Query 032339
Match_columns 142
No_of_seqs 109 out of 190
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 12:48:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032339.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032339hhsearch_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 1.2E-49 2.5E-54 300.1 9.2 106 35-140 5-110 (116)
2 PF02943 FeThRed_B: Ferredoxin 100.0 3.3E-45 7.1E-50 272.4 4.6 99 41-139 1-103 (108)
3 COG4802 FtrB Ferredoxin-thiore 100.0 8.9E-42 1.9E-46 254.1 8.2 96 38-138 1-100 (110)
4 PF05511 ATP-synt_F6: Mitochon 92.4 0.25 5.4E-06 36.9 4.4 81 1-85 1-84 (99)
5 PHA00425 DNA packaging protein 69.7 10 0.00022 27.9 4.3 45 40-84 29-76 (88)
6 PF03938 OmpH: Outer membrane 60.6 17 0.00036 27.1 4.2 37 39-75 111-157 (158)
7 PRK10780 periplasmic chaperone 57.3 19 0.00042 27.7 4.2 37 39-75 118-164 (165)
8 TIGR01924 rsbW_low_gc serine-p 53.8 40 0.00088 25.6 5.4 54 34-88 10-63 (159)
9 PF11123 DNA_Packaging_2: DNA 49.9 39 0.00084 24.7 4.4 45 40-84 27-74 (82)
10 PF03912 Psb28: Psb28 protein; 48.6 13 0.00028 28.3 1.9 24 38-61 84-107 (108)
11 PF10431 ClpB_D2-small: C-term 48.6 47 0.001 22.2 4.5 38 45-85 13-50 (81)
12 PRK13612 photosystem II reacti 48.4 18 0.00038 27.8 2.6 25 38-62 87-111 (113)
13 TIGR03047 PS_II_psb28 photosys 48.3 17 0.00038 27.7 2.5 24 38-61 84-107 (109)
14 PHA02745 hypothetical protein; 48.1 62 0.0013 28.1 6.1 54 32-85 211-264 (265)
15 PRK13611 photosystem II reacti 47.2 19 0.00041 27.3 2.5 24 38-61 80-103 (104)
16 CHL00128 psbW photosystem II p 47.1 19 0.00041 27.7 2.5 25 38-62 87-111 (113)
17 PLN00039 photosystem II reacti 46.8 19 0.00041 27.5 2.5 25 38-62 85-109 (111)
18 PF14791 DNA_pol_B_thumb: DNA 46.7 23 0.00051 23.9 2.7 20 45-64 10-29 (64)
19 KOG1671 Ubiquinol cytochrome c 42.6 8.5 0.00018 32.3 0.1 15 75-89 160-174 (210)
20 PF00356 LacI: Bacterial regul 40.6 22 0.00048 22.6 1.8 22 37-62 25-46 (46)
21 PRK05452 anaerobic nitric oxid 37.8 20 0.00044 32.4 1.7 35 31-67 370-404 (479)
22 PF00078 RVT_1: Reverse transc 37.5 41 0.00088 24.8 3.1 29 39-67 171-199 (214)
23 COG2825 HlpA Outer membrane pr 37.4 54 0.0012 26.0 3.9 39 37-75 119-167 (170)
24 TIGR01481 ccpA catabolite cont 36.4 56 0.0012 26.1 3.9 49 37-89 27-95 (329)
25 PRK11303 DNA-binding transcrip 34.4 64 0.0014 25.8 3.9 47 38-88 30-96 (328)
26 TIGR02417 fruct_sucro_rep D-fr 33.6 55 0.0012 26.3 3.4 51 38-92 29-99 (327)
27 PRK10401 DNA-binding transcrip 32.4 69 0.0015 26.1 3.9 46 38-87 28-93 (346)
28 COG5502 Uncharacterized conser 31.7 69 0.0015 25.3 3.6 41 39-79 71-112 (135)
29 PRK11041 DNA-binding transcrip 31.6 74 0.0016 25.0 3.8 41 45-85 7-67 (309)
30 KOG4634 Mitochondrial F1F0-ATP 31.0 1.2E+02 0.0025 23.1 4.6 37 47-83 39-77 (105)
31 KOG1220 Phosphoglucomutase/pho 30.5 39 0.00084 32.5 2.4 45 41-85 458-502 (607)
32 PF12683 DUF3798: Protein of u 30.1 1E+02 0.0023 26.9 4.7 50 42-92 187-236 (275)
33 cd01646 RT_Bac_retron_I RT_Bac 29.6 71 0.0015 23.8 3.3 36 39-74 98-133 (158)
34 TIGR02405 trehalos_R_Ecol treh 29.4 81 0.0018 25.3 3.8 44 38-85 28-91 (311)
35 PF11794 HpaB_N: 4-hydroxyphen 28.9 89 0.0019 26.7 4.1 47 38-84 74-120 (264)
36 PF01402 RHH_1: Ribbon-helix-h 28.3 1.3E+02 0.0027 17.4 3.6 30 44-76 8-37 (39)
37 PF13581 HATPase_c_2: Histidin 27.9 1.4E+02 0.0031 20.7 4.4 49 39-88 4-52 (125)
38 PRK10727 DNA-binding transcrip 26.6 1E+02 0.0022 25.0 4.0 46 37-86 27-92 (343)
39 PRK10423 transcriptional repre 26.6 1E+02 0.0022 24.5 3.9 45 37-85 24-88 (327)
40 cd01648 TERT TERT: Telomerase 26.4 86 0.0019 22.6 3.1 31 39-69 68-99 (119)
41 TIGR01463 mtaA_cmuA methyltran 26.3 1.1E+02 0.0023 25.6 4.1 44 41-84 293-340 (340)
42 PRK10703 DNA-binding transcrip 26.1 1.1E+02 0.0023 24.8 3.9 45 37-85 27-91 (341)
43 COG2861 Uncharacterized protei 25.8 2E+02 0.0043 24.9 5.6 46 33-78 182-230 (250)
44 PF04748 Polysacc_deac_2: Dive 24.9 2.2E+02 0.0047 23.1 5.5 47 33-79 150-199 (213)
45 PRK14987 gluconate operon tran 24.6 1.3E+02 0.0027 24.3 4.1 42 45-86 35-96 (331)
46 PRK05802 hypothetical protein; 24.6 41 0.0009 28.7 1.3 13 81-93 9-21 (320)
