Query 017005
Match_columns 379
No_of_seqs 25 out of 27
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 04:46:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017005hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2815 Mitochondrial/cholorop 99.9 1.1E-24 2.5E-29 205.9 4.0 167 206-376 23-195 (256)
2 TIGR00952 S15_bact ribosomal p 97.4 3E-05 6.6E-10 63.9 -0.1 30 347-376 2-31 (86)
3 PTZ00119 40S ribosomal protein 97.4 8.3E-05 1.8E-09 72.9 2.0 54 323-376 83-136 (302)
4 PRK05626 rpsO 30S ribosomal pr 97.3 6E-05 1.3E-09 62.5 0.0 30 347-376 5-34 (89)
5 cd00353 Ribosomal_S15p_S13e Ri 97.1 8.9E-05 1.9E-09 59.6 -0.4 26 350-375 2-27 (80)
6 PF00312 Ribosomal_S15: Riboso 96.3 0.00083 1.8E-08 54.3 -0.5 26 351-376 4-29 (83)
7 COG0184 RpsO Ribosomal protein 94.4 0.01 2.2E-07 49.6 -0.3 25 351-375 9-33 (89)
8 CHL00027 rps15 ribosomal prote 94.3 0.007 1.5E-07 50.8 -1.4 17 360-376 15-31 (90)
9 KOG1161 Protein involved in va 83.4 5.4 0.00012 40.3 8.2 115 212-341 3-158 (310)
10 PF04288 MukE: MukE-like famil 47.8 20 0.00044 35.1 3.5 37 226-271 82-120 (235)
11 PF03241 HpaB: 4-hydroxyphenyl 44.5 12 0.00027 34.7 1.5 40 309-348 105-152 (205)
12 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 41.9 18 0.00038 35.6 2.1 60 320-379 103-189 (251)
13 PF08945 Bclx_interact: Bcl-x 37.7 26 0.00057 26.1 2.0 24 336-359 10-33 (40)
14 PTZ00246 proteasome subunit al 33.9 88 0.0019 29.3 5.3 43 329-375 173-216 (253)
15 cd03763 proteasome_beta_type_7 31.9 95 0.0021 27.6 5.0 43 329-375 136-179 (189)
16 PF11629 Mst1_SARAH: C termina 31.2 18 0.00039 28.0 0.3 14 258-271 9-22 (49)
17 PF06698 DUF1192: Protein of u 28.7 47 0.001 26.3 2.2 18 254-271 18-35 (59)
18 PRK09726 antitoxin HipB; Provi 28.6 31 0.00068 27.5 1.2 30 234-266 6-35 (88)
19 cd04168 TetM_like Tet(M)-like 28.0 63 0.0014 30.2 3.3 44 327-371 178-221 (237)
20 cd03762 proteasome_beta_type_6 24.6 1.5E+02 0.0033 26.1 4.9 43 329-375 137-180 (188)
21 PF07540 NOC3p: Nucleolar comp 24.5 1.9E+02 0.0041 24.5 5.2 79 259-355 1-83 (95)
22 cd01886 EF-G Elongation factor 23.5 75 0.0016 30.4 3.0 44 327-371 211-254 (270)
23 cd03750 proteasome_alpha_type_ 23.4 1.8E+02 0.0039 26.8 5.3 43 329-375 167-209 (227)
24 TIGR03691 20S_bact_alpha prote 23.3 1.9E+02 0.004 27.3 5.5 47 328-375 162-208 (228)
25 TIGR03634 arc_protsome_B prote 22.8 1.9E+02 0.004 25.4 5.1 43 329-375 138-181 (185)
26 cd03759 proteasome_beta_type_3 22.7 1.7E+02 0.0037 26.2 5.0 43 329-375 142-185 (195)
27 KOG4289 Cadherin EGF LAG seven 22.2 63 0.0014 39.6 2.5 24 252-275 1149-1172(2531)
28 TIGR02309 HpaB-1 4-hydroxyphen 21.8 79 0.0017 33.1 3.0 39 310-348 379-423 (477)
29 PF13404 HTH_AsnC-type: AsnC-t 21.4 1.3E+02 0.0028 21.7 3.1 25 236-270 18-42 (42)
30 PRK05256 condesin subunit E; P 21.4 43 0.00094 33.0 0.9 115 226-360 91-212 (238)
No 1
>KOG2815 consensus Mitochondrial/choloroplast ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=1.1e-24 Score=205.87 Aligned_cols=167 Identities=29% Similarity=0.271 Sum_probs=141.8
Q ss_pred CCcccchhhhhhhHHHHHhhhhhhhHHHhhcChhHHHHHhhhcCCCCC--CCcccHHHHHHHHHHHHHhhhcccCcCCCC
Q 017005 206 ELPALVFGKEKKEEEKAVELERMKTDFVKMYSFEELGDKLKKLRPEGL--EGGFSLRELNERLMRLRVMEMNESNSKIGA 283 (379)
Q Consensus 206 ~lP~svFgkEl~~~~~~~~~e~~~~ef~k~Ys~eELGkKL~~LRP~g~--k~WFSL~ELn~RL~KLremE~~e~~s~~~g 283 (379)
