Query 032792
Match_columns 133
No_of_seqs 106 out of 238
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 06:01:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032792.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032792hhsearch_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 2.3E-55 5E-60 332.9 14.6 126 1-132 1-127 (161)
2 KOG1296 Uncharacterized conser 100.0 6.5E-54 1.4E-58 318.4 8.0 126 1-132 1-127 (161)
3 PF04502 DUF572: Family of unk 93.9 0.058 1.3E-06 45.0 3.3 63 29-93 35-102 (324)
4 PRK00415 rps27e 30S ribosomal 93.5 0.098 2.1E-06 33.8 3.1 34 27-76 5-39 (59)
5 PLN00209 ribosomal protein S27 93.3 0.16 3.4E-06 35.2 4.1 34 27-76 30-64 (86)
6 PF01667 Ribosomal_S27e: Ribos 93.0 0.12 2.6E-06 32.9 2.9 32 30-76 3-35 (55)
7 PTZ00083 40S ribosomal protein 92.6 0.23 4.9E-06 34.3 4.1 40 16-76 23-63 (85)
8 COG2051 RPS27A Ribosomal prote 91.0 0.45 9.7E-06 31.4 3.9 42 15-76 5-47 (67)
9 PF14205 Cys_rich_KTR: Cystein 85.9 0.94 2E-05 28.8 2.7 41 35-85 5-46 (55)
10 PF14255 Cys_rich_CPXG: Cystei 71.5 7.4 0.00016 24.3 3.5 41 35-85 1-42 (52)
11 KOG1779 40s ribosomal protein 59.8 18 0.00038 24.8 3.7 16 27-43 28-44 (84)
12 PF05180 zf-DNL: DNL zinc fing 59.0 11 0.00024 24.7 2.6 38 31-77 1-39 (66)
13 PRK00750 lysK lysyl-tRNA synth 58.4 30 0.00065 30.7 6.0 52 25-86 166-218 (510)
14 PF14353 CpXC: CpXC protein 58.0 2.8 6.2E-05 29.9 -0.4 47 34-80 1-51 (128)
15 cd00674 LysRS_core_class_I cat 57.0 39 0.00085 28.7 6.3 49 27-86 162-211 (353)
16 TIGR00467 lysS_arch lysyl-tRNA 55.7 31 0.00067 30.8 5.7 49 26-86 160-209 (515)
17 PF12760 Zn_Tnp_IS1595: Transp 52.8 8.8 0.00019 22.8 1.3 12 65-76 35-46 (46)
18 KOG2315 Predicted translation 51.9 27 0.00058 31.7 4.6 31 98-128 345-375 (566)
19 COG1066 Sms Predicted ATP-depe 49.2 11 0.00023 33.3 1.7 28 34-81 7-35 (456)
20 PRK03824 hypA hydrogenase nick 48.5 18 0.00038 26.5 2.5 47 33-85 69-124 (135)
21 PF01921 tRNA-synt_1f: tRNA sy 44.8 21 0.00045 30.6 2.8 50 27-85 167-217 (360)
22 PF10001 DUF2242: Uncharacteri 44.3 70 0.0015 23.4 5.0 57 9-68 19-79 (121)
23 KOG4497 Uncharacterized conser 39.0 30 0.00066 30.0 2.8 29 101-129 203-232 (447)
24 PRK03988 translation initiatio 39.0 29 0.00063 25.7 2.5 32 35-79 103-135 (138)
25 KOG0315 G-protein beta subunit 38.8 1.1E+02 0.0023 25.7 5.9 36 96-131 70-107 (311)
26 PF02146 SIR2: Sir2 family; I 38.4 10 0.00023 28.3 0.0 63 12-84 81-146 (178)
27 smart00440 ZnF_C2C2 C2C2 Zinc 37.6 67 0.0015 18.6 3.4 35 36-76 2-37 (40)
28 KOG2989 Uncharacterized conser 36.2 8 0.00017 31.6 -1.0 60 32-93 38-102 (253)
29 PF03367 zf-ZPR1: ZPR1 zinc-fi 35.6 75 0.0016 23.9 4.3 43 35-82 2-45 (161)
30 PF08662 eIF2A: Eukaryotic tra 35.3 54 0.0012 24.8 3.5 31 98-128 134-164 (194)
31 KOG3277 Uncharacterized conser 34.6 38 0.00082 26.0 2.5 37 63-111 75-111 (165)
32 TIGR02098 MJ0042_CXXC MJ0042 f 34.5 59 0.0013 18.0 2.8 34 34-78 2-36 (38)
33 cd01121 Sms Sms (bacterial rad 33.3 26 0.00056 29.9 1.6 12 36-47 2-14 (372)
34 PF04810 zf-Sec23_Sec24: Sec23 33.3 34 0.00073 19.7 1.7 26 48-79 11-36 (40)
35 PF13717 zinc_ribbon_4: zinc-r 32.3 27 0.00059 19.8 1.1 10 33-42 24-34 (36)
36 PF05129 Elf1: Transcription e 31.9 23 0.00051 23.8 0.9 33 66-111 21-53 (81)
37 TIGR00416 sms DNA repair prote 31.9 27 0.00058 30.5 1.5 28 34-81 7-35 (454)
38 TIGR00311 aIF-2beta translatio 31.5 45 0.00098 24.5 2.4 32 35-79 98-130 (133)
39 TIGR00310 ZPR1_znf ZPR1 zinc f 30.0 61 0.0013 25.3 3.1 42 35-81 1-44 (192)
40 PRK11823 DNA repair protein Ra 29.6 35 0.00076 29.6 1.8 15 34-48 7-22 (446)
41 PF08662 eIF2A: Eukaryotic tra 28.8 76 0.0017 24.0 3.4 31 99-129 92-122 (194)
42 PF01586 Basic: Myogenic Basic 28.6 20 0.00043 24.7 0.1 13 65-77 70-82 (86)
43 COG1637 Predicted nuclease of 27.3 42 0.0009 27.6 1.7 28 102-130 63-90 (253)
44 PF14803 Nudix_N_2: Nudix N-te 26.9 47 0.001 18.8 1.5 11 33-43 21-32 (34)
45 KOG2990 C2C2-type Zn-finger pr 26.5 17 0.00037 30.5 -0.6 51 29-82 47-100 (317)
46 PF10122 Mu-like_Com: Mu-like 26.4 83 0.0018 19.7 2.6 23 62-84 19-41 (51)
47 PF04502 DUF572: Family of unk 26.2 42 0.00091 28.0 1.6 13 30-42 73-86 (324)
48 PF06051 DUF928: Domain of Unk 25.8 66 0.0014 24.7 2.6 11 28-38 92-102 (189)
49 PF04216 FdhE: Protein involve 25.2 40 0.00086 27.4 1.3 43 29-78 205-249 (290)
50 TIGR01908 cas_CXXC_CXXC CRISPR 25.1 31 0.00066 28.8 0.6 36 36-71 7-44 (309)
51 PF12341 DUF3639: Protein of u 25.0 1.3E+02 0.0027 16.3 3.4 20 112-131 4-23 (27)
52 PRK12336 translation initiatio 24.9 68 0.0015 25.0 2.5 38 35-85 99-137 (201)
53 PRK03564 formate dehydrogenase 24.8 56 0.0012 27.5 2.1 43 29-79 220-264 (309)
54 PF09332 Mcm10: Mcm10 replicat 24.8 20 0.00044 30.5 -0.5 70 35-108 253-323 (344)
55 PF01096 TFIIS_C: Transcriptio 24.5 81 0.0018 18.1 2.2 11 65-75 26-36 (39)
56 TIGR02605 CxxC_CxxC_SSSS putat 23.8 84 0.0018 18.5 2.3 31 33-76 4-35 (52)
57 PF01927 Mut7-C: Mut7-C RNAse 23.5 64 0.0014 23.6 2.0 39 35-76 92-133 (147)
58 PF00400 WD40: WD domain, G-be 23.4 1.3E+02 0.0028 15.8 4.5 31 101-131 3-35 (39)
59 PF15411 PH_10: Pleckstrin hom 23.2 2.8E+02 0.0061 19.7 6.4 43 6-72 61-105 (116)
60 PF09723 Zn-ribbon_8: Zinc rib 23.1 97 0.0021 17.9 2.4 31 33-76 4-35 (42)
61 COG2260 Predicted Zn-ribbon RN 22.8 42 0.00091 21.6 0.8 15 29-43 12-27 (59)
62 PF15446 zf-PHD-like: PHD/FYVE 22.8 35 0.00076 26.5 0.5 12 62-73 46-57 (175)
63 KOG2055 WD40 repeat protein [G 22.7 62 0.0013 29.0 2.1 20 112-131 487-506 (514)
64 COG1631 RPL42A Ribosomal prote 22.6 84 0.0018 22.0 2.3 20 26-45 60-80 (94)
65 PF01807 zf-CHC2: CHC2 zinc fi 22.1 71 0.0015 21.7 1.9 33 33-78 32-65 (97)
66 PF06159 DUF974: Protein of un 21.4 3.5E+02 0.0076 21.6 6.1 17 111-127 154-170 (249)
67 PF13719 zinc_ribbon_5: zinc-r 21.4 57 0.0012 18.5 1.1 9 34-42 25-34 (37)
68 PF00935 Ribosomal_L44: Riboso 21.3 75 0.0016 21.4 1.8 17 30-46 49-66 (77)
69 COG1326 Uncharacterized archae 20.9 67 0.0014 25.5 1.7 32 32-63 28-60 (201)
