Query 031131
Match_columns 165
No_of_seqs 108 out of 244
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 09:40:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4168 Predicted RNA polymera 100.0 2.4E-34 5.2E-39 224.4 7.1 124 1-124 1-137 (149)
2 smart00657 RPOL4c DNA-directed 99.9 7.4E-28 1.6E-32 182.4 10.3 113 7-120 5-117 (118)
3 PF03874 RNA_pol_Rpb4: RNA pol 99.9 3.1E-27 6.7E-32 176.6 7.3 108 10-118 1-117 (117)
4 PRK14981 DNA-directed RNA poly 99.6 2.3E-14 5E-19 108.2 10.5 102 8-118 9-111 (112)
5 KOG2351 RNA polymerase II, fou 99.3 8.2E-12 1.8E-16 96.2 7.8 108 9-117 22-130 (134)
6 COG1460 Uncharacterized protei 98.7 1.5E-07 3.2E-12 71.7 10.8 102 8-118 10-112 (114)
7 COG5250 RPB4 RNA polymerase II 97.4 0.00079 1.7E-08 52.1 7.4 76 40-116 58-133 (138)
8 KOG4168 Predicted RNA polymera 84.3 1.4 2.9E-05 35.2 3.6 65 39-113 12-78 (149)
9 KOG0030 Myosin essential light 80.8 2.1 4.6E-05 34.2 3.5 86 9-112 42-131 (152)
10 PF02022 Integrase_Zn: Integra 70.4 2.4 5.2E-05 26.6 1.1 24 63-86 11-35 (40)
11 COG5126 FRQ1 Ca2+-binding prot 64.5 47 0.001 26.7 7.6 28 87-114 110-137 (160)
12 PLN03217 transcription factor 63.7 7.6 0.00017 28.6 2.7 22 100-121 15-36 (93)
13 COG4800 Predicted transcriptio 55.0 36 0.00079 27.4 5.4 57 56-117 13-70 (170)
14 PRK05445 hypothetical protein; 53.7 17 0.00036 29.5 3.4 45 71-115 2-67 (164)
15 smart00845 GatB_Yqey GatB doma 51.4 57 0.0012 25.1 6.0 76 40-115 20-101 (147)
16 PF13331 DUF4093: Domain of un 51.3 16 0.00035 26.4 2.7 23 59-81 64-86 (87)
17 PF00570 HRDC: HRDC domain Blo 44.8 12 0.00025 24.5 1.0 24 71-94 26-49 (68)
18 PRK15443 pduE propanediol dehy 43.7 30 0.00065 27.3 3.3 29 54-82 78-106 (138)
19 cd07313 terB_like_2 tellurium 43.6 31 0.00068 24.3 3.2 65 53-117 14-82 (104)
20 PF06569 DUF1128: Protein of u 41.4 39 0.00084 23.9 3.2 53 56-116 5-68 (71)
21 PF11829 DUF3349: Protein of u 41.1 1.1E+02 0.0024 22.7 5.8 73 41-115 6-86 (96)
22 PF13412 HTH_24: Winged helix- 40.7 44 0.00095 20.4 3.2 34 39-72 4-46 (48)
23 PF02287 Dehydratase_SU: Dehyd 40.2 38 0.00082 26.7 3.3 28 55-82 80-107 (136)
24 PHA00650 hypothetical protein 39.7 28 0.0006 24.5 2.3 13 66-78 67-79 (82)
25 PRK13689 hypothetical protein; 35.6 31 0.00067 24.6 2.0 19 100-118 5-23 (75)
26 PF13929 mRNA_stabil: mRNA sta 35.5 62 0.0013 28.6 4.3 59 5-69 155-214 (292)
27 TIGR02719 repress_PhaQ poly-be 34.9 76 0.0017 24.8 4.4 87 41-129 41-135 (138)
28 COG3013 Uncharacterized conser 34.8 24 0.00051 28.5 1.5 25 58-82 142-167 (168)
29 PF06207 DUF1002: Protein of u 34.4 59 0.0013 27.5 3.9 41 77-117 163-207 (225)
30 COG4840 Uncharacterized protei 34.2 70 0.0015 22.5 3.6 40 76-116 18-68 (71)
31 PRK05477 gatB aspartyl/glutamy 33.9 66 0.0014 30.1 4.5 79 40-120 347-430 (474)
32 cd04911 ACT_AKiii-YclM-BS_1 AC 33.8 40 0.00087 23.8 2.4 55 58-121 16-70 (76)
33 COG3082 Uncharacterized protei 31.7 40 0.00086 23.8 2.0 19 100-118 5-23 (74)
34 PF13543 KSR1-SAM: SAM like do 31.6 31 0.00068 26.9 1.7 73 37-113 34-110 (129)
35 TIGR02293 TAS_TIGR02293 putati 31.4 1.3E+02 0.0028 22.9 5.0 51 57-114 25-75 (133)
36 TIGR02220 phg_TIGR02220 phage 31.3 1.1E+02 0.0024 21.7 4.3 40 42-81 3-44 (77)
37 PF09832 DUF2059: Uncharacteri 30.8 20 0.00042 23.5 0.4 29 91-119 6-34 (64)
38 PRK07758 hypothetical protein; 29.8 53 0.0012 24.4 2.6 27 71-97 63-89 (95)
39 smart00341 HRDC Helicase and R 29.8 67 0.0015 21.4 2.9 50 70-120 28-77 (81)
40 COG4910 PduE Propanediol dehyd 29.5 68 0.0015 25.7 3.3 27 56-82 112-138 (170)
41 PRK14703 glutaminyl-tRNA synth 29.2 80 0.0017 31.4 4.4 75 40-114 645-723 (771)
42 cd04774 HTH_YfmP Helix-Turn-He 28.9 78 0.0017 22.7 3.3 69 39-115 12-93 (96)
43 PF03965 Penicillinase_R: Peni 28.9 2.3E+02 0.0049 20.5 7.3 24 91-116 92-115 (115)
44 COG1378 Predicted transcriptio 27.7 76 0.0016 26.9 3.5 32 61-92 3-37 (247)
45 PF08328 ASL_C: Adenylosuccina 26.8 1.3E+02 0.0027 23.2 4.2 42 41-87 72-113 (115)
46 cd08337 DED_c-FLIP_repeat1 Dea 26.8 1.1E+02 0.0024 21.8 3.7 37 36-72 13-49 (80)
47 cd03568 VHS_STAM VHS domain fa 25.3 1.5E+02 0.0032 23.0 4.5 65 41-116 22-91 (144)
48 PF03460 NIR_SIR_ferr: Nitrite 23.9 8.3 0.00018 25.5 -2.5 47 50-96 16-67 (69)
49 PF07693 KAP_NTPase: KAP famil 23.8 64 0.0014 26.9 2.3 34 87-121 170-203 (325)
50 PF07560 DUF1539: Domain of Un 23.6 1.2E+02 0.0027 23.6 3.7 43 41-83 42-92 (126)
51 PRK05445 hypothetical protein; 23.6 51 0.0011 26.7 1.6 25 58-82 138-163 (164)
52 PF12162 STAT1_TAZ2bind: STAT1 23.4 56 0.0012 18.3 1.3 17 77-94 2-18 (23)
53 TIGR00133 gatB glutamyl-tRNA(G 23.3 1.4E+02 0.0029 28.1 4.5 80 40-121 350-434 (478)
54 cd01107 HTH_BmrR Helix-Turn-He 23.2 1.4E+02 0.003 21.6 3.8 59 39-99 12-84 (108)
55 TIGR00134 gatE_arch glutamyl-t 22.6 1.4E+02 0.0031 28.9 4.7 68 44-114 500-573 (620)
56 TIGR02895 spore_sigI RNA polym 21.7 3.6E+02 0.0077 22.4 6.4 38 55-95 118-155 (218)
57 PF00034 Cytochrom_C: Cytochro 20.8 1E+02 0.0022 19.7 2.5 16 101-116 74-89 (91)
58 PF02637 GatB_Yqey: GatB domai 20.8 1.1E+02 0.0024 23.3 2.9 74 41-114 22-101 (148)
59 KOG2438 Glutamyl-tRNA amidotra 20.7 2.1E+02 0.0045 27.1 5.1 106 10-119 341-458 (505)
60 COG2511 GatE Archaeal Glu-tRNA 20.6 2.3E+02 0.005 27.5 5.5 74 41-116 504-583 (631)
61 cd04773 HTH_TioE_rpt2 Second H 20.4 2E+02 0.0042 20.9 4.1 76 40-116 13-103 (108)
62 PF05119 Terminase_4: Phage te 20.0 76 0.0016 22.1 1.8 40 46-85 56-95 (100)
63 cd03567 VHS_GGA VHS domain fam 20.0 2.8E+02 0.0061 21.4 5.1 65 41-116 23-92 (139)
No 1
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=100.00 E-value=2.4e-34 Score=224.40 Aligned_cols=124 Identities=43% Similarity=0.656 Sum_probs=112.7
Q ss_pred CeeecCCcccCcHHHHHHHHHhhc-----CCCCCCC------CCcccccchHHHHHHHhhCc-ccccCHHHHHHHHHHhh
Q 031131 1 MKILEANAGPLTNFEVFDFLRCKG-----ASKDPTR------VLVPVTPSEFKVYDYLVESA-ACNQTRNIINEFLEKSK 68 (165)
Q Consensus 1 MkIl~~~~a~LSN~EVl~~L~~~~-----~~~~~~~------~~~~l~~~e~e~l~YL~~~p-~~~qt~e~i~~l~~~L~ 68 (165)
|||+++|++.|||||||+||.+.+ +.+...+ ..+++.+++|+|++||..+| |+.|++|+|.+|+..|+
T Consensus 1 MKvl~ar~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~ 80 (149)
T KOG4168|consen 1 MKVLKARNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLK 80 (149)
T ss_pred CchhhhhHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhc
Confidence 999999999999999999999876 2222222 23568899999999999999 89999999999999999
Q ss_pred cCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCC-CHHHHHHHHHHHHHhCCCCCCC
Q 031131 69 KFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRF-QEEELQELVDLVIEVLPPLPNQ 124 (165)
Q Consensus 69 ~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~Rf-sEeqieeIL~iI~e~L~~~~~~ 124 (165)
.|+|||+|+|||+|++|++.|+||+|||+||+|| +++++.++++.|..+||+.|..
