Query psy2945
Match_columns 134
No_of_seqs 112 out of 231
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 21:36:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2945.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2945hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00924 Cyt_c_Oxidase_Vb Cytoc 100.0 3.2E-49 6.9E-54 284.2 10.2 95 39-134 2-97 (97)
2 PF01215 COX5B: Cytochrome c o 100.0 1.5E-49 3.2E-54 300.7 7.2 98 35-133 30-129 (136)
3 KOG3352|consensus 100.0 5.8E-48 1.3E-52 295.7 10.0 97 37-134 54-151 (153)
4 PLN02294 cytochrome c oxidase 100.0 5.5E-47 1.2E-51 295.5 10.7 94 39-133 62-158 (174)
5 PTZ00043 cytochrome c oxidase 100.0 7.1E-29 1.5E-33 201.9 7.3 87 43-130 105-195 (268)
6 KOG3456|consensus 96.8 0.0034 7.3E-08 46.8 5.7 40 89-128 74-116 (120)
7 PF10276 zf-CHCC: Zinc-finger 96.3 0.0068 1.5E-07 37.4 3.6 36 92-127 1-40 (40)
8 COG4391 Uncharacterized protei 84.5 1.7 3.7E-05 29.3 3.6 44 84-129 15-61 (62)
9 COG4647 AcxC Acetone carboxyla 65.9 2.8 6.1E-05 32.6 0.9 33 79-127 46-80 (165)
10 COG1326 Uncharacterized archae 65.7 2.5 5.3E-05 34.5 0.5 28 101-131 15-47 (201)
11 KOG3507|consensus 65.3 2.7 5.8E-05 28.3 0.6 15 111-125 31-46 (62)
12 PF04216 FdhE: Protein involve 63.5 4.3 9.4E-05 33.5 1.6 30 101-130 218-252 (290)
13 smart00834 CxxC_CXXC_SSSS Puta 62.3 6.6 0.00014 22.7 1.8 13 118-130 6-19 (41)
14 PF06397 Desulfoferrod_N: Desu 60.4 6.3 0.00014 23.8 1.5 19 114-132 3-22 (36)
15 PF13912 zf-C2H2_6: C2H2-type 60.3 5 0.00011 21.3 1.0 11 117-127 1-12 (27)
16 PF03604 DNA_RNApol_7kD: DNA d 56.8 5.1 0.00011 23.4 0.7 16 112-127 12-28 (32)
17 PF09723 Zn-ribbon_8: Zinc rib 56.6 11 0.00024 22.7 2.2 12 118-129 6-18 (42)
18 PF10571 UPF0547: Uncharacteri 56.0 3.5 7.5E-05 23.0 -0.1 11 117-127 14-25 (26)
19 PF08882 Acetone_carb_G: Aceto 55.9 11 0.00024 28.2 2.4 19 108-126 15-33 (112)
20 COG5189 SFP1 Putative transcri 54.6 5.6 0.00012 35.1 0.8 16 112-127 393-409 (423)
21 PF13465 zf-H2C2_2: Zinc-finge 52.4 9.9 0.00021 20.5 1.3 15 113-127 9-25 (26)
22 TIGR02605 CxxC_CxxC_SSSS putat 52.0 12 0.00027 22.9 1.9 12 118-129 6-18 (52)
23 PF13719 zinc_ribbon_5: zinc-r 51.9 10 0.00022 22.3 1.4 14 114-127 22-36 (37)
24 smart00659 RPOLCX RNA polymera 51.0 9.4 0.0002 23.6 1.2 15 111-125 13-28 (44)
25 PF12172 DUF35_N: Rubredoxin-l 50.9 7.9 0.00017 22.5 0.8 13 114-126 6-21 (37)
26 PF05191 ADK_lid: Adenylate ki 43.4 5.6 0.00012 23.7 -0.6 15 119-133 3-18 (36)
27 PRK03564 formate dehydrogenase 42.4 22 0.00048 30.5 2.6 29 103-131 234-267 (309)
28 PHA00616 hypothetical protein 42.1 5.3 0.00011 25.1 -0.9 11 117-127 1-12 (44)
29 COG3357 Predicted transcriptio 40.0 11 0.00023 27.5 0.2 17 48-64 14-30 (97)
30 PF00096 zf-C2H2: Zinc finger, 36.2 20 0.00043 18.1 0.9 10 118-127 1-11 (23)
31 TIGR00319 desulf_FeS4 desulfof 32.8 47 0.001 18.8 2.2 17 115-131 5-22 (34)
32 PF13717 zinc_ribbon_4: zinc-r 32.8 27 0.00058 20.5 1.1 14 114-127 22-36 (36)
33 TIGR02443 conserved hypothetic 32.5 48 0.001 22.1 2.4 34 95-128 7-43 (59)
34 smart00440 ZnF_C2C2 C2C2 Zinc 32.4 66 0.0014 19.2 2.9 24 104-127 8-39 (40)
35 PF10763 DUF2584: Protein of u 31.1 33 0.00072 24.2 1.6 26 106-132 6-31 (80)
36 PF09631 Sen15: Sen15 protein; 30.8 53 0.0011 23.1 2.6 23 92-115 72-94 (101)
37 PRK00398 rpoP DNA-directed RNA 30.6 65 0.0014 19.4 2.7 17 117-133 21-38 (46)
38 TIGR01562 FdhE formate dehydro 30.5 34 0.00074 29.3 1.8 28 104-131 233-267 (305)
39 COG1545 Predicted nucleic-acid 29.4 27 0.00058 26.3 0.9 9 118-126 30-39 (140)
40 PF05443 ROS_MUCR: ROS/MUCR tr 28.7 19 0.00041 27.3 0.0 11 118-128 73-84 (132)
41 cd00974 DSRD Desulforedoxin (D 28.6 65 0.0014 18.3 2.3 16 116-131 3-19 (34)
42 PF13894 zf-C2H2_4: C2H2-type 26.7 39 0.00085 16.4 1.0 9 119-127 2-11 (24)
43 TIGR02098 MJ0042_CXXC MJ0042 f 26.6 44 0.00095 19.1 1.3 12 118-129 3-15 (38)
44 PF14392 zf-CCHC_4: Zinc knuck 25.7 61 0.0013 19.9 2.0 21 106-126 19-41 (49)
45 PF09526 DUF2387: Probable met 25.3 1E+02 0.0022 20.9 3.2 37 95-131 6-45 (71)
46 TIGR01206 lysW lysine biosynth 25.0 79 0.0017 20.5 2.4 20 115-134 20-40 (54)
47 PF13451 zf-trcl: Probable zin 24.3 57 0.0012 20.9 1.6 14 115-128 2-16 (49)
48 PF11781 RRN7: RNA polymerase 23.2 48 0.001 19.6 1.1 16 109-125 18-34 (36)
49 PRK03824 hypA hydrogenase nick 23.0 70 0.0015 23.9 2.2 8 118-125 108-116 (135)
50 PF10083 DUF2321: Uncharacteri 22.9 36 0.00078 26.8 0.6 12 115-126 66-78 (158)
51 COG5188 PRP9 Splicing factor 3 22.9 18 0.0004 32.3 -1.1 27 99-125 354-383 (470)
52 COG1644 RPB10 DNA-directed RNA 22.9 38 0.00083 22.9 0.7 9 117-125 4-13 (63)
53 PRK00564 hypA hydrogenase nick 22.1 52 0.0011 24.0 1.3 8 118-125 89-97 (117)
54 PF05511 ATP-synt_F6: Mitochon 21.9 76 0.0017 23.1 2.1 15 22-36 17-31 (99)
55 PF04648 MF_alpha: Yeast matin 21.7 45 0.00097 16.0 0.6 11 108-118 2-12 (13)
56 PRK12380 hydrogenase nickel in 21.7 51 0.0011 23.9 1.2 20 110-129 62-83 (113)
57 PF00301 Rubredoxin: Rubredoxi 21.5 55 0.0012 20.5 1.1 10 118-127 2-12 (47)