70 COG4416 Com Mu-like prophage p 20.7 81 0.0018 20.1 1.8 22 62-83 19-40 (60)
71 PF05428 CRF-BP: Corticotropin 20.5 3.4E+02 0.0074 23.0 5.9 76 39-125 45-120 (311)
72 smart00709 Zpr1 Duplicated dom 20.4 1.5E+02 0.0032 22.4 3.5 38 36-78 2-40 (160)
73 PHA01634 hypothetical protein 20.3 61 0.0013 24.5 1.4 13 99-111 92-104 (156)
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=2.3e-55 Score=332.88 Aligned_cols=126 Identities=48% Similarity=0.915 Sum_probs=98.2
Q ss_pred CceEEEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032792 1 MVNCMLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (133)
Q Consensus 1 Mv~~~L~vkAeLenV~~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si 79 (133)
||+|+|+|||+||||++|+|.| ++|.|+|+|||+ |||+|+|+|+|+++|+++++||||+||||+|||+|+|++||
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 EEecCCCcccccccccCCCcccEEEEEccCceEEeEEeCCCEEEEEecCCeec
Q 032792 80 TMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESSPIGLLL 132 (133)
Q Consensus 80 ~i~~~~~~~~~~e~~~~~~~~~I~~fdCRG~ep~~f~p~~~w~~~s~~~~~~~ 132 (133)
+|++.+..+|++++ +++|++|++||||||||++|+|+++|+|+++++|+.|
T Consensus 77 ~i~~~~~~~~~~e~--~~~~~~i~~fdCRG~e~~~f~p~~~~~~~~~esG~~f 127 (161)
T PF05907_consen 77 DIIPGKGKPYTAED--SGKFVPILAFDCRGLEPVEFSPRGGWVAVSVESGTKF 127 (161)
T ss_dssp EEE--TTTEEEGGG--TTS-EEEEEEEEESEEEEEE---S-EEEEET-TS-EE
T ss_pred EEEecCcccccccc--ccCCceEEEEECCCcEeEEEecCCcEEEEEecCCCEE
Confidence 99999988999876 4799999999999999999999999999999999887
No 2
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.5e-54 Score=318.36 Aligned_cols=126 Identities=44% Similarity=0.865 Sum_probs=122.7
Q ss_pred CceEEEEEEEEecceeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032792 1 MVNCMLMISADLENLTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (133)
Q Consensus 1 Mv~~~L~vkAeLenV~~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si 79 (133)
||+|+|+++|.|||||+|+|.+ |+|+|+|++||+ |||.|++|++|+.+|.+.+|||||+||||||||+|+|++||
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 EEecCCCcccccccccCCCcccEEEEEccCceEEeEEeCCCEEEEEecCCeec
Q 032792 80 TMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFGVGWKVESSPIGLLL 132 (133)
Q Consensus 80 ~i~~~~~~~~~~e~~~~~~~~~I~~fdCRG~ep~~f~p~~~w~~~s~~~~~~~ 132 (133)
+|++.+++|||++++ ++|++|+.|||||+||++|+|+++|.++|+++|+.|
T Consensus 77 ~iv~~~~~pyt~ed~--e~~~~i~vfdCRG~EpidF~p~~~w~a~s~esG~~f 127 (161)
T KOG1296|consen 77 TIVAFEDKPYTAEDS--EKFKTIVVFDCRGLEPIDFYPRTGWFAVSAESGTAF 127 (161)
T ss_pred EEecCCCCccccccc--ccccceEEEeccCCcceeecCCceEEEEecccCcee
Confidence 999999999999875 699999999999999999999999999999999987
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=93.91 E-value=0.058 Score=44.98 Aligned_cols=63 Identities=22% Similarity=0.305 Sum_probs=45.4
Q ss_pred ceEEEEEEec-CCceeeceEEEecCeeEEeCC--CCce--eeEEEeeccCCCeeEEEEecCCCccccccc
Q 032792 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQG--GKGT--TNLIQKCKFCGREGTVTMIPGRGKPLTQEA 93 (133)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~g--srg~--aNfv~KCk~C~re~si~i~~~~~~~~~~e~ 93 (133)
|...|.|.|. |++-..+.+-+|. ++..+.+ -=|. =.|.|||..|..+.+|.=-|. +.-|..+.
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 4577999999 9999899999998 5665655 2243 379999999999865554333 34465543
No 4
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=93.52 E-value=0.098 Score=33.77 Aligned_cols=34 Identities=32% Similarity=0.850 Sum_probs=26.9
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
|+ .|+++|||. |+.+. +.+ +.|..+.+|..|++.
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=93.34 E-value=0.16 Score=35.16 Aligned_cols=34 Identities=29% Similarity=0.728 Sum_probs=27.2
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
|+ .|+++|||. |+.+. +.+ +.|..+.+|..|++.
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 64 899999999 99875 222 457889999999976
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=92.97 E-value=0.12 Score=32.88 Aligned_cols=32 Identities=34% Similarity=0.820 Sum_probs=19.3
Q ss_pred eEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 30 SYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 30 ~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
.|+++|||. |+.+. +.+ +.|..+.+|..|+..
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 222 346788999999975
No 7
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=92.63 E-value=0.23 Score=34.28 Aligned_cols=40 Identities=30% Similarity=0.715 Sum_probs=30.0
Q ss_pred eeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 16 TNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 16 ~~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
..|-|. |+ .|+++|||. |+.+. +.+ +.|..+.+|..|++.
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 345554 64 899999999 99875 222 456889999999875
No 8
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=90.95 E-value=0.45 Score=31.44 Aligned_cols=42 Identities=26% Similarity=0.620 Sum_probs=30.2
Q ss_pred eeeeeeCCCCCCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 15 LTNLQPQGGCDDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 15 V~~l~p~~~~~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
+.-+.|.. | ..++++|||. |+.+. +.+ +.|..+.+|-.|++.
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 4899999999 99764 222 456789999999985
No 9
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=85.91 E-value=0.94 Score=28.82 Aligned_cols=41 Identities=20% Similarity=0.430 Sum_probs=29.8
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~ 85 (133)
|.|. ||..++-. |.. ++ .+ -||-+-|+-|++|.-|++...+
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 5799 99877533 332 22 12 3999999999999999997654
No 10
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=71.54 E-value=7.4 Score=24.31 Aligned_cols=41 Identities=27% Similarity=0.578 Sum_probs=30.9
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~ 85 (133)
+.|. ||+.- .+. +.-|.|...++--|..|-|...+.+.-..
