Query 033909
Match_columns 109
No_of_seqs 112 out of 177
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 07:39:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033909hhsearch_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 1.3E-28 2.8E-33 178.8 7.6 70 35-104 5-74 (116)
2 COG4802 FtrB Ferredoxin-thiore 99.9 3.4E-27 7.3E-32 169.9 6.9 64 38-101 1-64 (110)
3 PF02943 FeThRed_B: Ferredoxin 99.9 4.1E-27 8.8E-32 168.5 6.5 58 41-98 1-58 (108)
4 PF05511 ATP-synt_F6: Mitochon 90.4 0.61 1.3E-05 33.5 4.5 81 1-85 1-84 (99)
5 PF03938 OmpH: Outer membrane 74.4 6.9 0.00015 27.8 4.3 37 39-75 111-157 (158)
6 PHA00425 DNA packaging protein 72.9 7.4 0.00016 27.6 4.1 45 40-84 29-76 (88)
7 PRK10780 periplasmic chaperone 71.7 8.4 0.00018 28.4 4.4 38 38-75 117-164 (165)
8 TIGR01924 rsbW_low_gc serine-p 69.8 24 0.00052 25.6 6.4 55 33-88 9-63 (159)
9 TIGR02417 fruct_sucro_rep D-fr 67.6 8.4 0.00018 29.4 3.7 48 45-92 32-99 (327)
10 KOG1671 Ubiquinol cytochrome c 63.8 2.1 4.6E-05 34.5 -0.2 15 75-89 160-174 (210)
11 PRK10401 DNA-binding transcrip 63.1 12 0.00025 29.1 3.8 46 44-89 30-95 (346)
12 PF12683 DUF3798: Protein of u 62.2 15 0.00033 30.6 4.5 49 42-91 187-235 (275)
13 TIGR01481 ccpA catabolite cont 60.4 14 0.00031 28.1 3.8 46 44-89 30-95 (329)
14 PF00356 LacI: Bacterial regul 57.9 9.5 0.00021 23.3 2.0 19 44-62 28-46 (46)
15 PRK11303 DNA-binding transcrip 57.2 22 0.00047 27.1 4.3 46 44-89 32-97 (328)
16 PF03912 Psb28: Psb28 protein; 55.1 11 0.00024 27.6 2.3 24 38-61 84-107 (108)
17 PRK11041 DNA-binding transcrip 54.9 25 0.00053 26.4 4.2 42 44-85 6-67 (309)
18 PRK13612 photosystem II reacti 54.3 15 0.00031 27.1 2.8 25 38-62 87-111 (113)
19 TIGR03047 PS_II_psb28 photosys 54.0 15 0.00031 27.0 2.8 24 38-61 84-107 (109)
20 PRK13611 photosystem II reacti 53.4 15 0.00033 26.7 2.8 24 38-61 80-103 (104)
21 COG2825 HlpA Outer membrane pr 53.2 26 0.00056 26.6 4.2 40 36-75 118-167 (170)
22 PLN00039 photosystem II reacti 53.0 16 0.00034 26.9 2.8 25 38-62 85-109 (111)
23 CHL00128 psbW photosystem II p 53.0 16 0.00034 27.0 2.8 25 38-62 87-111 (113)
24 PF10431 ClpB_D2-small: C-term 52.7 36 0.00078 21.7 4.3 38 45-85 13-50 (81)
25 TIGR02405 trehalos_R_Ecol treh 52.6 27 0.00058 26.7 4.2 42 44-85 30-91 (311)
26 PF14791 DNA_pol_B_thumb: DNA 50.9 20 0.00043 23.3 2.8 20 45-64 10-29 (64)
27 PF11123 DNA_Packaging_2: DNA 50.6 36 0.00077 23.9 4.1 45 40-84 27-74 (82)
28 PF00078 RVT_1: Reverse transc 49.6 27 0.00058 24.5 3.5 30 38-67 170-199 (214)
29 PRK10423 transcriptional repre 48.6 36 0.00078 25.8 4.3 45 45-89 28-94 (327)
30 TIGR00050 rRNA_methyl_1 RNA me 48.1 44 0.00095 26.1 4.8 40 37-76 169-208 (233)
31 PRK10727 DNA-binding transcrip 47.7 38 0.00082 26.2 4.4 43 44-86 30-92 (343)
32 PHA02745 hypothetical protein; 47.4 54 0.0012 27.4 5.4 52 34-85 213-264 (265)
33 PF01402 RHH_1: Ribbon-helix-h 47.0 49 0.0011 18.3 3.8 30 44-76 8-37 (39)
34 KOG1220 Phosphoglucomutase/pho 46.6 14 0.00031 33.8 2.2 46 40-85 457-502 (607)
35 PRK10339 DNA-binding transcrip 46.4 32 0.00069 26.4 3.8 25 65-89 79-103 (327)
36 PRK10703 DNA-binding transcrip 44.4 45 0.00097 25.6 4.3 45 37-85 27-91 (341)
37 PRK09492 treR trehalose repres 44.4 33 0.00071 25.9 3.5 43 45-87 34-96 (315)
38 PRK14987 gluconate operon tran 44.4 47 0.001 25.4 4.4 43 44-86 34-96 (331)
39 PF13410 GST_C_2: Glutathione 43.1 71 0.0015 19.0 5.1 45 40-84 8-52 (69)
40 COG5502 Uncharacterized conser 42.4 43 0.00093 25.4 3.8 35 44-78 76-111 (135)
41 KOG3651 Protein kinase C, alph 41.9 11 0.00023 32.9 0.6 10 82-91 24-33 (429)
42 KOG4634 Mitochondrial F1F0-ATP 40.3 64 0.0014 23.6 4.3 37 47-83 39-77 (105)
43 PF11794 HpaB_N: 4-hydroxyphen 39.5 53 0.0011 26.8 4.2 47 38-84 74-120 (264)
44 PRK05452 anaerobic nitric oxid 37.4 22 0.00048 30.7 1.8 72 31-104 370-446 (479)
45 PRK10014 DNA-binding transcrip 37.4 61 0.0013 24.8 4.1 42 45-86 36-97 (342)
46 PF02943 FeThRed_B: Ferredoxin 37.2 54 0.0012 23.6 3.5 47 37-91 22-70 (108)
47 PRK09526 lacI lac repressor; R 37.0 56 0.0012 25.0 3.8 43 44-86 34-96 (342)
48 PF08722 Tn7_Tnp_TnsA_N: TnsA 36.7 38 0.00082 22.1 2.5 31 32-62 54-84 (88)
49 PRK05802 hypothetical protein; 36.2 15 0.00033 29.9 0.6 13 81-93 9-21 (320)
50 cd01646 RT_Bac_retron_I RT_Bac 36.2 54 0.0012 23.3 3.4 47 38-85 97-143 (158)
51 TIGR01463 mtaA_cmuA methyltran 35.2 74 0.0016 25.4 4.4 44 41-84 293-340 (340)
52 PF04315 DUF462: Protein of un 34.6 13 0.00028 28.9 0.0 26 65-90 47-73 (164)
53 PHA01748 hypothetical protein 34.4 97 0.0021 19.7 4.1 31 45-78 12-42 (60)
54 KOG3820 Aromatic amino acid hy 33.0 24 0.00051 31.4 1.3 36 36-71 395-430 (461)
55 PLN02449 ferrochelatase 32.7 1.1E+02 0.0024 27.2 5.4 61 28-88 353-422 (485)
56 PF03445 DUF294: Putative nucl 32.4 57 0.0012 23.4 3.0 26 67-92 86-111 (138)
57 PF13963 Transpos_assoc: Trans 32.2 13 0.00027 24.6 -0.4 17 84-100 37-53 (77)
58 PF07308 DUF1456: Protein of u 32.0 40 0.00086 22.2 2.0 34 44-79 33-66 (68)
59 TIGR03164 UHCUDC OHCU decarbox 31.9 70 0.0015 23.9 3.5 25 37-61 87-111 (157)
60 PRK04069 serine-protein kinase 31.8 1.4E+02 0.0031 21.4 5.1 49 38-87 14-62 (161)
61 TIGR03180 UraD_2 OHCU decarbox 31.1 74 0.0016 23.8 3.6 25 37-61 87-111 (158)
62 KOG2681 Metal-dependent phosph 30.8 97 0.0021 28.0 4.7 60 42-109 317-377 (498)
63 PF14677 FANCI_S3: FANCI solen 30.6 82 0.0018 24.8 3.9 34 36-72 182-215 (219)
64 PHA01623 hypothetical protein 29.6 98 0.0021 19.5 3.4 31 44-77 22-52 (56)
65 COG1609 PurR Transcriptional r 29.0 1.1E+02 0.0023 24.7 4.4 51 37-91 26-98 (333)
66 PF08608 Wyosine_form: Wyosine 28.9 61 0.0013 21.0 2.4 25 36-63 26-50 (62)
67 PRK13798 putative OHCU decarbo 28.5 86 0.0019 23.7 3.5 25 37-61 92-116 (166)
68 cd01648 TERT TERT: Telomerase 28.4 83 0.0018 21.6 3.2 32 38-69 67-99 (119)
69 cd01651 RT_G2_intron RT_G2_int 27.9 89 0.0019 22.4 3.4 32 38-69 181-212 (226)
70 PRK07308 flavodoxin; Validated 27.8 85 0.0018 21.9 3.2 25 32-56 121-145 (146)
71 PRK15114 tRNA (cytidine/uridin 27.7 1.4E+02 0.0031 23.6 4.8 39 38-76 179-217 (245)
72 PF00570 HRDC: HRDC domain Blo 26.5 1.3E+02 0.0028 18.2 3.5 36 41-78 3-38 (68)
73 PRK03660 anti-sigma F factor; 26.4 2.1E+02 0.0046 19.4 5.0 50 38-88 11-60 (146)
74 PF10306 FLILHELTA: Hypothetic 26.3 93 0.002 21.6 3.1 30 37-66 57-86 (86)
75 PF12401 DUF3662: Protein of u 26.2 75 0.0016 22.5 2.7 25 38-62 70-94 (116)
76 COG3101 Uncharacterized protei 25.9 27 0.00058 27.5 0.4 19 70-88 62-81 (180)
77 PRK06242 flavodoxin; Provision 25.8 77 0.0017 21.8 2.7 22 35-56 128-149 (150)
78 TIGR01386 cztS_silS_copS heavy 25.8 2.3E+02 0.005 22.2 5.6 47 39-85 317-371 (457)
79 cd01650 RT_nLTR_like RT_nLTR: 25.7 89 0.0019 22.5 3.1 29 41-69 160-188 (220)
80 PF08369 PCP_red: Proto-chloro 25.5 72 0.0016 19.3 2.2 17 44-60 18-34 (45)
81 PRK13590 putative bifunctional 25.2 1.2E+02 0.0027 26.7 4.4 25 37-61 97-121 (591)
82 TIGR02793 nikR nickel-responsi 24.8 1.5E+02 0.0032 21.7 4.1 38 44-82 9-46 (129)
83 PRK06756 flavodoxin; Provision 24.5 1.1E+02 0.0024 21.3 3.3 22 35-56 125-146 (148)
84 PF14747 DUF4473: Domain of un 24.2 2.2E+02 0.0048 18.9 5.8 46 36-82 18-63 (82)
85 PF13581 HATPase_c_2: Histidin 24.0 2.2E+02 0.0048 18.7 5.0 49 39-88 4-52 (125)
86 PF03869 Arc: Arc-like DNA bin 23.4 1.6E+02 0.0035 18.0 3.5 31 44-76 13-43 (50)
87 PRK03922 hypothetical protein; 23.3 12 0.00027 27.6 -1.8 30 51-90 25-56 (113)
88 PF09213 M3: M3; InterPro: IP 23.0 25 0.00054 30.2 -0.3 17 82-98 330-346 (376)
89 PF02383 Syja_N: SacI homology 22.5 1.1E+02 0.0024 24.5 3.3 41 39-79 62-102 (319)
