Query 032901
Match_columns 130
No_of_seqs 103 out of 200
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:20:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032901hhsearch_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 5.9E-60 1.3E-64 348.9 7.8 105 1-105 1-107 (109)
2 PF01283 Ribosomal_S26e: Ribos 100.0 1.5E-60 3.3E-65 353.8 4.3 108 1-108 1-110 (113)
3 PTZ00172 40S ribosomal protein 100.0 2.1E-59 4.5E-64 345.6 8.1 102 1-102 1-104 (108)
4 PRK09335 30S ribosomal protein 100.0 1.3E-53 2.9E-58 309.0 6.9 92 1-96 1-94 (95)
5 KOG1768 40s ribosomal protein 100.0 3.6E-51 7.9E-56 304.3 4.2 106 1-106 1-108 (115)
6 COG4830 RPS26B Ribosomal prote 100.0 6.7E-49 1.4E-53 288.5 5.9 95 1-95 1-97 (108)
7 PF02591 DUF164: Putative zinc 58.2 5.5 0.00012 25.3 1.1 13 18-30 44-56 (56)
8 PF07503 zf-HYPF: HypF finger; 56.8 5.3 0.00011 24.2 0.7 13 15-27 16-28 (35)
9 PF08209 Sgf11: Sgf11 (transcr 56.3 6.1 0.00013 23.8 0.9 15 18-32 2-16 (33)
10 TIGR01031 rpmF_bact ribosomal 51.4 12 0.00026 24.5 1.8 30 2-31 2-37 (55)
11 COG1644 RPB10 DNA-directed RNA 50.7 7.3 0.00016 27.0 0.7 14 19-32 3-16 (63)
12 PF01194 RNA_pol_N: RNA polyme 50.0 3.3 7.2E-05 28.2 -1.0 14 19-32 3-16 (60)
13 PRK04016 DNA-directed RNA poly 49.9 8.3 0.00018 26.4 0.9 14 19-32 3-16 (62)
14 PF04726 Microvir_J: Microviru 49.1 9.4 0.0002 21.9 0.9 15 1-15 1-15 (24)
15 KOG2612 Predicted integral mem 48.7 6.8 0.00015 29.2 0.4 16 17-32 71-86 (103)
16 COG1150 HdrC Heterodisulfide r 47.3 7.3 0.00016 31.9 0.4 48 20-76 38-89 (195)
17 PLN00032 DNA-directed RNA poly 45.1 11 0.00024 26.6 0.9 14 19-32 3-16 (71)
18 COG5112 UFD2 U1-like Zn-finger 43.2 7.6 0.00017 29.8 -0.1 31 47-79 31-65 (126)
19 PF13119 DUF3973: Domain of un 41.4 12 0.00026 24.0 0.6 11 69-79 1-12 (41)
20 KOG3408 U1-like Zn-finger-cont 37.2 11 0.00023 29.4 -0.1 18 60-79 50-67 (129)
21 COG1400 SEC65 Signal recogniti 35.1 9.6 0.00021 27.9 -0.6 23 27-51 20-44 (93)
22 PF10122 Mu-like_Com: Mu-like 33.4 22 0.00047 23.7 0.9 14 19-32 3-16 (51)
23 COG5134 Uncharacterized conser 32.8 25 0.00053 30.1 1.4 44 20-75 42-85 (272)
24 PRK12286 rpmF 50S ribosomal pr 32.6 29 0.00062 23.0 1.4 31 2-32 4-39 (57)
25 COG4481 Uncharacterized protei 30.9 25 0.00055 24.0 0.9 15 16-30 30-44 (60)
26 KOG3497 DNA-directed RNA polym 30.4 22 0.00048 24.8 0.6 14 19-32 3-16 (69)
27 PF12838 Fer4_7: 4Fe-4S diclus 28.5 17 0.00036 22.1 -0.3 14 63-76 29-42 (52)
28 PF03604 DNA_RNApol_7kD: DNA d 27.5 23 0.00049 21.1 0.2 13 18-30 15-27 (32)
29 PF10589 NADH_4Fe-4S: NADH-ubi 27.0 20 0.00043 22.4 -0.1 9 24-32 14-22 (46)
30 PF00037 Fer4: 4Fe-4S binding 25.6 23 0.00049 19.2 -0.0 12 21-32 6-17 (24)
31 PF13717 zinc_ribbon_4: zinc-r 24.8 42 0.00092 20.0 1.1 14 16-29 21-34 (36)
32 PF06107 DUF951: Bacterial pro 23.9 40 0.00087 22.8 0.9 13 18-30 29-41 (57)
33 PF06639 BAP: Basal layer anti 23.4 20 0.00043 25.6 -0.7 22 73-94 5-26 (75)