T Consensus 81 ~fkLtKAE~LqiiN~rPss~vel~~~iE~~eeRf~~ee~i~elv~~i~~~~P~~P~~ 137 (149)
T KOG4168|consen 81 SFKLTKAEILQIINLRPSSSVELYLIIEEVEERFQDEEDIEELVETISKTLPATPKN 137 (149)
T ss_pred cccchHHHHHHHhccCcchHHHHHHHHHHHHHhccchhcHHHHHHhccccCCCCccc
Confidence 9999999999999999999999999999999999 9999999999999999977754
No 2
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=99.95 E-value=7.4e-28 Score=182.42 Aligned_cols=113 Identities=35% Similarity=0.376 Sum_probs=101.8
Q ss_pred CcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCC
Q 031131 7 NAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPS 86 (165)
Q Consensus 7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pt 86 (165)
++..|||+||+.+|++++..+.+.+...++.++.+++++||+++| ..+++++|.+|++.|++|+|||+|++||+|+||+
T Consensus 5 ~a~~L~n~Ev~~ll~~k~~~~~~~~~~~~l~~v~~~tl~Yl~~~~-~~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~ 83 (118)
T smart00657 5 NATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFA-RFKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPE 83 (118)
T ss_pred chhHhHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC
Confidence 457899999999999876555444445566777799999999998 6889999999999999999999999999999999
Q ss_pred cHHHHHHhhcccccCCCHHHHHHHHHHHHHhCCC
Q 031131 87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120 (165)
Q Consensus 87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~~ 120 (165)
|++|+++||++|++||+|+++++||++|++++|.
T Consensus 84 s~~E~~~lI~sl~~r~~ee~l~~iL~~i~~~~~~ 117 (118)
T smart00657 84 TAEEAQLLIPSLEERIDEEELEELLDDLSSLLPF 117 (118)
T ss_pred CHHHHHHHhhhhhccCCHHHHHHHHHHHHHhcCC
Confidence 9999999999999999999999999999999874
No 3
>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=99.94 E-value=3.1e-27 Score=176.64 Aligned_cols=108 Identities=35% Similarity=0.546 Sum_probs=89.2
Q ss_pred cCcHHHHHHHHHhhcCCC-CC--------CCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHH
Q 031131 10 PLTNFEVFDFLRCKGASK-DP--------TRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNI 80 (165)
Q Consensus 10 ~LSN~EVl~~L~~~~~~~-~~--------~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQI 80 (165)
+|||+||+++|+++.+.+ .. .+...++.++.+++++||++ |+..++++.+.+|++.|+.|+||++|++||
T Consensus 1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~-~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi 79 (117)
T PF03874_consen 1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEK-FSKFQNPESIKELREELKKFGLTEFEILQI 79 (117)
T ss_dssp EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHH-H-SSSSHHHHHHHHHHHTTSTS-HHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHc-cccCCCHHHHHHHHHHHhcccCCHHHHHHH
Confidence 589999999999543321 11 12334666777999999999 888889999999999999999999999999
Q ss_pred hcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131 81 INIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVL 118 (165)
Q Consensus 81 vNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L 118 (165)
+|++|+|++|+++||++|+.||+|+++++||++|+++.
T Consensus 80 ~Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~~v~~~~ 117 (117)
T PF03874_consen 80 INLRPTTAVELRAIIESLESRFSEEDLEEILDLVSKYR 117 (117)
T ss_dssp HHH--SSHHHHHHHSTTGTTTSTHHHHHHHHHHHHHHT
T ss_pred hcCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999863
No 4
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=99.57 E-value=2.3e-14 Score=108.18 Aligned_cols=102 Identities=20% Similarity=0.240 Sum_probs=88.7
Q ss_pred cccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcC-CCCHHHHHHHhcCCCC
Q 031131 8 AGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKF-KLAKAEILNIINIRPS 86 (165)
Q Consensus 8 ~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f-~LTk~E~LQIvNl~Pt 86 (165)
...|||.||..+|.++...+ .++....++++|++++. +.+++...++++.|... +|++.+..||+|+||.
T Consensus 9 e~~lt~sEa~~iL~~~~~~~-------els~~~~ktl~y~~kFs--k~~~e~a~elve~L~~~~~l~e~~a~~I~nL~P~ 79 (112)
T PRK14981 9 EEYITIAEAKEILSEIEEER-------ELSYELRRTLDYLNRFS--KLDPEDAEELVEELLELEKMKEKTAVKIADILPE 79 (112)
T ss_pred cccccHHHHHHHHHHHHhcc-------chhHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHccCCCHHHHHHHHhcCCC
Confidence 35899999999999887664 34444589999999995 45788888999998664 5799999999999999
Q ss_pred cHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131 87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVL 118 (165)
Q Consensus 87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L 118 (165)
|+.|+.+|+.....+|+++++++||++|+++.
T Consensus 80 ~~dElrai~~~~~~~~~~e~l~~ILd~l~k~~ 111 (112)
T PRK14981 80 TRDELRAIFAKERYTLSPEELDEILDIVKKYR 111 (112)
T ss_pred CHHHHHHHHHHhccCCCHHHHHHHHHHHHHhh
Confidence 99999999999988999999999999999873
No 5
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.30 E-value=8.2e-12 Score=96.23 Aligned_cols=108 Identities=14% Similarity=0.150 Sum_probs=91.7
Q ss_pred ccCcHHHHHHHHHhhcCCCC-CCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCc
Q 031131 9 GPLTNFEVFDFLRCKGASKD-PTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSS 87 (165)
Q Consensus 9 a~LSN~EVl~~L~~~~~~~~-~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts 87 (165)
..|.|.||.-+|.++..+.+ .....+.+..+-.+++.|+..+. +.-+++.+..+..-|...+|+|.|+-||-|+||.|
T Consensus 22 ~~L~~sEa~lllE~~~~q~~rs~d~~~~~s~Vf~kTl~Y~~~Fs-RfKn~etv~avr~iLs~~~lhkFE~A~lgnLcpet 100 (134)
T KOG2351|consen 22 DALMLSEARLLLEHRLEQRRRSEDDESEMSDVFKKTLQYLDRFS-RFKNRETVRAVRTILSGKGLHKFEVAQLGNLCPET 100 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHhhCCcchhhHHHHhccCccc
Confidence 35789999999998765443 33333344444489999999874 55689999999999999999999999999999999
Q ss_pred HHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131 88 LVEVDSIIEQCDTRFQEEELQELVDLVIEV 117 (165)
Q Consensus 88 ~veL~~iIEe~e~RfsEeqieeIL~iI~e~ 117 (165)
+.|-.++|..++.|++|+.+++||+-|+..
T Consensus 101 aEEAkaLvPSL~nkidD~~le~iL~dls~l 130 (134)
T KOG2351|consen 101 AEEAKALVPSLENKIDDDELEQILKDLSTL 130 (134)
T ss_pred HHHHHHhccccccccCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999864
No 6
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.75 E-value=1.5e-07 Score=71.67 Aligned_cols=102 Identities=20% Similarity=0.221 Sum_probs=87.7
Q ss_pred cccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhc-CCCCHHHHHHHhcCCCC
Q 031131 8 AGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKK-FKLAKAEILNIINIRPS 86 (165)
Q Consensus 8 ~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~-f~LTk~E~LQIvNl~Pt 86 (165)
...+|=.||..+|.++.... .++..++.+++|+.++. +..++..+++++.|.. +++.+.-..-|+.++|+
T Consensus 10 ~~yiti~Eak~il~~~~~~~-------eL~y~~~~al~y~~kFa--kldpe~a~e~veEL~~i~~~~e~~avkIadI~P~ 80 (114)
T COG1460 10 EKYITISEAKKILSKVEREE-------ELTYEQREALEYAEKFA--KLDPEKARELVEELLSIVKMSEKIAVKIADIMPR 80 (114)
T ss_pred ccCccHHHHHHHHHHhcccc-------cchHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHhhccccHHHHHHHHHhCCC
Confidence 45788999999998873332 56666789999999994 5779999999999976 45788888999999999
Q ss_pred cHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131 87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVL 118 (165)
Q Consensus 87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L 118 (165)
|..||++|..--..++|+|++++||++|..+.
T Consensus 81 t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~ 112 (114)
T COG1460 81 TPDELRSILAKERVMLSDEELDKILDIVDKYR 112 (114)
T ss_pred CHHHHHHHHHHccCCCCHHHHHHHHHHHHHHh
Confidence 99999999999889999999999999998763
No 7
>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]
Probab=97.41 E-value=0.00079 Score=52.07 Aligned_cols=76 Identities=12% Similarity=0.121 Sum_probs=68.6
Q ss_pred hHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHH
Q 031131 40 EFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIE 116 (165)
Q Consensus 40 e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e 116 (165)
-+.|+.||..+ |..-+.+....+..-|+.-||.+.|+-|+=-++|.|+.|...+|..+-.|.+|...+.|++.++.
