Query 031465
Match_columns 159
No_of_seqs 108 out of 182
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 14:29:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031465.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031465hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00165 ftrB ferredoxin thior 100.0 7E-46 1.5E-50 284.6 8.9 99 35-133 5-103 (116)
2 PF02943 FeThRed_B: Ferredoxin 100.0 1E-42 2.2E-47 263.5 5.0 94 41-134 1-98 (108)
3 COG4802 FtrB Ferredoxin-thiore 100.0 3.9E-40 8.4E-45 249.9 8.5 90 38-130 1-95 (110)
4 PF05511 ATP-synt_F6: Mitochon 86.9 1.2 2.7E-05 33.9 4.3 81 1-85 1-84 (99)
5 PHA00425 DNA packaging protein 69.2 8.9 0.00019 28.8 4.0 46 39-84 28-76 (88)
6 PF03938 OmpH: Outer membrane 57.9 21 0.00046 27.0 4.4 37 39-75 111-157 (158)
7 PRK10780 periplasmic chaperone 56.7 14 0.00031 28.9 3.4 38 38-75 117-164 (165)
8 TIGR01924 rsbW_low_gc serine-p 49.5 59 0.0013 25.2 5.7 56 32-88 8-63 (159)
9 PF11123 DNA_Packaging_2: DNA 47.2 41 0.00089 25.1 4.2 45 40-84 27-74 (82)
10 PF10431 ClpB_D2-small: C-term 41.8 69 0.0015 21.8 4.6 38 45-85 13-50 (81)
11 PRK05452 anaerobic nitric oxid 41.0 19 0.00041 33.2 2.1 35 31-67 370-404 (479)
12 PHA02745 hypothetical protein; 40.5 70 0.0015 28.4 5.4 53 33-85 212-264 (265)
13 COG2861 Uncharacterized protei 39.9 92 0.002 27.4 6.0 55 19-78 173-230 (250)
14 PF00078 RVT_1: Reverse transc 38.0 43 0.00093 25.1 3.3 29 39-67 171-199 (214)
15 PRK13612 photosystem II reacti 37.9 34 0.00073 26.8 2.7 25 38-62 87-111 (113)
16 TIGR02417 fruct_sucro_rep D-fr 37.9 47 0.001 27.1 3.8 66 45-110 32-127 (327)
17 TIGR03047 PS_II_psb28 photosys 37.9 33 0.00072 26.7 2.7 24 38-61 84-107 (109)
18 PF14791 DNA_pol_B_thumb: DNA 36.9 42 0.00092 23.1 2.8 20 45-64 10-29 (64)
19 PRK13611 photosystem II reacti 36.9 36 0.00078 26.3 2.7 24 38-61 80-103 (104)
20 PLN00039 photosystem II reacti 36.8 36 0.00078 26.6 2.7 25 38-62 85-109 (111)
21 CHL00128 psbW photosystem II p 36.8 36 0.00078 26.7 2.7 25 38-62 87-111 (113)
22 PF03912 Psb28: Psb28 protein; 36.6 27 0.00058 27.2 2.0 42 20-61 63-107 (108)
23 TIGR01481 ccpA catabolite cont 36.5 58 0.0013 26.5 4.1 46 44-89 30-95 (329)
24 COG2825 HlpA Outer membrane pr 35.8 43 0.00092 27.1 3.1 40 36-75 118-167 (170)
25 COG5502 Uncharacterized conser 35.8 55 0.0012 26.4 3.7 39 41-79 73-112 (135)
26 PF12683 DUF3798: Protein of u 35.8 73 0.0016 28.4 4.8 50 42-92 187-236 (275)
27 PF00356 LacI: Bacterial regul 35.3 33 0.0007 22.3 2.0 18 45-62 29-46 (46)
28 PRK11303 DNA-binding transcrip 34.1 68 0.0015 26.1 4.1 44 45-88 33-96 (328)
29 PRK10401 DNA-binding transcrip 32.7 70 0.0015 26.5 4.0 45 44-88 30-94 (346)
30 PRK11041 DNA-binding transcrip 30.8 81 0.0017 25.3 4.0 42 44-85 6-67 (309)
31 PF13410 GST_C_2: Glutathione 30.1 1.5E+02 0.0032 18.8 4.8 46 39-84 7-52 (69)
32 cd01646 RT_Bac_retron_I RT_Bac 29.6 75 0.0016 24.1 3.5 36 39-74 98-133 (158)
33 PF11794 HpaB_N: 4-hydroxyphen 29.6 94 0.002 27.0 4.4 47 38-84 74-120 (264)
34 PF01402 RHH_1: Ribbon-helix-h 28.1 1.3E+02 0.0029 17.6 3.8 30 44-76 8-37 (39)
35 TIGR02405 trehalos_R_Ecol treh 28.0 93 0.002 25.4 3.9 41 45-85 31-91 (311)
36 KOG1220 Phosphoglucomutase/pho 27.8 44 0.00096 32.7 2.3 46 40-85 457-502 (607)
37 PRK05802 hypothetical protein; 27.6 29 0.00064 30.1 1.0 13 81-93 9-21 (320)
38 KOG3820 Aromatic amino acid hy 27.2 34 0.00073 32.4 1.3 36 36-71 395-430 (461)
39 PRK10727 DNA-binding transcrip 26.8 1.1E+02 0.0023 25.4 4.1 43 44-86 30-92 (343)
40 KOG1671 Ubiquinol cytochrome c 26.3 21 0.00046 30.6 -0.1 15 75-89 160-174 (210)
41 PRK10423 transcriptional repre 26.1 1.1E+02 0.0024 24.8 4.0 41 45-85 28-88 (327)
42 PF04748 Polysacc_deac_2: Dive 26.1 2.2E+02 0.0047 23.6 5.8 49 31-79 148-199 (213)
43 KOG4634 Mitochondrial F1F0-ATP 25.4 1.3E+02 0.0029 23.4 4.1 36 48-83 40-77 (105)
44 PRK10703 DNA-binding transcrip 25.2 1.2E+02 0.0025 24.9 4.1 21 65-85 71-91 (341)
45 TIGR00050 rRNA_methyl_1 RNA me 24.1 1.7E+02 0.0036 24.5 4.8 38 38-75 170-207 (233)
46 PRK14987 gluconate operon tran 23.3 1.4E+02 0.0031 24.4 4.2 42 45-86 35-96 (331)
47 PRK09492 treR trehalose repres 23.3 1.2E+02 0.0025 24.5 3.7 42 45-86 34-95 (315)
48 cd01648 TERT TERT: Telomerase 23.1 1.1E+02 0.0024 22.4 3.3 30 40-69 69-99 (119)
49 KOG4198 RNA-binding Ran Zn-fin 23.1 32 0.0007 30.5 0.4 47 98-144 135-197 (280)
50 PHA01748 hypothetical protein 22.5 1.8E+02 0.004 19.6 4.0 29 45-75 12-40 (60)
51 KOG3651 Protein kinase C, alph 22.3 38 0.00082 31.4 0.7 25 82-106 24-51 (429)
52 TIGR00340 zpr1_rel ZPR1-relate 22.1 34 0.00075 27.7 0.4 39 114-157 28-67 (163)
53 cd01651 RT_G2_intron RT_G2_int 21.8 1.3E+02 0.0027 23.1 3.4 31 39-69 182-212 (226)
54 PF03869 Arc: Arc-like DNA bin 21.1 1.7E+02 0.0037 19.2 3.5 33 44-78 13-45 (50)
55 cd01650 RT_nLTR_like RT_nLTR: 21.1 1.2E+02 0.0026 23.3 3.2 29 41-69 160-188 (220)
56 COG1609 PurR Transcriptional r 21.0 1.8E+02 0.0039 25.0 4.5 54 34-91 23-98 (333)
57 PF13581 HATPase_c_2: Histidin 20.7 2.2E+02 0.0048 20.1 4.3 48 40-88 5-52 (125)
No 1