47 TIGR00050 rRNA_methyl_1 RNA me 24.2 1.6E+02 0.0035 24.1 4.7 40 37-76 169-208 (233)
48 PF07308 DUF1456: Protein of u 24.1 73 0.0016 21.9 2.2 35 43-79 32-66 (68)
49 cd01651 RT_G2_intron RT_G2_int 23.8 1E+02 0.0022 23.2 3.3 31 39-69 182-212 (226)
50 PRK09492 treR trehalose repres 23.7 1.1E+02 0.0024 24.3 3.5 46 37-86 30-95 (315)
51 PLN02449 ferrochelatase 23.6 1.6E+02 0.0036 27.3 5.1 51 39-89 366-423 (485)
52 PF03869 Arc: Arc-like DNA bin 23.3 1.4E+02 0.0029 19.2 3.3 33 44-78 13-45 (50)
53 cd01650 RT_nLTR_like RT_nLTR: 23.0 1E+02 0.0022 23.3 3.1 29 41-69 160-188 (220)
54 PF13410 GST_C_2: Glutathione 22.4 2E+02 0.0044 17.8 4.7 45 40-84 8-52 (69)
55 PHA01748 hypothetical protein 21.0 2E+02 0.0043 19.1 3.8 30 45-77 12-41 (60)
56 PRK04069 serine-protein kinase 20.8 2.9E+02 0.0063 20.7 5.2 49 38-87 14-62 (161)
57 PF03982 DAGAT: Diacylglycerol 20.2 2.4E+02 0.0051 24.3 5.1 33 35-84 256-288 (297)
No 1
>CHL00165 ftrB ferredoxin thioreductase subunit beta; Validated
Probab=100.00 E-value=1.2e-49 Score=300.09 Aligned_cols=106 Identities=62% Similarity=1.211 Sum_probs=101.8
Q ss_pred cCCCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccCCchhhhcCCceeecCcccccC
Q 032339 35 QVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVPMRER 114 (142)
Q Consensus 35 ~~~~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~~dk~~E~~d~diICPC~y~~e~ 114 (142)
+...+++++++|++|+++||+++||+||||+++|+.|++||++||++||+||||||+++|+++|+++++|||||++|+++
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 45688999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred ceeeeeeeeCCccccCCCceeecccC
Q 032339 115 KECHCMLFLTPENDFAGQDQVMLSTY 140 (142)
Q Consensus 115 G~ChCgLFvs~e~~~~G~~~~~~~~~ 140 (142)
|+|||||||++|++|+|++|+|+++.
T Consensus 85 g~CHC~LF~t~e~~~~~~~~~i~~~~ 110 (116)
T CHL00165 85 KECHCMLFLTPDNEFASQSQTISKKT 110 (116)
T ss_pred CCceEeeeecCCccccCcceeecHHH
Confidence 99999999999999999999999863
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=3.3e-45 Score=272.43 Aligned_cols=99 Identities=42% Similarity=0.725 Sum_probs=74.5
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccCCchhhhcCCceeecCcccc----cCce
Q 032339 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVPMR----ERKE 116 (142)
Q Consensus 41 ~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~~dk~~E~~d~diICPC~y~~----e~G~ 116 (142)
|++++|++|+++||+++||+||||+++|+.|++||++||++||++|||||+++|+++|++|++|||||++++ ++|+
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 689999999999999999999999999999999999999999999999999999888888999999999643 7999
Q ss_pred eeeeeeeCCccccCCCceeeccc
Q 032339 117 CHCMLFLTPENDFAGQDQVMLST 139 (142)
Q Consensus 117 ChCgLFvs~e~~~~G~~~~~~~~ 139 (142)
|||||||++|++++|++|+|+.+
T Consensus 81 ChC~Lf~~~e~~~~~~~~~~~~e 103 (108)
T PF02943_consen 81 CHCGLFVSPEYAEAGKKQEISHE 103 (108)
T ss_dssp -TTSSSB-TTSTTB-S-S---HH
T ss_pred ceEeeeECcccccchhhcccCHH
Confidence 99999999999999999999764
No 3
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=100.00 E-value=8.9e-42 Score=254.09 Aligned_cols=96 Identities=40% Similarity=0.725 Sum_probs=89.7
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCcccCCchhhhcCCceeecCcc----ccc
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHYDDKAAEAQQGFWNCPCVP----MRE 113 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~~dk~~E~~d~diICPC~y----~~e 113 (142)
.+++++++||+|+++||+|+||+||||.++|+.|++||+.||++||+++||||+++|+++| |++|||||+| +++
T Consensus 1 ~~~e~l~~my~~~eq~AeksG~~lnpD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~eee--dk~ivCPCvy~~ddi~e 78 (110)
T COG4802 1 ESDEELNKMYRFTEQYAEKSGYRLNPDREFTAEVLRGLASNKERYGYPSCPCRLVTGKEEE--DKDIVCPCVYRDDDIRE 78 (110)
T ss_pred CcHHHHHHHHHHHHHHHHhcCceeCCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCHHH--hhceeccCcCCccchhh
Confidence 3689999999999999999999999999999999999999999999999999999998888 6689999999 899
Q ss_pred CceeeeeeeeCCccccCCCceeecc
Q 032339 114 RKECHCMLFLTPENDFAGQDQVMLS 138 (142)
Q Consensus 114 ~G~ChCgLFvs~e~~~~G~~~~~~~ 138 (142)
||.||||||++++.. +-|.|+.
