Query 047023
Match_columns 82
No_of_seqs 108 out of 220
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 06:51:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047023.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047023hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1088 Uncharacterized conser 100.0 2.9E-37 6.2E-42 207.4 6.0 81 1-82 1-83 (124)
2 PF03966 Trm112p: Trm112p-like 98.7 2.2E-09 4.8E-14 65.1 -0.0 41 2-74 1-41 (68)
3 PF08671 SinI: Anti-repressor 72.6 3.1 6.7E-05 21.8 1.6 15 49-63 4-18 (30)
4 PF15392 Joubert: Joubert synd 71.3 3 6.5E-05 32.6 2.0 29 38-66 297-325 (329)
5 PF02954 HTH_8: Bacterial regu 65.1 2 4.3E-05 23.2 -0.1 28 35-63 4-31 (42)
6 PF02495 7kD_coat: 7kD viral c 62.9 12 0.00026 21.8 3.0 31 10-44 21-51 (59)
7 PF13959 DUF4217: Domain of un 61.8 8.5 0.00018 22.7 2.3 20 45-67 43-62 (65)
8 PF10884 DUF2683: Protein of u 56.1 6.8 0.00015 25.0 1.2 17 30-46 42-58 (80)
9 PF11336 DUF3138: Protein of u 49.5 5.4 0.00012 32.8 -0.1 11 1-11 232-242 (514)
10 PF11881 DUF3401: Domain of un 47.6 12 0.00026 28.1 1.6 15 47-61 165-179 (239)
11 PF15200 KRTDAP: Keratinocyte 42.1 16 0.00035 23.0 1.3 18 38-55 48-65 (77)
12 cd02425 Peptidase_C39F A sub-f 41.3 52 0.0011 20.2 3.6 29 34-62 26-58 (126)
13 PF14907 NTP_transf_5: Unchara 39.3 32 0.00069 24.0 2.6 24 40-63 211-234 (249)
14 cd02418 Peptidase_C39B A sub-f 37.4 61 0.0013 20.1 3.5 30 33-62 25-58 (136)
15 PF10381 Autophagy_Cterm: Auto 36.2 16 0.00034 18.5 0.4 13 39-51 10-22 (25)
16 cd02421 Peptidase_C39_likeD A 34.4 71 0.0015 19.7 3.4 30 33-62 20-53 (124)
17 PHA02503 putative transcriptio 33.2 22 0.00047 21.0 0.8 27 34-60 27-55 (57)
18 PF07582 AP_endonuc_2_N: AP en 31.5 45 0.00098 19.5 2.0 16 49-64 1-16 (55)
19 cd02423 Peptidase_C39G A sub-f 31.1 88 0.0019 19.2 3.4 29 34-62 27-59 (129)
20 PHA00212 putative transcriptio 30.1 28 0.0006 20.9 0.9 28 34-61 30-59 (63)
21 PF06935 DUF1284: Protein of u 29.5 30 0.00066 22.2 1.1 10 36-45 2-11 (103)
22 PF13935 Ead_Ea22: Ead/Ea22-li 28.9 41 0.0009 22.6 1.7 15 46-60 1-15 (139)
23 PF04516 CP2: CP2 transcriptio 28.4 46 0.001 24.8 2.0 26 7-33 166-194 (236)
24 cd02417 Peptidase_C39_likeA A 28.2 1.1E+02 0.0023 18.7 3.4 30 33-62 20-53 (121)
25 PF14030 DUF4245: Protein of u 27.6 79 0.0017 22.0 3.0 29 45-75 38-68 (169)
26 PF07572 BCNT: Bucentaur or cr 26.6 6.1 0.00013 25.0 -2.5 32 46-81 28-62 (81)
27 PF06544 DUF1115: Protein of u 25.4 33 0.00071 22.5 0.7 13 38-50 50-62 (128)
28 PF09116 gp45-slide_C: gp45 sl 24.5 39 0.00084 22.6 0.9 20 46-65 7-26 (112)
29 PF02016 Peptidase_S66: LD-car 24.2 48 0.001 24.7 1.5 17 42-58 76-92 (284)
30 cd02420 Peptidase_C39D A sub-f 24.1 1.4E+02 0.0031 18.3 3.5 30 33-62 25-58 (125)
31 COG1176 PotB ABC-type spermidi 22.8 54 0.0012 24.9 1.5 20 42-62 173-192 (287)
32 KOG3131 Uncharacterized conser 22.7 26 0.00056 26.9 -0.2 23 4-26 168-198 (281)
33 TIGR01323 nitrile_alph nitrile 22.4 31 0.00067 25.1 0.1 13 5-17 84-96 (185)
34 PF02969 TAF: TATA box binding 22.3 36 0.00079 20.5 0.4 18 51-68 7-24 (66)
35 PF15217 TSC21: TSC21 family 22.1 66 0.0014 23.0 1.8 32 46-78 62-99 (180)