34 PF13913 zf-C2HC_2: zinc-finge 22.2 39 0.00084 18.6 0.5 12 20-31 2-13 (25)
35 PF14832 Tautomerase_3: Putati 21.7 60 0.0013 24.7 1.6 25 46-72 20-44 (136)
36 PF08646 Rep_fac-A_C: Replicat 21.6 64 0.0014 23.6 1.7 32 9-40 25-57 (146)
37 PF04810 zf-Sec23_Sec24: Sec23 21.3 41 0.00089 20.3 0.5 13 20-32 2-14 (40)
38 PRK03954 ribonuclease P protei 21.3 75 0.0016 24.1 2.0 21 15-41 89-109 (121)
39 COG1326 Uncharacterized archae 21.2 50 0.0011 27.4 1.1 18 15-32 25-42 (201)
40 TIGR02174 CXXU_selWTH selT/sel 21.2 43 0.00092 22.4 0.6 14 67-80 1-14 (72)
41 PF10238 Eapp_C: E2F-associate 21.0 73 0.0016 24.6 1.9 11 20-30 109-119 (136)
42 PF04161 Arv1: Arv1-like famil 20.6 52 0.0011 26.1 1.1 19 14-32 18-36 (208)
43 PF00374 NiFeSe_Hases: Nickel- 20.5 23 0.0005 32.1 -1.0 8 71-78 500-507 (507)
44 PF13248 zf-ribbon_3: zinc-rib 20.3 41 0.00089 18.5 0.3 13 20-32 2-14 (26)
45 PF14424 Toxin-deaminase: The 20.0 64 0.0014 24.3 1.4 31 44-76 77-112 (133)
No 1
>PLN00186 ribosomal protein S26; Provisional
Probab=100.00 E-value=5.9e-60 Score=348.94 Aligned_cols=105 Identities=90% Similarity=1.439 Sum_probs=102.2
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
||+|||||||+|+|+|||++|+|+|||+|||| |||+|+|+||||++++|||+|||||++|.|||||+|+|||||||||
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 99999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccCCCCCCCcCCCCC
Q 032901 79 SHVVRVRSRTNRRIREPPQRFRRRDDV 105 (130)
Q Consensus 79 skVVRvRS~e~RK~r~pp~~~~~~~~~ 105 (130)
++||||||+|+||+|+||++|++.++.
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~~~~ 107 (109)
T PLN00186 81 SRVVRVRSRENRRIREPPPRFRRRKDD 107 (109)
T ss_pred cceeecCChHHccccCCCccccccccC
Confidence 999999999999999999999885543
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=1.5e-60 Score=353.76 Aligned_cols=108 Identities=68% Similarity=1.169 Sum_probs=71.0
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
||+|||||||+|||+||+++|+|+|||+|||| |||+|+|+||||++++|||+|||||++|+|||||+|+|||||||||
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 99999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccCCCCCCCcCCCCCCCC
Q 032901 79 SHVVRVRSRTNRRIREPPQRFRRRDDVPKA 108 (130)
Q Consensus 79 skVVRvRS~e~RK~r~pp~~~~~~~~~~~~ 108 (130)
++|||+||+|+||+|+||++|++.++..++
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 999999999999999999999997655543
No 3
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=100.00 E-value=2.1e-59 Score=345.61 Aligned_cols=102 Identities=74% Similarity=1.226 Sum_probs=99.9
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
||+|||||||+|+|+|||++|+|+|||+|||| |||+|+|+||||+++++||+|||+|++|+|||||+|+|||||||||
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 99999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccCCCCCCCcCC
Q 032901 79 SHVVRVRSRTNRRIREPPQRFRRR 102 (130)
Q Consensus 79 skVVRvRS~e~RK~r~pp~~~~~~ 102 (130)
++||||||+|+||+|+||+++...
