Query psy11384
Match_columns 137
No_of_seqs 126 out of 182
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 17:01:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11384.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11384hhsearch_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 1.3E-63 2.8E-68 371.7 7.4 105 1-105 1-105 (109)
2 PF01283 Ribosomal_S26e: Ribos 100.0 5.6E-64 1.2E-68 375.3 3.5 110 1-110 1-110 (113)
3 PTZ00172 40S ribosomal protein 100.0 3.7E-63 8.1E-68 368.8 7.8 104 1-104 1-104 (108)
4 PRK09335 30S ribosomal protein 100.0 1.5E-57 3.3E-62 332.5 6.4 94 1-98 1-94 (95)
5 KOG1768|consensus 100.0 2E-55 4.3E-60 330.2 4.6 111 1-111 1-111 (115)
6 COG4830 RPS26B Ribosomal prote 100.0 4E-52 8.6E-57 308.7 5.8 97 1-97 1-97 (108)
7 COG1400 SEC65 Signal recogniti 76.8 0.73 1.6E-05 34.0 -0.2 26 27-54 20-45 (93)
8 PF02591 DUF164: Putative zinc 56.4 6.1 0.00013 25.4 1.0 13 18-30 44-56 (56)
9 PF07503 zf-HYPF: HypF finger; 55.0 6.1 0.00013 24.2 0.8 14 15-28 16-29 (35)
10 PF08209 Sgf11: Sgf11 (transcr 49.6 9.4 0.0002 23.3 1.0 15 18-32 2-16 (33)
11 PF09889 DUF2116: Uncharacteri 48.6 7.7 0.00017 26.4 0.6 17 21-37 4-20 (59)
12 TIGR01031 rpmF_bact ribosomal 48.1 14 0.0003 24.5 1.8 28 2-29 2-35 (55)
13 PF04726 Microvir_J: Microviru 44.5 12 0.00027 21.7 0.9 15 1-15 1-15 (24)
14 PRK04016 DNA-directed RNA poly 41.7 13 0.00028 25.8 0.9 14 19-32 3-16 (62)
15 KOG2612|consensus 40.1 12 0.00026 28.3 0.5 15 17-31 71-85 (103)
16 PF01922 SRP19: SRP19 protein; 39.2 9.2 0.0002 27.6 -0.2 23 26-48 16-38 (95)
17 PF13248 zf-ribbon_3: zinc-rib 39.1 13 0.00028 20.8 0.5 15 20-34 2-16 (26)
18 COG1644 RPB10 DNA-directed RNA 38.3 14 0.00031 25.8 0.7 13 19-31 3-15 (63)
19 COG4481 Uncharacterized protei 37.6 16 0.00035 25.3 0.8 15 16-30 30-44 (60)
20 PF13119 DUF3973: Domain of un 36.5 16 0.00035 23.7 0.7 11 71-81 1-12 (41)
21 PF10122 Mu-like_Com: Mu-like 34.4 19 0.00042 24.2 0.8 18 19-36 3-20 (51)
22 PLN00032 DNA-directed RNA poly 34.3 20 0.00043 25.5 0.9 12 19-30 3-14 (71)
23 COG1150 HdrC Heterodisulfide r 33.8 22 0.00049 29.4 1.2 49 20-78 38-89 (195)
24 PF07496 zf-CW: CW-type Zinc F 33.3 20 0.00044 22.8 0.7 13 20-32 3-17 (50)
25 PF01194 RNA_pol_N: RNA polyme 33.2 18 0.00038 24.9 0.5 13 19-31 3-15 (60)
26 COG5112 UFD2 U1-like Zn-finger 33.1 14 0.00031 28.7 -0.0 45 35-81 17-65 (126)
27 PF03604 DNA_RNApol_7kD: DNA d 30.1 23 0.00049 21.4 0.5 12 18-29 15-26 (32)
28 COG5134 Uncharacterized conser 30.0 28 0.00061 30.1 1.3 46 19-78 41-86 (272)
29 PRK12286 rpmF 50S ribosomal pr 29.1 37 0.0008 22.7 1.5 29 2-30 4-37 (57)
30 PRK14890 putative Zn-ribbon RN 27.7 32 0.00069 23.7 1.0 26 18-44 5-31 (59)
31 PF10589 NADH_4Fe-4S: NADH-ubi 27.5 20 0.00043 22.7 -0.1 9 24-32 14-22 (46)
32 KOG3408|consensus 27.1 19 0.00041 28.3 -0.3 18 62-81 50-67 (129)
33 COG2888 Predicted Zn-ribbon RN 26.5 38 0.00083 23.6 1.2 34 18-52 7-41 (61)
34 KOG3198|consensus 26.2 22 0.00049 28.6 0.0 31 27-59 32-62 (152)
35 PF13240 zinc_ribbon_2: zinc-r 25.4 32 0.0007 19.1 0.6 12 22-33 1-12 (23)
36 PF12230 PRP21_like_P: Pre-mRN 24.7 25 0.00053 28.2 0.0 31 16-47 164-194 (229)
37 PF14832 Tautomerase_3: Putati 23.2 60 0.0013 24.9 1.9 25 48-74 20-44 (136)