T Consensus 1 i~CPyCge~~--~~~--------iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~ 42 (52)
T PF14255_consen 1 IQCPYCGEPI--EIL--------IDPSAGDQEYIEDCQVCCRPIEVQVTVDE 42 (52)
T ss_pred CCCCCCCCee--EEE--------EecCCCCeeEEeehhhcCCccEEEEEECC
Confidence 4799 99874 222 33355778999999999999999887543
No 11
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=59.76 E-value=18 Score=24.79 Aligned_cols=16 Identities=50% Similarity=1.190 Sum_probs=13.5
Q ss_pred CCceEEEEEEec-CCcee
Q 032792 27 PNFSYFFKLKCG-CGELS 43 (133)
Q Consensus 27 p~~~~~fkvkCt-C~e~~ 43 (133)
|+ .|+.+|||+ |.-++
T Consensus 28 ~n-syFm~VkC~gc~~iT 44 (84)
T KOG1779|consen 28 PN-SYFMDVKCPGCFKIT 44 (84)
T ss_pred CC-ceEEEEEcCCceEEE
Confidence 54 899999999 98765
No 12
>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=59.02 E-value=11 Score=24.73 Aligned_cols=38 Identities=32% Similarity=0.628 Sum_probs=20.1
Q ss_pred EEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCee
Q 032792 31 YFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREG 77 (133)
Q Consensus 31 ~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~ 77 (133)
|.+.+.|. |+..+.+ .|++. .. -+|. ...+|..|+...
T Consensus 1 ~~l~FTC~~C~~Rs~~--~~sk~-aY----~~Gv--Viv~C~gC~~~H 39 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAK--MFSKQ-AY----HKGV--VIVQCPGCKNRH 39 (66)
T ss_dssp EEEEEEETTTTEEEEE--EEEHH-HH----HTSE--EEEE-TTS--EE
T ss_pred CeEEEEcCCCCCccce--eeCHH-HH----hCCe--EEEECCCCccee
Confidence 55677888 8766543 34441 11 1244 677888887654
No 13
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=58.36 E-value=30 Score=30.66 Aligned_cols=52 Identities=27% Similarity=0.585 Sum_probs=34.4
Q ss_pred CCCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCC
Q 032792 25 DDPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (133)
Q Consensus 25 ~~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~~ 86 (133)
+.++--|.|..-|. ||-+..-.| + +.....|+..+ +|+ |+.+.++++..+.+
T Consensus 166 ~~~~~~~P~~pic~~cg~~~~~~~-~------~~d~~~~~v~y--~~~-cG~~~~~~~~~g~~ 218 (510)
T PRK00750 166 ERQATYSPFLPICPKCGKVLTTPV-I------SYDAEAGTVTY--DCE-CGHEGEVPVTGGHG 218 (510)
T ss_pred ccCCCeeeeeeeCCCCCccceEEE-E------EEeCCCCEEEE--EcC-CCCEEEEecCCCCc
Confidence 33445788999999 999864332 1 12222344444 676 99999999988643
No 14
>PF14353 CpXC: CpXC protein
Probab=58.03 E-value=2.8 Score=29.85 Aligned_cols=47 Identities=17% Similarity=0.308 Sum_probs=28.1
Q ss_pred EEEec-CCceeeceEE--EecCeeEEeC-CCCceeeEEEeeccCCCeeEEE
Q 032792 34 KLKCG-CGELSQKETC--VSLAETLPTQ-GGKGTTNLIQKCKFCGREGTVT 80 (133)
Q Consensus 34 kvkCt-C~e~~~~~v~--i~~~e~~e~~-gsrg~aNfv~KCk~C~re~si~ 80 (133)
+|.|. |+......++ ||..+.-++. .-....=|...|+.|++...+.
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 47899 9997765443 4443332221 1111124788999999997653
No 15
>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=56.99 E-value=39 Score=28.71 Aligned_cols=49 Identities=39% Similarity=0.688 Sum_probs=31.3
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCC
Q 032792 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (133)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~~ 86 (133)
++--|.|...|. ||-.. +.+. +..+..|+.- .+|+ |+.+.++++..+.+
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 444677999999 99432 2221 2222334444 4785 99999999986543
No 16
>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=55.70 E-value=31 Score=30.81 Aligned_cols=49 Identities=18% Similarity=0.365 Sum_probs=32.9
Q ss_pred CCCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCC
Q 032792 26 DPNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRG 86 (133)
Q Consensus 26 ~p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~~ 86 (133)
-++--|.|...|. ||-+....+. ..... ...++|+ |+.++++++..+.+
T Consensus 160 ~~~~~~P~~pic~~cGrv~~~~~~--------~~~~~---~v~Y~c~-cG~~g~~~~~~g~~ 209 (515)
T TIGR00467 160 LEENWYPISVFCENCGRDTTTVNN--------YDNEY---SIEYSCE-CGNQESVDIYTGAI 209 (515)
T ss_pred cCCCceeeeeecCCcCccCceEEE--------ecCCc---eEEEEcC-CCCEEEEeecCCCc
Confidence 3444677999999 9998652221 11111 2566896 99999999977644
No 17
>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=52.82 E-value=8.8 Score=22.79 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=9.6
Q ss_pred eEEEeeccCCCe
Q 032792 65 NLIQKCKFCGRE 76 (133)
Q Consensus 65 Nfv~KCk~C~re 76 (133)
...++|+.|+++
T Consensus 35 ~~~~~C~~C~~q 46 (46)
T PF12760_consen 35 RGRYRCKACRKQ 46 (46)
T ss_pred CCeEECCCCCCc
Confidence 567899999874
No 18
>KOG2315 consensus Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis]
Probab=51.94 E-value=27 Score=31.68 Aligned_cols=31 Identities=3% Similarity=0.013 Sum_probs=27.8
Q ss_pred CcccEEEEEccCceEEeEEeCCCEEEEEecC
Q 032792 98 GFSPLMLFDCRGYEPVDFVFGVGWKVESSPI 128 (133)
Q Consensus 98 ~~~~I~~fdCRG~ep~~f~p~~~w~~~s~~~ 128 (133)
+++.|..|+|-+.-..+|+|+|.|..+++-+
T Consensus 345 n~K~i~~~~a~~tt~~eW~PdGe~flTATTa 375 (566)
T KOG2315|consen 345 NRKLIAKFKAANTTVFEWSPDGEYFLTATTA 375 (566)
T ss_pred chhhccccccCCceEEEEcCCCcEEEEEecc
Confidence 4778999999999999999999999988754
No 19
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=49.24 E-value=11 Score=33.34 Aligned_cols=28 Identities=36% Similarity=0.630 Sum_probs=20.7
Q ss_pred EEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEE
Q 032792 34 KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (133)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i 81 (133)
...|+ ||.+|+||.. ||..|+.=+|+.=
T Consensus 7 ~f~C~~CG~~s~KW~G--------------------kCp~Cg~Wns~vE 35 (456)
T COG1066 7 AFVCQECGYVSPKWLG--------------------KCPACGAWNTLVE 35 (456)
T ss_pred EEEcccCCCCCccccc--------------------cCCCCCCccceEE
Confidence 36799 9999999954 6777776666543
No 20
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.54 E-value=18 Score=26.52 Aligned_cols=47 Identities=23% Similarity=0.440 Sum_probs=28.8
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCcee--------eEEEeeccCCCeeEEEEecCC
Q 032792 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTT--------NLIQKCKFCGREGTVTMIPGR 85 (133)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~a--------Nfv~KCk~C~re~si~i~~~~ 85 (133)
....|. ||...+-. .+...+++..+++ .+.++|+.|+.. .+.|+.+.
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 467899 99665321 1122344555555 677899999955 36666654
No 21
>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=44.82 E-value=21 Score=30.62 Aligned_cols=50 Identities=28% Similarity=0.538 Sum_probs=25.7
Q ss_pred CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032792 27 PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (133)
Q Consensus 27 p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~ 85 (133)
++--|.|..-|. ||-+.. +.|.. .+. +..-...+|+.|+.+.++++..+.