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=1.3e-53 Score=308.97 Aligned_cols=92 Identities=28% Similarity=0.644 Sum_probs=90.1
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
||+||+||||+|+|+||+++|+|+|||+|||| |||+|+|+||||+++++||+||++| |||||+|+|||||||||
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 99999999999999999999999999999999 9999999999999999999999988 99999999999999999
Q ss_pred cceeccccccccccCCCC
Q 032901 79 SHVVRVRSRTNRRIREPP 96 (130)
Q Consensus 79 skVVRvRS~e~RK~r~pp 96 (130)
++|||+||+|+||+|+|.
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=3.6e-51 Score=304.29 Aligned_cols=106 Identities=71% Similarity=1.187 Sum_probs=102.0
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
|++||+|+|++|+|+||+.+|+|+||++|||| |||+|+|+||||++++|||+|||+|++|+|||||+|||||||||||
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 99999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccCCCCCCCcCCCCCC
Q 032901 79 SHVVRVRSRTNRRIREPPQRFRRRDDVP 106 (130)
Q Consensus 79 skVVRvRS~e~RK~r~pp~~~~~~~~~~ 106 (130)
++|||+||.|.||+|+||++|.+.....
T Consensus 81 skVvR~rS~e~rrir~pp~rf~~~~~~~ 108 (115)
T KOG1768|consen 81 SKVVRVRSREARRIRTPPPRFSPRAPSL 108 (115)
T ss_pred eeeeccchhhhhcccCCCcccCcccccc
Confidence 9999999999999999999887744333
No 6
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.7e-49 Score=288.53 Aligned_cols=95 Identities=64% Similarity=1.125 Sum_probs=94.6
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
|||||+||||+|+|+||+.+|+|+|||..||| |||+|.|+|+||+++++||+++++|+.|.+||+|.|++||||||||
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 99999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccCCC
Q 032901 79 SHVVRVRSRTNRRIREP 95 (130)
Q Consensus 79 skVVRvRS~e~RK~r~p 95 (130)
++||||||+|+||+++|
T Consensus 81 ~~IvrVRSre~RK~r~p 97 (108)
T COG4830 81 ARIVRVRSREERKIRAP 97 (108)
T ss_pred eeEEEEecchhhhhcCC
Confidence 99999999999999998
No 7
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=58.16 E-value=5.5 Score=25.35 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=10.5
Q ss_pred cccEeccCccccc
Q 032901 18 VKFIRCSNCGKCC 30 (130)
Q Consensus 18 v~~V~C~NCgr~v 30 (130)
...+.|+||||.+
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 4678999999863
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=56.83 E-value=5.3 Score=24.23 Aligned_cols=13 Identities=62% Similarity=1.321 Sum_probs=8.7
Q ss_pred CCccccEeccCcc
Q 032901 15 RGHVKFIRCSNCG 27 (130)
Q Consensus 15 rGhv~~V~C~NCg 27 (130)
|=|-++|-|++||
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 4688999999999
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=56.26 E-value=6.1 Score=23.82 Aligned_cols=15 Identities=27% Similarity=0.895 Sum_probs=10.3
Q ss_pred cccEeccCccccccc
Q 032901 18 VKFIRCSNCGKCCPK 32 (130)
Q Consensus 18 v~~V~C~NCgr~vPK 32 (130)
...+.|.||+|-|..
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 457899999997754
No 10
>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=51.39 E-value=12 Score=24.51 Aligned_cols=30 Identities=23% Similarity=0.574 Sum_probs=19.8
Q ss_pred CcccccCCCCCCCCCc------cccEeccCcccccc
Q 032901 2 TFKRRNGGRNKHGRGH------VKFIRCSNCGKCCP 31 (130)
Q Consensus 2 ~kKRrNnGR~KkgrGh------v~~V~C~NCgr~vP 31 (130)
||+|-+..|..+=|.| ...+.|.+||...-
T Consensus 2 PKrk~Sksr~~~RRah~~kl~~p~l~~C~~cG~~~~ 37 (55)
T TIGR01031 2 PKRKTSKSRKRKRRSHDAKLTAPTLVVCPNCGEFKL 37 (55)
T ss_pred CCCcCCcccccchhcCcccccCCcceECCCCCCccc
Confidence 5566665555555555 45788999997543
No 11
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=50.69 E-value=7.3 Score=26.96 Aligned_cols=14 Identities=36% Similarity=0.731 Sum_probs=12.2
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||||-+||+.+--
T Consensus 3 iPiRCFsCGkvi~~ 16 (63)
T COG1644 3 IPVRCFSCGKVIGH 16 (63)
T ss_pred CceEeecCCCCHHH
Confidence 48999999998876
No 12
>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=50.04 E-value=3.3 Score=28.15 Aligned_cols=14 Identities=36% Similarity=0.726 Sum_probs=10.8
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||||-.||+.+-.
