Query 032492
Match_columns 139
No_of_seqs 107 out of 238
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 14:47:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032492hhsearch_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 1.2E-53 2.5E-58 327.4 14.6 126 1-133 1-127 (161)
2 KOG1296 Uncharacterized conser 100.0 1.6E-52 3.5E-57 314.9 7.9 124 1-130 1-125 (161)
3 PF04502 DUF572: Family of unk 93.1 0.12 2.5E-06 43.7 3.8 63 29-93 35-102 (324)
4 PRK00415 rps27e 30S ribosomal 92.7 0.15 3.2E-06 33.4 3.1 34 27-76 5-39 (59)
5 PLN00209 ribosomal protein S27 92.5 0.24 5.1E-06 34.7 4.1 34 27-76 30-64 (86)
6 PF01667 Ribosomal_S27e: Ribos 91.8 0.16 3.5E-06 32.7 2.4 32 30-76 3-35 (55)
7 PTZ00083 40S ribosomal protein 91.7 0.33 7.2E-06 33.9 4.1 34 27-76 29-63 (85)
8 COG2051 RPS27A Ribosomal prote 90.3 0.54 1.2E-05 31.5 3.9 42 15-76 5-47 (67)
9 PF14205 Cys_rich_KTR: Cystein 84.6 1.1 2.4E-05 28.9 2.6 41 35-85 5-46 (55)
10 PF14255 Cys_rich_CPXG: Cystei 65.7 11 0.00024 23.8 3.5 40 35-84 1-41 (52)
11 PF14353 CpXC: CpXC protein 56.1 3.2 7E-05 29.9 -0.4 46 34-80 1-51 (128)
12 KOG1779 40s ribosomal protein 53.9 24 0.00052 24.5 3.7 16 27-43 28-44 (84)
13 PF05428 CRF-BP: Corticotropin 53.7 40 0.00087 28.8 5.7 118 5-135 12-133 (311)
14 PF12760 Zn_Tnp_IS1595: Transp 53.2 8.5 0.00019 23.1 1.3 12 65-76 35-46 (46)
15 PF05180 zf-DNL: DNL zinc fing 51.4 17 0.00037 24.1 2.6 37 31-76 1-38 (66)
16 KOG2315 Predicted translation 49.3 32 0.00069 31.6 4.7 52 65-128 324-375 (566)
17 TIGR00467 lysS_arch lysyl-tRNA 48.3 47 0.001 30.1 5.7 48 27-86 161-209 (515)
18 PRK00750 lysK lysyl-tRNA synth 47.3 57 0.0012 29.3 6.0 50 27-86 168-218 (510)
19 cd00674 LysRS_core_class_I cat 46.9 69 0.0015 27.6 6.3 49 27-86 162-211 (353)
20 PRK03824 hypA hydrogenase nick 45.0 21 0.00046 26.4 2.5 47 33-85 69-124 (135)
21 COG1066 Sms Predicted ATP-depe 43.4 15 0.00032 32.9 1.7 15 34-48 7-22 (456)
22 PF10001 DUF2242: Uncharacteri 42.1 77 0.0017 23.5 5.0 56 9-67 19-78 (121)
23 TIGR02098 MJ0042_CXXC MJ0042 f 37.0 35 0.00075 19.3 2.1 35 33-78 1-36 (38)
24 KOG3277 Uncharacterized conser 36.8 32 0.0007 26.7 2.5 39 63-113 75-113 (165)
25 PF08662 eIF2A: Eukaryotic tra 36.0 55 0.0012 25.1 3.7 34 98-131 134-167 (194)
26 PF01921 tRNA-synt_1f: tRNA sy 35.6 33 0.00072 29.8 2.6 48 29-85 169-217 (360)
27 PF04810 zf-Sec23_Sec24: Sec23 35.6 29 0.00063 20.3 1.7 26 48-79 11-36 (40)
28 PF03367 zf-ZPR1: ZPR1 zinc-fi 34.1 81 0.0017 24.1 4.3 42 35-81 2-44 (161)
29 smart00440 ZnF_C2C2 C2C2 Zinc 33.3 85 0.0018 18.4 3.4 34 36-76 2-37 (40)
30 KOG2989 Uncharacterized conser 32.6 9.7 0.00021 31.5 -1.0 60 32-93 38-102 (253)
31 TIGR01206 lysW lysine biosynth 32.0 77 0.0017 20.1 3.3 32 34-79 2-34 (54)
32 PRK03988 translation initiatio 32.0 44 0.00095 25.1 2.5 15 65-79 121-135 (138)
33 PF02146 SIR2: Sir2 family; I 31.0 16 0.00035 27.5 0.0 62 13-84 82-146 (178)
34 PF05129 Elf1: Transcription e 30.4 26 0.00056 23.9 0.9 33 66-111 21-53 (81)
35 cd01121 Sms Sms (bacterial rad 30.2 31 0.00067 29.7 1.6 12 36-47 2-14 (372)
36 KOG4497 Uncharacterized conser 29.5 54 0.0012 28.9 2.9 26 101-126 203-229 (447)
37 TIGR00310 ZPR1_znf ZPR1 zinc f 29.2 53 0.0011 26.0 2.6 39 35-78 1-41 (192)
38 TIGR00416 sms DNA repair prote 29.1 32 0.00069 30.4 1.5 27 35-81 8-35 (454)
39 PF13717 zinc_ribbon_4: zinc-r 28.8 33 0.00073 19.7 1.1 10 33-42 24-34 (36)
40 PF15411 PH_10: Pleckstrin hom 28.4 2.3E+02 0.005 20.4 6.4 15 58-72 91-105 (116)
41 PF01586 Basic: Myogenic Basic 27.6 21 0.00046 24.9 0.1 13 65-77 70-82 (86)
42 PF06159 DUF974: Protein of un 27.0 2.2E+02 0.0048 23.0 6.0 17 111-127 154-170 (249)
43 PRK11823 DNA repair protein Ra 26.8 42 0.00091 29.5 1.8 15 35-49 8-23 (446)
44 KOG2990 C2C2-type Zn-finger pr 26.1 18 0.00038 30.8 -0.6 52 29-83 47-101 (317)
45 PF01927 Mut7-C: Mut7-C RNAse 25.9 53 0.0012 24.3 2.0 38 36-76 93-133 (147)
46 PF10122 Mu-like_Com: Mu-like 25.7 89 0.0019 19.8 2.7 23 62-84 19-41 (51)
47 KOG0315 G-protein beta subunit 25.6 2.5E+02 0.0054 23.9 6.1 37 96-132 70-108 (311)
48 TIGR00311 aIF-2beta translatio 25.6 66 0.0014 24.0 2.4 32 35-79 98-130 (133)
49 PF13670 PepSY_2: Peptidase pr 24.2 2.2E+02 0.0047 18.7 4.6 32 107-138 40-73 (83)
50 TIGR01908 cas_CXXC_CXXC CRISPR 24.2 33 0.00071 29.0 0.6 36 36-71 7-44 (309)
51 PF08630 Dfp1_Him1_M: Dfp1/Him 23.6 27 0.00058 25.9 0.0 35 96-134 87-123 (125)
52 PF08050 Tet_res_leader: Tetra 23.2 25 0.00055 18.0 -0.1 9 68-76 1-9 (20)
53 PF06051 DUF928: Domain of Unk 23.2 85 0.0018 24.4 2.8 11 28-38 92-102 (189)
54 PF01096 TFIIS_C: Transcriptio 22.4 93 0.002 18.1 2.2 11 65-75 26-36 (39)
55 PRK12336 translation initiatio 21.6 86 0.0019 24.7 2.5 38 35-85 99-137 (201)
56 PF09723 Zn-ribbon_8: Zinc rib 21.3 1.1E+02 0.0024 17.9 2.4 31 33-76 4-35 (42)
57 TIGR02605 CxxC_CxxC_SSSS putat 21.1 1E+02 0.0022 18.4 2.3 31 33-76 4-35 (52)