T Consensus 58 ~k~T~~Yl~~F-~Rfkd~e~~~a~~~~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nkidD~~lq~ilkels~ 133 (138)
T COG5250 58 FKSTLGYLDDF-CRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNKIDDAILQAILKELSL 133 (138)
T ss_pred HHHHHHHHHHH-HHhhhHHHHHHHHHHHccCCcchhhHHHhhccccccHHHHHhhcccccccccHHHHHHHHHHHHH
Confidence 37899999986 34556788999999999999999999999999999999999999999999999999999988764
No 8
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=84.35 E-value=1.4 Score=35.23 Aligned_cols=65 Identities=18% Similarity=0.249 Sum_probs=47.8
Q ss_pred chHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhccccc--CCCHHHHHHHHHH
Q 031131 39 SEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDT--RFQEEELQELVDL 113 (165)
Q Consensus 39 ~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~--RfsEeqieeIL~i 113 (165)
..|+|++||...+| + .......++.+-+-+++| |..|++.-+.+..|.+--. -.+.|-|-+++.+
T Consensus 12 tnyEVl~fL~el~~--~------n~~~~k~s~r~~~Q~~~~--~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k 78 (149)
T KOG4168|consen 12 TNYEVLQFLNELEC--M------NEEADKSSHRLGAQNILQ--NDLPTITYETLKYLSDNKNASTQTNESIIELITK 78 (149)
T ss_pred hhHHHHHHHHHhhh--h------hhhhhhhhhhhhcccccc--cccchhHHHHHHHHhcCcccccccHHHHHHHHHH
Confidence 35999999999998 3 333455778888999999 9999999999988887662 2455544444433
No 9
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=80.84 E-value=2.1 Score=34.21 Aligned_cols=86 Identities=20% Similarity=0.302 Sum_probs=53.2
Q ss_pred ccCcHHHHHHHHHhhcCCCCCCCCCcccccchHH----HHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCC
Q 031131 9 GPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFK----VYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIR 84 (165)
Q Consensus 9 a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e----~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~ 84 (165)
..=||.||.+.|.+-++.+- ++..+.++ ++.-+.+. . ..-....|++-|+.|+=-..=.+
T Consensus 42 ~nPT~aeV~k~l~~~~~~~~------~~~rl~FE~fLpm~q~vakn--k--~q~t~edfvegLrvFDkeg~G~i------ 105 (152)
T KOG0030|consen 42 QNPTNAEVLKVLGQPKRREM------NVKRLDFEEFLPMYQQVAKN--K--DQGTYEDFVEGLRVFDKEGNGTI------ 105 (152)
T ss_pred CCCcHHHHHHHHcCcccchh------hhhhhhHHHHHHHHHHHHhc--c--ccCcHHHHHHHHHhhcccCCcce------
Confidence 34589999999976555431 11112232 23334443 1 22466778888888853222221
Q ss_pred CCcHHHHHHhhcccccCCCHHHHHHHHH
Q 031131 85 PSSLVEVDSIIEQCDTRFQEEELQELVD 112 (165)
Q Consensus 85 Pts~veL~~iIEe~e~RfsEeqieeIL~ 112 (165)
..++|+-|+=-+-+|+|+++++++|+
T Consensus 106 --~~aeLRhvLttlGekl~eeEVe~Lla 131 (152)
T KOG0030|consen 106 --MGAELRHVLTTLGEKLTEEEVEELLA 131 (152)
T ss_pred --eHHHHHHHHHHHHhhccHHHHHHHHc
Confidence 24678888888899999999999986
No 10
>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=70.41 E-value=2.4 Score=26.56 Aligned_cols=24 Identities=21% Similarity=0.296 Sum_probs=18.0
Q ss_pred HHHHhh-cCCCCHHHHHHHhcCCCC
Q 031131 63 FLEKSK-KFKLAKAEILNIINIRPS 86 (165)
Q Consensus 63 l~~~L~-~f~LTk~E~LQIvNl~Pt 86 (165)
=++.|. .|+|++...=||||.||.
T Consensus 11 n~~~L~~~f~ip~~vAk~IV~~C~~ 35 (40)
T PF02022_consen 11 NAKALRHKFGIPRLVAKQIVNQCPK 35 (40)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHSCC
T ss_pred CHHHHHHHHccCHHHHHHHHHHCHH
Confidence 345666 799999999999999996
No 11
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=64.49 E-value=47 Score=26.71 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=20.1
Q ss_pred cHHHHHHhhcccccCCCHHHHHHHHHHH
Q 031131 87 SLVEVDSIIEQCDTRFQEEELQELVDLV 114 (165)
Q Consensus 87 s~veL~~iIEe~e~RfsEeqieeIL~iI 114 (165)
+.-+|..++-.+.+|++++++++||..+
T Consensus 110 s~~eL~~vl~~lge~~~deev~~ll~~~ 137 (160)
T COG5126 110 SIGELRRVLKSLGERLSDEEVEKLLKEY 137 (160)
T ss_pred cHHHHHHHHHhhcccCCHHHHHHHHHhc
Confidence 4566667777777777777777777654
No 12
>PLN03217 transcription factor ATBS1; Provisional
Probab=63.71 E-value=7.6 Score=28.59 Aligned_cols=22 Identities=27% Similarity=0.626 Sum_probs=20.0
Q ss_pred cCCCHHHHHHHHHHHHHhCCCC
Q 031131 100 TRFQEEELQELVDLVIEVLPPL 121 (165)
Q Consensus 100 ~RfsEeqieeIL~iI~e~L~~~ 121 (165)
.|+|||||.+++..++..||.-
T Consensus 15 ~risddqi~dLvsKLq~llPe~ 36 (93)
T PLN03217 15 SRISEDQINDLIIKLQQLLPEL 36 (93)
T ss_pred CCCCHHHHHHHHHHHHHHChHH
Confidence 3899999999999999999954
No 13
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=54.96 E-value=36 Score=27.39 Aligned_cols=57 Identities=19% Similarity=0.305 Sum_probs=45.1
Q ss_pred CHHHHHHHHHHh-hcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131 56 TRNIINEFLEKS-KKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEV 117 (165)
Q Consensus 56 t~e~i~~l~~~L-~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~ 117 (165)
+.|.|.+.++++ ...+||..|---..|++|+| ||-|+.-.+-|+ +.+.+|+..|+++
T Consensus 13 s~E~F~~~l~~~l~Elglt~~eFak~anIP~St---LYKil~G~dpr~--~tl~~I~ktir~~ 70 (170)
T COG4800 13 SGEDFGSCLQKLLDELGLTPSEFAKRANIPLST---LYKILKGSDPRY--DTLTRIFKTIRSY 70 (170)
T ss_pred chhHHHHHHHHHHHHcCCCHHHHHHHcCCCHHH---HHHHHhCCCccH--HHHHHHHHHHHHH
Confidence 456666666554 56899999999999999998 788998866565 5688999998766
No 14
>PRK05445 hypothetical protein; Validated
Probab=53.70 E-value=17 Score=29.47 Aligned_cols=45 Identities=16% Similarity=0.283 Sum_probs=32.4
Q ss_pred CCCHHHHHHHhcC-------CCCcHHHHHHhhcccccCC--------------CHHHHHHHHHHHH
Q 031131 71 KLAKAEILNIINI-------RPSSLVEVDSIIEQCDTRF--------------QEEELQELVDLVI 115 (165)
Q Consensus 71 ~LTk~E~LQIvNl-------~Pts~veL~~iIEe~e~Rf--------------sEeqieeIL~iI~ 115 (165)
.||++|.|.|.|+ -|.+...-..+++-+|+=| |++++..+++++.
T Consensus 2 ~mt~~eRliLsNQy~il~~l~pena~~Y~~~~~ile~Gy~l~~~el~~~~~~lse~~c~~ViDILe 67 (164)
T PRK05445 2 EMTNAQRLILSNQYKIMTMLDPENAERYRRLQTIIERGYGLQMRELDREFGELTEETCRTVIDIME 67 (164)
T ss_pred CCcHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhhhhhHHHHHHhhcccCCHHHHHHHHHHHH
Confidence 5788899998885 4777666555554444334 8999999998874
No 15
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=51.41 E-value=57 Score=25.05 Aligned_cols=76 Identities=18% Similarity=0.164 Sum_probs=47.5
Q ss_pred hHHHHHHHhhCcc----cccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccc-cCCCHH-HHHHHHHH
Q 031131 40 EFKVYDYLVESAA----CNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCD-TRFQEE-ELQELVDL 113 (165)
Q Consensus 40 e~e~l~YL~~~p~----~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e-~RfsEe-qieeIL~i 113 (165)
..+++.||.+.-. ...+++.+.+++..+..-.+|+.-.=+|+-..-.+.-....+|++.. .++|++ ++.+|++-
T Consensus 20 ~~el~~~l~~~~~~~~~~~i~~~~l~~li~lv~~g~It~~~ak~vl~~~~~~~~~~~~ii~~~~l~~isd~~el~~~v~~ 99 (147)
T smart00845 20 LGELLGELNKEGLEIEESPITPEHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEEIVEEKGLKQISDEGELEAIVDE 99 (147)
T ss_pred HHHHHHHHHhCCCCHhhCCCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCHHHHHHHcCCccCCCHHHHHHHHHH
Confidence 3566777765422 24678999999999988888865554444333222223556777765 467864 67776665
Q ss_pred HH
Q 031131 114 VI 115 (165)
Q Consensus 114 I~ 115 (165)
|-
T Consensus 100 vi 101 (147)
T smart00845 100 VI 101 (147)
T ss_pred HH
Confidence 43
No 16
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=51.25 E-value=16 Score=26.36 Aligned_cols=23 Identities=13% Similarity=0.332 Sum_probs=19.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHh
Q 031131 59 IINEFLEKSKKFKLAKAEILNII 81 (165)
Q Consensus 59 ~i~~l~~~L~~f~LTk~E~LQIv 81 (165)
.-++|+++|+.|++|+.|..+.|
T Consensus 64 N~KqllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 64 NAKQLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHh
Confidence 34679999999999999988764
No 17
>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=44.77 E-value=12 Score=24.53 Aligned_cols=24 Identities=29% Similarity=0.396 Sum_probs=18.4
Q ss_pred CCCHHHHHHHhcCCCCcHHHHHHh
Q 031131 71 KLAKAEILNIINIRPSSLVEVDSI 94 (165)
Q Consensus 71 ~LTk~E~LQIvNl~Pts~veL~~i 94 (165)
=|+..-...|+..+|+|..+|..|
T Consensus 26 Il~~~~L~~ia~~~P~s~~~L~~i 49 (68)
T PF00570_consen 26 ILSDEALLEIAKRLPTSIEELLQI 49 (68)
T ss_dssp HS-HHHHHHHHHH--SSHHHHHTS
T ss_pred ccCHHHHHHHHHhCCCCHHHHHHc
Confidence 367888889999999999999987
No 18
>PRK15443 pduE propanediol dehydratase small subunit; Provisional
Probab=43.66 E-value=30 Score=27.34 Aligned_cols=29 Identities=21% Similarity=0.334 Sum_probs=24.4
Q ss_pred ccCHHHHHHHHHHhhcCCCCHHHHHHHhc
Q 031131 54 NQTRNIINEFLEKSKKFKLAKAEILNIIN 82 (165)
Q Consensus 54 ~qt~e~i~~l~~~L~~f~LTk~E~LQIvN 82 (165)
...++.|-++.++|+||.=||.|.|.|.+
T Consensus 78 ~vpD~rvLeiYnaLRP~RStk~ELl~iA~ 106 (138)
T PRK15443 78 AVPDDRILEIYNALRPYRSTKEELLAIAD 106 (138)
T ss_pred CCCHHHHHHHHHhhCCCcccHHHHHHHHH
Confidence 35689999999999999999998887765
No 19
>cd07313 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=43.56 E-value=31 Score=24.28 Aligned_cols=65 Identities=17% Similarity=0.139 Sum_probs=41.3
Q ss_pred cccCHHHHHHHHHHhhc-CCCCHHHHHHHhcCCC---CcHHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131 53 CNQTRNIINEFLEKSKK-FKLAKAEILNIINIRP---SSLVEVDSIIEQCDTRFQEEELQELVDLVIEV 117 (165)
Q Consensus 53 ~~qt~e~i~~l~~~L~~-f~LTk~E~LQIvNl~P---ts~veL~~iIEe~e~RfsEeqieeIL~iI~e~ 117 (165)
+..+++.+..+...|.. |+|+..+.-++++..= .....++.....+-.+|+.++...++..+-+.
