Query 032076
Match_columns 148
No_of_seqs 108 out of 193
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:17:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032076.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032076hhsearch_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 5.5E-50 1.2E-54 303.7 10.5 112 35-146 5-116 (116)
2 PF02943 FeThRed_B: Ferredoxin 100.0 6.3E-46 1.4E-50 278.0 6.6 103 41-143 1-107 (108)
3 COG4802 FtrB Ferredoxin-thiore 100.0 2.8E-42 6.2E-47 258.2 9.5 98 39-141 2-103 (110)
4 PF05511 ATP-synt_F6: Mitochon 79.7 3.9 8.4E-05 30.8 4.4 50 36-85 34-84 (99)
5 PHA00425 DNA packaging protein 74.5 6.4 0.00014 29.1 4.2 46 39-84 28-76 (88)
6 PHA02745 hypothetical protein; 63.8 22 0.00048 31.0 5.9 60 26-85 205-264 (265)
7 PF03938 OmpH: Outer membrane 58.4 19 0.00041 27.0 4.2 37 39-75 111-157 (158)
8 PF11123 DNA_Packaging_2: DNA 57.1 25 0.00055 25.8 4.4 46 39-84 26-74 (82)
9 PRK10780 periplasmic chaperone 56.4 20 0.00044 27.8 4.2 37 39-75 118-164 (165)
10 TIGR01924 rsbW_low_gc serine-p 48.8 48 0.0011 25.3 5.1 50 37-87 13-62 (159)
11 PF14791 DNA_pol_B_thumb: DNA 46.4 24 0.00051 24.1 2.7 20 45-64 10-29 (64)
12 PRK13612 photosystem II reacti 46.4 20 0.00043 27.7 2.6 25 38-62 87-111 (113)
13 TIGR03047 PS_II_psb28 photosys 46.2 20 0.00043 27.6 2.5 24 38-61 84-107 (109)
14 KOG1671 Ubiquinol cytochrome c 46.0 6.9 0.00015 33.1 0.1 15 75-89 160-174 (210)
15 PF03912 Psb28: Psb28 protein; 45.7 15 0.00033 28.1 1.9 24 38-61 84-107 (108)
16 CHL00128 psbW photosystem II p 45.1 21 0.00045 27.6 2.6 25 38-62 87-111 (113)
17 PRK13611 photosystem II reacti 45.1 21 0.00046 27.2 2.5 24 38-61 80-103 (104)
18 PLN00039 photosystem II reacti 44.6 21 0.00047 27.4 2.5 25 38-62 85-109 (111)
19 PF00356 LacI: Bacterial regul 40.8 22 0.00048 22.7 1.8 18 45-62 29-46 (46)
20 PF10431 ClpB_D2-small: C-term 40.0 75 0.0016 21.3 4.5 38 45-85 13-50 (81)
21 TIGR01463 mtaA_cmuA methyltran 37.5 37 0.00081 28.6 3.2 45 40-84 292-340 (340)
22 TIGR01481 ccpA catabolite cont 36.5 56 0.0012 26.3 4.0 49 37-89 27-95 (329)
23 COG2825 HlpA Outer membrane pr 36.3 57 0.0012 26.1 3.9 38 38-75 120-167 (170)
24 PF12683 DUF3798: Protein of u 34.4 78 0.0017 27.8 4.7 50 42-92 187-236 (275)
25 PRK11303 DNA-binding transcrip 34.1 65 0.0014 25.9 4.0 44 45-88 33-96 (328)
26 PRK05452 anaerobic nitric oxid 33.4 25 0.00054 32.0 1.6 35 31-67 370-404 (479)
27 TIGR02417 fruct_sucro_rep D-fr 33.2 57 0.0012 26.4 3.5 48 45-92 32-99 (327)
28 PF00078 RVT_1: Reverse transc 32.7 54 0.0012 24.4 3.1 29 39-67 171-199 (214)
29 PRK11041 DNA-binding transcrip 32.3 71 0.0015 25.4 3.8 41 45-85 7-67 (309)
30 PRK10401 DNA-binding transcrip 32.2 69 0.0015 26.2 3.9 46 38-87 28-93 (346)
31 PF01402 RHH_1: Ribbon-helix-h 31.5 1.1E+02 0.0023 17.8 3.7 30 44-76 8-37 (39)
32 KOG4634 Mitochondrial F1F0-ATP 30.8 1.2E+02 0.0025 23.3 4.5 37 47-83 39-77 (105)
33 KOG1220 Phosphoglucomutase/pho 29.4 41 0.00089 32.5 2.4 45 41-85 458-502 (607)
34 COG5502 Uncharacterized conser 29.2 80 0.0017 25.1 3.6 39 40-78 72-111 (135)
35 TIGR02405 trehalos_R_Ecol treh 28.9 84 0.0018 25.4 3.8 45 37-85 27-91 (311)
36 PF11794 HpaB_N: 4-hydroxyphen 28.6 90 0.0019 26.8 4.1 47 38-84 74-120 (264)
37 PRK10423 transcriptional repre 26.7 1E+02 0.0022 24.7 3.9 20 66-85 69-88 (327)
38 PRK10727 DNA-binding transcrip 26.7 1E+02 0.0022 25.2 4.0 46 37-86 27-92 (343)
39 cd01646 RT_Bac_retron_I RT_Bac 26.1 89 0.0019 23.4 3.3 36 39-74 98-133 (158)
40 PRK10703 DNA-binding transcrip 25.2 1.1E+02 0.0024 24.8 3.9 21 65-85 71-91 (341)
41 PF08722 Tn7_Tnp_TnsA_N: TnsA 24.9 64 0.0014 22.2 2.1 31 32-62 54-84 (88)
42 TIGR00050 rRNA_methyl_1 RNA me 24.8 1.5E+02 0.0033 24.4 4.7 40 37-76 169-208 (233)
43 PRK14987 gluconate operon tran 24.4 1.3E+02 0.0028 24.4 4.1 42 45-86 35-96 (331)
44 PF13581 HATPase_c_2: Histidin 24.1 1.9E+02 0.0041 20.2 4.5 49 39-88 4-52 (125)
45 PRK09492 treR trehalose repres 23.1 1.1E+02 0.0025 24.4 3.5 46 37-86 30-95 (315)
46 PRK05802 hypothetical protein; 22.8 35 0.00076 29.3 0.6 13 81-93 9-21 (320)
47 PHA01748 hypothetical protein 22.7 1.7E+02 0.0038 19.5 3.9 32 44-78 11-42 (60)
48 PF04748 Polysacc_deac_2: Dive 21.8 2.4E+02 0.0053 23.0 5.3 45 35-79 152-199 (213)