.||..+++++.....+.+ +++...|++.|..+||+++++.++|.+. ++|||+.+|+.++.||+.+++.+ .+..-
T Consensus 23 ~lp~~~~~~~~~~~~~~e--~e~~~~~Lk~~~~~~lr~k~r~~~~~~~~~es~ksl~~l~~~~~k~~~~~~~e--l~ke~ 98 (256)
T KOG2815|consen 23 LLPKKGGAKEPDNSKGSE--SEKRSLFLKAYRGEELRKKYRDLKPLDKAPESVKSLFQLNPAIEKLDTVEKAE--LSKEV 98 (256)
T ss_pred hccccccccccccccccc--hHHHHHhcccccHHHHhhhhhhccccccCchhhHHHHHhhhhhHHHHHHHHHH--HHHHH
Confidence 688888888887777766 6789999999999999999999999998 99999999999999999998754 33333
Q ss_pred cChHHHHHHHHHHHHHHHhhh---hhhhhhhhhhcCCCCCcccCCChhHHHhhhcCCCCCCHHHHHHHHHHHHHHH-hcc
Q 017005 284 GTISALRSSLARIQIEKEEKA---RVQRINILEGFGGTPEYLLHPPKEHLVEKYFHPDNMSSAEKMKIELAKVREE-FKM 359 (379)
Q Consensus 284 ~~~~~LR~sl~~lk~~~~~k~---s~Q~~~~l~~lggtP~ym~~PPk~~Lve~Yfhpd~mss~Ek~K~el~kVR~e-Fkm 359 (379)
..+..+.++++---++.-.-. +.|..++++.++|++.|++.+|+.|++.||||++|||+.|+||+.|..||.| |++
T Consensus 99 ~~~~~~~~~~e~k~~k~t~a~~~d~~~~~~~~~e~~~~~r~~l~~~kr~~~lril~~~n~ss~e~~k~~lk~~~~e~~~~ 178 (256)
T KOG2815|consen 99 KNHKQDNNSLEEKFAKKTAAIRRDTFELEAIIIELSGKIRIKLLIDKREKILRILRRRNLSSFEKIKIKLKLVRKEPFQR 178 (256)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccHHHHhcchhhhhchhhHhhcccHHHHHHHHhhhhccccHHHHHHHHHHhccCCccc
Confidence 344555555543222221111 7789999999999999999999999999999999999999999999999999 999
Q ss_pred CcCccCccceeeeeeec
Q 017005 360 SESDCGSARVQSKGFFI 376 (379)
Q Consensus 360 se~DcGsarVQia~l~~ 376 (379)
.|.||||++||+|..|+
T Consensus 179 ~e~dtgs~~vQ~~~~t~ 195 (256)
T KOG2815|consen 179 FESDTGSAEVQAAFPTV 195 (256)
T ss_pred ccccccchhHhHHhHHH
Confidence 99999999999999884
No 2
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=97.43 E-value=3e-05 Score=63.89 Aligned_cols=30 Identities=30% Similarity=0.339 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhccCcCccCccceeeeeeec
Q 017005 347 KIELAKVREEFKMSESDCGSARVQSKGFFI 376 (379)
Q Consensus 347 K~el~kVR~eFkmse~DcGsarVQia~l~~ 376 (379)
+.+-+++-++|+.++.||||+.||||.||.
T Consensus 2 ~~~k~~li~~~~~~~~DtGS~eVQiA~LT~ 31 (86)
T TIGR00952 2 KERKQEIIKEFQLHEKDTGSPEVQIALLTE 31 (86)
T ss_pred HHHHHHHHHHHcCCCCCCCCHHHHHHHHHH
Confidence 456788999999999999999999999883
No 3
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=97.37 E-value=8.3e-05 Score=72.95 Aligned_cols=54 Identities=19% Similarity=0.060 Sum_probs=49.2
Q ss_pred cCCChhHHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCccceeeeeeec
Q 017005 323 LHPPKEHLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGSARVQSKGFFI 376 (379)
Q Consensus 323 ~~PPk~~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGsarVQia~l~~ 376 (379)
..-...+.|.+.++=+|=|..|++|..-+++.++|++++.|.||+.||||.||.
T Consensus 83 ~le~~~p~VkRILsLrNAs~kEi~K~rK~eIIkkfqr~~~DTGS~EVQIAiLTe 136 (302)
T PTZ00119 83 DIKHLRKNIINMLHLNCANSKQIHKYKKLCIRRCLQRRPFDTGSAPVQIGCLTE 136 (302)
T ss_pred chhhhCHHHHHHhccccCChHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHH
Confidence 344566789999999999999999999999999999999999999999999983
No 4
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=97.28 E-value=6e-05 Score=62.49 Aligned_cols=30 Identities=30% Similarity=0.289 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhccCcCccCccceeeeeeec
Q 017005 347 KIELAKVREEFKMSESDCGSARVQSKGFFI 376 (379)
Q Consensus 347 K~el~kVR~eFkmse~DcGsarVQia~l~~ 376 (379)
+.+-+.+.++|+.++.||||+.||||.||.