T Consensus 79 ~g~C~C~Lyl~~e~~---e~~sIp~ 100 (110)
T COG4802 79 YGECYCGLYLSPEKD---EAQSIPE 100 (110)
T ss_pred hCceeEEEEeccccc---chhhcch
Confidence 999999999999996 5666664
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=92.44 E-value=0.25 Score=36.93 Aligned_cols=81 Identities=14% Similarity=0.173 Sum_probs=39.6
Q ss_pred CcccccccccccccccCCCccccccCCcceeeccc--CCC-ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHH
Q 032339 1 MTLQSSLCGSGVSTFICTPRPIIARPRPVTQIRAQ--VEP-SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLAD 77 (142)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~-s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~ 77 (142)
|.+|+.+.++..++.+-..| |.-..+++.++ .+| ..-=+++++++..+-..+.|=..++.+++-..+-+-|.+
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 78888777777766665555 44444455544 334 555689999998888888898999999999999999999
Q ss_pred hHhhhCCC
Q 032339 78 HKDSLGAP 85 (142)
Q Consensus 78 NK~rYG~~ 85 (142)
-...||..
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 99999864
No 5
>PHA00425 DNA packaging protein, small subunit
Probab=69.72 E-value=10 Score=27.92 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=37.9
Q ss_pred hHHHHHHHHHHHHHhhhcCcE---eccChhhHHHHHHHHHHhHhhhCC
Q 032339 40 EKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (142)
Q Consensus 40 ~~~~e~~~~~~ekyaek~Gy~---lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (142)
++---.+|+-+.++-+++-|. +.||++++-.+..||+..+..+|.
T Consensus 29 ekRtPQLYnAIgKlL~RHkF~isKl~pD~~iLg~la~~l~ey~~~~g~ 76 (88)
T PHA00425 29 EKRTPQLYNAIGKLLDRHKFQISKLQPDENILGGLAAALEEYKEKVGA 76 (88)
T ss_pred cccChHHHHHHHHHHHHhcccccccCCcHHHHHHHHHHHHHHHHhcCC
Confidence 344457888899999988885 679999999999999999998885
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=60.55 E-value=17 Score=27.05 Aligned_cols=37 Identities=24% Similarity=0.275 Sum_probs=27.0
Q ss_pred ChHHHHHHHHHHHHHhhhcCc----------EeccChhhHHHHHHHH
Q 032339 39 SEKSVEIMRKFSEQYARRSDT----------FFCVDKSVTSVVIKGL 75 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy----------~lNPD~ev~~~Vi~GL 75 (142)
..+-.+++...++.||+..|| +.+|..++|+.|++.|
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 455667788899999999998 5577779999998866
No 7
>PRK10780 periplasmic chaperone; Provisional
Probab=57.32 E-value=19 Score=27.70 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=28.6
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEe----------ccChhhHHHHHHHH
Q 032339 39 SEKSVEIMRKFSEQYARRSDTFF----------CVDKSVTSVVIKGL 75 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~l----------NPD~ev~~~Vi~GL 75 (142)
.....+++.+.++++|++.||-+ +|..++|+.|++-|
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 45577888899999999999854 46678888887754
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=53.83 E-value=40 Score=25.60 Aligned_cols=54 Identities=11% Similarity=-0.005 Sum_probs=41.1
Q ss_pred ccCCCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCC
Q 032339 34 AQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (142)
Q Consensus 34 ~~~~~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CP 88 (142)
..-....+.+..++.|++.+|+..|+- ..+.+-+..++.-|+.|--+||++..|
T Consensus 10 l~~~a~~~~~~~vr~~~~~~a~~~g~~-~~~~~~l~lav~Ea~~Nai~ha~~~~~ 63 (159)
T TIGR01924 10 MTVPAKPEYVGLIRLTLSGIASRAGYT-YDDIEDLKIAVSEACTNAVKHAYKEGE 63 (159)
T ss_pred EEccCcHHHHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 344456788999999999999999964 233344666788899999999987553
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=49.92 E-value=39 Score=24.65 Aligned_cols=45 Identities=18% Similarity=0.179 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHHhhhcCcE---eccChhhHHHHHHHHHHhHhhhCC
Q 032339 40 EKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (142)
Q Consensus 40 ~~~~e~~~~~~ekyaek~Gy~---lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (142)
++---++|+-+.++-+++-|. +-||++++-.+..||...++.+|.