49 PF03869 Arc: Arc-like DNA bin 21.6 1.5E+02 0.0033 19.1 3.3 33 44-78 13-45 (50)
50 PF13410 GST_C_2: Glutathione 21.5 2.2E+02 0.0047 17.7 4.7 45 40-84 8-52 (69)
51 cd01648 TERT TERT: Telomerase 21.4 1.2E+02 0.0026 21.9 3.1 31 39-69 68-99 (119)
52 PLN02449 ferrochelatase 20.4 2.1E+02 0.0045 26.9 5.1 50 40-89 367-423 (485)
53 KOG3651 Protein kinase C, alph 20.3 42 0.00092 30.6 0.6 11 82-92 24-34 (429)
54 cd01651 RT_G2_intron RT_G2_int 20.2 1.3E+02 0.0029 22.8 3.3 31 39-69 182-212 (226)
No 1
>CHL00165 ftrB ferredoxin thioreductase subunit beta; Validated
Probab=100.00 E-value=5.5e-50 Score=303.66 Aligned_cols=112 Identities=61% Similarity=1.173 Sum_probs=107.7
Q ss_pred cCCCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccCCchhhhhCCceeecCcccccC
Q 032076 35 QVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVPMRER 114 (148)
Q Consensus 35 ~~~~s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~~dke~E~~d~diICPC~y~~e~ 114 (148)
+...+++++++|++|+++||+++||+||||+++|+.|++|||+||++||+||||||+++|+++|+++++|||||++|+++
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 56789999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred ceeeeeeeecCCCCCCCCcccccHHHHHHhhh
Q 032076 115 KECHCMLFLTPENDFAGQDQSISLDEIKESTA 146 (148)
Q Consensus 115 G~ChCgLFvs~e~~~~g~~q~i~~~~~~~~~~ 146 (148)
|+|||||||++|+.|+|+.|.|++++|.+++.
T Consensus 85 g~CHC~LF~t~e~~~~~~~~~i~~~~~~~~~~ 116 (116)
T CHL00165 85 KECHCMLFLTPDNEFASQSQTISKKTLLQNII 116 (116)
T ss_pred CCceEeeeecCCccccCcceeecHHHHHHhcC
Confidence 99999999999999999999999999998763
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=6.3e-46 Score=277.97 Aligned_cols=103 Identities=45% Similarity=0.758 Sum_probs=78.7
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccCCchhhhhCCceeecCcccc----cCce
Q 032076 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVPMR----ERKE 116 (148)
Q Consensus 41 k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~~dke~E~~d~diICPC~y~~----e~G~ 116 (148)
|++++|++|+++||+++||+||||+++|+.|++||++||++||++|||||+++|++++++|++|||||++++ ++|+
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 689999999999999999999999999999999999999999999999999999888888999999999632 7999
Q ss_pred eeeeeeecCCCCCCCCcccccHHHHHH
Q 032076 117 CHCMLFLTPENDFAGQDQSISLDEIKE 143 (148)
Q Consensus 117 ChCgLFvs~e~~~~g~~q~i~~~~~~~ 143 (148)
|||||||+++++++++.|+|+.++|.+
T Consensus 81 ChC~Lf~~~e~~~~~~~~~~~~e~~~~ 107 (108)
T PF02943_consen 81 CHCGLFVSPEYAEAGKKQEISHEEIEK 107 (108)
T ss_dssp -TTSSSB-TTSTTB-S-S---HHHHHH
T ss_pred ceEeeeECcccccchhhcccCHHHhhc
Confidence 999999999999999999999999975
No 3
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=100.00 E-value=2.8e-42 Score=258.17 Aligned_cols=98 Identities=41% Similarity=0.725 Sum_probs=92.8
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccCCchhhhhCCceeecCcc----cccC
Q 032076 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVP----MRER 114 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~~dke~E~~d~diICPC~y----~~e~ 114 (148)
+++++++||+|+++||+|+||+||||.++|+.|++|||.||++||+++||||+++|+++| |++|||||+| |++|
T Consensus 2 ~~e~l~~my~~~eq~AeksG~~lnpD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~eee--dk~ivCPCvy~~ddi~e~ 79 (110)
T COG4802 2 SDEELNKMYRFTEQYAEKSGYRLNPDREFTAEVLRGLASNKERYGYPSCPCRLVTGKEEE--DKDIVCPCVYRDDDIREY 79 (110)
T ss_pred cHHHHHHHHHHHHHHHHhcCceeCCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCHHH--hhceeccCcCCccchhhh
Confidence 689999999999999999999999999999999999999999999999999999998888 6789999999 8999
Q ss_pred ceeeeeeeecCCCCCCCCcccccHHHH
Q 032076 115 KECHCMLFLTPENDFAGQDQSISLDEI 141 (148)
Q Consensus 115 G~ChCgLFvs~e~~~~g~~q~i~~~~~ 141 (148)
|.||||||++++.. +.|.||...+
T Consensus 80 g~C~C~Lyl~~e~~---e~~sIp~r~~ 103 (110)
T COG4802 80 GECYCGLYLSPEKD---EAQSIPERRA 103 (110)
T ss_pred CceeEEEEeccccc---chhhcchhhH
Confidence 99999999999987 6788887776
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=79.68 E-value=3.9 Score=30.82 Aligned_cols=50 Identities=8% Similarity=0.197 Sum_probs=39.4
Q ss_pred CCC-ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032076 36 VEP-SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 36 ~~~-s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
.+| ..-=+++++++..+-..+.|=..++.+++-..+-+-|.+-...||..
