Query 028695
Match_columns 205
No_of_seqs 205 out of 1320
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 15:32:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028695hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03194 putative disease resi 100.0 2.1E-46 4.5E-51 310.0 16.2 153 12-169 19-175 (187)
2 PLN03210 Resistant to P. syrin 100.0 1.4E-44 3E-49 365.5 15.6 177 14-192 7-218 (1153)
3 PF01582 TIR: TIR domain; Int 99.9 3.7E-26 8.1E-31 180.2 3.7 121 22-142 1-140 (141)
4 smart00255 TIR Toll - interleu 99.9 8.4E-23 1.8E-27 158.8 9.7 126 19-146 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.7 3.1E-18 6.6E-23 127.3 2.9 87 22-116 1-87 (102)
6 KOG3678 SARM protein (with ste 99.0 1.9E-09 4E-14 100.8 8.0 94 15-115 608-709 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.5 1.7E-07 3.7E-12 73.2 6.2 91 20-116 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 97.4 0.00023 4.9E-09 56.2 4.8 65 21-85 2-70 (150)
9 PF10137 TIR-like: Predicted n 96.5 0.0093 2E-07 46.9 6.2 78 21-101 1-91 (125)
10 PF13271 DUF4062: Domain of un 90.5 1 2.3E-05 32.3 6.0 67 21-88 1-67 (83)
11 COG4916 Uncharacterized protei 84.3 1.2 2.6E-05 39.5 3.7 100 15-121 173-280 (329)
12 PF05014 Nuc_deoxyrib_tr: Nucl 83.4 13 0.00027 27.8 8.6 68 33-101 13-88 (113)
13 COG4271 Predicted nucleotide-b 76.5 9 0.0002 32.8 6.2 76 21-101 84-175 (233)
14 PF14258 DUF4350: Domain of un 74.6 17 0.00038 24.7 6.4 61 37-111 8-68 (70)
15 cd00860 ThrRS_anticodon ThrRS 66.3 28 0.00061 24.1 6.1 60 20-84 2-61 (91)
16 PF03129 HGTP_anticodon: Antic 59.6 11 0.00024 26.7 3.0 47 33-84 15-62 (94)
17 cd00738 HGTP_anticodon HGTP an 54.5 54 0.0012 22.7 5.9 60 20-84 2-64 (94)
18 PF11074 DUF2779: Domain of un 53.9 9.1 0.0002 30.1 1.9 33 64-98 61-93 (130)
19 cd02426 Pol_gamma_b_Cterm C-te 53.3 12 0.00027 29.1 2.5 32 33-64 43-77 (128)
20 cd02042 ParA ParA and ParB of 51.5 85 0.0019 22.3 7.9 74 22-99 3-83 (104)
21 PF01990 ATP-synt_F: ATP synth 45.8 87 0.0019 22.7 6.0 68 38-113 8-75 (95)
22 COG1658 Small primase-like pro 43.4 45 0.00098 26.3 4.3 56 19-76 29-84 (127)
23 PF03720 UDPG_MGDP_dh_C: UDP-g 42.7 28 0.00061 25.8 3.0 56 28-83 11-76 (106)
24 COG0400 Predicted esterase [Ge 42.3 93 0.002 26.3 6.4 57 14-72 141-199 (207)
25 PF09441 Abp2: ARS binding pro 40.5 7.4 0.00016 32.1 -0.5 57 88-145 54-114 (175)
26 KOG2792 Putative cytochrome C 39.8 24 0.00052 31.4 2.5 32 89-120 153-187 (280)
27 PF03709 OKR_DC_1_N: Orn/Lys/A 38.3 1.2E+02 0.0026 22.8 5.9 72 35-120 5-77 (115)
28 cd00858 GlyRS_anticodon GlyRS 38.2 1E+02 0.0022 23.1 5.5 60 19-84 26-87 (121)
29 PF02310 B12-binding: B12 bind 36.7 1.7E+02 0.0036 21.3 7.1 71 36-116 17-88 (121)
30 COG0125 Tmk Thymidylate kinase 36.3 2.4E+02 0.0052 23.8 8.0 98 22-121 4-140 (208)
31 PRK09194 prolyl-tRNA synthetas 35.7 44 0.00095 32.3 3.8 64 18-85 467-532 (565)
32 PF14359 DUF4406: Domain of un 34.1 1.9E+02 0.0041 21.2 7.3 62 37-101 19-85 (92)
33 PRK12325 prolyl-tRNA synthetas 34.1 56 0.0012 30.6 4.1 64 19-86 345-410 (439)
34 cd00861 ProRS_anticodon_short 33.6 1.1E+02 0.0024 21.2 4.8 47 34-84 18-64 (94)
35 TIGR00334 5S_RNA_mat_M5 ribonu 32.6 60 0.0013 27.0 3.6 50 33-86 35-84 (174)
36 PF00875 DNA_photolyase: DNA p 31.8 2.3E+02 0.0049 22.2 6.8 95 37-140 56-155 (165)
37 cd01424 MGS_CPS_II Methylglyox 31.1 1.8E+02 0.0039 21.2 5.8 30 21-52 2-31 (110)
38 PRK02228 V-type ATP synthase s 30.8 1.7E+02 0.0038 21.6 5.6 63 42-113 14-77 (100)
39 COG0710 AroD 3-dehydroquinate 29.3 1E+02 0.0022 26.7 4.6 76 34-114 79-155 (231)