90 PF03732 Retrotrans_gag: Retro 22.4 86 0.0019 19.3 2.2 36 39-75 59-94 (96)
91 smart00099 btg1 tob/btg1 famil 22.4 2.8E+02 0.006 20.1 5.1 50 40-90 2-53 (108)
92 PRK13697 cytochrome c6; Provis 22.0 1.1E+02 0.0023 20.3 2.8 23 37-60 89-111 (111)
93 PF09349 OHCU_decarbox: OHCU d 21.6 92 0.002 23.0 2.5 25 37-61 90-114 (159)
94 cd01586 AcnA_IRP Aconitase A c 21.4 25 0.00054 30.6 -0.6 42 67-108 58-99 (404)
95 cd07015 Clp_protease_NfeD Nodu 21.1 34 0.00073 26.0 0.1 20 39-58 113-132 (172)
96 PF07862 Nif11: Nitrogen fixat 21.0 40 0.00087 20.0 0.4 16 50-65 32-47 (49)
97 TIGR01565 homeo_ZF_HD homeobox 21.0 1.6E+02 0.0034 18.9 3.2 38 39-80 9-47 (58)
98 PF02786 CPSase_L_D2: Carbamoy 20.9 1.7E+02 0.0036 22.6 3.9 29 32-60 127-155 (211)
99 TIGR02309 HpaB-1 4-hydroxyphen 20.9 2.4E+02 0.0052 24.6 5.3 51 37-88 73-123 (477)
100 cd00304 RT_like RT_like: Rever 20.8 1.3E+02 0.0027 19.0 2.8 26 42-67 58-83 (98)
101 cd02892 SQCY_1 Squalene cyclas 20.8 1.6E+02 0.0036 26.1 4.3 43 38-80 326-389 (634)
102 PF03982 DAGAT: Diacylglycerol 20.7 2.2E+02 0.0048 23.3 4.8 16 33-48 254-269 (297)
103 TIGR02937 sigma70-ECF RNA poly 20.5 2.5E+02 0.0054 18.0 4.3 46 40-85 4-49 (158)
No 1
>CHL00165 ftrB ferredoxin thioreductase subunit beta; Validated
Probab=99.95 E-value=1.3e-28 Score=178.84 Aligned_cols=70 Identities=49% Similarity=0.782 Sum_probs=65.9
Q ss_pred cCCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCCCccCcchhhhhhhcCc
Q 033909 35 QVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCIMTTKLLKLSRASGI 104 (109)
Q Consensus 35 ~~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CPCRl~~g~re~dr~~~~ 104 (109)
+...+++++|+|++|+++||+++||+||||+++|+.||+||++||++||+||||||+++|++++++..-|
T Consensus 5 ~~~~~~~~~e~m~~f~ekya~~~G~~fnpD~~vt~~Vi~GLa~nK~~yG~p~CPCR~~~~k~~e~~~~~~ 74 (116)
T CHL00165 5 NEKSKPESLEAMRKFAETYAKRTNTFFCSDLSITAVVIEGLARHKDEYGAPLCPCRHYEDKKVEVSAAYW 74 (116)
T ss_pred ccccchhhHHHHHHHHHHHHHHhCCeeCCCHHHHHHHHHHHHHHHHHhCCCCCCCcCCCCcHHHhhcCCe
Confidence 4567899999999999999999999999999999999999999999999999999999999999887544
No 2
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=99.94 E-value=3.4e-27 Score=169.88 Aligned_cols=64 Identities=33% Similarity=0.588 Sum_probs=62.4
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCCCccCcchhhhhhh
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCIMTTKLLKLSRA 101 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CPCRl~~g~re~dr~ 101 (109)
.+++++++||+|+++||+++||+||||.++|+.|++||+.||++||+++||||+++|++++||.
T Consensus 1 ~~~e~l~~my~~~eq~AeksG~~lnpD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~eeedk~ 64 (110)
T COG4802 1 ESDEELNKMYRFTEQYAEKSGYRLNPDREFTAEVLRGLASNKERYGYPSCPCRLVTGKEEEDKD 64 (110)
T ss_pred CcHHHHHHHHHHHHHHHHhcCceeCCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCHHHhhc
Confidence 3689999999999999999999999999999999999999999999999999999999999997
No 3
>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=99.94 E-value=4.1e-27 Score=168.47 Aligned_cols=58 Identities=38% Similarity=0.606 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCCCccCcchhhh
Q 033909 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCIMTTKLLKL 98 (109)
Q Consensus 41 e~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CPCRl~~g~re~ 98 (109)
+++|+|++|+++||+++||+||||+++|+.|++||++||++||++|||||+++|++++
T Consensus 1 ~~le~~~~~~~~~a~~~G~~~NpD~~~~~~v~~GL~~nk~~yG~~~CPCr~~~~~~ee 58 (108)
T PF02943_consen 1 KELEKMYKFLEKYAEKSGYKLNPDEEVTDDVLEGLARNKERYGYPYCPCRLASGKEEE 58 (108)
T ss_dssp HHHHHHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCEECCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCchhh
Confidence 5899999999999999999999999999999999999999999999999999999987
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=90.42 E-value=0.61 Score=33.51 Aligned_cols=81 Identities=15% Similarity=0.193 Sum_probs=39.6
Q ss_pred CccccccccccccCccCCCCCcccCCCcceeee--ccCCCCHH-HHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHH
Q 033909 1 MTLQSSLCGSGVSTFICTPRPIIARPRPVTQIR--AQVEPSEK-SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLAD 77 (109)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~see-~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~ 77 (109)
|.+|+.+.++..|..+..-+ |.-.-.++. ...+|-++ =+++++++..|-..+.|=..++++++-..+-+-|.+
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 77888666666665555444 222212222 12344444 578999999999999999999999999999999999
Q ss_pred hHHhhCCC
Q 033909 78 HKDSLGAP 85 (109)
Q Consensus 78 NK~rYG~~ 85 (109)
-...||.-
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 99999863
No 5
>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=74.44 E-value=6.9 Score=27.78 Aligned_cols=37 Identities=24% Similarity=0.275 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHHHhhhcCc----------eeccChhhHHHHHHHH
Q 033909 39 SEKSVEIMRKFSEQYARRSDT----------FFCVDKSVTSVVIKGL 75 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~Gy----------~fNPD~evt~~VieGL 75 (109)
...-.+++...++.||+..|| +.+|..++|+.|++.|
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 344556788899999999998 5677889999999876
No 6
>PHA00425 DNA packaging protein, small subunit
Probab=72.94 E-value=7.4 Score=27.59 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHhhhcCce---eccChhhHHHHHHHHHHhHHhhCC
Q 033909 40 EKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (109)
Q Consensus 40 ee~lE~m~~f~ekyAek~Gy~---fNPD~evt~~VieGLa~NK~rYG~ 84 (109)
++.--++|+-+.|+-+++-|. +.||+++.-.+..+|...++.+|.
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 444567899999999999985 579999999999999999999985
No 7
>PRK10780 periplasmic chaperone; Provisional
Probab=71.74 E-value=8.4 Score=28.38 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHHHhhhcCcee----------ccChhhHHHHHHHH
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFF----------CVDKSVTSVVIKGL 75 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~f----------NPD~evt~~VieGL 75 (109)
..+.-++++.+.+++||++.||-+ +|..++|..|++-|
T Consensus 117 ~~~~i~~ki~~ai~~vak~~gy~~Vld~~~v~Y~~~~~DIT~~Vik~l 164 (165)
T PRK10780 117 ERNKILTRIQTAVKSVANKQGYDLVVDANAVAYNSSDKDITADVLKQV 164 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCeEEEeCCceeeeCCCCCchHHHHHhh
Confidence 345567788899999999999844 46778888888765
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=69.79 E-value=24 Score=25.60 Aligned_cols=55 Identities=11% Similarity=-0.002 Sum_probs=42.2
Q ss_pred eccCCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCC
Q 033909 33 RAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (109)
Q Consensus 33 ~~~~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CP 88 (109)
.-.-....+.+..++.|++.+|+..|+- ..+.+-+..++.-|+.|--+||+..++
T Consensus 9 ~l~~~a~~~~~~~vr~~~~~~a~~~g~~-~~~~~~l~lav~Ea~~Nai~ha~~~~~ 63 (159)
T TIGR01924 9 EMTVPAKPEYVGLIRLTLSGIASRAGYT-YDDIEDLKIAVSEACTNAVKHAYKEGE 63 (159)
T ss_pred EEEccCcHHHHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 3344456788899999999999999964 233345667888999999999997653
No 9
>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=67.56 E-value=8.4 Score=29.41 Aligned_cols=48 Identities=10% Similarity=-0.042 Sum_probs=34.6
Q ss_pred HHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCCCCCCccC
Q 033909 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCPCIMT 92 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~~CPCRl~ 92 (109)
++++.+.+.|++.||.-|. +..+...++.|+..--+++||...-|...