T Consensus 34 ~DPIQklFldKIREY~~Ksks~gGklVD~~Pe~~kel~eel~kL~r~YG~g 84 (99)
T PF05511_consen 34 LDPIQKLFLDKIREYNQKSKSSGGKLVDAGPEYEKELNEELEKLARQYGGG 84 (99)
T ss_dssp --TTTHHHHHHHHHHHHHHTTTSS-STT--THHHHHHHHHHHHHHHHHHSS
T ss_pred cChHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHHHHHhCCc
Confidence 344 44458999999988888899899999999999999999999999964
No 5
>PHA00425 DNA packaging protein, small subunit
Probab=74.48 E-value=6.4 Score=29.13 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=39.2
Q ss_pred ChHHHHHHHHHHHHHhhhcCcE---eccChhhHHHHHHHHHHhHhhhCC
Q 032076 39 SEKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~---lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (148)
.++---.+|+-+.++-+++.|. +.||++++-.+..+|+..+..+|.
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 3444567899999999999885 679999999999999999999885
No 6
>PHA02745 hypothetical protein; Provisional
Probab=63.76 E-value=22 Score=30.99 Aligned_cols=60 Identities=7% Similarity=0.078 Sum_probs=50.8
Q ss_pred CCCcccccccCCCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032076 26 PRPVTQIRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 26 ~~~~~~~~~~~~~s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
..+...+..++...+-.-..+-.|++.|+.+.||.---.+.+...+-.-|..-+-+||.+
T Consensus 205 a~d~~gt~vRPgLDe~Ar~vLL~fVe~yG~~~~W~t~D~~~I~ntiR~KiqeiR~K~g~~ 264 (265)
T PHA02745 205 AFDGEGTDVRPGLDEDARTVLLRYVEIYGEKQRWCTEDHQAIINVIRNKMQESRRKDRHR 264 (265)
T ss_pred cccccCcccCCCcchHHHHHHHHHHHHHhhccCCCCCchHHHHHHHHHHHHHHHHHhCCc
Confidence 334456667778889999999999999999999998888888888888888888889875
No 7
>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=58.43 E-value=19 Score=26.96 Aligned_cols=37 Identities=24% Similarity=0.275 Sum_probs=26.9
Q ss_pred ChHHHHHHHHHHHHHhhhcCc----------EeccChhhHHHHHHHH
Q 032076 39 SEKSVEIMRKFSEQYARRSDT----------FFCVDKSVTSVVIKGL 75 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy----------~lNPD~ev~~~Vi~GL 75 (148)
..+-.+++...++.||+..|| +.+|..++|+.|+..|
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 345567788899999999998 5677788999998866
No 8
>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=57.13 E-value=25 Score=25.78 Aligned_cols=46 Identities=17% Similarity=0.179 Sum_probs=38.9
Q ss_pred ChHHHHHHHHHHHHHhhhcCcE---eccChhhHHHHHHHHHHhHhhhCC
Q 032076 39 SEKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~---lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (148)
.++---.+|+-+.++-+++.|. +-||++++-.+..||...++.+|.
T Consensus 26 dekRsPQLYnAI~k~L~RHkF~iskl~pd~~~LG~L~~aL~ey~~~~g~ 74 (82)
T PF11123_consen 26 DEKRSPQLYNAIGKLLDRHKFQISKLQPDENILGELAAALEEYKKMVGA 74 (82)
T ss_pred hhhcChHHHHHHHHHHHHccchhhhcCccHHHHHHHHHHHHHHHHHcCC
Confidence 3444557889999999999885 579999999999999999998885
No 9
>PRK10780 periplasmic chaperone; Provisional
Probab=56.44 E-value=20 Score=27.80 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=28.4
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEe----------ccChhhHHHHHHHH
Q 032076 39 SEKSVEIMRKFSEQYARRSDTFF----------CVDKSVTSVVIKGL 75 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~l----------NPD~ev~~~Vi~GL 75 (148)
....++++.+.++++|++.||-+ +|..++|..|++-|
T Consensus 118 ~~~i~~ki~~ai~~vak~~gy~~Vld~~~v~Y~~~~~DIT~~Vik~l 164 (165)
T PRK10780 118 RNKILTRIQTAVKSVANKQGYDLVVDANAVAYNSSDKDITADVLKQV 164 (165)
T ss_pred HHHHHHHHHHHHHHHHHHcCCeEEEeCCceeeeCCCCCchHHHHHhh
Confidence 34567888899999999999844 46678888887754
No 10
>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=48.76 E-value=48 Score=25.34 Aligned_cols=50 Identities=10% Similarity=-0.020 Sum_probs=39.6
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCC
Q 032076 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLC 87 (148)
Q Consensus 37 ~~s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~C 87 (148)
....+.+..++.|++.+|+..|+- ..+.+-+..++.-|+.|--+||+...
