Query 033740
Match_columns 112
No_of_seqs 107 out of 183
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 05:45:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033740.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033740hhsearch_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 4.3E-65 9.3E-70 367.6 7.7 107 1-107 1-107 (109)
2 PTZ00172 40S ribosomal protein 100.0 1.1E-64 2.3E-69 365.2 7.9 105 1-105 1-105 (108)
3 PF01283 Ribosomal_S26e: Ribos 100.0 7.9E-65 1.7E-69 368.0 5.1 103 1-103 1-103 (113)
4 PRK09335 30S ribosomal protein 100.0 1.4E-58 3.1E-63 327.3 7.0 94 1-98 1-94 (95)
5 KOG1768 40s ribosomal protein 100.0 1.2E-55 2.7E-60 320.7 3.2 106 1-106 1-106 (115)
6 COG4830 RPS26B Ribosomal prote 100.0 6.3E-53 1.4E-57 302.8 6.0 97 1-97 1-97 (108)
7 COG1400 SEC65 Signal recogniti 77.0 0.49 1.1E-05 33.7 -1.0 38 27-66 20-58 (93)
8 PF07503 zf-HYPF: HypF finger; 64.1 2.9 6.3E-05 24.7 0.5 13 15-27 16-28 (35)
9 PF08209 Sgf11: Sgf11 (transcr 58.7 6.6 0.00014 23.1 1.4 15 18-32 2-16 (33)
10 PF02591 DUF164: Putative zinc 57.3 5.6 0.00012 24.7 0.9 13 18-30 44-56 (56)
11 PF09889 DUF2116: Uncharacteri 56.6 4.3 9.3E-05 26.6 0.3 17 21-37 4-20 (59)
12 PF13119 DUF3973: Domain of un 52.4 5.4 0.00012 24.9 0.3 11 71-81 1-12 (41)
13 TIGR01031 rpmF_bact ribosomal 50.5 11 0.00025 24.0 1.6 28 2-29 2-35 (55)
14 PF04726 Microvir_J: Microviru 49.5 9.4 0.0002 21.3 0.9 15 1-15 1-15 (24)
15 PRK04016 DNA-directed RNA poly 47.7 8.8 0.00019 25.6 0.8 14 19-32 3-16 (62)
16 COG1644 RPB10 DNA-directed RNA 46.7 8.7 0.00019 25.9 0.6 13 19-31 3-15 (63)
17 COG2888 Predicted Zn-ribbon RN 46.1 18 0.00038 24.3 2.0 36 17-53 6-42 (61)
18 PF13248 zf-ribbon_3: zinc-rib 44.0 8.6 0.00019 20.8 0.2 13 21-33 3-15 (26)
19 COG4481 Uncharacterized protei 43.7 14 0.00029 24.7 1.2 13 18-30 32-44 (60)
20 PLN00032 DNA-directed RNA poly 41.2 13 0.00028 25.5 0.8 12 19-30 3-14 (71)
21 PF01922 SRP19: SRP19 protein; 40.7 6.3 0.00014 27.5 -0.8 23 26-48 16-38 (95)
22 KOG2612 Predicted integral mem 38.8 11 0.00023 27.5 0.1 15 17-31 71-85 (103)
23 PF10122 Mu-like_Com: Mu-like 36.5 16 0.00035 23.6 0.7 15 19-33 3-17 (51)
24 COG5134 Uncharacterized conser 35.4 21 0.00045 29.7 1.3 44 20-77 42-85 (272)
25 PF01194 RNA_pol_N: RNA polyme 35.4 12 0.00026 24.8 -0.1 13 19-31 3-15 (60)
26 COG5112 UFD2 U1-like Zn-finger 35.3 13 0.00029 27.8 0.1 31 49-81 31-65 (126)
27 PRK14890 putative Zn-ribbon RN 32.9 22 0.00047 23.6 0.9 26 19-45 6-32 (59)
28 PF03604 DNA_RNApol_7kD: DNA d 32.0 16 0.00034 21.2 0.0 13 18-30 15-27 (32)
29 PF13240 zinc_ribbon_2: zinc-r 31.3 20 0.00044 19.1 0.4 12 22-33 1-12 (23)
30 PF10589 NADH_4Fe-4S: NADH-ubi 31.1 13 0.00029 22.6 -0.4 11 24-34 14-24 (46)
31 KOG3198 Signal recognition par 30.4 13 0.00028 28.8 -0.6 18 27-44 32-49 (152)
32 PRK12286 rpmF 50S ribosomal pr 30.0 33 0.00071 22.1 1.3 29 2-30 4-37 (57)
33 PF06639 BAP: Basal layer anti 29.6 12 0.00027 25.9 -0.8 21 75-95 5-25 (75)
34 KOG3497 DNA-directed RNA polym 28.1 28 0.00061 23.7 0.8 13 19-31 3-15 (69)
