Query 032843
Match_columns 132
No_of_seqs 109 out of 193
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:36:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032843.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032843hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00186 ribosomal protein S26 100.0 8.1E-64 1.8E-68 370.6 8.0 106 1-106 1-106 (109)
2 PF01283 Ribosomal_S26e: Ribos 100.0 2.4E-64 5.2E-69 375.1 4.8 110 1-110 1-110 (113)
3 PTZ00172 40S ribosomal protein 100.0 2.5E-63 5.5E-68 367.5 8.2 104 1-104 1-104 (108)
4 PRK09335 30S ribosomal protein 100.0 2.3E-57 5E-62 329.6 6.8 94 1-98 1-94 (95)
5 KOG1768 40s ribosomal protein 100.0 4.4E-55 9.6E-60 326.3 4.1 109 1-109 1-109 (115)
6 COG4830 RPS26B Ribosomal prote 100.0 8.2E-52 1.8E-56 305.0 5.8 97 1-97 1-97 (108)
7 COG1400 SEC65 Signal recogniti 73.1 0.78 1.7E-05 33.6 -0.8 26 27-54 20-45 (93)
8 PF08209 Sgf11: Sgf11 (transcr 56.9 7.2 0.00016 23.6 1.3 15 18-32 2-16 (33)
9 PF07503 zf-HYPF: HypF finger; 56.7 4.6 0.0001 24.6 0.5 14 15-28 16-29 (35)
10 PF02591 DUF164: Putative zinc 54.1 6.7 0.00015 25.0 0.9 13 18-30 44-56 (56)
11 TIGR01031 rpmF_bact ribosomal 46.4 15 0.00032 24.2 1.7 28 2-29 2-35 (55)
12 PRK04016 DNA-directed RNA poly 44.2 11 0.00023 26.0 0.8 14 19-32 3-16 (62)
13 PF09889 DUF2116: Uncharacteri 43.7 9.2 0.0002 25.8 0.4 17 21-37 4-20 (59)
14 PF04726 Microvir_J: Microviru 43.2 13 0.00029 21.4 0.9 15 1-15 1-15 (24)
15 COG1644 RPB10 DNA-directed RNA 43.2 11 0.00023 26.2 0.6 13 19-31 3-15 (63)
16 COG4481 Uncharacterized protei 42.8 14 0.0003 25.4 1.1 13 18-30 32-44 (60)
17 KOG2612 Predicted integral mem 41.7 8.9 0.00019 28.7 0.1 15 17-31 71-85 (103)
18 PF13119 DUF3973: Domain of un 39.8 14 0.00029 23.8 0.7 11 71-81 1-12 (41)
19 COG5112 UFD2 U1-like Zn-finger 38.7 11 0.00024 29.1 0.1 31 49-81 31-65 (126)
20 PF10122 Mu-like_Com: Mu-like 38.1 15 0.00032 24.6 0.7 18 19-36 3-20 (51)
21 PLN00032 DNA-directed RNA poly 38.0 16 0.00034 25.9 0.8 12 19-30 3-14 (71)
22 PF13248 zf-ribbon_3: zinc-rib 36.7 13 0.00029 20.6 0.3 13 21-33 3-15 (26)
23 PF01922 SRP19: SRP19 protein; 36.6 8.8 0.00019 27.5 -0.6 23 26-48 16-38 (95)
24 COG2888 Predicted Zn-ribbon RN 34.4 31 0.00068 23.8 1.8 36 18-54 7-43 (61)
25 KOG3408 U1-like Zn-finger-cont 32.5 14 0.00031 28.8 -0.1 18 62-81 50-67 (129)
26 PF01194 RNA_pol_N: RNA polyme 32.1 15 0.00032 25.1 -0.1 13 19-31 3-15 (60)
27 PRK12286 rpmF 50S ribosomal pr 26.2 41 0.00088 22.3 1.3 29 2-30 4-37 (57)
28 KOG3497 DNA-directed RNA polym 26.0 32 0.0007 24.2 0.8 12 19-30 3-14 (69)
29 PF13240 zinc_ribbon_2: zinc-r 25.9 29 0.00063 19.1 0.5 12 22-33 1-12 (23)
30 PF03604 DNA_RNApol_7kD: DNA d 25.5 24 0.00051 21.1 0.0 13 18-30 15-27 (32)
31 PF12230 PRP21_like_P: Pre-mRN 25.5 23 0.00051 28.2 0.0 32 16-48 164-195 (229)
32 COG1150 HdrC Heterodisulfide r 25.4 29 0.00063 28.6 0.5 48 21-78 39-89 (195)
33 PF10589 NADH_4Fe-4S: NADH-ubi 25.0 20 0.00044 22.5 -0.4 10 24-33 14-23 (46)
34 COG5134 Uncharacterized conser 24.8 38 0.00082 29.1 1.1 44 20-77 42-85 (272)
35 PRK14890 putative Zn-ribbon RN 24.5 37 0.00081 23.2 0.9 25 19-44 6-31 (59)
36 TIGR02174 CXXU_selWTH selT/sel 24.4 31 0.00068 23.1 0.5 14 69-82 1-14 (72)
37 PF13717 zinc_ribbon_4: zinc-r 24.3 45 0.00097 19.9 1.1 14 16-29 21-34 (36)
38 COG1326 Uncharacterized archae 24.3 69 0.0015 26.7 2.5 23 15-37 25-53 (201)
39 PF06639 BAP: Basal layer anti 23.8 20 0.00043 25.6 -0.6 22 75-96 5-26 (75)