>CHL00165 ftrB ferredoxin thioreductase subunit beta; Validated
Probab=100.00 E-value=7e-46 Score=284.56 Aligned_cols=99 Identities=55% Similarity=1.034 Sum_probs=95.3
Q ss_pred cCCcCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCccccchhhhhhCCceeecCcccccC
Q 031465 35 QVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVPMRER 114 (159)
Q Consensus 35 ~~~~see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~~CPCRl~~DkE~ev~D~diICPCvy~~E~ 114 (159)
+...+++++|+|++|+++||+++||+||||+++|+.|++|||+||++||+||||||+++++++|+++++|||||++|+|+
T Consensus 5 ~~~~~~~~~e~m~~f~ekya~~~G~~fnpD~~vt~~Vi~GLa~nK~~yG~p~CPCR~~~~k~~e~~~~~~iCPCv~m~e~ 84 (116)
T CHL00165 5 NEKSKPESLEAMRKFAETYAKRTNTFFCSDLSITAVVIEGLARHKDEYGAPLCPCRHYEDKKVEVSAAYWNCPCVPMRER 84 (116)
T ss_pred ccccchhhHHHHHHHHHHHHHHhCCeeCCCHHHHHHHHHHHHHHHHHhCCCCCCCcCCCCcHHHhhcCCeecCCHhHHHc
Confidence 45678999999999999999999999999999999999999999999999999999999998999999999999999999
Q ss_pred ceeeEeeeeccchhhccCC
Q 031465 115 NATACSFSLQRTILLARIS 133 (159)
Q Consensus 115 G~CHC~LFvs~e~~~a~~~ 133 (159)
|+||||||+++|++|||.+
T Consensus 85 g~CHC~LF~t~e~~~~~~~ 103 (116)
T CHL00165 85 KECHCMLFLTPDNEFASQS 103 (116)
T ss_pred CCceEeeeecCCccccCcc
Confidence 9999999999999999964
No 2
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=100.00 E-value=1e-42 Score=263.52 Aligned_cols=94 Identities=35% Similarity=0.556 Sum_probs=72.0
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCccccchhhhhhCCceeecCccc----ccCce
Q 031465 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVPM----RERNA 116 (159)
Q Consensus 41 e~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~~CPCRl~~DkE~ev~D~diICPCvy~----~E~G~ 116 (159)
+++++|++|+++||+++||+||||+++|+.|++||++||++||++|||||++++++++++|++|||||+++ .++|+
T Consensus 1 ~~le~~~~~~~~~a~~~G~~~NpD~~~~~~v~~GL~~nk~~yG~~~CPCr~~~~~~ee~~d~~iiCPC~~~r~~~~~~G~ 80 (108)
T PF02943_consen 1 KELEKMYKFLEKYAEKSGYKLNPDEEVTDDVLEGLARNKERYGYPYCPCRLASGKEEEVKDRDIICPCVPYREDDIEYGH 80 (108)
T ss_dssp HHHHHHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH------
T ss_pred ChHHHHHHHHHHHHHHhCCEECCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCchhhhccCCeecCCHHHHhhcccccc
Confidence 68999999999999999999999999999999999999999999999999999777779999999999952 38999
Q ss_pred eeEeeeeccchhhccCCC
Q 031465 117 TACSFSLQRTILLARISP 134 (159)
Q Consensus 117 CHC~LFvs~e~~~a~~~~ 134 (159)
|||||||++++.+++.+.
T Consensus 81 ChC~Lf~~~e~~~~~~~~ 98 (108)
T PF02943_consen 81 CHCGLFVSPEYAEAGKKQ 98 (108)
T ss_dssp -TTSSSB-TTSTTB-S-S
T ss_pred ceEeeeECcccccchhhc
Confidence 999999999999888754
No 3
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=100.00 E-value=3.9e-40 Score=249.90 Aligned_cols=90 Identities=33% Similarity=0.576 Sum_probs=84.3
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccc-chhhhhhCCceeecCcc----cc
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYD-DKAAEAQQGFWNCPCVP----MR 112 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~~CPCRl~~-DkE~ev~D~diICPCvy----~~ 112 (159)
.+++++++||+|+++||+|+||+||||+++|+.|++||+.||++||+++||||+++ ++++ |++|||||+| |+
T Consensus 1 ~~~e~l~~my~~~eq~AeksG~~lnpD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~eee---dk~ivCPCvy~~ddi~ 77 (110)
T COG4802 1 ESDEELNKMYRFTEQYAEKSGYRLNPDREFTAEVLRGLASNKERYGYPSCPCRLVTGKEEE---DKDIVCPCVYRDDDIR 77 (110)
T ss_pred CcHHHHHHHHHHHHHHHHhcCceeCCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCHHH---hhceeccCcCCccchh
Confidence 36899999999999999999999999999999999999999999999999999999 6666 7779999999 89
Q ss_pred cCceeeEeeeeccchhhc
Q 031465 113 ERNATACSFSLQRTILLA 130 (159)
Q Consensus 113 E~G~CHC~LFvs~e~~~a 130 (159)
+||.||||||++++..++
T Consensus 78 e~g~C~C~Lyl~~e~~e~ 95 (110)
T COG4802 78 EYGECYCGLYLSPEKDEA 95 (110)
T ss_pred hhCceeEEEEecccccch
Confidence 999999999999998644
No 4
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=86.88 E-value=1.2 Score=33.92 Aligned_cols=81 Identities=15% Similarity=0.185 Sum_probs=40.4
Q ss_pred CcccccccccccccccCCCccccccCCceeeeec--cCCcCHH-HHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHH
Q 031465 1 MTLQSSLCGSGVSTFICTPRPIIARPRPVTQIRA--QVEPSEK-SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLAD 77 (159)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~see-~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~ 77 (159)
|.+|+-+.++..++.+...+ |.-...++.+ ..+|.++ =+++++++..|-..+.|=..++.+++-..+-+-|.+
T Consensus 1 m~~~~~~~~~~~~~~s~~~~----Rni~~sa~~~~k~~DPIQklFldKIREY~~Ksks~gGklVD~~Pe~~kel~eel~k 76 (99)
T PF05511_consen 1 MALQRRLSSLLRSAVSVHLR----RNIGTSAVAFNKALDPIQKLFLDKIREYNQKSKSSGGKLVDAGPEYEKELNEELEK 76 (99)
T ss_dssp ------------------------------------S--TTTHHHHHHHHHHHHHHTTTSS-STT--THHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHHHH----HHhhhhHHHHhcccChHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHH
Confidence 67777555555544444333 2212223332 2456555 578999999999999998999999999999999999
Q ss_pred hHhhhCCC
Q 031465 78 HKDSLGAP 85 (159)
Q Consensus 78 NK~rYG~~ 85 (159)
-...||..