T Consensus 167 ~~~y~Pf~piC~~cGri~t--t~v~~---~d~----~~~~v~Y~c~~cG~~g~~~i~~g~ 217 (360)
T PF01921_consen 167 PETYSPFLPICEKCGRIDT--TEVTE---YDP----EGGTVTYRCEECGHEGEVDITGGN 217 (360)
T ss_dssp -TT--SEEEEETTTEE--E--EEEEE---E------SSSEEEEE--TTS---EEETTTT-
T ss_pred CCCeeeeeeeccccCCccc--ceeeE---eec----CCCEEEEEecCCCCEEEEecCCCc
Confidence 334678999999 998532 22222 111 223577899999999999998754
No 22
>PF10001 DUF2242: Uncharacterized protein conserved in bacteria (DUF2242); InterPro: IPR018718 This family includes putative lipoproteins and uncharacterised proteins.
Probab=44.33 E-value=70 Score=23.43 Aligned_cols=57 Identities=14% Similarity=0.226 Sum_probs=41.5
Q ss_pred EEEe-cceeeeeeCCCCCCCCceEEEEEEec--CCceeeceEEEecC-eeEEeCCCCceeeEEE
Q 032792 9 SADL-ENLTNLQPQGGCDDPNFSYFFKLKCG--CGELSQKETCVSLA-ETLPTQGGKGTTNLIQ 68 (133)
Q Consensus 9 kAeL-enV~~l~p~~~~~~p~~~~~fkvkCt--C~e~~~~~v~i~~~-e~~e~~gsrg~aNfv~ 68 (133)
++++ +|-++.||.+ +-+..-.|.|.|. -...+...+++|.- +...++-++..|++-.
T Consensus 19 ~~~~v~G~K~FQp~~---d~h~qi~~~vvCa~~~~~~~~s~~fvnAlQdrY~lKks~~SASvGV 79 (121)
T PF10001_consen 19 DPDRVDGRKNFQPED---DVHAQIEFRVVCAPDGSGGQSSTVFVNALQDRYALKKSNNSASVGV 79 (121)
T ss_pred CcceEeeeeccccCC---CceEEEEEEEEECCCCCCCeeEEEEEEeeeeeeeeeecCCcceEee
Confidence 3444 8999999975 2456788999999 44455678999875 5778888887776543
No 23
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=38.99 E-value=30 Score=29.96 Aligned_cols=29 Identities=10% Similarity=0.017 Sum_probs=24.7
Q ss_pred cEEEEEc-cCceEEeEEeCCCEEEEEecCC
Q 032792 101 PLMLFDC-RGYEPVDFVFGVGWKVESSPIG 129 (133)
Q Consensus 101 ~I~~fdC-RG~ep~~f~p~~~w~~~s~~~~ 129 (133)
.|++.|| -|+..++|+|.++|.+++..-+
T Consensus 203 kv~aYe~~lG~k~v~wsP~~qflavGsyD~ 232 (447)
T KOG4497|consen 203 KVYAYERGLGLKFVEWSPCNQFLAVGSYDQ 232 (447)
T ss_pred eeeeeeeccceeEEEeccccceEEeeccch
Confidence 3668898 8999999999999999987654
No 24
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=38.97 E-value=29 Score=25.70 Aligned_cols=32 Identities=31% Similarity=0.721 Sum_probs=21.3
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si 79 (133)
|.|. |+-.- ...+ . .+| -+.+||+-|+...++
T Consensus 103 VlC~~C~spd--T~l~-k-------~~r---~~~l~C~ACGa~~~V 135 (138)
T PRK03988 103 VICPECGSPD--TKLI-K-------EGR---IWVLKCEACGAETPV 135 (138)
T ss_pred EECCCCCCCC--cEEE-E-------cCC---eEEEEcccCCCCCcC
Confidence 7899 98743 2111 1 122 688999999988776
No 25
>KOG0315 consensus G-protein beta subunit-like protein (contains WD40 repeats) [General function prediction only]
Probab=38.77 E-value=1.1e+02 Score=25.66 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=31.1
Q ss_pred CCCcccEEEEEcc--CceEEeEEeCCCEEEEEecCCee
Q 032792 96 SGGFSPLMLFDCR--GYEPVDFVFGVGWKVESSPIGLL 131 (133)
Q Consensus 96 ~~~~~~I~~fdCR--G~ep~~f~p~~~w~~~s~~~~~~ 131 (133)
+++..|++.||=. .+--+.|+-+|.|..++.+-|+.
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 4677899999976 58889999999999999998863
No 26
>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=38.42 E-value=10 Score=28.28 Aligned_cols=63 Identities=21% Similarity=0.437 Sum_probs=34.6
Q ss_pred ecceeeeeeCCCCCC--CCceEEEEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecC
Q 032792 12 LENLTNLQPQGGCDD--PNFSYFFKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPG 84 (133)
Q Consensus 12 LenV~~l~p~~~~~~--p~~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~ 84 (133)
..||..|....+... +=|--.+.++|+ |+...+..-.....+..+.+ +|+.|+....=+|+-.
T Consensus 81 TQNIDgLh~~AG~~~vielHG~l~~~~C~~C~~~~~~~~~~~~~~~~~~~----------~C~~C~~~lrp~vv~f 146 (178)
T PF02146_consen 81 TQNIDGLHQKAGSPKVIELHGSLFRLRCSKCGKEYDREDIVDSIDEEEPP----------RCPKCGGLLRPDVVLF 146 (178)
T ss_dssp ES-SSSHHHHTTESCEEETTEEEEEEEETTTSBEEEGHHHHHHHHTTSSC----------BCTTTSCBEEEEE--B
T ss_pred ecccchhhhcccchhhHHHHhhhceeeecCCCccccchhhcccccccccc----------cccccCccCCCCeeec
Confidence 367776665332210 014566889999 99987654222221111122 9999999876666543
No 27
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=37.55 E-value=67 Score=18.56 Aligned_cols=35 Identities=23% Similarity=0.608 Sum_probs=18.2
Q ss_pred Eec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 36 KCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
+|. |+ |++-+++... --+..-+. .+..+|..|++.
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 577 76 5555555321 11122233 466778878753
No 28
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.17 E-value=8 Score=31.58 Aligned_cols=60 Identities=27% Similarity=0.408 Sum_probs=37.1
Q ss_pred EEEEEec-CCceeeceEEEecCeeEEeCCCC--c--eeeEEEeeccCCCeeEEEEecCCCccccccc
Q 032792 32 FFKLKCG-CGELSQKETCVSLAETLPTQGGK--G--TTNLIQKCKFCGREGTVTMIPGRGKPLTQEA 93 (133)
Q Consensus 32 ~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsr--g--~aNfv~KCk~C~re~si~i~~~~~~~~~~e~ 93 (133)
.|.++|- |||--.+.--+|.-+. +.-|-. | .--|.++|..|.++.++.=.|. +..|.+|.
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 4899999 9996555544444221 111111 2 2369999999999987766554 34465543
No 29
>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=35.64 E-value=75 Score=23.93 Aligned_cols=43 Identities=19% Similarity=0.258 Sum_probs=27.7
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEe
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMI 82 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~ 82 (133)
..|. |++.....+ -.+++|-.|-.-=..+.|..|+-.++=...
T Consensus 2 s~Cp~C~~~~~~~~-----~~~~IP~F~evii~sf~C~~CGyk~~ev~~ 45 (161)
T PF03367_consen 2 SLCPNCGENGTTRI-----LLTDIPYFKEVIIMSFECEHCGYKNNEVKS 45 (161)
T ss_dssp EE-TTTSSCCEEEE-----EEEEETTTEEEEEEEEE-TTT--EEEEEEE
T ss_pred CcCCCCCCCcEEEE-----EEEcCCCCceEEEEEeECCCCCCEeeeEEE
Confidence 4799 998643222 456789888888889999999988764443
No 30
>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=35.26 E-value=54 Score=24.81 Aligned_cols=31 Identities=6% Similarity=0.047 Sum_probs=25.0
Q ss_pred CcccEEEEEccCceEEeEEeCCCEEEEEecC
Q 032792 98 GFSPLMLFDCRGYEPVDFVFGVGWKVESSPI 128 (133)
Q Consensus 98 ~~~~I~~fdCRG~ep~~f~p~~~w~~~s~~~ 128 (133)
+...|..++=-++--++|+|+|.+.++++..