T Consensus 14 G~v~~~E~~~i~~~l~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~L~~v 82 (104)
T cd07313 14 GEYDEEERAAIDRLLAERFGLDAEEAAELLAEAEALEEEAPDLYEFTSLIKEHFDYEERLELVEALWEV 82 (104)
T ss_pred CCCCHHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 34566666666666665 7888777766655332 23344666666666677777777777776554
No 20
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=41.38 E-value=39 Score=23.87 Aligned_cols=53 Identities=19% Similarity=0.402 Sum_probs=35.7
Q ss_pred CHHHHHHHHHHhhcCCCCHHHHHHHhcCC---C--------CcHHHHHHhhcccccCCCHHHHHHHHHHHHH
Q 031131 56 TRNIINEFLEKSKKFKLAKAEILNIINIR---P--------SSLVEVDSIIEQCDTRFQEEELQELVDLVIE 116 (165)
Q Consensus 56 t~e~i~~l~~~L~~f~LTk~E~LQIvNl~---P--------ts~veL~~iIEe~e~RfsEeqieeIL~iI~e 116 (165)
+.+.+...++.++ ++|++||.. | ..+.+||-+|.- ..+||..+++.|.+-+.+
T Consensus 5 s~ENv~~MIe~Ik-------~KL~mvN~~~i~~~~f~~~~yedl~diy~~V~~-K~~fS~sEm~aI~~ELG~ 68 (71)
T PF06569_consen 5 SQENVEYMIEEIK-------QKLNMVNAGAIKPEDFSEEKYEDLKDIYEMVMS-KDSFSPSEMQAIAEELGQ 68 (71)
T ss_pred cHHHHHHHHHHHH-------HHHHHhhHHhCCHHhCChhhHHHHHHHHHHHHh-ccCCCHHHHHHHHHHHHh
Confidence 4555555554443 467777754 2 356788888887 668999999998876543
No 21
>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=41.09 E-value=1.1e+02 Score=22.66 Aligned_cols=73 Identities=11% Similarity=0.155 Sum_probs=46.1
Q ss_pred HHHHHHHhh-CcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCC------CCcHHHHHHhhcccccC-CCHHHHHHHHH
Q 031131 41 FKVYDYLVE-SAACNQTRNIINEFLEKSKKFKLAKAEILNIINIR------PSSLVEVDSIIEQCDTR-FQEEELQELVD 112 (165)
Q Consensus 41 ~e~l~YL~~-~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~------Pts~veL~~iIEe~e~R-fsEeqieeIL~ 112 (165)
..++++|+. +|.. .......-|+--|..- ||..|+-+|+... |.+.++|...|-..=.. -|+++|+.+..
T Consensus 6 ~~iv~WLRaGYP~G-vP~~Dy~PLlALL~r~-Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt~~~P~~~di~RV~~ 83 (96)
T PF11829_consen 6 ASIVDWLRAGYPEG-VPPTDYVPLLALLRRR-LTDDEVAEVAAELAARGDPPVDRIDIGVAITRVTDELPTPEDIERVRA 83 (96)
T ss_dssp HHHHHHHHHH-TT--B-HHHHHHHHHHHTTT-S-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHHHCSS-S-HHHHHHHHH
T ss_pred HHHHHHHHccCCCC-CCCCccHHHHHHhccc-CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHcCCcCHHHHHHHHH
Confidence 356777764 4432 3345555566555554 8888888877543 66888888888877666 48888888877
Q ss_pred HHH
Q 031131 113 LVI 115 (165)
Q Consensus 113 iI~ 115 (165)
.+.
T Consensus 84 ~La 86 (96)
T PF11829_consen 84 RLA 86 (96)
T ss_dssp HHH
T ss_pred HHH
Confidence 665
No 22
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=40.75 E-value=44 Score=20.38 Aligned_cols=34 Identities=26% Similarity=0.464 Sum_probs=21.7
Q ss_pred chHHHHHHHhhCcccc---------cCHHHHHHHHHHhhcCCC
Q 031131 39 SEFKVYDYLVESAACN---------QTRNIINEFLEKSKKFKL 72 (165)
Q Consensus 39 ~e~e~l~YL~~~p~~~---------qt~e~i~~l~~~L~~f~L 72 (165)
.+++++.||...|..+ .+...+...++.|...|+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence 3577888888877532 356677777777765554
No 23
>PF02287 Dehydratase_SU: Dehydratase small subunit; InterPro: IPR003207 This family contains the small subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances [, ].; PDB: 1IWP_M 1MMF_M 1UC4_M 1EEX_M 3AUJ_G 1IWB_M 1DIO_G 1UC5_G 1EGM_G 1EGV_M ....
Probab=40.16 E-value=38 Score=26.74 Aligned_cols=28 Identities=21% Similarity=0.347 Sum_probs=21.2
Q ss_pred cCHHHHHHHHHHhhcCCCCHHHHHHHhc
Q 031131 55 QTRNIINEFLEKSKKFKLAKAEILNIIN 82 (165)
Q Consensus 55 qt~e~i~~l~~~L~~f~LTk~E~LQIvN 82 (165)
..++.|-++.++|+||.=||.|.|.|.+
T Consensus 80 VPD~riLeiYnaLRP~RStK~ELl~iA~ 107 (136)
T PF02287_consen 80 VPDDRILEIYNALRPYRSTKQELLAIAD 107 (136)
T ss_dssp S-HHHHHHHHHHHSTTS--HHHHHHHHH
T ss_pred CCHHHHHHHHHhhCCCcccHHHHHHHHH
Confidence 4689999999999999989988877654
No 24
>PHA00650 hypothetical protein
Probab=39.69 E-value=28 Score=24.50 Aligned_cols=13 Identities=38% Similarity=0.685 Sum_probs=10.5
Q ss_pred HhhcCCCCHHHHH
Q 031131 66 KSKKFKLAKAEIL 78 (165)
Q Consensus 66 ~L~~f~LTk~E~L 78 (165)
.+..|++||+|.|
T Consensus 67 tierfgftkaell 79 (82)
T PHA00650 67 TIERFGFTKAELL 79 (82)
T ss_pred HHHHhcchHHhhh
Confidence 3467999999986
No 25
>PRK13689 hypothetical protein; Provisional
Probab=35.57 E-value=31 Score=24.63 Aligned_cols=19 Identities=21% Similarity=0.656 Sum_probs=16.8
Q ss_pred cCCCHHHHHHHHHHHHHhC
Q 031131 100 TRFQEEELQELVDLVIEVL 118 (165)
Q Consensus 100 ~RfsEeqieeIL~iI~e~L 118 (165)
+|+|++|+++||.-+-..|
T Consensus 5 SKYsd~qvE~il~el~~VL 23 (75)
T PRK13689 5 SKYSDEQVEQLLAELLAVL 23 (75)
T ss_pred ccccHHHHHHHHHHHHHHH
Confidence 6999999999999887776
No 26
>PF13929 mRNA_stabil: mRNA stabilisation
Probab=35.47 E-value=62 Score=28.58 Aligned_cols=59 Identities=22% Similarity=0.282 Sum_probs=38.4
Q ss_pred cCCcccCcHHHHHHHHHh-hcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhc
Q 031131 5 EANAGPLTNFEVFDFLRC-KGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKK 69 (165)
Q Consensus 5 ~~~~a~LSN~EVl~~L~~-~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~ 69 (165)
++....++|.||+..|=+ .-.+.+. . .+.. |++++|+..+-....++..|..+++.|..
T Consensus 155 ~~~~~Ii~d~evislLL~sMv~~~~~--~-l~al---YEvV~~l~~t~~~~l~~~vi~~Il~~L~~ 214 (292)
T PF13929_consen 155 NPDESIIFDEEVISLLLKSMVIDENT--K-LNAL---YEVVDFLVSTFSKSLTRNVIISILEILAE 214 (292)
T ss_pred CcccceeeChHHHHHHHHHHHhcccc--c-hhhH---HHHHHHHHhccccCCChhHHHHHHHHHHh
Confidence 344568899999987643 2221111 1 1233 99999999764466777888888888765
No 27
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=34.92 E-value=76 Score=24.79 Aligned_cols=87 Identities=14% Similarity=0.186 Sum_probs=49.0
Q ss_pred HHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCc--------HHHHHHhhcccccCCCHHHHHHHHH
Q 031131 41 FKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSS--------LVEVDSIIEQCDTRFQEEELQELVD 112 (165)
Q Consensus 41 ~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts--------~veL~~iIEe~e~RfsEeqieeIL~ 112 (165)
|++.+.+........++-++--.+..|..-+|-..+.-.--+-+|+. ...+...+++.. +|. ..++.++.