35 COG1326 Uncharacterized archae 27.5 58 0.0012 26.3 2.5 24 15-38 25-54 (201)
36 KOG3408 U1-like Zn-finger-cont 26.6 20 0.00044 27.1 -0.1 19 61-81 49-67 (129)
37 PF13717 zinc_ribbon_4: zinc-r 26.2 40 0.00087 19.5 1.1 14 16-29 21-34 (36)
38 PF07282 OrfB_Zn_ribbon: Putat 25.6 53 0.0011 20.5 1.7 19 15-33 41-59 (69)
39 PF12230 PRP21_like_P: Pre-mRN 24.8 24 0.00053 27.3 0.0 32 16-48 164-195 (229)
40 COG1150 HdrC Heterodisulfide r 24.4 29 0.00063 27.7 0.4 48 20-77 38-88 (195)
41 PF13913 zf-C2HC_2: zinc-finge 23.7 32 0.00069 18.5 0.3 13 20-32 2-14 (25)
42 PF07754 DUF1610: Domain of un 22.8 68 0.0015 17.7 1.5 15 13-27 9-23 (24)
43 smart00659 RPOLCX RNA polymera 22.8 42 0.00092 20.5 0.8 13 18-30 17-29 (44)
44 PF06107 DUF951: Bacterial pro 22.8 52 0.0011 21.6 1.3 15 20-34 31-47 (57)
45 PRK00398 rpoP DNA-directed RNA 22.6 67 0.0015 19.0 1.6 11 21-31 4-14 (46)
46 PF14832 Tautomerase_3: Putati 22.5 59 0.0013 24.1 1.7 25 48-74 20-44 (136)
47 PF04810 zf-Sec23_Sec24: Sec23 21.5 37 0.00079 20.0 0.3 11 20-30 2-12 (40)
48 PF10262 Rdx: Rdx family; Int 21.3 33 0.0007 22.3 0.1 16 69-84 3-18 (76)
49 TIGR02098 MJ0042_CXXC MJ0042 f 21.0 60 0.0013 18.2 1.1 11 20-30 25-35 (38)
50 PF10238 Eapp_C: E2F-associate 20.6 85 0.0018 23.5 2.2 11 20-30 109-119 (136)
51 PRK00754 signal recognition pa 20.2 19 0.00042 25.4 -1.3 15 27-41 23-37 (95)
52 TIGR02174 CXXU_selWTH selT/sel 20.0 43 0.00094 21.7 0.5 12 69-80 1-12 (72)
No 1
>PLN00186 ribosomal protein S26; Provisional
Probab=100.00 E-value=4.3e-65 Score=367.64 Aligned_cols=107 Identities=81% Similarity=1.345 Sum_probs=103.1
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeeecee
Q 033740 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (112)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSCAIH 80 (112)
||+|||||||+|+|+|||++|+|+|||+|||||||||+|+|+||||+||++||+||+||++|.|||||+|++||||||||
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 cceecccCchhhccCCCCccccccCCc
Q 033740 81 SHVVRVRSRTDRRNREPPKRFMRRRVS 107 (112)
Q Consensus 81 skVVR~RS~e~RK~r~~p~r~~~~~~~ 107 (112)
++|||+||+|+||+|+||++|+...++
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~~~~ 107 (109)
T PLN00186 81 SRVVRVRSRENRRIREPPPRFRRRKDD 107 (109)
T ss_pred cceeecCChHHccccCCCccccccccC
Confidence 999999999999999999999443443
No 2
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=100.00 E-value=1.1e-64 Score=365.19 Aligned_cols=105 Identities=70% Similarity=1.185 Sum_probs=102.5
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeeecee
Q 033740 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (112)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSCAIH 80 (112)
||+|||||||+|+|+|||++|+|+|||+|||||||||+|+|+||||+|+++||+||+||++|+|||||+|+|||||||||
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 cceecccCchhhccCCCCccccccC
Q 033740 81 SHVVRVRSRTDRRNREPPKRFMRRR 105 (112)
Q Consensus 81 skVVR~RS~e~RK~r~~p~r~~~~~ 105 (112)
++|||+||+|+||+|+||+++.++.