T Consensus 134 ~~~~i~~~~~~~~t~~~WsPdGr~~~ta~t~ 164 (194)
T PF08662_consen 134 KKKKISTFEHSDATDVEWSPDGRYLATATTS 164 (194)
T ss_pred CCEEeeccccCcEEEEEEcCCCCEEEEEEec
Confidence 5667777776677888999999999998754
No 31
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.55 E-value=38 Score=26.02 Aligned_cols=37 Identities=24% Similarity=0.588 Sum_probs=22.0
Q ss_pred eeeEEEeeccCCCeeEEEEecCCCcccccccccCCCcccEEEEEccCce
Q 032792 63 TTNLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYE 111 (133)
Q Consensus 63 ~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCRG~e 111 (133)
.-++++.||.|+-.++=+|.+ .+|. + | .+.+.|-||-
T Consensus 75 ~m~l~yTCkvCntRs~ktisk---~AY~--~---G----vVivqC~gC~ 111 (165)
T KOG3277|consen 75 RMQLAYTCKVCNTRSTKTISK---QAYE--K---G----VVIVQCPGCK 111 (165)
T ss_pred ceEEEEEeeccCCccccccCh---hhhh--C---c----eEEEECCCCc
Confidence 346777788887777765544 1232 1 2 5556677765
No 32
>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=34.49 E-value=59 Score=18.03 Aligned_cols=34 Identities=21% Similarity=0.392 Sum_probs=19.7
Q ss_pred EEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeE
Q 032792 34 KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (133)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~s 78 (133)
+++|. |+... .|.. +. ++...+ .++|..|+..-.
T Consensus 2 ~~~CP~C~~~~----~v~~-~~--~~~~~~----~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSF----RVVD-SQ--LGANGG----KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEE----EeCH-HH--cCCCCC----EEECCCCCCEEE
Confidence 68898 98763 3433 22 221111 477999987644
No 33
>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=33.33 E-value=26 Score=29.85 Aligned_cols=12 Identities=42% Similarity=0.750 Sum_probs=9.4
Q ss_pred Eec-CCceeeceE
Q 032792 36 KCG-CGELSQKET 47 (133)
Q Consensus 36 kCt-C~e~~~~~v 47 (133)
.|+ ||..+++|.
T Consensus 2 ~c~~cg~~~~~~~ 14 (372)
T cd01121 2 VCSECGYVSPKWL 14 (372)
T ss_pred CCCCCCCCCCCcc
Confidence 588 888888874
No 34
>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=33.33 E-value=34 Score=19.74 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=15.0
Q ss_pred EEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032792 48 CVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (133)
Q Consensus 48 ~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si 79 (133)
+||++-+++..| =.|+|.+|+..+.+
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 567766655533 24999999987664
No 35
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.25 E-value=27 Score=19.82 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=8.3
Q ss_pred EEEEec-CCce
Q 032792 33 FKLKCG-CGEL 42 (133)
Q Consensus 33 fkvkCt-C~e~ 42 (133)
.+|+|+ |+.+
T Consensus 24 ~~v~C~~C~~~ 34 (36)
T PF13717_consen 24 RKVRCSKCGHV 34 (36)
T ss_pred cEEECCCCCCE
Confidence 489999 9975
No 36
>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=31.93 E-value=23 Score=23.79 Aligned_cols=33 Identities=21% Similarity=0.500 Sum_probs=18.0
Q ss_pred EEEeeccCCCeeEEEEecCCCcccccccccCCCcccEEEEEccCce
Q 032792 66 LIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYE 111 (133)
Q Consensus 66 fv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCRG~e 111 (133)
=++.|.+|+.+.|+.+.-.+ -..+..+.||=|.
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 46899999999998886532 1338888888874
No 37
>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=31.89 E-value=27 Score=30.49 Aligned_cols=28 Identities=39% Similarity=0.614 Sum_probs=20.0
Q ss_pred EEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEE
Q 032792 34 KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTM 81 (133)
Q Consensus 34 kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i 81 (133)
...|+ ||..+++|. +||+.|+.=+|+.=
T Consensus 7 ~y~C~~Cg~~~~~~~--------------------g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 7 KFVCQHCGADSPKWQ--------------------GKCPACHAWNTITE 35 (454)
T ss_pred eEECCcCCCCCcccc--------------------EECcCCCCccccch
Confidence 35799 999988874 56777776666543
No 38
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=31.50 E-value=45 Score=24.53 Aligned_cols=32 Identities=22% Similarity=0.661 Sum_probs=20.8
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si 79 (133)
|.|. |+-.-.+ .+ . .+| -+.+||+-|+...++
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 7899 9875322 11 1 112 357899999998776
No 39
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=30.02 E-value=61 Score=25.28 Aligned_cols=42 Identities=21% Similarity=0.386 Sum_probs=28.2
Q ss_pred EEec-CCceeeceEEEecCeeEE-eCCCCceeeEEEeeccCCCeeEEEE
Q 032792 35 LKCG-CGELSQKETCVSLAETLP-TQGGKGTTNLIQKCKFCGREGTVTM 81 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e-~~gsrg~aNfv~KCk~C~re~si~i 81 (133)
+.|. |+..- ...+ -.+. +|..|-.-=..+.|..|+-.++=..
T Consensus 1 ~~Cp~C~~~~--~~~~---~~~~~IP~F~evii~sf~C~~CGyr~~ev~ 44 (192)
T TIGR00310 1 IDCPSCGGEC--ETVM---KTVNDIPYFGEVLETSTICEHCGYRSNDVK 44 (192)
T ss_pred CcCCCCCCCC--EEEE---EEEcCCCCcceEEEEEEECCCCCCccceeE
Confidence 4699 98642 2222 2344 8888877778999999998765433
No 40
>PRK11823 DNA repair protein RadA; Provisional
Probab=29.58 E-value=35 Score=29.61 Aligned_cols=15 Identities=33% Similarity=0.474 Sum_probs=11.4
Q ss_pred EEEec-CCceeeceEE
Q 032792 34 KLKCG-CGELSQKETC 48 (133)
Q Consensus 34 kvkCt-C~e~~~~~v~ 48 (133)
...|+ ||..+++|..
T Consensus 7 ~y~C~~Cg~~~~~~~g 22 (446)
T PRK11823 7 AYVCQECGAESPKWLG 22 (446)
T ss_pred eEECCcCCCCCcccCe
Confidence 35699 9999888753
No 41
>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=28.79 E-value=76 Score=23.99 Aligned_cols=31 Identities=6% Similarity=-0.038 Sum_probs=24.7
Q ss_pred cccEEEEEccCceEEeEEeCCCEEEEEecCC
Q 032792 99 FSPLMLFDCRGYEPVDFVFGVGWKVESSPIG 129 (133)
Q Consensus 99 ~~~I~~fdCRG~ep~~f~p~~~w~~~s~~~~ 129 (133)
..+|..|+-.-..-+.|+|.|.+.|.+.-|+
T Consensus 92 ~~~i~~~~~~~~n~i~wsP~G~~l~~~g~~n 122 (194)
T PF08662_consen 92 GKKIFSFGTQPRNTISWSPDGRFLVLAGFGN 122 (194)
T ss_pred ccEeEeecCCCceEEEECCCCCEEEEEEccC
Confidence 5667778766677899999999999976544
No 42
>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=28.59 E-value=20 Score=24.75 Aligned_cols=13 Identities=38% Similarity=0.756 Sum_probs=1.0
Q ss_pred eEEEeeccCCCee
Q 032792 65 NLIQKCKFCGREG 77 (133)
Q Consensus 65 Nfv~KCk~C~re~ 77 (133)
=|.|-||-|||-.