T Consensus 77 L~r~YG~g 84 (99)
T PF05511_consen 77 LARQYGGG 84 (99)
T ss_dssp HHHHHHSS
T ss_pred HHHHhCCc
Confidence 99999974
No 5
>PHA00425 DNA packaging protein, small subunit
Probab=69.17 E-value=8.9 Score=28.85 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=39.6
Q ss_pred CHHHHHHHHHHHHHHhhhcCcE---eccChhhHHHHHHHHHHhHhhhCC
Q 031465 39 SEKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (159)
Q Consensus 39 see~le~~~~f~ekyAek~Gy~---lNPD~evt~~Vi~GLa~NK~rYG~ 84 (159)
.++.--.+|+-+.|+-+++.|. +.||+++.-.+..||+.-+..+|.
T Consensus 28 dekRtPQLYnAIgKlL~RHkF~isKl~pD~~iLg~la~~l~ey~~~~g~ 76 (88)
T PHA00425 28 DEKRTPQLYNAIGKLLDRHKFQISKLQPDENILGGLAAALEEYKEKVGA 76 (88)
T ss_pred ccccChHHHHHHHHHHHHhcccccccCCcHHHHHHHHHHHHHHHHhcCC
Confidence 3445567899999999999985 679999999999999999999885
No 6
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=57.89 E-value=21 Score=27.00 Aligned_cols=37 Identities=24% Similarity=0.275 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHHHHhhhcCc----------EeccChhhHHHHHHHH
Q 031465 39 SEKSVEIMRKFSEQYARRSDT----------FFCVDKSVTSVVIKGL 75 (159)
Q Consensus 39 see~le~~~~f~ekyAek~Gy----------~lNPD~evt~~Vi~GL 75 (159)
...-.+++...++.||+..|| +.+|.-++|+.|++.|
T Consensus 111 ~~~i~~~i~~~v~~~a~~~g~~~Vl~~~~vly~~~~~DIT~~Vi~~L 157 (158)
T PF03938_consen 111 LQPIQKKINKAVEEYAKENGYDLVLDKNAVLYADPAYDITDEVIKAL 157 (158)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-SEEEEGGGEEEE-TTSE-HHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHcCCeEEEeCCceEeeCCCCChHHHHHHHh
Confidence 445566788899999999998 5677789999998876
No 7
>PRK10780 periplasmic chaperone; Provisional
Probab=56.73 E-value=14 Score=28.95 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=29.1
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEe----------ccChhhHHHHHHHH
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFF----------CVDKSVTSVVIKGL 75 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~l----------NPD~evt~~Vi~GL 75 (159)
....-++++.+.++++|++.||-+ +|..++|..|++-|
T Consensus 117 ~~~~i~~ki~~ai~~vak~~gy~~Vld~~~v~Y~~~~~DIT~~Vik~l 164 (165)
T PRK10780 117 ERNKILTRIQTAVKSVANKQGYDLVVDANAVAYNSSDKDITADVLKQV 164 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCeEEEeCCceeeeCCCCCchHHHHHhh
Confidence 345567788899999999999854 46678888888754
No 8
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=49.52 E-value=59 Score=25.18 Aligned_cols=56 Identities=13% Similarity=0.022 Sum_probs=42.2
Q ss_pred eeccCCcCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCC
Q 031465 32 IRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (159)
Q Consensus 32 ~~~~~~~see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~~CP 88 (159)
+........+.+..++.|++.+|+..|+- ..+.+-+..++.-|+.|--+||++..|
T Consensus 8 ~~l~~~a~~~~~~~vr~~~~~~a~~~g~~-~~~~~~l~lav~Ea~~Nai~ha~~~~~ 63 (159)
T TIGR01924 8 IEMTVPAKPEYVGLIRLTLSGIASRAGYT-YDDIEDLKIAVSEACTNAVKHAYKEGE 63 (159)
T ss_pred EEEEccCcHHHHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 44444556788999999999999999964 233344666788899999999997553
No 9
>PF11123 DNA_Packaging_2: DNA packaging protein ; InterPro: IPR024345 This entry represents Gp18 (gene 18 product), also known as DNA maturase A, from T7-like bacteriophages. In Bacteriophage T3, this protein is required for DNA packaging and functions in a complex with Gp19 [].
Probab=47.18 E-value=41 Score=25.09 Aligned_cols=45 Identities=18% Similarity=0.179 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHhhhcCcE---eccChhhHHHHHHHHHHhHhhhCC
Q 031465 40 EKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (159)
Q Consensus 40 ee~le~~~~f~ekyAek~Gy~---lNPD~evt~~Vi~GLa~NK~rYG~ 84 (159)
++.--.+|+-+.|+-+++.|. +-||+++.-.+..||..-++.+|.
T Consensus 27 ekRsPQLYnAI~k~L~RHkF~iskl~pd~~~LG~L~~aL~ey~~~~g~ 74 (82)
T PF11123_consen 27 EKRSPQLYNAIGKLLDRHKFQISKLQPDENILGELAAALEEYKKMVGA 74 (82)
T ss_pred hhcChHHHHHHHHHHHHccchhhhcCccHHHHHHHHHHHHHHHHHcCC
Confidence 445567899999999999986 579999999999999999998885
No 10
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=41.81 E-value=69 Score=21.80 Aligned_cols=38 Identities=16% Similarity=0.189 Sum_probs=26.8
Q ss_pred HHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 031465 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~ 85 (159)
++.+..+++++ .|..|+-|+++.+.+++-= ....||++
T Consensus 13 ~l~~l~~~l~~-~~i~l~~~~~~~~~l~~~~--~~~~~GAR 50 (81)
T PF10431_consen 13 QLKKLNERLKE-KGIELEFDDAVVDYLAEKG--YDPEYGAR 50 (81)
T ss_dssp HHHHHHHHHHH-TTEEEEE-HHHHHHHHHHH--HHTTTTTT
T ss_pred HHHHHHHHHHH-CCCeEEecHHHHHHHHHhC--cccCCCHH
Confidence 44555666666 9999999999999888742 34578875
No 11
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=41.01 E-value=19 Score=33.16 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=25.7
Q ss_pred eeeccCCcCHHHHHHHHHHHHHHhhhcCcEeccChhh
Q 031465 31 QIRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (159)
Q Consensus 31 ~~~~~~~~see~le~~~~f~ekyAek~Gy~lNPD~ev 67 (159)
.+...-.|+++++++.++|.+++|++-- +-|++..