T Consensus 5 ~~~k~~li~~f~~~~~DTGS~eVQiA~LT~ 34 (89)
T PRK05626 5 KEKKAEIIKEYGRHEGDTGSPEVQVALLTE 34 (89)
T ss_pred HHHHHHHHHHHcCCCCCCCCHHHHHHHHHH
Confidence 445678999999999999999999999873
No 5
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=97.14 E-value=8.9e-05 Score=59.58 Aligned_cols=26 Identities=31% Similarity=0.400 Sum_probs=24.4
Q ss_pred HHHHHHHhccCcCccCccceeeeeee
Q 017005 350 LAKVREEFKMSESDCGSARVQSKGFF 375 (379)
Q Consensus 350 l~kVR~eFkmse~DcGsarVQia~l~ 375 (379)
.++|.++|++++.||||+.||||.||
T Consensus 2 ~~~i~~~~~~~~~DtGs~evQia~LT 27 (80)
T cd00353 2 KQEILKEFGLAEGDTGSPEVQLALLT 27 (80)
T ss_pred HHHHHHHhCCCCCCCCChHHHHHHHH
Confidence 47899999999999999999999987
No 6
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 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 [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=96.30 E-value=0.00083 Score=54.27 Aligned_cols=26 Identities=27% Similarity=0.248 Sum_probs=23.9
Q ss_pred HHHHHHhccCcCccCccceeeeeeec
Q 017005 351 AKVREEFKMSESDCGSARVQSKGFFI 376 (379)
Q Consensus 351 ~kVR~eFkmse~DcGsarVQia~l~~ 376 (379)
+++.++|..+++||||+.||||.||.
T Consensus 4 ~~~i~~~~~~~~dtgs~evqia~LT~ 29 (83)
T PF00312_consen 4 QKSIKKFQRHPNDTGSPEVQIAILTE 29 (83)
T ss_dssp HHHHHHHSSSTTSSSSHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHH
Confidence 67889999999999999999999874
No 7
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=94.38 E-value=0.01 Score=49.62 Aligned_cols=25 Identities=32% Similarity=0.484 Sum_probs=23.4
Q ss_pred HHHHHHhccCcCccCccceeeeeee
Q 017005 351 AKVREEFKMSESDCGSARVQSKGFF 375 (379)
Q Consensus 351 ~kVR~eFkmse~DcGsarVQia~l~ 375 (379)
+++|+||..++.|-||..||||-||
T Consensus 9 ~~l~~eyg~~~~dtgs~evq~a~Lt 33 (89)
T COG0184 9 QELRDEYGIPEVDTGSGEVQLALLT 33 (89)
T ss_pred HHHHHHhCCCCCCCCCcHHHHHHHH
Confidence 5789999999999999999999887
No 8
>CHL00027 rps15 ribosomal protein S15
Probab=94.29 E-value=0.007 Score=50.79 Aligned_cols=17 Identities=29% Similarity=0.278 Sum_probs=15.7
Q ss_pred CcCccCccceeeeeeec
Q 017005 360 SESDCGSARVQSKGFFI 376 (379)
Q Consensus 360 se~DcGsarVQia~l~~ 376 (379)
+|.||||++||||.||-
T Consensus 15 ~~~DTGS~evQiA~LT~ 31 (90)
T CHL00027 15 KEENRGSVEFQVFSFTN 31 (90)
T ss_pred CCCCCCChHHHHHHHHH
Confidence 79999999999999873
No 9
>KOG1161 consensus Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism]
Probab=83.44 E-value=5.4 Score=40.25 Aligned_cols=115 Identities=24% Similarity=0.251 Sum_probs=67.1
Q ss_pred hhhhhhhHHHHHhhhhhhhHHH-hhcChhHHHHHhhhcCCCCCCCcccH-------------------------HHHHHH
Q 017005 212 FGKEKKEEEKAVELERMKTDFV-KMYSFEELGDKLKKLRPEGLEGGFSL-------------------------RELNER 265 (379)
Q Consensus 212 FgkEl~~~~~~~~~e~~~~ef~-k~Ys~eELGkKL~~LRP~g~k~WFSL-------------------------~ELn~R 265 (379)
|||.|.++.=.+ .. +.-+|++|-|+|+.+-+..+.+|.-. +||.+|
T Consensus 3 FGk~L~~~~l~e--------w~~~yinYk~LKK~lK~~~~~~~~~~~~~~~e~dFv~~Ld~ELEKv~~F~lek~~el~~R 74 (310)
T KOG1161|consen 3 FGKYLKEELLPE--------WKDKYINYKELKKLLKQYSIQTADSSPDSRDESDFVRLLDAELEKVNGFQLEKESELIIR 74 (310)
T ss_pred hhHHHHHhhhhh--------HhhhhcCHHHHHHHHHHhccccccCCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 899998443222 22 23489999999999966666555522 356666
Q ss_pred HHHHHHhhhcccCcCCCCcChHHHHHHHHHHHHHHHhhhhhhhhhhhhhcC--C-----------CCCcccCCChhHHHh
Q 017005 266 LMRLRVMEMNESNSKIGAGTISALRSSLARIQIEKEEKARVQRINILEGFG--G-----------TPEYLLHPPKEHLVE 332 (379)
Q Consensus 266 L~KLremE~~e~~s~~~g~~~~~LR~sl~~lk~~~~~k~s~Q~~~~l~~lg--g-----------tP~ym~~PPk~~Lve 332 (379)
|..|++-=.......+.--.+..||..|..+..+ +..|.-+..|+ | || |.+.||-...|.