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~~ 105 (108)
T PTZ00172 81 SRVVRVRSREDRKIRTPPKRPFRPT 105 (108)
T ss_pred CCeeecCChHHccccCCCCCCCCCc
Confidence 9999999999999999999985553
No 3
>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=7.9e-65 Score=368.03 Aligned_cols=103 Identities=69% Similarity=1.236 Sum_probs=73.0
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeeecee
Q 033740 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (112)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSCAIH 80 (112)
||+|||||||+|+|+||+++|+|+|||+|||||||||+|+|+||||+|++|||+||+||++|+|||||+|+|||||||||
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 cceecccCchhhccCCCCccccc
Q 033740 81 SHVVRVRSRTDRRNREPPKRFMR 103 (112)
Q Consensus 81 skVVR~RS~e~RK~r~~p~r~~~ 103 (112)
++|||+||+|+||+++||++|++
T Consensus 81 ~~IVr~Rs~e~RK~r~~p~~~~~ 103 (113)
T PF01283_consen 81 SKIVRVRSREERKDRTPPPRFRP 103 (113)
T ss_dssp TTSS----TCCCC--S-------
T ss_pred ccccccCChHHccccCCCCcCCc
Confidence 99999999999999999999943
No 4
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=100.00 E-value=1.4e-58 Score=327.26 Aligned_cols=94 Identities=30% Similarity=0.675 Sum_probs=92.0
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeeecee
Q 033740 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (112)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSCAIH 80 (112)
||+||+||||+|+|+||+++|+|+|||++||||||||+|+|+||||+++++||+||++| |||||+|++||||||||
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 99999999999999999999999999999999999999999999999999999999877 99999999999999999
Q ss_pred cceecccCchhhccCCCC
Q 033740 81 SHVVRVRSRTDRRNREPP 98 (112)
Q Consensus 81 skVVR~RS~e~RK~r~~p 98 (112)
++|||+||+|+||+++|.
T Consensus 77 ~~IVrvRs~e~Rk~r~~~ 94 (95)
T PRK09335 77 LGIIKIRPEEERKKKAPL 94 (95)
T ss_pred ccccccCChHHcccccCC
Confidence 999999999999999864
No 5
>KOG1768 consensus 40s ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-55 Score=320.72 Aligned_cols=106 Identities=71% Similarity=1.194 Sum_probs=102.8
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeeecee
Q 033740 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (112)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSCAIH 80 (112)
||+||+|+|++|+|+||+++|+|+||++|+|||||||+|+|+||||++++|||+|||||++|+|||||+|||||||||||
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 cceecccCchhhccCCCCccccccCC
Q 033740 81 SHVVRVRSRTDRRNREPPKRFMRRRV 106 (112)
Q Consensus 81 skVVR~RS~e~RK~r~~p~r~~~~~~ 106 (112)
++|||+||+|.||+|+||++|.+...
T Consensus 81 skVvR~rS~e~rrir~pp~rf~~~~~ 106 (115)
T KOG1768|consen 81 SKVVRVRSREARRIRTPPPRFSPRAP 106 (115)
T ss_pred eeeeccchhhhhcccCCCcccCcccc
Confidence 99999999999999999999855444
No 6
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-53 Score=302.77 Aligned_cols=97 Identities=63% Similarity=1.108 Sum_probs=96.6
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeeecee
Q 033740 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (112)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSCAIH 80 (112)
|||||+||||+|+|+||+.+|+|+|||..||||||||+|.|+|+||+|+++||++|+||+.|.+||+|.|+|||||||||
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 cceecccCchhhccCCC
Q 033740 81 SHVVRVRSRTDRRNREP 97 (112)
Q Consensus 81 skVVR~RS~e~RK~r~~ 97 (112)
++|||+||+|+||++.|
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=77.05 E-value=0.49 Score=33.72 Aligned_cols=38 Identities=24% Similarity=0.388 Sum_probs=26.2
Q ss_pred cceeecccceeeeeecccchhhHhhhHHHhc-cccccccce
Q 033740 27 GKCCPKDKAIKRFLVRNIVEQAAVRDVQDAC-IYDNYVLPK 66 (112)
Q Consensus 27 gr~vPKDKAIKrf~irNiVeaaa~rDi~eas-v~~~y~lPK 66 (112)
||.|||+.||..+...+|+| |+++|-=.. +.....-|+
T Consensus 20 GRrvpk~laV~~P~~~ei~~--a~~~LGl~~~v~~dk~yPr 58 (93)
T COG1400 20 GRRVPKELAVENPSLEEIAE--ALRELGLKPKVERDKKYPR 58 (93)
T ss_pred ccccchhhcccCCCHHHHHH--HHHHcCCCeeechhhcCCC
Confidence 59999999999999999888 455554332 333333444
No 8
>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=64.05 E-value=2.9 Score=24.72 Aligned_cols=13 Identities=62% Similarity=1.300 Sum_probs=8.8
Q ss_pred CCccceEeecCCc
Q 033740 15 RGHVNFIRCSNCG 27 (112)
Q Consensus 15 rGhv~~V~C~nCg 27 (112)
|=|-++|-|++||
T Consensus 16 R~~~~~isC~~CG 28 (35)
T PF07503_consen 16 RFHYQFISCTNCG 28 (35)
T ss_dssp TTT-TT--BTTCC
T ss_pred cccCcCccCCCCC
Confidence 5689999999999
No 9
>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=58.68 E-value=6.6 Score=23.06 Aligned_cols=15 Identities=27% Similarity=0.888 Sum_probs=10.4
Q ss_pred cceEeecCCcceeec
Q 033740 18 VNFIRCSNCGKCCPK 32 (112)
Q Consensus 18 v~~V~C~nCgr~vPK 32 (112)
.+.+.|.||+|-|.-
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 467899999998754
No 10
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=57.27 E-value=5.6 Score=24.69 Aligned_cols=13 Identities=31% Similarity=0.841 Sum_probs=10.4
Q ss_pred cceEeecCCccee
Q 033740 18 VNFIRCSNCGKCC 30 (112)
Q Consensus 18 v~~V~C~nCgr~v 30 (112)
...+.|+||||.+
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 4678999999863
No 11
>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=56.59 E-value=4.3 Score=26.65 Aligned_cols=17 Identities=35% Similarity=0.735 Sum_probs=14.6
Q ss_pred EeecCCcceeeccccee
Q 033740 21 IRCSNCGKCCPKDKAIK 37 (112)
Q Consensus 21 V~C~nCgr~vPKDKAIK 37 (112)
-||-+||.-+|-|++..