T Consensus 370 ~l~~~~~P~ee~~~~~~~~g~~la~~~~--~~~~~~~ 404 (479)
T PRK05452 370 SLKAKWRPDQDALELCREHGREIARQWA--LAPLPQS 404 (479)
T ss_pred cEEEEecCCHHHHHHHHHHHHHHHHHHh--hCCcccc
Confidence 3555566888899999999998886653 7777644
No 12
>PHA02745 hypothetical protein; Provisional
Probab=40.52 E-value=70 Score=28.36 Aligned_cols=53 Identities=8% Similarity=0.142 Sum_probs=44.6
Q ss_pred eccCCcCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 031465 33 RAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 33 ~~~~~~see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~ 85 (159)
....+..+-.-..+-.|++.|..+.||.---.+.+...+-.-|..-+-+||.+
T Consensus 212 ~vRPgLDe~Ar~vLL~fVe~yG~~~~W~t~D~~~I~ntiR~KiqeiR~K~g~~ 264 (265)
T PHA02745 212 DVRPGLDEDARTVLLRYVEIYGEKQRWCTEDHQAIINVIRNKMQESRRKDRHR 264 (265)
T ss_pred ccCCCcchHHHHHHHHHHHHHhhccCCCCCchHHHHHHHHHHHHHHHHHhCCc
Confidence 34445567777889999999999999998888888888888888888899875
No 13
>COG2861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.94 E-value=92 Score=27.43 Aligned_cols=55 Identities=22% Similarity=0.245 Sum_probs=43.3
Q ss_pred CccccccCCceeeeeccCCcCHHHHHHHHHHHHHHhhhcCcEe---ccChhhHHHHHHHHHHh
Q 031465 19 PRPIIARPRPVTQIRAQVEPSEKSVEIMRKFSEQYARRSDTFF---CVDKSVTSVVIKGLADH 78 (159)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~see~le~~~~f~ekyAek~Gy~l---NPD~evt~~Vi~GLa~N 78 (159)
..|.+.| -|.-+.+.+++++.+-.+-++++|+++|..+ +|-++-+..|.+++..-
T Consensus 173 gVp~~~r-----dvfLD~e~~~~~V~kql~~~~~~Ark~G~ai~IGh~~~~Tv~vl~~~~~~l 230 (250)
T COG2861 173 GVPVIKR-----DVFLDDEDTEAAVLKQLDAAEKLARKNGSAIGIGHPHKNTVAVLQQWLDEL 230 (250)
T ss_pred CCceeee-----eeeecCcCCHHHHHHHHHHHHHHHHhcCceEEecCCchhHHHHHHHHHHhC
Confidence 4455555 4556677889999999999999999999988 68788888877777543
No 14
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=38.04 E-value=43 Score=25.10 Aligned_cols=29 Identities=10% Similarity=0.079 Sum_probs=24.7
Q ss_pred CHHHHHHHHHHHHHHhhhcCcEeccChhh
Q 031465 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (159)
Q Consensus 39 see~le~~~~f~ekyAek~Gy~lNPD~ev 67 (159)
+.++++++.+.+.++.+..|..+||++-.
T Consensus 171 ~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~ 199 (214)
T PF00078_consen 171 SKEELQKILEKISQWLEELGLKLNPEKTK 199 (214)
T ss_dssp SHHHHHHHHHHHHHHHHHTTSBCSSTTTS
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEChHHEE
Confidence 36778888889999999999999999864
No 15
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=37.94 E-value=34 Score=26.83 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=22.2
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEec
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~lN 62 (159)
.++++-+.+.+|+++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T PRK13612 87 KSEQEWDRFMRFMERYAKENGLGFS 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 4899999999999999999997653
No 16
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=37.92 E-value=47 Score=27.07 Aligned_cols=66 Identities=14% Similarity=0.075 Sum_probs=42.2
Q ss_pred HHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCCCCccccchhhhh-----
Q 031465 45 IMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEA----- 99 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lN------------------P--D~evt~~Vi~GLa~NK~rYG~~~CPCRl~~DkE~ev----- 99 (159)
++++.+.+.|++.||.=| | +..+...++.|+.+--.++||..--+....+.+.|.
T Consensus 32 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~~~~~~~~ 111 (327)
T TIGR02417 32 ETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDDNPDQEKVVIEN 111 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHH
Confidence 566667777888887543 2 234677889999988888999876554433332221
Q ss_pred -----hCCceeecCcc
Q 031465 100 -----QQGFWNCPCVP 110 (159)
Q Consensus 100 -----~D~diICPCvy 110 (159)
-|.-|+.|...
T Consensus 112 l~~~~vdgiIi~~~~~ 127 (327)
T TIGR02417 112 LLARQVDALIVASCMP 127 (327)
T ss_pred HHHcCCCEEEEeCCCC
Confidence 15556777643
No 17
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=37.89 E-value=33 Score=26.71 Aligned_cols=24 Identities=25% Similarity=0.369 Sum_probs=21.6
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEe
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~l 61 (159)
.++++-+.+.+|+++||+.+|.-|
T Consensus 84 ~s~~~WdRFMRFmeRYA~~ngl~f 107 (109)
T TIGR03047 84 KSEDEWDRFMRFMERYAEANGLGY 107 (109)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 489999999999999999999755
No 18
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=36.91 E-value=42 Score=23.12 Aligned_cols=20 Identities=15% Similarity=0.130 Sum_probs=16.2
Q ss_pred HHHHHHHHHhhhcCcEeccC
Q 031465 45 IMRKFSEQYARRSDTFFCVD 64 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lNPD 64 (159)
.....+..+|.+.||.||+.
T Consensus 10 ~fnr~lR~~A~~~g~~L~~~ 29 (64)
T PF14791_consen 10 EFNRDLRQYAKKKGMKLSEY 29 (64)
T ss_dssp HHHHHHHHHHHHTTEEEESS
T ss_pred HHHHHHHHHHHHcCCeeCcc
Confidence 34567888999999999985
No 19
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=36.91 E-value=36 Score=26.34 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=21.3
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEe
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~l 61 (159)
.++++-+.+.+|+++||+.+|.-|
T Consensus 80 ~s~~~wdRFMRFmeRYA~~Ngl~f 103 (104)
T PRK13611 80 ETEAEWDRFLRFMERFSAANQMGM 103 (104)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 489999999999999999998643
No 20
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=36.78 E-value=36 Score=26.62 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=22.2
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEec
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~lN 62 (159)
.++++-+.+.+|+++||+.+|.-|.