T Consensus 75 l~~L~e~~~~~~~~~~~~~~~~~lr~~l~~~~~e------m~~L~~fs~LN~tGf~KILKK~DKrtg-~~l~~~f~~~l~ 147 (310)
T KOG1161|consen 75 LKELEEKIDALSLEPPSAEEMKELREELVDFHGE------MVLLENFSRLNYTGFAKILKKHDKRTG-YRLRPYFQVRLL 147 (310)
T ss_pred HHHHHHHhhccccCCcchhHHHHHHHHHHHHHHH------HHHHHHHHHHhHHHHHHHHHHHhcccc-cccccHHHHHHH
Confidence 6666653221122233333588999999988755 23344333333 2 77 888888655443
Q ss_pred h--hcCCCCCC
Q 017005 333 K--YFHPDNMS 341 (379)
Q Consensus 333 ~--Yfhpd~ms 341 (379)
- ||+-|.++
T Consensus 148 ~~Pf~~~e~~~ 158 (310)
T KOG1161|consen 148 HQPFFTTEQLF 158 (310)
T ss_pred hCCCchhhhHH
Confidence 2 33444443
No 10
>PF04288 MukE: MukE-like family; InterPro: IPR007385 This family contains MukE, which are proteins involved in the segregation and condensation of prokaryotic chromosomes. MukE along with MukF (IPR005582 from INTERPRO) interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli []. The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC []. ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; GO: 0007059 chromosome segregation, 0030261 chromosome condensation, 0005737 cytoplasm; PDB: 3EUK_M 3EUH_D 3RPU_Z.
Probab=47.78 E-value=20 Score=35.13 Aligned_cols=37 Identities=41% Similarity=0.445 Sum_probs=26.8
Q ss_pred hhhhhHHHhhcChhHHHHHhhhcCCCCC--CCcccHHHHHHHHHHHHH
Q 017005 226 ERMKTDFVKMYSFEELGDKLKKLRPEGL--EGGFSLRELNERLMRLRV 271 (379)
Q Consensus 226 e~~~~ef~k~Ys~eELGkKL~~LRP~g~--k~WFSL~ELn~RL~KLre 271 (379)
-+|.+..+--|- -|-|+.. +|||+.+||-+||.-|.-
T Consensus 82 LdMlVGkvLc~L---------yLsperLa~~gift~qeL~eeLl~lad 120 (235)
T PF04288_consen 82 LDMLVGKVLCYL---------YLSPERLAHEGIFTQQELYEELLSLAD 120 (235)
T ss_dssp CCCHHHHCCCCC---------CCSTCCHHHTTEEECHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHH---------hcCHHHHhcCCceeHHHHHHHHHHhhC
Confidence 456655555443 4778866 999999999999986643
No 11
>PF03241 HpaB: 4-hydroxyphenylacetate 3-hydroxylase C terminal; InterPro: IPR024719 This C-terminal domain is found in HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This domain is also found in pyoverdin chromophore biosynthetic protein PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=44.49 E-value=12 Score=34.65 Aligned_cols=40 Identities=25% Similarity=0.562 Sum_probs=27.1
Q ss_pred hhhhhhcCC-----CCCcc--cCCChhHHHhhhcCCC-CCCHHHHHHH
Q 017005 309 INILEGFGG-----TPEYL--LHPPKEHLVEKYFHPD-NMSSAEKMKI 348 (379)
Q Consensus 309 ~~~l~~lgg-----tP~ym--~~PPk~~Lve~Yfhpd-~mss~Ek~K~ 348 (379)
+.++-.||| +|+.. ..|+--++|+||+.-- .++++||+|+
T Consensus 105 ~eil~~l~gg~li~~Ps~~Df~npe~~~~l~kYl~g~~~~~aeeR~rl 152 (205)
T PF03241_consen 105 VEILQDLGGGGLITLPSEADFDNPEIGPYLDKYLQGANGVSAEERVRL 152 (205)
T ss_dssp HHHHHHHHGGGGTC---HHHHH-TTTHHHHHHHT-BTTTC-HHHHHHH
T ss_pred HHHHHHHhCCCeeeCCCHHHhCCcchhHHHHHHhcccCCCCHHHHHHH
Confidence 445555554 67665 4599999999999988 9999999987
No 12
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=41.86 E-value=18 Score=35.61 Aligned_cols=60 Identities=20% Similarity=0.329 Sum_probs=39.7
Q ss_pred CcccCCChhHHHhhhcCCCCCCHHHHHHHHH-----HHHHHHhc------cCcCccCc----------------cceeee
Q 017005 320 EYLLHPPKEHLVEKYFHPDNMSSAEKMKIEL-----AKVREEFK------MSESDCGS----------------ARVQSK 372 (379)
Q Consensus 320 ~ym~~PPk~~Lve~Yfhpd~mss~Ek~K~el-----~kVR~eFk------mse~DcGs----------------arVQia 372 (379)
+.|...+-+..+|.+|.++-+.+-+..+.-+ +.+.++|. +.+.-|+. -.+..+
T Consensus 103 eale~a~Dps~le~~lS~~Q~~~L~~y~~~~~~~kq~~lQ~~~~ka~~~a~~~~~~~~RdVtp~~klRV~d~~~~~~~~~ 182 (251)
T cd04494 103 EALEAAADPSFLEAELSEEQLEALSNYQQLQNEKKQARLQEEFRKAVEEALKEEGLSKRDVTPVWKLRVTDYRSKPEKSG 182 (251)
T ss_pred HHHHcCCChHHHHhhCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCCcceeEEEEEEeecccCCCceE
Confidence 4566778889999999999988876554443 23333332 23444433 445789
Q ss_pred eeecccC
Q 017005 373 GFFIWCP 379 (379)
Q Consensus 373 ~l~~~~~ 379 (379)
.||||-|
T Consensus 183 ~LTIWrP 189 (251)
T cd04494 183 LLSIWRP 189 (251)
T ss_pred EEEEeCC
Confidence 9999976
No 13