T Consensus 70 CL~WACKaCKRKt 82 (86)
T PF01586_consen 70 CLLWACKACKRKT 82 (86)
T ss_dssp ---------S---
T ss_pred chHHHhHhhhccC
Confidence 4999999999964
No 43
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=27.28 E-value=42 Score=27.56 Aligned_cols=28 Identities=25% Similarity=0.208 Sum_probs=22.8
Q ss_pred EEEEEccCceEEeEEeCCCEEEEEecCCe
Q 032792 102 LMLFDCRGYEPVDFVFGVGWKVESSPIGL 130 (133)
Q Consensus 102 I~~fdCRG~ep~~f~p~~~w~~~s~~~~~ 130 (133)
++--| |+-||+.|.|-+.|++...+.|.
T Consensus 63 ~vH~~-~~~eP~nW~pp~s~~~~~~~~g~ 90 (253)
T COG1637 63 LVHQD-RKREPLNWQPPGSSIAAAVRDGL 90 (253)
T ss_pred Eeccc-ccCCCcccCCCCceEEEeecCCc
Confidence 33344 99999999999999998777773
No 44
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.92 E-value=47 Score=18.83 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=8.9
Q ss_pred EEEEec-CCcee
Q 032792 33 FKLKCG-CGELS 43 (133)
Q Consensus 33 fkvkCt-C~e~~ 43 (133)
-+..|+ |+.+|
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 45
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=26.54 E-value=17 Score=30.48 Aligned_cols=51 Identities=14% Similarity=0.272 Sum_probs=37.0
Q ss_pred ceEEEEEEec-CCceeeceEEEecCeeEEeCCC--CceeeEEEeeccCCCeeEEEEe
Q 032792 29 FSYFFKLKCG-CGELSQKETCVSLAETLPTQGG--KGTTNLIQKCKFCGREGTVTMI 82 (133)
Q Consensus 29 ~~~~fkvkCt-C~e~~~~~v~i~~~e~~e~~gs--rg~aNfv~KCk~C~re~si~i~ 82 (133)
|+-.|.|-|. |...-...|-.|. |+..+.+- ----.|-|||..|... |.|.
T Consensus 47 FEMPynIWC~gC~nhIgmGvRyNA-eKkkvGnYYtTpiw~FrmKchlC~n~--i~iq 100 (317)
T KOG2990|consen 47 FEMPYNIWCDGCKNHIGMGVRYNA-EKKKVGNYYTTPIWSFRMKCHLCDNY--IVIQ 100 (317)
T ss_pred EecccchhhccHHHhhhccceech-hhhhccccccCcccchhhcccccCCc--eeee
Confidence 5567889999 9998888888888 56555211 1234799999999877 4443
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=26.44 E-value=83 Score=19.66 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=17.3
Q ss_pred ceeeEEEeeccCCCeeEEEEecC
Q 032792 62 GTTNLIQKCKFCGREGTVTMIPG 84 (133)
Q Consensus 62 g~aNfv~KCk~C~re~si~i~~~ 84 (133)
+..++.+||.-|+.-+.+.-...
T Consensus 19 ~~~~leIKCpRC~tiN~~~a~~~ 41 (51)
T PF10122_consen 19 EVIELEIKCPRCKTINHVRATSP 41 (51)
T ss_pred CccEEEEECCCCCccceEeccCC
Confidence 34478899999998888776543
No 47
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=26.16 E-value=42 Score=27.97 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=11.3
Q ss_pred eEEEEEEec-CCce
Q 032792 30 SYFFKLKCG-CGEL 42 (133)
Q Consensus 30 ~~~fkvkCt-C~e~ 42 (133)
.|.|.++|+ |.-.
T Consensus 73 I~rF~~kC~~C~~~ 86 (324)
T PF04502_consen 73 IYRFYIKCPRCSNE 86 (324)
T ss_pred EEEEEEEcCCCCCE
Confidence 799999999 9753
No 48
>PF06051 DUF928: Domain of Unknown Function (DUF928); InterPro: IPR010328 This is a family of uncharacterised bacterial proteins.
Probab=25.84 E-value=66 Score=24.75 Aligned_cols=11 Identities=27% Similarity=1.065 Sum_probs=10.0
Q ss_pred CceEEEEEEec
Q 032792 28 NFSYFFKLKCG 38 (133)
Q Consensus 28 ~~~~~fkvkCt 38 (133)
+|.|+|.|.|.
T Consensus 92 ~Y~W~~~l~Cd 102 (189)
T PF06051_consen 92 TYRWYFSLICD 102 (189)
T ss_pred eEEEEEEEEEC
Confidence 59999999995
No 49
>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=25.23 E-value=40 Score=27.37 Aligned_cols=43 Identities=19% Similarity=0.425 Sum_probs=20.2
Q ss_pred ceEEE-EEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeE
Q 032792 29 FSYFF-KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (133)
Q Consensus 29 ~~~~f-kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~s 78 (133)
++|.| +++|+ ||+..+..... ....+.+ +--+.-|+.|+.-.-
T Consensus 205 t~W~~~R~~Cp~Cg~~~~~~l~~--~~~e~~~-----~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 205 TEWRFVRIKCPYCGNTDHEKLEY--FTVEGEP-----AYRVEVCESCGSYLK 249 (290)
T ss_dssp -EEE--TTS-TTT---SS-EEE---------------SEEEEEETTTTEEEE
T ss_pred CeeeecCCCCcCCCCCCCcceee--EecCCCC-----cEEEEECCcccchHH
Confidence 67875 58999 99975443322 2111122 467888999997643
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=25.14 E-value=31 Score=28.79 Aligned_cols=36 Identities=28% Similarity=0.312 Sum_probs=27.1
Q ss_pred Eec-CCceeeceEEEecCeeEEeCCCCcee-eEEEeec
Q 032792 36 KCG-CGELSQKETCVSLAETLPTQGGKGTT-NLIQKCK 71 (133)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~~gsrg~a-Nfv~KCk 71 (133)
.|- ||+-|.+...+.+.+--.+.|+.|.+ ||.|-++
T Consensus 7 ~C~~Cg~r~a~~~~~~~t~~~~l~~~~~~~~Nffwn~~ 44 (309)
T TIGR01908 7 LCINCGERHAKKDTIFDTEIPLIGGLSGGVPNYFWNGK 44 (309)
T ss_pred cCCCcCCcchhccccccccCCccccCCCCccccccCCC
Confidence 699 99999876666666555556777777 9999864
No 51
>PF12341 DUF3639: Protein of unknown function (DUF3639) ; InterPro: IPR022100 This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with PF00400 from PFAM. There are two completely conserved residues (E and R) that may be functionally important.