40 PF06107 DUF951: Bacterial pro 23.2 50 0.0011 22.4 1.3 14 20-33 31-46 (57)
41 KOG3286 Selenoprotein T [Gener 22.9 52 0.0011 27.8 1.5 14 68-81 71-84 (226)
42 PF07282 OrfB_Zn_ribbon: Putat 22.3 65 0.0014 20.7 1.7 19 15-33 41-59 (69)
43 PF13913 zf-C2HC_2: zinc-finge 21.7 37 0.00079 18.8 0.3 13 20-32 2-14 (25)
44 PF14353 CpXC: CpXC protein 20.0 81 0.0017 22.7 1.9 45 21-79 2-46 (128)
No 1
>PLN00186 ribosomal protein S26; Provisional
Probab=100.00 E-value=8.1e-64 Score=370.58 Aligned_cols=106 Identities=91% Similarity=1.459 Sum_probs=103.9
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
||+|||||||+|+|+|||++|+|+|||+|||||||||+|+|+||||+++++||+||+||++|.|||||+|+|||||||||
T Consensus 1 M~kKRrN~GR~K~~rGhv~~V~C~nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~vy~~y~lPKly~K~~YCVSCAIH 80 (109)
T PLN00186 1 MTKKRRNGGRNKHGRGHVKRIRCSNCGKCVPKDKAIKRFLVRNIVEQAALRDVQEACVYDGYTLPKLYAKVQYCISCAIH 80 (109)
T ss_pred CCcccccCCCCCCCCCCCcceeeCCCcccccccceEEEEecccCccHHHHHHHHhhhcccccccchhhhceEEEEeehhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCchhhccCCCCCCCcCCCC
Q 032843 81 SHVVRVRSRTNRRIREPPQRFRRRDD 106 (132)
Q Consensus 81 skVVRvRS~e~RK~r~pp~r~~~~~~ 106 (132)
++||||||+|+||+|+||++|++.++
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~~~ 106 (109)
T PLN00186 81 SRVVRVRSRENRRIREPPPRFRRRKD 106 (109)
T ss_pred cceeecCChHHccccCCCcccccccc
Confidence 99999999999999999999988554
No 2
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=100.00 E-value=2.4e-64 Score=375.12 Aligned_cols=110 Identities=68% Similarity=1.171 Sum_probs=73.0
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
||+|||||||+|+|+|||++|+|+|||+|||||||||+|+|+||||++++|||+|||||++|+|||||+|+|||||||||
T Consensus 1 M~~KRrN~Gr~KkgrGhv~~V~C~nCgr~vPKDKAIkrf~i~niVeaaa~rdi~~a~v~~~y~lPKlyvK~~YCvSCAIH 80 (113)
T PF01283_consen 1 MTKKRRNNGRSKKGRGHVQPVRCDNCGRCVPKDKAIKRFVIRNIVEAAAVRDISEASVYDAYVLPKLYVKLYYCVSCAIH 80 (113)
T ss_dssp -----TTTTSS-SSSS---EEE-TTTB-EEECCCSEEEEEEEESS-CCCHHHHHHCB-SSS--S-EEEEEEEE-CHHHHH
T ss_pred CCcccccCCCCCCCCCCCcCEeeCcccccCcCCceEEEEEccCCccHHHHHHHhhcceeeecccccceeEEEEeeeeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCchhhccCCCCCCCcCCCCCCCC
Q 032843 81 SHVVRVRSRTNRRIREPPQRFRRRDDVPKA 110 (132)
Q Consensus 81 skVVRvRS~e~RK~r~pp~r~~~~~~~~~~ 110 (132)
++|||+||+|+||+|+||++|++..+..++
T Consensus 81 ~~IVr~Rs~e~RK~r~~p~~~~~~~~~~~~ 110 (113)
T PF01283_consen 81 SKIVRVRSREERKDRTPPPRFRPRKQGQKP 110 (113)
T ss_dssp TTSS----TCCCC--S--------------
T ss_pred ccccccCChHHccccCCCCcCCcccccccc
Confidence 999999999999999999999987665543
No 3
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=100.00 E-value=2.5e-63 Score=367.48 Aligned_cols=104 Identities=74% Similarity=1.227 Sum_probs=101.9
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
||+|||||||+|+|+|||++|+|+|||+|||||||||+|+|+||||+++++||+||+||++|+|||||+|+|||||||||
T Consensus 1 M~kKRrN~GR~K~~rGhv~~V~C~nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~v~~~y~lPKly~k~~YCVSCAIH 80 (108)
T PTZ00172 1 MTSKRRNNGRSKHGRGHVKPVRCSNCGRCVPKDKAIKRFVVRNIVDAASVRDIAEASVYYGYPLPKLYMKQQYCVSCAIH 80 (108)
T ss_pred CCcccccCCCCCCCCCCCccEEeCCccccccccceEEEEeccCCccHHHHHHHHHhhchhccccccceeeeEEeeehhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCchhhccCCCCCCCcCC
Q 032843 81 SHVVRVRSRTNRRIREPPQRFRRR 104 (132)
Q Consensus 81 skVVRvRS~e~RK~r~pp~r~~~~ 104 (132)
++||||||+|+||+|+||+++...
