)
T PF06207_consen 165 EVAKQKPKTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMKKIQNL 210 (225)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHcC
Confidence 56788899999999999866543223 6999999999999998753
No 18
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=34.87 E-value=55 Score=26.19 Aligned_cols=32 Identities=28% Similarity=0.294 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCCHhHHH---HHhcCCCCCHHHHH
Q 032568 75 RQVREILSRYQLAEFELC---VLGNLCPETVEEAI 106 (138)
Q Consensus 75 ~~v~~ll~~~~l~~~E~a---~l~NL~P~t~eEar 106 (138)
..+.+.|+.+||++.|+- .|+.+.|-|+.|+-
T Consensus 3 ~~~~~~L~~lGlt~yEa~vY~aLl~~g~~tA~eis 37 (247)
T COG1378 3 EELEENLQKLGLTEYEAKVYLALLCLGEATAKEIS 37 (247)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHhCCccHHHHH
Confidence 356778888999988876 67777888888764
No 19
>KOG4465 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.06 E-value=58 Score=28.41 Aligned_cols=66 Identities=12% Similarity=0.114 Sum_probs=39.8
Q ss_pred cccccHHHHHHHHHHHHHHhhhcCCCCCcchhHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCC
Q 032568 21 AKCLMNCEVAIILDHKYEQLQQTSDDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQL 86 (138)
Q Consensus 21 ~~~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l 86 (138)
..-+|.-||+++=+-..+..-........-+...+.++++||+-+-+.++......|-.+++.+||
T Consensus 246 krkmsvee~aeve~l~d~kalkl~~teeklikeeqsralnllea~~klknek~e~~iiaai~~h~l 311 (598)
T KOG4465|consen 246 KRKMSVEEVAEVEELWDEKALKLETTEEKLIKEEQSRALNLLEAVEKLKNEKDEEEIIAAIEEHGL 311 (598)
T ss_pred hhhccHHHHHHHHHHHHhhhcCCCchHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHhhh
Confidence 345777777766444433221111111223456788999999999998887766666666655544
No 20
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=32.91 E-value=54 Score=21.43 Aligned_cols=39 Identities=18% Similarity=0.330 Sum_probs=28.3
Q ss_pred HHhcCCC--CCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhh
Q 032568 93 VLGNLCP--ETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 135 (138)
Q Consensus 93 ~l~NL~P--~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r 135 (138)
-+++..| .+.+||+.|+.++.+ +...-|+.+|+.-.+++
T Consensus 9 E~l~~~p~~~s~e~a~~l~egL~n----Lrp~~lq~LL~~C~svK 49 (69)
T PF11459_consen 9 ELLSEVPKRQSFEEADELMEGLRN----LRPRVLQELLEHCTSVK 49 (69)
T ss_pred HHHHhCCccCCHHHHHHHHHHHhh----cCHHHHHHHHHHCccHH
Confidence 4566666 457889999998863 48888888888765543
No 21
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.61 E-value=1.6e+02 Score=20.00 Aligned_cols=74 Identities=15% Similarity=0.180 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHH
Q 032568 53 QVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 132 (138)
Q Consensus 53 ~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~ 132 (138)
..+++.++|+..--. ....+.+....||++-+|-.|-.=-|.+.+-...++-.+..+ .- ....++.+++.|.
T Consensus 4 ~~l~~~f~~i~~~V~------~~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~-~G-~~At~~~L~~aL~ 75 (96)
T cd08315 4 ETLRRSFDHFIKEVP------FDSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNK-TG-RKASVNTLLDALE 75 (96)
T ss_pred hHHHHHHHHHHHHCC------HHHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHh-hC-CCcHHHHHHHHHH
Confidence 345555555533221 133556666789999999988888899977778888877753 12 3456777776665
Q ss_pred hh
Q 032568 133 LI 134 (138)
Q Consensus 133 ~~ 134 (138)
+.
T Consensus 76 ~~ 77 (96)
T cd08315 76 AI 77 (96)
T ss_pred Hc
Confidence 43
No 22
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=32.54 E-value=43 Score=21.72 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcC
Q 032568 52 SQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNL 97 (138)
Q Consensus 52 ~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL 97 (138)
+..+.++...+..-.. +.+++..+||++.|+-.|.+|
T Consensus 31 ~~~Y~~A~klv~~Ga~---------~~el~~~CgL~~aEAeLl~~L 67 (70)
T PF10975_consen 31 SPLYSQAIKLVRQGAS---------VEELMEECGLSRAEAELLLSL 67 (70)
T ss_pred cchHHHHHHHHHcCCC---------HHHHHHHcCCCHHHHHHHHHH
Confidence 4456666666665432 457778899999999888765
No 23
>PHA00542 putative Cro-like protein
Probab=32.20 E-value=1.5e+02 Score=19.39 Aligned_cols=56 Identities=11% Similarity=0.077 Sum_probs=40.2
Q ss_pred HHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhhhc
Q 032568 76 QVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF 137 (138)
Q Consensus 76 ~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~f 137 (138)
.+...+...|++..++|....+.+.++.....--- +..+.+.+..|++.+.++-.|
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~------~~p~~~~l~ki~~~~~~~~~~ 77 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRH------KDPRYSVVEKLRHLVLNLDDF 77 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCC------CCCCHHHHHHHHHHHHHhchh
Confidence 34566777899999999999998877766543210 113778889998888777655
No 24
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=31.79 E-value=32 Score=17.80 Aligned_cols=14 Identities=14% Similarity=0.318 Sum_probs=7.7
Q ss_pred hcCCCCCHHHHHhh
Q 032568 95 GNLCPETVEEAIAM 108 (138)
Q Consensus 95 ~NL~P~t~eEar~L 108 (138)
.|++|-++|+-+.|
T Consensus 5 dnmmPMSPddy~~l 18 (23)
T PF12162_consen 5 DNMMPMSPDDYDEL 18 (23)
T ss_dssp TS---S-HHHHHHH
T ss_pred hcccCCCHHHHHHH
Confidence 68999999887765
No 25
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=31.00 E-value=85 Score=19.72 Aligned_cols=47 Identities=15% Similarity=0.144 Sum_probs=31.5
Q ss_pred CCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHhhh
Q 032568 85 QLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 135 (138)
Q Consensus 85 ~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r 135 (138)
-|+...+..|+...|.|..++..+-. +.. +. -...-..+++.|..+.
