Query psy16040
Match_columns 358
No_of_seqs 154 out of 243
Neff 2.3
Searched_HMMs 46136
Date Fri Aug 16 19:20:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16040.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16040hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4080|consensus 100.0 2.1E-43 4.5E-48 312.9 8.6 156 128-344 15-176 (176)
2 PRK12286 rpmF 50S ribosomal pr 99.5 1.1E-14 2.4E-19 109.5 2.5 45 172-223 1-45 (57)
3 PF01783 Ribosomal_L32p: Ribos 99.4 9.7E-14 2.1E-18 103.0 2.8 44 173-223 1-44 (56)
4 COG0333 RpmF Ribosomal protein 99.3 2.8E-13 6.1E-18 103.0 1.6 44 172-222 1-44 (57)
5 PRK01110 rpmF 50S ribosomal pr 99.3 5E-13 1.1E-17 101.4 1.7 43 172-221 1-43 (60)
6 TIGR01031 rpmF_bact ribosomal 99.3 1.3E-12 2.8E-17 97.6 2.3 44 174-223 1-44 (55)
7 CHL00152 rpl32 ribosomal prote 97.0 0.00015 3.2E-09 55.3 -0.3 18 172-189 1-18 (53)
8 PRK14892 putative transcriptio 95.2 0.011 2.3E-07 49.4 1.8 25 197-223 15-47 (99)
9 PF14446 Prok-RING_1: Prokaryo 77.1 1.3 2.7E-05 34.2 1.2 23 197-221 13-35 (54)
10 smart00729 Elp3 Elongator prot 63.8 16 0.00034 29.5 4.8 54 262-321 5-66 (216)
11 KOG4080|consensus 60.8 3.1 6.6E-05 38.7 0.3 26 74-99 40-69 (176)
12 TIGR03826 YvyF flagellar opero 60.3 7 0.00015 34.5 2.4 18 204-221 80-97 (137)
13 TIGR03826 YvyF flagellar opero 53.9 8.2 0.00018 34.1 1.7 23 279-301 22-44 (137)
14 COG4888 Uncharacterized Zn rib 48.4 9.3 0.0002 33.1 1.2 16 202-217 19-34 (104)
15 COG1545 Predicted nucleic-acid 47.9 15 0.00033 31.8 2.4 40 204-243 28-69 (140)
16 PF10186 Atg14: UV radiation r 42.9 18 0.0004 32.3 2.2 34 266-301 15-48 (302)
17 COG1579 Zn-ribbon protein, pos 42.9 11 0.00024 36.1 0.9 28 258-285 201-231 (239)
18 PF00403 HMA: Heavy-metal-asso 42.8 5.6 0.00012 28.3 -0.8 40 276-317 7-46 (62)
19 cd04860 AE_Prim_S AE_Prim_S: p 42.1 31 0.00066 32.5 3.6 36 277-316 101-136 (232)
20 KOG3014|consensus 41.8 44 0.00094 32.9 4.7 76 255-335 76-162 (257)
21 PF13913 zf-C2HC_2: zinc-finge 36.8 13 0.00028 24.0 0.3 16 204-219 1-16 (25)
22 PF07754 DUF1610: Domain of un 36.1 17 0.00036 24.2 0.7 10 204-213 15-24 (24)
23 PF12172 DUF35_N: Rubredoxin-l 36.0 15 0.00032 24.9 0.4 23 204-226 10-33 (37)
24 COG2608 CopZ Copper chaperone 35.3 15 0.00032 28.1 0.4 41 275-317 10-50 (71)
25 COG2051 RPS27A Ribosomal prote 34.0 22 0.00048 28.8 1.2 29 205-240 19-47 (67)
26 COG5222 Uncharacterized conser 33.8 15 0.00032 37.5 0.2 76 169-283 237-318 (427)
27 PF01896 DNA_primase_S: Eukary 33.8 73 0.0016 26.0 4.2 37 277-317 18-54 (145)
28 PF02591 DUF164: Putative zinc 32.0 23 0.0005 25.9 1.0 12 203-214 44-55 (56)
29 PF13540 RCC1_2: Regulator of 31.1 56 0.0012 21.4 2.6 22 53-74 1-22 (30)
30 PF14354 Lar_restr_allev: Rest 30.6 27 0.00058 25.4 1.1 13 204-216 2-14 (61)
31 PF05129 Elf1: Transcription e 30.0 24 0.00051 28.5 0.8 13 203-215 20-32 (81)
32 PF14353 CpXC: CpXC protein 28.8 25 0.00055 29.0 0.8 19 203-221 36-54 (128)
33 PF14394 DUF4423: Domain of un 28.1 95 0.002 27.7 4.3 33 270-302 122-154 (171)
34 PRK13130 H/ACA RNA-protein com 27.7 34 0.00074 26.5 1.2 18 203-221 3-20 (56)
35 PRK09710 lar restriction allev 25.8 32 0.00069 27.6 0.8 17 203-219 4-20 (64)
36 PF10571 UPF0547: Uncharacteri 25.8 38 0.00082 22.5 1.0 12 204-215 13-24 (26)
37 smart00834 CxxC_CXXC_SSSS Puta 25.5 39 0.00084 22.5 1.1 11 203-213 24-34 (41)
38 PF13248 zf-ribbon_3: zinc-rib 25.2 38 0.00083 21.8 1.0 16 206-221 3-19 (26)
39 KOG3214|consensus 24.8 25 0.00055 30.7 0.1 38 197-234 15-66 (109)
40 PF14535 AMP-binding_C_2: AMP- 24.6 1.9E+02 0.0041 22.9 5.0 43 284-332 52-94 (96)
41 COG1198 PriA Primosomal protei 23.7 71 0.0015 35.1 3.1 24 256-284 461-484 (730)
42 KOG0005|consensus 23.5 53 0.0011 26.8 1.6 28 288-317 22-49 (70)
43 PF01667 Ribosomal_S27e: Ribos 23.2 49 0.0011 25.6 1.4 28 206-240 8-35 (55)
44 COG0675 Transposase and inacti 22.9 40 0.00086 29.8 1.0 21 201-221 305-325 (364)
45 KOG0786|consensus 22.5 29 0.00062 34.9 0.0 47 74-122 181-232 (363)
46 PRK00419 DNA primase small sub 21.8 1.1E+02 0.0024 31.2 3.8 34 280-317 116-149 (376)
47 TIGR00595 priA primosomal prot 21.3 1E+02 0.0023 31.6 3.7 49 204-282 212-260 (505)
48 PRK08271 anaerobic ribonucleos 21.3 56 0.0012 35.1 1.8 21 204-224 565-586 (623)
49 PF10083 DUF2321: Uncharacteri 21.0 62 0.0013 29.8 1.8 31 278-308 74-104 (158)
50 PF14952 zf-tcix: Putative tre 20.9 47 0.001 25.1 0.9 13 203-215 9-21 (44)
51 TIGR00515 accD acetyl-CoA carb 20.7 45 0.00098 32.4 0.9 11 204-214 44-54 (285)
52 TIGR02605 CxxC_CxxC_SSSS putat 20.5 54 0.0012 23.2 1.1 12 204-215 25-36 (52)
53 PRK09335 30S ribosomal protein 20.4 58 0.0013 27.9 1.4 33 175-219 2-34 (95)
54 cd00350 rubredoxin_like Rubred 20.4 45 0.00097 22.5 0.6 13 204-216 16-28 (33)