T Consensus 3 iPVRCFTCGkvi~~ 16 (60)
T PF01194_consen 3 IPVRCFTCGKVIGN 16 (60)
T ss_dssp -SSS-STTTSBTCG
T ss_pred CceecCCCCCChhH
Confidence 38999999999876
No 13
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=49.92 E-value=8.3 Score=26.43 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=12.3
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||+|..||+.+--
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 48999999998865
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=49.15 E-value=9.4 Score=21.85 Aligned_cols=15 Identities=53% Similarity=0.851 Sum_probs=7.8
Q ss_pred CCcccccCCCCCCCC
Q 032901 1 MTFKRRNGGRNKHGR 15 (130)
Q Consensus 1 M~kKRrNnGR~Kkgr 15 (130)
|-++||+.|++|+.|
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 567899999999875
No 15
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=48.66 E-value=6.8 Score=29.18 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=13.0
Q ss_pred ccccEeccCccccccc
Q 032901 17 HVKFIRCSNCGKCCPK 32 (130)
Q Consensus 17 hv~~V~C~NCgr~vPK 32 (130)
..+.++|.||+|.|--
T Consensus 71 k~~~~hCeNC~RdVaA 86 (103)
T KOG2612|consen 71 KPMDCHCENCDRDVAA 86 (103)
T ss_pred CCccccCCCCccHHHH
Confidence 4568999999998754
No 16
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=47.29 E-value=7.3 Score=31.91 Aligned_cols=48 Identities=23% Similarity=0.546 Sum_probs=29.8
Q ss_pred cEeccCccccccc----ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeec
Q 032901 20 FIRCSNCGKCCPK----AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCA 76 (130)
Q Consensus 20 ~V~C~NCgr~vPK----AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCA 76 (130)
.-.|-|||-|.-- -.-.|..|-||.-+..-|.. .++... .+++|++|-
T Consensus 38 l~~C~QCG~CT~sCPs~r~t~y~pR~ii~~~~~g~~d--~il~~~-------~lW~C~tCy 89 (195)
T COG1150 38 LEGCYQCGTCTGSCPSGRFTDYSPRKIIRKARLGLVD--LILSSE-------SLWACVTCY 89 (195)
T ss_pred HhHhhccCcccCCCCCcccCCCCHHHHHHHHHcccHH--HHhcCC-------cceeeeech
Confidence 3448888888655 22445556688877765554 333222 378999983
No 17
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=45.14 E-value=11 Score=26.57 Aligned_cols=14 Identities=36% Similarity=0.726 Sum_probs=12.0
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||||-.||+.+--
T Consensus 3 iPVRCFTCGkvig~ 16 (71)
T PLN00032 3 IPVRCFTCGKVIGN 16 (71)
T ss_pred CceeecCCCCCcHH
Confidence 48999999998865
No 18
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=43.15 E-value=7.6 Score=29.83 Aligned_cols=31 Identities=23% Similarity=0.358 Sum_probs=19.2
Q ss_pred HHHhHHHhcccc----ccccceeeeeeeeeeeeceec
Q 032901 47 AVRDVQEACVYD----GYTLPKLYAKMQYCVSCAIHS 79 (130)
Q Consensus 47 avRDi~eAsv~~----~y~lPKlyvKl~YCVSCAIHs 79 (130)
+-.||++.--++ .-.||- .-.||||.||-|.
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 346776544443 223443 4589999999775
No 19
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=41.37 E-value=12 Score=23.98 Aligned_cols=11 Identities=55% Similarity=1.428 Sum_probs=8.1
Q ss_pred eeeeeee-ceec
Q 032901 69 MQYCVSC-AIHS 79 (130)
Q Consensus 69 l~YCVSC-AIHs 79 (130)
.+|||+| -||.
T Consensus 1 MyYCi~Cs~~h~ 12 (41)
T PF13119_consen 1 MYYCINCSEIHH 12 (41)
T ss_pred CEEEEEhHHhHH
Confidence 3799999 4653
No 20
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=37.21 E-value=11 Score=29.35 Aligned_cols=18 Identities=33% Similarity=0.598 Sum_probs=13.1
Q ss_pred cccceeeeeeeeeeeeceec
Q 032901 60 YTLPKLYAKMQYCVSCAIHS 79 (130)
Q Consensus 60 y~lPKlyvKl~YCVSCAIHs 79 (130)
+.||- .-++||+.||-|.