58 PF15446 zf-PHD-like: PHD/FYVE 20.2 42 0.00092 26.4 0.5 12 62-73 46-57 (175)
59 PF01807 zf-CHC2: CHC2 zinc fi 20.0 83 0.0018 21.7 1.9 33 33-78 32-65 (97)
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=1.2e-53 Score=327.38 Aligned_cols=126 Identities=48% Similarity=0.914 Sum_probs=97.1
Q ss_pred CceEEEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032492 1 MVNCMLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (139)
Q Consensus 1 Mv~~~L~vkAeLenVt~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si 79 (139)
||+|+|+|||+||||++|+|.+ ++|.|+|+|||+ |||+|+|+|+|+++|+++|+||||+||||+|||+|+|++||
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 EEecCCCcccccccccCCCCccEEEEEccCceEEeEEeCCCEEEEEeecCceee
Q 032492 80 TMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESVSFYSCPF 133 (139)
Q Consensus 80 ~i~~~~~~~~~~e~~~~~~~~~I~~fdCRGlEpv~f~P~~~w~~~s~~~~~~~~ 133 (139)
+|++++..+|+++++ ++|++|++||||||||++|+|+++|+|++++|+ ..|
T Consensus 77 ~i~~~~~~~~~~e~~--~~~~~i~~fdCRG~e~~~f~p~~~~~~~~~esG-~~f 127 (161)
T PF05907_consen 77 DIIPGKGKPYTAEDS--GKFVPILAFDCRGLEPVEFSPRGGWVAVSVESG-TKF 127 (161)
T ss_dssp EEE--TTTEEEGGGT--TS-EEEEEEEEESEEEEEE---S-EEEEET-TS--EE
T ss_pred EEEecCccccccccc--cCCceEEEEECCCcEeEEEecCCcEEEEEecCC-CEE
Confidence 999999889998764 799999999999999999999999999999777 455
No 2
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-52 Score=314.89 Aligned_cols=124 Identities=44% Similarity=0.852 Sum_probs=120.4
Q ss_pred CceEEEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032492 1 MVNCMLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (139)
Q Consensus 1 Mv~~~L~vkAeLenVt~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si 79 (139)
||+|+|+++|.|||||+|+|.+ |+|+|+|+|||+ |||.|++|++|+.+|.+.+|||||+||||||||+|+|++||
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 9999999999999999999987 789999999999 99999999999999999999999999999999999999999
Q ss_pred EEecCCCcccccccccCCCCccEEEEEccCceEEeEEeCCCEEEEEeecCc
Q 032492 80 TMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESVSFYS 130 (139)
Q Consensus 80 ~i~~~~~~~~~~e~~~~~~~~~I~~fdCRGlEpv~f~P~~~w~~~s~~~~~ 130 (139)
+|++.++++||++++ ++|++|+.|||||+||++|.|+++|.|+|++++.
T Consensus 77 ~iv~~~~~pyt~ed~--e~~~~i~vfdCRG~EpidF~p~~~w~a~s~esG~ 125 (161)
T KOG1296|consen 77 TIVAFEDKPYTAEDS--EKFKTIVVFDCRGLEPIDFYPRTGWFAVSAESGT 125 (161)
T ss_pred EEecCCCCccccccc--ccccceEEEeccCCcceeecCCceEEEEecccCc
Confidence 999999999999875 6899999999999999999999999999999983
No 3
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=93.08 E-value=0.12 Score=43.72 Aligned_cols=63 Identities=22% Similarity=0.305 Sum_probs=45.8
Q ss_pred ceEEEEEEec-CCceeeceEEEecCeeEEeCC--CCce--eeEEEeeccCCCeeEEEEecCCCccccccc
Q 032492 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQG--GKGT--TNLIQKCKFCGREGTVTMIPGRGKPLTQEA 93 (139)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~g--sRG~--aNfv~KCk~C~re~si~i~~~~~~~~~~e~ 93 (139)
|...|.|.|. |++--.+.+-+|. ++..+.+ ==|. =.|.|||..|+.+.+|.=.|. +.-|.++.
T Consensus 35 f~~Pf~i~C~~C~~~I~kG~rFNA-~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDPk-n~dY~~~~ 102 (324)
T PF04502_consen 35 FMMPFNIWCNTCGEYIYKGVRFNA-RKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDPK-NTDYVVES 102 (324)
T ss_pred EcCCccCcCCCCccccccceeeee-eeEecCCCccccceEEEEEEEcCCCCCEEeeecCCC-CCCeeeec
Confidence 4667999999 9999999999999 5655654 2243 379999999999866554443 34565543
No 4
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=92.74 E-value=0.15 Score=33.38 Aligned_cols=34 Identities=32% Similarity=0.850 Sum_probs=26.7
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
|+ .||++|||. |+.+. +.+ +.|..+.+|..|++.
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 54 899999999 99874 222 346789999999986
No 5
>PLN00209 ribosomal protein S27; Provisional
Probab=92.49 E-value=0.24 Score=34.71 Aligned_cols=34 Identities=29% Similarity=0.728 Sum_probs=26.9
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
|+ .|+++|||. |+.+. +.+ +.|..+.+|..|++.
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 222 456889999999976
No 6
>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=91.79 E-value=0.16 Score=32.72 Aligned_cols=32 Identities=34% Similarity=0.820 Sum_probs=19.2
Q ss_pred eEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 30 SYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 30 ~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
.|+++|||. |+.+. +.+ +.|..+.+|..|++.
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 699999999 99875 222 346788999999975
No 7
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=91.72 E-value=0.33 Score=33.91 Aligned_cols=34 Identities=32% Similarity=0.824 Sum_probs=26.7
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
|+ .|+++|||. |+.+. +.+ +.|..+.+|..|++.