36 PF07498 Rho_N: Rho terminatio 21.0 80 0.0017 17.1 1.6 19 46-64 3-21 (43)
37 cd02419 Peptidase_C39C A sub-f 21.0 1.8E+02 0.004 17.8 3.5 30 33-62 25-58 (127)
38 COG3544 Uncharacterized protei 21.0 42 0.00091 24.5 0.6 14 34-47 129-142 (190)
39 KOG1999 RNA polymerase II tran 20.3 36 0.00077 30.5 0.1 19 40-58 289-307 (1024)
No 1
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.9e-37 Score=207.44 Aligned_cols=81 Identities=53% Similarity=1.033 Sum_probs=77.0
Q ss_pred Ccccchhhhhhccccccc-CCCceeeeeeEEEeccCCCHHHHHhhcccccHHHHHHHHHhcCCCCCCCCCCCCCCCC-Cc
Q 047023 1 MRLLTHNMLSSNIKGVAN-GFPLLIEVEKVIEKQVDFNPDFLKNIFPKIEWQALVQASRSMGYAELPEESPESSMLD-SD 78 (82)
Q Consensus 1 MrLlThN~L~c~~k~c~~-gfPL~i~~~~~~~~e~efN~eFi~~mlpkldW~aL~~aA~~lg~~~LP~~~p~~~~~~-de 78 (82)
|||+|||||+|++|+|.+ ||||++++.+++++++||||+|+.+|+|||||+||+.||+++|..+||++.| +++.+ ||
T Consensus 1 MKLlthNfLsc~~k~~~s~gFPL~l~~~k~~~~~vEFnPdFl~~m~~kidW~All~~A~~l~~~~lP~~kP-e~~~e~de 79 (124)
T KOG1088|consen 1 MKLLTHNFLSCSVKKVVSVGFPLRLVAKKVVEKEVEFNPDFLIRMLPKIDWSALLEAARSLGNTELPDEKP-EKLVEDDE 79 (124)
T ss_pred CceeeeehhhheeecccccCCceEEEeeEEEEEeeecChHHHHHhhhhccHHHHHHHHHHhccccCCCCCc-cccccccH
Confidence 999999999999999985 9999999999999999999999999999999999999999999999999999 77766 77
Q ss_pred hhhC
Q 047023 79 DFLR 82 (82)
Q Consensus 79 efL~ 82 (82)
+|||
T Consensus 80 ~~Lr 83 (124)
T KOG1088|consen 80 EFLR 83 (124)
T ss_pred HHHH
Confidence 7885
No 2
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=98.72 E-value=2.2e-09 Score=65.10 Aligned_cols=41 Identities=41% Similarity=0.884 Sum_probs=33.4
Q ss_pred cccchhhhhhcccccccCCCceeeeeeEEEeccCCCHHHHHhhcccccHHHHHHHHHhcCCCCCCCCCCCCCC
Q 047023 2 RLLTHNMLSSNIKGVANGFPLLIEVEKVIEKQVDFNPDFLKNIFPKIEWQALVQASRSMGYAELPEESPESSM 74 (82)
Q Consensus 2 rLlThN~L~c~~k~c~~gfPL~i~~~~~~~~e~efN~eFi~~mlpkldW~aL~~aA~~lg~~~LP~~~p~~~~ 74 (82)
|++|||||+|++ |+ | || ||+||+++|+ +|..++|+..+ +++
T Consensus 1 k~~llniL~Cp~--ck-~-pL--------------------------~~~~l~~~~~-~~~~~lp~~~~-~~~ 41 (68)
T PF03966_consen 1 KLLLLNILACPV--CK-G-PL--------------------------DWEALVETAQ-LGLSELPKELP-EDY 41 (68)
T ss_dssp BGGGCGTBB-TT--TS-S-BE--------------------------HHHHHHHHHH-CCCCHCHHCHH-CHC
T ss_pred ChhHHhhhcCCC--CC-C-cc--------------------------hHHHHHHHHH-hCcccCCCCCc-cch
Confidence 689999999993 54 3 88 9999999999 99988888877 543
No 3
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=72.60 E-value=3.1 Score=21.76 Aligned_cols=15 Identities=27% Similarity=0.782 Sum_probs=12.5
Q ss_pred cHHHHHHHHHhcCCC
Q 047023 49 EWQALVQASRSMGYA 63 (82)
Q Consensus 49 dW~aL~~aA~~lg~~ 63 (82)
+|-+|..-|+++|++
T Consensus 4 EW~~Li~eA~~~Gls 18 (30)
T PF08671_consen 4 EWVELIKEAKESGLS 18 (30)
T ss_dssp HHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHcCCC
Confidence 799999999999975
No 4
>PF15392 Joubert: Joubert syndrome-associated
Probab=71.35 E-value=3 Score=32.63 Aligned_cols=29 Identities=21% Similarity=0.405 Sum_probs=23.1
Q ss_pred HHHHHhhcccccHHHHHHHHHhcCCCCCC
Q 047023 38 PDFLKNIFPKIEWQALVQASRSMGYAELP 66 (82)
Q Consensus 38 ~eFi~~mlpkldW~aL~~aA~~lg~~~LP 66 (82)