55 COG1579 Zn-ribbon protein, pos 20.3 43 0.00093 32.2 0.7 13 202-214 218-230 (239)
56 TIGR02147 Fsuc_second hypothet 20.3 1.5E+02 0.0033 28.5 4.3 31 270-300 220-250 (271)
57 COG5319 Uncharacterized protei 20.2 48 0.001 30.1 0.9 18 204-221 31-48 (142)
58 CHL00174 accD acetyl-CoA carbo 20.0 43 0.00094 33.0 0.7 12 204-215 56-67 (296)
59 TIGR03655 anti_R_Lar restricti 20.0 48 0.001 24.2 0.7 12 205-216 1-12 (53)
No 1
>KOG4080|consensus
Probab=100.00 E-value=2.1e-43 Score=312.92 Aligned_cols=156 Identities=38% Similarity=0.610 Sum_probs=141.2
Q ss_pred cccCCCCcccccCCcceeeeccCccCCCCCccCchhh----hccCCeEeecCCCCCChhHhhhccCCCCCCCccccccCC
Q psy16040 128 AMFSNSSLFFISDFNVAVTQISSVLTPKPVTKLSLKE----LFDTSILWAVPKKRRSLERRMNRKYGSKDQVWKMLMPRT 203 (358)
Q Consensus 128 ~~fs~~s~F~~~~f~pALavqsp~~~p~Ps~~~Slkd----l~~DGILwAVPKKRrSkERRRkRR~g~pk~~~KLLkPKt 203 (358)
+||+..+-+++.+|++||+++.+...+.++...|... ++++||||||||+|||++||++|+++.+ -|++++++
T Consensus 15 ~l~~lr~p~~s~p~~~~L~~~~~s~~~~ls~d~~~s~e~~~l~~n~illAVPK~r~S~eK~~kRk~~~~---~k~Lk~k~ 91 (176)
T KOG4080|consen 15 NLFSLRSPSPSIPFAKALGVFQSSTAPKLSQDYSSSRENSMLIDNSILLAVPKKRTSKEKKVKRKFLYT---RKLLKPKD 91 (176)
T ss_pred HHHhccCCCCCCCchhhhcccchhhccccccccccCCccccccccceEEeccccccchhhhhhhhccCc---cccccchh
Confidence 4788888899999999999999999999887776333 5667999999999999999999999865 38999999
Q ss_pred CcccCCCCCCcccCccccccccccccceeccCCCcceeeeccCccccccccccccccceeeeccccccccccccCcchHH
Q psy16040 204 DLTVCNTCGYTHHSKTLCGKYYSLSISRVKCSFPSLLKVMYPYGLTTNLEKDKYQSCDIVIQRNCIYNTILFLFTGNCYA 283 (358)
Q Consensus 204 NLv~CPqCGhlKl~HrLC~~~fsla~t~~s~sg~S~lkv~~~~pl~q~~~~ah~~gch~~~~~~~~~~~~~~~~~g~Cy~ 283 (358)
||++||+|||+|++|+|| .+||+
T Consensus 92 nl~~CP~CGh~k~a~~LC---------------------------------------------------------~~Cy~ 114 (176)
T KOG4080|consen 92 NLNTCPACGHIKPAHTLC---------------------------------------------------------DYCYA 114 (176)
T ss_pred ccccCcccCccccccccH---------------------------------------------------------HHHHH
Confidence 999999999999999999 99999
Q ss_pred HHHHHHHHHHHHHHHHcC--CCCCcceeEEEeCCCCCccccccccCceeEeccCCCCCCCchh
Q psy16040 284 KIKEETTRLQDKIVEALG--LNPVDKEVVVLYKGEKEHASEEFSETHRVIEVEGERPPWFSKN 344 (358)
Q Consensus 284 kik~eT~~iq~ki~~~lg--l~p~d~evvVlY~ge~~~~~~e~~~~~rvie~~~eRP~wFskn 344 (358)
||..||.+|+.||..+.+ ++++|+||+|||.||++.. ....++|||+|++++||.||.+|
T Consensus 115 kV~ket~ei~~k~~iq~~~~~e~~d~e~~Vly~Ge~d~~-t~dlk~Kri~e~~k~Rp~wftkn 176 (176)
T KOG4080|consen 115 KVHKETSEIKKKMMIQEPYVGEKQDKEVYVLYRGEPDAP-TADLKGKRILEIEKERPTWFTKN 176 (176)
T ss_pred HHHHHHHHHHHHHhccCCCCCCcCcceEEEEecCCCCcc-chhhccchhhhhhccCccccccC
Confidence 999999999997766655 7999999999999999766 67899999999999999999987
No 2
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=99.49 E-value=1.1e-14 Score=109.54 Aligned_cols=45 Identities=31% Similarity=0.632 Sum_probs=41.8
Q ss_pred eecCCCCCChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCcccccc
Q psy16040 172 WAVPKKRRSLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSKTLCGK 223 (358)
Q Consensus 172 wAVPKKRrSkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~HrLC~~ 223 (358)
|||||+|+|++||++||+ +||+..| +|+.||+||+++++|++|+.
T Consensus 1 MAvPKrk~S~srr~~RRs-----h~~l~~~--~l~~C~~CG~~~~~H~vC~~ 45 (57)
T PRK12286 1 MAVPKRKTSKSRKRKRRA-----HFKLKAP--GLVECPNCGEPKLPHRVCPS 45 (57)
T ss_pred CCcCcCcCChhhcchhcc-----cccccCC--cceECCCCCCccCCeEECCC
Confidence 899999999999999999 4788888 99999999999999999943
No 3
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=99.41 E-value=9.7e-14 Score=102.99 Aligned_cols=44 Identities=34% Similarity=0.731 Sum_probs=35.3
Q ss_pred ecCCCCCChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCcccccc
Q psy16040 173 AVPKKRRSLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSKTLCGK 223 (358)
Q Consensus 173 AVPKKRrSkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~HrLC~~ 223 (358)
||||+|+|++|+++||+ +|++-.| +|+.||+||+++++|++|+.
T Consensus 1 AvPKrk~Sksr~~~Rrs-----~~~l~~~--~l~~c~~cg~~~~~H~vc~~ 44 (56)
T PF01783_consen 1 AVPKRKTSKSRKRMRRS-----HWKLKAP--NLVKCPNCGEPKLPHRVCPS 44 (56)
T ss_dssp ---SS-SCHHHHHHHTT-----TTS--TT--SEEESSSSSSEESTTSBCTT
T ss_pred CCCCCcCChhHccchhc-----ccccccc--ceeeeccCCCEecccEeeCC
Confidence 89999999999999999 4777777 99999999999999999954
No 4
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=99.34 E-value=2.8e-13 Score=102.99 Aligned_cols=44 Identities=34% Similarity=0.561 Sum_probs=41.7
Q ss_pred eecCCCCCChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCccccc
Q psy16040 172 WAVPKKRRSLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSKTLCG 222 (358)
Q Consensus 172 wAVPKKRrSkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~HrLC~ 222 (358)
|||||+|+|++||++||. ++++..| +++.|++||+++++|++|.