38 PF10262 Rdx: Rdx family; Int 22.4 40 0.00087 22.6 0.7 19 69-87 3-21 (76)
39 PF13717 zinc_ribbon_4: zinc-r 22.4 54 0.0012 19.7 1.2 14 16-29 21-34 (36)
40 PF13913 zf-C2HC_2: zinc-finge 22.3 39 0.00084 18.9 0.5 14 20-33 2-15 (25)
41 TIGR02174 CXXU_selWTH selT/sel 21.7 38 0.00082 22.8 0.4 13 69-81 1-13 (72)
42 KOG3497|consensus 21.6 40 0.00087 23.9 0.6 13 19-31 3-15 (69)
43 PF04810 zf-Sec23_Sec24: Sec23 21.5 43 0.00094 20.4 0.7 11 20-30 2-12 (40)
44 PF07282 OrfB_Zn_ribbon: Putat 21.0 66 0.0014 20.8 1.5 19 15-33 41-59 (69)
45 PRK00754 signal recognition pa 20.8 28 0.00062 25.4 -0.3 20 27-46 23-42 (95)
46 PF10238 Eapp_C: E2F-associate 20.8 74 0.0016 24.8 2.0 12 19-30 108-119 (136)
47 KOG3286|consensus 20.3 63 0.0014 27.5 1.6 13 69-81 72-84 (226)
No 1
>PLN00186 ribosomal protein S26; Provisional
Probab=100.00 E-value=1.3e-63 Score=371.71 Aligned_cols=105 Identities=68% Similarity=1.199 Sum_probs=103.2
Q ss_pred CCccccCCCCCCCCCCCccceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeeeee
Q psy11384 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIH 80 (137)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCAIH 80 (137)
||+|||||||+|+|||||++|+|+|||+|||||||||+|+|+||||+||+|||+||+||++|.|||||+|+|||||||||
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 cCcccccCccccccCCCCCCCCCCC
Q psy11384 81 SKVVRNRSKSDRRIRTPPQRNFPRS 105 (137)
Q Consensus 81 skVVRvRS~e~RK~R~pp~~~~~~~ 105 (137)
++|||+||+|+||+|+||++|++..
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~~ 105 (109)
T PLN00186 81 SRVVRVRSRENRRIREPPPRFRRRK 105 (109)
T ss_pred cceeecCChHHccccCCCccccccc
Confidence 9999999999999999999998754
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=5.6e-64 Score=375.25 Aligned_cols=110 Identities=73% Similarity=1.160 Sum_probs=73.0
Q ss_pred CCccccCCCCCCCCCCCccceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeeeee
Q psy11384 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIH 80 (137)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCAIH 80 (137)
||+|||||||+|+|||||++|+|+|||+|||||||||+|+|+||||++++|||+||+||++|+|||||+|+|||||||||
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 cCcccccCccccccCCCCCCCCCCCCCCCc
Q psy11384 81 SKVVRNRSKSDRRIRTPPQRNFPRSVSLTE 110 (137)
Q Consensus 81 skVVRvRS~e~RK~R~pp~~~~~~~~~~~~ 110 (137)
++|||+||+|+||+|+||++|++......+
T Consensus 81 ~~IVr~Rs~e~RK~r~~p~~~~~~~~~~~~ 110 (113)
T PF01283_consen 81 SKIVRVRSREERKDRTPPPRFRPRKQGQKP 110 (113)
T ss_dssp TTSS----TCCCC--S--------------
T ss_pred ccccccCChHHccccCCCCcCCcccccccc
Confidence 999999999999999999999987665543
No 3
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=100.00 E-value=3.7e-63 Score=368.78 Aligned_cols=104 Identities=75% Similarity=1.270 Sum_probs=101.6
Q ss_pred CCccccCCCCCCCCCCCccceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeeeee
Q psy11384 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIH 80 (137)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCAIH 80 (137)
||+|||||||+|+|||||++|+|+|||+|||||||||+|+|+||||+||++||+||+||++|+|||||+|+|||||||||
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 cCcccccCccccccCCCCCCCCCC
Q psy11384 81 SKVVRNRSKSDRRIRTPPQRNFPR 104 (137)
Q Consensus 81 skVVRvRS~e~RK~R~pp~~~~~~ 104 (137)
++|||+||+|+||+|+||++|...