40 PF08902 DUF1848: Domain of un 28.5 4.2E+02 0.0091 23.5 9.9 132 19-155 47-201 (266)
41 TIGR00418 thrS threonyl-tRNA s 28.1 1.4E+02 0.0031 28.5 5.9 62 18-84 469-530 (563)
42 TIGR00409 proS_fam_II prolyl-t 27.7 45 0.00097 32.5 2.4 34 32-65 488-521 (568)
43 cd00859 HisRS_anticodon HisRS 27.4 1.9E+02 0.0041 19.2 5.0 34 21-55 3-36 (91)
44 cd07373 2A5CPDO_A The alpha su 26.6 3.3E+02 0.0072 23.6 7.5 78 33-113 90-172 (271)
45 cd00532 MGS-like MGS-like doma 26.6 1.8E+02 0.004 21.5 5.2 61 22-84 2-77 (112)
46 PF03437 BtpA: BtpA family; I 25.3 3E+02 0.0064 24.2 6.8 78 41-126 135-218 (254)
47 COG0276 HemH Protoheme ferro-l 25.1 3.2E+02 0.007 24.9 7.2 80 34-116 73-161 (320)
48 PRK01189 V-type ATP synthase s 25.0 1.2E+02 0.0025 22.9 3.8 41 42-87 16-57 (104)
49 cd03364 TOPRIM_DnaG_primases T 24.7 86 0.0019 21.6 2.8 37 40-78 36-74 (79)
50 cd06342 PBP1_ABC_LIVBP_like Ty 24.6 4E+02 0.0086 22.6 7.6 59 22-81 138-196 (334)
51 cd01857 HSR1_MMR1 HSR1/MMR1. 24.5 2.5E+02 0.0054 21.2 5.7 51 65-118 3-53 (141)
52 TIGR01093 aroD 3-dehydroquinat 24.4 2.3E+02 0.0049 23.8 5.9 69 37-108 82-150 (228)
53 PF03354 Terminase_1: Phage Te 24.2 5.3E+02 0.011 24.2 8.8 112 77-201 156-292 (477)
54 COG0683 LivK ABC-type branched 24.1 3.9E+02 0.0084 23.8 7.7 66 22-88 151-216 (366)
55 KOG1136 Predicted cleavage and 23.7 1.8E+02 0.0039 27.3 5.3 57 56-116 180-242 (501)
56 cd00138 PLDc Phospholipase D. 22.7 2.9E+02 0.0062 21.4 5.9 29 58-86 17-45 (176)
57 PF01113 DapB_N: Dihydrodipico 22.5 3.1E+02 0.0067 20.6 5.8 29 20-52 68-96 (124)
58 cd01423 MGS_CPS_I_III Methylgl 22.4 3.2E+02 0.007 20.1 6.3 29 22-52 3-31 (116)
59 PRK03991 threonyl-tRNA synthet 22.3 1E+02 0.0023 30.3 3.8 43 19-62 499-541 (613)
60 COG0512 PabA Anthranilate/para 22.3 1.6E+02 0.0034 24.9 4.4 47 30-86 8-56 (191)
61 cd00154 Rab Rab family. Rab G 22.1 2.4E+02 0.0052 20.4 5.1 29 59-87 57-86 (159)
62 PF08132 AdoMetDC_leader: S-ad 22.0 87 0.0019 20.9 2.2 24 9-32 10-33 (54)
63 cd06340 PBP1_ABC_ligand_bindin 21.4 4E+02 0.0088 23.1 7.1 63 22-85 147-209 (347)
64 PF10087 DUF2325: Uncharacteri 21.2 2.7E+02 0.006 20.0 5.1 58 35-94 11-69 (97)
65 PRK08661 prolyl-tRNA synthetas 20.3 1.2E+02 0.0027 28.7 3.7 61 19-84 287-354 (477)
66 PRK08350 hypothetical protein; 20.3 90 0.002 28.7 2.7 33 17-49 279-311 (341)
67 cd03411 Ferrochelatase_N Ferro 20.1 4.4E+02 0.0096 20.8 7.2 78 35-115 73-157 (159)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=2.1e-46 Score=309.97 Aligned_cols=153 Identities=23% Similarity=0.407 Sum_probs=133.3
Q ss_pred CCCCCCceeeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhH
Q 028695 12 HHQILQSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWC 91 (205)
Q Consensus 12 ss~~~~~~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wC 91 (205)
||++...+|||||||||+|+|++|++||+.+|+++||+||+|+.++.+|+.|.+.|.+||++|+++|+|||++|++|.||
T Consensus 19 ~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WC 98 (187)
T PLN03194 19 SSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFC 98 (187)
T ss_pred cCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhH
Confidence 33444568999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcccCCCCeEEEEEeecCccccccc-cCcchHHHHHHHHHHHHHhhcccceeecCC---cchhHHHHhHhh
Q 028695 92 LDELAKIVECGNKRKDRKVFAVFYGVDPADVRKQ-KGEDFERKVLKWRAALTTVASLAGWHLQDR---FFPLIYLLLFNY 167 (205)
Q Consensus 92 l~EL~~i~~~~~~~~~~~ViPIFy~v~PsdVr~q-~g~~f~e~v~~Wr~AL~~v~~~~G~~~~~~---~~~~~~~~~~~~ 167 (205)