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 5566678888888886542 23466788899988888899987666543
No 10
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=63.75 E-value=2.1 Score=34.45 Aligned_cols=15 Identities=27% Similarity=0.724 Sum_probs=13.2
Q ss_pred HHHhHHhhCCCCCCC
Q 033909 75 LADHKDSLGAPLCPC 89 (109)
Q Consensus 75 La~NK~rYG~~~CPC 89 (109)
.+.|+-.||..||||
T Consensus 160 p~~~AGd~gg~~CPC 174 (210)
T KOG1671|consen 160 PIANAGDYGGYYCPC 174 (210)
T ss_pred ccccccccCceeccc
Confidence 356899999999999
No 11
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=63.14 E-value=12 Score=29.06 Aligned_cols=46 Identities=4% Similarity=-0.147 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhhcCceec------------------c--ChhhHHHHHHHHHHhHHhhCCCCCCC
Q 033909 44 EIMRKFSEQYARRSDTFFC------------------V--DKSVTSVVIKGLADHKDSLGAPLCPC 89 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fN------------------P--D~evt~~VieGLa~NK~rYG~~~CPC 89 (109)
+++++.+.+.|++.||.-| | +..+...+++|+..--.++||...=|
T Consensus 30 ~~tr~kV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~ 95 (346)
T PRK10401 30 ADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIG 95 (346)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE
Confidence 4455667778888888754 3 24577789999999989999875433
No 12
>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=62.16 E-value=15 Score=30.64 Aligned_cols=49 Identities=18% Similarity=0.390 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCCCcc
Q 033909 42 SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCPCIM 91 (109)
Q Consensus 42 ~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CPCRl 91 (109)
-+|.+-+|++||-+... +|+-+..+++.||+.++.++-.|=...||+-+
T Consensus 187 IlE~vp~~i~kYGkdta-ff~TN~a~~epllk~~~~~g~i~~e~~~psp~ 235 (275)
T PF12683_consen 187 ILEDVPKWIKKYGKDTA-FFCTNDAMTEPLLKQALEYGGIFPEADLPSPL 235 (275)
T ss_dssp HHHHHHHHHHHH-S--E-EEESSHHHHHHHHHHHHHH--BB---SS--TT
T ss_pred HHHHHHHHHHHhCCcee-EEecCccccHHHHHHHHHcCCEEEeCCCCChh
Confidence 56788899999965554 57778889999999999999999999999876
No 13
>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=60.45 E-value=14 Score=28.12 Aligned_cols=46 Identities=13% Similarity=0.023 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCCCCCC
Q 033909 44 EIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCPC 89 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~~CPC 89 (109)
+++++.+.+.|++.||.-|+ +..+...++.|+..--.++||..--|
T Consensus 30 ~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~ 95 (329)
T TIGR01481 30 PATRKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILS 95 (329)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEE
Confidence 45566678888888887553 23567788999988888888876444
No 14
>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=57.91 E-value=9.5 Score=23.26 Aligned_cols=19 Identities=16% Similarity=-0.200 Sum_probs=13.2
Q ss_pred HHHHHHHHHHhhhcCceec
Q 033909 44 EIMRKFSEQYARRSDTFFC 62 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fN 62 (109)
+++++.+.+.|++.||.-|
T Consensus 28 ~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 28 EETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHHHHHHHHHHTB-SS
T ss_pred HHHHHHHHHHHHHHCCCCC
Confidence 3455667888899999765
No 15
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=57.20 E-value=22 Score=27.06 Aligned_cols=46 Identities=11% Similarity=0.008 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCCCCCC
Q 033909 44 EIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLCPC 89 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~~CPC 89 (109)
+++++.+.+.|++.||.-|. +..+...+++|+..--.++||..--+
T Consensus 32 ~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~ 97 (328)
T PRK11303 32 DKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIA 97 (328)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEE
Confidence 34666678888888887553 23466778999999889999876443
No 16
>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=55.10 E-value=11 Score=27.56 Aligned_cols=24 Identities=29% Similarity=0.405 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHHHHHHhhhcCcee
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~f 61 (109)
.++++-+.+.+|.++||+.+|.-|
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 578999999999999999999755
No 17
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=54.92 E-value=25 Score=26.38 Aligned_cols=42 Identities=17% Similarity=0.030 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCC
Q 033909 44 EIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~ 85 (109)
+++++.+.+.|++.||.-|. +..+...+++|+.+--.++|+.
T Consensus 6 ~~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~ 67 (309)
T PRK11041 6 QATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYL 67 (309)
T ss_pred HHHHHHHHHHHHHHCCCcCHHHHHhhcCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCE
Confidence 45667788999999998764 3456788999999999999864
No 18
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=54.30 E-value=15 Score=27.13 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceec
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fN 62 (109)
.++++-+.+.+|.++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T PRK13612 87 KSEQEWDRFMRFMERYAKENGLGFS 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 5899999999999999999997654
No 19
>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=54.04 E-value=15 Score=26.98 Aligned_cols=24 Identities=25% Similarity=0.369 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHHHHHHhhhcCcee
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~f 61 (109)
.++++-+.+.+|.++||+.+|.-|
T Consensus 84 ~s~~~WdRFMRFmeRYA~~ngl~f 107 (109)
T TIGR03047 84 KSEDEWDRFMRFMERYAEANGLGY 107 (109)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 589999999999999999999755
No 20
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=53.44 E-value=15 Score=26.67 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHHHHHhhhcCcee
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~f 61 (109)
.++++-+.+.+|.++||+.+|.-|
T Consensus 80 ~s~~~wdRFMRFmeRYA~~Ngl~f 103 (104)
T PRK13611 80 ETEAEWDRFLRFMERFSAANQMGM 103 (104)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcc
Confidence 589999999999999999998644
No 21
>COG2825 HlpA Outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=53.22 E-value=26 Score=26.61 Aligned_cols=40 Identities=25% Similarity=0.256 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHHHhhhcCce----------eccChhhHHHHHHHH
Q 033909 36 VEPSEKSVEIMRKFSEQYARRSDTF----------FCVDKSVTSVVIKGL 75 (109)
Q Consensus 36 ~~~see~lE~m~~f~ekyAek~Gy~----------fNPD~evt~~VieGL 75 (109)
.+...+.++++..-++.+|++.||- .+|-.++|+.||+-|
T Consensus 118 ~e~~~~~~~~i~~ai~~~a~~~gy~~vl~~~~V~y~~~~~DIT~~Vlk~l 167 (170)
T COG2825 118 AEEEQKLLEKIQRAIESVAEKGGYSLVLDSNAVLYAKPSKDITDDVLKAL 167 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCcceEecCCchhccCCCCCchHHHHHHH
Confidence 3455677888999999999999984 578888999999876
No 22
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=53.04 E-value=16 Score=26.90 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceec
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fN 62 (109)
.++++-+.+.+|.++||+.+|.-|.
T Consensus 85 ~s~~~WdRFMRFMeRYA~~ngl~f~ 109 (111)
T PLN00039 85 RSPREWDRFMRFMERYAEENGLGFV 109 (111)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 5899999999999999999997654
No 23
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=53.04 E-value=16 Score=26.98 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceec
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fN 62 (109)
.++++-+.+.+|.++||+.+|.-|.
T Consensus 87 ~s~~~WdRFMRFMeRYA~~ngl~f~ 111 (113)
T CHL00128 87 KNPEAWDRFMRFMERYAEDNGLTFT 111 (113)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCccc
Confidence 5899999999999999999997654
No 24
>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=52.71 E-value=36 Score=21.73 Aligned_cols=38 Identities=16% Similarity=0.189 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCC
Q 033909 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~ 85 (109)
++.+..+++++ .|..|+-|+++.+.+++-= ....||.+
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 44578765
No 25
>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=52.64 E-value=27 Score=26.68 Aligned_cols=42 Identities=14% Similarity=0.059 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhhhcCceec------------------cC--hhhHHHHHHHHHHhHHhhCCC
Q 033909 44 EIMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fN------------------PD--~evt~~VieGLa~NK~rYG~~ 85 (109)
+++++.+.+.|++.||.-| || ..+...+++|+..--.++||.
T Consensus 30 ~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~ 91 (311)
T TIGR02405 30 IETRERVEQVIQQSGFVPSKSARAMRGGSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYD 91 (311)
T ss_pred HHHHHHHHHHHHHHCCCcCHHHHHhhcCCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCe
Confidence 3445557778888888654 22 335677899999999999987
No 26
>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=50.91 E-value=20 Score=23.25 Aligned_cols=20 Identities=15% Similarity=0.130 Sum_probs=16.1
Q ss_pred HHHHHHHHHhhhcCceeccC
Q 033909 45 IMRKFSEQYARRSDTFFCVD 64 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fNPD 64 (109)
...+.+..+|.+.||.||..
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 34567888999999999974
No 27
>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=50.58 E-value=36 Score=23.91 Aligned_cols=45 Identities=18% Similarity=0.179 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHhhhcCce---eccChhhHHHHHHHHHHhHHhhCC
Q 033909 40 EKSVEIMRKFSEQYARRSDTF---FCVDKSVTSVVIKGLADHKDSLGA 84 (109)
Q Consensus 40 ee~lE~m~~f~ekyAek~Gy~---fNPD~evt~~VieGLa~NK~rYG~ 84 (109)
++.--++|+-+.|+-+++.|. +-||+++.-.+..||...++.+|.
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 444557899999999999986 569999999999999999999985
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=49.62 E-value=27 Score=24.51 Aligned_cols=30 Identities=10% Similarity=0.070 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhh
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSV 67 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~ev 67 (109)
.+.++++++.+.+.++.+..|..+|+++-.
T Consensus 170 ~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~ 199 (214)
T PF00078_consen 170 KSKEELQKILEKISQWLEELGLKLNPEKTK 199 (214)
T ss_dssp SSHHHHHHHHHHHHHHHHHTTSBCSSTTTS
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEChHHEE
Confidence 346778999999999999999999999864
No 29
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=48.57 E-value=36 Score=25.79 Aligned_cols=45 Identities=13% Similarity=0.128 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhhcCceec------------------cC--hhhHHHHHHHHHHhHHhhCCC--CCCC
Q 033909 45 IMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAP--LCPC 89 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fN------------------PD--~evt~~VieGLa~NK~rYG~~--~CPC 89 (109)
++++.+.+.|++.||.-| |+ ..+-..+++|+..--.++||. +|++
T Consensus 28 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~ 94 (327)
T PRK10423 28 AITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNT 94 (327)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeC
Confidence 445556677777787543 22 356788999999999999987 4444
No 30
>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=48.07 E-value=44 Score=26.15 Aligned_cols=40 Identities=8% Similarity=-0.063 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHH
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa 76 (109)
-++.++++.|++++++..++.||+-+..++.++..++-|.
T Consensus 169 ~a~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~lr~l~ 208 (233)
T TIGR00050 169 YATTDQLELLLEHLEEILLSLGFIPEHKIRRVMRKFRRLY 208 (233)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHH
Confidence 4688999999999999999999986666665555554443
No 31
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=47.75 E-value=38 Score=26.18 Aligned_cols=43 Identities=14% Similarity=0.010 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhhhcCceec------------------cC--hhhHHHHHHHHHHhHHhhCCCC
Q 033909 44 EIMRKFSEQYARRSDTFFC------------------VD--KSVTSVVIKGLADHKDSLGAPL 86 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fN------------------PD--~evt~~VieGLa~NK~rYG~~~ 86 (109)
+++++.+.+.|++.||.-| || ..+...+++|+..--.++||..