T Consensus 50 ~dlPG--~GqfyCi~CaRyF 67 (129)
T KOG3408|consen 50 PDLPG--GGQFYCIECARYF 67 (129)
T ss_pred CCCCC--Cceeehhhhhhhh
Confidence 44553 4589999999775
No 21
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=35.09 E-value=9.6 Score=27.88 Aligned_cols=23 Identities=30% Similarity=0.589 Sum_probs=18.4
Q ss_pred cccccc--ceeEeeecccchhHHHHhH
Q 032901 27 GKCCPK--AIKRFLVRNIVEQAAVRDV 51 (130)
Q Consensus 27 gr~vPK--AIKrf~irNiVEaaavRDi 51 (130)
||+||| ||..+....|+|+ +++|
T Consensus 20 GRrvpk~laV~~P~~~ei~~a--~~~L 44 (93)
T COG1400 20 GRRVPKELAVENPSLEEIAEA--LREL 44 (93)
T ss_pred ccccchhhcccCCCHHHHHHH--HHHc
Confidence 599999 9998888888774 5555
No 22
>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=33.41 E-value=22 Score=23.66 Aligned_cols=14 Identities=50% Similarity=0.873 Sum_probs=12.2
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
+-|||.+|++++-+
T Consensus 3 ~eiRC~~CnklLa~ 16 (51)
T PF10122_consen 3 KEIRCGHCNKLLAK 16 (51)
T ss_pred cceeccchhHHHhh
Confidence 56899999998877
No 23
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=32.82 E-value=25 Score=30.06 Aligned_cols=44 Identities=32% Similarity=0.493 Sum_probs=26.4
Q ss_pred cEeccCcccccccceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeee
Q 032901 20 FIRCSNCGKCCPKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSC 75 (130)
Q Consensus 20 ~V~C~NCgr~vPKAIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSC 75 (130)
+|+|-||+-.+|| =++| .++++|...--|.+. |+|-=..-|--|
T Consensus 42 ~~RCL~C~~YI~K-~~rf--------NavkE~~~dK~y~~~---kiYRf~I~C~~C 85 (272)
T COG5134 42 PVRCLNCENYIQK-GTRF--------NAVKEEIGDKSYYTT---KIYRFSIKCHLC 85 (272)
T ss_pred ceeecchhhhhhc-ccch--------hHHHHHhccccccee---EEEEEEEEccCC
Confidence 7999999999999 3334 246666443334333 445444444444
No 24
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=32.64 E-value=29 Score=22.97 Aligned_cols=31 Identities=23% Similarity=0.538 Sum_probs=18.9
Q ss_pred CcccccCCCCCCCCCc-----cccEeccCccccccc
Q 032901 2 TFKRRNGGRNKHGRGH-----VKFIRCSNCGKCCPK 32 (130)
Q Consensus 2 ~kKRrNnGR~KkgrGh-----v~~V~C~NCgr~vPK 32 (130)
||+|-+..|..+=|.| ...+.|.+||-....
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~~~ 39 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPKLP 39 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCccCC
Confidence 5555555554444555 336779999986554
No 25
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.93 E-value=25 Score=24.04 Aligned_cols=15 Identities=40% Similarity=0.855 Sum_probs=10.8
Q ss_pred CccccEeccCccccc
Q 032901 16 GHVKFIRCSNCGKCC 30 (130)
Q Consensus 16 Ghv~~V~C~NCgr~v 30 (130)
|-.-.|.|+|||+.|
T Consensus 30 GaDIkikC~nC~h~v 44 (60)
T COG4481 30 GADIKIKCENCGHSV 44 (60)
T ss_pred cCcEEEEecCCCcEE
Confidence 334468999999953
No 26
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=30.40 E-value=22 Score=24.84 Aligned_cols=14 Identities=43% Similarity=0.740 Sum_probs=11.7
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||+|..||..+-.
T Consensus 3 iPiRCFtCGKvig~ 16 (69)
T KOG3497|consen 3 IPIRCFTCGKVIGD 16 (69)
T ss_pred eeeEeeeccccccc
Confidence 38999999998765
No 27
>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3CF4_A 1K0T_A 2VKR_C 1JB0_C 3PCQ_C.
