Query 031077
Match_columns 166
No_of_seqs 105 out of 236
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 08:53:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031077.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031077hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05907 DUF866: Eukaryotic pr 100.0 4.8E-71 1.1E-75 436.5 19.0 159 1-165 1-161 (161)
2 KOG1296 Uncharacterized conser 100.0 1.9E-67 4.2E-72 406.1 11.7 159 1-165 1-161 (161)
3 PRK00415 rps27e 30S ribosomal 93.6 0.097 2.1E-06 35.2 3.4 34 27-76 5-39 (59)
4 PLN00209 ribosomal protein S27 93.3 0.17 3.6E-06 36.5 4.3 34 27-76 30-64 (86)
5 PF01667 Ribosomal_S27e: Ribos 93.1 0.1 2.3E-06 34.5 2.9 32 30-76 3-35 (55)
6 PTZ00083 40S ribosomal protein 92.7 0.22 4.9E-06 35.7 4.3 40 16-76 23-63 (85)
7 PF04502 DUF572: Family of unk 92.2 0.14 3E-06 44.7 3.3 54 29-83 35-93 (324)
8 COG2051 RPS27A Ribosomal prote 92.0 0.37 8E-06 33.2 4.4 42 15-76 5-47 (67)
9 PF14205 Cys_rich_KTR: Cystein 80.6 1.6 3.5E-05 28.9 2.3 41 35-85 5-46 (55)
10 PF14353 CpXC: CpXC protein 65.8 1.7 3.8E-05 32.4 -0.3 45 34-79 1-50 (128)
11 PF05180 zf-DNL: DNL zinc fing 65.2 6.2 0.00013 27.0 2.3 38 31-77 1-39 (66)
12 KOG2315 Predicted translation 62.9 26 0.00056 33.1 6.6 50 65-126 324-373 (566)
13 TIGR00467 lysS_arch lysyl-tRNA 59.3 22 0.00048 33.2 5.6 48 27-86 161-209 (515)
14 COG1066 Sms Predicted ATP-depe 58.6 5.7 0.00012 36.5 1.6 29 34-82 7-36 (456)
15 smart00709 Zpr1 Duplicated dom 55.2 81 0.0017 24.9 7.5 15 148-162 73-87 (160)
16 PF14255 Cys_rich_CPXG: Cystei 54.0 23 0.00051 23.0 3.5 40 35-84 1-41 (52)
17 PF09723 Zn-ribbon_8: Zinc rib 52.3 18 0.00039 22.0 2.7 30 33-75 4-34 (42)
18 cd00674 LysRS_core_class_I cat 52.2 44 0.00094 29.7 6.1 49 27-86 162-211 (353)
19 KOG1779 40s ribosomal protein 51.5 25 0.00054 25.1 3.6 16 27-43 28-44 (84)
20 COG5428 Uncharacterized conser 51.4 38 0.00082 23.4 4.4 42 113-155 3-46 (69)
21 PRK00750 lysK lysyl-tRNA synth 47.5 46 0.001 30.8 5.7 51 26-86 167-218 (510)
22 cd01121 Sms Sms (bacterial rad 47.4 11 0.00024 33.5 1.6 26 36-81 2-28 (372)
23 PF04810 zf-Sec23_Sec24: Sec23 46.7 15 0.00033 22.2 1.6 33 35-79 3-36 (40)
24 PF12760 Zn_Tnp_IS1595: Transp 46.0 13 0.00029 23.0 1.4 31 31-76 15-46 (46)
25 TIGR00416 sms DNA repair prote 46.0 11 0.00025 34.3 1.5 27 35-81 8-35 (454)
26 TIGR02605 CxxC_CxxC_SSSS putat 45.6 26 0.00057 21.8 2.7 31 33-76 4-35 (52)
27 PRK11823 DNA repair protein Ra 43.6 15 0.00032 33.4 1.8 26 35-80 8-34 (446)
28 PF01921 tRNA-synt_1f: tRNA sy 43.2 18 0.00039 32.4 2.2 50 28-86 168-218 (360)
29 PRK03824 hypA hydrogenase nick 42.6 23 0.0005 27.1 2.5 47 33-85 69-124 (135)
30 PF15411 PH_10: Pleckstrin hom 42.0 1.4E+02 0.003 22.3 6.6 43 6-72 61-105 (116)
31 PF10001 DUF2242: Uncharacteri 41.8 66 0.0014 24.6 4.8 53 12-67 23-78 (121)
32 TIGR01206 lysW lysine biosynth 36.3 55 0.0012 21.4 3.2 31 34-79 2-34 (54)
33 PF13670 PepSY_2: Peptidase pr 35.9 91 0.002 21.2 4.5 33 104-137 37-73 (83)
34 PRK03564 formate dehydrogenase 34.4 31 0.00068 30.2 2.3 43 29-79 220-264 (309)
35 KOG2989 Uncharacterized conser 33.6 10 0.00022 32.3 -0.8 59 32-92 38-101 (253)
36 PRK03988 translation initiatio 32.6 42 0.0009 26.0 2.5 32 35-79 103-135 (138)
37 smart00440 ZnF_C2C2 C2C2 Zinc 32.4 74 0.0016 19.2 3.1 34 36-76 2-37 (40)
38 PF03367 zf-ZPR1: ZPR1 zinc-fi 32.3 73 0.0016 25.1 3.9 41 35-80 2-43 (161)
39 KOG2110 Uncharacterized conser 32.3 2.8E+02 0.006 25.2 7.9 61 98-159 162-226 (391)
40 KOG3277 Uncharacterized conser 32.2 42 0.00092 26.8 2.5 44 62-117 74-117 (165)
41 PF09460 Saf-Nte_pilin: Saf-pi 31.0 1.8E+02 0.004 22.9 5.8 72 76-154 22-121 (145)
42 TIGR00310 ZPR1_znf ZPR1 zinc f 30.2 85 0.0018 25.6 4.1 41 35-80 1-43 (192)
43 PF05129 Elf1: Transcription e 28.9 52 0.0011 23.1 2.3 32 67-111 22-53 (81)
44 TIGR00311 aIF-2beta translatio 27.9 56 0.0012 25.1 2.5 32 35-79 98-130 (133)
45 PF02146 SIR2: Sir2 family; I 27.2 20 0.00043 28.0 -0.1 62 13-84 82-146 (178)
46 PF10122 Mu-like_Com: Mu-like 27.1 75 0.0016 20.7 2.6 23 62-84 19-41 (51)
47 PRK12336 translation initiatio 27.1 57 0.0012 26.6 2.5 37 35-84 99-136 (201)
48 PF01807 zf-CHC2: CHC2 zinc fi 26.2 54 0.0012 23.4 2.0 33 33-78 32-65 (97)
49 PF07433 DUF1513: Protein of u 26.1 1.5E+02 0.0032 26.1 5.0 55 102-163 30-90 (305)
50 KOG0315 G-protein beta subunit 25.6 2.1E+02 0.0046 25.0 5.8 35 96-130 70-107 (311)
51 KOG4497 Uncharacterized conser 25.0 70 0.0015 29.0 2.9 27 102-128 204-231 (447)
52 TIGR01908 cas_CXXC_CXXC CRISPR 24.8 31 0.00067 30.0 0.7 36 36-71 7-44 (309)
53 PF13717 zinc_ribbon_4: zinc-r 24.8 43 0.00094 19.8 1.1 10 33-42 24-34 (36)
54 PF04216 FdhE: Protein involve 24.6 46 0.001 28.2 1.7 42 28-77 204-248 (290)
55 KOG2990 C2C2-type Zn-finger pr 24.5 21 0.00046 31.2 -0.4 52 29-83 47-101 (317)
56 PF09332 Mcm10: Mcm10 replicat 24.5 20 0.00044 31.9 -0.6 47 35-83 253-300 (344)
57 COG4416 Com Mu-like prophage p 24.4 57 0.0012 21.7 1.7 23 61-83 18-40 (60)
58 COG5134 Uncharacterized conser 22.7 58 0.0013 27.6 1.8 51 31-83 39-95 (272)
59 PF07661 MORN_2: MORN repeat v 22.6 1.1E+02 0.0025 15.0 2.4 12 138-149 2-13 (22)
60 TIGR01562 FdhE formate dehydro 22.2 50 0.0011 28.9 1.4 44 29-79 218-264 (305)
61 PF01096 TFIIS_C: Transcriptio 21.3 1.4E+02 0.0031 17.7 3.0 11 65-75 26-36 (39)
62 PF07282 OrfB_Zn_ribbon: Putat 21.0 40 0.00087 22.1 0.5 32 34-81 28-60 (69)
63 PF14803 Nudix_N_2: Nudix N-te 20.2 74 0.0016 18.8 1.5 11 33-43 21-32 (34)
64 PF01586 Basic: Myogenic Basic 20.2 36 0.00078 24.5 0.1 13 65-77 70-82 (86)
No 1
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=100.00 E-value=4.8e-71 Score=436.47 Aligned_cols=159 Identities=47% Similarity=0.914 Sum_probs=125.3
Q ss_pred CceEEEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEE
Q 031077 1 MVNCMLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 1 Mv~~~L~vkAeLeNV~~l~p~~~~~~~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si 79 (166)