T Consensus 81 ~~iVRvRs~e~Rk~r~pp~r~~~~ 104 (108)
T PTZ00172 81 SRVVRVRSREDRKIRTPPKRPFRP 104 (108)
T ss_pred CCeeecCChHHccccCCCCCCCCC
Confidence 999999999999999999887543
No 4
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=100.00 E-value=1.5e-57 Score=332.53 Aligned_cols=94 Identities=32% Similarity=0.631 Sum_probs=92.2
Q ss_pred CCccccCCCCCCCCCCCccceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeeeee
Q psy11384 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIH 80 (137)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCAIH 80 (137)
||+||+||||+|+|+|||++|+|+|||+|||||||||+|+|+||||+++++||+||++| |||||+|+|||||||||
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 99999999999999999999999999999999999999999999999999999999887 99999999999999999
Q ss_pred cCcccccCccccccCCCC
Q psy11384 81 SKVVRNRSKSDRRIRTPP 98 (137)
Q Consensus 81 skVVRvRS~e~RK~R~pp 98 (137)
++|||+||+|+||+|+|.
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
Probab=100.00 E-value=2e-55 Score=330.15 Aligned_cols=111 Identities=75% Similarity=1.194 Sum_probs=107.3
Q ss_pred CCccccCCCCCCCCCCCccceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeeeee
Q psy11384 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIH 80 (137)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCAIH 80 (137)
||+||+|+|++|+|+||+.+|+|+||++|||||||||+|+|+||||++++|||+|||||++|+|||||+|||||||||||
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 cCcccccCccccccCCCCCCCCCCCCCCCcc
Q psy11384 81 SKVVRNRSKSDRRIRTPPQRNFPRSVSLTEG 111 (137)
Q Consensus 81 skVVRvRS~e~RK~R~pp~~~~~~~~~~~~~ 111 (137)
++|||+||+|.||+|+||++|.+++++.++.
T Consensus 81 skVvR~rS~e~rrir~pp~rf~~~~~~~~~~ 111 (115)
T KOG1768|consen 81 SKVVRVRSREARRIRTPPPRFSPRAPSLRPP 111 (115)
T ss_pred eeeeccchhhhhcccCCCcccCccccccCCC
Confidence 9999999999999999999999877765543
No 6
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-52 Score=308.65 Aligned_cols=97 Identities=63% Similarity=1.074 Sum_probs=96.7
Q ss_pred CCccccCCCCCCCCCCCccceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeeeee
Q psy11384 1 MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIH 80 (137)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCAIH 80 (137)
|||||+||||+|+||||+.+|+|+|||..||||||||+|.|+|+||+|+++||++|+||+.|.+||+|.|++||||||||
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 cCcccccCccccccCCC
Q psy11384 81 SKVVRNRSKSDRRIRTP 97 (137)
Q Consensus 81 skVVRvRS~e~RK~R~p 97 (137)
++|||+||+|+||++.|
T Consensus 81 ~~IvrVRSre~RK~r~p 97 (108)
T COG4830 81 ARIVRVRSREERKIRAP 97 (108)
T ss_pred eeEEEEecchhhhhcCC
Confidence 99999999999999999
No 7
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=76.82 E-value=0.73 Score=34.03 Aligned_cols=26 Identities=35% Similarity=0.585 Sum_probs=22.0
Q ss_pred CcccccccceeeceeecchhhHHhhhHH
Q psy11384 27 ARCVPKDKAIKKFVIRNIVEAAAVRDIT 54 (137)
Q Consensus 27 grcvPKDKAIKrf~irNiVEaaavRDis 54 (137)
||+|||+.||..+...+|+++ +++|-
T Consensus 20 GRrvpk~laV~~P~~~ei~~a--~~~LG 45 (93)
T COG1400 20 GRRVPKELAVENPSLEEIAEA--LRELG 45 (93)
T ss_pred ccccchhhcccCCCHHHHHHH--HHHcC
Confidence 599999999999999999886 55554
No 8
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=56.40 E-value=6.1 Score=25.38 Aligned_cols=13 Identities=38% Similarity=0.728 Sum_probs=10.5
Q ss_pred ccceeccCCCccc