T Consensus 41 YeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~-~~~-~~l~~ll~ 118 (138)
T TIGR02719 41 YKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFE-HYQ-NMLDSFFH 118 (138)
T ss_pred HHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHH-HHH-HHHHHHHH
Confidence 55555565533233456677777777766665443321111223321 222334444333 333 57889999
Q ss_pred HHHHhCCCCCCCCCccc
Q 031131 113 LVIEVLPPLPNQPNAAE 129 (165)
Q Consensus 113 iI~e~L~~~~~~e~~~~ 129 (165)
...+.||+.+...++++
T Consensus 119 ~~~~~~~~~~~~~~~~~ 135 (138)
T TIGR02719 119 LYTDAFFPFSSSPEKDE 135 (138)
T ss_pred HHHHhccCCCCCCCcCc
Confidence 99999999988766554
No 28
>COG3013 Uncharacterized conserved protein [Function unknown]
Probab=34.83 E-value=24 Score=28.50 Aligned_cols=25 Identities=20% Similarity=0.380 Sum_probs=19.6
Q ss_pred HHHHHHHHHh-hcCCCCHHHHHHHhc
Q 031131 58 NIINEFLEKS-KKFKLAKAEILNIIN 82 (165)
Q Consensus 58 e~i~~l~~~L-~~f~LTk~E~LQIvN 82 (165)
..+..+++.. ++|.|+..|+.||+|
T Consensus 142 ~rMl~~W~~cprqYhLs~~EI~~IlN 167 (168)
T COG3013 142 QRMLNVWHACPRQYHLSANEINQILN 167 (168)
T ss_pred HHHHHHHHhCchhccccHHHHHHHhc
Confidence 4455555554 689999999999999
No 29
>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=34.39 E-value=59 Score=27.46 Aligned_cols=41 Identities=17% Similarity=0.404 Sum_probs=34.6
Q ss_pred HHHHhcCCCCcHHHHHHhhcccccC----CCHHHHHHHHHHHHHh
Q 031131 77 ILNIINIRPSSLVEVDSIIEQCDTR----FQEEELQELVDLVIEV 117 (165)
Q Consensus 77 ~LQIvNl~Pts~veL~~iIEe~e~R----fsEeqieeIL~iI~e~ 117 (165)
|-+|....|.+..+++-||.+.-.- +|++|++.|++++.++
T Consensus 163 K~~va~~~~~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~~~ 207 (225)
T PF06207_consen 163 KEEVAKQKPKTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMKKI 207 (225)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 3477888899999999999887643 7999999999999875
No 30
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.18 E-value=70 Score=22.51 Aligned_cols=40 Identities=23% Similarity=0.438 Sum_probs=27.6
Q ss_pred HHHHHhcCCCC-----------cHHHHHHhhcccccCCCHHHHHHHHHHHHH
Q 031131 76 EILNIINIRPS-----------SLVEVDSIIEQCDTRFQEEELQELVDLVIE 116 (165)
Q Consensus 76 E~LQIvNl~Pt-----------s~veL~~iIEe~e~RfsEeqieeIL~iI~e 116 (165)
+||++||..-= .+-.||-+|-- -++||..+++.|-+-+.+
T Consensus 18 ~KLnmvN~gvl~~e~~d~~~~edLtdiy~mvkk-kenfSpsEmqaiA~eL~r 68 (71)
T COG4840 18 EKLNMVNVGVLDPEKYDNANYEDLTDIYDMVKK-KENFSPSEMQAIADELGR 68 (71)
T ss_pred HHHhhhhhhccCHHhcccccHHHHHHHHHHHHH-hccCCHHHHHHHHHHHHH
Confidence 67888887642 35567777776 458999888877665543
No 31
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=33.93 E-value=66 Score=30.11 Aligned_cols=79 Identities=16% Similarity=0.140 Sum_probs=49.5
Q ss_pred hHHHHHHHhhCcc----cccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccc-cCCCHHHHHHHHHHH
Q 031131 40 EFKVYDYLVESAA----CNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCD-TRFQEEELQELVDLV 114 (165)
Q Consensus 40 e~e~l~YL~~~p~----~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e-~RfsEeqieeIL~iI 114 (165)
..+++.+|.+.-. ...+++.+.+|+..+..-.+|+.-.=+|+-..-.+-.....+|++.. ...|++ .+|-++|
T Consensus 347 ~~el~~~l~~~~~~~~~~~i~~~~l~~Li~lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii~~~gl~~isd~--~~l~~iv 424 (474)
T PRK05477 347 MGELLGLLNEEGIEIEESPITPEQLAELIKLIDDGTISGKIAKEVFEEMLETGGDPDEIVEEKGLKQISDE--GALEAIV 424 (474)
T ss_pred HHHHHHHHHHCCCChhhcCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhcCCCHHHHHHHcCCcccCCH--HHHHHHH
Confidence 4667788876432 23688999999999999888876555544433222233667788776 346765 2444455
Q ss_pred HHhCCC
Q 031131 115 IEVLPP 120 (165)
Q Consensus 115 ~e~L~~ 120 (165)
.+.+..
T Consensus 425 ~evi~~ 430 (474)
T PRK05477 425 DEVLAA 430 (474)
T ss_pred HHHHHH
Confidence 555543
No 32
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=33.77 E-value=40 Score=23.81 Aligned_cols=55 Identities=18% Similarity=0.276 Sum_probs=44.4
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhCCCC
Q 031131 58 NIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPPL 121 (165)
Q Consensus 58 e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~~~ 121 (165)
.-.+++++-|..|+++ +-+.|+..+.+..+|.+ ..|+++-.++|++-|++.+.+.
T Consensus 16 GF~rk~L~I~E~~~is-------~Eh~PSGID~~Siii~~--~~~~~~~~~~i~~~i~~~~~pD 70 (76)
T cd04911 16 GFGRKLLSILEDNGIS-------YEHMPSGIDDISIIIRD--NQLTDEKEQKILAEIKEELHPD 70 (76)
T ss_pred cHHHHHHHHHHHcCCC-------EeeecCCCccEEEEEEc--cccchhhHHHHHHHHHHhcCCC
Confidence 3466777777777765 56899999999999986 4588889999999999988754
No 33
>COG3082 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.66 E-value=40 Score=23.85 Aligned_cols=19 Identities=21% Similarity=0.700 Sum_probs=16.3
Q ss_pred cCCCHHHHHHHHHHHHHhC
Q 031131 100 TRFQEEELQELVDLVIEVL 118 (165)
Q Consensus 100 ~RfsEeqieeIL~iI~e~L 118 (165)
+|+||++++.||.-+-..|
T Consensus 5 SkYsDe~ve~il~e~iaVL 23 (74)
T COG3082 5 SKYSDEQVEQILNELIAVL 23 (74)
T ss_pred ccccHHHHHHHHHHHHHHH
Confidence 6899999999998877666
No 34
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=31.64 E-value=31 Score=26.87 Aligned_cols=73 Identities=18% Similarity=0.355 Sum_probs=37.6
Q ss_pred ccchHHHHHHHhhCcccc--cCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhccccc--CCCHHHHHHHHH
Q 031131 37 TPSEFKVYDYLVESAACN--QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDT--RFQEEELQELVD 112 (165)
Q Consensus 37 ~~~e~e~l~YL~~~p~~~--qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~--RfsEeqieeIL~ 112 (165)
.+.|-++++|+++.-.++ .... .. -..|.+|. .=..-|.+||++|.++..+-.-+--+|. ..||+++.+|+.
T Consensus 34 r~lE~KLvK~fSkQL~~K~k~~~~-~~--~~~l~~yP-~l~~WL~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~ 109 (129)
T PF13543_consen 34 RTLEGKLVKYFSKQLQCKAKVAER-ER--AAELNSYP-SLRQWLRVVGLRPESIQAILSKVLTLEALLEMSDEELKEILN 109 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCc-cC--chhcccCC-cHHHHhhhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHH
Confidence 445678899988642211 1111 00 11223331 1234577788888777776433334443 356777776666
Q ss_pred H
Q 031131 113 L 113 (165)
Q Consensus 113 i 113 (165)
-
T Consensus 110 ~ 110 (129)
T PF13543_consen 110 R 110 (129)
T ss_pred H
Confidence 5
No 35
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=31.43 E-value=1.3e+02 Score=22.85 Aligned_cols=51 Identities=20% Similarity=0.309 Sum_probs=36.4
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHH
Q 031131 57 RNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLV 114 (165)
Q Consensus 57 ~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI 114 (165)
...+..+. ...+|+..|..+++.+.++|..-... -..|||-++-+.++.++
T Consensus 25 ~~~~~~l~---~~l~ls~~el~~~lgis~~Tl~R~~~----~~~~Ls~~~serl~~l~ 75 (133)
T TIGR02293 25 IGALDRLA---HLLAIGKAEIFKATGIPKATLQRRKM----AHQRLSSEESDRLARVA 75 (133)
T ss_pred HHHHHHHH---HHHCCCHHHHHHHHCCCHHHHHHHhh----cCCCCCHHHHHHHHHHH
Confidence 34455554 55689999999999988888655542 23499988888776665
No 36
>TIGR02220 phg_TIGR02220 phage conserved hypothetical protein, C-terminal domain. This model represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=31.27 E-value=1.1e+02 Score=21.72 Aligned_cols=40 Identities=15% Similarity=0.197 Sum_probs=18.2
Q ss_pred HHHHHHhhCccccc--CHHHHHHHHHHhhcCCCCHHHHHHHh
Q 031131 42 KVYDYLVESAACNQ--TRNIINEFLEKSKKFKLAKAEILNII 81 (165)
Q Consensus 42 e~l~YL~~~p~~~q--t~e~i~~l~~~L~~f~LTk~E~LQIv 81 (165)
++++||.+.+.+.. +...=..++.+.-.-|+|..+.-++|
T Consensus 3 eii~yLN~ktg~~y~~~~k~~~~lI~aR~~eg~~~~dfk~VI 44 (77)
T TIGR02220 3 EIIEYLNEKAGKSFKHTTAKHKKLIKARWNEGYTLEDFKKVI 44 (77)
T ss_pred HHHHHHHHhcCcccccccHhHHHHHHHHHHcCCCHHHHHHHH
Confidence 45666665443332 22344444444444444444444443
No 37
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=30.84 E-value=20 Score=23.53 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=21.7
Q ss_pred HHHhhcccccCCCHHHHHHHHHHHHHhCC
Q 031131 91 VDSIIEQCDTRFQEEELQELVDLVIEVLP 119 (165)
Q Consensus 91 L~~iIEe~e~RfsEeqieeIL~iI~e~L~ 119 (165)
...++.-....||+++++.|+..-++-+|
T Consensus 6 ~~~~~~~y~~~ft~~El~~i~~FY~Sp~G 34 (64)
T PF09832_consen 6 IDQMAPIYAEHFTEEELDAILAFYESPLG 34 (64)
T ss_dssp HHHHHHHHHHHS-HHHHHHHHHHHHSHHH
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHCCHHh
Confidence 34566777889999999999998776554
No 38
>PRK07758 hypothetical protein; Provisional
Probab=29.81 E-value=53 Score=24.41 Aligned_cols=27 Identities=30% Similarity=0.534 Sum_probs=23.9
Q ss_pred CCCHHHHHHHhcCCCCcHHHHHHhhcc
Q 031131 71 KLAKAEILNIINIRPSSLVEVDSIIEQ 97 (165)
Q Consensus 71 ~LTk~E~LQIvNl~Pts~veL~~iIEe 97 (165)
.+++.|.+.|=|+.|.|+.+|..-+.+
T Consensus 63 ~~te~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 63 KYSEKEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred cCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence 789999999999999999999866655
No 39
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=29.78 E-value=67 Score=21.39 Aligned_cols=50 Identities=14% Similarity=0.206 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhCCC
Q 031131 70 FKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120 (165)
Q Consensus 70 f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~~ 120 (165)
+=|+...++.|...+|+|..+|..+-.- ..++-...-..++++|+.+...