T Consensus 29 I~~~~~L~~ia~~~P~~~~~L~~i~g-~~~--~~-~~~~g~~~~~~i~~~~ 75 (81)
T smart00341 29 VLPDETLIKMAAALPTNVSELLAIDG-VGE--EK-ARRYGKDLLAVIQEAS 75 (81)
T ss_pred EECHHHHHHHHHHCCCCHHHHhcCCC-CCH--HH-HHHHHHHHHHHHHHHH
Confidence 36788889999999999999988543 221 11 2233456677776654
No 26
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=30.97 E-value=1.3e+02 Score=21.70 Aligned_cols=43 Identities=23% Similarity=0.277 Sum_probs=26.9
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcCCCCC
Q 032568 58 SLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPET 101 (138)
Q Consensus 58 Tl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t 101 (138)
.|+-++.|.+-+ .-..+.+++++...++.+.....|-+|.|.+
T Consensus 71 pYE~LK~lTRg~-~it~~~l~~fI~~L~ip~~~k~~L~~ltP~~ 113 (115)
T PF08328_consen 71 PYEKLKELTRGK-KITKEDLREFIESLDIPEEAKARLLALTPAT 113 (115)
T ss_dssp HHHHHHHHHTTS----HHHHHHHHHTSSS-HHHHHHHHH--CCC
T ss_pred HHHHHHHHHcCC-CCCHHHHHHHHHhCCCCHHHHHHHHhcCccc
Confidence 456666666655 3445667777777788888888888888876
No 27
>PF07299 FBP: Fibronectin-binding protein (FBP); InterPro: IPR010841 This entry consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [,].; PDB: 4ADO_B 4ADN_B 2YB5_F.
Probab=30.51 E-value=37 Score=26.76 Aligned_cols=71 Identities=21% Similarity=0.322 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 52 SQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 52 ~~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
+.+=+.+..=++.+....++..+++++.+... .|.+++|.-.+|.+.|+..+.+ .- +.++.+..|+.|
T Consensus 8 n~Ik~q~~~L~~~~~tvnD~~vi~a~~~~~~~---------ki~~~f~~~~~eq~~ll~~i~~--i~-~~~~~~~~L~~L 75 (208)
T PF07299_consen 8 NFIKKQVYQLVNAYRTVNDPKVIEAVKSLAIE---------KILELFPELTEEQKELLEQIMD--IK-TREEAEKYLEEL 75 (208)
T ss_dssp HHHHHHHHHHHHHHHC-T-CCCCHHHHHHHHH---------HHHHHHCTTTHHHCCHHHHHTS--TT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhccCCHHHHHHHHHHHHH---------HHHHHcccCCHHHHHHHHHHhc--cC-CHHHHHHHHHHH
Confidence 44445555556666666666655555554322 3445555555555555555542 12 455555555555
Q ss_pred Hhh
Q 032568 132 SLI 134 (138)
Q Consensus 132 ~~~ 134 (138)
..|
T Consensus 76 ~~y 78 (208)
T PF07299_consen 76 KPY 78 (208)
T ss_dssp HCC
T ss_pred HHH
Confidence 443
No 28
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=30.45 E-value=30 Score=20.16 Aligned_cols=48 Identities=19% Similarity=0.220 Sum_probs=30.4
Q ss_pred HHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 77 VREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 77 v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
+++++...|++..+.+..+++.|.++...-.= . +.++-+.+..|-..+
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g----~---~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENG----K---RNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTT----S---STSBHHHHHHHHHHH
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcC----C---CCCCHHHHHHHHHHH
Confidence 45667788999999999999777665543221 1 234777777766554
No 29
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=30.08 E-value=38 Score=20.79 Aligned_cols=23 Identities=22% Similarity=0.408 Sum_probs=18.3
Q ss_pred CCHhHHHHHhcCCCCCHHHHHhh
Q 032568 86 LAEFELCVLGNLCPETVEEAIAM 108 (138)
Q Consensus 86 l~~~E~a~l~NL~P~t~eEar~L 108 (138)
++...+..|+...|.|.+++..+
T Consensus 27 l~~~~L~~ia~~~P~s~~~L~~i 49 (68)
T PF00570_consen 27 LSDEALLEIAKRLPTSIEELLQI 49 (68)
T ss_dssp S-HHHHHHHHHH--SSHHHHHTS
T ss_pred cCHHHHHHHHHhCCCCHHHHHHc
Confidence 67788889999999999999998
No 30
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=28.72 E-value=1.6e+02 Score=18.65 Aligned_cols=52 Identities=23% Similarity=0.266 Sum_probs=39.5
Q ss_pred HHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHh
Q 032568 77 VREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 133 (138)
Q Consensus 77 v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~ 133 (138)
+..+++..-|+..|.-.|-+ +|+..+-++.|+-.+..| .+.-....++.|.+
T Consensus 22 ld~L~~~~vlt~~e~e~I~~-~~t~~~k~~~LLd~l~~k----g~~a~~~F~~~L~~ 73 (85)
T PF00619_consen 22 LDHLLSRGVLTEEEYEEIRS-EPTRQDKARKLLDILKRK----GPEAFDIFCQALRE 73 (85)
T ss_dssp HHHHHHTTSSSHHHHHHHHT-SSSHHHHHHHHHHHHHHC----CHHHHHHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHc-cCChHHHHHHHHHHHHHH----CHHHHHHHHHHHHh
Confidence 44555555589999998888 999999999999999865 56666666666654
No 31
>PF12763 EF-hand_4: Cytoskeletal-regulatory complex EF hand; PDB: 2QPT_A 2KSP_A 2KFG_A 2JQ6_A 2KFH_A 2KFF_A 1IQ3_A 3FIA_A 2KHN_A 2KGR_A ....