T Consensus 29 Pn-S~Fm~VkCp~C~n~q---~VF------------ShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 29 PN-SYFMDVKCPGCSQIT---TVF------------SHAQTVVLCGGCSSQ 63 (85)
T ss_pred CC-CeEEEEECCCCCCee---EEE------------ecCceEEEccccCCE
Confidence 54 899999999 99875 222 346789999999875
No 8
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=90.30 E-value=0.54 Score=31.48 Aligned_cols=42 Identities=26% Similarity=0.620 Sum_probs=30.1
Q ss_pred eeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 15 LTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 15 Vt~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
+.-+.|.. | ..++++|||. |+.+. +.+ +.|..+.+|-.|++.
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 34455532 5 3899999999 99874 222 446788999999985
No 9
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=84.59 E-value=1.1 Score=28.90 Aligned_cols=41 Identities=20% Similarity=0.430 Sum_probs=29.8
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032492 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~~ 85 (139)
+.|. ||..++-. |-. |+ .+ -||-+-|+-|++|.-|++....
T Consensus 5 i~CP~CgnKTR~k--ir~-DT-~L------kNfPlyCpKCK~EtlI~v~~~~ 46 (55)
T PF14205_consen 5 ILCPICGNKTRLK--IRE-DT-VL------KNFPLYCPKCKQETLIDVKQLK 46 (55)
T ss_pred EECCCCCCcccee--eec-Cc-ee------ccccccCCCCCceEEEEeeccE
Confidence 5699 99877533 222 22 12 3999999999999999997654
No 10
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=65.71 E-value=11 Score=23.79 Aligned_cols=40 Identities=28% Similarity=0.582 Sum_probs=30.3
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecC
Q 032492 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPG 84 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~ 84 (139)
+.|. ||+.- .+ .+.-|.|...++--|..|-|...+.+.-.
T Consensus 1 i~CPyCge~~--~~--------~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d 41 (52)
T PF14255_consen 1 IQCPYCGEPI--EI--------LIDPSAGDQEYIEDCQVCCRPIEVQVTVD 41 (52)
T ss_pred CCCCCCCCee--EE--------EEecCCCCeeEEeehhhcCCccEEEEEEC
Confidence 4689 99874 22 23345677799999999999999988654
No 11
>PF14353 CpXC: CpXC protein
Probab=56.10 E-value=3.2 Score=29.93 Aligned_cols=46 Identities=20% Similarity=0.423 Sum_probs=28.8
Q ss_pred EEEec-CCceeeceE--EEecCeeEEeCCC--CceeeEEEeeccCCCeeEEE
Q 032492 34 KLKCG-CGELSQKET--CVSLAETLPTQGG--KGTTNLIQKCKFCGREGTVT 80 (139)
Q Consensus 34 kvkCt-C~e~~~~~v--~i~~~e~~e~~gs--RG~aNfv~KCk~C~re~si~ 80 (139)
+|.|. |+......+ .||..+.-++.-. .|+ =|...|+.|++...++
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~-l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGS-LFSFTCPSCGHKFRLE 51 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCC-cCEEECCCCCCceecC
Confidence 37899 999765544 4554433333211 233 4788999999997653
No 12
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=53.95 E-value=24 Score=24.47 Aligned_cols=16 Identities=50% Similarity=1.190 Sum_probs=13.4
Q ss_pred CCceEEEEEEec-CCcee
Q 032492 27 PNFSYFFKLKCG-CGELS 43 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~ 43 (139)
|+ .|+++|||+ |..++
T Consensus 28 ~n-syFm~VkC~gc~~iT 44 (84)
T KOG1779|consen 28 PN-SYFMDVKCPGCFKIT 44 (84)
T ss_pred CC-ceEEEEEcCCceEEE
Confidence 44 899999999 98765
No 13
>PF05428 CRF-BP: Corticotropin-releasing factor binding protein (CRF-BP); InterPro: IPR008435 This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development [].
Probab=53.69 E-value=40 Score=28.78 Aligned_cols=118 Identities=16% Similarity=0.175 Sum_probs=66.9
Q ss_pred EEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEec
Q 032492 5 MLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIP 83 (139)
Q Consensus 5 ~L~vkAeLenVt~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~ 83 (139)
.|...+-|.|-.+..-.... .++ .-+.-+.-. =+|..+..+|--..+-.+|-.-.|.=.|.. ..=+-.+-+=++.
T Consensus 12 ~ll~l~~~~g~~R~~e~~~~-~~~-~~~~l~~~~~kre~~~e~~yrr~lrCldm~s~~G~f~f~a--~~pq~~Ca~y~ia 87 (311)
T PF05428_consen 12 LLLSLSALRGDSRYIELREE-ADD-DLFSLLSADLKRELSEEFIYRRPLRCLDMLSEEGQFTFTA--SRPQLVCAAYFIA 87 (311)
T ss_pred heeehhhhcCCchhhhhhhc-ccc-cchhhccchhhcccCccccccchhhheeeeccCceEEEec--CCCCceeEEEEEe
Confidence 34444455555554432211 111 223333334 667667777766666777766667433333 3323334445554
Q ss_pred CCCcccccccccCCCCccEEEEEccCceEEeEEeCCCEEEEEe---ecCceeeee
Q 032492 84 GRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESV---SFYSCPFPI 135 (139)
Q Consensus 84 ~~~~~~~~e~~~~~~~~~I~~fdCRGlEpv~f~P~~~w~~~s~---~~~~~~~~~ 135 (139)
.....++++-. -+.+||+|-.+++|. |||+.++. ++.+||+++
T Consensus 88 ePd~~IeI~~~-------~vdidC~~G~ll~v~--DGW~LnGe~FPs~~DHplpl 133 (311)
T PF05428_consen 88 EPDELIEIEFD-------HVDIDCEGGDLLKVF--DGWELNGEKFPSSQDHPLPL 133 (311)
T ss_pred CCCeEEEEEEE-------EeeccCCCCCEEEEE--eceEECccCCcCcccCCCch
Confidence 44444555432 578999999999987 79999886 456677765
No 14
>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=53.21 E-value=8.5 Score=23.15 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=9.6
Q ss_pred eEEEeeccCCCe
Q 032492 65 NLIQKCKFCGRE 76 (139)
Q Consensus 65 Nfv~KCk~C~re 76 (139)
...++|+.|+++
T Consensus 35 ~~~~~C~~C~~q 46 (46)
T PF12760_consen 35 RGRYRCKACRKQ 46 (46)
T ss_pred CCeEECCCCCCc
Confidence 567999999874
No 15
>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=51.42 E-value=17 Score=24.14 Aligned_cols=37 Identities=32% Similarity=0.658 Sum_probs=17.7
Q ss_pred EEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 31 YFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 31 ~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
|.+.+.|. |+..+.+ .|++. .. -+|. ...+|+.|+..