.|-.-.||.||||+|+-....++....|+
T Consensus 297 SeSTgSILSKlDW~AiedMvA~Vedk~~~ 325 (329)
T PF15392_consen 297 SESTGSILSKLDWNAIEDMVASVEDKSLS 325 (329)
T ss_pred ccchhhhhhhcchHHHHHHHhhhhccCcc
Confidence 45667899999999999998887665554
No 5
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=65.09 E-value=2 Score=23.23 Aligned_cols=28 Identities=14% Similarity=0.424 Sum_probs=22.3
Q ss_pred CCCHHHHHhhcccccHHHHHHHHHhcCCC
Q 047023 35 DFNPDFLKNIFPKIEWQALVQASRSMGYA 63 (82)
Q Consensus 35 efN~eFi~~mlpkldW~aL~~aA~~lg~~ 63 (82)
+|..++|...|.+-.|+ ..+||+.||++
T Consensus 4 ~~E~~~i~~aL~~~~gn-~~~aA~~Lgis 31 (42)
T PF02954_consen 4 EFEKQLIRQALERCGGN-VSKAARLLGIS 31 (42)
T ss_dssp HHHHHHHHHHHHHTTT--HHHHHHHHTS-
T ss_pred HHHHHHHHHHHHHhCCC-HHHHHHHHCCC
Confidence 35578999999999999 68999999975
No 6
>PF02495 7kD_coat: 7kD viral coat protein; InterPro: IPR003411 This family consists of a 7 kDa coat protein from Carlavirus and Potexvirus [].
Probab=62.95 E-value=12 Score=21.77 Aligned_cols=31 Identities=26% Similarity=0.484 Sum_probs=24.0
Q ss_pred hhcccccccCCCceeeeeeEEEeccCCCHHHHHhh
Q 047023 10 SSNIKGVANGFPLLIEVEKVIEKQVDFNPDFLKNI 44 (82)
Q Consensus 10 ~c~~k~c~~gfPL~i~~~~~~~~e~efN~eFi~~m 44 (82)
+...++|. ..|.-+.+.+...+|+|||++-+
T Consensus 21 ~~~~~~C~----I~ItGeSv~I~gC~~~~e~i~~i 51 (59)
T PF02495_consen 21 SPSSPSCV----IVITGESVTISGCEFTPEFIEAI 51 (59)
T ss_pred cCCCCCcE----EEEeCcEEEEECCCCCHHHHHHH
Confidence 44567787 56666788899999999999755
No 7
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=61.84 E-value=8.5 Score=22.74 Aligned_cols=20 Identities=30% Similarity=0.566 Sum_probs=15.9
Q ss_pred cccccHHHHHHHHHhcCCCCCCC
Q 047023 45 FPKIEWQALVQASRSMGYAELPE 67 (82)
Q Consensus 45 lpkldW~aL~~aA~~lg~~~LP~ 67 (82)
+.+|||..+ |+++|+.+.|.
T Consensus 43 ~~~L~l~~~---A~sfGL~~~P~ 62 (65)
T PF13959_consen 43 VKKLDLGHL---AKSFGLLEAPK 62 (65)
T ss_pred cccCCHHHH---HHHcCCCCCCC
Confidence 468899887 68899987775
No 8
>PF10884 DUF2683: Protein of unknown function (DUF2683); InterPro: IPR020271 This entry contains proteins with no known function.
Probab=56.08 E-value=6.8 Score=24.95 Aligned_cols=17 Identities=18% Similarity=0.387 Sum_probs=14.0
Q ss_pred EEeccCCCHHHHHhhcc
Q 047023 30 IEKQVDFNPDFLKNIFP 46 (82)
Q Consensus 30 ~~~e~efN~eFi~~mlp 46 (82)
...|.|++||||+.|..
T Consensus 42 ~~lEpElkPEfVeki~~ 58 (80)
T PF10884_consen 42 KILEPELKPEFVEKIKK 58 (80)
T ss_pred HhcccccCHHHHHHHHH
Confidence 45677999999999864
No 9
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=49.49 E-value=5.4 Score=32.76 Aligned_cols=11 Identities=55% Similarity=0.682 Sum_probs=9.4
Q ss_pred Ccccchhhhhh
Q 047023 1 MRLLTHNMLSS 11 (82)
Q Consensus 1 MrLlThN~L~c 11 (82)
|++||||+|=-
T Consensus 232 ~~~lTHNLLyD 242 (514)
T PF11336_consen 232 MLTLTHNLLYD 242 (514)
T ss_pred cceeeeceeee
Confidence 89999999854
No 10
>PF11881 DUF3401: Domain of unknown function (DUF3401); InterPro: IPR021818 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 231 to 250 amino acids in length. This domain is found associated with PF02145 from PFAM, PF00595 from PFAM.