T Consensus 30 ~~tr~rV~~~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~ 92 (343)
T PRK10727 30 EASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFL 92 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEE
Confidence 4556667777888888654 32 4577889999999989999864
No 32
>PHA02745 hypothetical protein; Provisional
Probab=47.38 E-value=54 Score=27.38 Aligned_cols=52 Identities=8% Similarity=0.146 Sum_probs=44.0
Q ss_pred ccCCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCC
Q 033909 34 AQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 34 ~~~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~ 85 (109)
..+...+-.--.+..|++.|..+.||.---.+.+...+=--|..-+-+||.+
T Consensus 213 vRPgLDe~Ar~vLL~fVe~yG~~~~W~t~D~~~I~ntiR~KiqeiR~K~g~~ 264 (265)
T PHA02745 213 VRPGLDEDARTVLLRYVEIYGEKQRWCTEDHQAIINVIRNKMQESRRKDRHR 264 (265)
T ss_pred cCCCcchHHHHHHHHHHHHHhhccCCCCCchHHHHHHHHHHHHHHHHHhCCc
Confidence 4455667777889999999999999998878888888888888888999976
No 33
>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=46.96 E-value=49 Score=18.31 Aligned_cols=30 Identities=7% Similarity=0.063 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhhhcCceeccChhhHHHHHHHHH
Q 033909 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa 76 (109)
+++++.++++|++.| -+-.+++..+|+..+
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 356777889999998 233445555554443
No 34
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=46.59 E-value=14 Score=33.81 Aligned_cols=46 Identities=15% Similarity=0.219 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCC
Q 033909 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 40 ee~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~ 85 (109)
.+.++++++-..-.-..+.|++|+|+++++.+.++|=.-...|+||
T Consensus 457 ~e~l~~l~e~yg~~~~~~~y~l~~~pe~~~~lf~~lR~~~~~~~yp 502 (607)
T KOG1220|consen 457 SEVLEDLYERYGYHSTANSYRLCIDPEVIKALFDGLRNYDTGYIYP 502 (607)
T ss_pred HHHHHHHHHhhCccceeeEEEEecCCchhHHHHHHHhhcccccccc
Confidence 4556666666666678899999999999999999986665555554
No 35
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=46.44 E-value=32 Score=26.38 Aligned_cols=25 Identities=20% Similarity=0.417 Sum_probs=18.3
Q ss_pred hhhHHHHHHHHHHhHHhhCCCCCCC
Q 033909 65 KSVTSVVIKGLADHKDSLGAPLCPC 89 (109)
Q Consensus 65 ~evt~~VieGLa~NK~rYG~~~CPC 89 (109)
..+-..+++|+...-...||..--|
T Consensus 79 ~~f~~~l~~~i~~~~~~~g~~~~~~ 103 (327)
T PRK10339 79 DPYYLAIRHGIETQCEKLGIELTNC 103 (327)
T ss_pred CchHHHHHHHHHHHHHHCCCEEEEe
Confidence 3455678899988888899875433
No 36
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=44.44 E-value=45 Score=25.60 Aligned_cols=45 Identities=7% Similarity=-0.054 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCC
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~ 85 (109)
..+++..++ +.+.|++.||.-|+ +..+...+++|+..--..+|+.
T Consensus 27 ~vs~~tr~~----V~~~a~elgY~pn~~a~~l~~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~ 91 (341)
T PRK10703 27 FVAEETRNA----VWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYT 91 (341)
T ss_pred CCCHHHHHH----HHHHHHHHCCCcCHHHHHHhhCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCE
Confidence 456666555 55556666665442 2357778999999988899975
No 37
>PRK09492 treR trehalose repressor; Provisional
Probab=44.36 E-value=33 Score=25.94 Aligned_cols=43 Identities=9% Similarity=-0.075 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCCCC
Q 033909 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPLC 87 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~~C 87 (109)
++++.+.+.|++.||.-|. +..+...+++|+..--.++||..-
T Consensus 34 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~ 96 (315)
T PRK09492 34 ETRERVEAVINQHGFSPSKSARAMRGQSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDPI 96 (315)
T ss_pred HHHHHHHHHHHHHCCCcCHHHHHhhcCCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeEE
Confidence 3455577788888886552 123456788999998899998753
No 38
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=44.35 E-value=47 Score=25.42 Aligned_cols=43 Identities=14% Similarity=0.081 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhhhcCceecc------------------C--hhhHHHHHHHHHHhHHhhCCCC
Q 033909 44 EIMRKFSEQYARRSDTFFCV------------------D--KSVTSVVIKGLADHKDSLGAPL 86 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNP------------------D--~evt~~VieGLa~NK~rYG~~~ 86 (109)
+++++.+.+.|++.||.-|+ + ..+...+++|+..--.++||..
T Consensus 34 ~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~ 96 (331)
T PRK14987 34 VALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQT 96 (331)
T ss_pred HHHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEE
Confidence 35677788888999996542 2 2367889999999999999873
No 39
>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=43.10 E-value=71 Score=18.97 Aligned_cols=45 Identities=11% Similarity=0.059 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCC
Q 033909 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (109)
Q Consensus 40 ee~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~ 84 (109)
.+.+++..+.+++....++|.+.....+++..+-+.+..-..+|.
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 456677778888888999999999999999999999988877764
No 40
>COG5502 Uncharacterized conserved protein [Function unknown]
Probab=42.44 E-value=43 Score=25.37 Aligned_cols=35 Identities=20% Similarity=0.076 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhhcCceeccChhhHH-HHHHHHHHh
Q 033909 44 EIMRKFSEQYARRSDTFFCVDKSVTS-VVIKGLADH 78 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNPD~evt~-~VieGLa~N 78 (109)
-.+.+|+.+++++.|+--|-|.+.+- +|.+-|.+|
T Consensus 76 ~s~~dFl~Rv~~~~g~~~~vd~e~a~~AVf~vL~r~ 111 (135)
T COG5502 76 FSLDDFLTRVANKFGLEPPVDPEHAIAAVFAVLKRH 111 (135)
T ss_pred ccHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHh
Confidence 35689999999999999999999888 787777766
No 41
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=41.94 E-value=11 Score=32.90 Aligned_cols=10 Identities=60% Similarity=1.510 Sum_probs=8.2
Q ss_pred hCCCCCCCcc
Q 033909 82 LGAPLCPCIM 91 (109)
Q Consensus 82 YG~~~CPCRl 91 (109)
=|.|||||-.
T Consensus 24 GGapyCPClY 33 (429)
T KOG3651|consen 24 GGAPYCPCLY 33 (429)
T ss_pred CCCCcCCeEE
Confidence 4899999954
No 42
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=40.30 E-value=64 Score=23.60 Aligned_cols=37 Identities=11% Similarity=0.168 Sum_probs=31.7
Q ss_pred HHHHHHHhhh--cCceeccChhhHHHHHHHHHHhHHhhC
Q 033909 47 RKFSEQYARR--SDTFFCVDKSVTSVVIKGLADHKDSLG 83 (109)
Q Consensus 47 ~~f~ekyAek--~Gy~fNPD~evt~~VieGLa~NK~rYG 83 (109)
...++.|..+ .|=-.|+|+++-..|-+-|-+-+..||
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 3445556666 999999999999999999999999999
No 43
>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=39.48 E-value=53 Score=26.79 Aligned_cols=47 Identities=21% Similarity=0.281 Sum_probs=41.5
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCC
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGA 84 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~ 84 (109)
-+.+++.+-++..+..++.+|-.+.--.+....++.++..+.+.||.
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 57889999999999999999999999999999999999999998887
No 44
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=37.41 E-value=22 Score=30.67 Aligned_cols=72 Identities=15% Similarity=0.203 Sum_probs=47.1
Q ss_pred eeeccCCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHH----HHHHHhHHhhCCCCCC-CccCcchhhhhhhcCc
Q 033909 31 QIRAQVEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVI----KGLADHKDSLGAPLCP-CIMTTKLLKLSRASGI 104 (109)
Q Consensus 31 ~~~~~~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~Vi----eGLa~NK~rYG~~~CP-CRl~~g~re~dr~~~~ 104 (109)
.+...-.|+++++++.++|.+++|++.= .-|++..+..-. ..-+.-.+.-+..-|+ |...-+..+-|..+||
T Consensus 370 ~l~~~~~P~ee~~~~~~~~g~~la~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~yd~~~g~~~~~~ 446 (479)
T PRK05452 370 SLKAKWRPDQDALELCREHGREIARQWA--LAPLPQSTVNTVVKEETSATTTADLGPRMQCSVCQWIYDPAKGEPMQDV 446 (479)
T ss_pred cEEEEecCCHHHHHHHHHHHHHHHHHHh--hCCccccccccccccccccccccCCCCeEEECCCCeEECCCCCCcccCC
Confidence 3556667999999999999999997664 777775411100 0002222366667787 8877777777777776
No 45
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=37.38 E-value=61 Score=24.77 Aligned_cols=42 Identities=10% Similarity=0.020 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhhcCceecc--------------------ChhhHHHHHHHHHHhHHhhCCCC
Q 033909 45 IMRKFSEQYARRSDTFFCV--------------------DKSVTSVVIKGLADHKDSLGAPL 86 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fNP--------------------D~evt~~VieGLa~NK~rYG~~~ 86 (109)
++++.+.+.|++.||.-|. +..+-..+++|+..--.++||..
T Consensus 36 ~tr~~V~~~a~elgY~p~~~a~~l~~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~ 97 (342)
T PRK10014 36 ATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMV 97 (342)
T ss_pred HHHHHHHHHHHHhCCCcCHHHHhhccCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEE
Confidence 4455677888888887652 23466788999999888999764
No 46
>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=37.18 E-value=54 Score=23.61 Aligned_cols=47 Identities=15% Similarity=0.338 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHh--hCCCCCCCcc
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDS--LGAPLCPCIM 91 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~r--YG~~~CPCRl 91 (109)
.|.++-.+.+.+-+.+.-++.||.+||=+-... .+++ =.+..|||-.
T Consensus 22 NpD~~~~~~v~~GL~~nk~~yG~~~CPCr~~~~--------~~ee~~d~~iiCPC~~ 70 (108)
T PF02943_consen 22 NPDEEVTDDVLEGLARNKERYGYPYCPCRLASG--------KEEEVKDRDIICPCVP 70 (108)
T ss_dssp BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S---------HHHHHHH-TTBSS-HH
T ss_pred CCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCC--------chhhhccCCeecCCHH
Confidence 467788888888899999999999999876411 1111 4677888873
No 47
>PRK09526 lacI lac repressor; Reviewed
Probab=36.97 E-value=56 Score=25.00 Aligned_cols=43 Identities=14% Similarity=0.080 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhhcCceecc------------------C--hhhHHHHHHHHHHhHHhhCCCC
Q 033909 44 EIMRKFSEQYARRSDTFFCV------------------D--KSVTSVVIKGLADHKDSLGAPL 86 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNP------------------D--~evt~~VieGLa~NK~rYG~~~ 86 (109)
+++++.+.+.|++.||.-|. | ..+...+++|+...-.++||..
T Consensus 34 ~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~ 96 (342)
T PRK09526 34 AKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSV 96 (342)
T ss_pred HHHHHHHHHHHHHHCCCcCHHHHHhhcCCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEE
Confidence 44566677788888886553 1 1345678999998888899874
No 48
>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=36.72 E-value=38 Score=22.10 Aligned_cols=31 Identities=10% Similarity=0.134 Sum_probs=19.1
Q ss_pred eeccCCCCHHHHHHHHHHHHHHhhhcCceec
Q 033909 32 IRAQVEPSEKSVEIMRKFSEQYARRSDTFFC 62 (109)
Q Consensus 32 ~~~~~~~see~lE~m~~f~ekyAek~Gy~fN 62 (109)
|.+..+.......+-.+..+.|+++.||.|.