>PF08945 Bclx_interact: Bcl-x interacting, BH3 domain; InterPro: IPR015040 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Members of this entry induce apoptosis. The isoform BimL is more potent than the isoform BimEL. They form heterodimers with a number of antiapoptotic Bcl-2 proteins including Mcl-1, Bcl-2, Bcl-X(L), BFL-1, and BHRF1, but do not heterodimerise with proapoptotic proteins such as BAD, BOK, BAX or BAK. They are peripheral membrane proteins, associated with intracytoplasmic membranes. The BH3 motif is required for Bcl-2 binding and cytotoxicity. After antigen-driven expansion, the majority of T cells involved in an immune response die rapidly by apoptosis dependent on the Bcl-2 related proteins; Bim and Bax or Bak []. Bcl-xL regulates Bax and Bim is an important regulator of bcl-x deficiency induced cell death during hematopoiesis and testicular development in mice []. Bim(L) displaces Bcl-x(L) in the mitochondria and promotes Bax translocation during TNFalpha-induced apoptosis []. A potent inhibitor of antiapoptotic Bcl-2 family members, including Bcl-X(L), is AT-101 []. The immunophilin protein FKBP8 and its splice variant are Bcl-XL-interacting proteins and regulate the apoptotic signalling pathways in the RPE []. This protein is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11 []. ; PDB: 2NL9_B 2V6Q_B 3KJ0_B 3KJ1_B 3FDL_B 3D7V_B 3IO8_D 2K7W_B 2VM6_B 3IO9_B ....
Probab=37.70 E-value=26 Score=26.14 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=17.8
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcc
Q 017005 336 HPDNMSSAEKMKIELAKVREEFKM 359 (379)
Q Consensus 336 hpd~mss~Ek~K~el~kVR~eFkm 359 (379)
.|.+|+.+.-.-.||.++-|||.-
T Consensus 10 ~P~~~~PE~wiAqELRRIgDEFna 33 (40)
T PF08945_consen 10 EPVDMRPEIWIAQELRRIGDEFNA 33 (40)
T ss_dssp -----HHHHHHHHHHHHHHHHHHH
T ss_pred CCccCCHHHHHHHHHHHHHHHhcc
Confidence 477899999999999999999964
No 14
>PTZ00246 proteasome subunit alpha; Provisional
Probab=33.87 E-value=88 Score=29.35 Aligned_cols=43 Identities=2% Similarity=0.166 Sum_probs=34.3
Q ss_pred HHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCc-cceeeeeee
Q 017005 329 HLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGS-ARVQSKGFF 375 (379)
Q Consensus 329 ~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGs-arVQia~l~ 375 (379)
.+||++|.| +|+-+|-.++=+.-++..+ +.||.+ ..|+|+-++
T Consensus 173 ~~Le~~~~~-~ms~eeai~l~~~al~~~~---~~d~~s~~~vev~ii~ 216 (253)
T PTZ00246 173 SILKQEWKE-DLTLEQGLLLAAKVLTKSM---DSTSPKADKIEVGILS 216 (253)
T ss_pred HHHHHhccC-CCCHHHHHHHHHHHHHHHH---hccCCCCCcEEEEEEe
Confidence 477899987 6999999988888888765 678874 678888775
No 15
>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=31.86 E-value=95 Score=27.56 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=30.9
Q ss_pred HHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCcc-Cccceeeeeee
Q 017005 329 HLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDC-GSARVQSKGFF 375 (379)
Q Consensus 329 ~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~Dc-GsarVQia~l~ 375 (379)
.+||++|+| +||-+|-.++=++-++.- .+.|| .+-.++|+-++
T Consensus 136 ~~L~~~~~~-~ls~~ea~~l~~~~l~~~---~~rd~~~~~~~~v~ii~ 179 (189)
T cd03763 136 SVLEDRYKP-DMTEEEAKKLVCEAIEAG---IFNDLGSGSNVDLCVIT 179 (189)
T ss_pred HHHHhhcCC-CCCHHHHHHHHHHHHHHH---HHhcCcCCCceEEEEEc
Confidence 477999998 599999888766666554 34676 45668887664
No 16
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=31.23 E-value=18 Score=27.97 Aligned_cols=14 Identities=43% Similarity=0.532 Sum_probs=7.8
Q ss_pred cHHHHHHHHHHHHH
Q 017005 258 SLRELNERLMRLRV 271 (379)
Q Consensus 258 SL~ELn~RL~KLre 271 (379)
|++||++||+-|=.
T Consensus 9 s~~eL~~rl~~LD~ 22 (49)
T PF11629_consen 9 SYEELQQRLASLDP 22 (49)
T ss_dssp -HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHhCCH
Confidence 55666666666643
No 17
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=28.72 E-value=47 Score=26.28 Aligned_cols=18 Identities=33% Similarity=0.386 Sum_probs=15.4
Q ss_pred CCcccHHHHHHHHHHHHH
Q 017005 254 EGGFSLRELNERLMRLRV 271 (379)
Q Consensus 254 k~WFSL~ELn~RL~KLre 271 (379)
-.-.|++||.+||+-|+.