T Consensus 28 ~I~~~~~L~~ia~~~P~~~~~L~~i~g~-~~~~~~~~g~~~~~~i~~~~~~ 77 (81)
T smart00341 28 FVLPDETLIKMAAALPTNVSELLAIDGV-GEEKARRYGKDLLAVIQEASDS 77 (81)
T ss_pred EEECHHHHHHHHHHCCCCHHHHhcCCCC-CHHHHHHHHHHHHHHHHHHHhc
Confidence 3578889999999999999988775333 2233334456788888876643
No 40
>COG4910 PduE Propanediol dehydratase, small subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.53 E-value=68 Score=25.68 Aligned_cols=27 Identities=22% Similarity=0.386 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHhhcCCCCHHHHHHHhc
Q 031131 56 TRNIINEFLEKSKKFKLAKAEILNIIN 82 (165)
Q Consensus 56 t~e~i~~l~~~L~~f~LTk~E~LQIvN 82 (165)
..+.|-++.+.|+||.=+|.|.|+|..
T Consensus 112 PddrIleiYnalRPyRsskEELLaiAd 138 (170)
T COG4910 112 PDDRILEIYNALRPYRSSKEELLAIAD 138 (170)
T ss_pred cHHHHHHHHHHhCcccccHHHHHHHHH
Confidence 468888889999999889999888864
No 41
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=29.25 E-value=80 Score=31.38 Aligned_cols=75 Identities=13% Similarity=0.129 Sum_probs=48.4
Q ss_pred hHHHHHHHhhC--cccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccc-cCCCH-HHHHHHHHHH
Q 031131 40 EFKVYDYLVES--AACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCD-TRFQE-EELQELVDLV 114 (165)
Q Consensus 40 e~e~l~YL~~~--p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e-~RfsE-eqieeIL~iI 114 (165)
..+++.+|.+. .....+++.+.+|+..+..=.+|..-.=+|+...-.+-.....||++.. .+.|+ ++++.|++-|
T Consensus 645 ~~El~~~Lne~~i~~~~l~pe~LaeLv~lV~~g~IS~~~AK~VL~~m~~~~~~p~~IIee~GL~qisDe~~Le~iV~eV 723 (771)
T PRK14703 645 VNDLAGLLRDRELAALPFTPAALARLVALVDAGRISTRIAKDVLAELAASGGDPEAIVEAKGLEQVSDAGALEPIVEEV 723 (771)
T ss_pred HHHHHHHHhcCCCccCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhcCCCHHHHHHhcCCcccCCHHHHHHHHHHH
Confidence 46778888764 3345788999999999988888876655555544232234567888876 34555 4455544433
No 42
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. 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=28.91 E-value=78 Score=22.69 Aligned_cols=69 Identities=13% Similarity=0.192 Sum_probs=41.7
Q ss_pred chHHHHHHHhhC----ccc------ccCHHHHH--HHHHHhhc-CCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHH
Q 031131 39 SEFKVYDYLVES----AAC------NQTRNIIN--EFLEKSKK-FKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEE 105 (165)
Q Consensus 39 ~e~e~l~YL~~~----p~~------~qt~e~i~--~l~~~L~~-f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEe 105 (165)
+...++.|..+. |.. .+++..+. .++..|+. +|++-.++-++++.++.- -+-+.++..+
T Consensus 12 vs~~tLR~ye~~Gll~p~r~~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~--------~~~~~~~~~~ 83 (96)
T cd04774 12 LTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEP--------VDGGHRYSAE 83 (96)
T ss_pred cCHHHHHHHHHCCCCCCCcCCCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccc--------cchhHHHHHH
Confidence 346666666542 211 24555554 44557888 999999999999998864 1223455555
Q ss_pred HHHHHHHHHH
Q 031131 106 ELQELVDLVI 115 (165)
Q Consensus 106 qieeIL~iI~ 115 (165)
-+.++.+.+.
T Consensus 84 ~l~~~~~~l~ 93 (96)
T cd04774 84 SLREIHDALA 93 (96)
T ss_pred HHHHHHHHHH
Confidence 5555555443
No 43
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=28.86 E-value=2.3e+02 Score=20.53 Aligned_cols=24 Identities=38% Similarity=0.541 Sum_probs=16.1
Q ss_pred HHHhhcccccCCCHHHHHHHHHHHHH
Q 031131 91 VDSIIEQCDTRFQEEELQELVDLVIE 116 (165)
Q Consensus 91 L~~iIEe~e~RfsEeqieeIL~iI~e 116 (165)
+..+++.. .+|++++++|-++|.+
T Consensus 92 ~~~l~~~~--~ls~~el~~L~~li~e 115 (115)
T PF03965_consen 92 VAALVESE--ELSPEELEELRKLIDE 115 (115)
T ss_dssp HHHHHHCT---S-HHHHHHHHHHHH-
T ss_pred HHHHHhcC--CCCHHHHHHHHHHHcC
Confidence 44555553 8999999999999864
No 44
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=27.69 E-value=76 Score=26.87 Aligned_cols=32 Identities=22% Similarity=0.352 Sum_probs=26.9
Q ss_pred HHHHHHhhcCCCCHHHH---HHHhcCCCCcHHHHH
Q 031131 61 NEFLEKSKKFKLAKAEI---LNIINIRPSSLVEVD 92 (165)
Q Consensus 61 ~~l~~~L~~f~LTk~E~---LQIvNl~Pts~veL~ 92 (165)
..+++.|+.||||+-|. +-|+++.|.|+-|++
T Consensus 3 ~~~~~~L~~lGlt~yEa~vY~aLl~~g~~tA~eis 37 (247)
T COG1378 3 EELEENLQKLGLTEYEAKVYLALLCLGEATAKEIS 37 (247)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHhCCccHHHHH
Confidence 35678889999999985 789999999988875
No 45
>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=26.79 E-value=1.3e+02 Score=23.20 Aligned_cols=42 Identities=14% Similarity=0.347 Sum_probs=26.7
Q ss_pred HHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCc
Q 031131 41 FKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSS 87 (165)
Q Consensus 41 ~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts 87 (165)
|+.++-|..- ...+.+.+.+|++.|. +....+-.+.++.|.+
T Consensus 72 YE~LK~lTRg--~~it~~~l~~fI~~L~---ip~~~k~~L~~ltP~~ 113 (115)
T PF08328_consen 72 YEKLKELTRG--KKITKEDLREFIESLD---IPEEAKARLLALTPAT 113 (115)
T ss_dssp HHHHHHHHTT--S---HHHHHHHHHTSS---S-HHHHHHHHH--CCC
T ss_pred HHHHHHHHcC--CCCCHHHHHHHHHhCC---CCHHHHHHHHhcCccc
Confidence 5666655543 3578899999996665 8888888888888876
No 46
>cd08337 DED_c-FLIP_repeat1 Death Effector Domain, repeat 1, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 1, similar to that found in FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association
Probab=26.78 E-value=1.1e+02 Score=21.82 Aligned_cols=37 Identities=16% Similarity=0.159 Sum_probs=29.2
Q ss_pred cccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCC
Q 031131 36 VTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKL 72 (165)
Q Consensus 36 l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~L 72 (165)
+...+.+.+.||..-+.+..+.+.++.++..|...++
T Consensus 13 Lds~E~e~L~FLC~D~ip~~~~e~~~~l~~~L~e~~~ 49 (80)
T cd08337 13 LDTDEDELLLFLCRDAAPDCTTAQLRDLLRALNERGK 49 (80)
T ss_pred cChHHHHHHHHHcccccccccchhHHHHHHHHHHcCC
Confidence 3444678899999887777777889999999988764
No 47
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=25.29 E-value=1.5e+02 Score=22.98 Aligned_cols=65 Identities=20% Similarity=0.378 Sum_probs=44.0
Q ss_pred HHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCC-----HHHHHHHHHHHH
Q 031131 41 FKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQ-----EEELQELVDLVI 115 (165)
Q Consensus 41 ~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~Rfs-----EeqieeIL~iI~ 115 (165)
.++.+.+...+ ...+++++.+.++|+.- ....|+. ++.-|.++|..|..||- .+-+++|..+|.