Q psy11384 18 VNPVRCTNCARCV 30 (137)
Q Consensus 18 v~~V~C~NCgrcv 30 (137)
...+.|+||||.+
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 4678999999863
No 9
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=55.00 E-value=6.1 Score=24.24 Aligned_cols=14 Identities=43% Similarity=0.788 Sum_probs=8.9
Q ss_pred CCCccceeccCCCc
Q psy11384 15 RGHVNPVRCTNCAR 28 (137)
Q Consensus 15 rGhv~~V~C~NCgr 28 (137)
|=|-++|-|++||-
T Consensus 16 R~~~~~isC~~CGP 29 (35)
T PF07503_consen 16 RFHYQFISCTNCGP 29 (35)
T ss_dssp TTT-TT--BTTCC-
T ss_pred cccCcCccCCCCCC
Confidence 46899999999994
No 10
>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=49.62 E-value=9.4 Score=23.29 Aligned_cols=15 Identities=40% Similarity=0.691 Sum_probs=10.2
Q ss_pred ccceeccCCCccccc
Q psy11384 18 VNPVRCTNCARCVPK 32 (137)
Q Consensus 18 v~~V~C~NCgrcvPK 32 (137)
...+.|.||+|-|.-
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 357899999997753
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=48.56 E-value=7.7 Score=26.39 Aligned_cols=17 Identities=24% Similarity=0.690 Sum_probs=15.0
Q ss_pred eeccCCCccccccccee
Q psy11384 21 VRCTNCARCVPKDKAIK 37 (137)
Q Consensus 21 V~C~NCgrcvPKDKAIK 37 (137)
-||-+||.-+|-|++.+
T Consensus 4 kHC~~CG~~Ip~~~~fC 20 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFC 20 (59)
T ss_pred CcCCcCCCcCCcchhhh
Confidence 37999999999998876
No 12
>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=48.11 E-value=14 Score=24.45 Aligned_cols=28 Identities=25% Similarity=0.545 Sum_probs=18.7
Q ss_pred CccccCCCCCCCCCCC------ccceeccCCCcc
Q psy11384 2 TCKRRNGGRSKHGRGH------VNPVRCTNCARC 29 (137)
Q Consensus 2 ~kKRrNnGR~KkgrGh------v~~V~C~NCgrc 29 (137)
||+|-+..|..+=|.| ...+.|.+||..
T Consensus 2 PKrk~Sksr~~~RRah~~kl~~p~l~~C~~cG~~ 35 (55)
T TIGR01031 2 PKRKTSKSRKRKRRSHDAKLTAPTLVVCPNCGEF 35 (55)
T ss_pred CCCcCCcccccchhcCcccccCCcceECCCCCCc
Confidence 5566665555555566 567889999963
No 13
>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=44.49 E-value=12 Score=21.72 Aligned_cols=15 Identities=53% Similarity=0.904 Sum_probs=7.9
Q ss_pred CCccccCCCCCCCCC
Q psy11384 1 MTCKRRNGGRSKHGR 15 (137)
Q Consensus 1 M~kKRrNnGR~Kkgr 15 (137)
|-++||+.|++|+.|
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 567899999999876
No 14
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=41.70 E-value=13 Score=25.77 Aligned_cols=14 Identities=36% Similarity=0.999 Sum_probs=11.6
Q ss_pred cceeccCCCccccc
Q psy11384 19 NPVRCTNCARCVPK 32 (137)
Q Consensus 19 ~~V~C~NCgrcvPK 32 (137)
-||+|..||+.+--
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 58999999997743
No 15
>KOG2612|consensus
Probab=40.14 E-value=12 Score=28.27 Aligned_cols=15 Identities=33% Similarity=0.625 Sum_probs=12.1
Q ss_pred CccceeccCCCcccc
Q psy11384 17 HVNPVRCTNCARCVP 31 (137)
Q Consensus 17 hv~~V~C~NCgrcvP 31 (137)
..+.++|.||+|.|.
T Consensus 71 k~~~~hCeNC~RdVa 85 (103)
T KOG2612|consen 71 KPMDCHCENCDRDVA 85 (103)
T ss_pred CCccccCCCCccHHH
Confidence 456799999999764
No 16
>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=39.23 E-value=9.2 Score=27.59 Aligned_cols=23 Identities=30% Similarity=0.469 Sum_probs=14.4
Q ss_pred CCcccccccceeeceeecchhhH
Q psy11384 26 CARCVPKDKAIKKFVIRNIVEAA 48 (137)
Q Consensus 26 CgrcvPKDKAIKrf~irNiVEaa 48 (137)
-||.|||+.|+..-.+..|.+|.