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 334456788888888888885 579999999999999999998885
No 10
>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=48.63 E-value=13 Score=28.31 Aligned_cols=24 Identities=29% Similarity=0.405 Sum_probs=19.0
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEe
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~l 61 (142)
.+++..+...+|+++||+.+|.-|
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 478999999999999999998654
No 11
>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=48.55 E-value=47 Score=22.20 Aligned_cols=38 Identities=16% Similarity=0.189 Sum_probs=27.0
Q ss_pred HHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032339 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 45 ~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
++.+..+++++ .|..|+-|+++.+.+++-= ....||.+
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 44556666666 9999999999999888742 34568865
No 12
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=48.40 E-value=18 Score=27.81 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=22.2
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN 62 (142)
.++++.+.+.+|+++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T PRK13612 87 KSEQEWDRFMRFMERYAKENGLGFS 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 3899999999999999999997653
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=48.30 E-value=17 Score=27.67 Aligned_cols=24 Identities=25% Similarity=0.369 Sum_probs=21.6
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEe
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~l 61 (142)
.++++.+...+|+++||+.+|.-|
T Consensus 84 ~s~~~WdRFMRFmeRYA~~ngl~f 107 (109)
T TIGR03047 84 KSEDEWDRFMRFMERYAEANGLGY 107 (109)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 389999999999999999999755
No 14
>PHA02745 hypothetical protein; Provisional
Probab=48.06 E-value=62 Score=28.10 Aligned_cols=54 Identities=7% Similarity=0.135 Sum_probs=46.9
Q ss_pred ecccCCCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032339 32 IRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 32 ~~~~~~~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
...++...+..-..+-.|++.|+.+.||.---.+.+...+---|..-+-+||.+
T Consensus 211 t~vRPgLDe~Ar~vLL~fVe~yG~~~~W~t~D~~~I~ntiR~KiqeiR~K~g~~ 264 (265)
T PHA02745 211 TDVRPGLDEDARTVLLRYVEIYGEKQRWCTEDHQAIINVIRNKMQESRRKDRHR 264 (265)
T ss_pred cccCCCcchHHHHHHHHHHHHHhhccCCCCCchHHHHHHHHHHHHHHHHHhCCc
Confidence 445667788888999999999999999998888888888888888888899875
No 15
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=47.22 E-value=19 Score=27.29 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=21.2
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEe
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~l 61 (142)
.++++.+.+.+|+++||+.+|.-|
T Consensus 80 ~s~~~wdRFMRFmeRYA~~Ngl~f 103 (104)
T PRK13611 80 ETEAEWDRFLRFMERFSAANQMGM 103 (104)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 389999999999999999998643
No 16
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=47.14 E-value=19 Score=27.66 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN 62 (142)
.++++.+...+|+++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T CHL00128 87 KNPEAWDRFMRFMERYAEDNGLTFT 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 3899999999999999999997653
No 17
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=46.78 E-value=19 Score=27.54 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN 62 (142)
.++++.+...+|+++||+.+|.-|.
T Consensus 85 ~s~~~WdRFMRFMeRYA~~ngl~f~ 109 (111)
T PLN00039 85 RSPREWDRFMRFMERYAEENGLGFV 109 (111)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 3899999999999999999997653
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=46.65 E-value=23 Score=23.91 Aligned_cols=20 Identities=15% Similarity=0.130 Sum_probs=16.4
Q ss_pred HHHHHHHHHhhhcCcEeccC
Q 032339 45 IMRKFSEQYARRSDTFFCVD 64 (142)
Q Consensus 45 ~~~~~~ekyaek~Gy~lNPD 64 (142)
...+.+..+|.+.||.||+.
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
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=42.56 E-value=8.5 Score=32.35 Aligned_cols=15 Identities=27% Similarity=0.724 Sum_probs=13.2
Q ss_pred HHHhHhhhCCCCCCC
Q 032339 75 LADHKDSLGAPLCPC 89 (142)
Q Consensus 75 La~NK~rYG~~~CPC 89 (142)
.+.|.-.||..||||
T Consensus 160 p~~~AGd~gg~~CPC 174 (210)
T KOG1671|consen 160 PIANAGDYGGYYCPC 174 (210)
T ss_pred ccccccccCceeccc
Confidence 356889999999999
No 20
>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=40.61 E-value=22 Score=22.56 Aligned_cols=22 Identities=18% Similarity=-0.123 Sum_probs=13.3
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFC 62 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lN 62 (142)
..++++.++ +.+.|++.||.-|
T Consensus 25 ~vs~~tr~r----I~~~a~~lgY~pN 46 (46)
T PF00356_consen 25 RVSEETRER----ILEAAEELGYRPN 46 (46)
T ss_dssp SSTHHHHHH----HHHHHHHHTB-SS
T ss_pred CCCHHHHHH----HHHHHHHHCCCCC
Confidence 356655555 6666777778765
No 21
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=37.79 E-value=20 Score=32.37 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=26.2
Q ss_pred eecccCCCChHHHHHHHHHHHHHhhhcCcEeccChhh
Q 032339 31 QIRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (142)
Q Consensus 31 ~~~~~~~~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev 67 (142)
.+..+-.|+++++++.++|.+++|++-= +-|++..
T Consensus 370 ~l~~~~~P~ee~~~~~~~~g~~la~~~~--~~~~~~~ 404 (479)
T PRK05452 370 SLKAKWRPDQDALELCREHGREIARQWA--LAPLPQS 404 (479)
T ss_pred cEEEEecCCHHHHHHHHHHHHHHHHHHh--hCCcccc
Confidence 3555666889999999999999996553 6776644
No 22
>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=37.54 E-value=41 Score=24.82 Aligned_cols=29 Identities=10% Similarity=0.079 Sum_probs=24.3
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhh
Q 032339 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~lNPD~ev 67 (142)
+.+.++++.+.+.++.+..|..+||++-.