Probab=28.37 E-value=42 Score=23.36 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=25.8
Q ss_pred HHHHhhcCCCCHH---HHHHHHHHHHhcCCCHhHHHHHhcCCC
Q 032568 60 QYVKRFSRYKNPD---AVRQVREILSRYQLAEFELCVLGNLCP 99 (138)
Q Consensus 60 ~Yl~~Fs~~~~~e---~~~~v~~ll~~~~l~~~E~a~l~NL~P 99 (138)
.|.+-|....+.. +-..++.++.+.||.....++|.+|+=
T Consensus 11 ~y~~~F~~l~~~~g~isg~~a~~~f~~S~L~~~~L~~IW~LaD 53 (104)
T PF12763_consen 11 KYDQIFQSLDPQDGKISGDQAREFFMKSGLPRDVLAQIWNLAD 53 (104)
T ss_dssp HHHHHHHCTSSSTTEEEHHHHHHHHHHTTSSHHHHHHHHHHH-
T ss_pred HHHHHHHhcCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHhhhc
Confidence 4666666554322 345566778888888888888877653
No 32
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=27.83 E-value=90 Score=23.43 Aligned_cols=32 Identities=9% Similarity=0.254 Sum_probs=20.9
Q ss_pred HHHhhcccccccCCCCCHHHHHHHH---------HHHHhhhh
Q 032568 104 EAIAMVPSIKTRGRAHDDEAIEKML---------NDLSLIKK 136 (138)
Q Consensus 104 Ear~Lipsl~~k~r~~~de~L~~IL---------~~l~~~r~ 136 (138)
.++.||..... ...+||++|.++| -.|++||.
T Consensus 108 ~i~~lI~~Ed~-~~PlSD~~i~~~L~~~gi~isRRTVaKYR~ 148 (160)
T PF04552_consen 108 RIKELIEEEDK-KKPLSDQEIAELLKEEGIKISRRTVAKYRE 148 (160)
T ss_dssp HHHHHHTTS-T-TS---HHHHHHHHTTTTS---HHHHHHHHH
T ss_pred HHHHHHHhcCC-CCCCCHHHHHHHHHHcCCCccHHHHHHHHH
Confidence 66777776643 2446999999999 56888885
No 33
>PRK11239 hypothetical protein; Provisional
Probab=27.34 E-value=3.2e+02 Score=21.75 Aligned_cols=48 Identities=19% Similarity=0.224 Sum_probs=37.0
Q ss_pred hcCCCHhHHHHHhcCC---CCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHh
Q 032568 83 RYQLAEFELCVLGNLC---PETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 133 (138)
Q Consensus 83 ~~~l~~~E~a~l~NL~---P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~ 133 (138)
.++|++-+.|.|+=|+ |+|+-|+|+=-.-+- +|-+=++++..|+.|..
T Consensus 92 ~l~l~~~~~All~~LlLRGPQT~gELRtRs~Rl~---~F~dv~~Ve~~L~~L~~ 142 (215)
T PRK11239 92 DLKLSAAEVALITTLLLRGAQTPGELRSRAARMY---EFSDMAEVESTLEQLAN 142 (215)
T ss_pred ccCCCHHHHHHHHHHHhcCCCChHHHHHhHhcCC---cCCCHHHHHHHHHHHHh
Confidence 3678888888877775 999999998777665 35344888998888764
No 34
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=27.07 E-value=1.9e+02 Score=23.00 Aligned_cols=58 Identities=14% Similarity=0.082 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhcC--CCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHH
Q 032568 72 DAVRQVREILSRYQ--LAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLN 129 (138)
Q Consensus 72 e~~~~v~~ll~~~~--l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~ 129 (138)
+....++..+...| +++..+..|+..+|.+..++...+.........++.+++++++.
T Consensus 188 ~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~~~~~ 247 (337)
T PRK12402 188 ELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEALG 247 (337)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhC
Confidence 44455555555555 56777889999999999888777654321111237777666554
No 35
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=26.83 E-value=1.1e+02 Score=21.73 Aligned_cols=28 Identities=7% Similarity=0.140 Sum_probs=17.7
Q ss_pred CCHHHHHHHH----HHHHhcCCCHhHHHHHhc
Q 032568 69 KNPDAVRQVR----EILSRYQLAEFELCVLGN 96 (138)
Q Consensus 69 ~~~e~~~~v~----~ll~~~~l~~~E~a~l~N 96 (138)
..++..+.++ .++...||++.|+..|.+
T Consensus 24 ~~a~~Re~F~aD~eAy~~~~gLTeEe~~AV~~ 55 (106)
T cd07921 24 NKAENREAFKADEEAYCDKFGLTEEQKQAVLD 55 (106)
T ss_pred CCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHh
Confidence 3455555444 566778888888776643
No 36
>PRK09726 antitoxin HipB; Provisional
Probab=26.68 E-value=73 Score=20.93 Aligned_cols=54 Identities=11% Similarity=0.054 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 71 PDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 71 ~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
..-...++.+....|++..+.|..+++.|.++-.... . .+.++-+.|..|.+.+
T Consensus 11 ~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~------g-~~~ps~~~l~~ia~~l 64 (88)
T PRK09726 11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN------N-PDNTTLTTFFKILQSL 64 (88)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC------C-CCCCCHHHHHHHHHHc
Confidence 3444667777888899999999999988777654332 1 1223667777776654
No 37
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=26.59 E-value=2.5e+02 Score=21.92 Aligned_cols=68 Identities=12% Similarity=0.111 Sum_probs=45.5
Q ss_pred hcCCCCHHHHHHHHHHHHhcC--CCHhHHHHHhcCCCCCHHHHHhhccccccc--CCCCCHHHHHHHHHHHH
Q 032568 65 FSRYKNPDAVRQVREILSRYQ--LAEFELCVLGNLCPETVEEAIAMVPSIKTR--GRAHDDEAIEKMLNDLS 132 (138)
Q Consensus 65 Fs~~~~~e~~~~v~~ll~~~~--l~~~E~a~l~NL~P~t~eEar~Lipsl~~k--~r~~~de~L~~IL~~l~ 132 (138)
|.+....+-..-|+..++..| +++..+..|++.++.+...++..+..|.-- ++.++.++++.++..-.