58 PF07710 P53_tetramer: P53 tet 21.5 74 0.0016 19.8 1.7 15 49-63 14-28 (42)
59 COG1594 RPB9 DNA-directed RNA 21.3 1.1E+02 0.0025 22.2 3.0 26 102-127 78-111 (113)
60 PHA02768 hypothetical protein; 20.9 39 0.00086 22.1 0.4 11 118-128 6-17 (55)
61 PF02748 PyrI_C: Aspartate car 20.8 1.6E+02 0.0034 18.8 3.2 21 108-128 24-47 (52)
62 cd00350 rubredoxin_like Rubred 20.8 54 0.0012 18.6 0.9 11 118-128 2-13 (33)
63 PF03966 Trm112p: Trm112p-like 20.7 59 0.0013 21.2 1.2 12 118-129 54-66 (68)
No 1
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=100.00 E-value=3.2e-49 Score=284.23 Aligned_cols=95 Identities=57% Similarity=0.994 Sum_probs=91.8
Q ss_pred CCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCCce
Q psy2945 39 DLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPK 118 (134)
Q Consensus 39 ~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~p~ 118 (134)
+.|+||||+||||||||+||+++++|+ |+|||+|+++++||++|||+|||++++|||||+|++|+|+|+||||++|+|+
T Consensus 2 ~~g~vp~d~e~aTGlEr~ELl~~~~G~-d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~h~v~W~~l~~g~~~ 80 (97)
T cd00924 2 AEGEVPTDLEQATGLERKELLAKLEGI-DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDSHDVIWMWLEKGKPK 80 (97)
T ss_pred CCcccCCchHhhhccHHHHHHHHHcCC-ccccccccccCCCCccCCeEecCCCCCeEEeeeCCCCCceEEEEEEeCCCce
Confidence 578999999999999999999999999 7799999999999999999999999999999999888999999999999999
Q ss_pred ee-eCCCEEEEEEeCCC
Q psy2945 119 RC-MCGHWFKLVYKAPI 134 (134)
Q Consensus 119 RC-eCG~~FkL~~~~p~ 134 (134)
|| +|||||||++++|.
T Consensus 81 rC~eCG~~fkL~~v~~~ 97 (97)
T cd00924 81 RCPECGHVFKLVDVGPP 97 (97)
T ss_pred eCCCCCcEEEEEECCCC
Confidence 99 89999999999985
No 2
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=100.00 E-value=1.5e-49 Score=300.71 Aligned_cols=98 Identities=48% Similarity=0.871 Sum_probs=69.7
Q ss_pred ccCCCCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeC-CCCCCcceEEEee
Q psy2945 35 WNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC-EEESPSINWMWLY 113 (134)
Q Consensus 35 ~~~~~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g-~~dsh~v~W~~l~ 113 (134)
.++++.|+||||+||||||||+|||++++|+ |||||+|++.++||+||||||||++++|||||+| +.|+|+|+||||+
T Consensus 30 ~~~a~~G~vptd~eqATGlER~Ella~~~G~-D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~sH~v~W~~l~ 108 (136)
T PF01215_consen 30 GPGAKPGTVPTDLEQATGLEREELLAKLEGI-DPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEPDDSHDVIWFWLH 108 (136)
T ss_dssp -------BS--HHHH--HHHHHHHHHHHTT---TT--S--B----SSSS-CEEEESSSCEEEEESSSTT-SSS-EEEEEE
T ss_pred cccccCCCCCChhHhhhHHHHHHHHHHhcCc-CcccccCccCCCCCccCCeEccCCCCceEEeeccCCCCcceeEEEEEe
Confidence 3456789999999999999999999999998 9999999999999999999999999999999999 6678899999999
Q ss_pred cCCceee-eCCCEEEEEEeCC
Q psy2945 114 EGKPKRC-MCGHWFKLVYKAP 133 (134)
Q Consensus 114 ~g~p~RC-eCG~~FkL~~~~p 133 (134)
+|+|+|| +||+||||+++|+
T Consensus 109 ~g~~~RCpeCG~~fkL~~vg~ 129 (136)
T PF01215_consen 109 KGKPQRCPECGQVFKLKYVGP 129 (136)
T ss_dssp TTSEEEETTTEEEEEEEE---
T ss_pred CCCccCCCCCCeEEEEEEcCC
Confidence 9999999 9999999999987
No 3
>KOG3352|consensus
Probab=100.00 E-value=5.8e-48 Score=295.71 Aligned_cols=97 Identities=53% Similarity=0.986 Sum_probs=92.8
Q ss_pred CCCCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCC
Q psy2945 37 KNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGK 116 (134)
Q Consensus 37 ~~~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~ 116 (134)
..+.|.||||+|||||+||+|||++++|+ ||||++.+++++|||+|||||||++|+|||||.|++|+|+|+||||+||+
T Consensus 54 ~~~~g~vpddle~aTGlEk~eLla~l~G~-d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~~~V~Wmwl~Kge 132 (153)
T KOG3352|consen 54 MAKGGGVPDDLEQATGLEKEELLAELEGR-DPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDSHAVVWMWLEKGE 132 (153)
T ss_pred cccCCCCCCchhhhhhHHHHHHHHHhhCC-CccccccccCCCCcccCCccccccCCceEEeecccCCCcceEEEEEEcCC
Confidence 34678999999999999999999999999 89999977789999999999999999999999999999999999999999
Q ss_pred ceee-eCCCEEEEEEeCCC
Q psy2945 117 PKRC-MCGHWFKLVYKAPI 134 (134)
Q Consensus 117 p~RC-eCG~~FkL~~~~p~ 134 (134)
.+|| ||||||||+.+||+
T Consensus 133 ~~rc~eCG~~fkL~~v~~~ 151 (153)
T KOG3352|consen 133 TQRCPECGHYFKLVPVGPV 151 (153)
T ss_pred cccCCcccceEEeeecCCC
Confidence 9998 99999999999985
No 4
>PLN02294 cytochrome c oxidase subunit Vb
Probab=100.00 E-value=5.5e-47 Score=295.45 Aligned_cols=94 Identities=35% Similarity=0.686 Sum_probs=91.4
Q ss_pred CCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeC--CCCCCcceEEEeecCC
Q psy2945 39 DLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC--EEESPSINWMWLYEGK 116 (134)
Q Consensus 39 ~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l~~g~ 116 (134)
.+++|+|+++|||||||+|||++++|+ |||||++++.++|||||||+|||++++|||||+| ++|+|+|+||||++|+
T Consensus 62 ~~~~~~d~~~~ATGLER~ELla~leG~-D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGk 140 (174)