Probab=24.98 E-value=1.3e+02 Score=16.29 Aligned_cols=20 Identities=20% Similarity=0.361 Sum_probs=15.0
Q ss_pred EEeEEeCCCEEEEEecCCee
Q 032792 112 PVDFVFGVGWKVESSPIGLL 131 (133)
Q Consensus 112 p~~f~p~~~w~~~s~~~~~~ 131 (133)
+..-.-.++|+++.+|.+++
T Consensus 4 i~aia~g~~~vavaTS~~~l 23 (27)
T PF12341_consen 4 IEAIAAGDSWVAVATSAGYL 23 (27)
T ss_pred EEEEEccCCEEEEEeCCCeE
Confidence 34445578999999998864
No 52
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=24.93 E-value=68 Score=24.97 Aligned_cols=38 Identities=24% Similarity=0.521 Sum_probs=25.7
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCC
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGR 85 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~ 85 (133)
|.|. |+-.-.+- + . . .--+.++|+-|+...++.-.+.+
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 99853221 1 1 1 12678999999999988765543
No 53
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.85 E-value=56 Score=27.46 Aligned_cols=43 Identities=23% Similarity=0.424 Sum_probs=25.8
Q ss_pred ceEEE-EEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEE
Q 032792 29 FSYFF-KLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTV 79 (133)
Q Consensus 29 ~~~~f-kvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si 79 (133)
++|.| +++|+ |++ +.+--|.+..+. ..+--+.-|..|+.-.-+
T Consensus 220 teW~~~R~~C~~Cg~-~~~l~y~~~~~~-------~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 220 SEWHVVRVKCSNCEQ-SGKLHYWSLDSE-------QAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CcccccCccCCCCCC-CCceeeeeecCC-------CcceEeeeccccccccee
Confidence 45654 79999 997 555444433211 123456789999877443
No 54
>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=24.76 E-value=20 Score=30.54 Aligned_cols=70 Identities=19% Similarity=0.248 Sum_probs=29.9
Q ss_pred EEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCCcccccccccCCCcccEEEEEcc
Q 032792 35 LKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCR 108 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCR 108 (133)
|.|. |...+...-..+..+.|.+.--.+. -=-+||+.|+.. ++++...... .-...++.+|.....++=|
T Consensus 253 v~C~~C~yt~~~~~~~C~~~~H~l~~~~a~-KRFFkC~~C~~R-t~sl~r~P~~--~C~~Cg~~~wer~~M~~ek 323 (344)
T PF09332_consen 253 VTCKQCKYTAFKPSDRCKEEGHPLKWHDAV-KRFFKCKDCGNR-TISLERLPKK--HCSNCGSSKWERTGMLKEK 323 (344)
T ss_dssp EEETTT--EESS--HHHHHTT--EEEEEEE--EEEE-T-TS-E-EEESSSS--S----TTT-S---EEE---SSS
T ss_pred EEcCCCCCcccCcchhHHhcCCceEEeeee-eeeEECCCCCCe-eeecccCCCC--CCCcCCcCceeehhhhhhh
Confidence 6789 9888887777777788887532222 235899999988 5566432211 1222333455555554433
No 55
>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=24.54 E-value=81 Score=18.06 Aligned_cols=11 Identities=36% Similarity=0.800 Sum_probs=7.3
Q ss_pred eEEEeeccCCC
Q 032792 65 NLIQKCKFCGR 75 (133)
Q Consensus 65 Nfv~KCk~C~r 75 (133)
.+...|..|++
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 55666777765
No 56
>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=23.76 E-value=84 Score=18.55 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=19.9
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
+..+|. ||.....+..++. .-...|..|+..
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 9998765533322 123569999984
No 57
>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=23.50 E-value=64 Score=23.59 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=22.7
Q ss_pred EEec-CCceeeceEEEecCee-EEe-CCCCceeeEEEeeccCCCe
Q 032792 35 LKCG-CGELSQKETCVSLAET-LPT-QGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 35 vkCt-C~e~~~~~v~i~~~e~-~e~-~gsrg~aNfv~KCk~C~re 76 (133)
-.|+ |+..- +.+.+.+. ..+ ++-....+-.+.|..|+|-
T Consensus 92 sRC~~CN~~L---~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 92 SRCPKCNGPL---RPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CccCCCCcEe---eechhhccccccCccccccCCeEEECCCCCCE
Confidence 3788 98832 33444322 123 2444455568899999884
No 58
>PF00400 WD40: WD domain, G-beta repeat; InterPro: IPR019781 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.; PDB: 2ZKQ_a 3CFV_B 3CFS_B 1PEV_A 1NR0_A 1VYH_T 3RFH_A 3O2Z_T 3FRX_C 3U5G_g ....
Probab=23.38 E-value=1.3e+02 Score=15.76 Aligned_cols=31 Identities=10% Similarity=0.109 Sum_probs=20.7
Q ss_pred cEEEEEccC--ceEEeEEeCCCEEEEEecCCee
Q 032792 101 PLMLFDCRG--YEPVDFVFGVGWKVESSPIGLL 131 (133)
Q Consensus 101 ~I~~fdCRG--~ep~~f~p~~~w~~~s~~~~~~ 131 (133)
++..|.... +.=+.|+|++.+.+++..-|+.
T Consensus 3 ~~~~~~~h~~~i~~i~~~~~~~~~~s~~~D~~i 35 (39)
T PF00400_consen 3 CVRTFRGHSSSINSIAWSPDGNFLASGSSDGTI 35 (39)
T ss_dssp EEEEEESSSSSEEEEEEETTSSEEEEEETTSEE
T ss_pred EEEEEcCCCCcEEEEEEecccccceeeCCCCEE
Confidence 344444443 4557899999999988776653
No 59
>PF15411 PH_10: Pleckstrin homology domain
Probab=23.23 E-value=2.8e+02 Score=19.68 Aligned_cols=43 Identities=19% Similarity=0.379 Sum_probs=24.3
Q ss_pred EEEEE--EecceeeeeeCCCCCCCCceEEEEEEecCCceeeceEEEecCeeEEeCCCCceeeEEEeecc
Q 032792 6 LMISA--DLENLTNLQPQGGCDDPNFSYFFKLKCGCGELSQKETCVSLAETLPTQGGKGTTNLIQKCKF 72 (133)
Q Consensus 6 L~vkA--eLenV~~l~p~~~~~~p~~~~~fkvkCtC~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~ 72 (133)
|++|. -+.||+++.+.+ .|. .|.+.|. ..|..+..||+++|+.
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---KPG-SYSLQIS--------------------WKGDPELENFTLRFRN 105 (116)
T ss_pred EEEeeEEEEEeeeeeeccC---CCC-ceEEEEE--------------------EcCCCCCceEEEEeCC
Confidence 44444 347788877764 232 4554431 2345566788888763
No 60
>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=23.11 E-value=97 Score=17.92 Aligned_cols=31 Identities=23% Similarity=0.546 Sum_probs=19.5
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCe
Q 032792 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGRE 76 (133)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re 76 (133)
+..+|. ||..-...+.+.. .-...|+.|+..
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 9987654444333 223568888873
No 61
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=22.82 E-value=42 Score=21.62 Aligned_cols=15 Identities=40% Similarity=0.678 Sum_probs=12.9
Q ss_pred ceEEEEEEec-CCcee
Q 032792 29 FSYFFKLKCG-CGELS 43 (133)
Q Consensus 29 ~~~~fkvkCt-C~e~~ 43 (133)
..|.|+=+|+ ||+.+
T Consensus 12 g~YTLke~Cp~CG~~t 27 (59)
T COG2260 12 GRYTLKEKCPVCGGDT 27 (59)
T ss_pred CceeecccCCCCCCcc
Confidence 4799999999 99975
No 62
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=22.77 E-value=35 Score=26.50 Aligned_cols=12 Identities=25% Similarity=1.007 Sum_probs=11.0
Q ss_pred ceeeEEEeeccC
Q 032792 62 GTTNLIQKCKFC 73 (133)
Q Consensus 62 g~aNfv~KCk~C 73 (133)
|..+||+.|++|
T Consensus 46 g~d~FVLQCr~C 57 (175)
T PF15446_consen 46 GDDDFVLQCRRC 57 (175)
T ss_pred cCCceEEechhh
Confidence 778999999998
No 63
>KOG2055 consensus WD40 repeat protein [General function prediction only]
Probab=22.72 E-value=62 Score=28.99 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=17.6
Q ss_pred EEeEEeCCCEEEEEecCCee
Q 032792 112 PVDFVFGVGWKVESSPIGLL 131 (133)
Q Consensus 112 p~~f~p~~~w~~~s~~~~~~ 131 (133)
-++|+|++||.|.+.++|..
T Consensus 487 c~aFSP~sG~lAvGNe~grv 506 (514)
T KOG2055|consen 487 CMAFSPNSGYLAVGNEAGRV 506 (514)
T ss_pred EEEecCCCceEEeecCCCce
Confidence 37899999999999999864
No 64
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=22.58 E-value=84 Score=22.03 Aligned_cols=20 Identities=30% Similarity=0.748 Sum_probs=16.1
Q ss_pred CCCceEEEEEEec-CCceeec
Q 032792 26 DPNFSYFFKLKCG-CGELSQK 45 (133)
Q Consensus 26 ~p~~~~~fkvkCt-C~e~~~~ 45 (133)
-|.-.--|.+.|+ |+..|..