T Consensus 13 ~a~~~~~~~vr~~~~~~a~~~g~~-~~~~~~l~lav~Ea~~Nai~ha~~~~ 62 (159)
T TIGR01924 13 PAKPEYVGLIRLTLSGIASRAGYT-YDDIEDLKIAVSEACTNAVKHAYKEG 62 (159)
T ss_pred cCcHHHHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 456788999999999999999964 23334566778889999999998755
No 11
>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=46.39 E-value=24 Score=24.05 Aligned_cols=20 Identities=15% Similarity=0.130 Sum_probs=16.5
Q ss_pred HHHHHHHHHhhhcCcEeccC
Q 032076 45 IMRKFSEQYARRSDTFFCVD 64 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lNPD 64 (148)
...+.+..+|.+.||.||+.
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 45667888999999999985
No 12
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=46.37 E-value=20 Score=27.72 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~lN 62 (148)
.+++..+.+.+|+++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T PRK13612 87 KSEQEWDRFMRFMERYAKENGLGFS 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 4899999999999999999997653
No 13
>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=46.17 E-value=20 Score=27.57 Aligned_cols=24 Identities=25% Similarity=0.369 Sum_probs=21.5
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEe
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~l 61 (148)
.+++..+.+.+|+++||+.+|.-|
T Consensus 84 ~s~~~WdRFMRFmeRYA~~ngl~f 107 (109)
T TIGR03047 84 KSEDEWDRFMRFMERYAEANGLGY 107 (109)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 489999999999999999998654
No 14
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=46.00 E-value=6.9 Score=33.05 Aligned_cols=15 Identities=27% Similarity=0.724 Sum_probs=13.2
Q ss_pred HHHhHhhhCCCCCCC
Q 032076 75 LADHKDSLGAPLCPC 89 (148)
Q Consensus 75 La~NK~rYG~~~CPC 89 (148)
.+.|+-.||..||||
T Consensus 160 p~~~AGd~gg~~CPC 174 (210)
T KOG1671|consen 160 PIANAGDYGGYYCPC 174 (210)
T ss_pred ccccccccCceeccc
Confidence 356889999999999
No 15
>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=45.67 E-value=15 Score=28.09 Aligned_cols=24 Identities=29% Similarity=0.405 Sum_probs=19.0
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEe
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~l 61 (148)
.+++..+.+.+|+++||+.+|.-|
T Consensus 84 ~s~~~WdRFMRFMeRYA~~Ngl~f 107 (108)
T PF03912_consen 84 KSEEEWDRFMRFMERYAEANGLGF 107 (108)
T ss_dssp -SSHHHHHHHHHHHHHHHH--SSS
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 478999999999999999998644
No 16
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=45.10 E-value=21 Score=27.57 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~lN 62 (148)
.+++..+.+.+|+++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T CHL00128 87 KNPEAWDRFMRFMERYAEDNGLTFT 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 4899999999999999999997653
No 17
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=45.08 E-value=21 Score=27.19 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=21.2
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEe
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~l 61 (148)
.+++..+.+.+|+++||+.+|.-|
T Consensus 80 ~s~~~wdRFMRFmeRYA~~Ngl~f 103 (104)
T PRK13611 80 ETEAEWDRFLRFMERFSAANQMGM 103 (104)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 489999999999999999998643
No 18
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=44.62 E-value=21 Score=27.43 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~lN 62 (148)
.+++..+.+.+|+++||+.+|.-|.
T Consensus 85 ~s~~~WdRFMRFMeRYA~~ngl~f~ 109 (111)
T PLN00039 85 RSPREWDRFMRFMERYAEENGLGFV 109 (111)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 4899999999999999999997553
No 19
>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=40.76 E-value=22 Score=22.71 Aligned_cols=18 Identities=11% Similarity=-0.278 Sum_probs=11.7
Q ss_pred HHHHHHHHHhhhcCcEec
Q 032076 45 IMRKFSEQYARRSDTFFC 62 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lN 62 (148)
++++.+.+.|++.||.-|
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 445557777788889765
No 20
>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=39.96 E-value=75 Score=21.34 Aligned_cols=38 Identities=16% Similarity=0.189 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032076 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
.+.+..+++++ .|..|+-|+++.+.+++-= ....||.+
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 34555666666 9999999999999887742 34567765
No 21
>TIGR01463 mtaA_cmuA methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.