T PLN02294 62 VKKRVEDVMPIATGHEREELEAELEGR-KLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGK 140 (174)
T ss_pred ccccCCCchhhccchHHHHHHHHHcCC-CccccccccCCCCCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCC
Confidence 467899999999999999999999999 9999999988999999999999999999999999 7999999999999999
Q ss_pred ceee-eCCCEEEEEEeCC
Q psy2945 117 PKRC-MCGHWFKLVYKAP 133 (134)
Q Consensus 117 p~RC-eCG~~FkL~~~~p 133 (134)
|+|| +||+||||+++||
T Consensus 141 p~RCpeCG~~fkL~~vG~ 158 (174)
T PLN02294 141 SFECPVCTQYFELEVVGP 158 (174)
T ss_pred ceeCCCCCCEEEEEEeCC
Confidence 9999 9999999999998
No 5
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=99.95 E-value=7.1e-29 Score=201.93 Aligned_cols=87 Identities=26% Similarity=0.346 Sum_probs=80.0
Q ss_pred CCCccc-ccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeC--CCCCCcceEEEeecCCcee
Q psy2945 43 LPDPLD-LATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC--EEESPSINWMWLYEGKPKR 119 (134)
Q Consensus 43 vptd~e-qATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l~~g~p~R 119 (134)
+..|+. |...-+.+.|+|.++|. +.+..+++.+++||+|||+||||++++|||||+| ++|+|+|+|||+++|+++|
T Consensus 105 la~d~gmqi~~~~~~hm~~~le~y-~~Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~EDeH~VvWFwLrEGkpqR 183 (268)
T PTZ00043 105 LARDMGMQIVNEPSEHMLGLLELY-EYLKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYR 183 (268)
T ss_pred HHHHhCceecCCchHHHHHHHHHH-HhcCcCCCCCCCCCccCCeEeccCCCceEEeccCCCccCCceeEEEEecCCCCcc
Confidence 333454 67777889999999998 9999999999999999999999999999999999 7889999999999999999
Q ss_pred e-eCCCEEEEEE
Q psy2945 120 C-MCGHWFKLVY 130 (134)
Q Consensus 120 C-eCG~~FkL~~ 130 (134)
| +||+||||++
T Consensus 184 CpECGqVFKLVr 195 (268)
T PTZ00043 184 CGECDQIFMLVR 195 (268)
T ss_pred CCCCCcEEEEEE
Confidence 9 9999999998
No 6
>KOG3456|consensus
Probab=96.83 E-value=0.0034 Score=46.80 Aligned_cols=40 Identities=23% Similarity=0.410 Sum_probs=35.2
Q ss_pred CCCCCeEEeeeC--CCCCCcceEEEeecCCceee-eCCCEEEE
Q psy2945 89 SAFEARIVGCIC--EEESPSINWMWLYEGKPKRC-MCGHWFKL 128 (134)
Q Consensus 89 S~~~~RiVGC~g--~~dsh~v~W~~l~~g~p~RC-eCG~~FkL 128 (134)
+.-++|||-|-| ++=-|-..|+.|.+..++-| -||.-|.-
T Consensus 74 ~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 74 IEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFVQ 116 (120)
T ss_pred hhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhhh
Confidence 455999999999 68889999999999989999 99987753
No 7
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=96.28 E-value=0.0068 Score=37.43 Aligned_cols=36 Identities=22% Similarity=0.425 Sum_probs=29.5
Q ss_pred CCeEEeeeC--CCCCCcceEEEeec-CCceee-eCCCEEE
Q psy2945 92 EARIVGCIC--EEESPSINWMWLYE-GKPKRC-MCGHWFK 127 (134)
Q Consensus 92 ~~RiVGC~g--~~dsh~v~W~~l~~-g~p~RC-eCG~~Fk 127 (134)
+.|+|-|-| .+-.|-.+|+.|.+ +++..| -||.-|+
T Consensus 1 ~~~~v~CdG~~~~lgHPrVyl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 1 DGRRVSCDGGGGALGHPRVYLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp -SSEEEEEESSTTSCCCCEEEE-TTTTCEEEETTTTEEEE
T ss_pred CCcEEEeCCCCCCCCCCeEEEecCCCCCeEECCCCCCEEC
Confidence 468999998 46788899999998 478999 9999885
No 8
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.50 E-value=1.7 Score=29.34 Aligned_cols=44 Identities=9% Similarity=0.142 Sum_probs=32.4
Q ss_pred CeeeeCCCCCeEEeeeC--CCCCCcceEEEeecCCceee-eCCCEEEEE
Q psy2945 84 PTEVPSAFEARIVGCIC--EEESPSINWMWLYEGKPKRC-MCGHWFKLV 129 (134)
Q Consensus 84 P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l~~g~p~RC-eCG~~FkL~ 129 (134)
++.|.+.+ --+-|.| ++-+|-=+|+-+.+..-.-| -||..|+|.
T Consensus 15 ~~~I~~~~--~~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 15 HETIEIGD--LPLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred ceEEEeCC--eeEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEEEec
Confidence 44454432 2367988 57888889999966556899 999999985
No 9
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=65.88 E-value=2.8 Score=32.57 Aligned_cols=33 Identities=24% Similarity=0.435 Sum_probs=21.3
Q ss_pred CCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEee--cCCceeeeCCCEEE
Q psy2945 79 GTKTQPTEVPSAFEARIVGCICEEESPSINWMWLY--EGKPKRCMCGHWFK 127 (134)
Q Consensus 79 GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~--~g~p~RCeCG~~Fk 127 (134)
=..+|||+.|-.. ++ |.+. +++..||+|||-|-
T Consensus 46 v~~~dpillpvg~--hl--------------fi~qs~~~rv~rcecghsf~ 80 (165)
T COG4647 46 VDWDDPILLPVGD--HL--------------FICQSAQKRVIRCECGHSFG 80 (165)
T ss_pred cccCCCeeeecCC--cE--------------EEEecccccEEEEecccccc
Confidence 3567899988432 12 3333 34579999999883
No 10
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=65.71 E-value=2.5 Score=34.45 Aligned_cols=28 Identities=29% Similarity=0.393 Sum_probs=17.5
Q ss_pred CCCCCcceEEEeecCC--ceee-eCCCEE--EEEEe
Q psy2945 101 EEESPSINWMWLYEGK--PKRC-MCGHWF--KLVYK 131 (134)
Q Consensus 101 ~~dsh~v~W~~l~~g~--p~RC-eCG~~F--kL~~~ 131 (134)
++-+|.++=. +|. .-|| +||++| .++..