|+||++|++| ++.||||||+|+|+|||+| .|....+++++||+||++|++++||++..+ ...++..+...+
T Consensus 99 LdEL~~I~e~-----~~~ViPIFY~VdPsdVr~q~~~~~~~e~v~~Wr~AL~~va~l~G~~~~~~~~~e~e~i~~iv~~v 173 (187)
T PLN03194 99 LHELALIMES-----KKRVIPIFCDVKPSQLRVVDNGTCPDEEIRRFNWALEEAKYTVGLTFDSLKGNWSEVVTMASDAV 173 (187)
T ss_pred HHHHHHHHHc-----CCEEEEEEecCCHHHhhccccCCCCHHHHHHHHHHHHHHhccccccCCCCCCCHHHHHHHHHHHH
Confidence 9999999998 3589999999999999997 443337899999999999999999988643 245554444444
Q ss_pred Hh
Q 028695 168 LF 169 (205)
Q Consensus 168 ~~ 169 (205)
..
T Consensus 174 ~k 175 (187)
T PLN03194 174 IK 175 (187)
T ss_pred HH
Confidence 33
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=1.4e-44 Score=365.55 Aligned_cols=177 Identities=38% Similarity=0.651 Sum_probs=154.4
Q ss_pred CCCCceeeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHH
Q 028695 14 QILQSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLD 93 (205)
Q Consensus 14 ~~~~~~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~ 93 (205)
+++.++|||||||||+|+|++|++||+++|.++||.+|+|+ ++++|+.|.+++.+||++|+++|||||++||+|.|||+
T Consensus 7 ~~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~ 85 (1153)
T PLN03210 7 SSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLN 85 (1153)
T ss_pred CCCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHH
Confidence 34578999999999999999999999999999999999987 69999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccCCCCeEEEEEeecCccccccccC---cch--------HHHHHHHHHHHHHhhcccceeecCCc--chhH
Q 028695 94 ELAKIVECGNKRKDRKVFAVFYGVDPADVRKQKG---EDF--------ERKVLKWRAALTTVASLAGWHLQDRF--FPLI 160 (205)
Q Consensus 94 EL~~i~~~~~~~~~~~ViPIFy~v~PsdVr~q~g---~~f--------~e~v~~Wr~AL~~v~~~~G~~~~~~~--~~~~ 160 (205)
||++|++| +++++++|+||||+|+|+|||+|+| +.| .+++++||+||++||+++||++.++- ..++
T Consensus 86 el~~i~~~-~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~~~~~~~~w~~al~~~~~~~g~~~~~~~~E~~~i 164 (1153)
T PLN03210 86 ELLEIVRC-KEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQNWPNEAKMI 164 (1153)
T ss_pred HHHHHHHh-hhhcCceEEEEEecccHHHHhhccchHHHHHHHHhcccchhHHHHHHHHHHHHhCcCceecCCCCCHHHHH
Confidence 99999999 8889999999999999999999999 334 57899999999999999999998751 2333
Q ss_pred HHHhHh----------------------hHhhhhhhhhhcCCCCcceeeccCce
Q 028695 161 YLLLFN----------------------YLFTLIIFCLFSGDVSPLAFYKHTHV 192 (205)
Q Consensus 161 ~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (205)
..+..+ .......++..+.+++..++|||.|+
T Consensus 165 ~~Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGi 218 (1153)
T PLN03210 165 EEIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGI 218 (1153)
T ss_pred HHHHHHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCC
Confidence 222222 23334566677888999999999986
No 3
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.92 E-value=3.7e-26 Score=180.25 Aligned_cols=121 Identities=36% Similarity=0.592 Sum_probs=104.2
Q ss_pred EEEecccccCCcchHHHHHHHHHcC--CeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHH
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRN--GFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIV 99 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~--Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~ 99 (205)
|||||++.+++..|+++|..+|+++ |+++|++++|+.+|..+.+++.++|++||++|+|||++|+.|.||+.||..++
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999444678999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred HhcccCC-CCeEEEEEeecCccccc-cccC---cc------h------HHHHHHHHHHHH