Probab=47.58 E-value=12 Score=28.12 Aligned_cols=15 Identities=27% Similarity=0.764 Sum_probs=13.6
Q ss_pred cccHHHHHHHHHhcC
Q 047023 47 KIEWQALVQASRSMG 61 (82)
Q Consensus 47 kldW~aL~~aA~~lg 61 (82)
-|||.-||.||++..
T Consensus 165 gLdWShLVdAAkAfE 179 (239)
T PF11881_consen 165 GLDWSHLVDAAKAFE 179 (239)
T ss_pred cccHHHHHHHHHHhh
Confidence 599999999999865
No 11
>PF15200 KRTDAP: Keratinocyte differentiation-associated
Probab=42.06 E-value=16 Score=22.98 Aligned_cols=18 Identities=22% Similarity=0.556 Sum_probs=15.5
Q ss_pred HHHHHhhcccccHHHHHH
Q 047023 38 PDFLKNIFPKIEWQALVQ 55 (82)
Q Consensus 38 ~eFi~~mlpkldW~aL~~ 55 (82)
-|.|++-||=|+|+|+=+
T Consensus 48 fe~iK~kLPFlNWdafPK 65 (77)
T PF15200_consen 48 FEAIKRKLPFLNWDAFPK 65 (77)
T ss_pred HHHHHHhCcccchhhhhh
Confidence 367899999999999875
No 12
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=41.35 E-value=52 Score=20.19 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=23.3
Q ss_pred cCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 34 VDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 34 ~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
.+++.+.+++-++ ..++..+.++|+.+|+
T Consensus 26 ~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~gl 58 (126)
T cd02425 26 YKVSLNELREKYELGRDGLSLSYLKQLLEEYGF 58 (126)
T ss_pred CCCCHHHHHHhccCCCCCcCHHHHHHHHHHCCC
Confidence 4567777777664 6889999999999996
No 13
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=39.27 E-value=32 Score=24.00 Aligned_cols=24 Identities=21% Similarity=0.628 Sum_probs=19.5
Q ss_pred HHHhhcccccHHHHHHHHHhcCCC
Q 047023 40 FLKNIFPKIEWQALVQASRSMGYA 63 (82)
Q Consensus 40 Fi~~mlpkldW~aL~~aA~~lg~~ 63 (82)
++++.-+.+||+.+.+.|+.+|+.
T Consensus 211 l~~~~~~~~dw~~l~~~~~~~~~~ 234 (249)
T PF14907_consen 211 LLRKYGSQIDWEYLLERAKRLGLR 234 (249)
T ss_pred HHHhcCCcccHHHHHHHHHHcCCH
Confidence 555555789999999999999964
No 14
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=37.38 E-value=61 Score=20.14 Aligned_cols=30 Identities=17% Similarity=0.337 Sum_probs=24.4
Q ss_pred ccCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 33 QVDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 33 e~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
...++++.+++.++ ..++..+..+|+.+|+
T Consensus 25 g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl 58 (136)
T cd02418 25 GKNYSLAKLRELAGTDREGTSLLGLVKAAEKLGF 58 (136)
T ss_pred CCCCCHHHHHHHcCCCCCCcCHHHHHHHHHHCCC
Confidence 34677788887764 6899999999999996
No 15
>PF10381 Autophagy_Cterm: Autophagocytosis associated protein C-terminal; InterPro: IPR019461 Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex []. It carries a highly characteristic conserved FLKF sequence motif. ; PDB: 2DYT_A.