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 47999999999877766666553
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.14 E-value=13 Score=20.85 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=10.8
Q ss_pred ceeccCCCccccccc
Q psy11384 20 PVRCTNCARCVPKDK 34 (137)
Q Consensus 20 ~V~C~NCgrcvPKDK 34 (137)
.+.|.|||.-++.|-
T Consensus 2 ~~~Cp~Cg~~~~~~~ 16 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDA 16 (26)
T ss_pred cCCCcccCCcCCccc
Confidence 357889998776663
No 18
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=38.34 E-value=14 Score=25.81 Aligned_cols=13 Identities=38% Similarity=1.007 Sum_probs=10.8
Q ss_pred cceeccCCCcccc
Q psy11384 19 NPVRCTNCARCVP 31 (137)
Q Consensus 19 ~~V~C~NCgrcvP 31 (137)
-||||-+||+.+-
T Consensus 3 iPiRCFsCGkvi~ 15 (63)
T COG1644 3 IPVRCFSCGKVIG 15 (63)
T ss_pred CceEeecCCCCHH
Confidence 4899999998764
No 19
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.61 E-value=16 Score=25.30 Aligned_cols=15 Identities=33% Similarity=0.813 Sum_probs=10.7
Q ss_pred CCccceeccCCCccc
Q psy11384 16 GHVNPVRCTNCARCV 30 (137)
Q Consensus 16 Ghv~~V~C~NCgrcv 30 (137)
|---.|.|+|||+.|
T Consensus 30 GaDIkikC~nC~h~v 44 (60)
T COG4481 30 GADIKIKCENCGHSV 44 (60)
T ss_pred cCcEEEEecCCCcEE
Confidence 333468899999853
No 20
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=36.53 E-value=16 Score=23.67 Aligned_cols=11 Identities=45% Similarity=1.367 Sum_probs=7.9
Q ss_pred EEEeeee-eeec
Q psy11384 71 LHYCVSC-AIHS 81 (137)
Q Consensus 71 l~YCVSC-AIHs 81 (137)
.+|||+| -||.
T Consensus 1 MyYCi~Cs~~h~ 12 (41)
T PF13119_consen 1 MYYCINCSEIHH 12 (41)
T ss_pred CEEEEEhHHhHH
Confidence 3799999 4553
No 21
>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=34.39 E-value=19 Score=24.16 Aligned_cols=18 Identities=22% Similarity=0.724 Sum_probs=13.8
Q ss_pred cceeccCCCcccccccce
Q psy11384 19 NPVRCTNCARCVPKDKAI 36 (137)
Q Consensus 19 ~~V~C~NCgrcvPKDKAI 36 (137)
+-|||.+|++++-+-...
T Consensus 3 ~eiRC~~CnklLa~~g~~ 20 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEV 20 (51)
T ss_pred cceeccchhHHHhhhcCc
Confidence 579999999988774333
No 22
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=34.31 E-value=20 Score=25.54 Aligned_cols=12 Identities=42% Similarity=1.124 Sum_probs=10.4
Q ss_pred cceeccCCCccc
Q psy11384 19 NPVRCTNCARCV 30 (137)
Q Consensus 19 ~~V~C~NCgrcv 30 (137)
-||||-.||+.+
T Consensus 3 iPVRCFTCGkvi 14 (71)
T PLN00032 3 IPVRCFTCGKVI 14 (71)
T ss_pred CceeecCCCCCc
Confidence 489999999876
No 23
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=33.75 E-value=22 Score=29.40 Aligned_cols=49 Identities=24% Similarity=0.523 Sum_probs=35.2
Q ss_pred ceeccCCCcc---cccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeee
Q psy11384 20 PVRCTNCARC---VPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCA 78 (137)
Q Consensus 20 ~V~C~NCgrc---vPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCA 78 (137)
.-.|.+||-| +|--.. -.|..|-||.-+...|.. .++.... +++|++|-
T Consensus 38 l~~C~QCG~CT~sCPs~r~-t~y~pR~ii~~~~~g~~d--~il~~~~-------lW~C~tCy 89 (195)
T COG1150 38 LEGCYQCGTCTGSCPSGRF-TDYSPRKIIRKARLGLVD--LILSSES-------LWACVTCY 89 (195)
T ss_pred HhHhhccCcccCCCCCccc-CCCCHHHHHHHHHcccHH--HHhcCCc-------ceeeeech
Confidence 3347777765 687777 678888999888777766 4554443 48999993
No 24
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=33.30 E-value=20 Score=22.84 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=7.7
Q ss_pred ceeccCCC--ccccc
Q psy11384 20 PVRCTNCA--RCVPK 32 (137)
Q Consensus 20 ~V~C~NCg--rcvPK 32 (137)
-|+|++|+ |.||.
T Consensus 3 WVQCd~C~KWR~lp~ 17 (50)
T PF07496_consen 3 WVQCDSCLKWRRLPE 17 (50)
T ss_dssp EEE-TTT--EEEE-C
T ss_pred EEECCCCCceeeCCh
Confidence 48999999 57773
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=33.19 E-value=18 Score=24.93 Aligned_cols=13 Identities=38% Similarity=0.996 Sum_probs=9.6
Q ss_pred cceeccCCCcccc
Q psy11384 19 NPVRCTNCARCVP 31 (137)
Q Consensus 19 ~~V~C~NCgrcvP 31 (137)
-||||-.||+.+-
T Consensus 3 iPVRCFTCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFTCGKVIG 15 (60)
T ss_dssp -SSS-STTTSBTC
T ss_pred CceecCCCCCChh
Confidence 3899999999874
No 26
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=33.14 E-value=14 Score=28.72 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=25.1
Q ss_pred ceeeceeecchhhHHhhhHHhhcccc----ccccceeeEeEEEeeeeeeec
Q psy11384 35 AIKKFVIRNIVEAAAVRDITEASYYQ----SYQLPKLYAKLHYCVSCAIHS 81 (137)
Q Consensus 35 AIKrf~irNiVEaaavRDiseAsV~~----~y~lPKlyvKl~YCVSCAIHs 81 (137)
+|+++.++--==...-.||++..-++ .-.||- .-.|||+.||-|.