T Consensus 1 ~~l~FTC~~C~~Rs~~--~~sk~-aY----~~Gv--Viv~C~gC~~~ 38 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAK--MFSKQ-AY----HKGV--VIVQCPGCKNR 38 (66)
T ss_dssp EEEEEEETTTTEEEEE--EEEHH-HH----HTSE--EEEE-TTS--E
T ss_pred CeEEEEcCCCCCccce--eeCHH-HH----hCCe--EEEECCCCcce
Confidence 45666777 7765543 33331 00 1244 66777777755
No 16
>KOG2315 consensus Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis]
Probab=49.31 E-value=32 Score=31.59 Aligned_cols=52 Identities=10% Similarity=0.075 Sum_probs=37.6
Q ss_pred eEEEeeccCCCeeEEEEecCCCcccccccccCCCCccEEEEEccCceEEeEEeCCCEEEEEeec
Q 032492 65 NLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESVSF 128 (139)
Q Consensus 65 Nfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCRGlEpv~f~P~~~w~~~s~~~ 128 (139)
|++.=+-|=.=.+++.|-... +++.|..|+|-+.-..+|+|+|.|.++++.+
T Consensus 324 ~ii~lAGFGNL~G~mEvwDv~------------n~K~i~~~~a~~tt~~eW~PdGe~flTATTa 375 (566)
T KOG2315|consen 324 NIILLAGFGNLPGDMEVWDVP------------NRKLIAKFKAANTTVFEWSPDGEYFLTATTA 375 (566)
T ss_pred CEEEEeecCCCCCceEEEecc------------chhhccccccCCceEEEEcCCCcEEEEEecc
Confidence 334444444444555554432 3788999999999999999999999888766
No 17
>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=48.28 E-value=47 Score=30.05 Aligned_cols=48 Identities=19% Similarity=0.379 Sum_probs=32.4
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCC
Q 032492 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~~~ 86 (139)
++-.|.|...|. ||-+....+.++. .. ...++|+ |+.++.+++..+.+
T Consensus 161 ~~~~~P~~pic~~cGrv~~~~~~~~~--------~~---~v~Y~c~-cG~~g~~~~~~g~~ 209 (515)
T TIGR00467 161 EENWYPISVFCENCGRDTTTVNNYDN--------EY---SIEYSCE-CGNQESVDIYTGAI 209 (515)
T ss_pred CCCceeeeeecCCcCccCceEEEecC--------Cc---eEEEEcC-CCCEEEEeecCCCc
Confidence 343677999999 9998652221111 11 2566896 99999999977644
No 18
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=47.29 E-value=57 Score=29.30 Aligned_cols=50 Identities=28% Similarity=0.593 Sum_probs=33.3
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCC
Q 032492 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~~~ 86 (139)
++-.|.|...|. ||-+..-.| + +...-.|+..+ +|+ |+.+.++++..+.+
T Consensus 168 ~~~~~P~~pic~~cg~~~~~~~-~------~~d~~~~~v~y--~~~-cG~~~~~~~~~g~~ 218 (510)
T PRK00750 168 QATYSPFLPICPKCGKVLTTPV-I------SYDAEAGTVTY--DCE-CGHEGEVPVTGGHG 218 (510)
T ss_pred CCCeeeeeeeCCCCCccceEEE-E------EEeCCCCEEEE--EcC-CCCEEEEecCCCCc
Confidence 444788999999 999864332 1 12222344444 676 99999999988643
No 19
>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=46.86 E-value=69 Score=27.57 Aligned_cols=49 Identities=39% Similarity=0.693 Sum_probs=30.9
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCC
Q 032492 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (139)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~~~ 86 (139)
++-.|.|...|. ||-.. +.+. +..+..|+ ..++|+ |+.+..++|..+.+
T Consensus 162 ~~~~~P~~p~c~~cg~~~---~~v~-----~~d~~~~~--v~y~c~-cG~~g~~~~~~g~~ 211 (353)
T cd00674 162 QETWYPFMPYCEKCGKDT---TTVE-----AYDAKAGT--VTYKCE-CGHEETVDIRTGRG 211 (353)
T ss_pred CCCceeeeeecCCcCcce---eEEE-----EEeCCCCe--EEEEcC-CCCEEEEeecCCCc
Confidence 333677999999 99332 2221 22223344 445785 99999999986543
No 20
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.02 E-value=21 Score=26.41 Aligned_cols=47 Identities=23% Similarity=0.440 Sum_probs=28.6
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCcee--------eEEEeeccCCCeeEEEEecCC
Q 032492 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTT--------NLIQKCKFCGREGTVTMIPGR 85 (139)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~a--------Nfv~KCk~C~re~si~i~~~~ 85 (139)
....|. ||...+-. .+...+++..+++ .+.++|+.|+.. .+.|+.+.
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 1122344555554 677899999955 36666654
No 21
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=43.44 E-value=15 Score=32.89 Aligned_cols=15 Identities=33% Similarity=0.561 Sum_probs=12.5
Q ss_pred EEEec-CCceeeceEE
Q 032492 34 KLKCG-CGELSQKETC 48 (139)
Q Consensus 34 kvkCt-C~e~~~~~v~ 48 (139)
...|+ ||.+|+||..
T Consensus 7 ~f~C~~CG~~s~KW~G 22 (456)
T COG1066 7 AFVCQECGYVSPKWLG 22 (456)
T ss_pred EEEcccCCCCCccccc
Confidence 35799 9999999954
No 22
>PF10001 DUF2242: Uncharacterized protein conserved in bacteria (DUF2242); InterPro: IPR018718 This family includes putative lipoproteins and uncharacterised proteins.
Probab=42.13 E-value=77 Score=23.55 Aligned_cols=56 Identities=14% Similarity=0.239 Sum_probs=40.7
Q ss_pred EEEe-cceeeeeeCCCCCCCCceEEEEEEec--CCceeeceEEEecC-eeEEeCCCCceeeEE
Q 032492 9 SADL-ENLTNLQPQGGCDDPNFSYFFKLKCG--CGELSQKETCVSLA-ETLPTQGGKGTTNLI 67 (139)
Q Consensus 9 kAeL-enVt~l~p~~~~~~p~~~~~fkvkCt--C~e~~~~~v~i~~~-e~~e~~gsRG~aNfv 67 (139)
++++ +|-.+.||.+ +-+..-.|.|.|. -...+...+++|.- |...++-++..|.+-
T Consensus 19 ~~~~v~G~K~FQp~~---d~h~qi~~~vvCa~~~~~~~~s~~fvnAlQdrY~lKks~~SASvG 78 (121)
T PF10001_consen 19 DPDRVDGRKNFQPED---DVHAQIEFRVVCAPDGSGGQSSTVFVNALQDRYALKKSNNSASVG 78 (121)
T ss_pred CcceEeeeeccccCC---CceEEEEEEEEECCCCCCCeeEEEEEEeeeeeeeeeecCCcceEe
Confidence 3444 8899999965 2456788999999 44455678999985 577888777777654
No 23
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=36.96 E-value=35 Score=19.28 Aligned_cols=35 Identities=20% Similarity=0.396 Sum_probs=20.2
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeE
Q 032492 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (139)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~s 78 (139)
++++|. |+... .|.. +. ++...+ ..+|..|+..-.