T Consensus 85 ~s~~~WdRFMRFMeRYA~~ngl~f~ 109 (111)
T PLN00039 85 RSPREWDRFMRFMERYAEENGLGFV 109 (111)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 4899999999999999999997653
No 21
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=36.77 E-value=36 Score=26.69 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=22.2
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEec
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~lN 62 (159)
.++++-+.+.+|+++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T CHL00128 87 KNPEAWDRFMRFMERYAEDNGLTFT 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 4899999999999999999997653
No 22
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=36.60 E-value=27 Score=27.17 Aligned_cols=42 Identities=24% Similarity=0.196 Sum_probs=25.1
Q ss_pred ccccccCCceeeee--ccCC-cCHHHHHHHHHHHHHHhhhcCcEe
Q 031465 20 RPIIARPRPVTQIR--AQVE-PSEKSVEIMRKFSEQYARRSDTFF 61 (159)
Q Consensus 20 ~~~~~~~~~~~~~~--~~~~-~see~le~~~~f~ekyAek~Gy~l 61 (159)
|||=+++-++.... +.-. .++++-+.+.+|+++||+.+|.-|
T Consensus 63 ~~v~~kFvnG~p~~iEa~y~m~s~~~WdRFMRFMeRYA~~Ngl~f 107 (108)
T PF03912_consen 63 RDVNAKFVNGKPQAIEATYIMKSEEEWDRFMRFMERYAEANGLGF 107 (108)
T ss_dssp --EEEEEETTEEEEEEEEEEE-SSHHHHHHHHHHHHHHHH--SSS
T ss_pred EecceEEECCceEEEEEEEEECCHHHHHHHHHHHHHHHHhcCCcc
Confidence 44545554443222 2222 578999999999999999998654
No 23
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=36.54 E-value=58 Score=26.47 Aligned_cols=46 Identities=13% Similarity=0.023 Sum_probs=32.8
Q ss_pred HHHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCCCCC
Q 031465 44 EIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCPC 89 (159)
Q Consensus 44 e~~~~f~ekyAek~Gy~lNP--------------------D~evt~~Vi~GLa~NK~rYG~~~CPC 89 (159)
+++++.+.+.|++.||.-|+ +..+...++.|+.+--.++|+..=-+
T Consensus 30 ~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~ 95 (329)
T TIGR01481 30 PATRKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILS 95 (329)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEE
Confidence 45566677778888886543 23577789999998888889876443
No 24
>COG2825 HlpA Outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=35.82 E-value=43 Score=27.14 Aligned_cols=40 Identities=25% Similarity=0.256 Sum_probs=32.5
Q ss_pred CCcCHHHHHHHHHHHHHHhhhcCcE----------eccChhhHHHHHHHH
Q 031465 36 VEPSEKSVEIMRKFSEQYARRSDTF----------FCVDKSVTSVVIKGL 75 (159)
Q Consensus 36 ~~~see~le~~~~f~ekyAek~Gy~----------lNPD~evt~~Vi~GL 75 (159)
.+...+.++++..-++.+|++.||- .+|-.++|+.|++-|
T Consensus 118 ~e~~~~~~~~i~~ai~~~a~~~gy~~vl~~~~V~y~~~~~DIT~~Vlk~l 167 (170)
T COG2825 118 AEEEQKLLEKIQRAIESVAEKGGYSLVLDSNAVLYAKPSKDITDDVLKAL 167 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCcceEecCCchhccCCCCCchHHHHHHH
Confidence 3455677888999999999999985 478888999998876
No 25
>COG5502 Uncharacterized conserved protein [Function unknown]
Probab=35.77 E-value=55 Score=26.39 Aligned_cols=39 Identities=21% Similarity=0.044 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHH-HHHHHHHHhH
Q 031465 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTS-VVIKGLADHK 79 (159)
Q Consensus 41 e~le~~~~f~ekyAek~Gy~lNPD~evt~-~Vi~GLa~NK 79 (159)
+..-.+..|+.+++++.|+--|.|.+.+- +|.+-|.+|-
T Consensus 73 ~~~~s~~dFl~Rv~~~~g~~~~vd~e~a~~AVf~vL~r~I 112 (135)
T COG5502 73 KLPFSLDDFLTRVANKFGLEPPVDPEHAIAAVFAVLKRHI 112 (135)
T ss_pred CCcccHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHhC
Confidence 33445689999999999999999999888 8888888774
No 26
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=35.77 E-value=73 Score=28.36 Aligned_cols=50 Identities=18% Similarity=0.361 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCccc
Q 031465 42 SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHY 92 (159)
Q Consensus 42 ~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~~CPCRl~ 92 (159)
-+|.+-+|+++|-+... +|+-+..+++.||+.++.++-.|=..-||+-+-
T Consensus 187 IlE~vp~~i~kYGkdta-ff~TN~a~~epllk~~~~~g~i~~e~~~psp~~ 236 (275)
T PF12683_consen 187 ILEDVPKWIKKYGKDTA-FFCTNDAMTEPLLKQALEYGGIFPEADLPSPLM 236 (275)
T ss_dssp HHHHHHHHHHHH-S--E-EEESSHHHHHHHHHHHHHH--BB---SS--TTT
T ss_pred HHHHHHHHHHHhCCcee-EEecCccccHHHHHHHHHcCCEEEeCCCCChhh
Confidence 57788899999965554 577788999999999999998888888888763
No 27
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=35.31 E-value=33 Score=22.26 Aligned_cols=18 Identities=11% Similarity=-0.278 Sum_probs=12.6
Q ss_pred HHHHHHHHHhhhcCcEec
Q 031465 45 IMRKFSEQYARRSDTFFC 62 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lN 62 (159)
++++.+.+.|++.||.-|
T Consensus 29 ~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 29 ETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHHHHHHHHHTB-SS
T ss_pred HHHHHHHHHHHHHCCCCC
Confidence 455667788889999755
No 28
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=34.15 E-value=68 Score=26.09 Aligned_cols=44 Identities=11% Similarity=-0.016 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCCCC
Q 031465 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCP 88 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lNP--------------------D~evt~~Vi~GLa~NK~rYG~~~CP 88 (159)
++++.+.+.|++.||.-|+ +..+...+++|+.+--..+|+..=-
T Consensus 33 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~ 96 (328)
T PRK11303 33 KTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLI 96 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEE
Confidence 4666677777787876442 2346678899999988899987543
No 29
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=32.72 E-value=70 Score=26.45 Aligned_cols=45 Identities=4% Similarity=-0.136 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCCC
Q 031465 44 EIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLCP 88 (159)
Q Consensus 44 e~~~~f~ekyAek~Gy~lN------------------P--D~evt~~Vi~GLa~NK~rYG~~~CP 88 (159)
+++++.+.+.|++.||.-| | +..+...+++|+..--.++|+..-=
T Consensus 30 ~~tr~kV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~ 94 (346)
T PRK10401 30 ADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLI 94 (346)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEE
Confidence 4455567777778888644 2 2457788999999998999987543
No 30
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=30.85 E-value=81 Score=25.26 Aligned_cols=42 Identities=17% Similarity=0.030 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCC
Q 031465 44 EIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 44 e~~~~f~ekyAek~Gy~lNP--------------------D~evt~~Vi~GLa~NK~rYG~~ 85 (159)
+++++.+.+.|++.||.=|. +..+...+++|+.+--..+|+.
T Consensus 6 ~~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~ 67 (309)
T PRK11041 6 QATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYL 67 (309)
T ss_pred HHHHHHHHHHHHHHCCCcCHHHHHhhcCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCE
Confidence 45677788888888888663 3456788999999998888864
No 31
>PF13410 GST_C_2: Glutathione S-transferase, C-terminal domain; PDB: 4DEJ_H 3IC8_A 2JL4_A 2V6K_B 3CBU_B 1JLW_B 3F6D_B 3G7I_A 3F63_A 3G7J_B ....