T Consensus 108 ~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~ 179 (302)
T TIGR01128 108 CKTPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSA 179 (302)
T ss_pred ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhh
Confidence 344444555667777777776 678878899999999988777666654310 11248888888776443
No 38
>TIGR02498 type_III_ssaH type III secretion system protein, SsaH family. This family describes a small protein, always smaller than 100 amino acids, encoded in pathogenicity islands for bacterial type III secretion systems in various strains of Yersinia, Salmonella, and enteropathogenic E. coli, as well as Chromobacterium violaceum and Citrobacter rodentium. Although strictly associated with type III secretion systems, this protein seems not yet to have been characterized as part of the apparatus or as an effector protein.
Probab=26.02 E-value=2.1e+02 Score=19.22 Aligned_cols=56 Identities=14% Similarity=0.119 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHH--HHhcCCCCCHHHHHhhc
Q 032568 54 VFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELC--VLGNLCPETVEEAIAMV 109 (138)
Q Consensus 54 ~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a--~l~NL~P~t~eEar~Li 109 (138)
.......-++-|..+-++.....+-+.+-.+||.+-+.| .|.+..++++.-.|+|+
T Consensus 21 L~~ea~ailnalP~li~D~~~r~vcea~llfGL~~~~~A~~~L~~~~~~eA~~Lr~l~ 78 (79)
T TIGR02498 21 LPKEAHSILNALPQIIPDKKDRLVCEAILLFGLNHKNDAVKLLENMDDEEAQLLRSLV 78 (79)
T ss_pred cHHHHHHHHHhcccccCCHhHHHHHHHHHHHhcCcHHHHHHHHhcCCcHHHHHHHHHh
Confidence 566677788888888777777888888889999877666 66776666666666655
No 39
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=25.82 E-value=1.5e+02 Score=17.60 Aligned_cols=49 Identities=14% Similarity=0.225 Sum_probs=28.7
Q ss_pred HHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 76 QVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 76 ~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
.++++....|++..++|...++. ++-|-.++.-.+.++.+.+..|.+.+
T Consensus 3 ~lk~~r~~~~lt~~~~a~~~~i~-------~~~i~~~e~g~~~~~~~~l~~i~~~~ 51 (64)
T PF12844_consen 3 RLKELREEKGLTQKDLAEKLGIS-------RSTISKIENGKRKPSVSTLKKIAEAL 51 (64)
T ss_dssp HHHHHHHHCT--HHHHHHHHTS--------HHHHHHHHTTSS--BHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHCcC-------HHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence 47777788899999999888885 33333343211335777777766654
No 40
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=25.45 E-value=1.6e+02 Score=19.25 Aligned_cols=18 Identities=28% Similarity=0.316 Sum_probs=11.5
Q ss_pred HHHHhcCCCHhHHHHHhc
Q 032568 79 EILSRYQLAEFELCVLGN 96 (138)
Q Consensus 79 ~ll~~~~l~~~E~a~l~N 96 (138)
.++..+||++.|+..|.+
T Consensus 28 a~~~~~~Lt~eE~~al~~ 45 (77)
T cd07321 28 AVLAEYGLTPEEKAALLA 45 (77)
T ss_pred HHHHHcCCCHHHHHHHHc
Confidence 456667777777766543
No 41
>PRK07168 bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed
Probab=25.41 E-value=60 Score=28.51 Aligned_cols=57 Identities=9% Similarity=0.064 Sum_probs=46.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhh-cccccccCCCCCHHHHHHHHHHH
Q 032568 67 RYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAM-VPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 67 ~~~~~e~~~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~L-ipsl~~k~r~~~de~L~~IL~~l 131 (138)
-|.++.++..+-+.++..|+.+...+.++.+-|.|...|+.. +- .-|.++|++|+.-
T Consensus 412 iFtS~ssV~~f~~~~~~~~~~~~~~~~~~~iGp~t~~~a~~~G~~--------~~~~~~~~~~~~~ 469 (474)
T PRK07168 412 VFEGRASIDTFLAEVKRLGFIDIVTLPFSYTDVPTLHYANKVGFH--------NIDHQLQETLMQK 469 (474)
T ss_pred EECCHHHHHHHHHHHHhhCchhhccCceEEeCHHHHHHHHHhCCC--------cccHHHHHHHhhh
Confidence 578899999999999999987776667899999999999876 33 2678899988753
No 42
>PF15076 DUF4543: Domain of unknown function (DUF4543)
Probab=24.99 E-value=1.2e+02 Score=19.93 Aligned_cols=30 Identities=10% Similarity=0.131 Sum_probs=21.7
Q ss_pred cccHHHHHHHHHHHHHHhhhcCCCCCcchh
Q 032568 23 CLMNCEVAIILDHKYEQLQQTSDDPMNQVS 52 (138)
Q Consensus 23 ~Ls~~EV~~iL~~~~~~~~~~~~~~~~~~~ 52 (138)
.|+-.+|+++|..++.++....+-|+..+.