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 3444455555556667778999999999874
No 49
>PRK05802 hypothetical protein; Provisional
Probab=36.19 E-value=15 Score=29.88 Aligned_cols=13 Identities=31% Similarity=0.979 Sum_probs=10.9
Q ss_pred hhCCCCCCCccCc
Q 033909 81 SLGAPLCPCIMTT 93 (109)
Q Consensus 81 rYG~~~CPCRl~~ 93 (109)
..|-.||||-|+.
T Consensus 9 d~~~~~cpc~la~ 21 (320)
T PRK05802 9 DAGSEYCPCHLAE 21 (320)
T ss_pred ccCCCcCceeeec
Confidence 4689999999985
No 50
>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=36.18 E-value=54 Score=23.27 Aligned_cols=47 Identities=17% Similarity=0.142 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCC
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~ 85 (109)
.+.+.++++.+.+....++.|..+||++.....+-+|. ...+-.|+.
T Consensus 97 ~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~~-~~~~flg~~ 143 (158)
T cd01646 97 DSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEGT-ASKDFLGYR 143 (158)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEChhhceeeecCCCC-ccccccceE
Confidence 45667778888888888899999999987665554443 223344443
No 51
>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=35.24 E-value=74 Score=25.36 Aligned_cols=44 Identities=9% Similarity=0.080 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHhhhcCceeccChh----hHHHHHHHHHHhHHhhCC
Q 033909 41 KSVEIMRKFSEQYARRSDTFFCVDKS----VTSVVIKGLADHKDSLGA 84 (109)
Q Consensus 41 e~lE~m~~f~ekyAek~Gy~fNPD~e----vt~~VieGLa~NK~rYG~ 84 (109)
.+.|++++.+++..++.||.|||+=+ .-..=++.+.+=-..|||
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 34577788888888889999999833 334445566665666665
No 52
>PF04315 DUF462: Protein of unknown function, DUF462; InterPro: IPR007411 This family consists of bacterial proteins of uncharacterised function.
Probab=34.59 E-value=13 Score=28.93 Aligned_cols=26 Identities=19% Similarity=0.307 Sum_probs=16.5
Q ss_pred hhhHHHHHHHHHHh-HHhhCCCCCCCc
Q 033909 65 KSVTSVVIKGLADH-KDSLGAPLCPCI 90 (109)
Q Consensus 65 ~evt~~VieGLa~N-K~rYG~~~CPCR 90 (109)
-|+.-=.|-|-.+- -..|||+|||.-
T Consensus 47 HEIaHWciAG~~RR~l~DfGYWY~PDG 73 (164)
T PF04315_consen 47 HEIAHWCIAGPERRQLEDFGYWYCPDG 73 (164)
T ss_pred HHHHHHHhccccccccccCCCCcCCCC
Confidence 34444455555543 467999999973
No 53
>PHA01748 hypothetical protein
Probab=34.45 E-value=97 Score=19.68 Aligned_cols=31 Identities=10% Similarity=0.163 Sum_probs=19.7
Q ss_pred HHHHHHHHHhhhcCceeccChhhHHHHHHHHHHh
Q 033909 45 IMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADH 78 (109)
Q Consensus 45 ~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~N 78 (109)
++.+.++.||++.|+ | -.+++...++.+..+
T Consensus 12 el~~eld~~a~~~g~--~-RSE~Ir~Ai~~~~~~ 42 (60)
T PHA01748 12 DLLELLDRYAIKHGL--N-RSEAIRKAIEKMVKD 42 (60)
T ss_pred HHHHHHHHHHHHhCC--C-HHHHHHHHHHHHHHH
Confidence 455668999999996 6 444455555544443
No 54
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=32.98 E-value=24 Score=31.44 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHH
Q 033909 36 VEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVV 71 (109)
Q Consensus 36 ~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~V 71 (109)
++.+++-.++|++|+...-++.|-.+||=.+-++.|
T Consensus 395 aeSFedAk~KlR~fa~ti~RPF~VrynpyT~svEvL 430 (461)
T KOG3820|consen 395 AESFEDAKEKLRKFASTIKRPFSVRYNPYTQSVEVL 430 (461)
T ss_pred hhhHHHHHHHHHHHHHhCCCCceeeeccccceehhh
Confidence 678999999999999999999999999977655543
No 55
>PLN02449 ferrochelatase
Probab=32.68 E-value=1.1e+02 Score=27.24 Aligned_cols=61 Identities=10% Similarity=-0.038 Sum_probs=39.2
Q ss_pred cceeeeccCCC--CHHHHHHHHHHHHHHhhhcCce-------eccChhhHHHHHHHHHHhHHhhCCCCCC
Q 033909 28 PVTQIRAQVEP--SEKSVEIMRKFSEQYARRSDTF-------FCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (109)
Q Consensus 28 ~~~~~~~~~~~--see~lE~m~~f~ekyAek~Gy~-------fNPD~evt~~VieGLa~NK~rYG~~~CP 88 (109)
...++.+-+=. --|.++++--..++.|++.|.. +|-++.+++.|.+=...+....|.+.|+
T Consensus 353 k~VlvvPigFvSDhiETL~EiDiE~re~a~e~G~~~~~rVP~LN~~p~FI~~La~lV~~~l~~~~~~~~~ 422 (485)
T PLN02449 353 KSLLAVPISFVSEHIETLEEIDMEYRELALESGIENWGRVPALGCEPTFISDLADAVIEALPYVGAMAVS 422 (485)
T ss_pred CeEEEECCcccccchHHHHHHHHHHHHHHHHcCCceEEEcCCCCCCHHHHHHHHHHHHHHhhcccccccc
Confidence 33444444333 3467777777788889998872 5889999987766655555444544444
No 56
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=32.37 E-value=57 Score=23.37 Aligned_cols=26 Identities=27% Similarity=0.373 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHhHHhhCCCCCCCccC
Q 033909 67 VTSVVIKGLADHKDSLGAPLCPCIMT 92 (109)
Q Consensus 67 vt~~VieGLa~NK~rYG~~~CPCRl~ 92 (109)
....+.+-+...-+.-|+++||=..-
T Consensus 86 ~f~~~a~~~~~~L~~~G~~~C~g~vm 111 (138)
T PF03445_consen 86 YFEAFAERLVDALDECGFPPCPGGVM 111 (138)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCCCcC
Confidence 33344455556667789999984443
No 57
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=32.22 E-value=13 Score=24.56 Aligned_cols=17 Identities=29% Similarity=0.487 Sum_probs=11.1
Q ss_pred CCCCCCccCcchhhhhh
Q 033909 84 APLCPCIMTTKLLKLSR 100 (109)
Q Consensus 84 ~~~CPCRl~~g~re~dr 100 (109)
...|||+-=-+.+..++
T Consensus 37 ~i~CPC~~C~N~~~~~~ 53 (77)
T PF13963_consen 37 MIRCPCRKCKNEKRQSR 53 (77)
T ss_pred ceECCchhhccCccCCH
Confidence 77899987655554433
No 58
>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=31.96 E-value=40 Score=22.24 Aligned_cols=34 Identities=18% Similarity=0.240 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhH
Q 033909 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHK 79 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK 79 (109)
+++..|++|- +..||.-|+|+.+ ...+.||...+
T Consensus 33 ~el~a~lrke-~~~~y~~c~D~~L-~~FL~GLi~~~ 66 (68)
T PF07308_consen 33 AELSAWLRKE-DEKGYKECSDQLL-RNFLNGLIIHK 66 (68)
T ss_pred HHHHHHHCCC-CCccccccChHHH-HHHHHHHHHHh
Confidence 4556677774 4459999999865 45678998765
No 59
>TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
Probab=31.85 E-value=70 Score=23.86 Aligned_cols=25 Identities=16% Similarity=0.264 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCcee
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~f 61 (109)
..++++.+++.+.-+.|-+|.|+.|
T Consensus 87 ~~~~~~~~~L~~lN~~Y~~kFGfpF 111 (157)
T TIGR03164 87 QLSQEEFARFTRLNNAYRARFGFPF 111 (157)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCee
Confidence 4567888899999999999999866
No 60
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=31.78 E-value=1.4e+02 Score=21.39 Aligned_cols=49 Identities=12% Similarity=0.014 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCC
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLC 87 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~C 87 (109)
...+.+...+.++..+++..|+-. .|.+-+..++.-++.|--+||+.-+
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 467788999999999999999854 3445566778889999999998755
No 61
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=31.07 E-value=74 Score=23.81 Aligned_cols=25 Identities=12% Similarity=0.226 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCcee
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~f 61 (109)
..++++.+++.+.-+.|-+|.|+.|
T Consensus 87 ~~~~~~~~~L~~lN~~Y~~kFGfpF 111 (158)
T TIGR03180 87 GADEETRAALLEGNAAYEEKFGRIF 111 (158)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCeE
Confidence 4677888888888888888888766
No 62
>KOG2681 consensus Metal-dependent phosphohydrolase [Function unknown]
Probab=30.76 E-value=97 Score=28.00 Aligned_cols=60 Identities=17% Similarity=0.192 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHh-hCCCCCCCccCcchhhhhhhcCceecCC
Q 033909 42 SVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDS-LGAPLCPCIMTTKLLKLSRASGIVHVFP 109 (109)
Q Consensus 42 ~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~r-YG~~~CPCRl~~g~re~dr~~~~~~~~~ 109 (109)
...++-+.+.+..+ ..+|++.+++ .+-|.+-..| | |+||||--.+++- .++..-|-||||
T Consensus 317 ~~~kldD~vl~~I~-----~~~DP~l~ea-qell~ri~~R~~-y~~~~Eta~~~~~-k~kie~~k~v~~ 377 (498)
T KOG2681|consen 317 AFSKLDDYVLAEIE-----QSTDPKLVEA-QELLLRIERRGY-YPYNPETAPNHDL-KRKIEDIKHVFP 377 (498)
T ss_pred HHHHhhHHHHHHhh-----cCCCchhHHH-HHHHHHHhhccc-cCCCCCcCCCccc-chhhhhhhccCh
Confidence 33444444444444 4577777654 3444444444 5 8999999998777 445555666665
No 63
>PF14677 FANCI_S3: FANCI solenoid 3; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=30.55 E-value=82 Score=24.81 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHH
Q 033909 36 VEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVI 72 (109)
Q Consensus 36 ~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~Vi 72 (109)
.++.+....+++.|+.++++.... .|.+++.+++
T Consensus 182 l~~~s~~~~q~~~W~~~~ck~~~l---~d~~~~k~ll 215 (219)
T PF14677_consen 182 LDPSSDQFTQMLSWTLKFCKENSL---EDSSFCKGLL 215 (219)
T ss_dssp S-SSSSHHHHHHHHHHHHHHS------S-HHHHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHHHhcCC---CcHHHHHHHH
Confidence 457778888999999999998775 7777777776
No 64
>PHA01623 hypothetical protein
Probab=29.55 E-value=98 Score=19.53 Aligned_cols=31 Identities=10% Similarity=0.081 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhhhcCceeccChhhHHHHHHHHHH
Q 033909 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLAD 77 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~ 77 (109)
+.+++.++.||+++|+. =.+++...|+-++.