T Consensus 17 ~i~rtr~~grDlDqi~nDls~~Es~~Klp~Dp~lPG--lGqhYCieCaryf 65 (126)
T COG5112 17 RIKRTRLFGRDLDQIKNDLSTKESQKKLPYDPELPG--LGQHYCIECARYF 65 (126)
T ss_pred HHHHHHHhcccHHHHHHhcchhhhhccCCCCCCCCC--CceeeeehhHHHH
Confidence 45555444311123456776644443 234554 5679999999774
No 27
>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=30.09 E-value=23 Score=21.36 Aligned_cols=12 Identities=33% Similarity=1.032 Sum_probs=9.0
Q ss_pred ccceeccCCCcc
Q psy11384 18 VNPVRCTNCARC 29 (137)
Q Consensus 18 v~~V~C~NCgrc 29 (137)
..+|+|.+||--
T Consensus 15 ~~~irC~~CG~R 26 (32)
T PF03604_consen 15 GDPIRCPECGHR 26 (32)
T ss_dssp SSTSSBSSSS-S
T ss_pred CCcEECCcCCCe
Confidence 457999999953
No 28
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=29.99 E-value=28 Score=30.06 Aligned_cols=46 Identities=33% Similarity=0.627 Sum_probs=28.8
Q ss_pred cceeccCCCcccccccceeeceeecchhhHHhhhHHhhccccccccceeeEeEEEeeeee
Q psy11384 19 NPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCA 78 (137)
Q Consensus 19 ~~V~C~NCgrcvPKDKAIKrf~irNiVEaaavRDiseAsV~~~y~lPKlyvKl~YCVSCA 78 (137)
-+|+|-||+-.+||.+- | .++++|...--|.+ -|.|.=.--|.-|+
T Consensus 41 F~~RCL~C~~YI~K~~r---f--------NavkE~~~dK~y~~---~kiYRf~I~C~~C~ 86 (272)
T COG5134 41 FPVRCLNCENYIQKGTR---F--------NAVKEEIGDKSYYT---TKIYRFSIKCHLCS 86 (272)
T ss_pred cceeecchhhhhhcccc---h--------hHHHHHhcccccce---eEEEEEEEEccCCC
Confidence 36999999999999863 3 25677666433333 34554444455553
No 29
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.13 E-value=37 Score=22.68 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=16.6
Q ss_pred CccccCCCCCCCCCCC-----ccceeccCCCccc
Q psy11384 2 TCKRRNGGRSKHGRGH-----VNPVRCTNCARCV 30 (137)
Q Consensus 2 ~kKRrNnGR~KkgrGh-----v~~V~C~NCgrcv 30 (137)
||+|-+..|..+=|.| ...+.|.+||-..
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPK 37 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCcc
Confidence 4555554444444444 4556799998643
No 30
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.73 E-value=32 Score=23.72 Aligned_cols=26 Identities=38% Similarity=0.883 Sum_probs=17.9
Q ss_pred ccceeccCCCc-ccccccceeeceeecc
Q psy11384 18 VNPVRCTNCAR-CVPKDKAIKKFVIRNI 44 (137)
Q Consensus 18 v~~V~C~NCgr-cvPKDKAIKrf~irNi 44 (137)
+.+..|++||+ +.|.++|.+ |.=-|=
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~-F~CPnC 31 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVK-FLCPNC 31 (59)
T ss_pred ccCccccCCCCcccCCCccCE-eeCCCC
Confidence 34557999998 566888876 655443
No 31
>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=27.50 E-value=20 Score=22.67 Aligned_cols=9 Identities=33% Similarity=1.176 Sum_probs=3.8
Q ss_pred cCCCccccc
Q psy11384 24 TNCARCVPK 32 (137)
Q Consensus 24 ~NCgrcvPK 32 (137)
.+||+|+|-
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 579999994
No 32
>KOG3408|consensus
Probab=27.12 E-value=19 Score=28.33 Aligned_cols=18 Identities=33% Similarity=0.650 Sum_probs=13.6
Q ss_pred cccceeeEeEEEeeeeeeec
Q psy11384 62 YQLPKLYAKLHYCVSCAIHS 81 (137)
Q Consensus 62 y~lPKlyvKl~YCVSCAIHs 81 (137)
+-||- .-++||+-||-|.