Q 028695 100 ECGNKRK-DRKVFAVFYGVDPADVR-KQKG---ED------F------ERKVLKWRAALT 142 (205)
Q Consensus 100 ~~~~~~~-~~~ViPIFy~v~PsdVr-~q~g---~~------f------~e~v~~Wr~AL~ 142 (205)
+++.+.+ ..+|+||||++.+++++ ++.+ .+ + .++...|++++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 9955533 58999999999999999 6776 11 1 247889998875
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.88 E-value=8.4e-23 Score=158.83 Aligned_cols=126 Identities=43% Similarity=0.723 Sum_probs=102.4
Q ss_pred eeeEEEeccc-ccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHH
Q 028695 19 KYDVFLSFRG-EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAK 97 (205)
Q Consensus 19 ~yDVFISfr~-~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~ 97 (205)
.|||||||++ ++..+.|+.+|..+|...|+.+|.|+.. ..|... .+|.++|++|++.|+|+|++|+.|.||..|+..
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~-~~~~~~-~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~ 78 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFE-PGGGDL-EEIDEAIEKSRIAIVVLSPNYAESEWCLDELVA 78 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcc-cccchH-HHHHHHHHHCcEEEEEECcccccChhHHHHHHH
Confidence 4999999999 4566889999999999999999999753 333333 399999999999999999999999999999999
Q ss_pred HHHhcccCCCCeEEEEEeecCccccccccC----------cchHHHH--HHHHHHHHHhhc
Q 028695 98 IVECGNKRKDRKVFAVFYGVDPADVRKQKG----------EDFERKV--LKWRAALTTVAS 146 (205)
Q Consensus 98 i~~~~~~~~~~~ViPIFy~v~PsdVr~q~g----------~~f~e~v--~~Wr~AL~~v~~ 146 (205)
++++..+.....||||+++..|.++.++.+ ..|.+.. +.|+.++..+.+
T Consensus 79 a~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~~fW~~~~~~l~~ 139 (140)
T smart00255 79 ALENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKERFWKKALYAVPS 139 (140)
T ss_pred HHHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhHHHHHHHHHHhcc
Confidence 998744446789999999988888888776 1221222 689888877653
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.71 E-value=3.1e-18 Score=127.29 Aligned_cols=87 Identities=34% Similarity=0.620 Sum_probs=75.6
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHh
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~ 101 (205)
|||||+++| ..++..|...|++.|+++|+|. ++.+|+.+.+.+.++|++|++.|+++|++|..|+||..|+..+.+
T Consensus 1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~- 76 (102)
T PF13676_consen 1 VFISYSSED--REFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK- 76 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC-
T ss_pred eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH-
Confidence 899999999 4699999999999999999997 999999999999999999999999999999999999999999844
Q ss_pred cccCCCCeEEEEEee
Q 028695 102 GNKRKDRKVFAVFYG 116 (205)
Q Consensus 102 ~~~~~~~~ViPIFy~ 116 (205)
.++.|+||..+
T Consensus 77 ----~~~~iipv~~~ 87 (102)
T PF13676_consen 77 ----RGKPIIPVRLD 87 (102)
T ss_dssp ----TSESEEEEECS
T ss_pred ----CCCEEEEEEEC
Confidence 35699999964
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=98.95 E-value=1.9e-09 Score=100.77 Aligned_cols=94 Identities=28% Similarity=0.473 Sum_probs=80.1
Q ss_pred CCCceeeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcC-------
Q 028695 15 ILQSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS------- 87 (205)
Q Consensus 15 ~~~~~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~------- 87 (205)
+.+.+.|||||||.. +.+..++-|...|+-+|++||+|-+.+..|+ +.+.+++.|...+.+|+|++||...