||+|+|+|||+|+||++|+|.+ ++|.|+|+|+|+ |||+|+|+|+|+++|+++++||||+|||++|||+|+|++||
T Consensus 1 M~~~~L~ikAeLeNVt~L~p~~----~~~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 1 MVKFALQIKAELENVTNLQPVD----PDFEWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp EEEEEEEEEEEEESEEEEE-------TT--EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred CcEEEEEEEEEEcCceEEEecC----CCCEEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 9999999999999999999986 568999999999 99999999999999999999999999999999999999999
Q ss_pred EEecCCCcccccccccCCCcccEEEEEecCceEEeeEeCCcEEEEEe-CCCEEEeeecCCCceeeecCCCCceEEEeeeE
Q 031077 80 TMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESL-AGTQYEDIDLSGGDYAEYDEKGECPVMISNLR 158 (166)
Q Consensus 80 ~i~~~~~~~~~~e~~~~~~~~~i~~fdCRG~E~~~f~p~~~w~~~~~-sG~~f~dvdLse~eW~dYDEk~~~~VsI~~~~ 158 (166)
+|++++..+|+.+++ ++|++|++||||||||++|+|+++|+|++. ||++|+||||+|+||+|||||++++|||++|+
T Consensus 77 ~i~~~~~~~~~~e~~--~~~~~i~~fdCRG~e~~~f~p~~~~~~~~~esG~~f~~vdL~e~eW~dYDek~~~~V~I~~~~ 154 (161)
T PF05907_consen 77 DIIPGKGKPYTAEDS--GKFVPILAFDCRGLEPVEFSPRGGWVAVSVESGTKFEDVDLSEGEWYDYDEKAGEEVSITEFE 154 (161)
T ss_dssp EEE--TTTEEEGGGT--TS-EEEEEEEEESEEEEEE---S-EEEEET-TS-EEEEE--TTS-EEEEETTTTEEEEEEEEE
T ss_pred EEEecCccccccccc--cCCceEEEEECCCcEeEEEecCCcEEEEEecCCCEEEeccCCCCceeeeccCCCceEEEEEEE
Confidence 999999889998754 899999999999999999999999999997 99999999999999999999999999999999
Q ss_pred EEEEEec
Q 031077 159 FKFEVVK 165 (166)
Q Consensus 159 ~~f~~~k 165 (166)
|+|+++|
T Consensus 155 ~~~~k~k 161 (161)
T PF05907_consen 155 WEFVKLK 161 (161)
T ss_dssp EEE----
T ss_pred EEEEecC
Confidence 9999987
No 2
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.9e-67 Score=406.12 Aligned_cols=159 Identities=43% Similarity=0.806 Sum_probs=154.8
Q ss_pred CceEEEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEE
Q 031077 1 MVNCMLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 1 Mv~~~L~vkAeLeNV~~l~p~~~~~~~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si 79 (166)
||+|+|+++|.|||||+|+|.+ |+|+|+|+|||+ |||.|++|++|+..|.+.+|||||+|||+||||+|+|++||
T Consensus 1 M~~~~l~i~a~lENvtkl~~~~----~~~rf~~kLkCtnCgE~~dkw~~I~l~E~~~~pg~Rgta~~v~KCK~C~Rensv 76 (161)
T KOG1296|consen 1 MVLFLLQIAATLENVTKLSPSG----PDFRFYLKLKCTNCGELSDKWQYITLNEEVAMPGSRGTASFVMKCKFCSRENSV 76 (161)
T ss_pred CceeeeeeehhhhcccccccCC----CCceeEEEeccccccccCCceEEEEeeeeecCCCCcchhhHhhhhhhhcccCcE
Confidence 9999999999999999999997 789999999999 99999999999999999999999999999999999999999
Q ss_pred EEecCCCcccccccccCCCcccEEEEEecCceEEeeEeCCcEEEEE-eCCCEEEeeecCCCceeeecCCCCceEEEeeeE
Q 031077 80 TMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVES-LAGTQYEDIDLSGGDYAEYDEKGECPVMISNLR 158 (166)
Q Consensus 80 ~i~~~~~~~~~~e~~~~~~~~~i~~fdCRG~E~~~f~p~~~w~~~~-~sG~~f~dvdLse~eW~dYDEk~~~~VsI~~~~ 158 (166)
+|++.+++|||.+++ ++|++|+.|||||+||++|.|+++|.|++ +||+.|++|||+++||+|||||++++|+|++|.
T Consensus 77 ~iv~~~~~pyt~ed~--e~~~~i~vfdCRG~EpidF~p~~~w~a~s~esG~~f~eidlse~ew~dYDdk~~e~V~i~efs 154 (161)
T KOG1296|consen 77 TIVAFEDKPYTAEDS--EKFKTIVVFDCRGLEPIDFYPRTGWFAVSAESGTAFSEIDLSEKEWTDYDDKAGESVGISEFS 154 (161)
T ss_pred EEecCCCCccccccc--ccccceEEEeccCCcceeecCCceEEEEecccCceeeeeecccccceehhhcCCCeeEEEeee
Confidence 999999999999875 68999999999999999999999999998 699999999999999999999999999999999
Q ss_pred EEEEEec
Q 031077 159 FKFEVVK 165 (166)
Q Consensus 159 ~~f~~~k 165 (166)
++|.+.|
T Consensus 155 ssfik~k 161 (161)
T KOG1296|consen 155 SSFIKGK 161 (161)
T ss_pred eeeEecC
Confidence 9999876
No 3
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=93.62 E-value=0.097 Score=35.19 Aligned_cols=34 Identities=32% Similarity=0.850 Sum_probs=26.8
Q ss_pred CCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 27 ~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
|+ .||++|+|. |+.+. +.+ +.|..+.+|..|++.
T Consensus 5 p~-S~F~~VkCp~C~n~q---~vF------------sha~t~V~C~~Cg~~ 39 (59)
T PRK00415 5 PR-SRFLKVKCPDCGNEQ---VVF------------SHASTVVRCLVCGKT 39 (59)
T ss_pred CC-CeEEEEECCCCCCeE---EEE------------ecCCcEEECcccCCC
Confidence 53 899999999 99875 333 446778999999985
No 4
>PLN00209 ribosomal protein S27; Provisional
Probab=93.25 E-value=0.17 Score=36.45 Aligned_cols=34 Identities=29% Similarity=0.728 Sum_probs=27.1
Q ss_pred CCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 27 ~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
|+ .||++|+|. |+.+. +.+ +.|..+.+|..|++.
T Consensus 30 Pn-S~Fm~VkCp~C~n~q---~VF------------ShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 30 PN-SFFMDVKCQGCFNIT---TVF------------SHSQTVVVCGSCQTV 64 (86)
T ss_pred CC-CEEEEEECCCCCCee---EEE------------ecCceEEEccccCCE
Confidence 54 899999999 99875 233 456789999999985
No 5
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=93.13 E-value=0.1 Score=34.54 Aligned_cols=32 Identities=34% Similarity=0.820 Sum_probs=19.4
Q ss_pred eEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 30 SYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 30 ~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
.||++|||. |+.+. +.+ +.|..+.+|..|+..
T Consensus 3 S~Fm~VkCp~C~~~q---~vF------------Sha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 3 SYFMDVKCPGCYNIQ---TVF------------SHAQTVVKCVVCGTV 35 (55)
T ss_dssp --EEEEE-TTT-SEE---EEE------------TT-SS-EE-SSSTSE
T ss_pred ccEEEEECCCCCCee---EEE------------ecCCeEEEcccCCCE
Confidence 799999999 99875 333 345678899999984
No 6
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=92.71 E-value=0.22 Score=35.73 Aligned_cols=40 Identities=30% Similarity=0.715 Sum_probs=29.9
Q ss_pred eeeeeCCCCCCCCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 16 TNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 16 ~~l~p~~~~~~~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
..|-|. |+ .||++|+|. |+.+. +.+ +.|..+.+|..|++.