T Consensus 22 l~icD~I~~~~--~~~k~a~ral~KRl~~~----n~~v~l~-----AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~ 90 (144)
T cd03568 22 LDVCDKVKSDE--NGAKDCLKAIMKRLNHK----DPNVQLR-----ALTLLDACAENCGKRFHQEVASRDFTQELKKLIN 90 (144)
T ss_pred HHHHHHHhcCC--ccHHHHHHHHHHHHcCC----CHHHHHH-----HHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhc
Confidence 46778887763 35679999999998753 3344443 67778899999998873 444455555554
Q ss_pred H
Q 031131 116 E 116 (165)
Q Consensus 116 e 116 (165)
.
T Consensus 91 ~ 91 (144)
T cd03568 91 D 91 (144)
T ss_pred c
Confidence 4
No 48
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=23.85 E-value=8.3 Score=25.53 Aligned_cols=47 Identities=11% Similarity=0.198 Sum_probs=36.5
Q ss_pred CcccccCHHHHHHHHHHhhcC-----CCCHHHHHHHhcCCCCcHHHHHHhhc
Q 031131 50 SAACNQTRNIINEFLEKSKKF-----KLAKAEILNIINIRPSSLVEVDSIIE 96 (165)
Q Consensus 50 ~p~~~qt~e~i~~l~~~L~~f-----~LTk~E~LQIvNl~Pts~veL~~iIE 96 (165)
.|+...+.+.++.|.+..+.| .||...-|+|.|+.+.++..+...+.
T Consensus 16 ~~~G~i~~~~l~~la~ia~~yg~~~irlT~~Q~l~l~~v~~~~~~~i~~~L~ 67 (69)
T PF03460_consen 16 IPGGRISAEQLRALAEIAEKYGDGEIRLTTRQNLQLRGVPEENLPAIFEELK 67 (69)
T ss_dssp -GGGEEEHHHHHHHHHHHHHHSTSEEEEETTSCEEEEEEEGGGHHHHHHHHH
T ss_pred CCCEEECHHHHHHHHHHHHHhCCCeEEECCCCeEEEeCCCHHHHHHHHHHHH
Confidence 466777888888888777766 47888899999999998888776554
No 49
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=23.82 E-value=64 Score=26.93 Aligned_cols=34 Identities=29% Similarity=0.317 Sum_probs=28.1
Q ss_pred cHHHHHHhhcccccCCCHHHHHHHHHHHHHhCCCC
Q 031131 87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPPL 121 (165)
Q Consensus 87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~~~ 121 (165)
.---+-.+|.|+| |++.+++-++|+.|+..+..+
T Consensus 170 ~~~~iViiIDdLD-R~~~~~i~~~l~~ik~~~~~~ 203 (325)
T PF07693_consen 170 SKKRIVIIIDDLD-RCSPEEIVELLEAIKLLLDFP 203 (325)
T ss_pred CCceEEEEEcchh-cCCcHHHHHHHHHHHHhcCCC
Confidence 3334667899998 999999999999999988764
No 50
>PF07560 DUF1539: Domain of Unknown Function (DUF1539); InterPro: IPR011436 This domain is found in a small number of Chlamydia proteins of unknown function. It occurs together with IPR013044 from INTERPRO.
Probab=23.63 E-value=1.2e+02 Score=23.56 Aligned_cols=43 Identities=21% Similarity=0.366 Sum_probs=33.3
Q ss_pred HHHHHHHhh-C-------cccccCHHHHHHHHHHhhcCCCCHHHHHHHhcC
Q 031131 41 FKVYDYLVE-S-------AACNQTRNIINEFLEKSKKFKLAKAEILNIINI 83 (165)
Q Consensus 41 ~e~l~YL~~-~-------p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl 83 (165)
+.+++||.. + |.....+..+..|...|+.-..++..|++++|.
T Consensus 42 ~~IL~~l~~~~~~~~~s~~~~~l~~~~m~~l~~aL~dp~Is~erK~~~l~y 92 (126)
T PF07560_consen 42 FKILDYLSTKSSPEDESHPDQSLFRSTMHQLIKALQDPTISKERKREALNY 92 (126)
T ss_pred HHHHHHHhccccccccCChhHHHHHHHHHHHHHHhcCCCCChHHHHHHHHH
Confidence 578999986 2 222234678888999999999999999999864
No 51
>PRK05445 hypothetical protein; Validated
Probab=23.57 E-value=51 Score=26.65 Aligned_cols=25 Identities=24% Similarity=0.460 Sum_probs=18.1
Q ss_pred HHHHHHHHHh-hcCCCCHHHHHHHhc
Q 031131 58 NIINEFLEKS-KKFKLAKAEILNIIN 82 (165)
Q Consensus 58 e~i~~l~~~L-~~f~LTk~E~LQIvN 82 (165)
..+-..+... ++|.|++.|+.||+|
T Consensus 138 ~RML~~w~~~~~~y~LS~eei~~Il~ 163 (164)
T PRK05445 138 QRMLTVWRACPRQYHLSANEILQILN 163 (164)
T ss_pred HHHHHHHHhCCCcCCCCHHHHHHHHh
Confidence 3444444433 479999999999998
No 52
>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=23.39 E-value=56 Score=18.32 Aligned_cols=17 Identities=29% Similarity=0.307 Sum_probs=7.3
Q ss_pred HHHHhcCCCCcHHHHHHh
Q 031131 77 ILNIINIRPSSLVEVDSI 94 (165)
Q Consensus 77 ~LQIvNl~Pts~veL~~i 94 (165)
+|| -|+.|-|+.+...+
T Consensus 2 rlq-dnmmPMSPddy~~l 18 (23)
T PF12162_consen 2 RLQ-DNMMPMSPDDYDEL 18 (23)
T ss_dssp ----TS---S-HHHHHHH
T ss_pred chh-hcccCCCHHHHHHH
Confidence 466 79999998876543
No 53
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=23.27 E-value=1.4e+02 Score=28.07 Aligned_cols=80 Identities=16% Similarity=0.229 Sum_probs=49.4
Q ss_pred hHHHHHHHhhCcc----cccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccc-cCCCHHHHHHHHHHH
Q 031131 40 EFKVYDYLVESAA----CNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCD-TRFQEEELQELVDLV 114 (165)
Q Consensus 40 e~e~l~YL~~~p~----~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e-~RfsEeqieeIL~iI 114 (165)
..+++.+|.+.-. ...+++.+.+|+..+..-.+|+.-.=+++-..=.+--....||++.. .+.|++ .+|-++|
T Consensus 350 ~~el~~~l~~~~~~i~~~~l~p~~l~~Li~lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii~~~gl~~isd~--~~l~~iv 427 (478)
T TIGR00133 350 CIELLGVLNKLQISLAECGLKPSDLAELIKLIKEGKISGKSAKQLIEEMLENGGDPSKLIEELGLEQISDE--KELIKII 427 (478)
T ss_pred HHHHHHHHHHCCCCHhhcCCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcCCCHHHHHHhcCCcccCCH--HHHHHHH
Confidence 4667788876422 24688999999999999988866554444432222233567777765 346654 3445555
Q ss_pred HHhCCCC
Q 031131 115 IEVLPPL 121 (165)
Q Consensus 115 ~e~L~~~ 121 (165)
.+.+...
T Consensus 428 ~evl~~n 434 (478)
T TIGR00133 428 EEVIKEN 434 (478)
T ss_pred HHHHHHC
Confidence 5555433
No 54
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=23.22 E-value=1.4e+02 Score=21.64 Aligned_cols=59 Identities=12% Similarity=0.138 Sum_probs=38.3
Q ss_pred chHHHHHHHhhC----ccc--------ccCHHHH--HHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccc
Q 031131 39 SEFKVYDYLVES----AAC--------NQTRNII--NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCD 99 (165)
Q Consensus 39 ~e~e~l~YL~~~----p~~--------~qt~e~i--~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e 99 (165)
+...++.|..+. |.. .++++.+ -.++..|+.+|++=.++..+++..+. .++..++...-
T Consensus 12 is~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~--~~~~~~l~~~~ 84 (108)
T cd01107 12 LSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND--DELRKLLREKL 84 (108)
T ss_pred cCHHHHHHHHHcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCH--HHHHHHHHHHH
Confidence 346777776643 211 2344433 35778889999999999999999875 55555554433
No 55
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA.