T Consensus 1 MAVPkrktSksrr~~RRs-----h~~l~~~--~~~~c~~cG~~~l~Hrvc~ 44 (57)
T COG0333 1 MAVPKRKTSKSRRRMRRS-----HDALKAP--TLSVCPNCGEYKLPHRVCL 44 (57)
T ss_pred CCCCcccCChhhhhhhhh-----hHhhhCc--cceeccCCCCcccCceEcC
Confidence 899999999999999999 5899999 8999999999999999993
No 5
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=99.31 E-value=5e-13 Score=101.40 Aligned_cols=43 Identities=35% Similarity=0.552 Sum_probs=41.2
Q ss_pred eecCCCCCChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCcccc
Q psy16040 172 WAVPKKRRSLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 172 wAVPKKRrSkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~HrLC 221 (358)
|||||+|+|++|+++||+ +|++..| +++.|++||+++++|++|
T Consensus 1 MAVPKrK~Sksr~~~RRa-----~~~~~~~--~~~~c~~cg~~~~pH~vc 43 (60)
T PRK01110 1 MAVPKRKTSKSKRRMRRS-----HWKLTAP--TLSVDKTTGEYHLPHHVS 43 (60)
T ss_pred CCCCcCccchhhchhhhh-----hhhccCC--ceeEcCCCCceeccceec
Confidence 899999999999999999 5899888 899999999999999998
No 6
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=99.28 E-value=1.3e-12 Score=97.55 Aligned_cols=44 Identities=32% Similarity=0.594 Sum_probs=40.1
Q ss_pred cCCCCCChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCcccccc
Q psy16040 174 VPKKRRSLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSKTLCGK 223 (358)
Q Consensus 174 VPKKRrSkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~HrLC~~ 223 (358)
|||+|+|++||++||+. .||+..| +|+.||+||+++++|++|+.
T Consensus 1 vPKrk~Sksr~~~RRah----~~kl~~p--~l~~C~~cG~~~~~H~vc~~ 44 (55)
T TIGR01031 1 VPKRKTSKSRKRKRRSH----DAKLTAP--TLVVCPNCGEFKLPHRVCPS 44 (55)
T ss_pred CCCCcCCcccccchhcC----cccccCC--cceECCCCCCcccCeeECCc
Confidence 89999999999999992 3788888 99999999999999999944
No 7
>CHL00152 rpl32 ribosomal protein L32; Validated
Probab=96.99 E-value=0.00015 Score=55.29 Aligned_cols=18 Identities=50% Similarity=0.575 Sum_probs=17.5
Q ss_pred eecCCCCCChhHhhhccC
Q psy16040 172 WAVPKKRRSLERRMNRKY 189 (358)
Q Consensus 172 wAVPKKRrSkERRRkRR~ 189 (358)
|||||||+|++|++.|+.
T Consensus 1 MAVPKKRtSksKk~~Rk~ 18 (53)
T CHL00152 1 MAVPKKRTSKSKKRIRKN 18 (53)
T ss_pred CCCCCCccchHHHHHHHH
Confidence 899999999999999998
No 8
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=95.18 E-value=0.011 Score=49.44 Aligned_cols=25 Identities=32% Similarity=0.659 Sum_probs=20.4
Q ss_pred cccccCCCcccCCCCCCcccC--------cccccc
Q psy16040 197 KMLMPRTDLTVCNTCGYTHHS--------KTLCGK 223 (358)
Q Consensus 197 KLLkPKtNLv~CPqCGhlKl~--------HrLC~~ 223 (358)
++-.| ++..||+||+..++ |++|+.
T Consensus 15 k~klp--t~f~CP~Cge~~v~v~~~k~~~h~~C~~ 47 (99)
T PRK14892 15 KPKLP--KIFECPRCGKVSISVKIKKNIAIITCGN 47 (99)
T ss_pred ccCCC--cEeECCCCCCeEeeeecCCCcceEECCC
Confidence 45556 89999999999986 999943
No 9
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.12 E-value=1.3 Score=34.20 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=19.7
Q ss_pred cccccCCCcccCCCCCCcccCcccc
Q psy16040 197 KMLMPRTDLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 197 KLLkPKtNLv~CPqCGhlKl~HrLC 221 (358)
+.++++.+++.||.||.++ ||-|
T Consensus 13 ~~~~~~dDiVvCp~Cgapy--HR~C 35 (54)
T PF14446_consen 13 KKFKDGDDIVVCPECGAPY--HRDC 35 (54)
T ss_pred CcccCCCCEEECCCCCCcc--cHHH
Confidence 5567788999999999987 7778
No 10
>smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Probab=63.78 E-value=16 Score=29.52 Aligned_cols=54 Identities=19% Similarity=0.132 Sum_probs=32.0
Q ss_pred eeeeccccccccccccCcchHHHH------HHHHHHHHHHHHHH--cCCCCCcceeEEEeCCCCCccc
Q psy16040 262 IVIQRNCIYNTILFLFTGNCYAKI------KEETTRLQDKIVEA--LGLNPVDKEVVVLYKGEKEHAS 321 (358)
Q Consensus 262 ~~~~~~~~~~~~~~~~~g~Cy~ki------k~eT~~iq~ki~~~--lgl~p~d~evvVlY~ge~~~~~ 321 (358)
+.+.|.|.++ |.+||... ......+.+.+.+. .|....+.+.+++.-||..-.+
T Consensus 5 i~~t~~C~~~------C~yC~~~~~~~~~~~~~~e~i~~~~~~~~~~~~~~~~~~~i~~~gg~~~~~~ 66 (216)
T smart00729 5 YIITRGCPRR------CTFCSFPSARGKLRSRYLEALVREIELLAEKGEKEILVGTVFIGGGTPTLLS 66 (216)
T ss_pred EEecCchhcc------CCcCCcCccccchhHHHHHHHHHHHHHHHhcccCCcceeEEEECCCCCCCCC
Confidence 5677889887 99998733 22334555555544 2332224566777777764433
No 11
>KOG4080|consensus
Probab=60.83 E-value=3.1 Score=38.67 Aligned_cols=26 Identities=50% Similarity=0.599 Sum_probs=18.2
Q ss_pred cccccccchhhh----hhccceeecccchh
Q psy16040 74 TPKPVTKLSLKE----LFDTSILWAVPKKV 99 (358)
Q Consensus 74 ~~~~~~~~~~~~----~~~~~~~~~~~~~~ 99 (358)
.|++-...|..+ +.|.+|||||||+-
T Consensus 40 ~~~ls~d~~~s~e~~~l~~n~illAVPK~r 69 (176)
T KOG4080|consen 40 APKLSQDYSSSRENSMLIDNSILLAVPKKR 69 (176)
T ss_pred ccccccccccCCccccccccceEEeccccc
Confidence 344444444444 88999999999974
No 12
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=60.29 E-value=7 Score=34.50 Aligned_cols=18 Identities=28% Similarity=0.567 Sum_probs=16.2
Q ss_pred CcccCCCCCCcccCcccc
Q psy16040 204 DLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 204 NLv~CPqCGhlKl~HrLC 221 (358)
-..+|..||.+...+++|
T Consensus 80 l~~~CE~CG~~I~~Gr~C 97 (137)
T TIGR03826 80 LGYPCERCGTSIREGRLC 97 (137)
T ss_pred CcCcccccCCcCCCCCcc
Confidence 346899999999999999
No 13
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=53.85 E-value=8.2 Score=34.08 Aligned_cols=23 Identities=13% Similarity=0.274 Sum_probs=19.0
Q ss_pred cchHHHHHHHHHHHHHHHHHHcC
Q psy16040 279 GNCYAKIKEETTRLQDKIVEALG 301 (358)
Q Consensus 279 g~Cy~kik~eT~~iq~ki~~~lg 301 (358)
+.||.+..++-..+++-|.+.-|
T Consensus 22 p~C~~~~e~~f~kV~~yLr~~p~ 44 (137)
T TIGR03826 22 PSCYEEEEREFEKVYKFLRKHEN 44 (137)
T ss_pred HHHhHHHHHHHHHHHHHHHHCCC
Confidence 99999998888888888876544
No 14
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=48.41 E-value=9.3 Score=33.09 Aligned_cols=16 Identities=25% Similarity=0.457 Sum_probs=12.6
Q ss_pred CCCcccCCCCCCcccC
Q psy16040 202 RTDLTVCNTCGYTHHS 217 (358)
Q Consensus 202 KtNLv~CPqCGhlKl~ 217 (358)
....-+||.|||.+..