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~ 104 (108)
T PTZ00172 81 SRVVRVRSREDRKIRTPPKRPFRP 104 (108)
T ss_pred CCeeecCChHHccccCCCCCCCCC
Confidence 999999999999999999887653
No 4
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=100.00 E-value=2.3e-57 Score=329.58 Aligned_cols=94 Identities=30% Similarity=0.658 Sum_probs=92.2
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
||+|||||||+|+|+||+++|+|+|||+|||||||||+|+|+||||+++++||+||++| |||||+|+|||||||||
T Consensus 1 M~kKRrn~GR~K~~rGhv~~V~C~nCgr~vPKDKAIkrf~i~n~Ve~a~~rdl~~a~~~----lpk~~~k~~YCvSCAiH 76 (95)
T PRK09335 1 MPKKRENRGRRKGDKGHVGYVQCDNCGRRVPRDKAVCVTKMYSPVDPQLAKELEKKGAI----IARYPVTKCYCVNCAVH 76 (95)
T ss_pred CCcccccCCCCCCCCCCCccEEeCCCCCcCcCCceEEEEEecCCCCHHHHHHHHhCcee----eeeeeeeeEEechhhhh
Confidence 99999999999999999999999999999999999999999999999999999999987 99999999999999999
Q ss_pred cccccccCchhhccCCCC
Q 032843 81 SHVVRVRSRTNRRIREPP 98 (132)
Q Consensus 81 skVVRvRS~e~RK~r~pp 98 (132)
++|||+||+|+||+|+|.
T Consensus 77 ~~IVrvRs~e~Rk~r~~~ 94 (95)
T PRK09335 77 LGIIKIRPEEERKKKAPL 94 (95)
T ss_pred ccccccCChHHcccccCC
Confidence 999999999999999863
No 5
>KOG1768 consensus 40s ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.4e-55 Score=326.25 Aligned_cols=109 Identities=71% Similarity=1.187 Sum_probs=104.5
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
||+||+|+|++|+|+||+.+|+|+||++|||||||||+|+|+||||++++|||+|||||++|+|||||+|||||||||||
T Consensus 1 m~~kr~~~gr~k~~~g~v~~i~c~~c~~~~~kdKaIk~f~i~niVEaaavrdiseasv~d~y~~pKly~Klhycvscaih 80 (115)
T KOG1768|consen 1 MTKKRRNAGRNKKGRGHVIPIRCTNCGRCMPKDKAIKRFVIRNIVEAAAVRDISEASVFDAYVLPKLYVKLHYCVSCAIH 80 (115)
T ss_pred CCcccccCCCCCCCCcceeeeeeccccccchHHHHHHHHHHHHHHHHHHhhhhhhheeccccccccccceeeeeEeeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCchhhccCCCCCCCcCCCCCCC
Q 032843 81 SHVVRVRSRTNRRIREPPQRFRRRDDVPK 109 (132)
Q Consensus 81 skVVRvRS~e~RK~r~pp~r~~~~~~~~~ 109 (132)
++|||+||.|.||+|+||++|.+.....+
T Consensus 81 skVvR~rS~e~rrir~pp~rf~~~~~~~~ 109 (115)
T KOG1768|consen 81 SKVVRVRSREARRIRTPPPRFSPRAPSLR 109 (115)
T ss_pred eeeeccchhhhhcccCCCcccCccccccC
Confidence 99999999999999999998877544333
No 6
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.2e-52 Score=304.96 Aligned_cols=97 Identities=65% Similarity=1.129 Sum_probs=96.6
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
|||||+||||+|+|+||+.+|+|+|||..||||||||+|.|+|+||+++++||+++++|+.|.+||+|.|+|||||||||
T Consensus 1 mpkkR~N~GR~K~~rGhv~~v~CdnCg~~vPkdKAikr~~i~s~Ve~a~~rdL~~asIy~~y~vpk~~~k~qyCVsCAih 80 (108)
T COG4830 1 MPKKRRNRGRNKKGRGHVKYVRCDNCGKAVPKDKAIKRTAIRSPVEAAAARDLSEASIYSEYAVPKTYNKLQYCVSCAIH 80 (108)
T ss_pred CcchhhhcCCCCCCCCCccceeeccccccCCccceeeEeeccCcccHHHHHHHhhceeeeeeeccccccceeeeeeeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCchhhccCCC
Q 032843 81 SHVVRVRSRTNRRIREP 97 (132)
Q Consensus 81 skVVRvRS~e~RK~r~p 97 (132)
++||||||+|+||++.|
T Consensus 81 ~~IvrVRSre~RK~r~p 97 (108)