T Consensus 1 M~~~CP~C~~~~----~v~~-~~--~~~~~~----~v~C~~C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSF----RVVD-SQ--LGANGG----KVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEE----EeCH-HH--cCCCCC----EEECCCCCCEEE
Confidence 368898 98763 3443 22 221112 477999987644
No 24
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.80 E-value=32 Score=26.73 Aligned_cols=39 Identities=23% Similarity=0.533 Sum_probs=25.9
Q ss_pred eeeEEEeeccCCCeeEEEEecCCCcccccccccCCCCccEEEEEccCceEE
Q 032492 63 TTNLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPV 113 (139)
Q Consensus 63 ~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCRGlEpv 113 (139)
.-++++.||.|+-.++-+|.+ .+|. . | ++-+.|-||-.-
T Consensus 75 ~m~l~yTCkvCntRs~ktisk---~AY~--~---G----vVivqC~gC~~~ 113 (165)
T KOG3277|consen 75 RMQLAYTCKVCNTRSTKTISK---QAYE--K---G----VVIVQCPGCKNH 113 (165)
T ss_pred ceEEEEEeeccCCccccccCh---hhhh--C---c----eEEEECCCCccc
Confidence 447888999998888866644 2333 2 2 566678888643
No 25
>PF08662 eIF2A: Eukaryotic translation initiation factor eIF2A; InterPro: IPR013979 This entry contains beta propellor domains found in eukaryotic translation initiation factors and TolB domain-containing proteins.
Probab=36.02 E-value=55 Score=25.06 Aligned_cols=34 Identities=6% Similarity=-0.015 Sum_probs=27.0
Q ss_pred CCccEEEEEccCceEEeEEeCCCEEEEEeecCce
Q 032492 98 GFSPLMLFDCRGYEPVDFVFGVGWKVESVSFYSC 131 (139)
Q Consensus 98 ~~~~I~~fdCRGlEpv~f~P~~~w~~~s~~~~~~ 131 (139)
+...|..++=-++--++|+|+|.+.++++...+.
T Consensus 134 ~~~~i~~~~~~~~t~~~WsPdGr~~~ta~t~~r~ 167 (194)
T PF08662_consen 134 KKKKISTFEHSDATDVEWSPDGRYLATATTSPRL 167 (194)
T ss_pred CCEEeeccccCcEEEEEEcCCCCEEEEEEeccce
Confidence 5677777777777888999999999998876443
No 26
>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=35.63 E-value=33 Score=29.79 Aligned_cols=48 Identities=27% Similarity=0.501 Sum_probs=25.2
Q ss_pred ceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032492 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (139)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~~ 85 (139)
-.|.|...|. ||-+.. +.|.. .+. +..-...+|+.|+.+.++++..+.
T Consensus 169 ~y~Pf~piC~~cGri~t--t~v~~---~d~----~~~~v~Y~c~~cG~~g~~~i~~g~ 217 (360)
T PF01921_consen 169 TYSPFLPICEKCGRIDT--TEVTE---YDP----EGGTVTYRCEECGHEGEVDITGGN 217 (360)
T ss_dssp T--SEEEEETTTEE--E--EEEEE---E------SSSEEEEE--TTS---EEETTTT-
T ss_pred CeeeeeeeccccCCccc--ceeeE---eec----CCCEEEEEecCCCCEEEEecCCCc
Confidence 3678999999 998531 22222 121 223577899999999999998754
No 27
>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=35.61 E-value=29 Score=20.29 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=14.9
Q ss_pred EEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032492 48 CVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (139)
Q Consensus 48 ~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si 79 (139)
+||+.-+++..| =.|+|.+|+..+.+
T Consensus 11 ylNp~~~~~~~~------~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 11 YLNPFCQFDDGG------KTWICNFCGTKNPL 36 (40)
T ss_dssp BS-TTSEEETTT------TEEEETTT--EEE-
T ss_pred EECCcceEcCCC------CEEECcCCCCcCCC
Confidence 566666655532 24999999997764
No 28
>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=34.09 E-value=81 Score=24.06 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=27.0
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEE
Q 032492 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i 81 (139)
..|. |++.....+ -.+++|..|-.-=..+.|..|+-.++=..
T Consensus 2 s~Cp~C~~~~~~~~-----~~~~IP~F~evii~sf~C~~CGyk~~ev~ 44 (161)
T PF03367_consen 2 SLCPNCGENGTTRI-----LLTDIPYFKEVIIMSFECEHCGYKNNEVK 44 (161)
T ss_dssp EE-TTTSSCCEEEE-----EEEEETTTEEEEEEEEE-TTT--EEEEEE
T ss_pred CcCCCCCCCcEEEE-----EEEcCCCCceEEEEEeECCCCCCEeeeEE
Confidence 4699 998643222 45678988888888899999998876433
No 29
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=33.26 E-value=85 Score=18.37 Aligned_cols=34 Identities=26% Similarity=0.651 Sum_probs=18.3
Q ss_pred Eec-CCceeeceEEEecCeeEEe-CCCCceeeEEEeeccCCCe
Q 032492 36 KCG-CGELSQKETCVSLAETLPT-QGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~-~gsRG~aNfv~KCk~C~re 76 (139)
+|. |+ |++-+++.. ++ ++.-|. .+..+|..|+..
T Consensus 2 ~Cp~C~--~~~a~~~q~----Q~RsaDE~m-T~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCG--NREATFFQL----QTRSADEPM-TVFYVCTKCGHR 37 (40)
T ss_pred cCCCCC--CCeEEEEEE----cccCCCCCC-eEEEEeCCCCCE
Confidence 577 76 455555532 12 122233 567788888753
No 30
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.61 E-value=9.7 Score=31.51 Aligned_cols=60 Identities=27% Similarity=0.396 Sum_probs=37.2
Q ss_pred EEEEEec-CCceeeceEEEecCeeEEeCCC--Cc--eeeEEEeeccCCCeeEEEEecCCCccccccc
Q 032492 32 FFKLKCG-CGELSQKETCVSLAETLPTQGG--KG--TTNLIQKCKFCGREGTVTMIPGRGKPLTQEA 93 (139)
Q Consensus 32 ~fkvkCt-C~e~~~~~v~i~~~e~~e~~gs--RG--~aNfv~KCk~C~re~si~i~~~~~~~~~~e~ 93 (139)
.|.++|- |||--.+.--+|.-++ +.-|- =| .--|.++|..|.++.++.=.|. +..|.++.