Probab=28.49 E-value=17 Score=22.12 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=6.2
Q ss_pred ceeeeeeeeeeeec
Q 032901 63 PKLYAKMQYCVSCA 76 (130)
Q Consensus 63 PKlyvKl~YCVSCA 76 (130)
+.+.+...+|+.|.
T Consensus 29 ~~~~~~~~~C~~C~ 42 (52)
T PF12838_consen 29 PKMVIDPDKCTGCG 42 (52)
T ss_dssp TTSEETGGG----S
T ss_pred eEEEEechhCcCcC
Confidence 44566677788774
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=27.46 E-value=23 Score=21.09 Aligned_cols=13 Identities=38% Similarity=0.777 Sum_probs=9.3
Q ss_pred cccEeccCccccc
Q 032901 18 VKFIRCSNCGKCC 30 (130)
Q Consensus 18 v~~V~C~NCgr~v 30 (130)
..+|+|.+||--+
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
>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=27.03 E-value=20 Score=22.44 Aligned_cols=9 Identities=56% Similarity=1.413 Sum_probs=4.2
Q ss_pred cCccccccc
Q 032901 24 SNCGKCCPK 32 (130)
Q Consensus 24 ~NCgr~vPK 32 (130)
.+||+|+|=
T Consensus 14 ESCGkC~PC 22 (46)
T PF10589_consen 14 ESCGKCTPC 22 (46)
T ss_dssp H--S--HHH
T ss_pred cCCCCCCCc
Confidence 589999997
No 30
>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1DUR_A 1H98_A 1BD6_A 1BQX_A 1BWE_A 1BC6_A 3BK7_A 1FCA_A 1FDN_A 2FDN_A ....
Probab=25.56 E-value=23 Score=19.18 Aligned_cols=12 Identities=33% Similarity=1.121 Sum_probs=7.4
Q ss_pred EeccCccccccc
Q 032901 21 IRCSNCGKCCPK 32 (130)
Q Consensus 21 V~C~NCgr~vPK 32 (130)
-.|.+||.|+.-
T Consensus 6 ~~C~~Cg~C~~~ 17 (24)
T PF00037_consen 6 DKCIGCGRCVEA 17 (24)
T ss_dssp TTSSS-THHHHH
T ss_pred HHCCCcchhhhh
Confidence 358888887643
No 31
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.77 E-value=42 Score=19.96 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=10.7
Q ss_pred CccccEeccCcccc
Q 032901 16 GHVKFIRCSNCGKC 29 (130)
Q Consensus 16 Ghv~~V~C~NCgr~ 29 (130)
++...|+|++||..
T Consensus 21 ~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 21 PKGRKVRCSKCGHV 34 (36)
T ss_pred CCCcEEECCCCCCE
Confidence 45568999999864
No 32
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=23.91 E-value=40 Score=22.77 Aligned_cols=13 Identities=31% Similarity=0.654 Sum_probs=9.9
Q ss_pred cccEeccCccccc
Q 032901 18 VKFIRCSNCGKCC 30 (130)
Q Consensus 18 v~~V~C~NCgr~v 30 (130)
.-.+.|++||+.|
T Consensus 29 DikikC~gCg~~i 41 (57)
T PF06107_consen 29 DIKIKCLGCGRQI 41 (57)
T ss_pred cEEEEECCCCCEE
Confidence 3468899999943
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=23.39 E-value=20 Score=25.57 Aligned_cols=22 Identities=23% Similarity=0.610 Sum_probs=17.6
Q ss_pred eeeceecceeccccccccccCC
Q 032901 73 VSCAIHSHVVRVRSRTNRRIRE 94 (130)
Q Consensus 73 VSCAIHskVVRvRS~e~RK~r~ 94 (130)
-||.||++|++-+-+|+-.-+.