T Consensus 4 kHC~~CG~~Ip~~~~fC 20 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFC 20 (59)
T ss_pred CcCCcCCCcCCcchhhh
Confidence 37999999999998765
No 12
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=52.44 E-value=5.4 Score=24.88 Aligned_cols=11 Identities=55% Similarity=1.428 Sum_probs=8.1
Q ss_pred EEEeeee-ceec
Q 033740 71 MQYCVSC-AIHS 81 (112)
Q Consensus 71 l~YCvSC-AIHs 81 (112)
.+|||+| -||.
T Consensus 1 MyYCi~Cs~~h~ 12 (41)
T PF13119_consen 1 MYYCINCSEIHH 12 (41)
T ss_pred CEEEEEhHHhHH
Confidence 3799999 5663
No 13
>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=50.52 E-value=11 Score=23.99 Aligned_cols=28 Identities=25% Similarity=0.680 Sum_probs=18.4
Q ss_pred CcccccCCCCCCCCCc------cceEeecCCcce
Q 033740 2 TFKRRNGGRNKHGRGH------VNFIRCSNCGKC 29 (112)
Q Consensus 2 ~kKRrNnGr~KkgrGh------v~~V~C~nCgr~ 29 (112)
||+|-+..|..+=|.| .+.+.|.+||..
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 567889999964
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=49.52 E-value=9.4 Score=21.29 Aligned_cols=15 Identities=53% Similarity=0.851 Sum_probs=7.8
Q ss_pred CCcccccCCCCCCCC
Q 033740 1 MTFKRRNGGRNKHGR 15 (112)
Q Consensus 1 M~kKRrNnGr~Kkgr 15 (112)
|-++||+.|++|+.|
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
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=47.70 E-value=8.8 Score=25.65 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=11.6
Q ss_pred ceEeecCCcceeec
Q 033740 19 NFIRCSNCGKCCPK 32 (112)
Q Consensus 19 ~~V~C~nCgr~vPK 32 (112)
-||+|..||+.+--
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 48999999997743
No 16
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=46.74 E-value=8.7 Score=25.90 Aligned_cols=13 Identities=38% Similarity=0.754 Sum_probs=10.8
Q ss_pred ceEeecCCcceee
Q 033740 19 NFIRCSNCGKCCP 31 (112)
Q Consensus 19 ~~V~C~nCgr~vP 31 (112)
-||+|-+||+.+-
T Consensus 3 iPiRCFsCGkvi~ 15 (63)
T COG1644 3 IPVRCFSCGKVIG 15 (63)
T ss_pred CceEeecCCCCHH
Confidence 4899999998653
No 17
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=46.08 E-value=18 Score=24.31 Aligned_cols=36 Identities=28% Similarity=0.412 Sum_probs=26.8
Q ss_pred ccceEeecCCccee-ecccceeeeeecccchhhHhhhH
Q 033740 17 HVNFIRCSNCGKCC-PKDKAIKRFLVRNIVEQAAVRDV 53 (112)
Q Consensus 17 hv~~V~C~nCgr~v-PKDKAIKrf~irNiVeaaa~rDi 53 (112)
+..+-.|++||+-+ |...|++ |.=.|==|....|..