T Consensus 15 eev~hEVik~---~g~~~lvrC~eCG~V~~~~i~~~ 47 (201)
T COG1326 15 EEVSHEVIKE---RGREPLVRCEECGTVHPAIIKTP 47 (201)
T ss_pred chhhHHHHHh---cCCceEEEccCCCcEeeceeecc
Confidence 3445665322 344 5999 999999 55443
No 11
>KOG3507|consensus
Probab=65.32 E-value=2.7 Score=28.30 Aligned_cols=15 Identities=40% Similarity=0.678 Sum_probs=12.9
Q ss_pred EeecCCceee-eCCCE
Q psy2945 111 WLYEGKPKRC-MCGHW 125 (134)
Q Consensus 111 ~l~~g~p~RC-eCG~~ 125 (134)
.|+.|.+-|| |||+-
T Consensus 31 ~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 31 TLKRGDVIRCRECGYR 46 (62)
T ss_pred cccCCCcEehhhcchH
Confidence 3889999999 99973
No 12
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=63.52 E-value=4.3 Score=33.52 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=15.5
Q ss_pred CCCCCcceEEEeecCC----ceee-eCCCEEEEEE
Q psy2945 101 EEESPSINWMWLYEGK----PKRC-MCGHWFKLVY 130 (134)
Q Consensus 101 ~~dsh~v~W~~l~~g~----p~RC-eCG~~FkL~~ 130 (134)
+.+++.-+|+.-.+|+ ...| .|++|+|.++
T Consensus 218 g~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 218 GNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp ---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 4666666666423333 3789 8999999987
No 13
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=62.32 E-value=6.6 Score=22.69 Aligned_cols=13 Identities=46% Similarity=1.071 Sum_probs=10.6
Q ss_pred eee-eCCCEEEEEE
Q psy2945 118 KRC-MCGHWFKLVY 130 (134)
Q Consensus 118 ~RC-eCG~~FkL~~ 130 (134)
.+| +||+.|.+..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (41)
T smart00834 6 YRCEDCGHTFEVLQ 19 (41)
T ss_pred EEcCCCCCEEEEEE
Confidence 589 9999998654
No 14
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=60.45 E-value=6.3 Score=23.76 Aligned_cols=19 Identities=26% Similarity=0.681 Sum_probs=11.4
Q ss_pred cCCceee-eCCCEEEEEEeC
Q psy2945 114 EGKPKRC-MCGHWFKLVYKA 132 (134)
Q Consensus 114 ~g~p~RC-eCG~~FkL~~~~ 132 (134)
+++-.+| .||+...+...|
T Consensus 3 ~~~~YkC~~CGniVev~~~g 22 (36)
T PF06397_consen 3 KGEFYKCEHCGNIVEVVHDG 22 (36)
T ss_dssp TTEEEE-TTT--EEEEEE--
T ss_pred cccEEEccCCCCEEEEEECC
Confidence 4667899 999999887765
No 15
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=60.31 E-value=5 Score=21.25 Aligned_cols=11 Identities=45% Similarity=1.105 Sum_probs=9.2
Q ss_pred ceee-eCCCEEE
Q psy2945 117 PKRC-MCGHWFK 127 (134)
Q Consensus 117 p~RC-eCG~~Fk 127 (134)
|.+| .|+..|.
T Consensus 1 ~~~C~~C~~~F~ 12 (27)
T PF13912_consen 1 PFECDECGKTFS 12 (27)
T ss_dssp SEEETTTTEEES
T ss_pred CCCCCccCCccC
Confidence 5789 9999984
No 16
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=56.80 E-value=5.1 Score=23.42 Aligned_cols=16 Identities=50% Similarity=1.032 Sum_probs=11.9
Q ss_pred eecCCceee-eCCCEEE
Q psy2945 112 LYEGKPKRC-MCGHWFK 127 (134)
Q Consensus 112 l~~g~p~RC-eCG~~Fk 127 (134)
+..+.+-|| +||+.-.
T Consensus 12 ~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRIL 28 (32)
T ss_dssp BSTSSTSSBSSSS-SEE
T ss_pred cCCCCcEECCcCCCeEE
Confidence 677888999 9998543
No 17
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=56.63 E-value=11 Score=22.74 Aligned_cols=12 Identities=50% Similarity=1.212 Sum_probs=10.1
Q ss_pred eee-eCCCEEEEE
Q psy2945 118 KRC-MCGHWFKLV 129 (134)
Q Consensus 118 ~RC-eCG~~FkL~ 129 (134)
.+| +||+.|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 689 999999864
No 18
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=56.03 E-value=3.5 Score=23.03 Aligned_cols=11 Identities=45% Similarity=0.890 Sum_probs=9.1
Q ss_pred ceee-eCCCEEE
Q psy2945 117 PKRC-MCGHWFK 127 (134)
Q Consensus 117 p~RC-eCG~~Fk 127 (134)
.+.| .||+.|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 4789 8999885
No 19
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=55.92 E-value=11 Score=28.16 Aligned_cols=19 Identities=37% Similarity=0.814 Sum_probs=14.4
Q ss_pred eEEEeecCCceeeeCCCEE
Q psy2945 108 NWMWLYEGKPKRCMCGHWF 126 (134)
Q Consensus 108 ~W~~l~~g~p~RCeCG~~F 126 (134)
.|..-.+++.-+|+|||.|
T Consensus 15 l~i~~~~~k~vkc~CGh~f 33 (112)
T PF08882_consen 15 LWIVQKKDKVVKCDCGHEF 33 (112)
T ss_pred EEEEEecCceeeccCCCee
Confidence 4555555678999999998
No 20
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=54.60 E-value=5.6 Score=35.11 Aligned_cols=16 Identities=38% Similarity=0.883 Sum_probs=14.5
Q ss_pred eecCCceee-eCCCEEE
Q psy2945 112 LYEGKPKRC-MCGHWFK 127 (134)
Q Consensus 112 l~~g~p~RC-eCG~~Fk 127 (134)
.-|+||.|| .|+.-||
T Consensus 393 ~~~~KPYrCevC~KRYK 409 (423)
T COG5189 393 SAKDKPYRCEVCDKRYK 409 (423)
T ss_pred cccCCceeccccchhhc
Confidence 668899999 7999998
No 21
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=52.36 E-value=9.9 Score=20.54 Aligned_cols=15 Identities=47% Similarity=1.099 Sum_probs=11.7
Q ss_pred ecC-Cceee-eCCCEEE
Q psy2945 113 YEG-KPKRC-MCGHWFK 127 (134)
Q Consensus 113 ~~g-~p~RC-eCG~~Fk 127 (134)
+.| +|..| .|+.-|.