T Consensus 38 Pf~~rC~tCgeyi~kg~kfN~r~E-~~~~e~yLgiki~Rf~i~Ct~cl~el~~rTDp~-N~dY~~E~ 102 (253)
T KOG2989|consen 38 PFRLRCNTCGEYIYKGKKFNAREE-DVIEETYLGIKIFRFYIKCTRCLRELSFRTDPK-NSDYVIES 102 (253)
T ss_pred cceeecccccchhhcCCCcchhHH-hhhccccccceeeeeeeeccchHhhhhhhcCCc-chHHHHHh
Confidence 3899999 9996655544554221 11111 13 2369999999999977766554 34455544
No 31
>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=31.99 E-value=77 Score=20.11 Aligned_cols=32 Identities=28% Similarity=0.589 Sum_probs=20.0
Q ss_pred EEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032492 34 KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (139)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si 79 (139)
+++|. |++. |.+... -+|. .+.|..|+.+--+
T Consensus 2 ~~~CP~CG~~----iev~~~-------~~Ge---iV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAE----IELENP-------ELGE---LVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCE----EecCCC-------ccCC---EEeCCCCCCEEEE
Confidence 46899 9883 222221 1344 5699999998655
No 32
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=31.98 E-value=44 Score=25.09 Aligned_cols=15 Identities=40% Similarity=0.780 Sum_probs=13.0
Q ss_pred eEEEeeccCCCeeEE
Q 032492 65 NLIQKCKFCGREGTV 79 (139)
Q Consensus 65 Nfv~KCk~C~re~si 79 (139)
-+.+||+-|+...++
T Consensus 121 ~~~l~C~ACGa~~~V 135 (138)
T PRK03988 121 IWVLKCEACGAETPV 135 (138)
T ss_pred eEEEEcccCCCCCcC
Confidence 688999999988776
No 33
>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=30.97 E-value=16 Score=27.54 Aligned_cols=62 Identities=21% Similarity=0.451 Sum_probs=33.3
Q ss_pred cceeeeeeCCCCCC--CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecC
Q 032492 13 ENLTNLQPQGGCDD--PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPG 84 (139)
Q Consensus 13 enVt~l~p~~~~~~--p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~ 84 (139)
.||..|....+... +=|--.+.++|+ |+...+..-.....+..+.+ +|+.|+....=+|+-.
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 56666665322110 014456889999 99987644222211111122 9999999776666543
No 34
>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=30.42 E-value=26 Score=23.91 Aligned_cols=33 Identities=21% Similarity=0.500 Sum_probs=18.1
Q ss_pred EEEeeccCCCeeEEEEecCCCcccccccccCCCCccEEEEEccCce
Q 032492 66 LIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYE 111 (139)
Q Consensus 66 fv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCRGlE 111 (139)
=++.|.+|+.+.|+.+.-.+ -..+..+.||=|.
T Consensus 21 ~~F~CPfC~~~~sV~v~idk-------------k~~~~~~~C~~Cg 53 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDK-------------KEGIGILSCRVCG 53 (81)
T ss_dssp S----TTT--SS-EEEEEET-------------TTTEEEEEESSS-
T ss_pred ceEcCCcCCCCCeEEEEEEc-------------cCCEEEEEecCCC
Confidence 47899999999998886432 1347888888874
No 35
>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=30.19 E-value=31 Score=29.72 Aligned_cols=12 Identities=42% Similarity=0.750 Sum_probs=9.3
Q ss_pred Eec-CCceeeceE
Q 032492 36 KCG-CGELSQKET 47 (139)
Q Consensus 36 kCt-C~e~~~~~v 47 (139)
.|+ ||.++++|.
T Consensus 2 ~c~~cg~~~~~~~ 14 (372)
T cd01121 2 VCSECGYVSPKWL 14 (372)
T ss_pred CCCCCCCCCCCcc
Confidence 588 888888774
No 36
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=29.55 E-value=54 Score=28.87 Aligned_cols=26 Identities=8% Similarity=0.079 Sum_probs=22.4
Q ss_pred cEEEEEc-cCceEEeEEeCCCEEEEEe
Q 032492 101 PLMLFDC-RGYEPVDFVFGVGWKVESV 126 (139)
Q Consensus 101 ~I~~fdC-RGlEpv~f~P~~~w~~~s~ 126 (139)
.|++.|| -|+..++|+|.++|.+++.
T Consensus 203 kv~aYe~~lG~k~v~wsP~~qflavGs 229 (447)
T KOG4497|consen 203 KVYAYERGLGLKFVEWSPCNQFLAVGS 229 (447)
T ss_pred eeeeeeeccceeEEEeccccceEEeec
Confidence 3668899 8999999999999998764
No 37
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=29.23 E-value=53 Score=25.96 Aligned_cols=39 Identities=21% Similarity=0.436 Sum_probs=25.2
Q ss_pred EEec-CCceeeceEEEecCeeEE-eCCCCceeeEEEeeccCCCeeE
Q 032492 35 LKCG-CGELSQKETCVSLAETLP-TQGGKGTTNLIQKCKFCGREGT 78 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e-~~gsRG~aNfv~KCk~C~re~s 78 (139)
+.|. |+..-. ..+ -.+. +|..|-.-=+.+.|..|+-.++
T Consensus 1 ~~Cp~C~~~~~--~~~---~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 1 IDCPSCGGECE--TVM---KTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred CcCCCCCCCCE--EEE---EEEcCCCCcceEEEEEEECCCCCCccc
Confidence 4688 886421 111 2344 7877777778888888887755
No 38
>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=29.11 E-value=32 Score=30.40 Aligned_cols=27 Identities=37% Similarity=0.597 Sum_probs=19.6
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEE
Q 032492 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i 81 (139)
..|+ ||..+++|. +||+.|+.=+|+.=
T Consensus 8 y~C~~Cg~~~~~~~--------------------g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 8 FVCQHCGADSPKWQ--------------------GKCPACHAWNTITE 35 (454)
T ss_pred EECCcCCCCCcccc--------------------EECcCCCCccccch
Confidence 5799 999988874 56777776666543
No 39
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=28.75 E-value=33 Score=19.70 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=8.3
Q ss_pred EEEEec-CCce
Q 032492 33 FKLKCG-CGEL 42 (139)
Q Consensus 33 fkvkCt-C~e~ 42 (139)
.+|+|+ |+.+
T Consensus 24 ~~v~C~~C~~~ 34 (36)
T PF13717_consen 24 RKVRCSKCGHV 34 (36)
T ss_pred cEEECCCCCCE
Confidence 489999 9975
No 40
>PF15411 PH_10: Pleckstrin homology domain
Probab=28.37 E-value=2.3e+02 Score=20.41 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=10.2
Q ss_pred CCCCceeeEEEeecc
Q 032492 58 QGGKGTTNLIQKCKF 72 (139)
Q Consensus 58 ~gsRG~aNfv~KCk~ 72 (139)
.|..+..||+++|+.