T Consensus 22 eel~~~Ld~y~~~~g~~---rSe~IreAI~~yL~ 52 (56)
T PHA01623 22 KDLKTRLKVYCAKNNLQ---LTQAIEEAIKEYLQ 52 (56)
T ss_pred HHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHH
Confidence 45677799999999984 44555555555443
No 65
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=29.02 E-value=1.1e+02 Score=24.65 Aligned_cols=51 Identities=14% Similarity=0.037 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCceeccC--------------------hhhHHHHHHHHHHhHHhhCCCC--CCCcc
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFFCVD--------------------KSVTSVVIKGLADHKDSLGAPL--CPCIM 91 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~fNPD--------------------~evt~~VieGLa~NK~rYG~~~--CPCRl 91 (109)
..++|. ++.+.+.+++.||.-|+- ..+...+++|+..--.++||.. |++..
T Consensus 26 ~Vs~eT----r~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~ 98 (333)
T COG1609 26 YVSEET----REKVLAAIKELGYRPNAVARSLRTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD 98 (333)
T ss_pred CCCHHH----HHHHHHHHHHHCCCCCHHHHHHHhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC
Confidence 455554 555777999999994431 1467789999999999988864 55555
No 66
>PF08608 Wyosine_form: Wyosine base formation; InterPro: IPR013917 The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW []. ; PDB: 2YX0_A 2Z2U_A.
Probab=28.88 E-value=61 Score=21.04 Aligned_cols=25 Identities=20% Similarity=0.101 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHHHHHHHHhhhcCceecc
Q 033909 36 VEPSEKSVEIMRKFSEQYARRSDTFFCV 63 (109)
Q Consensus 36 ~~~see~lE~m~~f~ekyAek~Gy~fNP 63 (109)
..|+-+++ .+|+++.++..||.+.-
T Consensus 26 nmp~h~eV---~~F~~~l~~~~~y~i~~ 50 (62)
T PF08608_consen 26 NMPWHEEV---LDFAEELAELLGYEITD 50 (62)
T ss_dssp GS--HHHH---HHHHHHHHTTSTEEEEE
T ss_pred CCCcHHHH---HHHHHHHHhhcCCEEEe
Confidence 33444444 99999999999987653
No 67
>PRK13798 putative OHCU decarboxylase; Provisional
Probab=28.49 E-value=86 Score=23.71 Aligned_cols=25 Identities=12% Similarity=0.232 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCcee
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~f 61 (109)
..++++.+++.++-..|-+|.|+.|
T Consensus 92 ~l~~~~~~~l~~lN~~Y~~kFGfpF 116 (166)
T PRK13798 92 DADEAVMAALAAGNRAYEEKFGFVF 116 (166)
T ss_pred cCCHHHHHHHHHHHHHHHHhCCCeE
Confidence 3577888888888888888888766
No 68
>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=28.36 E-value=83 Score=21.61 Aligned_cols=32 Identities=16% Similarity=0.048 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHHHHh-hhcCceeccChhhHH
Q 033909 38 PSEKSVEIMRKFSEQYA-RRSDTFFCVDKSVTS 69 (109)
Q Consensus 38 ~see~lE~m~~f~ekyA-ek~Gy~fNPD~evt~ 69 (109)
.++++.+++.+.+...- ++.|..+|+++..+-
T Consensus 67 ~~~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~ 99 (119)
T cd01648 67 TSLDKAIKFLNLLLRGFINQYKTFVNFDKTQIN 99 (119)
T ss_pred CCHHHHHHHHHHHHHhhHHhhCeEECcccceee
Confidence 34566666666666664 899999999987654
No 69
>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=27.89 E-value=89 Score=22.40 Aligned_cols=32 Identities=9% Similarity=0.151 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHH
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~ 69 (109)
.+++.++++.+.++.+++..|..+|+++....
T Consensus 181 ~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~ 212 (226)
T cd01651 181 RGPKEAEEIKELIREFLEELGLELNPEKTRIT 212 (226)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCeechhhccee
Confidence 44555888899999999999999999886443
No 70
>PRK07308 flavodoxin; Validated
Probab=27.84 E-value=85 Score=21.91 Aligned_cols=25 Identities=16% Similarity=0.514 Sum_probs=19.0
Q ss_pred eeccCCCCHHHHHHHHHHHHHHhhh
Q 033909 32 IRAQVEPSEKSVEIMRKFSEQYARR 56 (109)
Q Consensus 32 ~~~~~~~see~lE~m~~f~ekyAek 56 (109)
+.....|+++++++.++|.++++++
T Consensus 121 ~~~~~~p~~~~~~~~~~~~~~l~~~ 145 (146)
T PRK07308 121 VKVDLAAEDEDIERLEAFAEELAAK 145 (146)
T ss_pred EEEeCCCCHHHHHHHHHHHHHHHhh
Confidence 4444558889999999999888764
No 71
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=27.69 E-value=1.4e+02 Score=23.58 Aligned_cols=39 Identities=13% Similarity=-0.031 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHH
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa 76 (109)
.+.+++|.|++.+++.-++.||.--..++.++..++.|.
T Consensus 179 a~~~~l~~l~~~l~~~l~~i~f~~~~~~~~~~~~lrrll 217 (245)
T PRK15114 179 PLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRRLF 217 (245)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHH
Confidence 588999999999999999999963233444444444443
No 72
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=26.53 E-value=1.3e+02 Score=18.21 Aligned_cols=36 Identities=14% Similarity=0.270 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHh
Q 033909 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADH 78 (109)
Q Consensus 41 e~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~N 78 (109)
+-++++.+|=++.|++.| ..|..=+.+.++..|+.+
T Consensus 3 ~~~~~L~~~R~~~A~~~~--~~~~~Il~~~~L~~ia~~ 38 (68)
T PF00570_consen 3 ALLKALKEWREELAREED--VPPYRILSDEALLEIAKR 38 (68)
T ss_dssp HHHHHHHHHHHHHHHHHT--S-HHHHS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcC--cCcccccCHHHHHHHHHh
Confidence 567899999999999998 667777777788887765
No 73
>PRK03660 anti-sigma F factor; Provisional
Probab=26.44 E-value=2.1e+02 Score=19.37 Aligned_cols=50 Identities=10% Similarity=0.062 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCC
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CP 88 (109)
...+.+..++.++..++...|+-. .|...+..++..|+.|--+||+..-+
T Consensus 11 ~~~~~~~~~r~~~~~~~~~~~~~~-~~~~~l~~~l~eli~Nai~h~~~~~~ 60 (146)
T PRK03660 11 SLSENESFARVTVAAFAAQLDPTL-EELTEIKTAVSEAVTNAIIHGYENNP 60 (146)
T ss_pred chhhHHHHHHHHHHHHHHhcCCCh-HHHHhHHHHHHHHHHHHHHHhcCCCC
Confidence 445667778899999999988754 34456677889999999999987544
No 74
>PF10306 FLILHELTA: Hypothetical protein FLILHELTA; InterPro: IPR018811 This entry represents a family of conserved proteins found in fungi. They contain a characteristic FL(I)LHE(L)TA sequence motif, where the bracketed residues are I, L or V. Their function is not known.
Probab=26.26 E-value=93 Score=21.58 Aligned_cols=30 Identities=10% Similarity=-0.001 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCceeccChh
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKS 66 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~fNPD~e 66 (109)
+..+.-+++-.+..+++.+++||+...+++
T Consensus 57 ~lp~~~~~~g~~~~~r~~~k~G~~~~~~~~ 86 (86)
T PF10306_consen 57 WLPDWALDEGTERFERWFRKKGWFGFEKED 86 (86)
T ss_pred cchHHHHHHHHHHHHHHHHHcCCccccccC
Confidence 444456888889999999999999876653
No 75
>PF12401 DUF3662: Protein of unknown function (DUF2662) ; InterPro: IPR022128 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00498 from PFAM. ; PDB: 2LC0_A.
Probab=26.19 E-value=75 Score=22.51 Aligned_cols=25 Identities=12% Similarity=0.167 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHHHHHHhhhcCceec
Q 033909 38 PSEKSVEIMRKFSEQYARRSDTFFC 62 (109)
Q Consensus 38 ~see~lE~m~~f~ekyAek~Gy~fN 62 (109)
-.+...++|.+++.++|+..||.|-
T Consensus 70 ~~~~l~~el~~~l~~~a~~qgy~~~ 94 (116)
T PF12401_consen 70 WGDRLARELADYLAEHAREQGYTFV 94 (116)
T ss_dssp -SHHHHHHHHHHHHHHHHHHT-B-S
T ss_pred hHHHHHHHHHHHHHHHHHHCCCeec
Confidence 3466778899999999999999875
No 76
>COG3101 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.89 E-value=27 Score=27.46 Aligned_cols=19 Identities=32% Similarity=0.483 Sum_probs=8.3
Q ss_pred HHHHHHHHhH-HhhCCCCCC
Q 033909 70 VVIKGLADHK-DSLGAPLCP 88 (109)
Q Consensus 70 ~VieGLa~NK-~rYG~~~CP 88 (109)
-++.|-++-+ +.|||+|||
T Consensus 62 WcvAGk~Rr~l~DFGYWY~P 81 (180)
T COG3101 62 WCIAGKARRELVDFGYWYCP 81 (180)
T ss_pred HHHccHHHhhhhccCeeeCC
Confidence 3344444333 345555555
No 77
>PRK06242 flavodoxin; Provisional
Probab=25.83 E-value=77 Score=21.82 Aligned_cols=22 Identities=27% Similarity=0.570 Sum_probs=18.8
Q ss_pred cCCCCHHHHHHHHHHHHHHhhh
Q 033909 35 QVEPSEKSVEIMRKFSEQYARR 56 (109)
Q Consensus 35 ~~~~see~lE~m~~f~ekyAek 56 (109)
.-.|.++++++.++|.++.++|
T Consensus 128 ~~~p~~~d~~~~~~~gk~l~~~ 149 (150)
T PRK06242 128 KGHPNEKDLENAKEFAENLKKK 149 (150)
T ss_pred CCCcCHHHHHHHHHHHHHHhhc
Confidence 3458889999999999999876
No 78
>TIGR01386 cztS_silS_copS heavy metal sensor kinase. Members of this family contain a sensor histidine kinase domain (Pfam:PF00512) and a domain found in bacterial signal proteins (Pfam:PF00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc.
Probab=25.80 E-value=2.3e+02 Score=22.23 Aligned_cols=47 Identities=11% Similarity=0.056 Sum_probs=35.8
Q ss_pred CHHHHHHHHHHHHHHhhhcCc--------eeccChhhHHHHHHHHHHhHHhhCCC
Q 033909 39 SEKSVEIMRKFSEQYARRSDT--------FFCVDKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~Gy--------~fNPD~evt~~VieGLa~NK~rYG~~ 85 (109)
..+.++++....+..+++.|. .+..|+.....++.-|+.|--+|+..