T Consensus 23 k~Lv~~-----Pn-S~Fm~VkCp~C~n~q---~VF------------ShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 23 KRLVQG-----PN-SYFMDVKCPGCSQIT---TVF------------SHAQTVVLCGGCSSQ 63 (85)
T ss_pred eeEecC-----CC-CeEEEEECCCCCCee---EEE------------ecCceEEEccccCCE
Confidence 345553 54 899999999 99875 333 456778999999875
No 7
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=92.23 E-value=0.14 Score=44.72 Aligned_cols=54 Identities=24% Similarity=0.343 Sum_probs=40.3
Q ss_pred ceEEEEEEec-CCceecccEEEecCeeeeeCC--CCce--eeEEEEeccCCceeEEEEec
Q 031077 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQG--GKGT--TNLIQKCKFCGREGTVTMIP 83 (166)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~g--srg~--aNfv~KCk~C~r~~si~i~~ 83 (166)
|...|.|.|. |++-..+.+-+|. ++..+.+ ==|. =.|.|||..|..+.+|.=.|
T Consensus 35 f~~Pf~i~C~~C~~~I~kG~rFNA-~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDP 93 (324)
T PF04502_consen 35 FMMPFNIWCNTCGEYIYKGVRFNA-RKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDP 93 (324)
T ss_pred EcCCccCcCCCCccccccceeeee-eeEecCCCccccceEEEEEEEcCCCCCEEeeecCC
Confidence 4677999999 9999889999997 4544544 2243 37999999999985555433
No 8
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=91.95 E-value=0.37 Score=33.15 Aligned_cols=42 Identities=26% Similarity=0.620 Sum_probs=30.3
Q ss_pred eeeeeeCCCCCCCCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 15 LTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 15 V~~l~p~~~~~~~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
+.-+.|.. | ..+|++|+|. |+.+. +.+ +.|..+.+|-.|++.
T Consensus 5 ~k~~~p~~----p-~s~Fl~VkCpdC~N~q---~vF------------shast~V~C~~CG~~ 47 (67)
T COG2051 5 RKVKIPKE----P-RSRFLRVKCPDCGNEQ---VVF------------SHASTVVTCLICGTT 47 (67)
T ss_pred ceeeecCC----C-CceEEEEECCCCCCEE---EEe------------ccCceEEEecccccE
Confidence 34455542 5 4899999999 99874 333 456778999999984
No 9
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=80.57 E-value=1.6 Score=28.93 Aligned_cols=41 Identities=20% Similarity=0.372 Sum_probs=29.5
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecCC
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~~ 85 (166)
+.|. ||.-++-.|. . ++ ---||-+-|+-|++|.-|++....
T Consensus 5 i~CP~CgnKTR~kir--~-DT-------~LkNfPlyCpKCK~EtlI~v~~~~ 46 (55)
T PF14205_consen 5 ILCPICGNKTRLKIR--E-DT-------VLKNFPLYCPKCKQETLIDVKQLK 46 (55)
T ss_pred EECCCCCCccceeee--c-Cc-------eeccccccCCCCCceEEEEeeccE
Confidence 5699 9987754332 2 22 123999999999999999987654
No 10
>PF14353 CpXC: CpXC protein
Probab=65.77 E-value=1.7 Score=32.36 Aligned_cols=45 Identities=20% Similarity=0.445 Sum_probs=28.2
Q ss_pred EEEec-CCceecccE--EEecCeeeeeCCC--CceeeEEEEeccCCceeEE
Q 031077 34 KLKCG-CGELSQKET--CVSLAETLPTQGG--KGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 34 kvkCt-C~e~~~~~v--~i~~~e~~e~~gs--rg~aNfv~KCk~C~r~~si 79 (166)
+|+|. |+......+ .|+..+.-++.-. .|+- |...|+.|++...+
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l-~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSL-FSFTCPSCGHKFRL 50 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCc-CEEECCCCCCceec
Confidence 37899 999876644 4444333333211 2443 57799999998765
No 11
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=65.21 E-value=6.2 Score=27.05 Aligned_cols=38 Identities=32% Similarity=0.588 Sum_probs=20.5
Q ss_pred EEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCcee
Q 031077 31 YFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREG 77 (166)
Q Consensus 31 ~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~ 77 (166)
|.+.+.|. |+..+.+ .|++.- =-+|. ...+|+.|+...
T Consensus 1 ~~l~FTC~~C~~Rs~~--~~sk~a-----Y~~Gv--Viv~C~gC~~~H 39 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAK--MFSKQA-----YHKGV--VIVQCPGCKNRH 39 (66)
T ss_dssp EEEEEEETTTTEEEEE--EEEHHH-----HHTSE--EEEE-TTS--EE
T ss_pred CeEEEEcCCCCCccce--eeCHHH-----HhCCe--EEEECCCCccee
Confidence 56778888 8876644 343310 01355 677888888753
No 12
>KOG2315 consensus Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis]
Probab=62.91 E-value=26 Score=33.15 Aligned_cols=50 Identities=10% Similarity=0.075 Sum_probs=37.1
Q ss_pred eEEEEeccCCceeEEEEecCCCcccccccccCCCcccEEEEEecCceEEeeEeCCcEEEEEe
Q 031077 65 NLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESL 126 (166)
Q Consensus 65 Nfv~KCk~C~r~~si~i~~~~~~~~~~e~~~~~~~~~i~~fdCRG~E~~~f~p~~~w~~~~~ 126 (166)
|++.=|-|=.=.++|.|-... +++.|..|+|-+.-..+|+|+|.|.++.+
T Consensus 324 ~ii~lAGFGNL~G~mEvwDv~------------n~K~i~~~~a~~tt~~eW~PdGe~flTAT 373 (566)
T KOG2315|consen 324 NIILLAGFGNLPGDMEVWDVP------------NRKLIAKFKAANTTVFEWSPDGEYFLTAT 373 (566)
T ss_pred CEEEEeecCCCCCceEEEecc------------chhhccccccCCceEEEEcCCCcEEEEEe
Confidence 445555555555666665542 37889999999999999999999988764
No 13
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=59.25 E-value=22 Score=33.18 Aligned_cols=48 Identities=19% Similarity=0.383 Sum_probs=33.1
Q ss_pred CCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecCCC
Q 031077 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (166)
Q Consensus 27 ~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~~~ 86 (166)
++-.|.|..-|. ||-+....+.++. .. + ..++|+ |+.++++++..+.+
T Consensus 161 ~~~~~P~~pic~~cGrv~~~~~~~~~--------~~-~--v~Y~c~-cG~~g~~~~~~g~~ 209 (515)
T TIGR00467 161 EENWYPISVFCENCGRDTTTVNNYDN--------EY-S--IEYSCE-CGNQESVDIYTGAI 209 (515)
T ss_pred CCCceeeeeecCCcCccCceEEEecC--------Cc-e--EEEEcC-CCCEEEEeecCCCc
Confidence 444678999999 9998653322221 11 2 566896 99999999977644
No 14
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=58.56 E-value=5.7 Score=36.48 Aligned_cols=29 Identities=34% Similarity=0.578 Sum_probs=23.1
Q ss_pred EEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEe
Q 031077 34 KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMI 82 (166)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~ 82 (166)
...|+ ||..|+||.. ||..|+.=+|+.=.
T Consensus 7 ~f~C~~CG~~s~KW~G--------------------kCp~Cg~Wns~vE~ 36 (456)
T COG1066 7 AFVCQECGYVSPKWLG--------------------KCPACGAWNTLVEE 36 (456)
T ss_pred EEEcccCCCCCccccc--------------------cCCCCCCccceEEe
Confidence 35799 9999999953 88889888876543
No 15
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=55.16 E-value=81 Score=24.89 Aligned_cols=15 Identities=13% Similarity=0.315 Sum_probs=8.7
Q ss_pred CCceEEEeeeEEEEE
Q 031077 148 GECPVMISNLRFKFE 162 (166)
Q Consensus 148 ~~~~VsI~~~~~~f~ 162 (166)
....|.|.++.+++.
T Consensus 73 ~ta~i~IPEl~~ei~ 87 (160)
T smart00709 73 ETATISIPELDLEIP 87 (160)
T ss_pred CCcEEEeeeeeEEec
Confidence 344566666666654
No 16
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=53.96 E-value=23 Score=22.99 Aligned_cols=40 Identities=25% Similarity=0.573 Sum_probs=30.2
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecC
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPG 84 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~ 84 (166)
+.|. ||+.-. +. +.-|.|...++--|..|-|...+.+.-.