T Consensus 6 ~~~~~~CtSCg~~i~p~e~~v~-F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 6 MKDPPVCTSCGREIAPGETAVK-FPCPNCGEVEIYRCA 42 (61)
T ss_pred ccCCceeccCCCEeccCCceeE-eeCCCCCceeeehhh
Confidence 34466899999999 8888876 888877666665544
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=44.00 E-value=8.6 Score=20.77 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=9.7
Q ss_pred EeecCCcceeecc
Q 033740 21 IRCSNCGKCCPKD 33 (112)
Q Consensus 21 V~C~nCgr~vPKD 33 (112)
+.|.|||.-++.|
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 5688888876665
No 19
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.69 E-value=14 Score=24.71 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=10.0
Q ss_pred cceEeecCCccee
Q 033740 18 VNFIRCSNCGKCC 30 (112)
Q Consensus 18 v~~V~C~nCgr~v 30 (112)
--.|.|+|||+.|
T Consensus 32 DIkikC~nC~h~v 44 (60)
T COG4481 32 DIKIKCENCGHSV 44 (60)
T ss_pred cEEEEecCCCcEE
Confidence 3468899999954
No 20
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=41.16 E-value=13 Score=25.51 Aligned_cols=12 Identities=42% Similarity=0.850 Sum_probs=10.4
Q ss_pred ceEeecCCccee
Q 033740 19 NFIRCSNCGKCC 30 (112)
Q Consensus 19 ~~V~C~nCgr~v 30 (112)
-||||-.||+.+
T Consensus 3 iPVRCFTCGkvi 14 (71)
T PLN00032 3 IPVRCFTCGKVI 14 (71)
T ss_pred CceeecCCCCCc
Confidence 389999999876
No 21
>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=40.71 E-value=6.3 Score=27.47 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=14.0
Q ss_pred Ccceeecccceeeeeecccchhh
Q 033740 26 CGKCCPKDKAIKRFLVRNIVEQA 48 (112)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVeaa 48 (112)
-||.|||+.|+..-.+..|.+|.
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 47999999999866666665543
No 22
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=38.79 E-value=11 Score=27.46 Aligned_cols=15 Identities=20% Similarity=0.412 Sum_probs=11.9
Q ss_pred ccceEeecCCcceee
Q 033740 17 HVNFIRCSNCGKCCP 31 (112)
Q Consensus 17 hv~~V~C~nCgr~vP 31 (112)
..+.++|.||+|.|.
T Consensus 71 k~~~~hCeNC~RdVa 85 (103)
T KOG2612|consen 71 KPMDCHCENCDRDVA 85 (103)
T ss_pred CCccccCCCCccHHH
Confidence 456799999999763
No 23
>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=36.46 E-value=16 Score=23.60 Aligned_cols=15 Identities=40% Similarity=0.755 Sum_probs=12.4
Q ss_pred ceEeecCCcceeecc
Q 033740 19 NFIRCSNCGKCCPKD 33 (112)
Q Consensus 19 ~~V~C~nCgr~vPKD 33 (112)
+-|||.+|++++-+-
T Consensus 3 ~eiRC~~CnklLa~~ 17 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKA 17 (51)
T ss_pred cceeccchhHHHhhh
Confidence 568999999988774
No 24
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=35.44 E-value=21 Score=29.75 Aligned_cols=44 Identities=30% Similarity=0.486 Sum_probs=28.9
Q ss_pred eEeecCCcceeecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeee
Q 033740 20 FIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSC 77 (112)
Q Consensus 20 ~V~C~nCgr~vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSC 77 (112)
+|+|-||+-.+||.+-. | ++++|...--|++- |.|.-.--|.-|
T Consensus 42 ~~RCL~C~~YI~K~~rf------N-----avkE~~~dK~y~~~---kiYRf~I~C~~C 85 (272)
T COG5134 42 PVRCLNCENYIQKGTRF------N-----AVKEEIGDKSYYTT---KIYRFSIKCHLC 85 (272)
T ss_pred ceeecchhhhhhcccch------h-----HHHHHhccccccee---EEEEEEEEccCC
Confidence 79999999999998754 3 67777665444443 444444344444
No 25
>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=35.43 E-value=12 Score=24.81 Aligned_cols=13 Identities=38% Similarity=0.744 Sum_probs=9.5
Q ss_pred ceEeecCCcceee
Q 033740 19 NFIRCSNCGKCCP 31 (112)
Q Consensus 19 ~~V~C~nCgr~vP 31 (112)
-||||-.||+.+-
T Consensus 3 iPVRCFTCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFTCGKVIG 15 (60)
T ss_dssp -SSS-STTTSBTC
T ss_pred CceecCCCCCChh
Confidence 3899999999774
No 26
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=35.27 E-value=13 Score=27.83 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=19.9
Q ss_pred HhhhHHHhcccc----ccccceeeeeEEEeeeeceec
Q 033740 49 AVRDVQDACIYD----NYVLPKLYAKMQYCVSCAIHS 81 (112)
Q Consensus 49 a~rDi~easv~~----~y~lPKlyvKl~YCvSCAIHs 81 (112)
.-.||++..-++ .-.||- .-.|||+.||-|.