Probab=37.51 E-value=37 Score=28.61 Aligned_cols=45 Identities=9% Similarity=0.107 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHHhhhcCcEeccChhh----HHHHHHHHHHhHhhhCC
Q 032076 40 EKSVEIMRKFSEQYARRSDTFFCVDKSV----TSVVIKGLADHKDSLGA 84 (148)
Q Consensus 40 ~k~~e~~~~~~ekyAek~Gy~lNPD~ev----~~~Vi~GLa~NK~rYG~ 84 (148)
..+.+++++.+++..++.||.|||+-.+ -..=++.+.+--+.|||
T Consensus 292 ~gt~eeI~~~v~~~l~~~~~Il~~gcgi~~~tp~eni~a~v~a~~~~~~ 340 (340)
T TIGR01463 292 NGTPEKVKKLAKEVLYNGGDIVMPGCDIDWMTPLENLKAMIEACKSIKY 340 (340)
T ss_pred CCCHHHHHHHHHHHHHcCCeEECCCCCCCCCCCHHHHHHHHHHHHhccC
Confidence 3466788888888888899999998433 33444555555555654
No 22
>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=36.52 E-value=56 Score=26.33 Aligned_cols=49 Identities=12% Similarity=0.034 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCCCCC
Q 032076 37 EPSEKSVEIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCPC 89 (148)
Q Consensus 37 ~~s~k~~e~~~~~~ekyAek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~~CPC 89 (148)
..++++ ++.+.+.|++.||.-|+ +..+...++.|+...-.++||..=-+
T Consensus 27 ~vs~~t----r~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~ 95 (329)
T TIGR01481 27 NVKPAT----RKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILS 95 (329)
T ss_pred CCCHHH----HHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEE
Confidence 355555 44566667777776543 23577789999988888888876443
No 23
>COG2825 HlpA Outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=36.32 E-value=57 Score=26.08 Aligned_cols=38 Identities=24% Similarity=0.237 Sum_probs=31.0
Q ss_pred CChHHHHHHHHHHHHHhhhcCcE----------eccChhhHHHHHHHH
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTF----------FCVDKSVTSVVIKGL 75 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~----------lNPD~ev~~~Vi~GL 75 (148)
...+..+++...++.+|++.||- .+|-.++|+.|++-|
T Consensus 120 ~~~~~~~~i~~ai~~~a~~~gy~~vl~~~~V~y~~~~~DIT~~Vlk~l 167 (170)
T COG2825 120 EEQKLLEKIQRAIESVAEKGGYSLVLDSNAVLYAKPSKDITDDVLKAL 167 (170)
T ss_pred HHHHHHHHHHHHHHHHHHhCCcceEecCCchhccCCCCCchHHHHHHH
Confidence 34567788899999999999985 478888899998876
No 24
>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=34.43 E-value=78 Score=27.79 Aligned_cols=50 Identities=18% Similarity=0.361 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCccc
Q 032076 42 SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHY 92 (148)
Q Consensus 42 ~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~ 92 (148)
-+|.+-+|+++|-+... +|+-+..+++.||+.++.++-.|=..-||+-+-
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 46778889999976665 577788999999999999998888888887663
No 25
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=34.10 E-value=65 Score=25.95 Aligned_cols=44 Identities=11% Similarity=-0.016 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCCCC
Q 032076 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCP 88 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~~CP 88 (148)
++++.+.+.|++.||.-|+ +..+...++.|+.+.-.++|+..=-
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 3455566666777776442 2346677899999888899987543
No 26
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=33.37 E-value=25 Score=32.00 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=26.7
Q ss_pred cccccCCCChHHHHHHHHHHHHHhhhcCcEeccChhh
Q 032076 31 QIRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (148)
Q Consensus 31 ~~~~~~~~s~k~~e~~~~~~ekyAek~Gy~lNPD~ev 67 (148)
.+.....|+++++++.++|.+++|++-= +-|++..
T Consensus 370 ~l~~~~~P~ee~~~~~~~~g~~la~~~~--~~~~~~~ 404 (479)
T PRK05452 370 SLKAKWRPDQDALELCREHGREIARQWA--LAPLPQS 404 (479)
T ss_pred cEEEEecCCHHHHHHHHHHHHHHHHHHh--hCCcccc
Confidence 4555667899999999999999996653 7777644
No 27
>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=33.18 E-value=57 Score=26.37 Aligned_cols=48 Identities=10% Similarity=-0.061 Sum_probs=33.0
Q ss_pred HHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCCCCCccc
Q 032076 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCPCRHY 92 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~~CPCRl~ 92 (148)
++++.+.+.|++.||.-|. +..+...++.|+.+--.++||..--+...
T Consensus 32 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~ 99 (327)
T TIGR02417 32 ETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSD 99 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence 4455566677777775442 23467788999998888999987655443
No 28
>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=32.73 E-value=54 Score=24.36 Aligned_cols=29 Identities=10% Similarity=0.079 Sum_probs=23.9
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhh
Q 032076 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~lNPD~ev 67 (148)
+.+.++++.+.+.++.+..|..+||++-.
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 36678888888888888899999998754
No 29
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=32.28 E-value=71 Score=25.35 Aligned_cols=41 Identities=17% Similarity=0.017 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCC
Q 032076 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
++++.+.+.|++.||.-|. +..+...+++|+.+--..+|+.