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 36678888888899999999999998864
No 23
>COG2825 HlpA Outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=37.40 E-value=54 Score=26.03 Aligned_cols=39 Identities=26% Similarity=0.261 Sum_probs=31.6
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcE----------eccChhhHHHHHHHH
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTF----------FCVDKSVTSVVIKGL 75 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~----------lNPD~ev~~~Vi~GL 75 (142)
+.-.+..+++...++.+|++.||- .+|-.++|+.|++-|
T Consensus 119 e~~~~~~~~i~~ai~~~a~~~gy~~vl~~~~V~y~~~~~DIT~~Vlk~l 167 (170)
T COG2825 119 EEEQKLLEKIQRAIESVAEKGGYSLVLDSNAVLYAKPSKDITDDVLKAL 167 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCcceEecCCchhccCCCCCchHHHHHHH
Confidence 345677888899999999999985 477888899998866
No 24
>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=36.45 E-value=56 Score=26.12 Aligned_cols=49 Identities=8% Similarity=-0.030 Sum_probs=32.6
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCCCC
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLCPC 89 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~CPC 89 (142)
..++++.++ +.+.|++.||.-| | +..+...++.|+...-.++|+..=-+
T Consensus 27 ~vs~~tr~r----V~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~ 95 (329)
T TIGR01481 27 NVKPATRKK----VLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILS 95 (329)
T ss_pred CCCHHHHHH----HHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEE
Confidence 366666555 5556666667554 3 23577789999988888888876433
No 25
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=34.36 E-value=64 Score=25.78 Aligned_cols=47 Identities=19% Similarity=0.110 Sum_probs=31.0
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCCC
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLCP 88 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~CP 88 (142)
.++++.++ +.+.|++.||.-| | +..+...+++|+.+.-.++|+..=-
T Consensus 30 Vs~~tr~r----V~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~ 96 (328)
T PRK11303 30 VSDKTVEK----VMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLI 96 (328)
T ss_pred cCHHHHHH----HHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEE
Confidence 56665555 5555666666544 2 2346677899999988899987543
No 26
>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=33.59 E-value=55 Score=26.25 Aligned_cols=51 Identities=16% Similarity=0.014 Sum_probs=33.7
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCCCCccc
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLCPCRHY 92 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~CPCRl~ 92 (142)
.++++.++ +.+.|++.||.-| | +..+...++.|+..--.++||..--+...
T Consensus 29 vs~~tr~r----V~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~ 99 (327)
T TIGR02417 29 ISQETVER----VMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSD 99 (327)
T ss_pred cCHHHHHH----HHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence 55555444 5566666666543 2 23467788999998888999987655443
No 27
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=32.39 E-value=69 Score=26.05 Aligned_cols=46 Identities=7% Similarity=-0.085 Sum_probs=31.8
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCCC
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLC 87 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~C 87 (142)
.++++.++ +.+.|+..||.-| | +..+...+++|+..--.++|+..-
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 56666666 4555555667644 2 245777899999999899998754
No 28
>COG5502 Uncharacterized conserved protein [Function unknown]
Probab=31.68 E-value=69 Score=25.28 Aligned_cols=41 Identities=20% Similarity=0.041 Sum_probs=34.4
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHH-HHHHHHHHhH
Q 032339 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTS-VVIKGLADHK 79 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~-~Vi~GLa~NK 79 (142)
..+..-..++|+.+++.+-|+--|-|.+.+- +|.+-|.+|-
T Consensus 71 ~~~~~~s~~dFl~Rv~~~~g~~~~vd~e~a~~AVf~vL~r~I 112 (135)
T COG5502 71 PPKLPFSLDDFLTRVANKFGLEPPVDPEHAIAAVFAVLKRHI 112 (135)
T ss_pred CCCCcccHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHhC
Confidence 3445556789999999999999999999988 8888888873
No 29
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=31.58 E-value=74 Score=25.05 Aligned_cols=41 Identities=17% Similarity=0.017 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCC
Q 032339 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 45 ~~~~~~ekyaek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
++++.+.+.|++.||.-|. +..+...+++|+.+--.++|+.
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 3444466677777787663 3456788899999988888864
No 30
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=30.96 E-value=1.2e+02 Score=23.12 Aligned_cols=37 Identities=11% Similarity=0.168 Sum_probs=32.0
Q ss_pred HHHHHHHhhh--cCcEeccChhhHHHHHHHHHHhHhhhC
Q 032339 47 RKFSEQYARR--SDTFFCVDKSVTSVVIKGLADHKDSLG 83 (142)
Q Consensus 47 ~~~~ekyaek--~Gy~lNPD~ev~~~Vi~GLa~NK~rYG 83 (142)
...++.|..+ +|=-.|+|+++-..|.+-|-+-+..||
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 3445666666 999999999999999999999999999
No 31
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=30.46 E-value=39 Score=32.45 Aligned_cols=45 Identities=16% Similarity=0.222 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCC
Q 032339 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 41 ~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
+-++.+++...-+-..+.|++++|+++++.+.++|=.-...|+|+
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 445555555555667889999999999999999986665544443
No 32
>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=30.08 E-value=1e+02 Score=26.86 Aligned_cols=50 Identities=18% Similarity=0.361 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCCCccc
Q 032339 42 SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCRHY 92 (142)
Q Consensus 42 ~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CPCRl~ 92 (142)
-+|.+-+|+++|.+... +|+-+..+++.||+.++.++-.|=..-||+-+-
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 46778899999976665 567788899999999999998888888888664
No 33
>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=29.58 E-value=71 Score=23.78 Aligned_cols=36 Identities=11% Similarity=0.091 Sum_probs=26.5
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHH
Q 032339 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKG 74 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~G 74 (142)
+.+.++++.+.++.+.++.|..+||++.....+-+|
T Consensus 98 ~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~ 133 (158)
T cd01646 98 SKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEG 133 (158)
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEChhhceeeecCCC
Confidence 456667777778888888999999998665555444
No 34
>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=29.45 E-value=81 Score=25.29 Aligned_cols=44 Identities=16% Similarity=0.078 Sum_probs=29.4
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCC
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lN------------------PD--~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
.++++.++ +.+.|++.||.-| || ..+...+++|+..--.++||.