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 345776654443 234555 5789999999764
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=32.90 E-value=22 Score=23.60 Aligned_cols=26 Identities=38% Similarity=0.781 Sum_probs=18.2
Q ss_pred ceEeecCCcc-eeecccceeeeeecccc
Q 033740 19 NFIRCSNCGK-CCPKDKAIKRFLVRNIV 45 (112)
Q Consensus 19 ~~V~C~nCgr-~vPKDKAIKrf~irNiV 45 (112)
.+..|++||+ +.|.++|.+ |.=.|==
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~-F~CPnCG 32 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVK-FLCPNCG 32 (59)
T ss_pred cCccccCCCCcccCCCccCE-eeCCCCC
Confidence 4557999998 556888875 6655543
No 28
>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=32.01 E-value=16 Score=21.22 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=9.3
Q ss_pred cceEeecCCccee
Q 033740 18 VNFIRCSNCGKCC 30 (112)
Q Consensus 18 v~~V~C~nCgr~v 30 (112)
..+|+|.+||--+
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 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.26 E-value=20 Score=19.11 Aligned_cols=12 Identities=42% Similarity=0.894 Sum_probs=9.3
Q ss_pred eecCCcceeecc
Q 033740 22 RCSNCGKCCPKD 33 (112)
Q Consensus 22 ~C~nCgr~vPKD 33 (112)
.|.+||.-++.|
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 388999888755
No 30
>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=31.12 E-value=13 Score=22.61 Aligned_cols=11 Identities=45% Similarity=1.183 Sum_probs=4.6
Q ss_pred cCCcceeeccc
Q 033740 24 SNCGKCCPKDK 34 (112)
Q Consensus 24 ~nCgr~vPKDK 34 (112)
.+||+|+|-=.
T Consensus 14 ESCGkC~PCR~ 24 (46)
T PF10589_consen 14 ESCGKCTPCRE 24 (46)
T ss_dssp H--S--HHHHC
T ss_pred cCCCCCCCcHh
Confidence 47999999533
No 31
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.36 E-value=13 Score=28.81 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=13.1
Q ss_pred cceeecccceeeeeeccc
Q 033740 27 GKCCPKDKAIKRFLVRNI 44 (112)
Q Consensus 27 gr~vPKDKAIKrf~irNi 44 (112)
||++||||||..=.-.+|
T Consensus 32 GRripke~aVeNP~a~eI 49 (152)
T KOG3198|consen 32 GRRIPKEKAVENPLAKEI 49 (152)
T ss_pred ccccCHHHhhcCcchhHH
Confidence 699999999974444443
No 32
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.96 E-value=33 Score=22.10 Aligned_cols=29 Identities=24% Similarity=0.626 Sum_probs=16.7
Q ss_pred CcccccCCCCCCCCCc-----cceEeecCCccee
Q 033740 2 TFKRRNGGRNKHGRGH-----VNFIRCSNCGKCC 30 (112)
Q Consensus 2 ~kKRrNnGr~KkgrGh-----v~~V~C~nCgr~v 30 (112)
||+|-+..|.-+=|.| .+.+.|.+||...
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPK 37 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCcc
Confidence 4555444444444454 3466799998743
No 33
>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=29.61 E-value=12 Score=25.92 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=17.5
Q ss_pred eeeceecceecccCchhhccC
Q 033740 75 VSCAIHSHVVRVRSRTDRRNR 95 (112)
Q Consensus 75 vSCAIHskVVR~RS~e~RK~r 95 (112)
.||.+|+.|++-+-+|+-.-+
T Consensus 5 AS~V~hA~ii~Gqtke~~nt~ 25 (75)
T PF06639_consen 5 ASCVIHAHIISGQTKEDSNTG 25 (75)
T ss_pred hhhHhhHHhhcCceeeccCCC
Confidence 489999999999988876554
No 34
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=28.11 E-value=28 Score=23.72 Aligned_cols=13 Identities=46% Similarity=0.767 Sum_probs=10.5
Q ss_pred ceEeecCCcceee
Q 033740 19 NFIRCSNCGKCCP 31 (112)
Q Consensus 19 ~~V~C~nCgr~vP 31 (112)
-||+|-.||..+-
T Consensus 3 iPiRCFtCGKvig 15 (69)
T KOG3497|consen 3 IPIRCFTCGKVIG 15 (69)
T ss_pred eeeEeeecccccc
Confidence 3899999998653
No 35
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=27.52 E-value=58 Score=26.33 Aligned_cols=24 Identities=33% Similarity=0.833 Sum_probs=17.1
Q ss_pred CCccceEeecCCccee------ecccceee
Q 033740 15 RGHVNFIRCSNCGKCC------PKDKAIKR 38 (112)
Q Consensus 15 rGhv~~V~C~nCgr~v------PKDKAIKr 38 (112)
+|....++|.|||..- ||-.+++.
T Consensus 25 ~g~~~lvrC~eCG~V~~~~i~~~k~~~v~v 54 (201)
T COG1326 25 RGREPLVRCEECGTVHPAIIKTPKPVRVRV 54 (201)
T ss_pred cCCceEEEccCCCcEeeceeeccccceEEE
Confidence 4555899999999865 55555553
No 36
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=26.62 E-value=20 Score=27.10 Aligned_cols=19 Identities=32% Similarity=0.555 Sum_probs=14.1
Q ss_pred ccccceeeeeEEEeeeeceec
Q 033740 61 NYVLPKLYAKMQYCVSCAIHS 81 (112)
Q Consensus 61 ~y~lPKlyvKl~YCvSCAIHs 81 (112)
.+-||- .-++||+.||-|.