T Consensus 19 L~k~FtCp~Cghe~vs 34 (104)
T COG4888 19 LPKTFTCPRCGHEKVS 34 (104)
T ss_pred CCceEecCccCCeeee
Confidence 3467899999998764
No 15
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=47.94 E-value=15 Score=31.83 Aligned_cols=40 Identities=23% Similarity=0.277 Sum_probs=29.0
Q ss_pred CcccCCCCCCcc-cCccccccccccc-cceeccCCCcceeee
Q psy16040 204 DLTVCNTCGYTH-HSKTLCGKYYSLS-ISRVKCSFPSLLKVM 243 (358)
Q Consensus 204 NLv~CPqCGhlK-l~HrLC~~~fsla-~t~~s~sg~S~lkv~ 243 (358)
--..|++||+.. .++..|++|++.. ..-+--||-+.|.-+
T Consensus 28 ~g~kC~~CG~v~~PPr~~Cp~C~~~~~~E~vels~~G~V~t~ 69 (140)
T COG1545 28 LGTKCKKCGRVYFPPRAYCPKCGSETELEWVELSGEGKVETY 69 (140)
T ss_pred EEEEcCCCCeEEcCCcccCCCCCCCCceEEEEeCCCeEEEEE
Confidence 345899999964 6788999999995 356666666665433
No 16
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=42.90 E-value=18 Score=32.35 Aligned_cols=34 Identities=32% Similarity=0.489 Sum_probs=24.6
Q ss_pred ccccccccccccCcchHHHHHHHHHHHHHHHHHHcC
Q psy16040 266 RNCIYNTILFLFTGNCYAKIKEETTRLQDKIVEALG 301 (358)
Q Consensus 266 ~~~~~~~~~~~~~g~Cy~kik~eT~~iq~ki~~~lg 301 (358)
.+|+-|.+ .---.+...++++.+.++++|.+.+.
T Consensus 15 ~~C~~~~L--~~~~~~l~~~~~~~~~l~~~i~~~l~ 48 (302)
T PF10186_consen 15 ANCVNNRL--LELRSELQQLKEENEELRRRIEEILE 48 (302)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56766652 22256778888999999999998774
No 17
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=42.86 E-value=11 Score=36.06 Aligned_cols=28 Identities=11% Similarity=0.265 Sum_probs=21.1
Q ss_pred cccceeeec---cccccccccccCcchHHHH
Q psy16040 258 QSCDIVIQR---NCIYNTILFLFTGNCYAKI 285 (358)
Q Consensus 258 ~gch~~~~~---~~~~~~~~~~~~g~Cy~ki 285 (358)
-||||+|.+ +++-|-==..||++|-+-+
T Consensus 201 ~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 201 GGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred cCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 599999986 4566655567999997644
No 18
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=42.79 E-value=5.6 Score=28.28 Aligned_cols=40 Identities=20% Similarity=0.388 Sum_probs=28.1
Q ss_pred ccCcchHHHHHHHHHHHHHHHHHHcCCCCCcceeEEEeCCCC
Q psy16040 276 LFTGNCYAKIKEETTRLQDKIVEALGLNPVDKEVVVLYKGEK 317 (358)
Q Consensus 276 ~~~g~Cy~kik~eT~~iq~ki~~~lgl~p~d~evvVlY~ge~ 317 (358)
+.|++|.++|++-...+..- ...-.|..+.++.|.|..+.
T Consensus 7 m~C~~C~~~v~~~l~~~~GV--~~v~vd~~~~~v~v~~~~~~ 46 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGV--KSVKVDLETKTVTVTYDPDK 46 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTE--EEEEEETTTTEEEEEESTTT
T ss_pred cccHHHHHHHHHHHhcCCCC--cEEEEECCCCEEEEEEecCC
Confidence 68999999998766554221 11225777899999998776
No 19
>cd04860 AE_Prim_S AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulat
Probab=42.08 E-value=31 Score=32.48 Aligned_cols=36 Identities=22% Similarity=0.504 Sum_probs=32.6
Q ss_pred cCcchHHHHHHHHHHHHHHHHHHcCCCCCcceeEEEeCCC
Q psy16040 277 FTGNCYAKIKEETTRLQDKIVEALGLNPVDKEVVVLYKGE 316 (358)
Q Consensus 277 ~~g~Cy~kik~eT~~iq~ki~~~lgl~p~d~evvVlY~ge 316 (358)
.|..|...++.++..|.+.+.+.+|++. +.++|.|-
T Consensus 101 ic~kCw~~~~~a~~~l~~~L~~dFGf~~----i~~vfSG~ 136 (232)
T cd04860 101 ICEKCWKFAKEAVKILDDILREDFGFKH----ILWVFSGR 136 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCce----EEEEEECC
Confidence 5789999999999999999999999985 78999994
No 20
>KOG3014|consensus
Probab=41.80 E-value=44 Score=32.86 Aligned_cols=76 Identities=18% Similarity=0.182 Sum_probs=41.9
Q ss_pred ccccccceee-eccccccccccccCcchHHHHHHHHHHHHHHHHHHcCCCCC-----cceeEEEeCCCCCc-----cccc
Q psy16040 255 DKYQSCDIVI-QRNCIYNTILFLFTGNCYAKIKEETTRLQDKIVEALGLNPV-----DKEVVVLYKGEKEH-----ASEE 323 (358)
Q Consensus 255 ah~~gch~~~-~~~~~~~~~~~~~~g~Cy~kik~eT~~iq~ki~~~lgl~p~-----d~evvVlY~ge~~~-----~~~e 323 (358)
..-+|-|+-. +.+|||=.--+-- -+. +.-.+++...+.++||..+. ++.-++||--.... -.|.