T Consensus 9 H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HSSSSSEEESSSSEEES
T ss_pred cCCCCCCCCCCCcCeeC
Confidence 444 68999 9999884
No 22
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=52.04 E-value=12 Score=22.88 Aligned_cols=12 Identities=50% Similarity=1.323 Sum_probs=10.1
Q ss_pred eee-eCCCEEEEE
Q psy2945 118 KRC-MCGHWFKLV 129 (134)
Q Consensus 118 ~RC-eCG~~FkL~ 129 (134)
.+| +||+.|.+.
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 589 999999875
No 23
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=51.87 E-value=10 Score=22.34 Aligned_cols=14 Identities=50% Similarity=1.241 Sum_probs=11.5
Q ss_pred cCCceee-eCCCEEE
Q psy2945 114 EGKPKRC-MCGHWFK 127 (134)
Q Consensus 114 ~g~p~RC-eCG~~Fk 127 (134)
+|..-|| .|++.|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 3567999 9999985
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=51.03 E-value=9.4 Score=23.64 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=11.7
Q ss_pred EeecCCceee-eCCCE
Q psy2945 111 WLYEGKPKRC-MCGHW 125 (134)
Q Consensus 111 ~l~~g~p~RC-eCG~~ 125 (134)
.+..+.+-|| +||+-
T Consensus 13 ~~~~~~~irC~~CG~r 28 (44)
T smart00659 13 EIKSKDVVRCRECGYR 28 (44)
T ss_pred ecCCCCceECCCCCce
Confidence 3456788999 99984
No 25
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=50.91 E-value=7.9 Score=22.46 Aligned_cols=13 Identities=46% Similarity=0.994 Sum_probs=6.5
Q ss_pred cCCc--eee-eCCCEE
Q psy2945 114 EGKP--KRC-MCGHWF 126 (134)
Q Consensus 114 ~g~p--~RC-eCG~~F 126 (134)
+|+. +|| .||+++
T Consensus 6 ~~~l~~~rC~~Cg~~~ 21 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQ 21 (37)
T ss_dssp TT-EEEEE-TTT--EE
T ss_pred CCEEEEEEcCCCCCEe
Confidence 4543 999 999985
No 26
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=43.44 E-value=5.6 Score=23.68 Aligned_cols=15 Identities=27% Similarity=0.999 Sum_probs=11.3
Q ss_pred ee-eCCCEEEEEEeCC
Q psy2945 119 RC-MCGHWFKLVYKAP 133 (134)
Q Consensus 119 RC-eCG~~FkL~~~~p 133 (134)
-| .||..|-+.+.+|
T Consensus 3 ~C~~Cg~~Yh~~~~pP 18 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPP 18 (36)
T ss_dssp EETTTTEEEETTTB--
T ss_pred CcCCCCCccccccCCC
Confidence 48 8999999887766
No 27
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.37 E-value=22 Score=30.50 Aligned_cols=29 Identities=28% Similarity=0.699 Sum_probs=20.7
Q ss_pred CCCcceEEEeecC----Cceee-eCCCEEEEEEe
Q psy2945 103 ESPSINWMWLYEG----KPKRC-MCGHWFKLVYK 131 (134)
Q Consensus 103 dsh~v~W~~l~~g----~p~RC-eCG~~FkL~~~ 131 (134)
++..+.++.+..+ +..-| .|++|.|..+.
T Consensus 234 ~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~ 267 (309)
T PRK03564 234 QSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQ 267 (309)
T ss_pred CCCceeeeeecCCCcceEeeecccccccceeccc
Confidence 3445777777654 33789 89999998754
No 28
>PHA00616 hypothetical protein
Probab=42.11 E-value=5.3 Score=25.12 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=8.9
Q ss_pred ceee-eCCCEEE
Q psy2945 117 PKRC-MCGHWFK 127 (134)
Q Consensus 117 p~RC-eCG~~Fk 127 (134)
|.+| +||..|.
T Consensus 1 pYqC~~CG~~F~ 12 (44)
T PHA00616 1 MYQCLRCGGIFR 12 (44)
T ss_pred CCccchhhHHHh
Confidence 5689 9999875
No 29
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=40.01 E-value=11 Score=27.52 Aligned_cols=17 Identities=24% Similarity=0.317 Sum_probs=9.7
Q ss_pred cccccHHHHHHHHHHcC
Q psy2945 48 DLATGLEKRELLAELAG 64 (134)
Q Consensus 48 eqATGlEr~ELla~~~G 64 (134)
||-++++-.|+...+-+
T Consensus 14 e~~eplt~~ei~~~~~~ 30 (97)
T COG3357 14 ESDEPLTVAEIFELLNG 30 (97)
T ss_pred cCCCcchHHHHHHHHcC
Confidence 44566666666655544
No 30
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=36.15 E-value=20 Score=18.06 Aligned_cols=10 Identities=40% Similarity=1.235 Sum_probs=8.0
Q ss_pred eee-eCCCEEE
Q psy2945 118 KRC-MCGHWFK 127 (134)
Q Consensus 118 ~RC-eCG~~Fk 127 (134)
..| .||..|.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 369 8999885
No 31
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=32.83 E-value=47 Score=18.84 Aligned_cols=17 Identities=24% Similarity=0.780 Sum_probs=13.7
Q ss_pred CCceee-eCCCEEEEEEe
Q psy2945 115 GKPKRC-MCGHWFKLVYK 131 (134)
Q Consensus 115 g~p~RC-eCG~~FkL~~~ 131 (134)
++-.+| .||+.+.+...
T Consensus 5 ~~~ykC~~Cgniv~v~~~ 22 (34)
T TIGR00319 5 GQVYKCEVCGNIVEVLHA 22 (34)
T ss_pred CcEEEcCCCCcEEEEEEC
Confidence 567899 89999987653
No 32
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.77 E-value=27 Score=20.54 Aligned_cols=14 Identities=50% Similarity=1.146 Sum_probs=11.0
Q ss_pred cCCceee-eCCCEEE
Q psy2945 114 EGKPKRC-MCGHWFK 127 (134)
Q Consensus 114 ~g~p~RC-eCG~~Fk 127 (134)
+|.--+| .||+.|.
T Consensus 22 ~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 22 KGRKVRCSKCGHVFF 36 (36)
T ss_pred CCcEEECCCCCCEeC
Confidence 4566899 9999883
No 33
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=32.53 E-value=48 Score=22.11 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=19.4
Q ss_pred EEeeeCCC-CCCcceEEEeecC-Cceee-eCCCEEEE
Q psy2945 95 IVGCICEE-ESPSINWMWLYEG-KPKRC-MCGHWFKL 128 (134)
Q Consensus 95 iVGC~g~~-dsh~v~W~~l~~g-~p~RC-eCG~~FkL 128 (134)
|-|-+||. .+-+.+=||-..| +...| +||+--..