T Consensus 49 D~dlPG--~GqfyCi~CaRyF 67 (129)
T KOG3408|consen 49 DPDLPG--GGQFYCIECARYF 67 (129)
T ss_pred CCCCCC--Cceeehhhhhhhh
Confidence 445665 5789999999764
No 37
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.19 E-value=40 Score=19.53 Aligned_cols=14 Identities=36% Similarity=0.802 Sum_probs=10.8
Q ss_pred CccceEeecCCcce
Q 033740 16 GHVNFIRCSNCGKC 29 (112)
Q Consensus 16 Ghv~~V~C~nCgr~ 29 (112)
+....++|++||..
T Consensus 21 ~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 21 PKGRKVRCSKCGHV 34 (36)
T ss_pred CCCcEEECCCCCCE
Confidence 45568999999964
No 38
>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=25.61 E-value=53 Score=20.52 Aligned_cols=19 Identities=32% Similarity=0.609 Sum_probs=13.0
Q ss_pred CCccceEeecCCcceeecc
Q 033740 15 RGHVNFIRCSNCGKCCPKD 33 (112)
Q Consensus 15 rGhv~~V~C~nCgr~vPKD 33 (112)
........|.+||..+..|
T Consensus 41 ~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 41 RRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred ccccceEEcCCCCCEECcH
Confidence 3455566788888777766
No 39
>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=24.75 E-value=24 Score=27.27 Aligned_cols=32 Identities=16% Similarity=0.324 Sum_probs=0.0
Q ss_pred CccceEeecCCcceeecccceeeeeecccchhh
Q 033740 16 GHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQA 48 (112)
Q Consensus 16 Ghv~~V~C~nCgr~vPKDKAIKrf~irNiVeaa 48 (112)
..+..+.|..||..||-|+-=. -.--+++|+.
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 2222455543
No 40
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=24.36 E-value=29 Score=27.72 Aligned_cols=48 Identities=29% Similarity=0.711 Sum_probs=34.4
Q ss_pred eEeecCCcce---eecccceeeeeecccchhhHhhhHHHhccccccccceeeeeEEEeeee
Q 033740 20 FIRCSNCGKC---CPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSC 77 (112)
Q Consensus 20 ~V~C~nCgr~---vPKDKAIKrf~irNiVeaaa~rDi~easv~~~y~lPKlyvKl~YCvSC 77 (112)
.-.|.|||-| .|--.. -.|..|-|+.-+...|.. .++.... ++.|++|
T Consensus 38 l~~C~QCG~CT~sCPs~r~-t~y~pR~ii~~~~~g~~d--~il~~~~-------lW~C~tC 88 (195)
T COG1150 38 LEGCYQCGTCTGSCPSGRF-TDYSPRKIIRKARLGLVD--LILSSES-------LWACVTC 88 (195)
T ss_pred HhHhhccCcccCCCCCccc-CCCCHHHHHHHHHcccHH--HHhcCCc-------ceeeeec
Confidence 3347787776 577777 678888899888877765 4444443 4899998
No 41
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=23.74 E-value=32 Score=18.47 Aligned_cols=13 Identities=23% Similarity=0.743 Sum_probs=10.1
Q ss_pred eEeecCCcceeec
Q 033740 20 FIRCSNCGKCCPK 32 (112)
Q Consensus 20 ~V~C~nCgr~vPK 32 (112)
.+.|.+|||-..-
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 5789999997643
No 42
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=22.79 E-value=68 Score=17.66 Aligned_cols=15 Identities=33% Similarity=0.682 Sum_probs=10.2
Q ss_pred CCCCccceEeecCCc
Q 033740 13 HGRGHVNFIRCSNCG 27 (112)
Q Consensus 13 kgrGhv~~V~C~nCg 27 (112)
-++++.-.-.|.|||
T Consensus 9 ~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 9 APREQAVPFPCPNCG 23 (24)
T ss_pred cCcccCceEeCCCCC
Confidence 456666667777777
No 43
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.79 E-value=42 Score=20.45 Aligned_cols=13 Identities=31% Similarity=0.853 Sum_probs=10.6
Q ss_pred cceEeecCCccee
Q 033740 18 VNFIRCSNCGKCC 30 (112)
Q Consensus 18 v~~V~C~nCgr~v 30 (112)
..+|+|.+||--+
T Consensus 17 ~~~irC~~CG~rI 29 (44)
T smart00659 17 KDVVRCRECGYRI 29 (44)
T ss_pred CCceECCCCCceE
Confidence 4689999999854
No 44
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=22.79 E-value=52 Score=21.64 Aligned_cols=15 Identities=40% Similarity=0.979 Sum_probs=11.1
Q ss_pred eEeecCCcce--eeccc
Q 033740 20 FIRCSNCGKC--CPKDK 34 (112)
Q Consensus 20 ~V~C~nCgr~--vPKDK 34 (112)
.+.|++||+. +|+-+
T Consensus 31 kikC~gCg~~imlpR~~ 47 (57)
T PF06107_consen 31 KIKCLGCGRQIMLPRSK 47 (57)
T ss_pred EEEECCCCCEEEEeHHH
Confidence 5789999994 56543
No 45
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.55 E-value=67 Score=18.99 Aligned_cols=11 Identities=27% Similarity=0.975 Sum_probs=5.3
Q ss_pred EeecCCcceee
Q 033740 21 IRCSNCGKCCP 31 (112)
Q Consensus 21 V~C~nCgr~vP 31 (112)
.+|.|||..+-
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 34555555443
No 46
>PF14832 Tautomerase_3: Putative oxalocrotonate tautomerase enzyme; PDB: 3C6V_C 3N4D_I 3N4G_C 3N4H_A 2FLZ_C 3MF8_A 3MF7_A 2FLT_A.