T Consensus 1 i~CPyCge~~~--~~--------iD~s~~~Q~yiEDC~vCC~PI~~~v~~d 41 (52)
T PF14255_consen 1 IQCPYCGEPIE--IL--------IDPSAGDQEYIEDCQVCCRPIEVQVTVD 41 (52)
T ss_pred CCCCCCCCeeE--EE--------EecCCCCeeEEeehhhcCCccEEEEEEC
Confidence 4789 998742 33 3335577899999999999999888654
No 17
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=52.28 E-value=18 Score=22.04 Aligned_cols=30 Identities=23% Similarity=0.565 Sum_probs=19.6
Q ss_pred EEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCc
Q 031077 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGR 75 (166)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r 75 (166)
+..+|. ||..-...+.++. .-...|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~-------------~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE-------------DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC-------------CCCCcCCCCCC
Confidence 466899 9987765555443 12347888887
No 18
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=52.21 E-value=44 Score=29.71 Aligned_cols=49 Identities=39% Similarity=0.688 Sum_probs=31.6
Q ss_pred CCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecCCC
Q 031077 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (166)
Q Consensus 27 ~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~~~ 86 (166)
++-.|.|..-|. ||-.+ +.+. +.....|+.- .+|+ |+.++++++..+.+
T Consensus 162 ~~~~~P~~p~c~~cg~~~---~~v~-----~~d~~~~~v~--y~c~-cG~~g~~~~~~g~~ 211 (353)
T cd00674 162 QETWYPFMPYCEKCGKDT---TTVE-----AYDAKAGTVT--YKCE-CGHEETVDIRTGRG 211 (353)
T ss_pred CCCceeeeeecCCcCcce---eEEE-----EEeCCCCeEE--EEcC-CCCEEEEeecCCCc
Confidence 344678999999 99443 2221 2222334444 4784 99999999987644
No 19
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=51.55 E-value=25 Score=25.07 Aligned_cols=16 Identities=50% Similarity=1.190 Sum_probs=13.5
Q ss_pred CCceEEEEEEec-CCcee
Q 031077 27 PNFSYFFKLKCG-CGELS 43 (166)
Q Consensus 27 ~~~~~~fkvkCt-C~e~~ 43 (166)
|+ .|+++|||+ |.-.+
T Consensus 28 ~n-syFm~VkC~gc~~iT 44 (84)
T KOG1779|consen 28 PN-SYFMDVKCPGCFKIT 44 (84)
T ss_pred CC-ceEEEEEcCCceEEE
Confidence 53 899999999 98775
No 20
>COG5428 Uncharacterized conserved small protein [Function unknown]
Probab=51.43 E-value=38 Score=23.44 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=27.1
Q ss_pred EeeEeCCc--EEEEEeCCCEEEeeecCCCceeeecCCCCceEEEe
Q 031077 113 VDFVFGVG--WKVESLAGTQYEDIDLSGGDYAEYDEKGECPVMIS 155 (166)
Q Consensus 113 ~~f~p~~~--w~~~~~sG~~f~dvdLse~eW~dYDEk~~~~VsI~ 155 (166)
+.|.|+.. |+-...++..-+..++.|+=|-||||++. -++|.
T Consensus 3 v~YD~daD~lYI~~~~~~~~~dt~e~~edi~Idide~Gk-V~GiE 46 (69)
T COG5428 3 VKYDTDADILYILLEEGKVVEDTIELGEDILIDIDENGK-VIGIE 46 (69)
T ss_pred eeecCCCcEEEEEEecCcceeehhhcCCcEEEEecCCCc-EEEEE
Confidence 34555544 44333344567778898889999999853 45554
No 21
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=47.54 E-value=46 Score=30.84 Aligned_cols=51 Identities=27% Similarity=0.552 Sum_probs=34.5
Q ss_pred CCCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecCCC
Q 031077 26 DPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (166)
Q Consensus 26 ~~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~~~ 86 (166)
-++-.|.|..-|. ||-+..-.|. +.....|+..+ .|+ |+.++++++..+.+
T Consensus 167 ~~~~~~P~~pic~~cg~~~~~~~~-------~~d~~~~~v~y--~~~-cG~~~~~~~~~g~~ 218 (510)
T PRK00750 167 RQATYSPFLPICPKCGKVLTTPVI-------SYDAEAGTVTY--DCE-CGHEGEVPVTGGHG 218 (510)
T ss_pred cCCCeeeeeeeCCCCCccceEEEE-------EEeCCCCEEEE--EcC-CCCEEEEecCCCCc
Confidence 3445788999999 9998644331 12222344444 676 99999999988644
No 22
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=47.38 E-value=11 Score=33.52 Aligned_cols=26 Identities=38% Similarity=0.681 Sum_probs=19.3
Q ss_pred Eec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEE
Q 031077 36 KCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (166)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i 81 (166)
.|+ ||..+++|. .||+.|+.=+|+.=
T Consensus 2 ~c~~cg~~~~~~~--------------------g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYVSPKWL--------------------GKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCcc--------------------EECcCCCCceeeee
Confidence 588 999998884 47777777776654
No 23
>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=46.74 E-value=15 Score=22.21 Aligned_cols=33 Identities=21% Similarity=0.619 Sum_probs=15.8
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si 79 (166)
++|. |+- +||+.-+++..|. .|+|.+|+..+.+
T Consensus 3 ~rC~~C~a------ylNp~~~~~~~~~------~w~C~~C~~~N~l 36 (40)
T PF04810_consen 3 VRCRRCRA------YLNPFCQFDDGGK------TWICNFCGTKNPL 36 (40)
T ss_dssp -B-TTT--------BS-TTSEEETTTT------EEEETTT--EEE-
T ss_pred cccCCCCC------EECCcceEcCCCC------EEECcCCCCcCCC
Confidence 4566 654 5556555444222 5999999987654
No 24
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=46.05 E-value=13 Score=22.97 Aligned_cols=31 Identities=19% Similarity=0.439 Sum_probs=19.2
Q ss_pred EEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 31 YFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 31 ~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
|.=-+.|. ||... ...+.. ...++|+.|+++
T Consensus 15 W~~g~~CP~Cg~~~--~~~~~~-------------~~~~~C~~C~~q 46 (46)
T PF12760_consen 15 WPDGFVCPHCGSTK--HYRLKT-------------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCCCCee--eEEeCC-------------CCeEECCCCCCc
Confidence 33346799 99872 222221 457899999874
No 25
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=45.96 E-value=11 Score=34.27 Aligned_cols=27 Identities=37% Similarity=0.574 Sum_probs=21.3
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i 81 (166)
..|+ ||..+++| .++|+.|+.=+|+.=
T Consensus 8 y~C~~Cg~~~~~~--------------------~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 8 FVCQHCGADSPKW--------------------QGKCPACHAWNTITE 35 (454)
T ss_pred EECCcCCCCCccc--------------------cEECcCCCCccccch
Confidence 5799 99999888 468888887777654
No 26
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=45.61 E-value=26 Score=21.78 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=20.0
Q ss_pred EEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCce
Q 031077 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~ 76 (166)
+..+|. ||...+.+..++. .-...|+.|+..
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~-------------~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSD-------------DPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEEEecCC-------------CCCCCCCCCCCC
Confidence 445899 9988765544332 123579999974
No 27
>PRK11823 DNA repair protein RadA; Provisional
Probab=43.55 E-value=15 Score=33.39 Aligned_cols=26 Identities=35% Similarity=0.645 Sum_probs=19.5
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVT 80 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~ 80 (166)
..|+ ||..+++|. ++|+.|+.=+|+.
T Consensus 8 y~C~~Cg~~~~~~~--------------------g~Cp~C~~w~t~~ 34 (446)
T PRK11823 8 YVCQECGAESPKWL--------------------GRCPECGAWNTLV 34 (446)
T ss_pred EECCcCCCCCcccC--------------------eeCcCCCCcccee
Confidence 5699 999998884 5777777666654
No 28
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=43.17 E-value=18 Score=32.41 Aligned_cols=50 Identities=28% Similarity=0.517 Sum_probs=25.8
Q ss_pred CceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecCCC
Q 031077 28 NFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (166)
Q Consensus 28 ~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~~~ 86 (166)
.-.|.|..-|. ||-+.. +.|... +. +..-...+|+.|+.++++++..+.+
T Consensus 168 ~~y~Pf~piC~~cGri~t--t~v~~~---d~----~~~~v~Y~c~~cG~~g~~~i~~g~g 218 (360)
T PF01921_consen 168 ETYSPFLPICEKCGRIDT--TEVTEY---DP----EGGTVTYRCEECGHEGEVDITGGNG 218 (360)
T ss_dssp TT--SEEEEETTTEE--E--EEEEEE---------SSSEEEEE--TTS---EEETTTT-E
T ss_pred CCeeeeeeeccccCCccc--ceeeEe---ec----CCCEEEEEecCCCCEEEEecCCCcc
Confidence 34788999999 998532 222211 11 2234578999999999999987643
No 29
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.57 E-value=23 Score=27.06 Aligned_cols=47 Identities=23% Similarity=0.440 Sum_probs=28.6
Q ss_pred EEEEec-CCceecccEEEecCeeeeeCCCCcee--------eEEEEeccCCceeEEEEecCC
Q 031077 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTT--------NLIQKCKFCGREGTVTMIPGR 85 (166)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~a--------Nfv~KCk~C~r~~si~i~~~~ 85 (166)
....|. ||..++-. .+...+++..+++ ++.++|+.|+.. .+.|+.+.