T Consensus 18 Ls~lSv~EL~~RIa~L~a 35 (59)
T PF06698_consen 18 LSLLSVEELEERIALLEA 35 (59)
T ss_pred chhcCHHHHHHHHHHHHH
Confidence 456899999999998876
No 18
>PRK09726 antitoxin HipB; Provisional
Probab=28.59 E-value=31 Score=27.49 Aligned_cols=30 Identities=30% Similarity=0.628 Sum_probs=22.9
Q ss_pred hhcChhHHHHHhhhcCCCCCCCcccHHHHHHHH
Q 017005 234 KMYSFEELGDKLKKLRPEGLEGGFSLRELNERL 266 (379)
Q Consensus 234 k~Ys~eELGkKL~~LRP~g~k~WFSL~ELn~RL 266 (379)
+.|+..+||++|+.+|=. .| .|.+||-+++
T Consensus 6 ~~~~~~~l~~~lk~~R~~--~g-ltq~elA~~~ 35 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQ--NG-WTQSELAKKI 35 (88)
T ss_pred cccCHHHHHHHHHHHHHH--cC-CCHHHHHHHH
Confidence 789999999999999832 34 4777777765
No 19
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=27.97 E-value=63 Score=30.16 Aligned_cols=44 Identities=25% Similarity=0.212 Sum_probs=31.3
Q ss_pred hhHHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCccceee
Q 017005 327 KEHLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGSARVQS 371 (379)
Q Consensus 327 k~~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGsarVQi 371 (379)
-|+|+|+||.-+-++.+|-.. -|.+.=.+=++-+==||||.--|
T Consensus 178 dd~l~e~yl~~~~~~~~el~~-~l~~~~~~~~~~Pv~~gsa~~~~ 221 (237)
T cd04168 178 DDELLEKYLEGGPIEELELDN-ELSARIAKRKVFPVYHGSALKGI 221 (237)
T ss_pred CHHHHHHHhCCCCCCHHHHHH-HHHHHHHhCCeEEEEEccccCCc
Confidence 478999999999999887443 44443334577777899986544
No 20
>cd03762 proteasome_beta_type_6 proteasome beta type-6 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=24.58 E-value=1.5e+02 Score=26.13 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=33.2
Q ss_pred HHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCc-cceeeeeee
Q 017005 329 HLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGS-ARVQSKGFF 375 (379)
Q Consensus 329 ~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGs-arVQia~l~ 375 (379)
-++|+.+.| +|+-+|-.++=++-++.-.+ .||.+ -.|+|+-++
T Consensus 137 ~~Le~~~~~-~~s~~ea~~l~~~al~~~~~---rd~~~~~~~~i~~i~ 180 (188)
T cd03762 137 GYVDANYKP-GMTLEECIKFVKNALSLAMS---RDGSSGGVIRLVIIT 180 (188)
T ss_pred HHHHhcCCC-CCCHHHHHHHHHHHHHHHHH---hccccCCCEEEEEEC
Confidence 377888887 69999999998888887754 56655 588888664
No 21
>PF07540 NOC3p: Nucleolar complex-associated protein; InterPro: IPR011501 Nucleolar complex-associated protein (Noc3p, Q07896 from SWISSPROT) is conserved in eukaryotes and plays essential roles in replication and rRNA processing in Saccharomyces cerevisiae [].
Probab=24.52 E-value=1.9e+02 Score=24.55 Aligned_cols=79 Identities=24% Similarity=0.405 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHhhhcccCcCCCCcChHHHHHHHHHHHHHHHhhhhhhhhhhhhhc---CC-CCCcccCCChhHHHhhh
Q 017005 259 LRELNERLMRLRVMEMNESNSKIGAGTISALRSSLARIQIEKEEKARVQRINILEGF---GG-TPEYLLHPPKEHLVEKY 334 (379)
Q Consensus 259 L~ELn~RL~KLremE~~e~~s~~~g~~~~~LR~sl~~lk~~~~~k~s~Q~~~~l~~l---gg-tP~ym~~PPk~~Lve~Y 334 (379)
+++..++|+.|...=-++++.. +..||.-+.-.... ....++.|++|+.+ -. .|.|.-.|+-+. |
T Consensus 1 i~~~K~~IA~l~~~ile~PE~n-----i~~lk~l~~~~~~~--~~~~v~kLa~lSl~~VFkDIiPgYrIR~~te~--e-- 69 (95)
T PF07540_consen 1 IEEAKEEIASLASSILEDPEEN-----IGSLKRLLKLCESK--VDVTVRKLAILSLLAVFKDIIPGYRIRPLTEK--E-- 69 (95)
T ss_pred ChHHHHHHHHHHHHHHHCHHHH-----HHHHHHHHHHHhcc--chHHHHHHHHHHHHHHHhhcCCCcccCCCChH--H--
Confidence 4678899999887644544433 44455433322222 11266777775543 34 999999998664 2
Q ss_pred cCCCCCCHHHHHHHHHHHHHH
Q 017005 335 FHPDNMSSAEKMKIELAKVRE 355 (379)
Q Consensus 335 fhpd~mss~Ek~K~el~kVR~ 355 (379)
-.+|++.|.+++|+
T Consensus 70 -------~~~kvsKev~~lr~ 83 (95)
T PF07540_consen 70 -------KKEKVSKEVRKLRD 83 (95)
T ss_pred -------hhhhHHHHHHHHHH
Confidence 26789999999986
No 22
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=23.53 E-value=75 Score=30.44 Aligned_cols=44 Identities=23% Similarity=0.283 Sum_probs=32.7
Q ss_pred hhHHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCccceee
Q 017005 327 KEHLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGSARVQS 371 (379)