T Consensus 7 IAGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 7 IAGAVCPACSAQDTLAMWKENNIELVECVECGYQEQQ 43 (59)
T ss_pred eccccCCCCcCccEEEEEEeCCceEEEeccCCCcccc
Confidence 55777752 2223333334444 45889 99987654
No 34
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=32.39 E-value=66 Score=19.21 Aligned_cols=24 Identities=25% Similarity=0.673 Sum_probs=15.4
Q ss_pred CCcceEEEee---cCCc----eee-eCCCEEE
Q psy2945 104 SPSINWMWLY---EGKP----KRC-MCGHWFK 127 (134)
Q Consensus 104 sh~v~W~~l~---~g~p----~RC-eCG~~Fk 127 (134)
.+...|+.+. .++| ..| .||+.|+
T Consensus 8 ~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 8 NREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 4556666653 2333 788 9999875
No 35
>PF10763 DUF2584: Protein of unknown function (DUF2584); InterPro: IPR019699 This entry is represented by Bacteriophage 0305phi8-36, Orf221. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2NWA_F.
Probab=31.11 E-value=33 Score=24.19 Aligned_cols=26 Identities=31% Similarity=0.387 Sum_probs=17.7
Q ss_pred cceEEEeecCCceeeeCCCEEEEEEeC
Q psy2945 106 SINWMWLYEGKPKRCMCGHWFKLVYKA 132 (134)
Q Consensus 106 ~v~W~~l~~g~p~RCeCG~~FkL~~~~ 132 (134)
+++||-+.+|+..|-+ .+.|.|...|
T Consensus 6 E~nt~ivtkgke~rie-~n~f~l~KeG 31 (80)
T PF10763_consen 6 EVNTMIVTKGKEKRIE-ENIFQLEKEG 31 (80)
T ss_dssp EE-SSEE--S--EESS-SSEEEEEEES
T ss_pred EEEEEEEecCcceEcc-ccEEEEEeCc
Confidence 4788889999999987 7999998776
No 36
>PF09631 Sen15: Sen15 protein; InterPro: IPR018593 The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly []. ; PDB: 2GW6_B.
Probab=30.83 E-value=53 Score=23.09 Aligned_cols=23 Identities=22% Similarity=0.443 Sum_probs=13.7
Q ss_pred CCeEEeeeCCCCCCcceEEEeecC
Q psy2945 92 EARIVGCICEEESPSINWMWLYEG 115 (134)
Q Consensus 92 ~~RiVGC~g~~dsh~v~W~~l~~g 115 (134)
.+||+=++..+|++.|+| .+++|
T Consensus 72 ~~ri~LAiv~~DsTiVYY-~i~~G 94 (101)
T PF09631_consen 72 PKRILLAIVDDDSTIVYY-KIHDG 94 (101)
T ss_dssp --EEEEEEE-TTS-EEEE-EEE--
T ss_pred CcEEEEEEEcCCCCEEEE-EEeCC
Confidence 789999999999985555 58988
No 37
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.64 E-value=65 Score=19.39 Aligned_cols=17 Identities=29% Similarity=0.669 Sum_probs=12.7
Q ss_pred ceee-eCCCEEEEEEeCC
Q psy2945 117 PKRC-MCGHWFKLVYKAP 133 (134)
Q Consensus 117 p~RC-eCG~~FkL~~~~p 133 (134)
..+| .||+-+.++.-++
T Consensus 21 ~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 21 GVRCPYCGYRILFKERPP 38 (46)
T ss_pred ceECCCCCCeEEEccCCC
Confidence 6899 8999777765444
No 38
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=30.52 E-value=34 Score=29.29 Aligned_cols=28 Identities=25% Similarity=0.658 Sum_probs=19.6
Q ss_pred CCcceEEEeec--C----Cceee-eCCCEEEEEEe
Q psy2945 104 SPSINWMWLYE--G----KPKRC-MCGHWFKLVYK 131 (134)
Q Consensus 104 sh~v~W~~l~~--g----~p~RC-eCG~~FkL~~~ 131 (134)
+..+.++.+.. + +..-| .|++|.|..+.
T Consensus 233 ~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~ 267 (305)
T TIGR01562 233 SKHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQ 267 (305)
T ss_pred CCceeeEeecCCCCCcceEEeeccccccchhhhcc
Confidence 34576777764 2 23679 89999998754
No 39
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=29.42 E-value=27 Score=26.30 Aligned_cols=9 Identities=33% Similarity=1.261 Sum_probs=7.4
Q ss_pred eee-eCCCEE
Q psy2945 118 KRC-MCGHWF 126 (134)
Q Consensus 118 ~RC-eCG~~F 126 (134)
.|| .||++|
T Consensus 30 ~kC~~CG~v~ 39 (140)
T COG1545 30 TKCKKCGRVY 39 (140)
T ss_pred EEcCCCCeEE
Confidence 688 888887
No 40
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=28.75 E-value=19 Score=27.35 Aligned_cols=11 Identities=45% Similarity=0.881 Sum_probs=5.7
Q ss_pred eee-eCCCEEEE
Q psy2945 118 KRC-MCGHWFKL 128 (134)
Q Consensus 118 ~RC-eCG~~FkL 128 (134)
--| |||..||.
T Consensus 73 i~clecGk~~k~ 84 (132)
T PF05443_consen 73 IICLECGKKFKT 84 (132)
T ss_dssp EE-TBT--EESB
T ss_pred eEEccCCcccch
Confidence 456 88888874
No 41
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=28.62 E-value=65 Score=18.31 Aligned_cols=16 Identities=19% Similarity=0.694 Sum_probs=12.1
Q ss_pred Cceee-eCCCEEEEEEe
Q psy2945 116 KPKRC-MCGHWFKLVYK 131 (134)
Q Consensus 116 ~p~RC-eCG~~FkL~~~ 131 (134)
+-.+| .||+...+...
T Consensus 3 ~~ykC~~CGniv~v~~~ 19 (34)
T cd00974 3 EVYKCEICGNIVEVLNV 19 (34)
T ss_pred cEEEcCCCCcEEEEEEC
Confidence 45789 89998877653
No 42
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=26.72 E-value=39 Score=16.37 Aligned_cols=9 Identities=44% Similarity=1.501 Sum_probs=5.5
Q ss_pred ee-eCCCEEE
Q psy2945 119 RC-MCGHWFK 127 (134)
Q Consensus 119 RC-eCG~~Fk 127 (134)
.| .||..|.