T Consensus 69 ~~~~C~~CG~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~-~~~i~~G~ 124 (135)
T PRK03824 69 AVLKCRNCGNEWSLK-----EVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR-DFEIVKGR 124 (135)
T ss_pred eEEECCCCCCEEecc-----cccccccccccccccccccccccCcCCcCCCCC-CcEEecCc
Confidence 457899 99665321 1122344555544 677899999964 46666654
No 30
>PF15411 PH_10: Pleckstrin homology domain
Probab=41.97 E-value=1.4e+02 Score=22.25 Aligned_cols=43 Identities=19% Similarity=0.355 Sum_probs=26.3
Q ss_pred EEEEEE--ecceeeeeeCCCCCCCCceEEEEEEecCCceecccEEEecCeeeeeCCCCceeeEEEEecc
Q 031077 6 LMISAD--LENLTNLQPQGGCDDPNFSYFFKLKCGCGELSQKETCVSLAETLPTQGGKGTTNLIQKCKF 72 (166)
Q Consensus 6 L~vkAe--LeNV~~l~p~~~~~~~~~~~~fkvkCtC~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~ 72 (166)
|++|.. +.||+++.+.+ .| -.|.+.|. ..|..+..||+++|+.
T Consensus 61 L~LKGrI~i~~i~~v~~~s---~~-g~~~L~i~--------------------w~~d~e~~~F~lrf~n 105 (116)
T PF15411_consen 61 LQLKGRIYISNITEVSSSS---KP-GSYSLQIS--------------------WKGDPELENFTLRFRN 105 (116)
T ss_pred EEEeeEEEEEeeeeeeccC---CC-CceEEEEE--------------------EcCCCCCceEEEEeCC
Confidence 455554 47888888765 23 24555543 2355567788888864
No 31
>PF10001 DUF2242: Uncharacterized protein conserved in bacteria (DUF2242); InterPro: IPR018718 This family includes putative lipoproteins and uncharacterised proteins.
Probab=41.85 E-value=66 Score=24.57 Aligned_cols=53 Identities=13% Similarity=0.243 Sum_probs=39.9
Q ss_pred ecceeeeeeCCCCCCCCceEEEEEEec--CCceecccEEEecC-eeeeeCCCCceeeEE
Q 031077 12 LENLTNLQPQGGCDDPNFSYFFKLKCG--CGELSQKETCVSLA-ETLPTQGGKGTTNLI 67 (166)
Q Consensus 12 LeNV~~l~p~~~~~~~~~~~~fkvkCt--C~e~~~~~v~i~~~-e~~e~~gsrg~aNfv 67 (166)
+++-++.||.+ +-+..-.|.|.|. -...+...+++|.- +...++.++..|.+-
T Consensus 23 v~G~K~FQp~~---d~h~qi~~~vvCa~~~~~~~~s~~fvnAlQdrY~lKks~~SASvG 78 (121)
T PF10001_consen 23 VDGRKNFQPED---DVHAQIEFRVVCAPDGSGGQSSTVFVNALQDRYALKKSNNSASVG 78 (121)
T ss_pred EeeeeccccCC---CceEEEEEEEEECCCCCCCeeEEEEEEeeeeeeeeeecCCcceEe
Confidence 48889999975 3457788999999 34445678999875 678888888777654
No 32
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=36.30 E-value=55 Score=21.39 Aligned_cols=31 Identities=29% Similarity=0.615 Sum_probs=20.0
Q ss_pred EEEec-CCceecccEEEecCeeeeeCCC-CceeeEEEEeccCCceeEE
Q 031077 34 KLKCG-CGELSQKETCVSLAETLPTQGG-KGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gs-rg~aNfv~KCk~C~r~~si 79 (166)
+++|. ||+. |. +++. +|. .+.|..|+.+--|
T Consensus 2 ~~~CP~CG~~----ie--------v~~~~~Ge---iV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAE----IE--------LENPELGE---LVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCE----Ee--------cCCCccCC---EEeCCCCCCEEEE
Confidence 45899 9883 22 3322 344 5699999988655
No 33
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=35.85 E-value=91 Score=21.22 Aligned_cols=33 Identities=21% Similarity=0.449 Sum_probs=24.0
Q ss_pred EEEecCceEEeeEe-CC-cEEEEE--eCCCEEEeeecC
Q 031077 104 LFDCRGYEPVDFVF-GV-GWKVES--LAGTQYEDIDLS 137 (166)
Q Consensus 104 ~fdCRG~E~~~f~p-~~-~w~~~~--~sG~~f~dvdLs 137 (166)
.+.=+|.++.++.. ++ .|.+.. .+|+.++ |.+.
T Consensus 37 ~l~~~G~~v~~ve~~~~g~yev~~~~~dG~~~e-v~vD 73 (83)
T PF13670_consen 37 KLEAQGYQVREVEFDDDGCYEVEARDKDGKKVE-VYVD 73 (83)
T ss_pred HHHhcCCceEEEEEcCCCEEEEEEEECCCCEEE-EEEc
Confidence 33447888888888 55 499884 4999987 7664
No 34
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.44 E-value=31 Score=30.21 Aligned_cols=43 Identities=23% Similarity=0.418 Sum_probs=24.2
Q ss_pred ceEEE-EEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEE
Q 031077 29 FSYFF-KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 29 ~~~~f-kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si 79 (166)
++|.| +++|+ ||+ +.+--|.+..+ . ..+--+--|..|+.-.-+
T Consensus 220 teW~~~R~~C~~Cg~-~~~l~y~~~~~------~-~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 220 SEWHVVRVKCSNCEQ-SGKLHYWSLDS------E-QAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CcccccCccCCCCCC-CCceeeeeecC------C-CcceEeeeccccccccee
Confidence 45665 58899 987 44544443321 1 112346678888876433
No 35
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.62 E-value=10 Score=32.31 Aligned_cols=59 Identities=27% Similarity=0.408 Sum_probs=36.5
Q ss_pred EEEEEec-CCceecccEEEecCeeeeeCCCC--c--eeeEEEEeccCCceeEEEEecCCCcccccc
Q 031077 32 FFKLKCG-CGELSQKETCVSLAETLPTQGGK--G--TTNLIQKCKFCGREGTVTMIPGRGKPLTQE 92 (166)
Q Consensus 32 ~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsr--g--~aNfv~KCk~C~r~~si~i~~~~~~~~~~e 92 (166)
.|.++|. ||+--.+.--+|.-+. +..|-. | .--|.++|..|.++.++.=.|. +..|..+
T Consensus 38 Pf~~rC~tCgeyi~kg~kfN~r~E-~~~~e~yLgiki~Rf~i~Ct~cl~el~~rTDp~-N~dY~~E 101 (253)
T KOG2989|consen 38 PFRLRCNTCGEYIYKGKKFNAREE-DVIEETYLGIKIFRFYIKCTRCLRELSFRTDPK-NSDYVIE 101 (253)
T ss_pred cceeecccccchhhcCCCcchhHH-hhhccccccceeeeeeeeccchHhhhhhhcCCc-chHHHHH
Confidence 4899999 9996655544443221 111111 3 2369999999999987766554 2344444
No 36
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=32.58 E-value=42 Score=25.99 Aligned_cols=32 Identities=34% Similarity=0.777 Sum_probs=21.4
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si 79 (166)
|.|. |+..-.. .+- .+| -+.++|+.|+...++
T Consensus 103 VlC~~C~spdT~--l~k--------~~r---~~~l~C~ACGa~~~V 135 (138)
T PRK03988 103 VICPECGSPDTK--LIK--------EGR---IWVLKCEACGAETPV 135 (138)
T ss_pred EECCCCCCCCcE--EEE--------cCC---eEEEEcccCCCCCcC
Confidence 8899 9985322 221 112 678899999988776
No 37
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=32.37 E-value=74 Score=19.20 Aligned_cols=34 Identities=26% Similarity=0.651 Sum_probs=18.7
Q ss_pred Eec-CCceecccEEEecCeeeee-CCCCceeeEEEEeccCCce
Q 031077 36 KCG-CGELSQKETCVSLAETLPT-QGGKGTTNLIQKCKFCGRE 76 (166)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~-~gsrg~aNfv~KCk~C~r~ 76 (166)
+|. || |++.+++... + ++.-+. .+..+|..|+..
T Consensus 2 ~Cp~C~--~~~a~~~q~Q----~RsaDE~m-T~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCG--NREATFFQLQ----TRSADEPM-TVFYVCTKCGHR 37 (40)
T ss_pred cCCCCC--CCeEEEEEEc----ccCCCCCC-eEEEEeCCCCCE
Confidence 578 87 5566665321 1 111122 466788888763
No 38
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=32.35 E-value=73 Score=25.09 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=23.4
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVT 80 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~ 80 (166)
..|. |+......+ -.+++|..|-.-=..+.|..|+-.++=.