T Consensus 5 AS~V~hA~ii~Gqtke~~nt~s 26 (75)
T PF06639_consen 5 ASCVIHAHIISGQTKEDSNTGS 26 (75)
T ss_pred hhhHhhHHhhcCceeeccCCCc
Confidence 4899999999988888755443
No 34
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.21 E-value=39 Score=18.62 Aligned_cols=12 Identities=25% Similarity=0.822 Sum_probs=9.3
Q ss_pred cEeccCcccccc
Q 032901 20 FIRCSNCGKCCP 31 (130)
Q Consensus 20 ~V~C~NCgr~vP 31 (130)
.+.|.+|||-.-
T Consensus 2 l~~C~~CgR~F~ 13 (25)
T PF13913_consen 2 LVPCPICGRKFN 13 (25)
T ss_pred CCcCCCCCCEEC
Confidence 578999998653
No 35
>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=21.69 E-value=60 Score=24.67 Aligned_cols=25 Identities=20% Similarity=0.610 Sum_probs=17.3
Q ss_pred HHHHhHHHhccccccccceeeeeeeee
Q 032901 46 AAVRDVQEACVYDGYTLPKLYAKMQYC 72 (130)
Q Consensus 46 aavRDi~eAsv~~~y~lPKlyvKl~YC 72 (130)
+++++|.+ +|.++-||.+||-..+.
T Consensus 20 ~LA~~IT~--~y~~~glP~FyV~V~F~ 44 (136)
T PF14832_consen 20 ALAEAITD--IYTSIGLPAFYVNVRFI 44 (136)
T ss_dssp HHHHHHHH--HHHHTTTTGGG-EEEEE
T ss_pred HHHHHHHH--HHhCCCCCCEEEEEEEE
Confidence 44555544 67777899999988775
No 36
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=21.57 E-value=64 Score=23.57 Aligned_cols=32 Identities=22% Similarity=0.325 Sum_probs=20.1
Q ss_pred CCCCCCCCc-cccEeccCcccccccceeEeeec
Q 032901 9 GRNKHGRGH-VKFIRCSNCGKCCPKAIKRFLVR 40 (130)
Q Consensus 9 GR~KkgrGh-v~~V~C~NCgr~vPKAIKrf~ir 40 (130)
.++||-.-. ...-+|.+|+..++....||.+.
T Consensus 25 ~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~ 57 (146)
T PF08646_consen 25 KCNKKVTENGDGSYRCEKCNKTVENPKYRYRLS 57 (146)
T ss_dssp TTS-B-EEETTTEEEETTTTEEESS-EEEEEEE
T ss_pred cCCCEeecCCCcEEECCCCCCcCCCeeEEEEEE
Confidence 455653322 23579999999987766777766
No 37
>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=21.29 E-value=41 Score=20.27 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=6.6
Q ss_pred cEeccCccccccc
Q 032901 20 FIRCSNCGKCCPK 32 (130)
Q Consensus 20 ~V~C~NCgr~vPK 32 (130)
+++|.+|+..+-.
T Consensus 2 p~rC~~C~aylNp 14 (40)
T PF04810_consen 2 PVRCRRCRAYLNP 14 (40)
T ss_dssp S-B-TTT--BS-T
T ss_pred ccccCCCCCEECC
Confidence 7899999987765
No 38
>PRK03954 ribonuclease P protein component 4; Validated
Probab=21.29 E-value=75 Score=24.06 Aligned_cols=21 Identities=38% Similarity=0.732 Sum_probs=15.6
Q ss_pred CCccccEeccCcccccccceeEeeecc
Q 032901 15 RGHVKFIRCSNCGKCCPKAIKRFLVRN 41 (130)
Q Consensus 15 rGhv~~V~C~NCgr~vPKAIKrf~irN 41 (130)
.||+ .|.|.+||. +++|-+..