T Consensus 91 ~~d~e~~~F~lrf~n 105 (116)
T PF15411_consen 91 KGDPELENFTLRFRN 105 (116)
T ss_pred cCCCCCceEEEEeCC
Confidence 355567788888763
No 41
>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=27.62 E-value=21 Score=24.94 Aligned_cols=13 Identities=38% Similarity=0.756 Sum_probs=1.0
Q ss_pred eEEEeeccCCCee
Q 032492 65 NLIQKCKFCGREG 77 (139)
Q Consensus 65 Nfv~KCk~C~re~ 77 (139)
=|.|-||-|||-.
T Consensus 70 CL~WACKaCKRKt 82 (86)
T PF01586_consen 70 CLLWACKACKRKT 82 (86)
T ss_dssp ---------S---
T ss_pred chHHHhHhhhccC
Confidence 5999999999964
No 42
>PF06159 DUF974: Protein of unknown function (DUF974); InterPro: IPR010378 This is a family of uncharacterised eukaryotic proteins.
Probab=27.00 E-value=2.2e+02 Score=23.01 Aligned_cols=17 Identities=29% Similarity=0.427 Sum_probs=11.6
Q ss_pred eEEeEEeCCCEEEEEee
Q 032492 111 EPVDFVFGVGWKVESVS 127 (139)
Q Consensus 111 Epv~f~P~~~w~~~s~~ 127 (139)
|=+.|.|..+|.+...+
T Consensus 154 e~v~lep~~~~~~~~ln 170 (249)
T PF06159_consen 154 EKVKLEPSPGFKVTDLN 170 (249)
T ss_pred EEEEeecCCCceeEecc
Confidence 44667777777776665
No 43
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.84 E-value=42 Score=29.50 Aligned_cols=15 Identities=33% Similarity=0.439 Sum_probs=11.4
Q ss_pred EEec-CCceeeceEEE
Q 032492 35 LKCG-CGELSQKETCV 49 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i 49 (139)
..|+ ||..+++|..-
T Consensus 8 y~C~~Cg~~~~~~~g~ 23 (446)
T PRK11823 8 YVCQECGAESPKWLGR 23 (446)
T ss_pred EECCcCCCCCcccCee
Confidence 5699 99998887543
No 44
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=26.13 E-value=18 Score=30.80 Aligned_cols=52 Identities=13% Similarity=0.267 Sum_probs=38.0
Q ss_pred ceEEEEEEec-CCceeeceEEEecCeeEEeCCC--CceeeEEEeeccCCCeeEEEEec
Q 032492 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQGG--KGTTNLIQKCKFCGREGTVTMIP 83 (139)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gs--RG~aNfv~KCk~C~re~si~i~~ 83 (139)
|+-.|.|-|. |...-...|-.|. |+..+.+- --.-.|-|||..|... |.|..
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 5566889999 9998888999998 56555222 1234799999999877 55543
No 45
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=25.93 E-value=53 Score=24.31 Aligned_cols=38 Identities=24% Similarity=0.298 Sum_probs=22.7
Q ss_pred Eec-CCceeeceEEEecCeeE-EeC-CCCceeeEEEeeccCCCe
Q 032492 36 KCG-CGELSQKETCVSLAETL-PTQ-GGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~-e~~-gsRG~aNfv~KCk~C~re 76 (139)
.|+ |+.. -+.+.+.+.. .+| +-....+-.+.|..|+|-
T Consensus 93 RC~~CN~~---L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 93 RCPKCNGP---LRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred ccCCCCcE---eeechhhccccccCccccccCCeEEECCCCCCE
Confidence 699 9883 3444443221 232 334455668999999984
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=25.70 E-value=89 Score=19.81 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=17.5
Q ss_pred ceeeEEEeeccCCCeeEEEEecC
Q 032492 62 GTTNLIQKCKFCGREGTVTMIPG 84 (139)
Q Consensus 62 G~aNfv~KCk~C~re~si~i~~~ 84 (139)
+..++-+||.-|+.-+.+.-...
T Consensus 19 ~~~~leIKCpRC~tiN~~~a~~~ 41 (51)
T PF10122_consen 19 EVIELEIKCPRCKTINHVRATSP 41 (51)
T ss_pred CccEEEEECCCCCccceEeccCC
Confidence 34578999999999888776543
No 47
>KOG0315 consensus G-protein beta subunit-like protein (contains WD40 repeats) [General function prediction only]
Probab=25.63 E-value=2.5e+02 Score=23.86 Aligned_cols=37 Identities=16% Similarity=0.208 Sum_probs=30.4
Q ss_pred CCCCccEEEEEcc--CceEEeEEeCCCEEEEEeecCcee
Q 032492 96 SGGFSPLMLFDCR--GYEPVDFVFGVGWKVESVSFYSCP 132 (139)
Q Consensus 96 ~~~~~~I~~fdCR--GlEpv~f~P~~~w~~~s~~~~~~~ 132 (139)
+++..|++.||=. .+--+.|+-+|-|..++.+-+.|.
T Consensus 70 S~np~Pv~t~e~h~kNVtaVgF~~dgrWMyTgseDgt~k 108 (311)
T KOG0315|consen 70 SNNPNPVATFEGHTKNVTAVGFQCDGRWMYTGSEDGTVK 108 (311)
T ss_pred CCCCCceeEEeccCCceEEEEEeecCeEEEecCCCceEE
Confidence 4677799999976 588899999999999988776553
No 48
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=25.56 E-value=66 Score=23.97 Aligned_cols=32 Identities=22% Similarity=0.644 Sum_probs=20.8
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032492 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si 79 (139)
|.|. |+..-.+. + . .+| -+.+||+-|+...++
T Consensus 98 VlC~~C~sPdT~l--~-k-------~~r---~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNRPDTRI--I-K-------EGR---VSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCCCCcEE--E-E-------eCC---eEEEecccCCCCCcc
Confidence 7899 98743221 1 1 122 357899999998776
No 49
>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=24.19 E-value=2.2e+02 Score=18.67 Aligned_cols=32 Identities=16% Similarity=0.258 Sum_probs=21.5
Q ss_pred ccCceEEeEEe-CC-CEEEEEeecCceeeeeeee
Q 032492 107 CRGYEPVDFVF-GV-GWKVESVSFYSCPFPIVFE 138 (139)
Q Consensus 107 CRGlEpv~f~P-~~-~w~~~s~~~~~~~~~~~~~ 138 (139)
=+|.++.++.. ++ .|.++.....--.++|..|
T Consensus 40 ~~G~~v~~ve~~~~g~yev~~~~~dG~~~ev~vD 73 (83)
T PF13670_consen 40 AQGYQVREVEFDDDGCYEVEARDKDGKKVEVYVD 73 (83)
T ss_pred hcCCceEEEEEcCCCEEEEEEEECCCCEEEEEEc
Confidence 37777777777 55 4988866555566666554
No 50
>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=24.18 E-value=33 Score=28.98 Aligned_cols=36 Identities=28% Similarity=0.312 Sum_probs=26.9
Q ss_pred Eec-CCceeeceEEEecCeeEEeCCCCcee-eEEEeec
Q 032492 36 KCG-CGELSQKETCVSLAETLPTQGGKGTT-NLIQKCK 71 (139)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~~gsRG~a-Nfv~KCk 71 (139)
.|- ||+-+.+...+.+++--.+.|+.|.+ ||.|-++
T Consensus 7 ~C~~Cg~r~a~~~~~~~t~~~~l~~~~~~~~Nffwn~~ 44 (309)
T TIGR01908 7 LCINCGERHAKKDTIFDTEIPLIGGLSGGVPNYFWNGK 44 (309)
T ss_pred cCCCcCCcchhccccccccCCccccCCCCccccccCCC
Confidence 588 99999876666665555557777776 9999864
No 51
>PF08630 Dfp1_Him1_M: Dfp1/Him1, central region; InterPro: IPR013939 This region, together with the C-terminal zinc finger (IPR006572 from INTERPRO) is essential for the mitotic and kinase activation functions of Dfp1/Him1 []. ; PDB: 3OQ0_J 3OQ4_D 3QBZ_A.