T Consensus 8 il~Ek~AKqlLRsrR~dr~~K~Gfpdepmr 37 (75)
T PF15076_consen 8 ILTEKQAKQLLRSRRQDRPRKPGFPDEPMR 37 (75)
T ss_pred cccHHHHHHHHHHHHhcCCCCCCCCcchHH
Confidence 478899999999998877545555554443
No 43
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.45 E-value=1.6e+02 Score=17.45 Aligned_cols=49 Identities=14% Similarity=0.301 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 77 VREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 77 v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
++++|...|++..+.+.-+++.+.|......==+ ..+ +-+.|..|-..+
T Consensus 2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~-----~~~-~~~~l~~ia~~l 50 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKTGISRSTLSRILNGKP-----SNP-SLDTLEKIAKAL 50 (63)
T ss_dssp HHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----------HHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhccc-----ccc-cHHHHHHHHHHc
Confidence 6778888889999999988888877766654110 123 667777766554
No 44
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=24.27 E-value=1.4e+02 Score=20.64 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=17.7
Q ss_pred CHHHHHHHH----HHHHhcCCCHhHHHHHhc
Q 032568 70 NPDAVRQVR----EILSRYQLAEFELCVLGN 96 (138)
Q Consensus 70 ~~e~~~~v~----~ll~~~~l~~~E~a~l~N 96 (138)
.++..+.++ .++...||++.|+..|.+
T Consensus 17 ~a~~RerF~~D~ea~~~e~gLt~Ee~~av~~ 47 (94)
T cd07923 17 EPAHRERFLEDPEALFDEAGLTEEERTLIRN 47 (94)
T ss_pred CHHHHHHHHhCHHHHHHHcCCCHHHHHHHHc
Confidence 455544443 567788888888877654
No 45
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=24.24 E-value=2.2e+02 Score=18.75 Aligned_cols=40 Identities=20% Similarity=0.320 Sum_probs=31.4
Q ss_pred HHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccC
Q 032568 77 VREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRG 116 (138)
Q Consensus 77 v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~ 116 (138)
+..++...-|++.|+-.|..=.++..+-||.||-++..||
T Consensus 22 lD~Ll~~~Vl~~~E~e~i~~~~~t~~dkar~Lid~v~~KG 61 (83)
T cd08325 22 LDDLLEKNVLNEEEMEKIKEENNTIMDKARVLVDSVTEKG 61 (83)
T ss_pred HHHHHHcCCCCHHHHHHHHhccCCHHHHHHHHHHHHHHHh
Confidence 4455566668888888887767778999999999998763
No 46
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=24.22 E-value=1.3e+02 Score=18.52 Aligned_cols=24 Identities=17% Similarity=0.329 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHhcCCCHhHHHHHh
Q 032568 71 PDAVRQVREILSRYQLAEFELCVLG 95 (138)
Q Consensus 71 ~e~~~~v~~ll~~~~l~~~E~a~l~ 95 (138)
..+++.|.+||.. |++..|+.+|+
T Consensus 14 Q~AvE~Iq~LMaq-GmSsgEAI~~V 37 (51)
T PF03701_consen 14 QQAVERIQELMAQ-GMSSGEAIAIV 37 (51)
T ss_pred HHHHHHHHHHHHh-cccHHHHHHHH
Confidence 4578888888876 78888887765
No 47
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=24.15 E-value=1e+02 Score=20.85 Aligned_cols=17 Identities=29% Similarity=0.233 Sum_probs=9.4
Q ss_pred HHHHhcCCCHhHHHHHh
Q 032568 79 EILSRYQLAEFELCVLG 95 (138)
Q Consensus 79 ~ll~~~~l~~~E~a~l~ 95 (138)
.++..+||++.|+..|.
T Consensus 23 a~~~~~~Lt~eer~av~ 39 (88)
T PF07746_consen 23 AYLDEYGLTEEERQAVL 39 (88)
T ss_dssp HHHHCCT--HHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHH
Confidence 45566777777766553
No 48
>PF12125 Beta-TrCP_D: D domain of beta-TrCP; InterPro: IPR021977 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found associated with PF00646 from PFAM, PF00400 from PFAM. The protein that contains this domain functions as a ubiquitin ligase. Ubiquitination is required to direct proteins towards the proteasome for degradation. This protein is part of the WD40 class of F box proteins. The D domain of these F box proteins is involved in mediating the dimerisation of the protein. Dimerisation is necessary to polyubiquitinate substrates so this D domain is vital in directing substrates towards the proteasome for degradation. ; PDB: 2P64_A 1P22_A.
Probab=24.07 E-value=91 Score=18.29 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=22.1
Q ss_pred HHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHH
Q 032568 62 VKRFSRYKNPDAVRQVREILSRYQLAEFELCVL 94 (138)
Q Consensus 62 l~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l 94 (138)
++.|.++...+.+.-|+.++.++ ..+.--+|
T Consensus 1 ~~~F~~Wse~eQvdFVe~Ll~rM--~H~Qhg~I 31 (40)
T PF12125_consen 1 VEYFDKWSESEQVDFVEQLLSRM--CHYQHGQI 31 (40)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHTS---HHHHHHH
T ss_pred CchhhccCchhHHHHHHHHHHHH--HHHHHHhH
Confidence 46799999999999999999875 44444444
No 49
>COG3612 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.03 E-value=1.7e+02 Score=22.04 Aligned_cols=42 Identities=19% Similarity=0.337 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHHH
Q 032568 53 QVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVL 94 (138)
Q Consensus 53 ~~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~l 94 (138)
+.+.+.++.+.-=.+++..+++..+++++.+.|+-.|.++.|
T Consensus 91 ~~~driLDa~aA~g~~~rqe~Va~vn~~qe~l~lvtf~~aaL 132 (157)
T COG3612 91 PSFDRILDAAAASGKLDRQEAVAEVNSLQENLGLVTFQTAAL 132 (157)
T ss_pred chHHHHHHHHHHhcCccHHHHHHHHHHHHHHhcceehHHHHH
Confidence 378899999999899999999999999999999767766655
No 50
>KOG4646 consensus Uncharacterized conserved protein, contains ARM repeats [Function unknown]
Probab=23.55 E-value=74 Score=24.13 Aligned_cols=17 Identities=41% Similarity=0.620 Sum_probs=14.1
Q ss_pred CCCHhHHHHHhcCCCCC
Q 032568 85 QLAEFELCVLGNLCPET 101 (138)
Q Consensus 85 ~l~~~E~a~l~NL~P~t 101 (138)
.|.+|-|.-|+|+||+-
T Consensus 73 ~LvefgIgglCNlC~d~ 89 (173)
T KOG4646|consen 73 LLVEFGIGGLCNLCLDK 89 (173)
T ss_pred HHHHHhHHHHHhhccCh
Confidence 36688899999999964
No 51
>PF06287 DUF1039: Protein of unknown function (DUF1039); InterPro: IPR010437 This family describes a small protein, always smaller than 100 amino acids, encoded in pathogenicity islands for bacterial type III secretion systems in various strains of Yersinia, Salmonella, and enteropathogenic Escherichia coli, as well as Chromobacterium violaceum and Citrobacter rodentium. Although strictly associated with type III secretion systems, this protein seems not yet to have been characterised as part of the apparatus or as an effector protein.