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 68 8999884
No 43
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=26.57 E-value=44 Score=19.13 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=9.2
Q ss_pred eee-eCCCEEEEE
Q psy2945 118 KRC-MCGHWFKLV 129 (134)
Q Consensus 118 ~RC-eCG~~FkL~ 129 (134)
-.| +||..|++.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 368 888888875
No 44
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=25.69 E-value=61 Score=19.90 Aligned_cols=21 Identities=29% Similarity=0.585 Sum_probs=15.7
Q ss_pred cceEEEee-cCCceee-eCCCEE
Q psy2945 106 SINWMWLY-EGKPKRC-MCGHWF 126 (134)
Q Consensus 106 ~v~W~~l~-~g~p~RC-eCG~~F 126 (134)
...|+.++ +.-|..| .||.+.
T Consensus 19 ~~~~~~v~YE~lp~~C~~C~~~g 41 (49)
T PF14392_consen 19 ESFWVKVKYERLPRFCFHCGRIG 41 (49)
T ss_pred cEEEEEEEECCcChhhcCCCCcC
Confidence 35667776 7788999 999764
No 45
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=25.32 E-value=1e+02 Score=20.89 Aligned_cols=37 Identities=24% Similarity=0.487 Sum_probs=23.5
Q ss_pred EEeeeCCC-CCCcceEEEeecCC-ceee-eCCCEEEEEEe
Q psy2945 95 IVGCICEE-ESPSINWMWLYEGK-PKRC-MCGHWFKLVYK 131 (134)
Q Consensus 95 iVGC~g~~-dsh~v~W~~l~~g~-p~RC-eCG~~FkL~~~ 131 (134)
|-|-+||. .+-+.+=+|-.+|. -..| +||+...+...
T Consensus 6 IAGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 6 IAGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ecCccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 55777852 33344445556664 5899 99998766443
No 46
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=25.02 E-value=79 Score=20.46 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=17.0
Q ss_pred CCceee-eCCCEEEEEEeCCC
Q psy2945 115 GKPKRC-MCGHWFKLVYKAPI 134 (134)
Q Consensus 115 g~p~RC-eCG~~FkL~~~~p~ 134 (134)
|..-.| .||.-|.++...|+
T Consensus 20 GeiV~Cp~CGaeleVv~~~p~ 40 (54)
T TIGR01206 20 GELVICDECGAELEVVSLDPL 40 (54)
T ss_pred CCEEeCCCCCCEEEEEeCCCC
Confidence 777899 89999999888774
No 47
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=24.31 E-value=57 Score=20.89 Aligned_cols=14 Identities=36% Similarity=0.712 Sum_probs=10.8
Q ss_pred CCceee-eCCCEEEE
Q psy2945 115 GKPKRC-MCGHWFKL 128 (134)
Q Consensus 115 g~p~RC-eCG~~FkL 128 (134)
+++-.| +||.-|..
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 456789 99998875
No 48
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.17 E-value=48 Score=19.60 Aligned_cols=16 Identities=38% Similarity=1.005 Sum_probs=10.6
Q ss_pred EEEeecCCceee-eCCCE
Q psy2945 109 WMWLYEGKPKRC-MCGHW 125 (134)
Q Consensus 109 W~~l~~g~p~RC-eCG~~ 125 (134)
|+...+|. ..| +||+.
T Consensus 18 ~~~~~dG~-~yC~~cG~~ 34 (36)
T PF11781_consen 18 WFYSDDGF-YYCDRCGHQ 34 (36)
T ss_pred EeEccCCE-EEhhhCceE
Confidence 66555555 677 78775
No 49
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.02 E-value=70 Score=23.86 Aligned_cols=8 Identities=38% Similarity=1.124 Sum_probs=4.3
Q ss_pred eee-eCCCE
Q psy2945 118 KRC-MCGHW 125 (134)
Q Consensus 118 ~RC-eCG~~ 125 (134)
.+| .||+.
T Consensus 108 ~~CP~Cgs~ 116 (135)
T PRK03824 108 LKCPKCGSR 116 (135)
T ss_pred cCCcCCCCC
Confidence 446 56654
No 50
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.94 E-value=36 Score=26.84 Aligned_cols=12 Identities=33% Similarity=0.910 Sum_probs=10.3
Q ss_pred CCceee-eCCCEE
Q psy2945 115 GKPKRC-MCGHWF 126 (134)
Q Consensus 115 g~p~RC-eCG~~F 126 (134)
..|.+| .||+-|
T Consensus 66 ~~PsYC~~CGkpy 78 (158)
T PF10083_consen 66 EAPSYCHNCGKPY 78 (158)
T ss_pred CCChhHHhCCCCC
Confidence 478999 999977
No 51
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.93 E-value=18 Score=32.33 Aligned_cols=27 Identities=22% Similarity=0.701 Sum_probs=19.3
Q ss_pred eCCCCCCcceEEEeecC--Cceee-eCCCE
Q psy2945 99 ICEEESPSINWMWLYEG--KPKRC-MCGHW 125 (134)
Q Consensus 99 ~g~~dsh~v~W~~l~~g--~p~RC-eCG~~ 125 (134)
.|++.-....|+|=..| .-.+| .||++
T Consensus 354 LG~DG~PmP~WL~klhgLd~ef~CEICgNy 383 (470)
T COG5188 354 LGPDGLPMPRWLCKLHGLDIEFECEICGNY 383 (470)
T ss_pred CCCCCCCCchHHHHhcCCCcceeeeecccc
Confidence 35666666788886665 56999 79964
No 52
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=22.88 E-value=38 Score=22.90 Aligned_cols=9 Identities=56% Similarity=1.361 Sum_probs=7.7
Q ss_pred ceee-eCCCE
Q psy2945 117 PKRC-MCGHW 125 (134)
Q Consensus 117 p~RC-eCG~~ 125 (134)
|-|| .||.+
T Consensus 4 PiRCFsCGkv 13 (63)
T COG1644 4 PVRCFSCGKV 13 (63)
T ss_pred ceEeecCCCC
Confidence 7899 99975
No 53
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.14 E-value=52 Score=23.97 Aligned_cols=8 Identities=25% Similarity=0.559 Sum_probs=5.0
Q ss_pred eee-eCCCE
Q psy2945 118 KRC-MCGHW 125 (134)
Q Consensus 118 ~RC-eCG~~ 125 (134)
.+| .||+.