T Consensus 76 ~~~~~~~~~~~~~~rIv~V~~~~s----~~~-~kk~~Ev~~~VnnELg~~~~~~~~~~~~k~~lFIS~rk~~VGcLvaE~ 150 (257)
T KOG3014|consen 76 DERLGVEYPLQSDGRIVYVNPEDS----PAA-LKKVEEVMKMVNNELGYQQIENQCWPKIKTFLFISVRKIVVGCLVAEP 150 (257)
T ss_pred ccceeeeccccCCCeEEEEeCCCC----hHH-HHHHHHHHHHHHhhcCCcccccccccceeEEEEEEecceeeeEEEehh
Confidence 3344444443 5677764332221 122 33456778889999997544 34434444333322 1255
Q ss_pred cccCceeEeccC
Q psy16040 324 FSETHRVIEVEG 335 (358)
Q Consensus 324 ~~~~~rvie~~~ 335 (358)
.++..|+|+.++
T Consensus 151 Is~a~~~i~~~~ 162 (257)
T KOG3014|consen 151 ISQAFRVIESPG 162 (257)
T ss_pred hhhhhhhccCcC
Confidence 778899999777
No 21
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=36.82 E-value=13 Score=23.98 Aligned_cols=16 Identities=25% Similarity=0.690 Sum_probs=12.0
Q ss_pred CcccCCCCCCcccCcc
Q psy16040 204 DLTVCNTCGYTHHSKT 219 (358)
Q Consensus 204 NLv~CPqCGhlKl~Hr 219 (358)
+++.||.||.-..+..
T Consensus 1 ~l~~C~~CgR~F~~~~ 16 (25)
T PF13913_consen 1 ELVPCPICGRKFNPDR 16 (25)
T ss_pred CCCcCCCCCCEECHHH
Confidence 4788999998765543
No 22
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=36.14 E-value=17 Score=24.19 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=8.2
Q ss_pred CcccCCCCCC
Q psy16040 204 DLTVCNTCGY 213 (358)
Q Consensus 204 NLv~CPqCGh 213 (358)
..-.||+||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 5668999995
No 23
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=35.95 E-value=15 Score=24.92 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=12.1
Q ss_pred CcccCCCCCCc-ccCccccccccc
Q psy16040 204 DLTVCNTCGYT-HHSKTLCGKYYS 226 (358)
Q Consensus 204 NLv~CPqCGhl-Kl~HrLC~~~fs 226 (358)
-+..|..||+. ..+...|+++.|
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEcCCCCCEecCCCcCCCCcCc
Confidence 35689999998 557788865544
No 24
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=35.33 E-value=15 Score=28.06 Aligned_cols=41 Identities=12% Similarity=0.310 Sum_probs=28.4
Q ss_pred cccCcchHHHHHHHHHHHHHHHHHHcCCCCCcceeEEEeCCCC
Q psy16040 275 FLFTGNCYAKIKEETTRLQDKIVEALGLNPVDKEVVVLYKGEK 317 (358)
Q Consensus 275 ~~~~g~Cy~kik~eT~~iq~ki~~~lgl~p~d~evvVlY~ge~ 317 (358)
=+-|++|..+|++..+.+.- +..-..++..+.+.|.|++..
T Consensus 10 ~MtC~~C~~~V~~al~~v~g--v~~v~v~l~~~~~~V~~d~~~ 50 (71)
T COG2608 10 GMTCGHCVKTVEKALEEVDG--VASVDVDLEKGTATVTFDSNK 50 (71)
T ss_pred CcCcHHHHHHHHHHHhcCCC--eeEEEEEcccCeEEEEEcCCc
Confidence 46799999999988776654 223335566666778888764
No 25
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=33.99 E-value=22 Score=28.79 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=21.4
Q ss_pred cccCCCCCCcccCccccccccccccceeccCCCcce
Q psy16040 205 LTVCNTCGYTHHSKTLCGKYYSLSISRVKCSFPSLL 240 (358)
Q Consensus 205 Lv~CPqCGhlKl~HrLC~~~fsla~t~~s~sg~S~l 240 (358)
-+.||.||+- -+ +||.|.+.++|-.=+..
T Consensus 19 ~VkCpdC~N~-----q~--vFshast~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNE-----QV--VFSHASTVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCE-----EE--EeccCceEEEecccccE
Confidence 4689999963 33 69999998887655443
No 26
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.80 E-value=15 Score=37.48 Aligned_cols=76 Identities=25% Similarity=0.382 Sum_probs=51.7
Q ss_pred CeEeecCCCCC--ChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCc--cccccccccccceeccCCCcceeeec
Q psy16040 169 SILWAVPKKRR--SLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSK--TLCGKYYSLSISRVKCSFPSLLKVMY 244 (358)
Q Consensus 169 GILwAVPKKRr--SkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~H--rLC~~~fsla~t~~s~sg~S~lkv~~ 244 (358)
+++.++|..-. ...+|+.-+...|+..||+--| +--..||-||-+.+.- +-|
T Consensus 237 ~yVv~qpdvqsWe~Yq~r~~a~~~~~Dqv~k~~~~-~i~LkCplc~~Llrnp~kT~c----------------------- 292 (427)
T COG5222 237 GYVVAQPDVQSWEKYQQRTKAVAEIPDQVYKMQPP-NISLKCPLCHCLLRNPMKTPC----------------------- 292 (427)
T ss_pred CeEEeccchHHHHHHHHHHHhhhhCchhhhccCCC-CccccCcchhhhhhCcccCcc-----------------------
Confidence 36677876532 2234444455566778988766 2237899999775432 235
Q ss_pred cCccccccccccccccceeeecccccccccc--ccCcchHH
Q psy16040 245 PYGLTTNLEKDKYQSCDIVIQRNCIYNTILF--LFTGNCYA 283 (358)
Q Consensus 245 ~~pl~q~~~~ah~~gch~~~~~~~~~~~~~~--~~~g~Cy~ 283 (358)
|.+..-..||-|.+|= .-|+||-.
T Consensus 293 ---------------C~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 293 ---------------CGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ---------------ccchHHHHHHhhhhhhccccCCCccc
Confidence 8888889999998874 57999976
No 27
>PF01896 DNA_primase_S: Eukaryotic and archaeal DNA primase small subunit; InterPro: IPR002755 DNA primase [] synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large (p60) and small (p50) subunits in eukaryotes. This family represents sequences of the small subunit and the DNA primase sequences of the Archaea []. No sequence similarity can be detected between the eukaryotic p50 and p60 subunits and the primases purified from bacteriophage and bacteria, IPR006295 from INTERPRO. ; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 1V33_A 1V34_A 2FAR_B 2FAQ_A 2FAO_B 1G71_A 2R9L_B 3PKY_B 2IRU_B 2IRY_B ....
Probab=33.76 E-value=73 Score=25.97 Aligned_cols=37 Identities=24% Similarity=0.532 Sum_probs=28.3
Q ss_pred cCcchHHHHHHHHHHHHHHHHHHcCCCCCcceeEEEeCCCC
Q psy16040 277 FTGNCYAKIKEETTRLQDKIVEALGLNPVDKEVVVLYKGEK 317 (358)
Q Consensus 277 ~~g~Cy~kik~eT~~iq~ki~~~lgl~p~d~evvVlY~ge~ 317 (358)
.|..|-..++++...+-+.+.+.+|++. +.+.|.|.+
T Consensus 18 ~~~~~i~~~~~~~~~~~~~l~~~~g~~~----~~~~~SG~r 54 (145)
T PF01896_consen 18 VCEKCIEFVVEEAAKLLDFLLEDFGFRC----IFVKFSGNR 54 (145)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHTTT--S----EEEEE-SSS
T ss_pred ccchhhHHHHHHHHHHHHhhhhhcCCcc----cEEEeCCCc
Confidence 5789999999999999999999999987 557788754
No 28
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.04 E-value=23 Score=25.92 Aligned_cols=12 Identities=25% Similarity=0.899 Sum_probs=10.1
Q ss_pred CCcccCCCCCCc
Q psy16040 203 TDLTVCNTCGYT 214 (358)
Q Consensus 203 tNLv~CPqCGhl 214 (358)
+.++.||+||..