T Consensus 608 ~~skq~DVFISYRRs-tGnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~n 685 (832)
T KOG3678|consen 608 MLSKQIDVFISYRRS-TGNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDDN 685 (832)
T ss_pred cccCCcceEEEeecc-ccHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhcccc
Confidence 345689999999876 4577999999999999999999988898887 4678999999999999999999763
Q ss_pred -ChhHHHHHHHHHHhcccCCCCeEEEEEe
Q 028695 88 -SPWCLDELAKIVECGNKRKDRKVFAVFY 115 (205)
Q Consensus 88 -S~wCl~EL~~i~~~~~~~~~~~ViPIFy 115 (205)
-.|.-+||.-+++| ++.|||||-
T Consensus 686 CeDWVHKEl~~Afe~-----~KNIiPI~D 709 (832)
T KOG3678|consen 686 CEDWVHKELKCAFEH-----QKNIIPIFD 709 (832)
T ss_pred HHHHHHHHHHHHHHh-----cCCeeeeec
Confidence 35777788888888 678999984
No 7
>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.
Probab=98.55 E-value=1.7e-07 Score=73.23 Aligned_cols=91 Identities=23% Similarity=0.404 Sum_probs=49.3
Q ss_pred eeEEEecccccCCcchHHHHHHHHHcC-------CeEE----------EEcCCCCCCCccchHHHHHHHHhcCceEEEec
Q 028695 20 YDVFLSFRGEDTRNNFTDNLHTALIRN-------GFIA----------FKDDETLDRGNEISSELSKAIEESNVSIVILS 82 (205)
Q Consensus 20 yDVFISfr~~D~r~~Fv~~L~~aL~~~-------Gi~v----------f~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S 82 (205)
|.|||||++.|.. ..+..|...+... .+.. +.+..+....+.|...|.++|.+|.++||+++
T Consensus 1 ~~vFIS~~~~d~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDDD-WYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------THH--HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCcH-HHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 6899999999843 3677777777663 1211 12222333445788899999999999999999
Q ss_pred cCCcCChhHHHHHHHHHHhcccCCCCeEEEEEee
Q 028695 83 KNYASSPWCLDELAKIVECGNKRKDRKVFAVFYG 116 (205)
Q Consensus 83 ~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPIFy~ 116 (205)
++-..|+|+..|+..+++. +..||.|-..
T Consensus 80 ~~T~~s~wV~~EI~~A~~~-----~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALKK-----GKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTTT--------EEEEETT
T ss_pred CCcccCcHHHHHHHHHHHC-----CCCEEEEECC
Confidence 9999999999999998875 7788888654
No 8
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=97.42 E-value=0.00023 Score=56.22 Aligned_cols=65 Identities=20% Similarity=0.339 Sum_probs=52.4
Q ss_pred eEEEecccccCC-cchHHHHHHHHHcC-CeEEEEcCCCCCC--CccchHHHHHHHHhcCceEEEeccCC
Q 028695 21 DVFLSFRGEDTR-NNFTDNLHTALIRN-GFIAFKDDETLDR--GNEISSELSKAIEESNVSIVILSKNY 85 (205)
Q Consensus 21 DVFISfr~~D~r-~~Fv~~L~~aL~~~-Gi~vf~D~~dl~~--G~~i~~~i~~aI~~Sri~IvV~S~~y 85 (205)
.|||||+..... ...|..|...|++. |+.|.+|.-+... +.....=+.+++++++..|+|+||.+
T Consensus 2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~ 70 (150)
T PF08357_consen 2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 599999885543 36789999999999 9999999766633 55666667888999999999999544
No 9
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=96.46 E-value=0.0093 Score=46.91 Aligned_cols=78 Identities=18% Similarity=0.250 Sum_probs=61.4
Q ss_pred eEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccC-Cc------------C
Q 028695 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN-YA------------S 87 (205)
Q Consensus 21 DVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~-y~------------~ 87 (205)
.|||.|. +|. .....+...|+..|+.+.+-.+....|..+.+.+.++..+++.+|++++|+ .. -
T Consensus 1 kVFIvhg-~~~--~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RDL--AAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CCH--HHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 3899997 553 578889999998888877655567999999999999999999999999995 22 1
Q ss_pred ChhHHHHHHHHHHh
Q 028695 88 SPWCLDELAKIVEC 101 (205)
Q Consensus 88 S~wCl~EL~~i~~~ 101 (205)
-...+.|+-..+..
T Consensus 78 R~NVifE~G~f~g~ 91 (125)
T PF10137_consen 78 RQNVIFELGLFIGK 91 (125)
T ss_pred ccceeehhhHHHhh
Confidence 23456788887754
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=90.52 E-value=1 Score=32.26 Aligned_cols=67 Identities=24% Similarity=0.222 Sum_probs=47.3
Q ss_pred eEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCC
Q 028695 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASS 88 (205)
Q Consensus 21 DVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S 88 (205)
.||||-.-.|.. .--..|.+.|.+.|.....-+.--..+....+.+++.|++|++.|.++-.+|-..