T Consensus 60 KptKKv~Lr~~Ct~Cgkah~~ 80 (94)
T COG1631 60 KPTKKVDLRLRCTECGKAHQR 80 (94)
T ss_pred CccceEEEEEEehhhcccccc
Confidence 3555778999999 9998865
No 65
>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=22.13 E-value=71 Score=21.74 Aligned_cols=33 Identities=21% Similarity=0.462 Sum_probs=16.3
Q ss_pred EEEEec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeE
Q 032792 33 FKLKCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (133)
Q Consensus 33 fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~s 78 (133)
+...|. |++.|++ .+|+.. ++ .++|-.|++.+.
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 8888764 466652 12 699999998764
No 66
>PF06159 DUF974: Protein of unknown function (DUF974); InterPro: IPR010378 This is a family of uncharacterised eukaryotic proteins.
Probab=21.42 E-value=3.5e+02 Score=21.57 Aligned_cols=17 Identities=29% Similarity=0.315 Sum_probs=12.2
Q ss_pred eEEeEEeCCCEEEEEec
Q 032792 111 EPVDFVFGVGWKVESSP 127 (133)
Q Consensus 111 ep~~f~p~~~w~~~s~~ 127 (133)
|=+.|.|..+|.+...+
T Consensus 154 e~v~lep~~~~~~~~ln 170 (249)
T PF06159_consen 154 EKVKLEPSPGFKVTDLN 170 (249)
T ss_pred EEEEeecCCCceeEecc
Confidence 45778888888777655
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=21.38 E-value=57 Score=18.47 Aligned_cols=9 Identities=44% Similarity=1.401 Sum_probs=7.7
Q ss_pred EEEec-CCce
Q 032792 34 KLKCG-CGEL 42 (133)
Q Consensus 34 kvkCt-C~e~ 42 (133)
+|+|+ |+.+
T Consensus 25 ~vrC~~C~~~ 34 (37)
T PF13719_consen 25 KVRCPKCGHV 34 (37)
T ss_pred EEECCCCCcE
Confidence 89999 9875
No 68
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=21.29 E-value=75 Score=21.40 Aligned_cols=17 Identities=24% Similarity=0.763 Sum_probs=12.0
Q ss_pred eEEEEEEec-CCceeece
Q 032792 30 SYFFKLKCG-CGELSQKE 46 (133)
Q Consensus 30 ~~~fkvkCt-C~e~~~~~ 46 (133)
.--|++.|+ |+-.|-..
T Consensus 49 Ki~Lrl~C~~C~~~~~~~ 66 (77)
T PF00935_consen 49 KIVLRLECTECGKAHMRP 66 (77)
T ss_dssp BBEEEEEETTTS-EEEEE
T ss_pred cEEEEEEeCCCCcccccc
Confidence 456899999 99887543
No 69
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.92 E-value=67 Score=25.50 Aligned_cols=32 Identities=9% Similarity=0.128 Sum_probs=19.9
Q ss_pred EEEEEec-CCceeeceEEEecCeeEEeCCCCce
Q 032792 32 FFKLKCG-CGELSQKETCVSLAETLPTQGGKGT 63 (133)
Q Consensus 32 ~fkvkCt-C~e~~~~~v~i~~~e~~e~~gsrg~ 63 (133)
...+.|. ||.+|+..+..-....+.+==||..
T Consensus 28 ~~lvrC~eCG~V~~~~i~~~k~~~v~viVS~~~ 60 (201)
T COG1326 28 EPLVRCEECGTVHPAIIKTPKPVRVRVIVSRHE 60 (201)
T ss_pred ceEEEccCCCcEeeceeeccccceEEEEEecCC
Confidence 3688999 9999966555544444444334433
No 70
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=20.66 E-value=81 Score=20.14 Aligned_cols=22 Identities=23% Similarity=0.407 Sum_probs=19.0
Q ss_pred ceeeEEEeeccCCCeeEEEEec
Q 032792 62 GTTNLIQKCKFCGREGTVTMIP 83 (133)
Q Consensus 62 g~aNfv~KCk~C~re~si~i~~ 83 (133)
|.|.+-.||+-|+--+-+.+..
T Consensus 19 ~~~yle~KCPrCK~vN~~~~~~ 40 (60)
T COG4416 19 GQAYLEKKCPRCKEVNEFYIKE 40 (60)
T ss_pred cceeeeecCCccceeeeeeccc
Confidence 7789999999999988888764
No 71
>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=20.55 E-value=3.4e+02 Score=22.96 Aligned_cols=76 Identities=16% Similarity=0.165 Sum_probs=46.1
Q ss_pred CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeEEEEecCCCcccccccccCCCcccEEEEEccCceEEeEEeC
Q 032792 39 CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGTVTMIPGRGKPLTQEAAQSGGFSPLMLFDCRGYEPVDFVFG 118 (133)
Q Consensus 39 C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~~~I~~fdCRG~ep~~f~p~ 118 (133)
=+|..+..+|--..+-.+|-.-.|.=.|.. ..=+-.+-+=++-.++..+.++- .-+.+||+|-.+++|.
T Consensus 45 kre~~~e~~yrr~lrCldm~s~~G~f~f~a--~~pq~~Ca~y~iaePd~~IeI~~-------~~vdidC~~G~ll~v~-- 113 (311)
T PF05428_consen 45 KRELSEEFIYRRPLRCLDMLSEEGQFTFTA--SRPQLVCAAYFIAEPDELIEIEF-------DHVDIDCEGGDLLKVF-- 113 (311)
T ss_pred hcccCccccccchhhheeeeccCceEEEec--CCCCceeEEEEEeCCCeEEEEEE-------EEeeccCCCCCEEEEE--
Confidence 566666666655555666665556433333 33233344445544444444432 2568899999999987
Q ss_pred CCEEEEE
Q 032792 119 VGWKVES 125 (133)
Q Consensus 119 ~~w~~~s 125 (133)
|||+.++
T Consensus 114 DGW~LnG 120 (311)
T PF05428_consen 114 DGWELNG 120 (311)
T ss_pred eceEECc
Confidence 8999874
No 72
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=20.45 E-value=1.5e+02 Score=22.39 Aligned_cols=38 Identities=16% Similarity=0.326 Sum_probs=26.9
Q ss_pred Eec-CCceeeceEEEecCeeEEeCCCCceeeEEEeeccCCCeeE
Q 032792 36 KCG-CGELSQKETCVSLAETLPTQGGKGTTNLIQKCKFCGREGT 78 (133)
Q Consensus 36 kCt-C~e~~~~~v~i~~~e~~e~~gsrg~aNfv~KCk~C~re~s 78 (133)
.|. |++.-. ++.-.+++|-.|---=..+.|..|+-.++
T Consensus 2 ~Cp~C~~~~~-----~~~~~~~IP~F~evii~sf~C~~CGyk~~ 40 (160)
T smart00709 2 DCPSCGGNGT-----TRMLLTSIPYFREVIIMSFECEHCGYRNN 40 (160)
T ss_pred cCCCCCCCCE-----EEEEEecCCCcceEEEEEEECCCCCCccc
Confidence 488 886521 33345678888777778899999997755
No 73
>PHA01634 hypothetical protein
Probab=20.30 E-value=61 Score=24.50 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=11.4
Q ss_pred cccEEEEEccCce
Q 032792 99 FSPLMLFDCRGYE 111 (133)
Q Consensus 99 ~~~I~~fdCRG~e 111 (133)
...|+.+||-|||
T Consensus 92 ~~Di~~iDCeGCE 104 (156)
T PHA01634 92 DVDIFVMDCEGCE 104 (156)
T ss_pred CcceEEEEccchH
Confidence 4679999999998
Done!