Probab=30.12 E-value=1.5e+02 Score=18.78 Aligned_cols=46 Identities=11% Similarity=0.066 Sum_probs=36.9
Q ss_pred CHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 031465 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (159)
Q Consensus 39 see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~ 84 (159)
..+.+++..+.++.....++|.+.....+++..+-+.+..-..+|.
T Consensus 7 ~~~~~~~~l~~le~~L~~~~fl~G~~~s~aD~~l~~~l~~~~~~~~ 52 (69)
T PF13410_consen 7 ARAQLEAALDALEDHLADGPFLFGDRPSLADIALAPFLWRLRFVGP 52 (69)
T ss_dssp HHHHHHHHHHHHHHHHTTSSBTTBSS--HHHHHHHHHHHHHHHCTH
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHHHHHhCc
Confidence 4566777778888899999999999999999999999988777654
No 32
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=29.60 E-value=75 Score=24.10 Aligned_cols=36 Identities=11% Similarity=0.091 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHH
Q 031465 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKG 74 (159)
Q Consensus 39 see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~G 74 (159)
+.+.++++.+.+....++.|..+||++.....+-.|
T Consensus 98 ~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~ 133 (158)
T cd01646 98 SKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEG 133 (158)
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEChhhceeeecCCC
Confidence 456677788888888888999999998766555444
No 33
>PF11794 HpaB_N: 4-hydroxyphenylacetate 3-hydroxylase N terminal; InterPro: IPR024674 This domain is found in the N terminus of HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. The domain is also found in pyoverdin chromophore biosynthetic protein (PvcC), which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=29.58 E-value=94 Score=27.05 Aligned_cols=47 Identities=21% Similarity=0.281 Sum_probs=42.3
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~ 84 (159)
-+.++|.+-++.++..++.+|-.+.--.+....++.|+....+.||.
T Consensus 74 ~s~eDL~~rr~~~~~~a~~t~G~~gR~pD~~n~~~~~~~~~~~~~~~ 120 (264)
T PF11794_consen 74 RSKEDLVKRRKAIREWARYTGGCMGRSPDYMNALLAGLAAAADFFGT 120 (264)
T ss_dssp -SHHHHHHHHHHHHHHHHHCCC--STCHHHHHHHHHHHHHCCHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHcCceeecChhHHHHHHHHHHHHHHHHhH
Confidence 47899999999999999999999999999999999999999999998
No 34
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=28.10 E-value=1.3e+02 Score=17.62 Aligned_cols=30 Identities=7% Similarity=0.063 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHH
Q 031465 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (159)
Q Consensus 44 e~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa 76 (159)
+++++.++++|++.| -+-.+++..++...+
T Consensus 8 ~~~~~~l~~~a~~~g---~s~s~~ir~ai~~~l 37 (39)
T PF01402_consen 8 DELYERLDELAKELG---RSRSELIREAIREYL 37 (39)
T ss_dssp HHHHHHHHHHHHHHT---SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHC---cCHHHHHHHHHHHHH
Confidence 356777888999998 233444544444443
No 35
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=27.96 E-value=93 Score=25.38 Aligned_cols=41 Identities=15% Similarity=0.082 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCC
Q 031465 45 IMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lN------------------PD--~evt~~Vi~GLa~NK~rYG~~ 85 (159)
++++.+.+.|++.||.-| || ..+...+++|+..--..+||.
T Consensus 31 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~ 91 (311)
T TIGR02405 31 ETRERVEQVIQQSGFVPSKSARAMRGGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYD 91 (311)
T ss_pred HHHHHHHHHHHHHCCCcCHHHHHhhcCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCe
Confidence 345556677777777543 32 235667899999999999987
No 36
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=27.83 E-value=44 Score=32.71 Aligned_cols=46 Identities=15% Similarity=0.219 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 031465 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 40 ee~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~ 85 (159)
.+.++.+++-..-+-..+.|++++|+++++.+.++|=.-...|+||
T Consensus 457 ~e~l~~l~e~yg~~~~~~~y~l~~~pe~~~~lf~~lR~~~~~~~yp 502 (607)
T KOG1220|consen 457 SEVLEDLYERYGYHSTANSYRLCIDPEVIKALFDGLRNYDTGYIYP 502 (607)
T ss_pred HHHHHHHHHhhCccceeeEEEEecCCchhHHHHHHHhhcccccccc
Confidence 4556666666666778899999999999999999986655544443
No 37
>PRK05802 hypothetical protein; Provisional
Probab=27.60 E-value=29 Score=30.12 Aligned_cols=13 Identities=31% Similarity=0.930 Sum_probs=11.3
Q ss_pred hhCCCCCCCcccc
Q 031465 81 SLGAPLCPCRHYD 93 (159)
Q Consensus 81 rYG~~~CPCRl~~ 93 (159)
..|..||||-|+.
T Consensus 9 d~~~~~cpc~la~ 21 (320)
T PRK05802 9 DAGSEYCPCHLAE 21 (320)
T ss_pred ccCCCcCceeeec
Confidence 4699999999986
No 38
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=27.17 E-value=34 Score=32.38 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=31.0
Q ss_pred CCcCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHH
Q 031465 36 VEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVV 71 (159)
Q Consensus 36 ~~~see~le~~~~f~ekyAek~Gy~lNPD~evt~~V 71 (159)
+|.+++..++|++|+...-+..|-++||=.+-++.|
T Consensus 395 aeSFedAk~KlR~fa~ti~RPF~VrynpyT~svEvL 430 (461)
T KOG3820|consen 395 AESFEDAKEKLRKFASTIKRPFSVRYNPYTQSVEVL 430 (461)
T ss_pred hhhHHHHHHHHHHHHHhCCCCceeeeccccceehhh
Confidence 567899999999999999999999999977655543
No 39
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=26.85 E-value=1.1e+02 Score=25.36 Aligned_cols=43 Identities=14% Similarity=0.010 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCCC
Q 031465 44 EIMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAPL 86 (159)
Q Consensus 44 e~~~~f~ekyAek~Gy~lN------------------PD--~evt~~Vi~GLa~NK~rYG~~~ 86 (159)
+++++.+.+.|++.||.-| || ..+...+++|+.+--.++|+..
T Consensus 30 ~~tr~rV~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~ 92 (343)
T PRK10727 30 EASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFL 92 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEE
Confidence 3455556677777777544 32 4577889999999888899764
No 40
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=26.25 E-value=21 Score=30.62 Aligned_cols=15 Identities=27% Similarity=0.724 Sum_probs=13.1
Q ss_pred HHHhHhhhCCCCCCC
Q 031465 75 LADHKDSLGAPLCPC 89 (159)
Q Consensus 75 La~NK~rYG~~~CPC 89 (159)
.+.|+-.||..||||
T Consensus 160 p~~~AGd~gg~~CPC 174 (210)
T KOG1671|consen 160 PIANAGDYGGYYCPC 174 (210)
T ss_pred ccccccccCceeccc
Confidence 356889999999999
No 41
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=26.14 E-value=1.1e+02 Score=24.78 Aligned_cols=41 Identities=10% Similarity=0.026 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCC
Q 031465 45 IMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lN------------------PD--~evt~~Vi~GLa~NK~rYG~~ 85 (159)
++++.+.+.|++.||.-| |+ ..+-..+++|+..--.++|+.