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~l~~~~~nll~Nai~~~~~ 371 (457)
T TIGR01386 317 LAAELAKVAEYFEPLAEERGVRIRVEGEGLVRGDPQMFRRAISNLLSNALRHTPD 371 (457)
T ss_pred HHHHHHHHHHHHHHHHHhCCeEEEecCCceEEECHHHHHHHHHHHHHHHHHcCCC
Confidence 455566666666777777774 45578888999999999999999843
No 79
>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=25.71 E-value=89 Score=22.46 Aligned_cols=29 Identities=10% Similarity=0.117 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhhhcCceeccChhhHH
Q 033909 41 KSVEIMRKFSEQYARRSDTFFCVDKSVTS 69 (109)
Q Consensus 41 e~lE~m~~f~ekyAek~Gy~fNPD~evt~ 69 (109)
+.++.+.+.+..+++..|..+|+++....
T Consensus 160 ~~~~~~~~~~~~~~~~~gl~in~~Kt~~~ 188 (220)
T cd01650 160 RKLQELLQRLQEWSKESGLKINPSKSKVM 188 (220)
T ss_pred HHHHHHHHHHHHHHHHcCCEEChhheEEE
Confidence 47888888899999999999999987543
No 80
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=25.45 E-value=72 Score=19.34 Aligned_cols=17 Identities=29% Similarity=0.389 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhhhcCce
Q 033909 44 EIMRKFSEQYARRSDTF 60 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~ 60 (109)
.++++-+|+||.+.|+.
T Consensus 18 ~~~r~~~E~~Ar~~G~~ 34 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYD 34 (45)
T ss_dssp HHHHHHHHHHHHHCT-S
T ss_pred HHHHHHHHHHHHHcCCC
Confidence 67899999999999984
No 81
>PRK13590 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional
Probab=25.17 E-value=1.2e+02 Score=26.66 Aligned_cols=25 Identities=12% Similarity=0.223 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCcee
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~f 61 (109)
..++++.+++.+.-+.|-+|+|+.|
T Consensus 97 ~~~~~~~~~l~~lN~~Y~~kFGf~f 121 (591)
T PRK13590 97 HCTPEEFARIQQLNADYNARFGFPF 121 (591)
T ss_pred cCCHHHHHHHHHHHHHHHHhCCCeE
Confidence 4578888999999999999999887
No 82
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=24.81 E-value=1.5e+02 Score=21.69 Aligned_cols=38 Identities=8% Similarity=0.113 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhh
Q 033909 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSL 82 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rY 82 (109)
+++.+.+++++++.|| -|.-+-+-+.+-+.|..++..-
T Consensus 9 ~~ll~~lD~~~~~~g~-~~RSe~ir~~ir~~l~e~~~~~ 46 (129)
T TIGR02793 9 DDLLETLDRLIARRGY-QNRSEAIRDLLRSGLQQEAAEQ 46 (129)
T ss_pred HHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHHHhhhhc
Confidence 3556678999999999 3445555555555777776443
No 83
>PRK06756 flavodoxin; Provisional
Probab=24.47 E-value=1.1e+02 Score=21.32 Aligned_cols=22 Identities=18% Similarity=0.554 Sum_probs=15.2
Q ss_pred cCCCCHHHHHHHHHHHHHHhhh
Q 033909 35 QVEPSEKSVEIMRKFSEQYARR 56 (109)
Q Consensus 35 ~~~~see~lE~m~~f~ekyAek 56 (109)
.-.|++++++++++|.++++++
T Consensus 125 ~~~p~~~d~~~~~~~~~~~~~~ 146 (148)
T PRK06756 125 ELTPEDEDVEKCLQFGAEFVKH 146 (148)
T ss_pred ecCCCHHHHHHHHHHHHHHHHh
Confidence 4456777777777777777654
No 84
>PF14747 DUF4473: Domain of unknown function (DUF4473)
Probab=24.21 E-value=2.2e+02 Score=18.86 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhh
Q 033909 36 VEPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSL 82 (109)
Q Consensus 36 ~~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rY 82 (109)
+-+|++.++.|.++.+++..+..-. ++|.+-...++.-+...-+.|
T Consensus 18 AGmS~~aidgi~~i~~~~~~~~~~~-~~~~e~~~~~~~~~~~e~~~f 63 (82)
T PF14747_consen 18 AGMSEKAIDGIVKIAEKFKSQFAKA-KGNKEAAKKFFEKYKAEVDAF 63 (82)
T ss_pred cCCCHHHHHHHHHHHHHHHhccccc-cCCHHHHHHHHHHHHHHHHHH
Confidence 4589999999999999999887777 999999998888887766654
No 85
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=24.05 E-value=2.2e+02 Score=18.74 Aligned_cols=49 Identities=14% Similarity=0.160 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCC
Q 033909 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CP 88 (109)
.-+.+..++.|+...+++.|+-- .+...+..++.=++.|--+||+.-.+
T Consensus 4 ~~~~i~~~r~~~~~~~~~~~~~~-~~~~~~~lav~E~~~Nav~H~~~~~~ 52 (125)
T PF13581_consen 4 DPEDIREARAFLREFLERLGLPE-EDRDDLELAVSEALTNAVEHGYPGDP 52 (125)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 34688999999999999966531 12334556667778899999998765
No 86
>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=23.41 E-value=1.6e+02 Score=18.05 Aligned_cols=31 Identities=10% Similarity=0.113 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhhhcCceeccChhhHHHHHHHHH
Q 033909 44 EIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLA 76 (109)
Q Consensus 44 E~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa 76 (109)
+.+++++++.|+..|==+| .+++..|.+.|.
T Consensus 13 ~~l~~~lk~~A~~~gRS~N--sEIv~~L~~~l~ 43 (50)
T PF03869_consen 13 EELKEKLKERAEENGRSMN--SEIVQRLEEALK 43 (50)
T ss_dssp HHHHHHHHHHHHHTTS-HH--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCChH--HHHHHHHHHHHh
Confidence 4678889999999987665 345555555444
No 87
>PRK03922 hypothetical protein; Provisional
Probab=23.35 E-value=12 Score=27.58 Aligned_cols=30 Identities=20% Similarity=0.372 Sum_probs=22.6
Q ss_pred HHHhhhcCceecc-ChhhHHHHHHHHHHhHHhhCCCCCC-Cc
Q 033909 51 EQYARRSDTFFCV-DKSVTSVVIKGLADHKDSLGAPLCP-CI 90 (109)
Q Consensus 51 ekyAek~Gy~fNP-D~evt~~VieGLa~NK~rYG~~~CP-CR 90 (109)
.--.-+.|-.||| |.++++. .-|...|| |-
T Consensus 25 ~iAIseaGkrLn~~~l~yVei----------evG~~~cP~cg 56 (113)
T PRK03922 25 GVAISEAGKRLNPEDLDYVEV----------EVGLTICPKCG 56 (113)
T ss_pred HHHHHHHHhhcCcccCCeEEE----------ecCcccCCCCC
Confidence 3345677889999 8887753 56999999 85
No 88
>PF09213 M3: M3; InterPro: IPR015296 This entry represents a group of viral chemokine binding proteins, which bind with CC-chemokine MCP-1, acting as cytokine decoy receptors []. For example, the murine herpesvirus decoy receptor M3 acts as an immune system saboteur by altering host anti-viral inflammatory repsonses. M3 adopts a structure consisting of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds.; PDB: 2NYZ_A 2NZ1_A 1ML0_A 1MKF_B.
Probab=23.01 E-value=25 Score=30.19 Aligned_cols=17 Identities=29% Similarity=0.565 Sum_probs=10.0
Q ss_pred hCCCCCCCccCcchhhh
Q 033909 82 LGAPLCPCIMTTKLLKL 98 (109)
Q Consensus 82 YG~~~CPCRl~~g~re~ 98 (109)
-|.+-||||+..|.-+.
T Consensus 330 ~~~~~CP~~~~~G~~e~ 346 (376)
T PF09213_consen 330 RGDPDCPCHFSLGRDEN 346 (376)
T ss_dssp E--SS-SEEEEE-SSTT
T ss_pred cCCCCCceEEeecCcce
Confidence 37789999999886553
No 89
>PF02383 Syja_N: SacI homology domain; InterPro: IPR002013 Synaptic vesicles are recycled with remarkable speed and precision in nerve terminals. A major recycling pathway involves clathrin-mediated endocytosis at endocytic zones located around sites of release. Different 'accessory' proteins linked to this pathway have been shown to alter the shape and composition of lipid membranes, to modify membrane-coat protein interactions, and to influence actin polymerisation. These include the GTPase dynamin, the lysophosphatidic acid acyl transferase endophilin, and the phosphoinositide phosphatase synaptojanin []. The recessive suppressor of secretory defect in yeast Golgi and yeast actin function belongs to this family. This protein may be involved in the coordination of the activities of the secretory pathway and the actin cytoskeleton. Human synaptojanin which may be localised on coated endocytic intermediates in nerve terminals also belongs to this family.; GO: 0042578 phosphoric ester hydrolase activity; PDB: 3LWT_X.
Probab=22.48 E-value=1.1e+02 Score=24.46 Aligned_cols=41 Identities=5% Similarity=0.158 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhH
Q 033909 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHK 79 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK 79 (109)
.+++.++..+.++++-...|++|+.|-++|..+......+.
T Consensus 62 ~~~~e~~~~~~l~~~l~~~~fYfS~~~DLT~slQ~~~~~~~ 102 (319)
T PF02383_consen 62 QSRDEQRYLSLLKKLLSSGSFYFSYTYDLTNSLQRQFENNS 102 (319)
T ss_dssp --HHHHHHHHHHHHHHHH---EE-SSS-TTS-HHHHHHH-S
T ss_pred cchHHHHHHHHHHHHhcCCCEEEECCCChhHhhcccccccc
Confidence 34667778888999999999999999999999988877654
No 90
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=22.36 E-value=86 Score=19.33 Aligned_cols=36 Identities=22% Similarity=0.234 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHH
Q 033909 39 SEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGL 75 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGL 75 (109)
..+++.+..+..++.+...+. --+++..+..+++||
T Consensus 59 ~~esv~~y~~rf~~l~~~~~~-~~~e~~~v~~f~~GL 94 (96)
T PF03732_consen 59 GNESVREYVNRFRELARRAPP-PMDEEMLVERFIRGL 94 (96)
T ss_pred cCCcHHHHHHHHHHHHHHCCC-CcCHHHHHHHHHHCC
Confidence 567777777778888888887 556677788888887
No 91
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=22.35 E-value=2.8e+02 Score=20.07 Aligned_cols=50 Identities=10% Similarity=0.123 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHhhhcCceeccCh--hhHHHHHHHHHHhHHhhCCCCCCCc
Q 033909 40 EKSVEIMRKFSEQYARRSDTFFCVDK--SVTSVVIKGLADHKDSLGAPLCPCI 90 (109)
Q Consensus 40 ee~lE~m~~f~ekyAek~Gy~fNPD~--evt~~VieGLa~NK~rYG~~~CPCR 90 (109)
..++++.-.|+.+|.+++|- ++.++ .|.+.|...|..+-.-+=||-.|++
T Consensus 2 ~~EI~~av~Fl~~~l~~~~~-l~~~~v~~F~~~L~~~L~~~y~~HWyP~~P~k 53 (108)
T smart00099 2 KLEIAAAVNFITSLLRKHNK-LSKRRVEIFAEKLTRLLKEKYKNHWYPEKPYK 53 (108)
T ss_pred hHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Confidence 35788999999999999985 55442 4667788888999898889999998
No 92
>PRK13697 cytochrome c6; Provisional
Probab=22.04 E-value=1.1e+02 Score=20.34 Aligned_cols=23 Identities=13% Similarity=0.024 Sum_probs=17.8
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCce
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTF 60 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~ 60 (109)
..++++++.+-.|+.+.+ ++||.