Probab=36.22 E-value=16 Score=18.52 Aligned_cols=13 Identities=31% Similarity=0.915 Sum_probs=9.2
Q ss_pred HHHHhhcccccHH
Q 047023 39 DFLKNIFPKIEWQ 51 (82)
Q Consensus 39 eFi~~mlpkldW~ 51 (82)
-|+..++|.|+|+
T Consensus 10 KFi~sViPtIeyD 22 (25)
T PF10381_consen 10 KFISSVIPTIEYD 22 (25)
T ss_dssp HHHHHHSTTB--T
T ss_pred HHHhhcCCceeee
Confidence 3889999999885
No 16
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=34.42 E-value=71 Score=19.66 Aligned_cols=30 Identities=17% Similarity=0.145 Sum_probs=24.6
Q ss_pred ccCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 33 QVDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 33 e~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
...++++.+++.++ ..+-..|.++|+.+|+
T Consensus 20 g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl 53 (124)
T cd02421 20 GKPASRDSLVAGLPLDDGRLSPALFPRAAARAGL 53 (124)
T ss_pred CCCCCHHHHHhcCCCCCCCcCHHHHHHHHHHCCC
Confidence 35678888888864 6888999999999995
No 17
>PHA02503 putative transcription regulator; Provisional
Probab=33.18 E-value=22 Score=20.99 Aligned_cols=27 Identities=30% Similarity=0.736 Sum_probs=20.9
Q ss_pred cCCCHHHHHh-hcccc-cHHHHHHHHHhc
Q 047023 34 VDFNPDFLKN-IFPKI-EWQALVQASRSM 60 (82)
Q Consensus 34 ~efN~eFi~~-mlpkl-dW~aL~~aA~~l 60 (82)
.+|..+||++ +||.+ +|+--++||-+|
T Consensus 27 ~~~s~~fl~~slipql~ewsnaykaavel 55 (57)
T PHA02503 27 SVYSKDFLQNSLIPQLYEWSNAYKAAVEL 55 (57)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence 4788899986 56654 899999998654
No 18
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=31.51 E-value=45 Score=19.47 Aligned_cols=16 Identities=31% Similarity=0.873 Sum_probs=12.2
Q ss_pred cHHHHHHHHHhcCCCC
Q 047023 49 EWQALVQASRSMGYAE 64 (82)
Q Consensus 49 dW~aL~~aA~~lg~~~ 64 (82)
||.++..+-++.|+.+
T Consensus 1 dw~~i~~~L~~~GYdG 16 (55)
T PF07582_consen 1 DWKRIFSALREIGYDG 16 (55)
T ss_dssp -HHHHHHHHHHTT--S
T ss_pred CHHHHHHHHHHcCCCc
Confidence 7999999999999865
No 19
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=31.05 E-value=88 Score=19.21 Aligned_cols=29 Identities=7% Similarity=0.194 Sum_probs=22.8
Q ss_pred cCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 34 VDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 34 ~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
..++++.+++-++ +.++..+.++|+.+|+
T Consensus 27 ~~~~~~~l~~~~~~~~~~~s~~~l~~~a~~~Gl 59 (129)
T cd02423 27 INITEQEVLKLMLIRSEGFSMLDLKRYAEALGL 59 (129)
T ss_pred CCCCHHHHHHHhCcccCCcCHHHHHHHHHHCCC
Confidence 4567777777653 7899999999999995
No 20
>PHA00212 putative transcription regulator
Probab=30.12 E-value=28 Score=20.92 Aligned_cols=28 Identities=29% Similarity=0.719 Sum_probs=21.6
Q ss_pred cCCCHHHHHh-hccc-ccHHHHHHHHHhcC
Q 047023 34 VDFNPDFLKN-IFPK-IEWQALVQASRSMG 61 (82)
Q Consensus 34 ~efN~eFi~~-mlpk-ldW~aL~~aA~~lg 61 (82)
.+|..+||++ +||. .+|+--++||-+|-
T Consensus 30 ~~~s~~f~~~~l~pql~ewsnaykaavelt 59 (63)
T PHA00212 30 KDFSVQFIKDSLLPQLFEWSNAYKAAVELT 59 (63)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHh
Confidence 4678888886 5565 49999999997764
No 21
>PF06935 DUF1284: Protein of unknown function (DUF1284); InterPro: IPR009702 This family consists of several hypothetical bacterial and archaeal proteins of around 130 residues in length. The function of this family is unknown, although it is thought that they may be iron-sulphur binding proteins.
Probab=29.49 E-value=30 Score=22.17 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=8.1
Q ss_pred CCHHHHHhhc
Q 047023 36 FNPDFLKNIF 45 (82)
Q Consensus 36 fN~eFi~~ml 45 (82)
|+++|++||=
T Consensus 2 YS~~Fv~Nm~ 11 (103)
T PF06935_consen 2 YSPEFVENMK 11 (103)
T ss_pred CCHHHHHHHH
Confidence 7889998873
No 22
>PF13935 Ead_Ea22: Ead/Ea22-like protein
Probab=28.91 E-value=41 Score=22.57 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.8
Q ss_pred ccccHHHHHHHHHhc
Q 047023 46 PKIEWQALVQASRSM 60 (82)
Q Consensus 46 pkldW~aL~~aA~~l 60 (82)
++|||.||+++|+.-
T Consensus 1 S~Id~QaLREaAEkA 15 (139)
T PF13935_consen 1 SNIDYQALREAAEKA 15 (139)
T ss_pred CcccHHHHHHHHHHh
Confidence 479999999999874
No 23
>PF04516 CP2: CP2 transcription factor; InterPro: IPR007604 This entry represents a conserved region in the CP2 transcription factor family.