Probab=22.60 E-value=1.4e+02 Score=28.91 Aligned_cols=68 Identities=13% Similarity=0.176 Sum_probs=46.5
Q ss_pred HHHHhhCc--ccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCC---CCcHHHHHHhhcccc-cCCCHHHHHHHHHHH
Q 031131 44 YDYLVESA--ACNQTRNIINEFLEKSKKFKLAKAEILNIINIR---PSSLVEVDSIIEQCD-TRFQEEELQELVDLV 114 (165)
Q Consensus 44 l~YL~~~p--~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~---Pts~veL~~iIEe~e-~RfsEeqieeIL~iI 114 (165)
+.+|.+.- ....+++.+.+|+..+..=.+++.-.=+|+... |.++ ..||++.. ..+|++++.+|++-|
T Consensus 500 ~~~l~~~~~~~~~~~~~~l~~l~~~~~~g~is~~~~k~vl~~~~~~~~~~---~~iiee~gL~qlsdeel~~iV~ev 573 (620)
T TIGR00134 500 LRELRREGHDIDGLELRHLRDAIKLLEVGKIAKEGLREILKCMCDEPLAA---EDAARKLKLKLLAEEEIESIIQEI 573 (620)
T ss_pred HHHHHhCCCCcccCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHhCCCCH---HHHHHHcCCcCCCHHHHHHHHHHH
Confidence 77777642 234678999999999999888876655555433 3343 44888887 578987666655544
No 56
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=21.74 E-value=3.6e+02 Score=22.38 Aligned_cols=38 Identities=21% Similarity=0.279 Sum_probs=29.6
Q ss_pred cCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhh
Q 031131 55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSII 95 (165)
Q Consensus 55 qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iI 95 (165)
.+.+.|..|.+.|+.||+|=.+ |++.+|....--..+|
T Consensus 118 ~~~eEI~~~~~~L~~~gi~~~d---Lv~~sPkh~d~r~~~i 155 (218)
T TIGR02895 118 NRRLEILEYKKLLKQFGIEFVE---LVKVSPKHRDTRKKAI 155 (218)
T ss_pred cHHHHHHHHHHHHHHcCCcHHH---HhhcCCCCHHHHHHHH
Confidence 4678999999999999998665 6788998765544444
No 57
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=20.76 E-value=1e+02 Score=19.73 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=13.3
Q ss_pred CCCHHHHHHHHHHHHH
Q 031131 101 RFQEEELQELVDLVIE 116 (165)
Q Consensus 101 RfsEeqieeIL~iI~e 116 (165)
+||++|+..|+.-|.+
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 8888888888888765
No 58
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=20.75 E-value=1.1e+02 Score=23.28 Aligned_cols=74 Identities=18% Similarity=0.201 Sum_probs=41.4
Q ss_pred HHHHHHHhhCc----ccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccc-cCCCH-HHHHHHHHHH
Q 031131 41 FKVYDYLVESA----ACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCD-TRFQE-EELQELVDLV 114 (165)
Q Consensus 41 ~e~l~YL~~~p----~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e-~RfsE-eqieeIL~iI 114 (165)
.+++.+|.+.. .+..+++.+.+++..+..-.+|+.-.=+|+-..-.+--...-+|++.. .+.++ +++.+|++-|
T Consensus 22 ~el~~~l~~~~~~~~~~~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~~~~~~~~~ii~~~~l~~i~d~~el~~~v~~v 101 (148)
T PF02637_consen 22 NELLGLLNKKGLDIEDSPISPEHLAELINLLEDGKISKKSAKELLRELLENGKSPEEIIEENGLWQISDEEELEALVEEV 101 (148)
T ss_dssp THHHHHHHHHT--TTTSSSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTS-HHHHHHHTT---B--CCHHHHHHHHH
T ss_pred HHHHHHHHHCCCChhhcCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCcCCCHHHHHHHHHHH
Confidence 56667776532 134678999999998888888875444443333222333456666654 24554 5555555544
No 59
>KOG2438 consensus Glutamyl-tRNA amidotransferase subunit B [Translation, ribosomal structure and biogenesis]
Probab=20.74 E-value=2.1e+02 Score=27.12 Aligned_cols=106 Identities=14% Similarity=0.150 Sum_probs=67.6
Q ss_pred cCcHHHHHHHHHhhc---CCCCC--CCCCcccccchHHHHHHHhhCcc----cccCHHHHHHHHHHhhcCCCCHHHHHHH
Q 031131 10 PLTNFEVFDFLRCKG---ASKDP--TRVLVPVTPSEFKVYDYLVESAA----CNQTRNIINEFLEKSKKFKLAKAEILNI 80 (165)
Q Consensus 10 ~LSN~EVl~~L~~~~---~~~~~--~~~~~~l~~~e~e~l~YL~~~p~----~~qt~e~i~~l~~~L~~f~LTk~E~LQI 80 (165)
++.+.|++++.++.- +.+.. .+.+.+| +..+.+-||++-+- ...++..+.+|+..|..-.+|..-..|+
T Consensus 341 L~~~~~~~~~~~d~v~i~k~~ae~~~k~~~~W--i~~~~~g~lrq~~ls~~~~~~~p~~la~ll~ll~~~~Is~~~ak~l 418 (505)
T KOG2438|consen 341 LANEVELLEFYKDSVRIIKYKAETTPKLITYW--IKEEFLGYLRQIALSPNQSIVTPRQLADLLKLLSEETISALSAKQL 418 (505)
T ss_pred hhcchhHHHHHhhhhhhhhhcccccccchHHH--HHHHHHHHHhhccCCccccccChHHHHHHHHHhhhhhhhHHHHHHH
Confidence 567788888886321 11111 2222233 34678899986433 3457899999999999999999999999
Q ss_pred hcCCCCcHH--HHHHhhcccc-cCCCHHHHHHHHHHHHHhCC
Q 031131 81 INIRPSSLV--EVDSIIEQCD-TRFQEEELQELVDLVIEVLP 119 (165)
Q Consensus 81 vNl~Pts~v--eL~~iIEe~e-~RfsEeqieeIL~iI~e~L~ 119 (165)
+-+.=.+.- .+..+||+-+ .+.. +-.+|-++|.+.+.
T Consensus 419 l~~l~~~~~~~~~s~LIeek~l~~I~--dp~eIe~lv~~vm~ 458 (505)
T KOG2438|consen 419 LRHLLKNPGVMTVSILIEEKRLWQIR--DPAEIEELVRSVME 458 (505)
T ss_pred HHHHHhCCCcCCHHHHHhhhhhhhcC--CHHHHHHHHHHHHH
Confidence 887655554 7888888744 2333 22344445554443
No 60
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=20.63 E-value=2.3e+02 Score=27.52 Aligned_cols=74 Identities=27% Similarity=0.342 Sum_probs=52.4
Q ss_pred HHHHHHHhhC--cccccCHHHHHHHHHHhhcCCCCHH---HHHHHhcCCCCcHHHHHHhhcccc-cCCCHHHHHHHHHHH
Q 031131 41 FKVYDYLVES--AACNQTRNIINEFLEKSKKFKLAKA---EILNIINIRPSSLVEVDSIIEQCD-TRFQEEELQELVDLV 114 (165)
Q Consensus 41 ~e~l~YL~~~--p~~~qt~e~i~~l~~~L~~f~LTk~---E~LQIvNl~Pts~veL~~iIEe~e-~RfsEeqieeIL~iI 114 (165)
..++.||++- +..+.+.+.|..++..++.-.++|. |+|-.+=.-|.+- ...++++.- .+|++|++++|++-|
T Consensus 504 ~~~~~~L~reg~~i~~l~~~~i~~~~~~~~~g~iake~iee~l~~l~~~p~~~--~~e~~~~~gL~~ls~eEve~iI~ei 581 (631)
T COG2511 504 VNTLPELRREGVEIDNLDDEHIEELLRLVSEGKIAKEAIEEILKALAENPGKD--AAEIAEKLGLKELSEEEVEKIIDEI 581 (631)
T ss_pred HHHHHHHHhcCCccccCCHHHHHHHHHHHhcccchHHHHHHHHHHHHhCCCCC--HHHHHHHhccccCCHHHHHHHHHHH
Confidence 4678888764 4456789999999999988888775 4444444435443 334666664 679999999999876
Q ss_pred HH
Q 031131 115 IE 116 (165)
Q Consensus 115 ~e 116 (165)
-+
T Consensus 582 i~ 583 (631)
T COG2511 582 IE 583 (631)
T ss_pred HH
Confidence 53
No 61
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.38 E-value=2e+02 Score=20.92 Aligned_cols=76 Identities=5% Similarity=0.019 Sum_probs=47.4
Q ss_pred hHHHHHHHhhC----cc-------cccCHHHHH--HHHHHhhcCCCCHHHHHHHhcCCC--CcHHHHHHhhcccccCCCH
Q 031131 40 EFKVYDYLVES----AA-------CNQTRNIIN--EFLEKSKKFKLAKAEILNIINIRP--SSLVEVDSIIEQCDTRFQE 104 (165)
Q Consensus 40 e~e~l~YL~~~----p~-------~~qt~e~i~--~l~~~L~~f~LTk~E~LQIvNl~P--ts~veL~~iIEe~e~RfsE 104 (165)
...++.|..+. |. ...+++.+. .++..|+..|++=.++-++++... .+..++..+++.--..+ +
T Consensus 13 s~~tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l-~ 91 (108)
T cd04773 13 PPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRRVAL-T 91 (108)
T ss_pred CHHHHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHH-H
Confidence 36667766542 21 124555544 456788899999999999988642 23456666666555445 4
Q ss_pred HHHHHHHHHHHH
Q 031131 105 EELQELVDLVIE 116 (165)
Q Consensus 105 eqieeIL~iI~e 116 (165)
.++.++++-+..
T Consensus 92 ~~~~~~~~~~~~ 103 (108)
T cd04773 92 QRGRAMLDAAAA 103 (108)
T ss_pred HHHHHHHHHHHH
Confidence 667777666654
No 62
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=20.04 E-value=76 Score=22.15 Aligned_cols=40 Identities=8% Similarity=0.055 Sum_probs=30.1
Q ss_pred HHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCC
Q 031131 46 YLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRP 85 (165)
Q Consensus 46 YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~P 85 (165)
+...+|...+-....+++...++.||||.+-...|....+
T Consensus 56 ~~~~nP~~~~~~~~~~~~~~l~~~lGLtP~sR~kl~~~~~ 95 (100)
T PF05119_consen 56 NPKKNPAVSILNKAMKQMRSLASELGLTPASRAKLAVPKK 95 (100)
T ss_pred CcccCHHHHHHHHHHHHHHHHHHHcCCCHHHHhhccCCCc
Confidence 4455666566677888888888999999998888766443
No 63
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=20.04 E-value=2.8e+02 Score=21.39 Aligned_cols=65 Identities=18% Similarity=0.298 Sum_probs=45.9
Q ss_pred HHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCC-----CHHHHHHHHHHHH
Q 031131 41 FKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRF-----QEEELQELVDLVI 115 (165)
Q Consensus 41 ~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~Rf-----sEeqieeIL~iI~ 115 (165)
.++.+.....|. ..+++++.+.++|+.-+ ..+.|. ++.-|.++|..|-.|| +.+-+.+++.+|.
T Consensus 23 leicD~In~~~~--~~k~a~rai~krl~~~n--~~v~l~-------AL~LLe~~vkNCG~~fh~evas~~Fl~el~kl~~ 91 (139)
T cd03567 23 QAFCEQINKEPE--GPQLAVRLLAHKIQSPQ--EKEALQ-------ALTVLEACMKNCGERFHSEVGKFRFLNELIKLVS 91 (139)
T ss_pred HHHHHHHHcCCc--cHHHHHHHHHHHHcCCC--HHHHHH-------HHHHHHHHHHHcCHHHHHHHHhHHHHHHHHHHhc
Confidence 477888877763 45789999999987543 333332 4556889999999988 4556667777775
Q ss_pred H
Q 031131 116 E 116 (165)
Q Consensus 116 e 116 (165)
.
T Consensus 92 ~ 92 (139)
T cd03567 92 P 92 (139)
T ss_pred c
Confidence 3
Done!