T Consensus 89 ~~CP~Cgs~ 97 (117)
T PRK00564 89 GVCEKCHSK 97 (117)
T ss_pred CcCcCCCCC
Confidence 357 67765
No 54
>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=21.95 E-value=76 Score=23.14 Aligned_cols=15 Identities=20% Similarity=0.220 Sum_probs=0.0
Q ss_pred cccCcceeeeeeecc
Q psy2945 22 TATGNSFSTCAQRWN 36 (134)
Q Consensus 22 ~~~~R~fsts~~~~~ 36 (134)
...+|.+++|+++.+
T Consensus 17 ~~~~Rni~~sa~~~~ 31 (99)
T PF05511_consen 17 VHLRRNIGTSAVAFN 31 (99)
T ss_dssp ---------------
T ss_pred HHHHHHhhhhHHHHh
Confidence 445799999998766
No 55
>PF04648 MF_alpha: Yeast mating factor alpha hormone; InterPro: IPR006742 This repeated sequence,WHWLQLKPGQPMY, characterises the mating factor alpha-1 or alpha-1 mating pheromone [contains: Mating factor alpha].The hormone is excreted into the culture medium by haploid cells of the alpha mating type and acts on cells of the opposite mating type (type A) by binding to a cognate G-protein coupled receptor which is coupled to a downstream signal transduction pathway. It inhibits DNA synthesis in type A cells synchronising them with type alpha, and so mediates the conjugation process.; GO: 0000772 mating pheromone activity, 0019953 sexual reproduction, 0005576 extracellular region
Probab=21.70 E-value=45 Score=16.04 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=8.0
Q ss_pred eEEEeecCCce
Q psy2945 108 NWMWLYEGKPK 118 (134)
Q Consensus 108 ~W~~l~~g~p~ 118 (134)
.|+.+..|+|-
T Consensus 2 hWL~~~~GqP~ 12 (13)
T PF04648_consen 2 HWLRLSPGQPM 12 (13)
T ss_pred cceeccCCCcC
Confidence 47777788873
No 56
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.67 E-value=51 Score=23.87 Aligned_cols=20 Identities=10% Similarity=0.313 Sum_probs=13.8
Q ss_pred EEeecCCc-eee-eCCCEEEEE
Q psy2945 110 MWLYEGKP-KRC-MCGHWFKLV 129 (134)
Q Consensus 110 ~~l~~g~p-~RC-eCG~~FkL~ 129 (134)
+.+..=++ -|| .||+.|.+.
T Consensus 62 L~I~~vp~~~~C~~Cg~~~~~~ 83 (113)
T PRK12380 62 LHIVYKPAQAWCWDCSQVVEIH 83 (113)
T ss_pred EEEEeeCcEEEcccCCCEEecC
Confidence 33444343 899 999999875
No 57
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=21.54 E-value=55 Score=20.55 Aligned_cols=10 Identities=30% Similarity=1.046 Sum_probs=8.2
Q ss_pred eee-eCCCEEE
Q psy2945 118 KRC-MCGHWFK 127 (134)
Q Consensus 118 ~RC-eCG~~Fk 127 (134)
.+| .||.+|-
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 579 8999885
No 58
>PF07710 P53_tetramer: P53 tetramerisation motif; InterPro: IPR010991 The p53 protein is a tetrameric transcription factor that plays a central role in the prevention of neoplastic transformation []. Oligomerization appears to be essential for the tumour suppressing activity of p53. p53 can be divided into different functional domains: an N-terminal transactivation domain, a proline-rich domain, a DNA-binding domain (IPR008967 from INTERPRO), a tetramerisation domain and a C-terminal regulatory region. The tetramerisation domain of human p53 extends from residues 325 to 356, and has a 4-helical bundle fold. The tetramerisation domain is essential for DNA binding, protein-protein interactions, post-translational modifications, and p53 degradation [].; GO: 0051262 protein tetramerization; PDB: 3Q06_B 1SAL_B 1OLH_B 1AIE_A 1PES_D 1SAK_D 1SAE_B 2J11_D 1PET_A 1OLG_A ....
Probab=21.49 E-value=74 Score=19.79 Aligned_cols=15 Identities=27% Similarity=0.465 Sum_probs=13.1
Q ss_pred ccccHHHHHHHHHHc
Q psy2945 49 LATGLEKRELLAELA 63 (134)
Q Consensus 49 qATGlEr~ELla~~~ 63 (134)
|.-|.||+||+-++.
T Consensus 14 ~VrGRe~yE~l~kin 28 (42)
T PF07710_consen 14 QVRGRERYEMLKKIN 28 (42)
T ss_dssp EEESHHHHHHHHHHH
T ss_pred EEecHHHHHHHHHHH
Confidence 788999999998873
No 59
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.30 E-value=1.1e+02 Score=22.21 Aligned_cols=26 Identities=19% Similarity=0.475 Sum_probs=16.6
Q ss_pred CCCCcceEEEeec---CCc----eee-eCCCEEE
Q psy2945 102 EESPSINWMWLYE---GKP----KRC-MCGHWFK 127 (134)
Q Consensus 102 ~dsh~v~W~~l~~---g~p----~RC-eCG~~Fk 127 (134)
-+.+.+.|+.+.. ++| .+| .||+.|+
T Consensus 78 Cg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 78 CGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred CCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 4555555555552 444 689 9999886
No 60
>PHA02768 hypothetical protein; Provisional
Probab=20.93 E-value=39 Score=22.09 Aligned_cols=11 Identities=27% Similarity=0.905 Sum_probs=8.3
Q ss_pred eee-eCCCEEEE
Q psy2945 118 KRC-MCGHWFKL 128 (134)
Q Consensus 118 ~RC-eCG~~FkL 128 (134)
..| +||..|.-
T Consensus 6 y~C~~CGK~Fs~ 17 (55)
T PHA02768 6 YECPICGEIYIK 17 (55)
T ss_pred cCcchhCCeecc
Confidence 478 89888853
No 61
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=20.81 E-value=1.6e+02 Score=18.75 Aligned_cols=21 Identities=14% Similarity=0.396 Sum_probs=11.7
Q ss_pred eEEEe-ecCC-ceee-eCCCEEEE
Q psy2945 108 NWMWL-YEGK-PKRC-MCGHWFKL 128 (134)
Q Consensus 108 ~W~~l-~~g~-p~RC-eCG~~FkL 128 (134)
.-|.| .+++ .-|| -|+..|..
T Consensus 24 ~~F~v~~~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 24 SRFYVIDKEPIKLRCHYCERIITE 47 (52)
T ss_dssp -EEEEEETTTCEEEETTT--EEEH
T ss_pred ceEEEEeCCCCEEEeeCCCCEecc
Confidence 44555 3343 4999 89999864
No 62
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.80 E-value=54 Score=18.64 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=8.5
Q ss_pred eee-eCCCEEEE
Q psy2945 118 KRC-MCGHWFKL 128 (134)
Q Consensus 118 ~RC-eCG~~FkL 128 (134)
.+| .||+.|.-
T Consensus 2 ~~C~~CGy~y~~ 13 (33)
T cd00350 2 YVCPVCGYIYDG 13 (33)
T ss_pred EECCCCCCEECC
Confidence 478 89998864
No 63
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=20.73 E-value=59 Score=21.19 Aligned_cols=12 Identities=25% Similarity=0.686 Sum_probs=9.7
Q ss_pred eee-eCCCEEEEE
Q psy2945 118 KRC-MCGHWFKLV 129 (134)
Q Consensus 118 ~RC-eCG~~FkL~ 129 (134)
=.| +||.+|-+.
T Consensus 54 L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 54 LICPECGREYPIR 66 (68)
T ss_dssp EEETTTTEEEEEE
T ss_pred EEcCCCCCEEeCC
Confidence 568 999999764
Done!