T COG4830 81 ARIVRVRSREERKIRAP 97 (108)
T ss_pred eeEEEEecchhhhhcCC
Confidence 99999999999999998
No 7
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=73.10 E-value=0.78 Score=33.64 Aligned_cols=26 Identities=27% Similarity=0.516 Sum_probs=21.7
Q ss_pred cceeecccceeeeeecccchhhHHhhHH
Q 032843 27 GKCCPKDKAIKRFLVRNIVEQAAVRDVQ 54 (132)
Q Consensus 27 gr~vPKDKAIKrf~irNiVEaaavrDis 54 (132)
||+|||+.||..+...+|+|+ +++|-
T Consensus 20 GRrvpk~laV~~P~~~ei~~a--~~~LG 45 (93)
T COG1400 20 GRRVPKELAVENPSLEEIAEA--LRELG 45 (93)
T ss_pred ccccchhhcccCCCHHHHHHH--HHHcC
Confidence 599999999999999999875 55554
No 8
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=56.88 E-value=7.2 Score=23.61 Aligned_cols=15 Identities=27% Similarity=0.895 Sum_probs=10.4
Q ss_pred cceEeecCCcceeec
Q 032843 18 VKFIRCSNCGKCCPK 32 (132)
Q Consensus 18 v~~V~C~NCgr~vPK 32 (132)
...+.|.||+|-|.-
T Consensus 2 ~~~~~C~nC~R~v~a 16 (33)
T PF08209_consen 2 SPYVECPNCGRPVAA 16 (33)
T ss_dssp S-EEE-TTTSSEEEG
T ss_pred CCeEECCCCcCCcch
Confidence 467899999998753
No 9
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=56.71 E-value=4.6 Score=24.59 Aligned_cols=14 Identities=57% Similarity=1.212 Sum_probs=8.8
Q ss_pred CCccceEeecCCcc
Q 032843 15 RGHVKFIRCSNCGK 28 (132)
Q Consensus 15 rGhv~~V~C~NCgr 28 (132)
|=|-++|-|++||=
T Consensus 16 R~~~~~isC~~CGP 29 (35)
T PF07503_consen 16 RFHYQFISCTNCGP 29 (35)
T ss_dssp TTT-TT--BTTCC-
T ss_pred cccCcCccCCCCCC
Confidence 46889999999993
No 10
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=54.08 E-value=6.7 Score=25.03 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=10.4
Q ss_pred cceEeecCCccee
Q 032843 18 VKFIRCSNCGKCC 30 (132)
Q Consensus 18 v~~V~C~NCgr~v 30 (132)
...+.|.||||.+
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 4678999999863
No 11
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=46.36 E-value=15 Score=24.17 Aligned_cols=28 Identities=25% Similarity=0.675 Sum_probs=18.3
Q ss_pred CcccccCCCCCCCCCc------cceEeecCCcce
Q 032843 2 TFKRRNGGRNKHGRGH------VKFIRCSNCGKC 29 (132)
Q Consensus 2 ~kKRrNnGR~KkgrGh------v~~V~C~NCgr~ 29 (132)
||+|-+..|..+=|.| ...+.|.+||..
T Consensus 2 PKrk~Sksr~~~RRah~~kl~~p~l~~C~~cG~~ 35 (55)
T TIGR01031 2 PKRKTSKSRKRKRRSHDAKLTAPTLVVCPNCGEF 35 (55)
T ss_pred CCCcCCcccccchhcCcccccCCcceECCCCCCc
Confidence 5555555555555555 457889999963
No 12
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=44.17 E-value=11 Score=25.99 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=11.5
Q ss_pred ceEeecCCcceeec
Q 032843 19 KFIRCSNCGKCCPK 32 (132)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (132)
-||+|..||+.+--
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 48999999997743
No 13
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=43.67 E-value=9.2 Score=25.84 Aligned_cols=17 Identities=35% Similarity=0.735 Sum_probs=14.7
Q ss_pred EeecCCcceeeccccee
Q 032843 21 IRCSNCGKCCPKDKAIK 37 (132)
Q Consensus 21 V~C~NCgr~vPKDKAIK 37 (132)
-||-+||.-+|-|++..