T Consensus 2 s~Cp~C~~~~~~~~-----~~~~IP~F~evii~sf~C~~CGyk~~ev 43 (161)
T PF03367_consen 2 SLCPNCGENGTTRI-----LLTDIPYFKEVIIMSFECEHCGYKNNEV 43 (161)
T ss_dssp EE-TTTSSCCEEEE-----EEEEETTTEEEEEEEEE-TTT--EEEEE
T ss_pred CcCCCCCCCcEEEE-----EEEcCCCCceEEEEEeECCCCCCEeeeE
Confidence 3688 887543222 3456777777777778888888765533
No 39
>KOG2110 consensus Uncharacterized conserved protein, contains WD40 repeats [Function unknown]
Probab=32.32 E-value=2.8e+02 Score=25.24 Aligned_cols=61 Identities=20% Similarity=0.327 Sum_probs=47.5
Q ss_pred CcccEEEEEecC--ceEEeeEeCCcEEEEE-eCCCEEEeeecCCCc-eeeecCCCCceEEEeeeEE
Q 031077 98 GFSPLMLFDCRG--YEPVDFVFGVGWKVES-LAGTQYEDIDLSGGD-YAEYDEKGECPVMISNLRF 159 (166)
Q Consensus 98 ~~~~i~~fdCRG--~E~~~f~p~~~w~~~~-~sG~~f~dvdLse~e-W~dYDEk~~~~VsI~~~~~ 159 (166)
+-+|+..|+|+- +--+.|+|+|-..|+. +.||+..=...++|+ -++|= .+--+|+|+.+.|
T Consensus 162 nl~~v~~I~aH~~~lAalafs~~G~llATASeKGTVIRVf~v~~G~kl~eFR-RG~~~~~IySL~F 226 (391)
T KOG2110|consen 162 NLQPVNTINAHKGPLAALAFSPDGTLLATASEKGTVIRVFSVPEGQKLYEFR-RGTYPVSIYSLSF 226 (391)
T ss_pred cceeeeEEEecCCceeEEEECCCCCEEEEeccCceEEEEEEcCCccEeeeee-CCceeeEEEEEEE
Confidence 567778888875 5668899999999995 799988855667764 77777 4555999998876
No 40
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.24 E-value=42 Score=26.85 Aligned_cols=44 Identities=23% Similarity=0.513 Sum_probs=30.0
Q ss_pred ceeeEEEEeccCCceeEEEEecCCCcccccccccCCCcccEEEEEecCceEEeeEe
Q 031077 62 GTTNLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVF 117 (166)
Q Consensus 62 g~aNfv~KCk~C~r~~si~i~~~~~~~~~~e~~~~~~~~~i~~fdCRG~E~~~f~p 117 (166)
..-++++.||.|+-.++=+|-+ .+| ++ | ++.+.|-||-.--...
T Consensus 74 p~m~l~yTCkvCntRs~ktisk---~AY--~~---G----vVivqC~gC~~~Hlia 117 (165)
T KOG3277|consen 74 PRMQLAYTCKVCNTRSTKTISK---QAY--EK---G----VVIVQCPGCKNHHLIA 117 (165)
T ss_pred cceEEEEEeeccCCccccccCh---hhh--hC---c----eEEEECCCCccceeeh
Confidence 4558899999999988866644 223 32 2 6777899997544433
No 41
>PF09460 Saf-Nte_pilin: Saf-pilin pilus formation protein; InterPro: IPR018569 This domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N terminus of another, incoming, pilus subunit which is not involved in the Ig-fold. The N terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit []. ; PDB: 2CNZ_A 2CO7_A 2CO3_A 2CO1_A 2CNY_A 3CRF_A 2CO4_A 3CRE_A 2CO6_A 2CO2_A ....
Probab=30.96 E-value=1.8e+02 Score=22.86 Aligned_cols=72 Identities=21% Similarity=0.338 Sum_probs=41.1
Q ss_pred eeEEEEecCCCcccccccccCCCcccEEEEEecCceEEeeEeCC-----------c--EEEEEe-CCCEEEeeecCC---
Q 031077 76 EGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGV-----------G--WKVESL-AGTQYEDIDLSG--- 138 (166)
Q Consensus 76 ~~si~i~~~~~~~~~~e~~~~~~~~~i~~fdCRG~E~~~f~p~~-----------~--w~~~~~-sG~~f~dvdLse--- 138 (166)
.-+++|.++.+ +..-.. ..-..|+.|--.|.-+-+|--+| | |.+.+. +|+... |-|+.
T Consensus 22 ~ltvsl~pV~G--L~AG~~--~~~~~IA~ltVss~s~k~f~vrG~~~s~~~~~~~g~~W~I~GKNsGn~I~-V~f~~~~~ 96 (145)
T PF09460_consen 22 QLTVSLTPVPG--LMAGRN--KGGMAIAKLTVSSTSIKEFGVRGDYVSPTTVGNTGDVWRITGKNSGNGII-VGFSSNAA 96 (145)
T ss_dssp SEEEEEEE-TT--BBSEE----TT-EEEEEEEESSS-SEEEEEE--ESSEESSTTSSEEEEE-TTT--EEE-EEE-HHHH
T ss_pred CcEEEEEecCc--hhccCC--CCCCEEEEEEEcccchhheeEeecccCccccCCCcceEEEEeccCCCEEE-EEEecccc
Confidence 45667777655 322111 12347888877777777776665 3 999985 999887 88741
Q ss_pred -----------CceeeecCCCCceEEE
Q 031077 139 -----------GDYAEYDEKGECPVMI 154 (166)
Q Consensus 139 -----------~eW~dYDEk~~~~VsI 154 (166)
-+|.=|| .+.++.|
T Consensus 97 ~~~~~~~~~ng~~W~~y~--tn~~~~i 121 (145)
T PF09460_consen 97 ANKGSLVMWNGHKWFTYD--TNDPLDI 121 (145)
T ss_dssp HT-SEEEEETTEEEEEEE--SSEEEEE
T ss_pred ccCCCccccCCceEEEec--CCCcEEE
Confidence 2689998 4455555
No 42
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=30.25 E-value=85 Score=25.58 Aligned_cols=41 Identities=20% Similarity=0.391 Sum_probs=26.3
Q ss_pred EEec-CCceecccEEEecCeeee-eCCCCceeeEEEEeccCCceeEEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLP-TQGGKGTTNLIQKCKFCGREGTVT 80 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e-~~gsrg~aNfv~KCk~C~r~~si~ 80 (166)
+.|. |+..-. ..+ -.+. +|..|-.-=+.+.|..|+-.++=.
T Consensus 1 ~~Cp~C~~~~~--~~~---~~~~~IP~F~evii~sf~C~~CGyr~~ev 43 (192)
T TIGR00310 1 IDCPSCGGECE--TVM---KTVNDIPYFGEVLETSTICEHCGYRSNDV 43 (192)
T ss_pred CcCCCCCCCCE--EEE---EEEcCCCCcceEEEEEEECCCCCCcccee
Confidence 4688 886422 111 1334 788877777888899998765533
No 43
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=28.87 E-value=52 Score=23.09 Aligned_cols=32 Identities=22% Similarity=0.537 Sum_probs=16.5
Q ss_pred EEEeccCCceeEEEEecCCCcccccccccCCCcccEEEEEecCce
Q 031077 67 IQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYE 111 (166)
Q Consensus 67 v~KCk~C~r~~si~i~~~~~~~~~~e~~~~~~~~~i~~fdCRG~E 111 (166)
++.|++|+.+.|+.+.-.+ -..+..+.|+=+.
T Consensus 22 ~F~CPfC~~~~sV~v~idk-------------k~~~~~~~C~~Cg 53 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDK-------------KEGIGILSCRVCG 53 (81)
T ss_dssp ----TTT--SS-EEEEEET-------------TTTEEEEEESSS-
T ss_pred eEcCCcCCCCCeEEEEEEc-------------cCCEEEEEecCCC
Confidence 6789999988887775422 1337788888873
No 44
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=27.90 E-value=56 Score=25.10 Aligned_cols=32 Identities=22% Similarity=0.661 Sum_probs=21.3
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEE
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si 79 (166)
|.|. |+..-.. .+ . .+| -+.+||+.|+...++
T Consensus 98 VlC~~C~sPdT~--l~-k-------~~r---~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNRPDTR--II-K-------EGR---VSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCCCCcE--EE-E-------eCC---eEEEecccCCCCCcc
Confidence 8899 9985432 22 1 112 357899999998776
No 45
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=27.18 E-value=20 Score=27.98 Aligned_cols=62 Identities=21% Similarity=0.451 Sum_probs=32.5
Q ss_pred cceeeeeeCCCCCC--CCceEEEEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecC
Q 031077 13 ENLTNLQPQGGCDD--PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPG 84 (166)
Q Consensus 13 eNV~~l~p~~~~~~--~~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~ 84 (166)
.||.+|....+... +=|--.+.++|+ |+...+..-........+.+ +|+.|+....=+|+-.