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 479999999964
No 29
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=31.08 E-value=56 Score=21.37 Aligned_cols=22 Identities=23% Similarity=0.262 Sum_probs=18.0
Q ss_pred eeEEEEeeeeeeeeeecccccc
Q psy16040 53 VTSVIIGLDFNVAVTQNSSVLT 74 (358)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~ 74 (358)
|++|-.|.++.++++++..|..
T Consensus 1 V~~ia~G~~ht~al~~~g~v~~ 22 (30)
T PF13540_consen 1 VVQIACGGYHTCALTSDGEVYC 22 (30)
T ss_dssp EEEEEEESSEEEEEE-TTEEEE
T ss_pred CEEEEecCCEEEEEEcCCCEEE
Confidence 6788999999999999987753
No 30
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.58 E-value=27 Score=25.39 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=10.0
Q ss_pred CcccCCCCCCccc
Q psy16040 204 DLTVCNTCGYTHH 216 (358)
Q Consensus 204 NLv~CPqCGhlKl 216 (358)
.|.+||-||+...
T Consensus 2 ~LkPCPFCG~~~~ 14 (61)
T PF14354_consen 2 ELKPCPFCGSADV 14 (61)
T ss_pred CCcCCCCCCCcce
Confidence 5778999997654
No 31
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=30.02 E-value=24 Score=28.48 Aligned_cols=13 Identities=15% Similarity=0.409 Sum_probs=5.0
Q ss_pred CCcccCCCCCCcc
Q psy16040 203 TDLTVCNTCGYTH 215 (358)
Q Consensus 203 tNLv~CPqCGhlK 215 (358)
...-.||.|||-+
T Consensus 20 ~~~F~CPfC~~~~ 32 (81)
T PF05129_consen 20 PKVFDCPFCNHEK 32 (81)
T ss_dssp SS----TTT--SS
T ss_pred CceEcCCcCCCCC
Confidence 3788999999653
No 32
>PF14353 CpXC: CpXC protein
Probab=28.77 E-value=25 Score=28.99 Aligned_cols=19 Identities=16% Similarity=0.210 Sum_probs=15.9
Q ss_pred CCcccCCCCCCcccCcccc
Q psy16040 203 TDLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 203 tNLv~CPqCGhlKl~HrLC 221 (358)
-+..+||+||+......-|
T Consensus 36 l~~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLEYPL 54 (128)
T ss_pred cCEEECCCCCCceecCCCE
Confidence 3788999999988877777
No 33
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=28.08 E-value=95 Score=27.72 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=27.3
Q ss_pred ccccccccCcchHHHHHHHHHHHHHHHHHHcCC
Q psy16040 270 YNTILFLFTGNCYAKIKEETTRLQDKIVEALGL 302 (358)
Q Consensus 270 ~~~~~~~~~g~Cy~kik~eT~~iq~ki~~~lgl 302 (358)
|-++.+-....+|++|++|+...+.+|.....=
T Consensus 122 ~s~~T~~vs~~~~~ki~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 122 FSGLTMSVSREDYEKIKKEIREFRKKIIAIAEE 154 (171)
T ss_pred eeeeEEEeCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445667778999999999999999999876543
No 34
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=27.66 E-value=34 Score=26.47 Aligned_cols=18 Identities=28% Similarity=0.813 Sum_probs=14.7
Q ss_pred CCcccCCCCCCcccCcccc
Q psy16040 203 TDLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 203 tNLv~CPqCGhlKl~HrLC 221 (358)
..|..|++||.+-+ ...|
T Consensus 3 s~mr~C~~CgvYTL-k~~C 20 (56)
T PRK13130 3 SKIRKCPKCGVYTL-KEIC 20 (56)
T ss_pred ccceECCCCCCEEc-cccC
Confidence 37889999999988 6666
No 35
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=25.78 E-value=32 Score=27.60 Aligned_cols=17 Identities=18% Similarity=0.512 Sum_probs=13.4
Q ss_pred CCcccCCCCCCcccCcc
Q psy16040 203 TDLTVCNTCGYTHHSKT 219 (358)
Q Consensus 203 tNLv~CPqCGhlKl~Hr 219 (358)
++|.+||.||.....+.
T Consensus 4 d~lKPCPFCG~~~~~v~ 20 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVK 20 (64)
T ss_pred ccccCCCCCCCceeEEE
Confidence 37888999998776654
No 36
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=25.77 E-value=38 Score=22.47 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=8.7
Q ss_pred CcccCCCCCCcc
Q psy16040 204 DLTVCNTCGYTH 215 (358)
Q Consensus 204 NLv~CPqCGhlK 215 (358)
+-..||.||+..
T Consensus 13 ~~~~Cp~CG~~F 24 (26)
T PF10571_consen 13 SAKFCPHCGYDF 24 (26)
T ss_pred hcCcCCCCCCCC
Confidence 567788888754
No 37
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS 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=25.46 E-value=39 Score=22.52 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=9.5
Q ss_pred CCcccCCCCCC
Q psy16040 203 TDLTVCNTCGY 213 (358)
Q Consensus 203 tNLv~CPqCGh 213 (358)
..+..||+||.
T Consensus 24 ~~~~~CP~Cg~ 34 (41)
T smart00834 24 DPLATCPECGG 34 (41)
T ss_pred CCCCCCCCCCC
Confidence 47889999998
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=25.23 E-value=38 Score=21.80 Aligned_cols=16 Identities=25% Similarity=0.796 Sum_probs=10.6
Q ss_pred ccCCCCCCcccC-cccc
Q psy16040 206 TVCNTCGYTHHS-KTLC 221 (358)
Q Consensus 206 v~CPqCGhlKl~-HrLC 221 (358)
..||+||..... .+.|
T Consensus 3 ~~Cp~Cg~~~~~~~~fC 19 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFC 19 (26)
T ss_pred CCCcccCCcCCcccccC
Confidence 479999996433 3445
No 39
>KOG3214|consensus
Probab=24.82 E-value=25 Score=30.68 Aligned_cols=38 Identities=16% Similarity=0.333 Sum_probs=24.2
Q ss_pred cccccCCCcccCCCCCCccc--------------Cccccccccccccceecc
Q psy16040 197 KMLMPRTDLTVCNTCGYTHH--------------SKTLCGKYYSLSISRVKC 234 (358)
Q Consensus 197 KLLkPKtNLv~CPqCGhlKl--------------~HrLC~~~fsla~t~~s~ 234 (358)
|...|+..--.||.|.|.+. .-++|+.-|+.-+|.||.
T Consensus 15 r~~~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~Lse 66 (109)
T KOG3214|consen 15 RRVEPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSE 66 (109)
T ss_pred hhccchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhcc
Confidence 33445555667999999763 235676677776666554
No 40
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=24.59 E-value=1.9e+02 Score=22.89 Aligned_cols=43 Identities=26% Similarity=0.494 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCcceeEEEeCCCCCccccccccCceeEe
Q psy16040 284 KIKEETTRLQDKIVEALGLNPVDKEVVVLYKGEKEHASEEFSETHRVIE 332 (358)
Q Consensus 284 kik~eT~~iq~ki~~~lgl~p~d~evvVlY~ge~~~~~~e~~~~~rvie 332 (358)
...+-..+|++++.+.+|++| +|.++=.|.-+.. -.+.+|||.