T Consensus 4 kHC~~CG~~Ip~~~~fC 20 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFC 20 (59)
T ss_pred CcCCcCCCcCCcchhhh
Confidence 37999999999998765
No 14
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=43.24 E-value=13 Score=21.37 Aligned_cols=15 Identities=53% Similarity=0.851 Sum_probs=7.7
Q ss_pred CCcccccCCCCCCCC
Q 032843 1 MTFKRRNGGRNKHGR 15 (132)
Q Consensus 1 M~kKRrNnGR~Kkgr 15 (132)
|-++||+.|++|+.|
T Consensus 1 ~k~~rrs~~~~kgar 15 (24)
T PF04726_consen 1 MKSKRRSGGKRKGAR 15 (24)
T ss_dssp --GGGS---SSSSS-
T ss_pred CcccccCCCccCceE
Confidence 567899999999865
No 15
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=43.19 E-value=11 Score=26.24 Aligned_cols=13 Identities=38% Similarity=0.772 Sum_probs=10.7
Q ss_pred ceEeecCCcceee
Q 032843 19 KFIRCSNCGKCCP 31 (132)
Q Consensus 19 ~~V~C~NCgr~vP 31 (132)
-||||-+||+.+-
T Consensus 3 iPiRCFsCGkvi~ 15 (63)
T COG1644 3 IPVRCFSCGKVIG 15 (63)
T ss_pred CceEeecCCCCHH
Confidence 4899999998653
No 16
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.84 E-value=14 Score=25.41 Aligned_cols=13 Identities=38% Similarity=0.838 Sum_probs=10.0
Q ss_pred cceEeecCCccee
Q 032843 18 VKFIRCSNCGKCC 30 (132)
Q Consensus 18 v~~V~C~NCgr~v 30 (132)
--.|.|+|||+.|
T Consensus 32 DIkikC~nC~h~v 44 (60)
T COG4481 32 DIKIKCENCGHSV 44 (60)
T ss_pred cEEEEecCCCcEE
Confidence 3468899999954
No 17
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=41.68 E-value=8.9 Score=28.68 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=11.9
Q ss_pred ccceEeecCCcceee
Q 032843 17 HVKFIRCSNCGKCCP 31 (132)
Q Consensus 17 hv~~V~C~NCgr~vP 31 (132)
..+.++|.||+|.|-
T Consensus 71 k~~~~hCeNC~RdVa 85 (103)
T KOG2612|consen 71 KPMDCHCENCDRDVA 85 (103)
T ss_pred CCccccCCCCccHHH
Confidence 456899999999763
No 18
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=39.84 E-value=14 Score=23.82 Aligned_cols=11 Identities=55% Similarity=1.428 Sum_probs=8.1
Q ss_pred eEEeeee-ceec
Q 032843 71 MQYCVSC-AIHS 81 (132)
Q Consensus 71 l~YCVSC-AIHs 81 (132)
.+|||+| -||.
T Consensus 1 MyYCi~Cs~~h~ 12 (41)
T PF13119_consen 1 MYYCINCSEIHH 12 (41)
T ss_pred CEEEEEhHHhHH
Confidence 3799999 5663
No 19
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=38.67 E-value=11 Score=29.11 Aligned_cols=31 Identities=23% Similarity=0.345 Sum_probs=19.8
Q ss_pred HHhhHHhhccccc----cccccceeeeEEeeeeceec
Q 032843 49 AVRDVQEACVYDG----YTLPKLYAKMQYCVSCAIHS 81 (132)
Q Consensus 49 avrDiseAsv~~~----y~lPKlyvKl~YCVSCAIHs 81 (132)
.-.||++..-++- -.||- .-.|||+.||-|.
T Consensus 31 i~nDls~~Es~~Klp~Dp~lPG--lGqhYCieCaryf 65 (126)
T COG5112 31 IKNDLSTKESQKKLPYDPELPG--LGQHYCIECARYF 65 (126)
T ss_pred HHHhcchhhhhccCCCCCCCCC--CceeeeehhHHHH
Confidence 3567766554432 23443 4689999999774
No 20
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=38.13 E-value=15 Score=24.56 Aligned_cols=18 Identities=39% Similarity=0.711 Sum_probs=13.7
Q ss_pred ceEeecCCcceeecccce
Q 032843 19 KFIRCSNCGKCCPKDKAI 36 (132)
Q Consensus 19 ~~V~C~NCgr~vPKDKAI 36 (132)
+-|||.+|++++-+-..+
T Consensus 3 ~eiRC~~CnklLa~~g~~ 20 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEV 20 (51)
T ss_pred cceeccchhHHHhhhcCc
Confidence 579999999988774333
No 21
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=38.04 E-value=16 Score=25.88 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=10.3
Q ss_pred ceEeecCCccee
Q 032843 19 KFIRCSNCGKCC 30 (132)
Q Consensus 19 ~~V~C~NCgr~v 30 (132)
-||||-.||+.+
T Consensus 3 iPVRCFTCGkvi 14 (71)
T PLN00032 3 IPVRCFTCGKVI 14 (71)
T ss_pred CceeecCCCCCc
Confidence 389999999866
No 22
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=36.72 E-value=13 Score=20.63 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=9.7
Q ss_pred EeecCCcceeecc
Q 032843 21 IRCSNCGKCCPKD 33 (132)
Q Consensus 21 V~C~NCgr~vPKD 33 (132)
+.|.|||.-++.|
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 5688888876665
No 23
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=36.56 E-value=8.8 Score=27.51 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=14.9
Q ss_pred Ccceeecccceeeeeecccchhh
Q 032843 26 CGKCCPKDKAIKRFLVRNIVEQA 48 (132)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVEaa 48 (132)
-||.|||+.|+..-.+..|.++.