Q Consensus 327 k~~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGsarVQi 371 (379)
-|+|+||||.-+-++.+|-.+.-.+-|+ .=++-+==||||.-.|
T Consensus 211 dd~L~e~yl~~~~~~~~el~~~l~~~~~-~~~~~PV~~gSa~~~~ 254 (270)
T cd01886 211 DDELMEKYLEGEEITEEEIKAAIRKGTI-ANKIVPVLCGSAFKNK 254 (270)
T ss_pred CHHHHHHHhCCCCCCHHHHHHHHHHHHH-cCcEEEEEeCcCCCCc
Confidence 5899999999999998885444334444 3477788899987554
No 23
>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=23.44 E-value=1.8e+02 Score=26.82 Aligned_cols=43 Identities=9% Similarity=0.236 Sum_probs=34.4
Q ss_pred HHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCccceeeeeee
Q 017005 329 HLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGSARVQSKGFF 375 (379)
Q Consensus 329 ~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGsarVQia~l~ 375 (379)
.+||+++++ +|+-+|-.++=+.-+++-++ .||-+..+.|+-++
T Consensus 167 ~~Le~~~~~-~ms~eeai~l~~~~l~~~~~---~~l~~~~iev~iv~ 209 (227)
T cd03750 167 TFLEKRYNE-DLELEDAIHTAILTLKEGFE---GQMTEKNIEIGICG 209 (227)
T ss_pred HHHHhhccC-CCCHHHHHHHHHHHHHHHhc---ccCCCCcEEEEEEE
Confidence 467898887 59999999988888887664 47888888888664
No 24
>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type. Members of this family are the alpha subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In most Actinobacteria (an exception is Propionibacterium acnes), the proteasome is accompanied by a system of tagging proteins for degradation with Pup.
Probab=23.30 E-value=1.9e+02 Score=27.33 Aligned_cols=47 Identities=9% Similarity=0.140 Sum_probs=34.6
Q ss_pred hHHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCccCccceeeeeee
Q 017005 328 EHLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDCGSARVQSKGFF 375 (379)
Q Consensus 328 ~~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~DcGsarVQia~l~ 375 (379)
...||++|+| +||-+|-.++-+.-++..............|.||-++
T Consensus 162 ~~~Lek~y~~-~ms~eeai~la~~aL~~~~~~~r~~~~~~~iEv~ii~ 208 (228)
T TIGR03691 162 ATALKESYRD-GLSLADALGLAVQALRAGGNGEKRELDAASLEVAVLD 208 (228)
T ss_pred HHHHHHhcCC-CCCHHHHHHHHHHHHHHHhccccccCCccceEEEEEe
Confidence 5678889987 7999999999888888664433223555668887765
No 25
>TIGR03634 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit. This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
Probab=22.83 E-value=1.9e+02 Score=25.44 Aligned_cols=43 Identities=14% Similarity=0.276 Sum_probs=31.2
Q ss_pred HHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCcc-Cccceeeeeee
Q 017005 329 HLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDC-GSARVQSKGFF 375 (379)
Q Consensus 329 ~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~Dc-GsarVQia~l~ 375 (379)
.++|++|+| +||-+|-.++=++-++.-++ .|| .+-.++|+-++
T Consensus 138 ~~Le~~~~~-~~s~~ea~~l~~~~l~~~~~---r~~~~~~~~~v~ii~ 181 (185)
T TIGR03634 138 GVLEDEYRE-DMSVEEAKKLAVRAIKSAIE---RDVASGNGIDVAVIT 181 (185)
T ss_pred HHHHhcCCC-CCCHHHHHHHHHHHHHHHHH---hcccCCCCEEEEEEc
Confidence 478999986 59999999887777776554 443 34568887654
No 26
>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=22.73 E-value=1.7e+02 Score=26.22 Aligned_cols=43 Identities=12% Similarity=0.106 Sum_probs=30.9
Q ss_pred HHHhhhcCCCCCCHHHHHHHHHHHHHHHhccCcCcc-Cccceeeeeee
Q 017005 329 HLVEKYFHPDNMSSAEKMKIELAKVREEFKMSESDC-GSARVQSKGFF 375 (379)
Q Consensus 329 ~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkmse~Dc-GsarVQia~l~ 375 (379)
.+||++++| +|+-+|-.++=+.-++.-+. .|| .+..++|+-++
T Consensus 142 ~~Le~~~~~-~~s~~ea~~l~~~~l~~~~~---rd~~~~~~~~i~ii~ 185 (195)
T cd03759 142 GMCESLWRP-DMEPDELFETISQALLSAVD---RDALSGWGAVVYIIT 185 (195)
T ss_pred HHHHhccCC-CCCHHHHHHHHHHHHHHHHh---hCcccCCceEEEEEc
Confidence 479999988 59999998887777766443 443 34567887654
No 27
>KOG4289 consensus Cadherin EGF LAG seven-pass G-type receptor [Signal transduction mechanisms]
Probab=22.16 E-value=63 Score=39.57 Aligned_cols=24 Identities=25% Similarity=0.506 Sum_probs=19.8
Q ss_pred CCCCcccHHHHHHHHHHHHHhhhc
Q 017005 252 GLEGGFSLRELNERLMRLRVMEMN 275 (379)
Q Consensus 252 g~k~WFSL~ELn~RL~KLremE~~ 275 (379)
|..|||..|+|||+|.+|..|--.