Probab=23.14 E-value=2e+02 Score=18.65 Aligned_cols=56 Identities=14% Similarity=0.176 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHH--HHhcCCCCCHHHHHhhc
Q 032568 54 VFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELC--VLGNLCPETVEEAIAMV 109 (138)
Q Consensus 54 ~~~kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a--~l~NL~P~t~eEar~Li 109 (138)
.......-++-|...-++.....+=+.+-.+||.+-..| .|.++-|+++.=+|.|+
T Consensus 8 L~~ea~aIL~alP~Li~D~~~r~~c~alllfGL~~~~~Al~~L~~~~~eeA~~Lr~L~ 65 (66)
T PF06287_consen 8 LLKEARAILNALPQLIPDEEDRAVCEALLLFGLGEQAAALQLLADSDSEEAQALRFLF 65 (66)
T ss_pred cHHHHHHHHHhchhhcCCHhHHHHHHHHHHHHcCChHHHHHHHhCCChHHHHHHHHHc
Confidence 344555666667776666667777788888888765555 56666666666666554
No 52
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.11 E-value=2.2e+02 Score=18.42 Aligned_cols=55 Identities=9% Similarity=0.206 Sum_probs=42.0
Q ss_pred HHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHHHh
Q 032568 77 VREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 133 (138)
Q Consensus 77 v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l~~ 133 (138)
...+....||++-+|-.|-+-.|...+.+..++-.+..| .- ....++.+++.|.+
T Consensus 14 Wk~laR~LGls~~~I~~ie~~~~~~~eq~~~mL~~W~~k-~G-~~At~~~L~~aL~~ 68 (79)
T cd08784 14 HKRFFRKLGLSDNEIKVAELDNPQHRDRVYELLRIWRNK-EG-RKATLNTLIKALKD 68 (79)
T ss_pred HHHHHHHcCCCHHHHHHHHHcCCchHHHHHHHHHHHHhc-cC-cCcHHHHHHHHHHH
Confidence 445556789999999999999999778888888888754 22 45677777777654
No 53
>PF10041 DUF2277: Uncharacterized conserved protein (DUF2277); InterPro: IPR018735 Members of this family of hypothetical bacterial proteins have no known function.
Probab=22.74 E-value=1.3e+02 Score=20.15 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=21.1
Q ss_pred CCCcchhHHHHHHHHHHHhhcCCCCHH
Q 032568 46 DPMNQVSQVFEKSLQYVKRFSRYKNPD 72 (138)
Q Consensus 46 ~~~~~~~~~~~kTl~Yl~~Fs~~~~~e 72 (138)
+|.....++..-+++||++.|.+..+.
T Consensus 12 ePpaT~~EI~aAAlQyVRKvSG~~~Ps 38 (78)
T PF10041_consen 12 EPPATDEEIRAAALQYVRKVSGFRKPS 38 (78)
T ss_pred CCCCCHHHHHHHHHHHHHHHccCCCcc
Confidence 455555678888999999999997655
No 54
>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095); InterPro: IPR018662 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=22.04 E-value=96 Score=22.55 Aligned_cols=6 Identities=33% Similarity=1.149 Sum_probs=2.6
Q ss_pred HHHHHh
Q 032568 59 LQYVKR 64 (138)
Q Consensus 59 l~Yl~~ 64 (138)
+||+++
T Consensus 68 iD~lrR 73 (128)
T PF09868_consen 68 IDYLRR 73 (128)
T ss_pred HHHHHH
Confidence 344443
No 55
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. 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 substrates.
Probab=21.89 E-value=1.3e+02 Score=20.38 Aligned_cols=47 Identities=17% Similarity=0.113 Sum_probs=26.4
Q ss_pred hHHHHHhcCCCCCH---HHHHhhcccccccCCCCCHHHHHHHHHHHHhhhh
Q 032568 89 FELCVLGNLCPETV---EEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 136 (138)
Q Consensus 89 ~E~a~l~NL~P~t~---eEar~Lipsl~~k~r~~~de~L~~IL~~l~~~r~ 136 (138)
-|+|.+.++.+.|. |+.-.|-|.-.+..|.|+++++ .-|..|..+|+
T Consensus 4 ge~a~~~gvs~~tlRyYe~~GLl~p~~~~g~r~Y~~~~~-~~l~~I~~lr~ 53 (107)
T cd04777 4 GKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQ-DDLEFILELKG 53 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCcCCccCCCccccCHHHH-HHHHHHHHHHH
Confidence 35666666666663 3444444422122245688888 56666666664
No 56
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=21.66 E-value=1.3e+02 Score=15.09 Aligned_cols=26 Identities=15% Similarity=0.280 Sum_probs=16.8
Q ss_pred HHhhcCCCCHHHHHHHHHHHHhcCCC
Q 032568 62 VKRFSRYKNPDAVRQVREILSRYQLA 87 (138)
Q Consensus 62 l~~Fs~~~~~e~~~~v~~ll~~~~l~ 87 (138)
++-|++.++.+.+..+-..|...|+.