T Consensus 16 ~GRrv~k~~aV~~P~~~EI~~a~ 38 (95)
T PF01922_consen 16 EGRRVPKELAVENPTLEEIADAC 38 (95)
T ss_dssp TT--SSTTTSBSS--HHHHHHHH
T ss_pred hccccChhhcCCCCCHHHHHHHH
Confidence 47999999999877777776654
No 24
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=34.44 E-value=31 Score=23.83 Aligned_cols=36 Identities=28% Similarity=0.422 Sum_probs=26.6
Q ss_pred cceEeecCCccee-ecccceeeeeecccchhhHHhhHH
Q 032843 18 VKFIRCSNCGKCC-PKDKAIKRFLVRNIVEQAAVRDVQ 54 (132)
Q Consensus 18 v~~V~C~NCgr~v-PKDKAIKrf~irNiVEaaavrDis 54 (132)
..+-.|++||+-+ |..++++ |.--|-=|....|...
T Consensus 7 ~~~~~CtSCg~~i~p~e~~v~-F~CPnCGe~~I~Rc~~ 43 (61)
T COG2888 7 KDPPVCTSCGREIAPGETAVK-FPCPNCGEVEIYRCAK 43 (61)
T ss_pred cCCceeccCCCEeccCCceeE-eeCCCCCceeeehhhh
Confidence 3456899999999 8878776 8888776666655543
No 25
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=32.48 E-value=14 Score=28.80 Aligned_cols=18 Identities=33% Similarity=0.598 Sum_probs=13.1
Q ss_pred cccccceeeeEEeeeeceec
Q 032843 62 YTLPKLYAKMQYCVSCAIHS 81 (132)
Q Consensus 62 y~lPKlyvKl~YCVSCAIHs 81 (132)
+-||- .-++||+-||-|.
T Consensus 50 ~dlPG--~GqfyCi~CaRyF 67 (129)
T KOG3408|consen 50 PDLPG--GGQFYCIECARYF 67 (129)
T ss_pred CCCCC--Cceeehhhhhhhh
Confidence 44553 4589999999774
No 26
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=32.05 E-value=15 Score=25.11 Aligned_cols=13 Identities=38% Similarity=0.761 Sum_probs=9.5
Q ss_pred ceEeecCCcceee
Q 032843 19 KFIRCSNCGKCCP 31 (132)
Q Consensus 19 ~~V~C~NCgr~vP 31 (132)
-||||-.||+.+-
T Consensus 3 iPVRCFTCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFTCGKVIG 15 (60)
T ss_dssp -SSS-STTTSBTC
T ss_pred CceecCCCCCChh
Confidence 3899999998774
No 27
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.16 E-value=41 Score=22.32 Aligned_cols=29 Identities=24% Similarity=0.608 Sum_probs=16.7
Q ss_pred CcccccCCCCCCCCCc-----cceEeecCCccee
Q 032843 2 TFKRRNGGRNKHGRGH-----VKFIRCSNCGKCC 30 (132)
Q Consensus 2 ~kKRrNnGR~KkgrGh-----v~~V~C~NCgr~v 30 (132)
||+|-+..|..+=|.| ...+.|.+||-..
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPK 37 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCcc
Confidence 4555555444444455 3466799998643
No 28
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=25.95 E-value=32 Score=24.16 Aligned_cols=12 Identities=50% Similarity=0.894 Sum_probs=10.0
Q ss_pred ceEeecCCccee
Q 032843 19 KFIRCSNCGKCC 30 (132)
Q Consensus 19 ~~V~C~NCgr~v 30 (132)
-||||-.||..+
T Consensus 3 iPiRCFtCGKvi 14 (69)
T KOG3497|consen 3 IPIRCFTCGKVI 14 (69)
T ss_pred eeeEeeeccccc
Confidence 389999999865
No 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.89 E-value=29 Score=19.07 Aligned_cols=12 Identities=42% Similarity=0.894 Sum_probs=9.3
Q ss_pred eecCCcceeecc
Q 032843 22 RCSNCGKCCPKD 33 (132)
Q Consensus 22 ~C~NCgr~vPKD 33 (132)
.|.+||.-++.|
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 388999888755
No 30
>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=25.49 E-value=24 Score=21.10 Aligned_cols=13 Identities=38% Similarity=0.777 Sum_probs=9.3
Q ss_pred cceEeecCCccee
Q 032843 18 VKFIRCSNCGKCC 30 (132)
Q Consensus 18 v~~V~C~NCgr~v 30 (132)
..+|+|.+||--+
T Consensus 15 ~~~irC~~CG~RI 27 (32)
T PF03604_consen 15 GDPIRCPECGHRI 27 (32)
T ss_dssp SSTSSBSSSS-SE
T ss_pred CCcEECCcCCCeE
Confidence 3579999999643
No 31
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=25.46 E-value=23 Score=28.17 Aligned_cols=32 Identities=19% Similarity=0.349 Sum_probs=0.0
Q ss_pred CccceEeecCCcceeecccceeeeeecccchhh
Q 032843 16 GHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQA 48 (132)
Q Consensus 16 Ghv~~V~C~NCgr~vPKDKAIKrf~irNiVEaa 48 (132)
..+..+.|..||..||-|+-=. -+--+++|+.