T Consensus 1149 gvrgw~~sE~lqE~iy~L~~~sll 1172 (2531)
T KOG4289|consen 1149 GVRGWFPSEDLQEQIYLLTAISLL 1172 (2531)
T ss_pred cccccccHHHHHHHHHHHHHhhhe
Confidence 337899999999999999887433
No 28
>TIGR02309 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence above trusted although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241).
Probab=21.76 E-value=79 Score=33.09 Aligned_cols=39 Identities=26% Similarity=0.528 Sum_probs=29.4
Q ss_pred hhhhhcCC-----CCCcc-cCCChhHHHhhhcCCCCCCHHHHHHH
Q 017005 310 NILEGFGG-----TPEYL-LHPPKEHLVEKYFHPDNMSSAEKMKI 348 (379)
Q Consensus 310 ~~l~~lgg-----tP~ym-~~PPk~~Lve~Yfhpd~mss~Ek~K~ 348 (379)
.++-.+|| +|+.. +.|+--.+|+||+.-.+++++||+|+
T Consensus 379 ~alq~lGG~G~~~~Ps~~df~~e~~~~l~kyl~~~~~~a~eR~kl 423 (477)
T TIGR02309 379 EILEQLGASGLITLPSEKDFKGPLGPFLEKFLQGANLEAKERVAL 423 (477)
T ss_pred HHHHHHhCCcEEecCChHHhChhhHHHHHHHhCCCCCCHHHHHHH
Confidence 44555555 66553 35777789999999888999999987
No 29
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=21.38 E-value=1.3e+02 Score=21.68 Aligned_cols=25 Identities=32% Similarity=0.465 Sum_probs=18.0
Q ss_pred cChhHHHHHhhhcCCCCCCCcccHHHHHHHHHHHH
Q 017005 236 YSFEELGDKLKKLRPEGLEGGFSLRELNERLMRLR 270 (379)
Q Consensus 236 Ys~eELGkKL~~LRP~g~k~WFSL~ELn~RL~KLr 270 (379)
=++.|||++|+. |-.+...||.||+
T Consensus 18 ~s~~~la~~lgl----------S~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 18 RSYAELAEELGL----------SESTVRRRIRRLE 42 (42)
T ss_dssp S-HHHHHHHHTS-----------HHHHHHHHHHHH
T ss_pred ccHHHHHHHHCc----------CHHHHHHHHHHhC
Confidence 367899999874 6677888888874
No 30
>PRK05256 condesin subunit E; Provisional
Probab=21.37 E-value=43 Score=32.97 Aligned_cols=115 Identities=20% Similarity=0.279 Sum_probs=59.9
Q ss_pred hhhhhHHHhhcChhHHHHHhhhcCCCCC--CCcccHHHHHHHHHHHHHhhhc--ccCcCCCCcChHHHHHHHHHHHHHHH
Q 017005 226 ERMKTDFVKMYSFEELGDKLKKLRPEGL--EGGFSLRELNERLMRLRVMEMN--ESNSKIGAGTISALRSSLARIQIEKE 301 (379)
Q Consensus 226 e~~~~ef~k~Ys~eELGkKL~~LRP~g~--k~WFSL~ELn~RL~KLremE~~--e~~s~~~g~~~~~LR~sl~~lk~~~~ 301 (379)
-+|.+..+--|-| |-|+.. +|||+.+||-+||.-|.--++- -...+-+|..+ ...+|+.+ -
T Consensus 91 ldMlvGkvLc~Ly---------LsperLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDl-----D~~Kl~ek-v 155 (238)
T PRK05256 91 LDMLVGKILCYLY---------LSPERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDL-----DKQKLQEK-V 155 (238)
T ss_pred HHHHHHHHHHHHh---------cCHHHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchh-----hHHHHHHH-H
Confidence 4566655555543 445554 8999999999999866532111 01133334222 22333322 2
Q ss_pred hhh--hhhhhhhhhhcC-CCCCcccCCChhHHHhhhcCCCCCCHHHHHHHHHHHHHHHhccC
Q 017005 302 EKA--RVQRINILEGFG-GTPEYLLHPPKEHLVEKYFHPDNMSSAEKMKIELAKVREEFKMS 360 (379)
Q Consensus 302 ~k~--s~Q~~~~l~~lg-gtP~ym~~PPk~~Lve~Yfhpd~mss~Ek~K~el~kVR~eFkms 360 (379)
.++ ..+++.++-.+| .+-.|+.-+ -|=||-.| -=+.+.--.+.+.=|||.+-|.
T Consensus 156 r~sLrrLrRlgmI~~l~~d~~kF~ite----AvfRFgad-vR~~dd~~eaqlrLIrdGea~~ 212 (238)
T PRK05256 156 RTSLNRLRRLGMVWFMGHDSSKFRITE----SVFRFGAD-VRSGDDPREAQLRLIRDGEAMP 212 (238)
T ss_pred HHHHHHHHhccceeeecCCCceEEecH----HHHhhccc-cccCCCHHHHHHHHHhccceec
Confidence 233 566777766666 355555332 23333332 2222223344578889888874
Done!