T Consensus 28 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~ 88 (327)
T PRK10423 28 AITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVERSCFERGYS 88 (327)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCE
Confidence 444456666666676433 32 356788999999988899987
No 42
>PF04748 Polysacc_deac_2: Divergent polysaccharide deacetylase; InterPro: IPR006837 This is a family of uncharacterised proteins that includes YibQ.; PDB: 2QV5_A 2NLY_A.
Probab=26.12 E-value=2.2e+02 Score=23.62 Aligned_cols=49 Identities=8% Similarity=0.080 Sum_probs=37.5
Q ss_pred eeeccCCcCHHHHHHHHHHHHHHhhhcCcEe---ccChhhHHHHHHHHHHhH
Q 031465 31 QIRAQVEPSEKSVEIMRKFSEQYARRSDTFF---CVDKSVTSVVIKGLADHK 79 (159)
Q Consensus 31 ~~~~~~~~see~le~~~~f~ekyAek~Gy~l---NPD~evt~~Vi~GLa~NK 79 (159)
-+.-+.+.+.+.+++.-+.+.+.|++.|+.+ +|.++-++.|.+.+...+
T Consensus 148 dvfLD~~~~~~~I~~ql~~~~~~A~~~G~aI~Igh~~p~Tl~~L~~~~~~l~ 199 (213)
T PF04748_consen 148 DVFLDNDQDEAAIRRQLDQAARIARKQGSAIAIGHPRPETLEALEEWLPELE 199 (213)
T ss_dssp SEETTST-SHHHHHHHHHHHHHHHHCCSEEEEEEE-SCCHHHHHHHHHHHHH
T ss_pred ceecCCCCCHHHHHHHHHHHHHhhhhcCcEEEEEcCCHHHHHHHHHHHhHHh
Confidence 3445566899999999999999999999976 788887777777766544
No 43
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=25.43 E-value=1.3e+02 Score=23.36 Aligned_cols=36 Identities=11% Similarity=0.193 Sum_probs=30.8
Q ss_pred HHHHHHhhh--cCcEeccChhhHHHHHHHHHHhHhhhC
Q 031465 48 KFSEQYARR--SDTFFCVDKSVTSVVIKGLADHKDSLG 83 (159)
Q Consensus 48 ~f~ekyAek--~Gy~lNPD~evt~~Vi~GLa~NK~rYG 83 (159)
..++.|..+ .|=-.|+|+++-..|-+-|-+-+..||
T Consensus 40 dKvREy~~ks~~Gklvds~pe~e~eLk~el~rla~qfg 77 (105)
T KOG4634|consen 40 DKVREYKKKSPAGKLVDSDPEYEQELKEELFRLAQQFG 77 (105)
T ss_pred HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 344555555 899999999999999999999999999
No 44
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=25.19 E-value=1.2e+02 Score=24.94 Aligned_cols=21 Identities=10% Similarity=0.085 Sum_probs=17.3
Q ss_pred hhhHHHHHHHHHHhHhhhCCC
Q 031465 65 KSVTSVVIKGLADHKDSLGAP 85 (159)
Q Consensus 65 ~evt~~Vi~GLa~NK~rYG~~ 85 (159)
..+...+++|+.+--..+|+.
T Consensus 71 ~~~~~~~~~gi~~~~~~~g~~ 91 (341)
T PRK10703 71 APYFAEIIEAVEKNCYQKGYT 91 (341)
T ss_pred CchHHHHHHHHHHHHHHCCCE
Confidence 357788999999988889975
No 45
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen
Probab=24.13 E-value=1.7e+02 Score=24.47 Aligned_cols=38 Identities=8% Similarity=-0.024 Sum_probs=29.6
Q ss_pred cCHHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHH
Q 031465 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGL 75 (159)
Q Consensus 38 ~see~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GL 75 (159)
.+.++++.|++.+++..+..||+-+..++.+...++-|
T Consensus 170 a~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~lr~l 207 (233)
T TIGR00050 170 ATTDQLELLLEHLEEILLSLGFIPEHKIRRVMRKFRRL 207 (233)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCCccCHHHHHHHHHHH
Confidence 68899999999999999999987655665555444433
No 46
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=23.31 E-value=1.4e+02 Score=24.38 Aligned_cols=42 Identities=14% Similarity=0.100 Sum_probs=31.9
Q ss_pred HHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCCC
Q 031465 45 IMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAPL 86 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lN------------------PD--~evt~~Vi~GLa~NK~rYG~~~ 86 (159)
++++.+.+.|++.||.-| |+ -.+...+++|+.+--..+|+..
T Consensus 35 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~ 96 (331)
T PRK14987 35 ALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQT 96 (331)
T ss_pred HHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEE
Confidence 567778888888888644 22 2367889999999999999873
No 47
>PRK09492 treR trehalose repressor; Provisional
Probab=23.26 E-value=1.2e+02 Score=24.55 Aligned_cols=42 Identities=10% Similarity=-0.069 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCC
Q 031465 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPL 86 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lNP--------------------D~evt~~Vi~GLa~NK~rYG~~~ 86 (159)
++++.+.+.|++.||.-|. +..+...++.|+..--.++||..