Probab=23.56 E-value=27 Score=25.94 Aligned_cols=35 Identities=26% Similarity=0.412 Sum_probs=0.0
Q ss_pred CCCCccEEEEEccCceEEeEEeCCC-E-EEEEeecCceeee
Q 032492 96 SGGFSPLMLFDCRGYEPVDFVFGVG-W-KVESVSFYSCPFP 134 (139)
Q Consensus 96 ~~~~~~I~~fdCRGlEpv~f~P~~~-w-~~~s~~~~~~~~~ 134 (139)
.+++.|||.-|=. --=.+.++ | +..+...++|||-
T Consensus 87 ~q~~rPImvrEy~----k~~~~~~~~wP~~r~~~~GrCPFi 123 (125)
T PF08630_consen 87 DQKTRPIMVREYP----KVADKQDGPWPQFRSGTFGRCPFI 123 (125)
T ss_dssp -----------------------------------------
T ss_pred CcCCCcEEEEecc----ccccccCCCCCEEecCCCCCCCCC
Confidence 4689999984331 11144444 9 8899999999984
No 52
>PF08050 Tet_res_leader: Tetracycline resistance leader peptide; InterPro: IPR012618 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the tetracycline resistance leader peptide, which can be found in Tet(L) efflux proteins. Tet(L) is a transmembrane protein that can function as a metal-tetracycline/H+ antiporter. Its sequence is preceded by a leader region region that contains a 20-amino-acid open reading frame and an appropriately spaced ribosome binding site []. Expression of the gene is induced by addition of tetracycline, which is thought to act by binding to ribosomes that translate the tet(L) leader peptide coding sequence. The presence of three inverted repeats, which can form two different conformations of mRNA, suggests that the tetracycline resistance (TcR) region is regulated by a translational attenuation mechanism. A Rho-independent transcriptional terminator structure is present immediately after the translational stop codon of the Tet protein [].; GO: 0046677 response to antibiotic
Probab=23.24 E-value=25 Score=18.03 Aligned_cols=9 Identities=33% Similarity=0.501 Sum_probs=6.5
Q ss_pred EeeccCCCe
Q 032492 68 QKCKFCGRE 76 (139)
Q Consensus 68 ~KCk~C~re 76 (139)
|||+.|.|.
T Consensus 1 MkC~k~Nrv 9 (20)
T PF08050_consen 1 MKCNKMNRV 9 (20)
T ss_pred CcccccceE
Confidence 578888764
No 53
>PF06051 DUF928: Domain of Unknown Function (DUF928); InterPro: IPR010328 This is a family of uncharacterised bacterial proteins.
Probab=23.24 E-value=85 Score=24.45 Aligned_cols=11 Identities=27% Similarity=1.065 Sum_probs=10.0
Q ss_pred CceEEEEEEec
Q 032492 28 NFSYFFKLKCG 38 (139)
Q Consensus 28 ~~~~~fkvkCt 38 (139)
+|.|+|.|.|.
T Consensus 92 ~Y~W~~~l~Cd 102 (189)
T PF06051_consen 92 TYRWYFSLICD 102 (189)
T ss_pred eEEEEEEEEEC
Confidence 59999999995
No 54
>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=22.44 E-value=93 Score=18.05 Aligned_cols=11 Identities=36% Similarity=0.800 Sum_probs=7.3
Q ss_pred eEEEeeccCCC
Q 032492 65 NLIQKCKFCGR 75 (139)
Q Consensus 65 Nfv~KCk~C~r 75 (139)
.+..+|..|++
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 56666777765
No 55
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=21.58 E-value=86 Score=24.71 Aligned_cols=38 Identities=24% Similarity=0.521 Sum_probs=25.8
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032492 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (139)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~si~i~~~~ 85 (139)
|.|. |+..-.+. + . . .--+.+||+-|+...++.-...+
T Consensus 99 V~C~~C~~pdT~l--~-k------~----~~~~~l~C~aCGa~~~v~~~~~~ 137 (201)
T PRK12336 99 VICSECGLPDTRL--V-K------E----DRVLMLRCDACGAHRPVKKRKAS 137 (201)
T ss_pred EECCCCCCCCcEE--E-E------c----CCeEEEEcccCCCCccccccccc
Confidence 8899 99843222 1 1 1 12678999999999998866543
No 56
>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=21.29 E-value=1.1e+02 Score=17.94 Aligned_cols=31 Identities=23% Similarity=0.546 Sum_probs=19.7
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
+..+|. ||..-...+.+.. .-...|+.|+..
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~-------------~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE-------------DDPVPCPECGST 35 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC-------------CCCCcCCCCCCC
Confidence 567899 9987755444433 223568888773
No 57
>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=21.07 E-value=1e+02 Score=18.42 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=20.1
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032492 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (139)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re 76 (139)
+..+|. |+.+...+..+.. .-...|..|+..
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~-------------~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSD-------------DPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEEEecCC-------------CCCCCCCCCCCC
Confidence 455899 9998765543322 123569999984
No 58
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=20.22 E-value=42 Score=26.39 Aligned_cols=12 Identities=25% Similarity=1.007 Sum_probs=10.9
Q ss_pred ceeeEEEeeccC
Q 032492 62 GTTNLIQKCKFC 73 (139)
Q Consensus 62 G~aNfv~KCk~C 73 (139)
|..+||+.|++|
T Consensus 46 g~d~FVLQCr~C 57 (175)
T PF15446_consen 46 GDDDFVLQCRRC 57 (175)
T ss_pred cCCceEEechhh
Confidence 678999999998
No 59
>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=20.03 E-value=83 Score=21.68 Aligned_cols=33 Identities=21% Similarity=0.462 Sum_probs=16.3
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeE
Q 032492 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (139)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsRG~aNfv~KCk~C~re~s 78 (139)
+...|. |++.+++ .+|+.. +| .++|-.|++.+.
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 346699 9988875 466652 22 699999998764
Done!