T Consensus 50 ~dlPG--~GqfyCi~CaRyF 67 (129)
T KOG3408|consen 50 PDLPG--GGQFYCIECARYF 67 (129)
T ss_pred CCCCC--Cceeehhhhhhhh
Confidence 45665 5689999999764
No 33
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=26.51 E-value=38 Score=23.58 Aligned_cols=34 Identities=35% Similarity=0.588 Sum_probs=24.8
Q ss_pred ccceeccCCCccc-ccccceeeceeecchhhHHhhh
Q psy11384 18 VNPVRCTNCARCV-PKDKAIKKFVIRNIVEAAAVRD 52 (137)
Q Consensus 18 v~~V~C~NCgrcv-PKDKAIKrf~irNiVEaaavRD 52 (137)
..+-.|++||+-+ |..+|++ |.=-|==|....|.
T Consensus 7 ~~~~~CtSCg~~i~p~e~~v~-F~CPnCGe~~I~Rc 41 (61)
T COG2888 7 KDPPVCTSCGREIAPGETAVK-FPCPNCGEVEIYRC 41 (61)
T ss_pred cCCceeccCCCEeccCCceeE-eeCCCCCceeeehh
Confidence 3466899999999 8888877 87777665554444
No 34
>KOG3198|consensus
Probab=26.22 E-value=22 Score=28.56 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=19.3
Q ss_pred CcccccccceeeceeecchhhHHhhhHHhhccc
Q psy11384 27 ARCVPKDKAIKKFVIRNIVEAAAVRDITEASYY 59 (137)
Q Consensus 27 grcvPKDKAIKrf~irNiVEaaavRDiseAsV~ 59 (137)
||++||||||..=.-.+|-| ++++|.=.+.+
T Consensus 32 GRripke~aVeNP~a~eI~D--vl~~lgl~~~~ 62 (152)
T KOG3198|consen 32 GRRIPKEKAVENPLAKEIAD--VLRALGLNCLL 62 (152)
T ss_pred ccccCHHHhhcCcchhHHHH--HHHHhCCcccc
Confidence 69999999987655555533 24444433333
No 35
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.42 E-value=32 Score=19.06 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=9.3
Q ss_pred eccCCCcccccc
Q psy11384 22 RCTNCARCVPKD 33 (137)
Q Consensus 22 ~C~NCgrcvPKD 33 (137)
.|.+||.-++.|
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 388999888765
No 36
>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=24.68 E-value=25 Score=28.18 Aligned_cols=31 Identities=10% Similarity=0.245 Sum_probs=0.0
Q ss_pred CCccceeccCCCcccccccceeeceeecchhh
Q psy11384 16 GHVNPVRCTNCARCVPKDKAIKKFVIRNIVEA 47 (137)
Q Consensus 16 Ghv~~V~C~NCgrcvPKDKAIKrf~irNiVEa 47 (137)
..+..+.|..||..||-|+-=. -.--+++|+
T Consensus 164 ~~~~~~~cPitGe~IP~~e~~e-HmRi~LlDP 194 (229)
T PF12230_consen 164 PKEKMIICPITGEMIPADEMDE-HMRIELLDP 194 (229)
T ss_dssp --------------------------------
T ss_pred cccccccccccccccccccccc-ccccccccc
Confidence 4567899999999999998654 233344444
No 37
>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=23.20 E-value=60 Score=24.91 Aligned_cols=25 Identities=32% Similarity=0.620 Sum_probs=18.3
Q ss_pred HHhhhHHhhccccccccceeeEeEEEe
Q psy11384 48 AAVRDITEASYYQSYQLPKLYAKLHYC 74 (137)
Q Consensus 48 aavRDiseAsV~~~y~lPKlyvKl~YC 74 (137)
+++++|.+ +|.++-||.+||-..+.
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 46666666 67777899999988775
No 38
>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=22.44 E-value=40 Score=22.64 Aligned_cols=19 Identities=21% Similarity=0.677 Sum_probs=14.2
Q ss_pred EeEEEeeeeeeecCccccc
Q psy11384 69 AKLHYCVSCAIHSKVVRNR 87 (137)
Q Consensus 69 vKl~YCVSCAIHskVVRvR 87 (137)
|...||.+|-.|.+.....
T Consensus 3 V~IeYC~~C~~~~~a~~l~ 21 (76)
T PF10262_consen 3 VTIEYCTSCGYRPRALELA 21 (76)
T ss_dssp EEEEEETTTTCHHHHHHHH
T ss_pred EEEEECCCCCCHHHHHHHH
Confidence 6789999998877655433
No 39
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=22.39 E-value=54 Score=19.72 Aligned_cols=14 Identities=29% Similarity=0.712 Sum_probs=10.6
Q ss_pred CCccceeccCCCcc
Q psy11384 16 GHVNPVRCTNCARC 29 (137)
Q Consensus 16 Ghv~~V~C~NCgrc 29 (137)
+....++|++||..