T Consensus 164 ~~~~~~~cPitGe~IP~~e~~e-HmRi~LlDP~ 195 (229)
T PF12230_consen 164 PKEKMIICPITGEMIPADEMDE-HMRIELLDPR 195 (229)
T ss_dssp ---------------------------------
T ss_pred cccccccccccccccccccccc-cccccccccc
Confidence 3567899999999999998654 2223344443
No 32
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=25.45 E-value=29 Score=28.58 Aligned_cols=48 Identities=27% Similarity=0.680 Sum_probs=34.1
Q ss_pred EeecCCcce---eecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeec
Q 032843 21 IRCSNCGKC---CPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCA 78 (132)
Q Consensus 21 V~C~NCgr~---vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCA 78 (132)
-.|.|||-| +|--.. -.|..|-||.-+...|.+ .++... .+++|++|-
T Consensus 39 ~~C~QCG~CT~sCPs~r~-t~y~pR~ii~~~~~g~~d--~il~~~-------~lW~C~tCy 89 (195)
T COG1150 39 EGCYQCGTCTGSCPSGRF-TDYSPRKIIRKARLGLVD--LILSSE-------SLWACVTCY 89 (195)
T ss_pred hHhhccCcccCCCCCccc-CCCCHHHHHHHHHcccHH--HHhcCC-------cceeeeech
Confidence 347777776 577777 678889999888877665 344333 368899983
No 33
>PF10589 NADH_4Fe-4S: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; InterPro: IPR019575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the F subunit of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. This entry represents the iron-sulphur binding domain of the F subunit.; GO: 0055114 oxidation-reduction process; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=24.97 E-value=20 Score=22.47 Aligned_cols=10 Identities=50% Similarity=1.262 Sum_probs=4.2
Q ss_pred cCCcceeecc
Q 032843 24 SNCGKCCPKD 33 (132)
Q Consensus 24 ~NCgr~vPKD 33 (132)
.+||+|+|-=
T Consensus 14 ESCGkC~PCR 23 (46)
T PF10589_consen 14 ESCGKCTPCR 23 (46)
T ss_dssp H--S--HHHH
T ss_pred cCCCCCCCcH
Confidence 5799999953
No 34
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=24.81 E-value=38 Score=29.07 Aligned_cols=44 Identities=27% Similarity=0.443 Sum_probs=27.1
Q ss_pred eEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeee
Q 032843 20 FIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSC 77 (132)
Q Consensus 20 ~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSC 77 (132)
+|+|-||+-.+||.+-. .++++|-..--|.+. |.|.-..-|--|
T Consensus 42 ~~RCL~C~~YI~K~~rf-----------NavkE~~~dK~y~~~---kiYRf~I~C~~C 85 (272)
T COG5134 42 PVRCLNCENYIQKGTRF-----------NAVKEEIGDKSYYTT---KIYRFSIKCHLC 85 (272)
T ss_pred ceeecchhhhhhcccch-----------hHHHHHhccccccee---EEEEEEEEccCC
Confidence 79999999999998632 246666543334333 445444444444
No 35
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.53 E-value=37 Score=23.19 Aligned_cols=25 Identities=40% Similarity=0.860 Sum_probs=17.7
Q ss_pred ceEeecCCcc-eeecccceeeeeeccc
Q 032843 19 KFIRCSNCGK-CCPKDKAIKRFLVRNI 44 (132)
Q Consensus 19 ~~V~C~NCgr-~vPKDKAIKrf~irNi 44 (132)
.+..|++||+ +.|.+++.+ |.=-|=
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~-F~CPnC 31 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVK-FLCPNC 31 (59)
T ss_pred cCccccCCCCcccCCCccCE-eeCCCC
Confidence 4557999998 556888875 665554
No 36
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=24.37 E-value=31 Score=23.09 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=10.1
Q ss_pred eeeEEeeeeceecc
Q 032843 69 AKMQYCVSCAIHSH 82 (132)
Q Consensus 69 vKl~YCVSCAIHsk 82 (132)
|...||.+|-...+
T Consensus 1 V~IeyC~~C~y~~R 14 (72)
T TIGR02174 1 VEIEYCGSCGYKPR 14 (72)
T ss_pred CEEEECCCCCChHH
Confidence 46789999975443
No 37
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.31 E-value=45 Score=19.94 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=10.9
Q ss_pred CccceEeecCCcce
Q 032843 16 GHVKFIRCSNCGKC 29 (132)
Q Consensus 16 Ghv~~V~C~NCgr~ 29 (132)
++...|+|++|+..