T Consensus 8 l~a~~~~g~~~~a~~~~~~M~~~gv~ 33 (34)
T PF13812_consen 8 LRACAKAGDPDAALQLFDEMKEQGVK 33 (34)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 34466777777766666666666654
No 57
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=21.34 E-value=1.6e+02 Score=20.87 Aligned_cols=16 Identities=6% Similarity=0.088 Sum_probs=9.1
Q ss_pred HHHHhcCCCHhHHHHH
Q 032568 79 EILSRYQLAEFELCVL 94 (138)
Q Consensus 79 ~ll~~~~l~~~E~a~l 94 (138)
.++...||++.+...|
T Consensus 38 Ay~~~~~Lteeqr~av 53 (106)
T cd07925 38 AYCEKFGLTPEQKQAV 53 (106)
T ss_pred HHHHHcCCCHHHHHHH
Confidence 4555666666655544
No 58
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=21.20 E-value=2.6e+02 Score=20.72 Aligned_cols=73 Identities=18% Similarity=0.264 Sum_probs=48.8
Q ss_pred ccccccHHHHHHHHHHHHHHh-hhcCC-------C-----------CCc---chhHHHHHHHHHHHhhcCCCCHHHHHHH
Q 032568 20 KAKCLMNCEVAIILDHKYEQL-QQTSD-------D-----------PMN---QVSQVFEKSLQYVKRFSRYKNPDAVRQV 77 (138)
Q Consensus 20 ~~~~Ls~~EV~~iL~~~~~~~-~~~~~-------~-----------~~~---~~~~~~~kTl~Yl~~Fs~~~~~e~~~~v 77 (138)
+-+-+|..+|+.+++...+.= -.... + |+. .-...|.+.++|+-.-......+.+..+
T Consensus 30 D~~WmspdqAk~li~~A~~eGLl~~~~~~l~~~Fd~~~v~iP~~FkP~~~~l~e~~~fe~ild~ia~~~g~~~~evv~~i 109 (144)
T PF09999_consen 30 DRKWMSPDQAKRLIDEAIEEGLLEEEGGYLVPNFDPSEVEIPLGFKPDEEILQERDPFERILDYIAAKTGIEKQEVVAEI 109 (144)
T ss_pred ecCCCCHHHHHHHHHHHHHCCCeeecCCEEEEecCccccccCCCCCCcHHHHhcccHHHHHHHHHHHhcCCCHHHHHHHH
Confidence 345678889999887755321 00000 0 110 1245889999999998889889999999
Q ss_pred HHHHHhcC--CCHhHHH
Q 032568 78 REILSRYQ--LAEFELC 92 (138)
Q Consensus 78 ~~ll~~~~--l~~~E~a 92 (138)
.+....+| ++..-+|
T Consensus 110 n~~q~~~~~~l~~e~aa 126 (144)
T PF09999_consen 110 NELQEELGGLLDPEAAA 126 (144)
T ss_pred HHHHHHHhccCCHHHHH
Confidence 99888888 5444333
No 59
>PRK10945 gene expression modulator; Provisional
Probab=21.03 E-value=2.6e+02 Score=18.47 Aligned_cols=35 Identities=29% Similarity=0.454 Sum_probs=25.7
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHH
Q 032568 57 KSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELC 92 (138)
Q Consensus 57 kTl~Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a 92 (138)
...+|+=+|-++.+.++.+.|-+-+. ..|+..|+.
T Consensus 7 tk~dyL~~fRrcss~eTLEkvie~~~-~~L~~~E~~ 41 (72)
T PRK10945 7 TKTDYLMRLRRCQTIDTLERVIEKNK-YELSDDELA 41 (72)
T ss_pred cHHHHHHHHHhcCcHHHHHHHHHHhh-ccCCHHHHH
Confidence 44899999999999999887776543 346654444
No 60
>PF06603 UpxZ: UpxZ family of transcription anti-terminator antagonists; InterPro: IPR010570 This family consists of several hypothetical proteins of unknown function and seems to be specific to Bacteroides species.
Probab=21.02 E-value=1.2e+02 Score=21.58 Aligned_cols=32 Identities=25% Similarity=0.287 Sum_probs=25.0
Q ss_pred HHHhhcCCCCHHHHHHHHHHHHhcCCCHhHHHH
Q 032568 61 YVKRFSRYKNPDAVRQVREILSRYQLAEFELCV 93 (138)
Q Consensus 61 Yl~~Fs~~~~~e~~~~v~~ll~~~~l~~~E~a~ 93 (138)
|+..|++. |.+.-.....+....|-+..|-|.