T Consensus 1 rVFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 1 RVFISSTFRDLK-EERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CEEEecChhhHH-HHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 389998777753 3446788888777765443221112355566788999999999999999999754
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=84.35 E-value=1.2 Score=39.47 Aligned_cols=100 Identities=19% Similarity=0.088 Sum_probs=67.6
Q ss_pred CCCceeeEEEecccccCCcchHHHHHHHHH--cCCeEEEEcCCC---CCCCccchHHHHHHH--HhcCceEEEeccCCcC
Q 028695 15 ILQSKYDVFLSFRGEDTRNNFTDNLHTALI--RNGFIAFKDDET---LDRGNEISSELSKAI--EESNVSIVILSKNYAS 87 (205)
Q Consensus 15 ~~~~~yDVFISfr~~D~r~~Fv~~L~~aL~--~~Gi~vf~D~~d---l~~G~~i~~~i~~aI--~~Sri~IvV~S~~y~~ 87 (205)
...+.||+=+||.|+- .+.|+....+++ ..-+..|+|-.- +-+|+ +. .++.-+ +.|++.+|.+..+|..
T Consensus 173 ~~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~-~~L~~~Y~~rC~~~~VF~~~~Y~~ 248 (329)
T COG4916 173 SSEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LV-STLDPGYDIRCVVTTVFNTGSYIC 248 (329)
T ss_pred ccccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HH-HhcccccCceEEEEEEEeCCceEE
Confidence 3467899999999986 469999999998 445788888531 23333 22 223222 2588899999999999
Q ss_pred ChhHHHHHHHHHHhcccCCCCeEEEEEe-ecCccc
Q 028695 88 SPWCLDELAKIVECGNKRKDRKVFAVFY-GVDPAD 121 (205)
Q Consensus 88 S~wCl~EL~~i~~~~~~~~~~~ViPIFy-~v~Psd 121 (205)
..||.-|-..+-+- ..-....||-| +++-+-
T Consensus 249 K~~c~~E~~~~r~~---~~~d~~~rI~~~~~d~~a 280 (329)
T COG4916 249 KSTCHIEGLEGRLN---PILDTGFRIKYLYADNIA 280 (329)
T ss_pred eeeeccchhhcccc---ccccccceEEEEecCCcc
Confidence 99999887776332 11235667766 444443
No 12
>PF05014 Nuc_deoxyrib_tr: Nucleoside 2-deoxyribosyltransferase; InterPro: IPR007710 Nucleoside 2-deoxyribosyltransferase (2.4.2.6 from EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [] and class II [] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.; GO: 0050144 nucleoside deoxyribosyltransferase activity, 0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity, 0009159 deoxyribonucleoside monophosphate catabolic process; PDB: 1S2L_A 1S2D_C 1S2I_A 1S3F_B 1S2G_C 2A0K_A 2F67_A 2F64_B 2F62_A 2F2T_A ....
Probab=83.38 E-value=13 Score=27.78 Aligned_cols=68 Identities=21% Similarity=0.196 Sum_probs=49.6
Q ss_pred cchHHHHHHHHHcCCeEEEEcCC-CCC-------CCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHh
Q 028695 33 NNFTDNLHTALIRNGFIAFKDDE-TLD-------RGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (205)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~-dl~-------~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~ 101 (205)
..+...+.++|++.|+.+|...+ +.. ....|...-.++|++|++.|+++...- -+.=+.-|+..+...