T Consensus 7 ~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~ 67 (309)
T PRK11041 7 ATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYL 67 (309)
T ss_pred HHHHHHHHHHHHHCCCcCHHHHHhhcCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCE
Confidence 4555577778888887663 3456788899999988888864
No 30
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=32.18 E-value=69 Score=26.22 Aligned_cols=46 Identities=7% Similarity=-0.085 Sum_probs=31.9
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCC
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLC 87 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~C 87 (148)
.++++.++ +.+.|+..||.-| | +..+...+++|+..--.++||..-
T Consensus 28 Vs~~tr~k----V~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~ 93 (346)
T PRK10401 28 VSADTREA----VMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVL 93 (346)
T ss_pred CCHHHHHH----HHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEE
Confidence 55555555 5666666677644 2 235777899999998899998754
No 31
>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=31.51 E-value=1.1e+02 Score=17.83 Aligned_cols=30 Identities=7% Similarity=0.063 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHH
Q 032076 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (148)
Q Consensus 44 e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa 76 (148)
+++++.++++|++.| -+-.+++..++...+
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 456677888888888 233445555554443
No 32
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=30.83 E-value=1.2e+02 Score=23.29 Aligned_cols=37 Identities=11% Similarity=0.168 Sum_probs=32.0
Q ss_pred HHHHHHHhhh--cCcEeccChhhHHHHHHHHHHhHhhhC
Q 032076 47 RKFSEQYARR--SDTFFCVDKSVTSVVIKGLADHKDSLG 83 (148)
Q Consensus 47 ~~~~ekyAek--~Gy~lNPD~ev~~~Vi~GLa~NK~rYG 83 (148)
...++.|+.+ .|=-.|+|+++-..|-+-|-+-+..||
T Consensus 39 ldKvREy~~ks~~Gklvds~pe~e~eLk~el~rla~qfg 77 (105)
T KOG4634|consen 39 LDKVREYKKKSPAGKLVDSDPEYEQELKEELFRLAQQFG 77 (105)
T ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 4445666666 999999999999999999999999999
No 33
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=29.42 E-value=41 Score=32.49 Aligned_cols=45 Identities=16% Similarity=0.222 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032076 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 41 k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
+-++.+++...-+-..+.|++++|+++++.+.++|=.-...|+||
T Consensus 458 e~l~~l~e~yg~~~~~~~y~l~~~pe~~~~lf~~lR~~~~~~~yp 502 (607)
T KOG1220|consen 458 EVLEDLYERYGYHSTANSYRLCIDPEVIKALFDGLRNYDTGYIYP 502 (607)
T ss_pred HHHHHHHHhhCccceeeEEEEecCCchhHHHHHHHhhcccccccc
Confidence 445555555555667889999999999999999986665545444
No 34
>COG5502 Uncharacterized conserved protein [Function unknown]
Probab=29.18 E-value=80 Score=25.09 Aligned_cols=39 Identities=21% Similarity=0.058 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHHHhhhcCcEeccChhhHH-HHHHHHHHh
Q 032076 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTS-VVIKGLADH 78 (148)
Q Consensus 40 ~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~-~Vi~GLa~N 78 (148)
.+..-.+++|+.+++.+.|+-.|-|.+.+. +|.+-|.+|
T Consensus 72 ~~~~~s~~dFl~Rv~~~~g~~~~vd~e~a~~AVf~vL~r~ 111 (135)
T COG5502 72 PKLPFSLDDFLTRVANKFGLEPPVDPEHAIAAVFAVLKRH 111 (135)
T ss_pred CCCcccHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHh
Confidence 344556789999999999999999999988 888888877
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=28.88 E-value=84 Score=25.39 Aligned_cols=45 Identities=16% Similarity=0.085 Sum_probs=29.8
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCC
Q 032076 37 EPSEKSVEIMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 37 ~~s~k~~e~~~~~~ekyAek~Gy~lN------------------PD--~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
..++++-++ +.+.|++.||.-| || ..+...+++|+..--.++||.
T Consensus 27 ~vs~~tr~r----V~~~a~~lgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~ 91 (311)
T TIGR02405 27 KVSIETRER----VEQVIQQSGFVPSKSARAMRGGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYD 91 (311)
T ss_pred CCCHHHHHH----HHHHHHHHCCCcCHHHHHhhcCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCe
Confidence 355555444 5666666666544 32 235667899999998999987
No 36
>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=28.64 E-value=90 Score=26.83 Aligned_cols=47 Identities=21% Similarity=0.281 Sum_probs=42.2
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 032076 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (148)
Q Consensus 38 ~s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (148)
-+.++|.+-++.++..++.+|-.+.--.+....++.++....+.||.
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 48899999999999999999999999999999999999999999998
No 37
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=26.67 E-value=1e+02 Score=24.74 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHHhHhhhCCC
Q 032076 66 SVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 66 ev~~~Vi~GLa~NK~rYG~~ 85 (148)
.+-..+++|+..--.++|+.
T Consensus 69 ~~~~~~~~gi~~~~~~~g~~ 88 (327)
T PRK10423 69 PFYSELVRGVERSCFERGYS 88 (327)
T ss_pred CcHHHHHHHHHHHHHHcCCE
Confidence 46778999999988889986
No 38
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=26.67 E-value=1e+02 Score=25.19 Aligned_cols=46 Identities=13% Similarity=-0.008 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCC
Q 032076 37 EPSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPL 86 (148)
Q Consensus 37 ~~s~k~~e~~~~~~ekyAek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~ 86 (148)
..++++-++ +.+.|++.||.-| | +..+...+++|+..--.++|+..
T Consensus 27 ~Vs~~tr~r----V~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~ 92 (343)
T PRK10727 27 KASEASRLA----VHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFL 92 (343)
T ss_pred CCCHHHHHH----HHHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEE
Confidence 356555554 5556666666544 3 23577889999999888888763
No 39
>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=26.10 E-value=89 Score=23.43 Aligned_cols=36 Identities=11% Similarity=0.091 Sum_probs=26.1
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHH
Q 032076 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKG 74 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~G 74 (148)
+.+.++++.+.+..+.++.|..+||++.....+-.|
T Consensus 98 ~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~ 133 (158)
T cd01646 98 SKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEG 133 (158)
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEChhhceeeecCCC
Confidence 456667777778888888999999987665544333
No 40
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=25.23 E-value=1.1e+02 Score=24.82 Aligned_cols=21 Identities=10% Similarity=0.085 Sum_probs=16.9
Q ss_pred hhhHHHHHHHHHHhHhhhCCC
Q 032076 65 KSVTSVVIKGLADHKDSLGAP 85 (148)
Q Consensus 65 ~ev~~~Vi~GLa~NK~rYG~~ 85 (148)
..+...+++|+..--..+|+.