T Consensus 34 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~ 95 (315)
T PRK09492 34 ETRERVEAVINQHGFSPSKSARAMRGQSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDP 95 (315)
T ss_pred HHHHHHHHHHHHHCCCcCHHHHHhhcCCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeE
Confidence 3455566777777775442 12355678899999989999875
No 48
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=23.07 E-value=1.1e+02 Score=22.38 Aligned_cols=30 Identities=13% Similarity=0.026 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHh-hhcCcEeccChhhHH
Q 031465 40 EKSVEIMRKFSEQYA-RRSDTFFCVDKSVTS 69 (159)
Q Consensus 40 ee~le~~~~f~ekyA-ek~Gy~lNPD~evt~ 69 (159)
+++.+++.+.+...- ++.|..+|+++..+-
T Consensus 69 ~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~ 99 (119)
T cd01648 69 LDKAIKFLNLLLRGFINQYKTFVNFDKTQIN 99 (119)
T ss_pred HHHHHHHHHHHHHhhHHhhCeEECcccceee
Confidence 455566666666664 889999999987654
No 49
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=23.07 E-value=32 Score=30.49 Aligned_cols=47 Identities=15% Similarity=0.215 Sum_probs=26.4
Q ss_pred hhhCCceeec-Cccc--ccCc---eeeEeeee----------ccchhhccCCCCccccccccc
Q 031465 98 EAQQGFWNCP-CVPM--RERN---ATACSFSL----------QRTILLARISPSPWMKSRNQQ 144 (159)
Q Consensus 98 ev~D~diICP-Cvy~--~E~G---~CHC~LFv----------s~e~~~a~~~~~~~~~~~~~~ 144 (159)
+.+-.||+|| |.|+ ...- .|-|.--. ..+....++...+|...|+++
T Consensus 135 ~~~~GDW~Cp~C~fhNfarn~~C~rC~~~r~~~a~~~~~~s~~~~~~~~s~~~~~~~~t~~~~ 197 (280)
T KOG4198|consen 135 PWRSGDWECPGCNFHNFARNSECFRCGAKRPLAALLGNQASEATEHDWLSKVADSSSSTRFES 197 (280)
T ss_pred CccccCcccCCCCceeccccchhhhcCCcCcccccccccccccccccccccccccccceeccc
Confidence 3458999999 9996 2222 33333322 123344555566666666655
No 50
>PHA01748 hypothetical protein
Probab=22.54 E-value=1.8e+02 Score=19.63 Aligned_cols=29 Identities=10% Similarity=0.177 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhhcCcEeccChhhHHHHHHHH
Q 031465 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGL 75 (159)
Q Consensus 45 ~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GL 75 (159)
++.+.+++||++.|+ |-.+-+-.+|-..+
T Consensus 12 el~~eld~~a~~~g~--~RSE~Ir~Ai~~~~ 40 (60)
T PHA01748 12 DLLELLDRYAIKHGL--NRSEAIRKAIEKMV 40 (60)
T ss_pred HHHHHHHHHHHHhCC--CHHHHHHHHHHHHH
Confidence 455668899999996 64444444444333
No 51
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=22.29 E-value=38 Score=31.40 Aligned_cols=25 Identities=44% Similarity=0.824 Sum_probs=14.3
Q ss_pred hCCCCCCCcccc---chhhhhhCCceee
Q 031465 82 LGAPLCPCRHYD---DKAAEAQQGFWNC 106 (159)
Q Consensus 82 YG~~~CPCRl~~---DkE~ev~D~diIC 106 (159)
=|.|||||-..- |+.-..+|+.|-|
T Consensus 24 GGapyCPClYiVQvFD~tPAa~dG~i~~ 51 (429)
T KOG3651|consen 24 GGAPYCPCLYIVQVFDKTPAAKDGRIRC 51 (429)
T ss_pred CCCCcCCeEEEEEeccCCchhccCcccc
Confidence 378888886542 5544444554443
No 52
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=22.09 E-value=34 Score=27.73 Aligned_cols=39 Identities=18% Similarity=0.202 Sum_probs=27.4
Q ss_pred Ccee-eEeeeeccchhhccCCCCccccccccccccccccccceee
Q 031465 114 RNAT-ACSFSLQRTILLARISPSPWMKSRNQQQICDVTDYNRQVL 157 (159)
Q Consensus 114 ~G~C-HC~LFvs~e~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (159)
-..| |||.=-++=.....++| -|=.-.+.+..|.||||+
T Consensus 28 sf~C~~CGyr~~ev~~~~~~~p-----~r~~l~V~~~~DL~r~Vv 67 (163)
T TIGR00340 28 TYICEKCGYRSTDVYQLEEKEP-----VRYIIKIENEDDLFTLVY 67 (163)
T ss_pred EEECCCCCCchhheeEcCCcCC-----EEEEEEECChhhccceEE
Confidence 4567 89876554444444555 466777888899999997
No 53
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=21.77 E-value=1.3e+02 Score=23.14 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHHHHHhhhcCcEeccChhhHH
Q 031465 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (159)
Q Consensus 39 see~le~~~~f~ekyAek~Gy~lNPD~evt~ 69 (159)
.++.++++.+.++.+++..|..||+++....
T Consensus 182 ~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~ 212 (226)
T cd01651 182 GPKEAEEIKELIREFLEELGLELNPEKTRIT 212 (226)
T ss_pred CHHHHHHHHHHHHHHHHHcCCeechhhccee
Confidence 4455888888899999999999999986543
No 54
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=21.08 E-value=1.7e+02 Score=19.15 Aligned_cols=33 Identities=9% Similarity=0.115 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHh
Q 031465 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADH 78 (159)
Q Consensus 44 e~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~N 78 (159)
+.++++++..|+..|=-+| .+++..|.+.|.++
T Consensus 13 ~~l~~~lk~~A~~~gRS~N--sEIv~~L~~~l~~e 45 (50)
T PF03869_consen 13 EELKEKLKERAEENGRSMN--SEIVQRLEEALKKE 45 (50)
T ss_dssp HHHHHHHHHHHHHTTS-HH--HHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHhCCChH--HHHHHHHHHHHhcc
Confidence 3678889999999997776 45666666666644
No 55
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=21.08 E-value=1.2e+02 Score=23.35 Aligned_cols=29 Identities=10% Similarity=0.117 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHH
Q 031465 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (159)
Q Consensus 41 e~le~~~~f~ekyAek~Gy~lNPD~evt~ 69 (159)
+.++.+.+.+..+++..|..+|+++..+.
T Consensus 160 ~~~~~~~~~~~~~~~~~gl~in~~Kt~~~ 188 (220)
T cd01650 160 RKLQELLQRLQEWSKESGLKINPSKSKVM 188 (220)
T ss_pred HHHHHHHHHHHHHHHHcCCEEChhheEEE
Confidence 57888888888899999999999987554
No 56
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=20.96 E-value=1.8e+02 Score=24.98 Aligned_cols=54 Identities=13% Similarity=0.058 Sum_probs=36.9
Q ss_pred ccCCcCHHHHHHHHHHHHHHhhhcCcEeccC--------------------hhhHHHHHHHHHHhHhhhCCCC--CCCcc
Q 031465 34 AQVEPSEKSVEIMRKFSEQYARRSDTFFCVD--------------------KSVTSVVIKGLADHKDSLGAPL--CPCRH 91 (159)
Q Consensus 34 ~~~~~see~le~~~~f~ekyAek~Gy~lNPD--------------------~evt~~Vi~GLa~NK~rYG~~~--CPCRl 91 (159)
.....++| +++.+.+.+++.||.=|+- -.+...++.|+..--.++||.. |++..
T Consensus 23 ~~~~Vs~e----Tr~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~ 98 (333)
T COG1609 23 GSPYVSEE----TREKVLAAIKELGYRPNAVARSLRTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD 98 (333)
T ss_pred CCCCCCHH----HHHHHHHHHHHHCCCCCHHHHHHHhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC
Confidence 33345555 4555777899999983321 1467789999999888888864 55554
No 57
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=20.73 E-value=2.2e+02 Score=20.06 Aligned_cols=48 Identities=15% Similarity=0.152 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCC
Q 031465 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (159)
Q Consensus 40 ee~le~~~~f~ekyAek~Gy~lNPD~evt~~Vi~GLa~NK~rYG~~~CP 88 (159)
-+.+..++.|+...+++.|+--. +...+..++.=++.|--+||+.-.+
T Consensus 5 ~~~i~~~r~~~~~~~~~~~~~~~-~~~~~~lav~E~~~Nav~H~~~~~~ 52 (125)
T PF13581_consen 5 PEDIREARAFLREFLERLGLPEE-DRDDLELAVSEALTNAVEHGYPGDP 52 (125)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 46889999999999999765422 2233444555667799999998655
Done!