T Consensus 21 ~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 21 PKGRKVRCSKCGHV 34 (36)
T ss_pred CCCcEEECCCCCCE
Confidence 45568999999864
No 38
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.29 E-value=69 Score=26.67 Aligned_cols=23 Identities=35% Similarity=0.902 Sum_probs=16.3
Q ss_pred CCccceEeecCCccee------eccccee
Q 032843 15 RGHVKFIRCSNCGKCC------PKDKAIK 37 (132)
Q Consensus 15 rGhv~~V~C~NCgr~v------PKDKAIK 37 (132)
+|..-.++|.|||-.- ||-..++
T Consensus 25 ~g~~~lvrC~eCG~V~~~~i~~~k~~~v~ 53 (201)
T COG1326 25 RGREPLVRCEECGTVHPAIIKTPKPVRVR 53 (201)
T ss_pred cCCceEEEccCCCcEeeceeeccccceEE
Confidence 4555899999999865 4555554
No 39
>PF06639 BAP: Basal layer antifungal peptide (BAP); InterPro: IPR009540 This family consists of several basal layer antifungal peptide (BAP) sequences specific to Zea mays (Maize). The BAP2 peptide exhibits potent broad-range activity against a range of filamentous fungi, including several plant pathogens [].
Probab=23.77 E-value=20 Score=25.64 Aligned_cols=22 Identities=23% Similarity=0.610 Sum_probs=17.7
Q ss_pred eeeceecccccccCchhhccCC
Q 032843 75 VSCAIHSHVVRVRSRTNRRIRE 96 (132)
Q Consensus 75 VSCAIHskVVRvRS~e~RK~r~ 96 (132)
-||.||++|++=+-+|+-.-+.
T Consensus 5 AS~V~hA~ii~Gqtke~~nt~s 26 (75)
T PF06639_consen 5 ASCVIHAHIISGQTKEDSNTGS 26 (75)
T ss_pred hhhHhhHHhhcCceeeccCCCc
Confidence 4899999999998888765443
No 40
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=23.18 E-value=50 Score=22.42 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=10.6
Q ss_pred eEeecCCcce--eecc
Q 032843 20 FIRCSNCGKC--CPKD 33 (132)
Q Consensus 20 ~V~C~NCgr~--vPKD 33 (132)
.+.|++||+. +|+-
T Consensus 31 kikC~gCg~~imlpR~ 46 (57)
T PF06107_consen 31 KIKCLGCGRQIMLPRS 46 (57)
T ss_pred EEEECCCCCEEEEeHH
Confidence 5789999994 4553
No 41
>KOG3286 consensus Selenoprotein T [General function prediction only]
Probab=22.85 E-value=52 Score=27.82 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=11.2
Q ss_pred eeeeEEeeeeceec
Q 032843 68 YAKMQYCVSCAIHS 81 (132)
Q Consensus 68 yvKl~YCVSCAIHs 81 (132)
-++..|||||-.-.
T Consensus 71 tl~i~fCvSCgYk~ 84 (226)
T KOG3286|consen 71 TLEINFCVSCGYKQ 84 (226)
T ss_pred cEEEEEEEecCcHH
Confidence 47899999997644
No 42
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.34 E-value=65 Score=20.69 Aligned_cols=19 Identities=32% Similarity=0.651 Sum_probs=12.9
Q ss_pred CCccceEeecCCcceeecc
Q 032843 15 RGHVKFIRCSNCGKCCPKD 33 (132)
Q Consensus 15 rGhv~~V~C~NCgr~vPKD 33 (132)
....+...|.+||..+..|
T Consensus 41 ~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 41 RRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred ccccceEEcCCCCCEECcH
Confidence 3455566788888777666
No 43
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.70 E-value=37 Score=18.80 Aligned_cols=13 Identities=23% Similarity=0.743 Sum_probs=10.2
Q ss_pred eEeecCCcceeec
Q 032843 20 FIRCSNCGKCCPK 32 (132)
Q Consensus 20 ~V~C~NCgr~vPK 32 (132)
.+.|.+|||-..-
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 5789999997643
No 44
>PF14353 CpXC: CpXC protein
Probab=20.00 E-value=81 Score=22.71 Aligned_cols=45 Identities=27% Similarity=0.530 Sum_probs=26.8
Q ss_pred EeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeece
Q 032843 21 IRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAI 79 (132)
Q Consensus 21 V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAI 79 (132)
|.|.+||.-.- +.+..+|+++.--|+.++-. +|-.. .+-|.+|.-
T Consensus 2 itCP~C~~~~~-------~~v~~~I~~~~~p~l~e~il-~g~l~------~~~CP~Cg~ 46 (128)
T PF14353_consen 2 ITCPHCGHEFE-------FEVWTSINADEDPELKEKIL-DGSLF------SFTCPSCGH 46 (128)
T ss_pred cCCCCCCCeeE-------EEEEeEEcCcCCHHHHHHHH-cCCcC------EEECCCCCC
Confidence 67999987543 45555666555555554433 33322 677888854
Done!