T Consensus 82 QNIDgLh~~AG~~~vielHG~l~~~~C~~C~~~~~~~~~~~~~~~~~~~----------~C~~C~~~lrp~vv~f 146 (178)
T PF02146_consen 82 QNIDGLHQKAGSPKVIELHGSLFRLRCSKCGKEYDREDIVDSIDEEEPP----------RCPKCGGLLRPDVVLF 146 (178)
T ss_dssp S-SSSHHHHTTESCEEETTEEEEEEEETTTSBEEEGHHHHHHHHTTSSC----------BCTTTSCBEEEEE--B
T ss_pred cccchhhhcccchhhHHHHhhhceeeecCCCccccchhhcccccccccc----------cccccCccCCCCeeec
Confidence 56666654332110 013456889999 99987543222111111111 9999999766666543
No 46
>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=27.08 E-value=75 Score=20.71 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=17.3
Q ss_pred ceeeEEEEeccCCceeEEEEecC
Q 031077 62 GTTNLIQKCKFCGREGTVTMIPG 84 (166)
Q Consensus 62 g~aNfv~KCk~C~r~~si~i~~~ 84 (166)
+..++.+||+-|+.-+.+.-...
T Consensus 19 ~~~~leIKCpRC~tiN~~~a~~~ 41 (51)
T PF10122_consen 19 EVIELEIKCPRCKTINHVRATSP 41 (51)
T ss_pred CccEEEEECCCCCccceEeccCC
Confidence 34578899999999887776543
No 47
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=27.05 E-value=57 Score=26.59 Aligned_cols=37 Identities=24% Similarity=0.537 Sum_probs=25.5
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEecC
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPG 84 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~~ 84 (166)
|.|. |+..-..- + . . .--+.++|+-|+...++.-...
T Consensus 99 V~C~~C~~pdT~l--~-k------~----~~~~~l~C~aCGa~~~v~~~~~ 136 (201)
T PRK12336 99 VICSECGLPDTRL--V-K------E----DRVLMLRCDACGAHRPVKKRKA 136 (201)
T ss_pred EECCCCCCCCcEE--E-E------c----CCeEEEEcccCCCCcccccccc
Confidence 8899 99854322 1 1 1 1256799999999998876554
No 48
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=26.22 E-value=54 Score=23.38 Aligned_cols=33 Identities=21% Similarity=0.462 Sum_probs=16.3
Q ss_pred EEEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeE
Q 031077 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (166)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~s 78 (166)
+...|. |++.||+ .+|+.. ++ .++|-.|++.+.
T Consensus 32 ~~~~CPfH~d~~pS-~~i~~~--------k~----~~~Cf~Cg~~Gd 65 (97)
T PF01807_consen 32 YRCLCPFHDDKTPS-FSINPD--------KN----RFKCFGCGKGGD 65 (97)
T ss_dssp EEE--SSS--SS---EEEETT--------TT----EEEETTT--EE-
T ss_pred EEEECcCCCCCCCc-eEEECC--------CC----eEEECCCCCCCc
Confidence 446699 9988875 466542 12 799999998764
No 49
>PF07433 DUF1513: Protein of unknown function (DUF1513); InterPro: IPR008311 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.07 E-value=1.5e+02 Score=26.06 Aligned_cols=55 Identities=18% Similarity=0.273 Sum_probs=28.8
Q ss_pred EEEEEecCceEEeeE-eCCcEE-----EEEeCCCEEEeeecCCCceeeecCCCCceEEEeeeEEEEEE
Q 031077 102 LMLFDCRGYEPVDFV-FGVGWK-----VESLAGTQYEDIDLSGGDYAEYDEKGECPVMISNLRFKFEV 163 (166)
Q Consensus 102 i~~fdCRG~E~~~f~-p~~~w~-----~~~~sG~~f~dvdLse~eW~dYDEk~~~~VsI~~~~~~f~~ 163 (166)
.+.||||+-++.... +..+.. +-+..|+.+- -+|+ ||+ .+.--|+|++.+-.+++
T Consensus 30 ~~v~D~~~g~~~~~~~a~~gRHFyGHg~fs~dG~~Ly---tTEn---d~~-~g~G~IgVyd~~~~~~r 90 (305)
T PF07433_consen 30 ALVFDCRTGQLLQRLWAPPGRHFYGHGVFSPDGRLLY---TTEN---DYE-TGRGVIGVYDAARGYRR 90 (305)
T ss_pred EEEEEcCCCceeeEEcCCCCCEEecCEEEcCCCCEEE---Eecc---ccC-CCcEEEEEEECcCCcEE
Confidence 678899987766432 222221 1122343221 1343 564 34446899998855544
No 50
>KOG0315 consensus G-protein beta subunit-like protein (contains WD40 repeats) [General function prediction only]
Probab=25.60 E-value=2.1e+02 Score=24.99 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=29.1
Q ss_pred CCCcccEEEEEec--CceEEeeEeCCcEEEEE-eCCCE
Q 031077 96 SGGFSPLMLFDCR--GYEPVDFVFGVGWKVES-LAGTQ 130 (166)
Q Consensus 96 ~~~~~~i~~fdCR--G~E~~~f~p~~~w~~~~-~sG~~ 130 (166)
+++..|++.||-. .+-.+.|+-+|.|..++ +.|+.
T Consensus 70 S~np~Pv~t~e~h~kNVtaVgF~~dgrWMyTgseDgt~ 107 (311)
T KOG0315|consen 70 SNNPNPVATFEGHTKNVTAVGFQCDGRWMYTGSEDGTV 107 (311)
T ss_pred CCCCCceeEEeccCCceEEEEEeecCeEEEecCCCceE
Confidence 5677899999976 58889999999999997 67763
No 51
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=25.04 E-value=70 Score=28.96 Aligned_cols=27 Identities=7% Similarity=0.044 Sum_probs=23.0
Q ss_pred EEEEEe-cCceEEeeEeCCcEEEEEeCC
Q 031077 102 LMLFDC-RGYEPVDFVFGVGWKVESLAG 128 (166)
Q Consensus 102 i~~fdC-RG~E~~~f~p~~~w~~~~~sG 128 (166)
|++.+| -|+-.++|+|.+.|.+++...
T Consensus 204 v~aYe~~lG~k~v~wsP~~qflavGsyD 231 (447)
T KOG4497|consen 204 VYAYERGLGLKFVEWSPCNQFLAVGSYD 231 (447)
T ss_pred eeeeeeccceeEEEeccccceEEeeccc
Confidence 568888 899999999999999998644
No 52
>TIGR01908 cas_CXXC_CXXC CRISPR-associated CXXC_CXXC protein Cst1. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a conserved region from an otherwise highly divergent protein found in the Tneap subtype of CRISPR/Cas regions. This Cys-rich region features two motifs of CXXC.
Probab=24.83 E-value=31 Score=30.04 Aligned_cols=36 Identities=28% Similarity=0.312 Sum_probs=26.6
Q ss_pred Eec-CCceecccEEEecCeeeeeCCCCcee-eEEEEec
Q 031077 36 KCG-CGELSQKETCVSLAETLPTQGGKGTT-NLIQKCK 71 (166)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~~gsrg~a-Nfv~KCk 71 (166)
.|- ||+.|.+...+.+++--.+.|+-|.+ ||.|-++
T Consensus 7 ~C~~Cg~r~a~~~~~~~t~~~~l~~~~~~~~Nffwn~~ 44 (309)
T TIGR01908 7 LCINCGERHAKKDTIFDTEIPLIGGLSGGVPNYFWNGK 44 (309)
T ss_pred cCCCcCCcchhccccccccCCccccCCCCccccccCCC
Confidence 699 99999876666666555556777776 9998864
No 53
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.80 E-value=43 Score=19.80 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=8.2
Q ss_pred EEEEec-CCce
Q 031077 33 FKLKCG-CGEL 42 (166)
Q Consensus 33 fkvkCt-C~e~ 42 (166)
.+|+|+ |+.+
T Consensus 24 ~~v~C~~C~~~ 34 (36)
T PF13717_consen 24 RKVRCSKCGHV 34 (36)
T ss_pred cEEECCCCCCE
Confidence 489999 9875
No 54
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=24.55 E-value=46 Score=28.22 Aligned_cols=42 Identities=21% Similarity=0.530 Sum_probs=18.6
Q ss_pred CceEEEE-EEec-CCceecccE-EEecCeeeeeCCCCceeeEEEEeccCCcee
Q 031077 28 NFSYFFK-LKCG-CGELSQKET-CVSLAETLPTQGGKGTTNLIQKCKFCGREG 77 (166)
Q Consensus 28 ~~~~~fk-vkCt-C~e~~~~~v-~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~ 77 (166)
.++|.|. ++|+ ||+..+... +++. + +. .+--+.-|+.|+.-.