T Consensus 28 vs~~tr~r----V~~~a~~lgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~ 91 (311)
T TIGR02405 28 VSIETRER----VEQVIQQSGFVPSKSARAMRGGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYD 91 (311)
T ss_pred CCHHHHHH----HHHHHHHHCCCcCHHHHHhhcCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCe
Confidence 56666555 5555666666543 32 235667899999998999987
No 35
>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=28.92 E-value=89 Score=26.67 Aligned_cols=47 Identities=21% Similarity=0.281 Sum_probs=42.0
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (142)
-|.+++.+-++.++..++.+|-.+.--.+....++.++....+.||.
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 36
>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=28.31 E-value=1.3e+02 Score=17.37 Aligned_cols=30 Identities=7% Similarity=0.063 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHH
Q 032339 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (142)
Q Consensus 44 e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa 76 (142)
+++++.++++|++.| -+-.+++..+++..+
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 345666788888888 233344444444433
No 37
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=27.90 E-value=1.4e+02 Score=20.68 Aligned_cols=49 Identities=14% Similarity=0.152 Sum_probs=34.8
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCCC
Q 032339 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~CP 88 (142)
..+.+..++.|+..++++.|+--. +...+..++.=++.|--+||+.-.+
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 346889999999999988665422 2233444555667799999998655
No 38
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=26.63 E-value=1e+02 Score=24.99 Aligned_cols=46 Identities=13% Similarity=0.011 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCCC
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPL 86 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~~ 86 (142)
..|+++-+++ .+.|++.||.-| | +..+...+++|+..--.++|+..
T Consensus 27 ~Vs~~tr~rV----~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~ 92 (343)
T PRK10727 27 KASEASRLAV----HSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFL 92 (343)
T ss_pred CCCHHHHHHH----HHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEE
Confidence 3666666654 455555556443 3 24577889999999888898763
No 39
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=26.57 E-value=1e+02 Score=24.53 Aligned_cols=45 Identities=11% Similarity=-0.005 Sum_probs=30.3
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec------------------cC--hhhHHHHHHHHHHhHhhhCCC
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lN------------------PD--~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
..++++.+++.+.+ ++.||.-| |+ ..+-..+++|+..--.++|+.
T Consensus 24 ~vs~~tr~rV~~~a----~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~ 88 (327)
T PRK10423 24 FVSEAITAKVEAAI----KELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVERSCFERGYS 88 (327)
T ss_pred CCCHHHHHHHHHHH----HHHCCCccHHHHHHhhCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCE
Confidence 36777766655554 44455332 32 356778999999988899987
No 40
>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=26.35 E-value=86 Score=22.57 Aligned_cols=31 Identities=16% Similarity=0.049 Sum_probs=22.9
Q ss_pred ChHHHHHHHHHHHHHh-hhcCcEeccChhhHH
Q 032339 39 SEKSVEIMRKFSEQYA-RRSDTFFCVDKSVTS 69 (142)
Q Consensus 39 s~~~~e~~~~~~ekya-ek~Gy~lNPD~ev~~ 69 (142)
+.++.+++.+.+..+- ++.|..+|+++..+-
T Consensus 68 ~~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~ 99 (119)
T cd01648 68 SLDKAIKFLNLLLRGFINQYKTFVNFDKTQIN 99 (119)
T ss_pred CHHHHHHHHHHHHHhhHHhhCeEECcccceee
Confidence 3556666666666664 889999999987754
No 41
>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=26.28 E-value=1.1e+02 Score=25.63 Aligned_cols=44 Identities=9% Similarity=0.103 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhh----HHHHHHHHHHhHhhhCC
Q 032339 41 KSVEIMRKFSEQYARRSDTFFCVDKSV----TSVVIKGLADHKDSLGA 84 (142)
Q Consensus 41 ~~~e~~~~~~ekyaek~Gy~lNPD~ev----~~~Vi~GLa~NK~rYG~ 84 (142)
.+.|++++.+++..++.||.|||+-.+ -..=++.+.+--..|||
T Consensus 293 gt~eeI~~~v~~~l~~~~~Il~~gcgi~~~tp~eni~a~v~a~~~~~~ 340 (340)
T TIGR01463 293 GTPEKVKKLAKEVLYNGGDIVMPGCDIDWMTPLENLKAMIEACKSIKY 340 (340)
T ss_pred CCHHHHHHHHHHHHHcCCeEECCCCCCCCCCCHHHHHHHHHHHHhccC
Confidence 466788888888888899999997333 33334444444455554
No 42
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=26.08 E-value=1.1e+02 Score=24.77 Aligned_cols=45 Identities=7% Similarity=-0.027 Sum_probs=30.3
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEec------------------c--ChhhHHHHHHHHHHhHhhhCCC
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAP 85 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lN------------------P--D~ev~~~Vi~GLa~NK~rYG~~ 85 (142)
..|+++.+++.+.+++ .||.-| | +..+...+++|+..--..+|+.