T Consensus 52 ~~~~l~~~i~~~lk~~lgv~~---~V~lv~~gtLpr~---~~K~~RviD 94 (96)
T PF14535_consen 52 DLEALAERIAERLKERLGVRP---EVELVPPGTLPRS---EGKAKRVID 94 (96)
T ss_dssp HHHHHHHHHHHHHHHHHSS-E---EEEEE-TT-S------SSSS-SEEE
T ss_pred HHHHHHHHHHHHHHhhcCceE---EEEEECCCCccCC---CCcceEEEe
Confidence 344555688999999999987 5667777776542 247888875
No 41
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=23.73 E-value=71 Score=35.09 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=19.5
Q ss_pred cccccceeeeccccccccccccCcchHHH
Q psy16040 256 KYQSCDIVIQRNCIYNTILFLFTGNCYAK 284 (358)
Q Consensus 256 h~~gch~~~~~~~~~~~~~~~~~g~Cy~k 284 (358)
+.+=||. |-|..-....|++|-..
T Consensus 461 ~~L~CH~-----Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHY-----CGYQEPIPQSCPECGSE 484 (730)
T ss_pred CeeEeCC-----CCCCCCCCCCCCCCCCC
Confidence 6777885 88888888999999755
No 42
>KOG0005|consensus
Probab=23.50 E-value=53 Score=26.75 Aligned_cols=28 Identities=21% Similarity=0.665 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHcCCCCCcceeEEEeCCCC
Q psy16040 288 ETTRLQDKIVEALGLNPVDKEVVVLYKGEK 317 (358)
Q Consensus 288 eT~~iq~ki~~~lgl~p~d~evvVlY~ge~ 317 (358)
-..+|+++|.|..|+.|+.+. ++|.|..
T Consensus 22 kverIKErvEEkeGIPp~qqr--li~~gkq 49 (70)
T KOG0005|consen 22 KVERIKERVEEKEGIPPQQQR--LIYAGKQ 49 (70)
T ss_pred HHHHHHHHhhhhcCCCchhhh--hhhcccc
Confidence 356899999999999999988 6788876
No 43
>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=23.20 E-value=49 Score=25.64 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=16.9
Q ss_pred ccCCCCCCcccCccccccccccccceeccCCCcce
Q psy16040 206 TVCNTCGYTHHSKTLCGKYYSLSISRVKCSFPSLL 240 (358)
Q Consensus 206 v~CPqCGhlKl~HrLC~~~fsla~t~~s~sg~S~l 240 (358)
+.||.|++. +.+||.|.+.+.|.+=|++
T Consensus 8 VkCp~C~~~-------q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 8 VKCPGCYNI-------QTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EE-TTT-SE-------EEEETT-SS-EE-SSSTSE
T ss_pred EECCCCCCe-------eEEEecCCeEEEcccCCCE
Confidence 679999875 2379999998888776654
No 44
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.94 E-value=40 Score=29.79 Aligned_cols=21 Identities=24% Similarity=0.475 Sum_probs=13.7
Q ss_pred cCCCcccCCCCCCcccCcccc
Q psy16040 201 PRTDLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 201 PKtNLv~CPqCGhlKl~HrLC 221 (358)
|-..=..||.||++......|
T Consensus 305 ~~~tS~~C~~cg~~~~r~~~C 325 (364)
T COG0675 305 PYYTSKTCPCCGHLSGRLFKC 325 (364)
T ss_pred CCCCcccccccCCccceeEEC
Confidence 344557899999844445567
No 45
>KOG0786|consensus
Probab=22.52 E-value=29 Score=34.93 Aligned_cols=47 Identities=32% Similarity=0.472 Sum_probs=38.1
Q ss_pred cccccccchhhhhhccceeecccchhhhhhccCCcch-HHHHH----HHhhhcc
Q psy16040 74 TPKPVTKLSLKELFDTSILWAVPKKVEDAHAENRPDS-LQHMC----KMIDVSS 122 (358)
Q Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~~~----~~~~~~~ 122 (358)
.|-|++.+.-....++|+||. |.|+.+.++..|+. |+||. .|+.|.+
T Consensus 181 pp~pl~slDKANVLaaSrLWR--KtV~~~~k~EyP~l~l~hqliDsAAM~Lvk~ 232 (363)
T KOG0786|consen 181 PPGPLCSLDKANVLAASRLWR--KTVTKALKSEYPDLELSHQLIDSAAMQLVKD 232 (363)
T ss_pred CCCCccccchhhHHHHHHHHH--HHHHHHHHhhCCCcchhhhhhhHHHHHHhcC
Confidence 477888888889999999996 88999999999985 78874 4555543
No 46
>PRK00419 DNA primase small subunit; Reviewed
Probab=21.78 E-value=1.1e+02 Score=31.15 Aligned_cols=34 Identities=29% Similarity=0.686 Sum_probs=29.9
Q ss_pred chHHHHHHHHHHHHHHHHHHcCCCCCcceeEEEeCCCC
Q psy16040 280 NCYAKIKEETTRLQDKIVEALGLNPVDKEVVVLYKGEK 317 (358)
Q Consensus 280 ~Cy~kik~eT~~iq~ki~~~lgl~p~d~evvVlY~ge~ 317 (358)
.|..++++++..|-+-+.+.+|++ ++.++|.|-.
T Consensus 116 ~cl~~~k~~a~klld~L~~DFGf~----~i~~vFSG~R 149 (376)
T PRK00419 116 ECLERAKEEALRLLDFLEDDFGFE----DIHVVFSGGR 149 (376)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCC----eeEEEEeCCC
Confidence 899999999999999999999993 4778999944
No 47
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.34 E-value=1e+02 Score=31.57 Aligned_cols=49 Identities=22% Similarity=0.438 Sum_probs=32.4
Q ss_pred CcccCCCCCCcccCccccccccccccceeccCCCcceeeeccCccccccccccccccceeeeccccccccccccCcchH
Q psy16040 204 DLTVCNTCGYTHHSKTLCGKYYSLSISRVKCSFPSLLKVMYPYGLTTNLEKDKYQSCDIVIQRNCIYNTILFLFTGNCY 282 (358)
Q Consensus 204 NLv~CPqCGhlKl~HrLC~~~fsla~t~~s~sg~S~lkv~~~~pl~q~~~~ah~~gch~~~~~~~~~~~~~~~~~g~Cy 282 (358)
....|..||+.- .|++| +..|.+|. +...+-|| .|-|-.-..-.|++|-
T Consensus 212 ~~~~C~~Cg~~~----~C~~C------------~~~l~~h~---------~~~~l~Ch-----~Cg~~~~~~~~Cp~C~ 260 (505)
T TIGR00595 212 KNLLCRSCGYIL----CCPNC------------DVSLTYHK---------KEGKLRCH-----YCGYQEPIPKTCPQCG 260 (505)
T ss_pred CeeEhhhCcCcc----CCCCC------------CCceEEec---------CCCeEEcC-----CCcCcCCCCCCCCCCC
Confidence 357899999864 35322 22333332 24467788 6888888889999994
No 48
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.27 E-value=56 Score=35.06 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=18.0
Q ss_pred CcccCCCCCCc-ccCccccccc
Q psy16040 204 DLTVCNTCGYT-HHSKTLCGKY 224 (358)
Q Consensus 204 NLv~CPqCGhl-Kl~HrLC~~~ 224 (358)
.+..|+.||.. ...|..||+|
T Consensus 565 ~~~iC~~CG~~~~g~~~~CP~C 586 (623)
T PRK08271 565 KITICNDCHHIDKRTGKRCPIC 586 (623)
T ss_pred CCccCCCCCCcCCCCCcCCcCC
Confidence 79999999987 7789999654
No 49
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.98 E-value=62 Score=29.85 Aligned_cols=31 Identities=26% Similarity=0.312 Sum_probs=19.8
Q ss_pred CcchHHHHHHHHHHHHHHHHHHcCCCCCcce
Q psy16040 278 TGNCYAKIKEETTRLQDKIVEALGLNPVDKE 308 (358)
Q Consensus 278 ~g~Cy~kik~eT~~iq~ki~~~lgl~p~d~e 308 (358)
||.=|--...-++..++-+.+..+|+|-++|
T Consensus 74 CGkpyPWt~~~L~aa~el~ee~eeLs~deke 104 (158)
T PF10083_consen 74 CGKPYPWTENALEAANELIEEDEELSPDEKE 104 (158)
T ss_pred CCCCCchHHHHHHHHHHHHHHhhcCCHHHHH
Confidence 3444555666666666666666778777666
No 50
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=20.90 E-value=47 Score=25.08 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=11.3
Q ss_pred CCcccCCCCCCcc
Q psy16040 203 TDLTVCNTCGYTH 215 (358)
Q Consensus 203 tNLv~CPqCGhlK 215 (358)
..|..||+||-+.