T Consensus 204 ~t~W~~~R~~Cp~Cg~~~~~~l~~~~~-e--~~-----~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 204 GTEWRFVRIKCPYCGNTDHEKLEYFTV-E--GE-----PAYRVEVCESCGSYL 248 (290)
T ss_dssp --EEE--TTS-TTT---SS-EEE----------------SEEEEEETTTTEEE
T ss_pred CCeeeecCCCCcCCCCCCCcceeeEec-C--CC-----CcEEEEECCcccchH
Confidence 3678765 8899 999755433 2221 1 11 145678999999753
No 55
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=24.48 E-value=21 Score=31.20 Aligned_cols=52 Identities=13% Similarity=0.267 Sum_probs=37.2
Q ss_pred ceEEEEEEec-CCceecccEEEecCeeeeeCCC--CceeeEEEEeccCCceeEEEEec
Q 031077 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQGG--KGTTNLIQKCKFCGREGTVTMIP 83 (166)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gs--rg~aNfv~KCk~C~r~~si~i~~ 83 (166)
|+-.|.|-|. |...-...|-.|. |+..+-+- ----.|-|||..|... |.|-.
T Consensus 47 FEMPynIWC~gC~nhIgmGvRyNA-eKkkvGnYYtTpiw~FrmKchlC~n~--i~iqT 101 (317)
T KOG2990|consen 47 FEMPYNIWCDGCKNHIGMGVRYNA-EKKKVGNYYTTPIWSFRMKCHLCDNY--IVIQT 101 (317)
T ss_pred EecccchhhccHHHhhhccceech-hhhhccccccCcccchhhcccccCCc--eeeec
Confidence 5567889999 9998888888887 45455221 2234799999999876 55543
No 56
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=24.46 E-value=20 Score=31.87 Aligned_cols=47 Identities=23% Similarity=0.395 Sum_probs=25.2
Q ss_pred EEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEEec
Q 031077 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIP 83 (166)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i~~ 83 (166)
|.|. |...+...-.....+.|.+..-.+.=- -+||+.|+.. +|++..
T Consensus 253 v~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KR-FFkC~~C~~R-t~sl~r 300 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKR-FFKCKDCGNR-TISLER 300 (344)
T ss_dssp EEETTT--EESS--HHHHHTT--EEEEEEE-E-EEE-T-TS-E-EEESSS
T ss_pred EEcCCCCCcccCcchhHHhcCCceEEeeeeee-eEECCCCCCe-eeeccc
Confidence 6799 988887777777777777753333334 4699999996 666643
No 57
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=24.42 E-value=57 Score=21.73 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=19.5
Q ss_pred CceeeEEEEeccCCceeEEEEec
Q 031077 61 KGTTNLIQKCKFCGREGTVTMIP 83 (166)
Q Consensus 61 rg~aNfv~KCk~C~r~~si~i~~ 83 (166)
.|.|.+-.||+-|+-.+-+.|..
T Consensus 18 ~~~~yle~KCPrCK~vN~~~~~~ 40 (60)
T COG4416 18 EGQAYLEKKCPRCKEVNEFYIKE 40 (60)
T ss_pred ccceeeeecCCccceeeeeeccc
Confidence 37789999999999988888754
No 58
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=22.69 E-value=58 Score=27.58 Aligned_cols=51 Identities=25% Similarity=0.384 Sum_probs=33.6
Q ss_pred EEEEEEec-CCceecccEEEecCeeeeeCCCC---c--eeeEEEEeccCCceeEEEEec
Q 031077 31 YFFKLKCG-CGELSQKETCVSLAETLPTQGGK---G--TTNLIQKCKFCGREGTVTMIP 83 (166)
Q Consensus 31 ~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsr---g--~aNfv~KCk~C~r~~si~i~~ 83 (166)
=.|.+.|- |++--++.--.|. ..|+-+-+ | .--|.++|..|++..-+.-.|
T Consensus 39 TPF~~RCL~C~~YI~K~~rfNa--vkE~~~dK~y~~~kiYRf~I~C~~C~n~i~~RTDP 95 (272)
T COG5134 39 TPFPVRCLNCENYIQKGTRFNA--VKEEIGDKSYYTTKIYRFSIKCHLCSNPIDVRTDP 95 (272)
T ss_pred cCcceeecchhhhhhcccchhH--HHHHhcccccceeEEEEEEEEccCCCCceeeecCC
Confidence 35889999 9997777666665 22333333 2 235999999999875444433
No 59
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=22.58 E-value=1.1e+02 Score=15.01 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=9.4
Q ss_pred CCceeeecCCCC
Q 031077 138 GGDYAEYDEKGE 149 (166)
Q Consensus 138 e~eW~dYDEk~~ 149 (166)
+|+|.-|++++.
T Consensus 2 ~G~~~~yy~nG~ 13 (22)
T PF07661_consen 2 DGEWKFYYENGK 13 (22)
T ss_pred cceEEEEeCCCC
Confidence 478999998765
No 60
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.23 E-value=50 Score=28.86 Aligned_cols=44 Identities=18% Similarity=0.418 Sum_probs=25.5
Q ss_pred ceEEE-EEEec-CCceecccEEEecCeeeeeCCCCc-eeeEEEEeccCCceeEE
Q 031077 29 FSYFF-KLKCG-CGELSQKETCVSLAETLPTQGGKG-TTNLIQKCKFCGREGTV 79 (166)
Q Consensus 29 ~~~~f-kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg-~aNfv~KCk~C~r~~si 79 (166)
++|.| +++|+ ||+. .+--|++.. +..+ .+--+--|..|+.-.-+
T Consensus 218 teW~~~R~~C~~Cg~~-~~l~y~~~e------~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 218 TEWHYVRVKCSHCEES-KHLAYLSLE------HDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred CcccccCccCCCCCCC-CceeeEeec------CCCCCcceEEeeccccccchhh
Confidence 45664 69999 9985 343344432 1111 23456689999876433
No 61
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=21.26 E-value=1.4e+02 Score=17.74 Aligned_cols=11 Identities=36% Similarity=0.800 Sum_probs=7.7
Q ss_pred eEEEEeccCCc
Q 031077 65 NLIQKCKFCGR 75 (166)
Q Consensus 65 Nfv~KCk~C~r 75 (166)
.+...|..|++
T Consensus 26 T~fy~C~~C~~ 36 (39)
T PF01096_consen 26 TLFYVCCNCGH 36 (39)
T ss_dssp EEEEEESSSTE
T ss_pred eEEEEeCCCCC
Confidence 55667888875
No 62
>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=20.99 E-value=40 Score=22.07 Aligned_cols=32 Identities=25% Similarity=0.529 Sum_probs=21.3
Q ss_pred EEEec-CCceecccEEEecCeeeeeCCCCceeeEEEEeccCCceeEEEE
Q 031077 34 KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (166)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~r~~si~i 81 (166)
--.|+ ||..... .+ ..=.+.|+.|+.....++
T Consensus 28 Sq~C~~CG~~~~~----~~------------~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RR------------SGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred ccCccCccccccc----cc------------ccceEEcCCCCCEECcHH
Confidence 45699 9998765 11 122679999998765444
No 63
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.21 E-value=74 Score=18.79 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=8.8
Q ss_pred EEEEec-CCcee
Q 031077 33 FKLKCG-CGELS 43 (166)
Q Consensus 33 fkvkCt-C~e~~ 43 (166)
-+..|+ ||.+|
T Consensus 21 ~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 21 ERLVCPACGFIH 32 (34)
T ss_dssp -EEEETTTTEEE
T ss_pred cceECCCCCCEE
Confidence 467899 99987
No 64
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=20.20 E-value=36 Score=24.49 Aligned_cols=13 Identities=38% Similarity=0.756 Sum_probs=1.0
Q ss_pred eEEEEeccCCcee
Q 031077 65 NLIQKCKFCGREG 77 (166)
Q Consensus 65 Nfv~KCk~C~r~~ 77 (166)
=|.|-||-|||-.
T Consensus 70 CL~WACKaCKRKt 82 (86)
T PF01586_consen 70 CLLWACKACKRKT 82 (86)
T ss_dssp ---------S---
T ss_pred chHHHhHhhhccC
Confidence 4999999999953
Done!