T Consensus 27 ~vs~~tr~~V~~~a~e----lgY~pn~~a~~l~~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~ 91 (341)
T PRK10703 27 FVAEETRNAVWAAIKE----LHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYT 91 (341)
T ss_pred CCCHHHHHHHHHHHHH----HCCCcCHHHHHHhhCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCE
Confidence 4677777776655544 444333 2 3457788999999988888875
No 43
>COG2861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.76 E-value=2e+02 Score=24.90 Aligned_cols=46 Identities=20% Similarity=0.153 Sum_probs=38.2
Q ss_pred cccCCCChHHHHHHHHHHHHHhhhcCcEe---ccChhhHHHHHHHHHHh
Q 032339 33 RAQVEPSEKSVEIMRKFSEQYARRSDTFF---CVDKSVTSVVIKGLADH 78 (142)
Q Consensus 33 ~~~~~~s~~~~e~~~~~~ekyaek~Gy~l---NPD~ev~~~Vi~GLa~N 78 (142)
.-+.+.+++++.+-.+-++++|+++|..+ +|-++-++.|.+++..-
T Consensus 182 fLD~e~~~~~V~kql~~~~~~Ark~G~ai~IGh~~~~Tv~vl~~~~~~l 230 (250)
T COG2861 182 FLDDEDTEAAVLKQLDAAEKLARKNGSAIGIGHPHKNTVAVLQQWLDEL 230 (250)
T ss_pred eecCcCCHHHHHHHHHHHHHHHHhcCceEEecCCchhHHHHHHHHHHhC
Confidence 34667789999999999999999999988 68888888888777543
No 44
>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=24.93 E-value=2.2e+02 Score=23.14 Aligned_cols=47 Identities=9% Similarity=0.055 Sum_probs=36.5
Q ss_pred cccCCCChHHHHHHHHHHHHHhhhcCcEe---ccChhhHHHHHHHHHHhH
Q 032339 33 RAQVEPSEKSVEIMRKFSEQYARRSDTFF---CVDKSVTSVVIKGLADHK 79 (142)
Q Consensus 33 ~~~~~~s~~~~e~~~~~~ekyaek~Gy~l---NPD~ev~~~Vi~GLa~NK 79 (142)
.-+.+.+.+.+++.-+.+.+.|++.|+.+ +|.++.++.|.+.+...+
T Consensus 150 fLD~~~~~~~I~~ql~~~~~~A~~~G~aI~Igh~~p~Tl~~L~~~~~~l~ 199 (213)
T PF04748_consen 150 FLDNDQDEAAIRRQLDQAARIARKQGSAIAIGHPRPETLEALEEWLPELE 199 (213)
T ss_dssp ETTST-SHHHHHHHHHHHHHHHHCCSEEEEEEE-SCCHHHHHHHHHHHHH
T ss_pred ecCCCCCHHHHHHHHHHHHHhhhhcCcEEEEEcCCHHHHHHHHHHHhHHh
Confidence 33556899999999999999999999975 788888887777776554
No 45
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.63 E-value=1.3e+02 Score=24.29 Aligned_cols=42 Identities=14% Similarity=0.098 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhhcCcEecc------------------C--hhhHHHHHHHHHHhHhhhCCCC
Q 032339 45 IMRKFSEQYARRSDTFFCV------------------D--KSVTSVVIKGLADHKDSLGAPL 86 (142)
Q Consensus 45 ~~~~~~ekyaek~Gy~lNP------------------D--~ev~~~Vi~GLa~NK~rYG~~~ 86 (142)
++++.+.+.|++.||.-|+ + ..+...+++|+.+--.++|+..
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 4555566777777776442 2 2367889999999999999873
No 46
>PRK05802 hypothetical protein; Provisional
Probab=24.58 E-value=41 Score=28.67 Aligned_cols=13 Identities=31% Similarity=0.930 Sum_probs=11.2
Q ss_pred hhCCCCCCCcccC
Q 032339 81 SLGAPLCPCRHYD 93 (142)
Q Consensus 81 rYG~~~CPCRl~~ 93 (142)
..|-.||||-|+.
T Consensus 9 d~~~~~cpc~la~ 21 (320)
T PRK05802 9 DAGSEYCPCHLAE 21 (320)
T ss_pred ccCCCcCceeeec
Confidence 3689999999985
No 47
>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=24.16 E-value=1.6e+02 Score=24.11 Aligned_cols=40 Identities=8% Similarity=-0.063 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHH
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa 76 (142)
-.+.++++.+++++++..+..||+-+..++.+...++-|.
T Consensus 169 ~a~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~lr~l~ 208 (233)
T TIGR00050 169 YATTDQLELLLEHLEEILLSLGFIPEHKIRRVMRKFRRLY 208 (233)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHH
Confidence 3688999999999999999999976566665554444443
No 48
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=24.05 E-value=73 Score=21.91 Aligned_cols=35 Identities=17% Similarity=0.217 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhH
Q 032339 43 VEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHK 79 (142)
Q Consensus 43 ~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK 79 (142)
..++..|+++-- ..||.-++|+.+ ...+.||...+
T Consensus 32 ~~el~a~lrke~-~~~y~~c~D~~L-~~FL~GLi~~~ 66 (68)
T PF07308_consen 32 KAELSAWLRKED-EKGYKECSDQLL-RNFLNGLIIHK 66 (68)
T ss_pred HHHHHHHHCCCC-CccccccChHHH-HHHHHHHHHHh
Confidence 345666777744 459999999765 56778998775
No 49
>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=23.79 E-value=1e+02 Score=23.23 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=25.2
Q ss_pred ChHHHHHHHHHHHHHhhhcCcEeccChhhHH
Q 032339 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~ 69 (142)
+++.++++.+.++.+++..|..+|+++..+.
T Consensus 182 ~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~ 212 (226)
T cd01651 182 GPKEAEEIKELIREFLEELGLELNPEKTRIT 212 (226)
T ss_pred CHHHHHHHHHHHHHHHHHcCCeechhhccee
Confidence 4455888888899999999999999886543
No 50
>PRK09492 treR trehalose repressor; Provisional
Probab=23.67 E-value=1.1e+02 Score=24.31 Aligned_cols=46 Identities=13% Similarity=-0.021 Sum_probs=30.2
Q ss_pred CCChHHHHHHHHHHHHHhhhcCcEecc--------------------ChhhHHHHHHHHHHhHhhhCCCC
Q 032339 37 EPSEKSVEIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPL 86 (142)
Q Consensus 37 ~~s~~~~e~~~~~~ekyaek~Gy~lNP--------------------D~ev~~~Vi~GLa~NK~rYG~~~ 86 (142)
..|+++.++ +.+.|++.||+-|. +..+...++.|+...-.++||..