T Consensus 21 ~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 21 PKGRKVRCSKCGHV 34 (36)
T ss_pred CCCcEEECCCCCCE
Confidence 45568999999864
No 40
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.34 E-value=39 Score=18.86 Aligned_cols=14 Identities=36% Similarity=0.624 Sum_probs=10.6
Q ss_pred ceeccCCCcccccc
Q psy11384 20 PVRCTNCARCVPKD 33 (137)
Q Consensus 20 ~V~C~NCgrcvPKD 33 (137)
.+.|.+|||-..-|
T Consensus 2 l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 2 LVPCPICGRKFNPD 15 (25)
T ss_pred CCcCCCCCCEECHH
Confidence 57899999976443
No 41
>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=21.67 E-value=38 Score=22.84 Aligned_cols=13 Identities=31% Similarity=0.897 Sum_probs=9.5
Q ss_pred EeEEEeeeeeeec
Q psy11384 69 AKLHYCVSCAIHS 81 (137)
Q Consensus 69 vKl~YCVSCAIHs 81 (137)
|...||.+|-...
T Consensus 1 V~IeyC~~C~y~~ 13 (72)
T TIGR02174 1 VEIEYCGSCGYKP 13 (72)
T ss_pred CEEEECCCCCChH
Confidence 4578999997443
No 42
>KOG3497|consensus
Probab=21.59 E-value=40 Score=23.91 Aligned_cols=13 Identities=31% Similarity=0.989 Sum_probs=10.5
Q ss_pred cceeccCCCcccc
Q psy11384 19 NPVRCTNCARCVP 31 (137)
Q Consensus 19 ~~V~C~NCgrcvP 31 (137)
-||||-.||..+-
T Consensus 3 iPiRCFtCGKvig 15 (69)
T KOG3497|consen 3 IPIRCFTCGKVIG 15 (69)
T ss_pred eeeEeeecccccc
Confidence 4899999998653
No 43
>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=21.47 E-value=43 Score=20.39 Aligned_cols=11 Identities=45% Similarity=1.177 Sum_probs=5.3
Q ss_pred ceeccCCCccc
Q psy11384 20 PVRCTNCARCV 30 (137)
Q Consensus 20 ~V~C~NCgrcv 30 (137)
+++|.+|+..+
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 78899998654
No 44
>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=21.03 E-value=66 Score=20.79 Aligned_cols=19 Identities=26% Similarity=0.494 Sum_probs=13.4
Q ss_pred CCCccceeccCCCcccccc
Q psy11384 15 RGHVNPVRCTNCARCVPKD 33 (137)
Q Consensus 15 rGhv~~V~C~NCgrcvPKD 33 (137)
....+...|.+||..+.+|
T Consensus 41 ~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 41 RRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred ccccceEEcCCCCCEECcH
Confidence 3455667788888877776
No 45
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=20.85 E-value=28 Score=25.44 Aligned_cols=20 Identities=25% Similarity=0.461 Sum_probs=13.7
Q ss_pred Ccccccccceeeceeecchh
Q psy11384 27 ARCVPKDKAIKKFVIRNIVE 46 (137)
Q Consensus 27 grcvPKDKAIKrf~irNiVE 46 (137)
||.|||+.|+..=.+..|.|
T Consensus 23 GRrv~k~~aV~~P~~~EI~~ 42 (95)
T PRK00754 23 GRIISRKLAVKEPRLEEIIE 42 (95)
T ss_pred cCccCHHHhccCCCHHHHHH
Confidence 69999999977544443333
No 46
>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=20.81 E-value=74 Score=24.75 Aligned_cols=12 Identities=42% Similarity=1.154 Sum_probs=9.7
Q ss_pred cceeccCCCccc
Q psy11384 19 NPVRCTNCARCV 30 (137)
Q Consensus 19 ~~V~C~NCgrcv 30 (137)
.||.|+.|+--|
T Consensus 108 hPV~Cs~C~TeV 119 (136)
T PF10238_consen 108 HPVKCSECSTEV 119 (136)
T ss_pred eceecccCCCEE
Confidence 489999998654
No 47
>KOG3286|consensus
Probab=20.33 E-value=63 Score=27.50 Aligned_cols=13 Identities=31% Similarity=0.981 Sum_probs=10.7
Q ss_pred EeEEEeeeeeeec
Q psy11384 69 AKLHYCVSCAIHS 81 (137)
Q Consensus 69 vKl~YCVSCAIHs 81 (137)
++..|||||-.-.
T Consensus 72 l~i~fCvSCgYk~ 84 (226)
T KOG3286|consen 72 LEINFCVSCGYKQ 84 (226)
T ss_pred EEEEEEEecCcHH
Confidence 7889999997643
Done!