Probab=22.48 E-value=59 Score=24.05 Aligned_cols=25 Identities=24% Similarity=0.562 Sum_probs=17.4
Q ss_pred hHhhhHHHhccccccccceeeeeEEEe
Q 033740 48 AAVRDVQDACIYDNYVLPKLYAKMQYC 74 (112)
Q Consensus 48 aa~rDi~easv~~~y~lPKlyvKl~YC 74 (112)
+++.+|.+. |.++-||.+||-..+.
T Consensus 20 ~LA~~IT~~--y~~~glP~FyV~V~F~ 44 (136)
T PF14832_consen 20 ALAEAITDI--YTSIGLPAFYVNVRFI 44 (136)
T ss_dssp HHHHHHHHH--HHHTTTTGGG-EEEEE
T ss_pred HHHHHHHHH--HhCCCCCCEEEEEEEE
Confidence 456666654 7667899999998775
No 47
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=21.49 E-value=37 Score=19.96 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=5.2
Q ss_pred eEeecCCccee
Q 033740 20 FIRCSNCGKCC 30 (112)
Q Consensus 20 ~V~C~nCgr~v 30 (112)
|++|.+|+..+
T Consensus 2 p~rC~~C~ayl 12 (40)
T PF04810_consen 2 PVRCRRCRAYL 12 (40)
T ss_dssp S-B-TTT--BS
T ss_pred ccccCCCCCEE
Confidence 68888888754
No 48
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=21.31 E-value=33 Score=22.29 Aligned_cols=16 Identities=25% Similarity=0.847 Sum_probs=12.6
Q ss_pred eeEEEeeeeceeccee
Q 033740 69 AKMQYCVSCAIHSHVV 84 (112)
Q Consensus 69 vKl~YCvSCAIHskVV 84 (112)
|...||.+|-.|.+..
T Consensus 3 V~IeYC~~C~~~~~a~ 18 (76)
T PF10262_consen 3 VTIEYCTSCGYRPRAL 18 (76)
T ss_dssp EEEEEETTTTCHHHHH
T ss_pred EEEEECCCCCCHHHHH
Confidence 7789999998776543
No 49
>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=20.95 E-value=60 Score=18.23 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=8.8
Q ss_pred eEeecCCccee
Q 033740 20 FIRCSNCGKCC 30 (112)
Q Consensus 20 ~V~C~nCgr~v 30 (112)
.|+|.+||..+
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 68999999753
No 50
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=20.61 E-value=85 Score=23.55 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=9.2
Q ss_pred eEeecCCccee
Q 033740 20 FIRCSNCGKCC 30 (112)
Q Consensus 20 ~V~C~nCgr~v 30 (112)
||.|+.|+--|
T Consensus 109 PV~Cs~C~TeV 119 (136)
T PF10238_consen 109 PVKCSECSTEV 119 (136)
T ss_pred ceecccCCCEE
Confidence 89999999644
No 51
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=20.23 E-value=19 Score=25.38 Aligned_cols=15 Identities=20% Similarity=0.302 Sum_probs=11.5
Q ss_pred cceeecccceeeeee
Q 033740 27 GKCCPKDKAIKRFLV 41 (112)
Q Consensus 27 gr~vPKDKAIKrf~i 41 (112)
||.||++.|+..=.+
T Consensus 23 GRrv~k~~aV~~P~~ 37 (95)
T PRK00754 23 GRIISRKLAVKEPRL 37 (95)
T ss_pred cCccCHHHhccCCCH
Confidence 799999999874333
No 52
>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=20.03 E-value=43 Score=21.74 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=8.8
Q ss_pred eeEEEeeeecee
Q 033740 69 AKMQYCVSCAIH 80 (112)
Q Consensus 69 vKl~YCvSCAIH 80 (112)
|...||.+|-..
T Consensus 1 V~IeyC~~C~y~ 12 (72)
T TIGR02174 1 VEIEYCGSCGYK 12 (72)
T ss_pred CEEEECCCCCCh
Confidence 457899999743
Done!