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 366666555 55556666665442 12355678899998888999875
No 51
>PLN02449 ferrochelatase
Probab=23.59 E-value=1.6e+02 Score=27.35 Aligned_cols=51 Identities=12% Similarity=0.044 Sum_probs=38.6
Q ss_pred ChHHHHHHHHHHHHHhhhcCcE-------eccChhhHHHHHHHHHHhHhhhCCCCCCC
Q 032339 39 SEKSVEIMRKFSEQYARRSDTF-------FCVDKSVTSVVIKGLADHKDSLGAPLCPC 89 (142)
Q Consensus 39 s~~~~e~~~~~~ekyaek~Gy~-------lNPD~ev~~~Vi~GLa~NK~rYG~~~CPC 89 (142)
--|+++++.-..++.|++.|.. ||-++.+++.|.+=..++....|.+.|+|
T Consensus 366 hiETL~EiDiE~re~a~e~G~~~~~rVP~LN~~p~FI~~La~lV~~~l~~~~~~~~~~ 423 (485)
T PLN02449 366 HIETLEEIDMEYRELALESGIENWGRVPALGCEPTFISDLADAVIEALPYVGAMAVSN 423 (485)
T ss_pred chHHHHHHHHHHHHHHHHcCCceEEEcCCCCCCHHHHHHHHHHHHHHhhccccccccc
Confidence 4578888888888899999973 58899999987776666655456666655
No 52
>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=23.26 E-value=1.4e+02 Score=19.19 Aligned_cols=33 Identities=9% Similarity=0.115 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHh
Q 032339 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADH 78 (142)
Q Consensus 44 e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~N 78 (142)
+.++++++..|+..|=-+| .+++..|.+.|.++
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 4678889999999987776 45677776666644
No 53
>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=23.00 E-value=1e+02 Score=23.34 Aligned_cols=29 Identities=10% Similarity=0.117 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhhhcCcEeccChhhHH
Q 032339 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (142)
Q Consensus 41 ~~~e~~~~~~ekyaek~Gy~lNPD~ev~~ 69 (142)
+.++.+.+.+..+++..|..+|+++..+.
T Consensus 160 ~~~~~~~~~~~~~~~~~gl~in~~Kt~~~ 188 (220)
T cd01650 160 RKLQELLQRLQEWSKESGLKINPSKSKVM 188 (220)
T ss_pred HHHHHHHHHHHHHHHHcCCEEChhheEEE
Confidence 47888888899999999999999987654
No 54
>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=22.36 E-value=2e+02 Score=17.75 Aligned_cols=45 Identities=11% Similarity=0.059 Sum_probs=34.8
Q ss_pred hHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 032339 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (142)
Q Consensus 40 ~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (142)
.+.+++..+.++.....++|.+.....+++..+-+....-..++.
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 345666677788888888899999999999999999988776654
No 55
>PHA01748 hypothetical protein
Probab=21.04 E-value=2e+02 Score=19.05 Aligned_cols=30 Identities=7% Similarity=0.223 Sum_probs=17.4
Q ss_pred HHHHHHHHHhhhcCcEeccChhhHHHHHHHHHH
Q 032339 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGLAD 77 (142)
Q Consensus 45 ~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~ 77 (142)
++.+.+++||++.|+ |-.+-+-.+| +-+..
T Consensus 12 el~~eld~~a~~~g~--~RSE~Ir~Ai-~~~~~ 41 (60)
T PHA01748 12 DLLELLDRYAIKHGL--NRSEAIRKAI-EKMVK 41 (60)
T ss_pred HHHHHHHHHHHHhCC--CHHHHHHHHH-HHHHH
Confidence 445557888888886 6444444444 44443
No 56
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=20.81 E-value=2.9e+02 Score=20.74 Aligned_cols=49 Identities=12% Similarity=0.014 Sum_probs=38.9
Q ss_pred CChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCCCCC
Q 032339 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLC 87 (142)
Q Consensus 38 ~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~~~C 87 (142)
...+.+..++.++..+++..|+-. .+.+-+..++.-++.|--+||+.-.
T Consensus 14 a~~~~~~~vr~~v~~~~~~~g~~~-~~~~~l~lav~Ea~~Nai~Hg~~~~ 62 (161)
T PRK04069 14 AKAEYVSIIRLTLSGVANRMGFSY-DDIEDMKIAVSEACTNAVQHAYKED 62 (161)
T ss_pred CcHHHHHHHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHHHHHhccCCC
Confidence 367889999999999999999854 3344456677888899999998654
No 57
>PF03982 DAGAT: Diacylglycerol acyltransferase ; InterPro: IPR007130 The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT) [, ].; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=20.17 E-value=2.4e+02 Score=24.25 Aligned_cols=33 Identities=18% Similarity=0.379 Sum_probs=21.8
Q ss_pred cCCCChHHHHHHHHHHHHHhhhcCcEeccChhhHHHHHHHHHHhHhhhCC
Q 032339 35 QVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (142)
Q Consensus 35 ~~~~s~~~~e~~~~~~ekyaek~Gy~lNPD~ev~~~Vi~GLa~NK~rYG~ 84 (142)
..+||+|+++++++ +| +++|.+=--+||.+||.
T Consensus 256 ~~~Pt~e~Vd~~H~---~Y--------------~~~L~~LFd~~K~~~g~ 288 (297)
T PF03982_consen 256 IENPTQEDVDKLHA---RY--------------IEALRELFDKHKAKYGY 288 (297)
T ss_pred CCCcCHHHHHHHHH---HH--------------HHHHHHHHHHHHHhcCC
Confidence 56788888887764 22 34455555677888875
Done!