T Consensus 89 ~~~v-vitCl~CG~-----~kR~P~~~ 109 (121)
T PRK03954 89 MPHV-VITCLECGH-----IMRYPYLR 109 (121)
T ss_pred cceE-EEECccCCC-----EEeeccch
Confidence 3676 888999997 67776543
No 39
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=21.22 E-value=50 Score=27.37 Aligned_cols=18 Identities=39% Similarity=1.034 Sum_probs=14.1
Q ss_pred CCccccEeccCccccccc
Q 032901 15 RGHVKFIRCSNCGKCCPK 32 (130)
Q Consensus 15 rGhv~~V~C~NCgr~vPK 32 (130)
+|....++|.|||-.-|-
T Consensus 25 ~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 25 RGREPLVRCEECGTVHPA 42 (201)
T ss_pred cCCceEEEccCCCcEeec
Confidence 456689999999997643
No 40
>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=21.22 E-value=43 Score=22.38 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=9.8
Q ss_pred eeeeeeeeeceecc
Q 032901 67 AKMQYCVSCAIHSH 80 (130)
Q Consensus 67 vKl~YCVSCAIHsk 80 (130)
|...||.+|-...+
T Consensus 1 V~IeyC~~C~y~~R 14 (72)
T TIGR02174 1 VEIEYCGSCGYKPR 14 (72)
T ss_pred CEEEECCCCCChHH
Confidence 45789999974433
No 41
>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=20.97 E-value=73 Score=24.55 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=9.1
Q ss_pred cEeccCccccc
Q 032901 20 FIRCSNCGKCC 30 (130)
Q Consensus 20 ~V~C~NCgr~v 30 (130)
||.|+.|+--|
T Consensus 109 PV~Cs~C~TeV 119 (136)
T PF10238_consen 109 PVKCSECSTEV 119 (136)
T ss_pred ceecccCCCEE
Confidence 89999998644
No 42
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=20.62 E-value=52 Score=26.08 Aligned_cols=19 Identities=37% Similarity=1.003 Sum_probs=16.6
Q ss_pred CCCccccEeccCccccccc
Q 032901 14 GRGHVKFIRCSNCGKCCPK 32 (130)
Q Consensus 14 grGhv~~V~C~NCgr~vPK 32 (130)
+.|+-+.-+|.||++.+-|
T Consensus 18 s~~~irLt~C~~C~~vaDk 36 (208)
T PF04161_consen 18 SPGNIRLTKCPNCGKVADK 36 (208)
T ss_pred CCCcEEEeeccccCCcccc
Confidence 4578888999999999998
No 43
>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium (the [NiFe] and [NiFeSe] hydrogenases) and those lacking nickel (the [Fe] hydrogenases). The [NiFe] and [NiFeSe] hydrogenases are heterodimer that consist of a small subunit that contains a signal peptide and a large subunit. All the known large subunits seem to be evolutionary related []; they contain two Cys-x-x-Cys motifs; one at their N-terminal end; the other at their C-terminal end. These four cysteines are involved in the binding of nickel []. In the [NiFeSe] hydrogenases the first cysteine of the C-terminal motif is a selenocysteine which has experimentally been shown to be a nickel ligand [].; GO: 0016151 nickel ion binding; PDB: 1E3D_D 3USC_M 3USE_L 3UQY_M 3RGW_L 1CC1_L 1YQ9_I 2FRV_D 1FRV_B 3MYR_F ....
Probab=20.47 E-value=23 Score=32.11 Aligned_cols=8 Identities=63% Similarity=1.526 Sum_probs=5.2
Q ss_pred eeeeecee
Q 032901 71 YCVSCAIH 78 (130)
Q Consensus 71 YCVSCAIH 78 (130)
=|+|||+|
T Consensus 500 PCisCavH 507 (507)
T PF00374_consen 500 PCISCAVH 507 (507)
T ss_dssp -BHHHHH-
T ss_pred ccccccCc
Confidence 48888888
No 44
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.34 E-value=41 Score=18.53 Aligned_cols=13 Identities=31% Similarity=0.600 Sum_probs=8.9
Q ss_pred cEeccCccccccc
Q 032901 20 FIRCSNCGKCCPK 32 (130)
Q Consensus 20 ~V~C~NCgr~vPK 32 (130)
.+.|.|||.-++.
T Consensus 2 ~~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 2 EMFCPNCGAEIDP 14 (26)
T ss_pred cCCCcccCCcCCc
Confidence 3568888886654
No 45
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=20.01 E-value=64 Score=24.35 Aligned_cols=31 Identities=19% Similarity=0.403 Sum_probs=20.1
Q ss_pred hhHHHHhHHHhcccccccc-----ceeeeeeeeeeeec
Q 032901 44 EQAAVRDVQEACVYDGYTL-----PKLYAKMQYCVSCA 76 (130)
Q Consensus 44 EaaavRDi~eAsv~~~y~l-----PKlyvKl~YCVSCA 76 (130)
|+-++++|.+.- ..-.+ -+||..+.+|-||-
T Consensus 77 E~KiL~~ia~~l--~~~~~~~~G~i~l~te~~pC~SC~ 112 (133)
T PF14424_consen 77 EYKILEDIAKKL--GDNPDPSGGTIDLFTELPPCESCS 112 (133)
T ss_pred HHHHHHHHHHHh--ccccccCCceEEEEecCCcChhHH
Confidence 445677775532 22222 26999999999994
Done!