Probab=28.39 E-value=46 Score=24.84 Aligned_cols=26 Identities=35% Similarity=0.576 Sum_probs=19.0
Q ss_pred hhhh---hcccccccCCCceeeeeeEEEec
Q 047023 7 NMLS---SNIKGVANGFPLLIEVEKVIEKQ 33 (82)
Q Consensus 7 N~L~---c~~k~c~~gfPL~i~~~~~~~~e 33 (82)
|+|+ ++.||++ |-||+|.+....+.+
T Consensus 166 ncLSTdFS~~KGvK-GvP~RlqidT~~~~~ 194 (236)
T PF04516_consen 166 NCLSTDFSPSKGVK-GVPFRLQIDTYMISS 194 (236)
T ss_pred EeccccccccCCcC-CCCeEEEEeeeecCC
Confidence 5555 4578996 999999986655544
No 24
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=28.19 E-value=1.1e+02 Score=18.71 Aligned_cols=30 Identities=23% Similarity=0.445 Sum_probs=24.6
Q ss_pred ccCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 33 QVDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 33 e~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
...++.+.+++.++ +.+-..+..+|+.+|+
T Consensus 20 g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl 53 (121)
T cd02417 20 GIAADPEQLRHEFGLAGEPFNSTELLLAAKSLGL 53 (121)
T ss_pred CCCCCHHHHHHHhcCCCCCCCHHHHHHHHHHcCC
Confidence 45677888888875 7889999999999995
No 25
>PF14030 DUF4245: Protein of unknown function (DUF4245)
Probab=27.56 E-value=79 Score=21.97 Aligned_cols=29 Identities=21% Similarity=0.458 Sum_probs=18.9
Q ss_pred cccccHHHHHHHHHh-cCCCC-CCCCCCCCCCC
Q 047023 45 FPKIEWQALVQASRS-MGYAE-LPEESPESSML 75 (82)
Q Consensus 45 lpkldW~aL~~aA~~-lg~~~-LP~~~p~~~~~ 75 (82)
.|.+||.+.+++|+. +|++- .|+ +| +++.
T Consensus 38 v~~VD~~~~l~~aar~a~~pv~~P~-lP-~gW~ 68 (169)
T PF14030_consen 38 VPEVDYSAALQTAARAAPFPVRAPE-LP-EGWK 68 (169)
T ss_pred CcccchhHHHHHHHHhCCCCeeCCC-CC-CCce
Confidence 578899887666555 88754 455 66 5543
No 26
>PF07572 BCNT: Bucentaur or craniofacial development; InterPro: IPR011421 Vertebrate BCNT (named after Bucentaur) or human craniofacial development protein 1 (CFDP1) are characterised by an N-terminal acidic region, a central and single IR element (inverted repeat) from the retrotransposable element-1 family (RTE-1) and a highly conserved 82-amino acid region at the C terminus. This entry represents the BCNT C-terminal domain that is also found in Drosophila YETI, a protein that binds to a microtubule-based motor kinesin-1, and the yeast SWR1-complex protein 5 (SWC5), a component of the SWR1 chromatin remodeling complex [, ]. In the bovine genome recombination of BCNT through the IR element with a member of the retrotransposable element-1 family, leads to gene duplications, the insertion of the RTE-1 apurinic/apyrimidinic endonuclease (APE)-like domain (see IPR005135 from INTERPRO) with the concomitant loss of the conserved C-terminal domain of BCNT and with the additional recruitment of either 2 (p97bcnt) or 3 (p97bcnt-2) C-terminal IR-elements [].
Probab=26.60 E-value=6.1 Score=24.99 Aligned_cols=32 Identities=25% Similarity=0.660 Sum_probs=20.2
Q ss_pred ccccHHHHHHHHHhcCCCC-CCCCC--CCCCCCCCchhh
Q 047023 46 PKIEWQALVQASRSMGYAE-LPEES--PESSMLDSDDFL 81 (82)
Q Consensus 46 pkldW~aL~~aA~~lg~~~-LP~~~--p~~~~~~deefL 81 (82)
.++||..++..- |+.+ |-... - ++|.+..+||
T Consensus 28 S~lDW~~fk~~e---gi~deL~~~~k~k-~gYLekq~FL 62 (81)
T PF07572_consen 28 SKLDWASFKDKE---GIEDELEKHNKGK-DGYLEKQDFL 62 (81)
T ss_pred HHHhHHHHHHhc---chHHHHHHHhhcc-hhhhHHHHHH
Confidence 478999999864 5433 44333 2 5666667776
No 27
>PF06544 DUF1115: Protein of unknown function (DUF1115); InterPro: IPR010541 This entry represents the C terminus of several eukaryotic RWD domain-containing proteins of unknown function.
Probab=25.44 E-value=33 Score=22.53 Aligned_cols=13 Identities=23% Similarity=0.795 Sum_probs=11.8
Q ss_pred HHHHHhhcccccH
Q 047023 38 PDFLKNIFPKIEW 50 (82)
Q Consensus 38 ~eFi~~mlpkldW 50 (82)
.+|.+.|+.||+|
T Consensus 50 ~~y~~lmlrri~W 62 (128)
T PF06544_consen 50 KEYKKLMLRRIKW 62 (128)
T ss_pred HHHHHHHhceecc
Confidence 4799999999999
No 28
>PF09116 gp45-slide_C: gp45 sliding clamp, C terminal; InterPro: IPR015200 This domain is essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. It adopts a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry []. ; PDB: 1B8H_A 1B77_B 3U61_F 3U60_G 3U5Z_R 1CZD_B.