T Consensus 9 RGirkCp~CGt~N 21 (44)
T PF14952_consen 9 RGIRKCPKCGTYN 21 (44)
T ss_pred hccccCCcCcCcc
Confidence 3899999999876
No 51
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.65 E-value=45 Score=32.39 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=5.3
Q ss_pred CcccCCCCCCc
Q psy16040 204 DLTVCNTCGYT 214 (358)
Q Consensus 204 NLv~CPqCGhl 214 (358)
|+.+||+|||.
T Consensus 44 ~~~vc~~c~~h 54 (285)
T TIGR00515 44 NLEVCPKCDHH 54 (285)
T ss_pred hCCCCCCCCCc
Confidence 44455555543
No 52
>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=20.50 E-value=54 Score=23.23 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=9.5
Q ss_pred CcccCCCCCCcc
Q psy16040 204 DLTVCNTCGYTH 215 (358)
Q Consensus 204 NLv~CPqCGhlK 215 (358)
....||.||...
T Consensus 25 ~~~~CP~Cg~~~ 36 (52)
T TIGR02605 25 PLATCPECGGEK 36 (52)
T ss_pred CCCCCCCCCCCc
Confidence 567899999843
No 53
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=20.43 E-value=58 Score=27.88 Aligned_cols=33 Identities=30% Similarity=0.517 Sum_probs=21.3
Q ss_pred CCCCCChhHhhhccCCCCCCCccccccCCCcccCCCCCCcccCcc
Q psy16040 175 PKKRRSLERRMNRKYGSKDQVWKMLMPRTDLTVCNTCGYTHHSKT 219 (358)
Q Consensus 175 PKKRrSkERRRkRR~g~pk~~~KLLkPKtNLv~CPqCGhlKl~Hr 219 (358)
||||++..|..+=|- ....+.|.+||.....+-
T Consensus 2 ~kKRrn~GR~K~~rG------------hv~~V~C~nCgr~vPKDK 34 (95)
T PRK09335 2 PKKRENRGRRKGDKG------------HVGYVQCDNCGRRVPRDK 34 (95)
T ss_pred CcccccCCCCCCCCC------------CCccEEeCCCCCcCcCCc
Confidence 677776654432222 347899999998766553
No 54
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.43 E-value=45 Score=22.48 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=9.9
Q ss_pred CcccCCCCCCccc
Q psy16040 204 DLTVCNTCGYTHH 216 (358)
Q Consensus 204 NLv~CPqCGhlKl 216 (358)
.--.||.||..+.
T Consensus 16 ~~~~CP~Cg~~~~ 28 (33)
T cd00350 16 APWVCPVCGAPKD 28 (33)
T ss_pred CCCcCcCCCCcHH
Confidence 4458999998764
No 55
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.35 E-value=43 Score=32.19 Aligned_cols=13 Identities=23% Similarity=0.838 Sum_probs=11.4
Q ss_pred CCCcccCCCCCCc
Q psy16040 202 RTDLTVCNTCGYT 214 (358)
Q Consensus 202 KtNLv~CPqCGhl 214 (358)
++.++.||.||..
T Consensus 218 ~d~iv~CP~CgRI 230 (239)
T COG1579 218 KDEIVFCPYCGRI 230 (239)
T ss_pred CCCCccCCccchH
Confidence 5799999999975
No 56
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=20.30 E-value=1.5e+02 Score=28.52 Aligned_cols=31 Identities=13% Similarity=0.335 Sum_probs=27.5
Q ss_pred ccccccccCcchHHHHHHHHHHHHHHHHHHc
Q psy16040 270 YNTILFLFTGNCYAKIKEETTRLQDKIVEAL 300 (358)
Q Consensus 270 ~~~~~~~~~g~Cy~kik~eT~~iq~ki~~~l 300 (358)
|-++.+-....+|++|++|+...|++|....
T Consensus 220 ~S~lT~~i~~~~~~~i~~~i~~fRk~i~~i~ 250 (271)
T TIGR02147 220 VSTVTFGISEEAYKEIVKKIQEFRKEVLAIA 250 (271)
T ss_pred cceeeEecCHHHHHHHHHHHHHHHHHHHHHH
Confidence 6778888899999999999999999998644
No 57
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.16 E-value=48 Score=30.12 Aligned_cols=18 Identities=44% Similarity=0.722 Sum_probs=14.2
Q ss_pred CcccCCCCCCcccCcccc
Q psy16040 204 DLTVCNTCGYTHHSKTLC 221 (358)
Q Consensus 204 NLv~CPqCGhlKl~HrLC 221 (358)
.|++||.||+.-....+=
T Consensus 31 gLv~CPvCgs~~VsK~lm 48 (142)
T COG5319 31 GLVTCPVCGSTEVSKLLM 48 (142)
T ss_pred CceeCCCCCcHHHHHHhc
Confidence 899999999876655544
No 58
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=20.04 E-value=43 Score=33.04 Aligned_cols=12 Identities=33% Similarity=1.193 Sum_probs=6.7
Q ss_pred CcccCCCCCCcc
Q psy16040 204 DLTVCNTCGYTH 215 (358)
Q Consensus 204 NLv~CPqCGhlK 215 (358)
|+.+||+|||..
T Consensus 56 ~~~vcp~c~~h~ 67 (296)
T CHL00174 56 KMNICEQCGYHL 67 (296)
T ss_pred cCCCCCCCCCCc
Confidence 555666666543
No 59
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=20.01 E-value=48 Score=24.21 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=8.4
Q ss_pred cccCCCCCCccc
Q psy16040 205 LTVCNTCGYTHH 216 (358)
Q Consensus 205 Lv~CPqCGhlKl 216 (358)
|.+||.||.--.
T Consensus 1 LkPCPfCGg~~~ 12 (53)
T TIGR03655 1 LKPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCCcce
Confidence 457999997433
Done!