T Consensus 71 ~~~~~~~~~gi~~~~~~~g~~ 91 (341)
T PRK10703 71 APYFAEIIEAVEKNCYQKGYT 91 (341)
T ss_pred CchHHHHHHHHHHHHHHCCCE
Confidence 357778899998888888875
No 41
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=24.93 E-value=64 Score=22.17 Aligned_cols=31 Identities=10% Similarity=0.134 Sum_probs=19.1
Q ss_pred ccccCCCChHHHHHHHHHHHHHhhhcCcEec
Q 032076 32 IRAQVEPSEKSVEIMRKFSEQYARRSDTFFC 62 (148)
Q Consensus 32 ~~~~~~~s~k~~e~~~~~~ekyAek~Gy~lN 62 (148)
|.+..+.......+-.+..++|+++.||.|.
T Consensus 54 VK~~~~l~~~~~~~k~~~~~~y~~~~g~~f~ 84 (88)
T PF08722_consen 54 VKPSSELEKPRTKEKLEIEREYWEEQGIPFR 84 (88)
T ss_dssp E--GGGGGSHHHHHHHHHHHHHHHHCT--EE
T ss_pred EccHHHhcChhHHHHHHHHHHHHHHcCCeEE
Confidence 4555555555555566778899999999873
No 42
>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=24.81 E-value=1.5e+02 Score=24.43 Aligned_cols=40 Identities=8% Similarity=-0.063 Sum_probs=30.9
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHH
Q 032076 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (148)
Q Consensus 37 ~~s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa 76 (148)
-++.++++.+++++++..+..||+-+..++.+...++-|.
T Consensus 169 ~a~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~lr~l~ 208 (233)
T TIGR00050 169 YATTDQLELLLEHLEEILLSLGFIPEHKIRRVMRKFRRLY 208 (233)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHH
Confidence 3688999999999999999999976666666555444443
No 43
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.38 E-value=1.3e+02 Score=24.44 Aligned_cols=42 Identities=14% Similarity=0.098 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhhcCcEecc------------------C--hhhHHHHHHHHHHhHhhhCCCC
Q 032076 45 IMRKFSEQYARRSDTFFCV------------------D--KSVTSVVIKGLADHKDSLGAPL 86 (148)
Q Consensus 45 ~~~~~~ekyAek~Gy~lNP------------------D--~ev~~~Vi~GLa~NK~rYG~~~ 86 (148)
++++.+.+.|++.||.-|+ + ..+...++.|+.+--.++|+..
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 4566677777778886442 2 2367889999999999999873
No 44
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=24.09 E-value=1.9e+02 Score=20.16 Aligned_cols=49 Identities=14% Similarity=0.152 Sum_probs=35.3
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCC
Q 032076 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CP 88 (148)
..+.+..++.|+..++++.|+--. +...+..++.=++.|--+||+.-.+
T Consensus 4 ~~~~i~~~r~~~~~~~~~~~~~~~-~~~~~~lav~E~~~Nav~H~~~~~~ 52 (125)
T PF13581_consen 4 DPEDIREARAFLREFLERLGLPEE-DRDDLELAVSEALTNAVEHGYPGDP 52 (125)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 456889999999999988665321 2234455566677799999998655
No 45
>PRK09492 treR trehalose repressor; Provisional
Probab=23.10 E-value=1.1e+02 Score=24.39 Aligned_cols=46 Identities=13% Similarity=-0.021 Sum_probs=30.2
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCC
Q 032076 37 EPSEKSVEIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPL 86 (148)
Q Consensus 37 ~~s~k~~e~~~~~~ekyAek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~~ 86 (148)
..++++.++ +.+.|++.||.-|. +..+...++.|+...-.++||..
T Consensus 30 ~vs~~tr~r----V~~~a~elgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~ 95 (315)
T PRK09492 30 GVSEETRER----VEAVINQHGFSPSKSARAMRGQSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDP 95 (315)
T ss_pred CCCHHHHHH----HHHHHHHHCCCcCHHHHHhhcCCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeE
Confidence 356555544 55666667775442 12345678899988888999875
No 46
>PRK05802 hypothetical protein; Provisional
Probab=22.78 E-value=35 Score=29.32 Aligned_cols=13 Identities=31% Similarity=0.930 Sum_probs=11.4
Q ss_pred hhCCCCCCCcccC
Q 032076 81 SLGAPLCPCRHYD 93 (148)
Q Consensus 81 rYG~~~CPCRl~~ 93 (148)
..|..||||-|+.