Probab=24.47 E-value=39 Score=22.56 Aligned_cols=20 Identities=35% Similarity=0.586 Sum_probs=14.1
Q ss_pred ccccHHHHHHHHHhcCCCCC
Q 047023 46 PKIEWQALVQASRSMGYAEL 65 (82)
Q Consensus 46 pkldW~aL~~aA~~lg~~~L 65 (82)
.-=||..|..||+.+|+++|
T Consensus 7 ~~edl~ql~kas~~l~l~dl 26 (112)
T PF09116_consen 7 KAEDLQQLMKASRTLGLPDL 26 (112)
T ss_dssp -HHHHHHHHHHHHHCT--EE
T ss_pred cHHHHHHHHHHHHhcCCCeE
Confidence 33478999999999997654
No 29
>PF02016 Peptidase_S66: LD-carboxypeptidase; InterPro: IPR003507 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature is found in the Escherichia coli microcin C7 self-immunity protein mccF and in muramoyltetrapeptide carboxypeptidase (3.4.17.13 from EC, LD-carboxypeptidase A). LD-carboxypeptidase A belongs to MEROPS peptidase family S66 (clan SS). The entry also contains uncharacterised proteins including hypothetical proteins from various bacteria archaea.; PDB: 1ZRS_A 1ZL0_B 2AUM_B 2AUN_B 3TLG_A 3TLC_A 3TLZ_B 3TLY_B 3TLE_A 3TLB_B ....
Probab=24.20 E-value=48 Score=24.65 Aligned_cols=17 Identities=12% Similarity=0.577 Sum_probs=13.5
Q ss_pred HhhcccccHHHHHHHHH
Q 047023 42 KNIFPKIEWQALVQASR 58 (82)
Q Consensus 42 ~~mlpkldW~aL~~aA~ 58 (82)
.++||.|||+++.+.-+
T Consensus 76 ~rlL~~ld~~~i~~~pK 92 (284)
T PF02016_consen 76 NRLLPYLDYDAIRKNPK 92 (284)
T ss_dssp GGGGGGCHHHHHHHSG-
T ss_pred HHHHhcccccccccCCC
Confidence 58999999999987543
No 30
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=24.05 E-value=1.4e+02 Score=18.29 Aligned_cols=30 Identities=17% Similarity=0.056 Sum_probs=23.1
Q ss_pred ccCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 33 QVDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 33 e~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
-..++++.+++.++ ..+-..|.++|+.+|+
T Consensus 25 g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl 58 (125)
T cd02420 25 GRYVPLSELRIACGVSRDGSNASNLLKAAREYGL 58 (125)
T ss_pred CCCCCHHHHHHHcCCCCCCCCHHHHHHHHHHcCc
Confidence 34667788887764 4778889999999995
No 31
>COG1176 PotB ABC-type spermidine/putrescine transport system, permease component I [Amino acid transport and metabolism]
Probab=22.80 E-value=54 Score=24.92 Aligned_cols=20 Identities=30% Similarity=0.448 Sum_probs=16.4
Q ss_pred HhhcccccHHHHHHHHHhcCC
Q 047023 42 KNIFPKIEWQALVQASRSMGY 62 (82)
Q Consensus 42 ~~mlpkldW~aL~~aA~~lg~ 62 (82)
-.-+.|+|.+ |++||++||-
T Consensus 173 y~al~~id~~-L~eAA~dLGA 192 (287)
T COG1176 173 YAALEKIDPS-LLEAARDLGA 192 (287)
T ss_pred HHHHHhCCHH-HHHHHHHcCC
Confidence 3456799988 9999999994
No 32
>KOG3131 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.75 E-value=26 Score=26.93 Aligned_cols=23 Identities=30% Similarity=0.343 Sum_probs=17.5
Q ss_pred cchhhhhh--------cccccccCCCceeee
Q 047023 4 LTHNMLSS--------NIKGVANGFPLLIEV 26 (82)
Q Consensus 4 lThN~L~c--------~~k~c~~gfPL~i~~ 26 (82)
|+||.|++ +++-|.|+||+-...