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~al 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYAL 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHC
Confidence 56889999999999999997542 111 122344555678999999999998765 456678899998765
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=76.52 E-value=9 Score=32.82 Aligned_cols=76 Identities=21% Similarity=0.291 Sum_probs=57.1
Q ss_pred eEEEecccccCCcchHHHHHHHHHcC-Ce-EEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCc--------CChh
Q 028695 21 DVFLSFRGEDTRNNFTDNLHTALIRN-GF-IAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA--------SSPW 90 (205)
Q Consensus 21 DVFISfr~~D~r~~Fv~~L~~aL~~~-Gi-~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~--------~S~w 90 (205)
.|||-|+++ ..+.....+|.+. .. .+|.|. -+..|..+.+.+.+-|.+++.+|++.+|+=. +-.|
T Consensus 84 kvFvv~ghd----~iArael~allrd~~l~~vi~d~-~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~ 158 (233)
T COG4271 84 KVFVVSGHD----AIARAELEALLRDWKLEPVILDG-LFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAF 158 (233)
T ss_pred eEEEEeccH----HHHHHHHHHHhhccccceEEecC-cccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhcc
Confidence 999999654 2666667777643 33 456565 6889999999999999999999999999843 1223
Q ss_pred ------HHHHHHHHHHh
Q 028695 91 ------CLDELAKIVEC 101 (205)
Q Consensus 91 ------Cl~EL~~i~~~ 101 (205)
.+.||...+.+
T Consensus 159 praRqNVifELGm~mgr 175 (233)
T COG4271 159 PRARQNVIFELGMFMGR 175 (233)
T ss_pred ccccccchhhHhhHHhh
Confidence 56788888765
No 14
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=74.57 E-value=17 Score=24.65 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=38.2
Q ss_pred HHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEE
Q 028695 37 DNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVF 111 (205)
Q Consensus 37 ~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~Vi 111 (205)
.-|+.-|++.|+++-.... ..++++..+-.++++++.+.-+. -.|+..+.+. .+.++..||
T Consensus 8 ~a~~~~L~~~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~-v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEW-VEAGNTLVL 68 (70)
T ss_pred HHHHHHHHHCCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHH-HHcCCEEEE
Confidence 4577888888998754432 12345568889999999965543 3455555555 334555544
No 15
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=66.28 E-value=28 Score=24.07 Aligned_cols=60 Identities=10% Similarity=0.153 Sum_probs=37.4
Q ss_pred eeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccC
Q 028695 20 YDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (205)
Q Consensus 20 yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~ 84 (205)
++|+|...+++. ...+-.+...|.+.|+.+-+|.+. ..+...+..|-..---.++++.++
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~~----~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLRN----EKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHHcCCCEEEEECcc
Confidence 677776655443 346788999999999999998743 344445555533222244555544
No 16
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=59.57 E-value=11 Score=26.72 Aligned_cols=47 Identities=17% Similarity=0.274 Sum_probs=31.3
Q ss_pred cchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHH-hcCceEEEeccC
Q 028695 33 NNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIE-ESNVSIVILSKN 84 (205)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~-~Sri~IvV~S~~ 84 (205)
..++.+|...|.+.||.+.+|+.+. .+...+..|-. +... ++|+.++
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~~~----~~~k~~~~a~~~g~p~-~iiiG~~ 62 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDSDK----SLGKQIKYADKLGIPF-IIIIGEK 62 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESSSS----THHHHHHHHHHTTESE-EEEEEHH
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCC----chhHHHHHHhhcCCeE-EEEECch
Confidence 3578999999999999999997544 44444555543 3444 4445544
No 17
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=54.51 E-value=54 Score=22.68 Aligned_cols=60 Identities=20% Similarity=0.300 Sum_probs=37.8
Q ss_pred eeEEEecccc---cCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccC
Q 028695 20 YDVFLSFRGE---DTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (205)
Q Consensus 20 yDVFISfr~~---D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~ 84 (205)
++|+|-.-++ . ....+-.+...|.+.|+.+-+|.. +..+...+..|-..---.++++.++
T Consensus 2 ~~v~ii~~~~~~~~-~~~~a~~~~~~Lr~~g~~v~~~~~----~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVE-AREYAQKLLNALLANGIRVLYDDR----ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHH-HHHHHHHHHHHHHHCCCEEEecCC----CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 5666665343 2 235677889999999999999774 3455545555533333456677764
No 18
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=53.91 E-value=9.1 Score=30.13 Aligned_cols=33 Identities=36% Similarity=0.443 Sum_probs=18.8
Q ss_pred hHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHH
Q 028695 64 SSELSKAIEESNVSIVILSKNYASSPWCLDELAKI 98 (205)
Q Consensus 64 ~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i 98 (205)
...+.++|..-..+|+|++..|-++ |+.||..+
T Consensus 61 ~~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 61 IEALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 3344444444435677777766543 77777665
No 19
>cd02426 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase.
Probab=53.27 E-value=12 Score=29.06 Aligned_cols=32 Identities=9% Similarity=0.146 Sum_probs=25.3
Q ss_pred cchHHHHHHHHHcCCeEEEEcCCCC---CCCccch
Q 028695 33 NNFTDNLHTALIRNGFIAFKDDETL---DRGNEIS 64 (205)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~dl---~~G~~i~ 64 (205)
...+..|+..|...|+.+..|+++- .+|..+.