T Consensus 23 YsD~~~rL-N~ev~~~~~~Ly~~~G~t~EeeA~ 54 (106)
T PF06603_consen 23 YSDDFSRL-NKEVYEQSNDLYSQHGSTPEEEAN 54 (106)
T ss_pred ehHHHHHH-hHHHHHHHHHHHhccCCCHHHHHH
Confidence 78888888 577778888888888887776653
No 61
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=20.99 E-value=42 Score=24.97 Aligned_cols=15 Identities=40% Similarity=0.645 Sum_probs=10.3
Q ss_pred cCCCCCHHHHHHHHH
Q 032568 115 RGRAHDDEAIEKMLN 129 (138)
Q Consensus 115 k~r~~~de~L~~IL~ 129 (138)
+.|.++||+|+.||-
T Consensus 83 RNrpLTDEELD~mLP 97 (144)
T PF08920_consen 83 RNRPLTDEELDAMLP 97 (144)
T ss_dssp CTS-S-HHHHHHTS-
T ss_pred ccCcCCHHHHHHhCC
Confidence 457789999999983
No 62
>PRK04081 hypothetical protein; Provisional
Probab=20.99 E-value=58 Score=25.67 Aligned_cols=36 Identities=17% Similarity=0.340 Sum_probs=30.1
Q ss_pred HHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHH
Q 032568 93 VLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLND 130 (138)
Q Consensus 93 ~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~ 130 (138)
.|++=.|.+ +.|.++-.+...+|+++.++++.++++
T Consensus 62 KI~eE~Ps~--~Trvilr~~dG~ER~LS~eE~dkLi~e 97 (207)
T PRK04081 62 KILEEYPSS--ETRVVLRDLDGTERVLSQEEIDKLIKE 97 (207)
T ss_pred EeeeecCCC--cceEEEecCCCcccccCHHHHHHHHHH
Confidence 355556877 799999998887899999999999976
No 63
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=20.90 E-value=1.1e+02 Score=20.90 Aligned_cols=46 Identities=17% Similarity=0.181 Sum_probs=28.3
Q ss_pred hHHHHHhcCCCCC---HHHHHhhcccccc--cCCCCCHHHHHHHHHHHHhhh
Q 032568 89 FELCVLGNLCPET---VEEAIAMVPSIKT--RGRAHDDEAIEKMLNDLSLIK 135 (138)
Q Consensus 89 ~E~a~l~NL~P~t---~eEar~Lipsl~~--k~r~~~de~L~~IL~~l~~~r 135 (138)
-|+|.++++.|.| .++.-.|.|.-.+ ..|.|+++++ ..|..|..+|
T Consensus 4 ~eva~~~gvs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl-~~l~~I~~~r 54 (124)
T COG0789 4 GEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDL-ELLQIIKTLR 54 (124)
T ss_pred HHHHHHhCCCHHHHHHHHHcCCCCCcccCCCCceecCHHHH-HHHHHHHHHH
Confidence 4677788888877 3455555555333 2367899994 4455555554
No 64
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=20.30 E-value=1.6e+02 Score=16.51 Aligned_cols=20 Identities=40% Similarity=0.665 Sum_probs=12.0
Q ss_pred HHHHHhhcccccccCCCCCHHHHHHHH
Q 032568 102 VEEAIAMVPSIKTRGRAHDDEAIEKML 128 (138)
Q Consensus 102 ~eEar~Lipsl~~k~r~~~de~L~~IL 128 (138)
+..++.++|++ +.+.|+..|
T Consensus 5 v~~L~~mFP~~-------~~~~I~~~L 24 (42)
T PF02845_consen 5 VQQLQEMFPDL-------DREVIEAVL 24 (42)
T ss_dssp HHHHHHHSSSS--------HHHHHHHH
T ss_pred HHHHHHHCCCC-------CHHHHHHHH
Confidence 45667777754 556666665
No 65
>PRK06424 transcription factor; Provisional
Probab=20.11 E-value=3.3e+02 Score=20.02 Aligned_cols=50 Identities=16% Similarity=0.100 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 75 RQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 75 ~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
..|+.+....||++.+.|..+++- +..|-.+++-.+..+.+.+..|-+.+
T Consensus 87 ~~Ir~lRe~~GLSQ~eLA~~iGvs-------~stIskiE~G~~~Ps~~~l~kLa~~L 136 (144)
T PRK06424 87 ELVKNARERLSMSQADLAAKIFER-------KNVIASIERGDLLPDIKTARKLEKIL 136 (144)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCC-------HHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence 456777778999999999999985 44455555422345666666665544
No 66
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.11 E-value=1.1e+02 Score=21.05 Aligned_cols=46 Identities=9% Similarity=0.204 Sum_probs=23.3
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHhcC-CCHhHHHHHhcCCCCCHH--HHHhhcc
Q 032568 58 SLQYVKRFSRYKNPDAVRQVREILSRYQ-LAEFELCVLGNLCPETVE--EAIAMVP 110 (138)
Q Consensus 58 Tl~Yl~~Fs~~~~~e~~~~v~~ll~~~~-l~~~E~a~l~NL~P~t~e--Ear~Lip 110 (138)
.+||+.+. +..+-+-.|.+.|.+-| +++. .| |-.-.+.. -+|+++|
T Consensus 37 V~D~L~rC---dT~EEAlEii~yleKrGEi~~E-~A---~~L~~~~~~kgvrs~~~ 85 (98)
T COG4003 37 VIDFLRRC---DTEEEALEIINYLEKRGEITPE-MA---KALRVTLVHKGVRSFGP 85 (98)
T ss_pred HHHHHHHh---CcHHHHHHHHHHHHHhCCCCHH-HH---HHHHhhHHHHHHHHhcc
Confidence 46777764 34444444555555544 6654 22 22223333 4667776
No 67
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=20.07 E-value=1e+02 Score=17.62 Aligned_cols=50 Identities=14% Similarity=0.153 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCHhHHHHHhcCCCCCHHHHHhhcccccccCCCCCHHHHHHHHHHH
Q 032568 75 RQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 131 (138)
Q Consensus 75 ~~v~~ll~~~~l~~~E~a~l~NL~P~t~eEar~Lipsl~~k~r~~~de~L~~IL~~l 131 (138)
..++.+....|++..+.|..+.+.|.++..... .+ +.++.+.+..|.+.+
T Consensus 5 ~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~------g~-~~~~~~~~~~i~~~l 54 (58)
T TIGR03070 5 MLVRARRKALGLTQADLADLAGVGLRFIRDVEN------GK-PTVRLDKVLRVLDAL 54 (58)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC------CC-CCCCHHHHHHHHHHc
Confidence 446666677899999999999888766554331 11 123667777766544
Done!