T Consensus 168 LyeNiL~snw~~Drl~k~~LcgNsfqml~~~ 198 (281)
T KOG3131|consen 168 LYENILWSNWKRDRLPKVFLCGNSFQMLTMT 198 (281)
T ss_pred HHHHHHHHhhhhccccceEEecCcHHHHHhh
Confidence 68999999 466788888876543
No 33
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=22.38 E-value=31 Score=25.09 Aligned_cols=13 Identities=15% Similarity=0.284 Sum_probs=11.2
Q ss_pred chhhhhhcccccc
Q 047023 5 THNMLSSNIKGVA 17 (82)
Q Consensus 5 ThN~L~c~~k~c~ 17 (82)
+||+..|...+|-
T Consensus 84 vHN~vVCTLCSCy 96 (185)
T TIGR01323 84 VHNVVVCTLCSCY 96 (185)
T ss_pred ceeEEEecccccc
Confidence 6999999997774
No 34
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=22.29 E-value=36 Score=20.52 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=10.0
Q ss_pred HHHHHHHHhcCCCCCCCC
Q 047023 51 QALVQASRSMGYAELPEE 68 (82)
Q Consensus 51 ~aL~~aA~~lg~~~LP~~ 68 (82)
+.+...|.++|++.||++
T Consensus 7 esvk~iAes~Gi~~l~de 24 (66)
T PF02969_consen 7 ESVKDIAESLGISNLSDE 24 (66)
T ss_dssp HHHHHHHHHTT---B-HH
T ss_pred HHHHHHHHHcCCCCCCHH
Confidence 345667899999878764
No 35
>PF15217 TSC21: TSC21 family
Probab=22.14 E-value=66 Score=23.01 Aligned_cols=32 Identities=22% Similarity=0.555 Sum_probs=22.0
Q ss_pred cccc--HHHHH---HHHHhcCCCC-CCCCCCCCCCCCCc
Q 047023 46 PKIE--WQALV---QASRSMGYAE-LPEESPESSMLDSD 78 (82)
Q Consensus 46 pkld--W~aL~---~aA~~lg~~~-LP~~~p~~~~~~de 78 (82)
|||+ |+|+. -+|+.||+++ .|++-. ..-.+||
T Consensus 62 PkL~dGYpAFkrphmTA~DLG~PGFFPpqd~-~~t~ede 99 (180)
T PF15217_consen 62 PKLEDGYPAFKRPHMTARDLGLPGFFPPQDR-VATAEDE 99 (180)
T ss_pred cccccCchhhccccccHhhcCCCCcCCCCCC-ccccccc
Confidence 4554 66664 5899999998 788765 5444554
No 36
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=21.01 E-value=80 Score=17.06 Aligned_cols=19 Identities=11% Similarity=0.286 Sum_probs=13.6
Q ss_pred ccccHHHHHHHHHhcCCCC
Q 047023 46 PKIEWQALVQASRSMGYAE 64 (82)
Q Consensus 46 pkldW~aL~~aA~~lg~~~ 64 (82)
.++...-|++-|+++|++.
T Consensus 3 ~~~~~~eL~~iAk~lgI~~ 21 (43)
T PF07498_consen 3 KSMTLSELREIAKELGIEG 21 (43)
T ss_dssp HCS-HHHHHHHHHCTT-TT
T ss_pred ccCCHHHHHHHHHHcCCCC
Confidence 4556778999999999863
No 37
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=21.00 E-value=1.8e+02 Score=17.75 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=23.8
Q ss_pred ccCCCHHHHHhhcc----cccHHHHHHHHHhcCC
Q 047023 33 QVDFNPDFLKNIFP----KIEWQALVQASRSMGY 62 (82)
Q Consensus 33 e~efN~eFi~~mlp----kldW~aL~~aA~~lg~ 62 (82)
...++++.+++.++ ..+-..+.++|+.+|+
T Consensus 25 g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl 58 (127)
T cd02419 25 GHHVDLASLRQRFPVSLKGATLADLIDIAQQLGL 58 (127)
T ss_pred CCCCCHHHHHHHcCCCCCCcCHHHHHHHHHHCCC
Confidence 45677788887764 6888899999999995
No 38
>COG3544 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.99 E-value=42 Score=24.50 Aligned_cols=14 Identities=29% Similarity=0.683 Sum_probs=12.7
Q ss_pred cCCCHHHHHhhccc
Q 047023 34 VDFNPDFLKNIFPK 47 (82)
Q Consensus 34 ~efN~eFi~~mlpk 47 (82)
.+|+.+||+.|||-
T Consensus 129 ~naDr~Flr~MIpH 142 (190)
T COG3544 129 GNADRDFLRQMIPH 142 (190)
T ss_pred cchHHHHHHHhhhh
Confidence 68999999999995
No 39
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.27 E-value=36 Score=30.49 Aligned_cols=19 Identities=21% Similarity=0.466 Sum_probs=15.8
Q ss_pred HHHhhcccccHHHHHHHHH
Q 047023 40 FLKNIFPKIEWQALVQASR 58 (82)
Q Consensus 40 Fi~~mlpkldW~aL~~aA~ 58 (82)
-..+|||||||.++.+.-.
T Consensus 289 v~lKlIPRIDyq~~~~~~~ 307 (1024)
T KOG1999|consen 289 VRLKLIPRIDYQKLLGKLE 307 (1024)
T ss_pred EEEEEeccccHHhhhcccc
Confidence 4568999999999998754
Done!