T Consensus 89 ~ls~~di~~l~~Yi~~~~-~~~~~ 111 (111)
T PRK13697 89 RLSPDQIEDVAAYVLEQA-EKGWK 111 (111)
T ss_pred CCCHHHHHHHHHHHHHHH-HccCC
Confidence 368999999999999954 45563
No 93
>PF09349 OHCU_decarbox: OHCU decarboxylase; InterPro: IPR018020 The proteins in this entry are OHCU decarboxylase, an enzyme of the purine catabolism that catalyses the conversion of OHCU into S(+)-allantoin []; it is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (IPR002042 from INTERPRO) and step two is catalysed by hydroxyisourate hydrolase (IPR000895 from INTERPRO). ; PDB: 3O7I_B 3O7H_B 3O7J_A 3O7K_A 2Q37_A 2O70_B 2O73_C 2O74_C 2O8I_A.
Probab=21.59 E-value=92 Score=22.98 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCcee
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFF 61 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~f 61 (109)
..+++.++++.+.-+.|-+|.||.|
T Consensus 90 ~~~~~~~~~L~~lN~~Y~~kFGf~F 114 (159)
T PF09349_consen 90 SLDEEELAELAALNQAYEEKFGFPF 114 (159)
T ss_dssp STHHHHHHHHHHHHHHHHHHHSS--
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCce
Confidence 4678899999999999999999876
No 94
>cd01586 AcnA_IRP Aconitase A catalytic domain. Aconitase A catalytic domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydrolyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes.
Probab=21.43 E-value=25 Score=30.64 Aligned_cols=42 Identities=10% Similarity=0.082 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHhHHhhCCCCCCCccCcchhhhhhhcCceecC
Q 033909 67 VTSVVIKGLADHKDSLGAPLCPCIMTTKLLKLSRASGIVHVF 108 (109)
Q Consensus 67 vt~~VieGLa~NK~rYG~~~CPCRl~~g~re~dr~~~~~~~~ 108 (109)
+-..+++-|-+|.++|+...==|+.+.+-+-.+.-.||+|+.
T Consensus 58 ~~~~~~~~~~~N~e~~~~~~~~~~~~~~~~~~~pg~GI~Hqv 99 (404)
T cd01586 58 LAKNMKLEFERNRERYEFLKWGQKAFKNLRVVPPGTGIIHQV 99 (404)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHhCCCCCCCCCCCEeeee
Confidence 346788888899999988766666665455555667999974
No 95
>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cle
Probab=21.07 E-value=34 Score=25.98 Aligned_cols=20 Identities=15% Similarity=0.195 Sum_probs=16.9
Q ss_pred CHHHHHHHHHHHHHHhhhcC
Q 033909 39 SEKSVEIMRKFSEQYARRSD 58 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~G 58 (109)
.++....+..+++.+|+++|
T Consensus 113 ~~ki~~~~~~~~r~~A~~~G 132 (172)
T cd07015 113 PPKITNYFIAYIKSLAQESG 132 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHC
Confidence 45777788889999999998
No 96
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=21.00 E-value=40 Score=19.99 Aligned_cols=16 Identities=19% Similarity=0.162 Sum_probs=12.4
Q ss_pred HHHHhhhcCceeccCh
Q 033909 50 SEQYARRSDTFFCVDK 65 (109)
Q Consensus 50 ~ekyAek~Gy~fNPD~ 65 (109)
+-++|...||.|.+++
T Consensus 32 ~~~lA~~~Gy~ft~~e 47 (49)
T PF07862_consen 32 VVALAREAGYDFTEEE 47 (49)
T ss_pred HHHHHHHcCCCCCHHH
Confidence 3467899999998753
No 97
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=20.97 E-value=1.6e+02 Score=18.94 Aligned_cols=38 Identities=5% Similarity=0.027 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHHhhhcCc-eeccChhhHHHHHHHHHHhHH
Q 033909 39 SEKSVEIMRKFSEQYARRSDT-FFCVDKSVTSVVIKGLADHKD 80 (109)
Q Consensus 39 see~lE~m~~f~ekyAek~Gy-~fNPD~evt~~VieGLa~NK~ 80 (109)
+.+.+++ ++.++++.|| .-.||.+..+.+..-|-..+.
T Consensus 9 t~~Q~~~----Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~ 47 (58)
T TIGR01565 9 TAEQKEK----MRDFAEKLGWKLKDKRREEVREFCEEIGVTRK 47 (58)
T ss_pred CHHHHHH----HHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHH
Confidence 4555555 5667788999 455888877777665544433
No 98
>PF02786 CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain; InterPro: IPR005479 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the ATP-binding domain found in the large subunit of carbamoyl phosphate synthase, as well as in related proteins.; GO: 0003824 catalytic activity, 0005524 ATP binding, 0008152 metabolic process; PDB: 3U9S_A 3U9T_A 2C00_B 2VQD_A 1W96_B 1W93_A 1M6V_C 1CS0_C 1C30_E 1C3O_G ....
Probab=20.95 E-value=1.7e+02 Score=22.57 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=22.5
Q ss_pred eeccCCCCHHHHHHHHHHHHHHhhhcCce
Q 033909 32 IRAQVEPSEKSVEIMRKFSEQYARRSDTF 60 (109)
Q Consensus 32 ~~~~~~~see~lE~m~~f~ekyAek~Gy~ 60 (109)
+-|....+++..++|++.+.++|+..||.
T Consensus 127 ~~P~~~L~~~~~~~l~~~a~~ia~~l~~~ 155 (211)
T PF02786_consen 127 EAPAQTLSDEERQKLREAAKKIARALGYV 155 (211)
T ss_dssp EES-SSS-HHHHHHHHHHHHHHHHHTT-E
T ss_pred EeeccccchHHHHHHHHHHHHHHHhhCee
Confidence 34445689999999999999999999984
No 99
>TIGR02309 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence above trusted although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241).
Probab=20.92 E-value=2.4e+02 Score=24.58 Aligned_cols=51 Identities=10% Similarity=0.094 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCCCCC
Q 033909 37 EPSEKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAPLCP 88 (109)
Q Consensus 37 ~~see~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~~CP 88 (109)
.-+.+++.+-++.++..++.+|-.+---.+.+..++.++..+.+-|++ ++|
T Consensus 73 p~s~edL~~r~~~~~~~~~~~~g~~gR~pD~~n~~~~~~~~~~~~~~~-~~~ 123 (477)
T TIGR02309 73 PKTKEDLKRRGEAYKLWADQNLGMMGRSPDYLNAVVMAYAASADYFGK-SNS 123 (477)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCeeecChHHHHHHHHHHHhhHHHHhh-cCc
Confidence 357788889999999999999888887799999999999999977763 444
No 100
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=20.78 E-value=1.3e+02 Score=18.96 Aligned_cols=26 Identities=12% Similarity=0.153 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHhhhcCceeccChhh
Q 033909 42 SVEIMRKFSEQYARRSDTFFCVDKSV 67 (109)
Q Consensus 42 ~lE~m~~f~ekyAek~Gy~fNPD~ev 67 (109)
+.+...+-+....++.|..+|+++..
T Consensus 58 ~~~~~~~~l~~~l~~~gl~ln~~Kt~ 83 (98)
T cd00304 58 QQAVKKRELEEFLARLGLNLSDEKTQ 83 (98)
T ss_pred HHHHHHHHHHHHHHHcCcEEChheeE
Confidence 56666666777778899999998864
No 101
>cd02892 SQCY_1 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds. This group contains bacterial SQCY which catalyzes the convertion of squalene to hopene or diplopterol and eukaryotic OSQCY which transforms the 2,3-epoxide of squalene to compounds such as, lanosterol in mammals and fungi or, cycloartenol in plants. Deletion of a single glycine residue of Alicyclobacillus acidocaldarius SQCY alters its substrate specificity into that of eukaryotic OSQCY. Both enzymes have a second minor domain, which forms an alpha-alpha barrel that is inserted into the major domain.
Probab=20.76 E-value=1.6e+02 Score=26.11 Aligned_cols=43 Identities=14% Similarity=0.154 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHHHh---------------hhcCceec------cChhhHHHHHHHHHHhHH
Q 033909 38 PSEKSVEIMRKFSEQYA---------------RRSDTFFC------VDKSVTSVVIKGLADHKD 80 (109)
Q Consensus 38 ~see~lE~m~~f~ekyA---------------ek~Gy~fN------PD~evt~~VieGLa~NK~ 80 (109)
..++.+++..+|+.+-+ .+.||-|. ||.+.|..+++.|+....
T Consensus 326 ~~~~~l~ka~~wL~~~Q~~~~~gdw~~~~~~~~~GGW~fs~~~~~~pd~d~Ta~~l~AL~~~~~ 389 (634)
T cd02892 326 EFDPALKKALDWLLESQILDNPGDWKVKYRHLRKGGWAFSTANQGYPDSDDTAEALKALLRLQE 389 (634)
T ss_pred cchHHHHHHHHHHHHHHcCCCCCchhhhCCCCCCCCCCCCCCCCCCCCcCchHHHHHHHHHhhc
Confidence 56778999999998776 36688775 899999999999987653
No 102
>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=20.74 E-value=2.2e+02 Score=23.31 Aligned_cols=16 Identities=13% Similarity=0.320 Sum_probs=11.3
Q ss_pred eccCCCCHHHHHHHHH
Q 033909 33 RAQVEPSEKSVEIMRK 48 (109)
Q Consensus 33 ~~~~~~see~lE~m~~ 48 (109)
.-..+|++|+++++++
T Consensus 254 ~~~~~Pt~e~Vd~~H~ 269 (297)
T PF03982_consen 254 PKIENPTQEDVDKLHA 269 (297)
T ss_pred cCCCCcCHHHHHHHHH
Confidence 3456799998887654
No 103
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=20.45 E-value=2.5e+02 Score=18.00 Aligned_cols=46 Identities=17% Similarity=0.061 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHhhhcCceeccChhhHHHHHHHHHHhHHhhCCC
Q 033909 40 EKSVEIMRKFSEQYARRSDTFFCVDKSVTSVVIKGLADHKDSLGAP 85 (109)
Q Consensus 40 ee~lE~m~~f~ekyAek~Gy~fNPD~evt~~VieGLa~NK~rYG~~ 85 (109)
++-++..+.++.+++.+....-.--++++..+..+|..+-+.|...
T Consensus 4 ~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~ 49 (158)
T TIGR02937 4 EELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE 49 (158)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc
Confidence 4455666667777777632222223467777777777777777655
Done!