T Consensus 9 d~~~~~cpc~la~ 21 (320)
T PRK05802 9 DAGSEYCPCHLAE 21 (320)
T ss_pred ccCCCcCceeeec
Confidence 4699999999985
No 47
>PHA01748 hypothetical protein
Probab=22.73 E-value=1.7e+02 Score=19.47 Aligned_cols=32 Identities=13% Similarity=0.182 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHh
Q 032076 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADH 78 (148)
Q Consensus 44 e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~N 78 (148)
+++.+.+++||++.|+ |-. +++...++.+..+
T Consensus 11 ~el~~eld~~a~~~g~--~RS-E~Ir~Ai~~~~~~ 42 (60)
T PHA01748 11 EDLLELLDRYAIKHGL--NRS-EAIRKAIEKMVKD 42 (60)
T ss_pred HHHHHHHHHHHHHhCC--CHH-HHHHHHHHHHHHH
Confidence 4556668889999996 644 4444444444433
No 48
>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=21.78 E-value=2.4e+02 Score=23.02 Aligned_cols=45 Identities=9% Similarity=0.090 Sum_probs=35.2
Q ss_pred cCCCChHHHHHHHHHHHHHhhhcCcEe---ccChhhHHHHHHHHHHhH
Q 032076 35 QVEPSEKSVEIMRKFSEQYARRSDTFF---CVDKSVTSVVIKGLADHK 79 (148)
Q Consensus 35 ~~~~s~k~~e~~~~~~ekyAek~Gy~l---NPD~ev~~~Vi~GLa~NK 79 (148)
+.+.+.+.+++.-+.+.+.|++.|+.+ +|.++.++.|.+.+...+
T Consensus 152 D~~~~~~~I~~ql~~~~~~A~~~G~aI~Igh~~p~Tl~~L~~~~~~l~ 199 (213)
T PF04748_consen 152 DNDQDEAAIRRQLDQAARIARKQGSAIAIGHPRPETLEALEEWLPELE 199 (213)
T ss_dssp TST-SHHHHHHHHHHHHHHHHCCSEEEEEEE-SCCHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhhhhcCcEEEEEcCCHHHHHHHHHHHhHHh
Confidence 455889999999999999999999975 788888877777776554
No 49
>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=21.65 E-value=1.5e+02 Score=19.10 Aligned_cols=33 Identities=9% Similarity=0.115 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHh
Q 032076 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADH 78 (148)
Q Consensus 44 e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~N 78 (148)
+.++++++..|+..|=-+| .+++..|.+.|.++
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 5788889999999997776 35666666666544
No 50
>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=21.47 E-value=2.2e+02 Score=17.75 Aligned_cols=45 Identities=11% Similarity=0.059 Sum_probs=35.1
Q ss_pred hHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 032076 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (148)
Q Consensus 40 ~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (148)
.+.+.+..+.++.....++|.+.....+++..+-+.+..-..++.
T Consensus 8 ~~~~~~~l~~le~~L~~~~fl~G~~~s~aD~~l~~~l~~~~~~~~ 52 (69)
T PF13410_consen 8 RAQLEAALDALEDHLADGPFLFGDRPSLADIALAPFLWRLRFVGP 52 (69)
T ss_dssp HHHHHHHHHHHHHHHTTSSBTTBSS--HHHHHHHHHHHHHHHCTH
T ss_pred HHHHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHHHHHhCc
Confidence 355666777788888888999999999999999999988777654
No 51
>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=21.44 E-value=1.2e+02 Score=21.94 Aligned_cols=31 Identities=16% Similarity=0.049 Sum_probs=22.3
Q ss_pred ChHHHHHHHHHHHHHh-hhcCcEeccChhhHH
Q 032076 39 SEKSVEIMRKFSEQYA-RRSDTFFCVDKSVTS 69 (148)
Q Consensus 39 s~k~~e~~~~~~ekyA-ek~Gy~lNPD~ev~~ 69 (148)
+.++.+++.+.+..+- ++.|..+|+++..+-
T Consensus 68 ~~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~ 99 (119)
T cd01648 68 SLDKAIKFLNLLLRGFINQYKTFVNFDKTQIN 99 (119)
T ss_pred CHHHHHHHHHHHHHhhHHhhCeEECcccceee
Confidence 3456666666666664 889999999887654
No 52
>PLN02449 ferrochelatase
Probab=20.37 E-value=2.1e+02 Score=26.89 Aligned_cols=50 Identities=12% Similarity=0.046 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHHhhhcCcE-------eccChhhHHHHHHHHHHhHhhhCCCCCCC
Q 032076 40 EKSVEIMRKFSEQYARRSDTF-------FCVDKSVTSVVIKGLADHKDSLGAPLCPC 89 (148)
Q Consensus 40 ~k~~e~~~~~~ekyAek~Gy~-------lNPD~ev~~~Vi~GLa~NK~rYG~~~CPC 89 (148)
-|++.++.--.++.|++.|.. ||-++.+++.|.+=..++....|.+.|+|
T Consensus 367 iETL~EiDiE~re~a~e~G~~~~~rVP~LN~~p~FI~~La~lV~~~l~~~~~~~~~~ 423 (485)
T PLN02449 367 IETLEEIDMEYRELALESGIENWGRVPALGCEPTFISDLADAVIEALPYVGAMAVSN 423 (485)
T ss_pred hHHHHHHHHHHHHHHHHcCCceEEEcCCCCCCHHHHHHHHHHHHHHhhccccccccc
Confidence 478888888888889998873 58899999987776666655456666665
No 53
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=20.32 E-value=42 Score=30.64 Aligned_cols=11 Identities=55% Similarity=1.141 Sum_probs=8.4
Q ss_pred hCCCCCCCccc
Q 032076 82 LGAPLCPCRHY 92 (148)
Q Consensus 82 YG~~~CPCRl~ 92 (148)
=|.|||||-..
T Consensus 24 GGapyCPClYi 34 (429)
T KOG3651|consen 24 GGAPYCPCLYI 34 (429)
T ss_pred CCCCcCCeEEE
Confidence 37899999654
No 54
>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=20.21 E-value=1.3e+02 Score=22.78 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=25.4
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHH
Q 032076 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (148)
Q Consensus 39 s~k~~e~~~~~~ekyAek~Gy~lNPD~ev~~ 69 (148)
+++.++++.+.++.+++..|..||+++..+.
T Consensus 182 ~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~ 212 (226)
T cd01651 182 GPKEAEEIKELIREFLEELGLELNPEKTRIT 212 (226)
T ss_pred CHHHHHHHHHHHHHHHHHcCCeechhhccee
Confidence 4555888899999999999999999876543
Done!