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~~ 77 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLLD 77 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHHH
Confidence 5678999999999999999998753 4555543
No 20
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=51.55 E-value=85 Score=22.29 Aligned_cols=74 Identities=18% Similarity=0.178 Sum_probs=46.7
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCC-------CCccchHHHHHHHHhcCceEEEeccCCcCChhHHHH
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLD-------RGNEISSELSKAIEESNVSIVILSKNYASSPWCLDE 94 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~-------~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~E 94 (205)
+|.+..|--.+-.++.+|...|.++|.++.+-|-|.. -+-...+....++..|+..|+++.++.. .+..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~----s~~~ 78 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL----DLDG 78 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH----HHHH
Confidence 3566655544455679999999989988776433322 1112234455788889988888887643 4444
Q ss_pred HHHHH
Q 028695 95 LAKIV 99 (205)
Q Consensus 95 L~~i~ 99 (205)
+..++
T Consensus 79 ~~~~~ 83 (104)
T cd02042 79 LEKLL 83 (104)
T ss_pred HHHHH
Confidence 44443
No 21
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=45.82 E-value=87 Score=22.67 Aligned_cols=68 Identities=16% Similarity=0.221 Sum_probs=43.6
Q ss_pred HHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEE
Q 028695 38 NLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAV 113 (205)
Q Consensus 38 ~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPI 113 (205)
.+...|.-.|+..+... ...+++...+.+.+++..+.|++++++++.. -.+++....+. ...-.|++|
T Consensus 8 ~~v~gFrLaGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~--~~~~l~~~~~~---~~~P~iv~I 75 (95)
T PF01990_consen 8 DTVLGFRLAGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAEK--IRDELDEYREE---SSLPLIVEI 75 (95)
T ss_dssp HHHHHHHHTTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT--HHHHHHHHHHT---SSSSEEEEE
T ss_pred HHHHHHHHcCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH--HHHHHHHHHhc---cCCceEEEc
Confidence 34556777899988765 1235566667777778999999999998773 23444444332 233445554
No 22
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=43.45 E-value=45 Score=26.31 Aligned_cols=56 Identities=14% Similarity=0.200 Sum_probs=42.4
Q ss_pred eeeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCc
Q 028695 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNV 76 (205)
Q Consensus 19 ~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri 76 (205)
..++|+-..+.=....+++.|..++..+|+-++.|.+ .+|+.|...+.+.+.++.-
T Consensus 29 ~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D--~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 29 DAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD--RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC--cchHHHHHHHHHHhccccc
Confidence 4567776654322256889999999999999999975 6899999888888877544
No 23
>PF03720 UDPG_MGDP_dh_C: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; InterPro: IPR014027 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the C-terminal substrate-binding domain of these enzymes. Structural studies indicate that this domain forms an incomplete dinucleotide binding fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3GG2_D 1DLI_A 1DLJ_A 2Y0E_D 2Y0D_B 2Y0C_D 1MV8_B 1MUU_A 1MFZ_C 3TDK_B ....
Probab=42.69 E-value=28 Score=25.76 Aligned_cols=56 Identities=20% Similarity=0.273 Sum_probs=34.0
Q ss_pred cccCCcchHHHHHHHHHcCCeEEEEcCCCCCC----------CccchHHHHHHHHhcCceEEEecc
Q 028695 28 GEDTRNNFTDNLHTALIRNGFIAFKDDETLDR----------GNEISSELSKAIEESNVSIVILSK 83 (205)
Q Consensus 28 ~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~----------G~~i~~~i~~aI~~Sri~IvV~S~ 83 (205)
..|+|.+=+-.|.+.|.++|+.+.+.|--+.. |-.+.+.+.++++.+++.|+.-..
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h 76 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDH 76 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecC
Confidence 35889999999999999999998876532211 222334567888888876654433
No 24
>COG0400 Predicted esterase [General function prediction only]
Probab=42.31 E-value=93 Score=26.29 Aligned_cols=57 Identities=21% Similarity=0.120 Sum_probs=43.3
Q ss_pred CCCCceeeEEEecccccC--CcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHH
Q 028695 14 QILQSKYDVFLSFRGEDT--RNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIE 72 (205)
Q Consensus 14 ~~~~~~yDVFISfr~~D~--r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~ 72 (205)
.......-|||++-..|. -.....+|.+.|+..|..+..... ..|-.|.++-.++++
T Consensus 141 ~~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~--~~GH~i~~e~~~~~~ 199 (207)
T COG0400 141 LPDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWH--EGGHEIPPEELEAAR 199 (207)
T ss_pred ccccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEEe--cCCCcCCHHHHHHHH
Confidence 445667889999988886 355679999999999999988763 477788766555544
No 25
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=40.54 E-value=7.4 Score=32.09 Aligned_cols=57 Identities=28% Similarity=0.441 Sum_probs=37.5
Q ss_pred ChhHHHHHHHHHHhcccCCCCeEEEEEeecCcccccc-ccC---cchHHHHHHHHHHHHHhh
Q 028695 88 SPWCLDELAKIVECGNKRKDRKVFAVFYGVDPADVRK-QKG---EDFERKVLKWRAALTTVA 145 (205)
Q Consensus 88 S~wCl~EL~~i~~~~~~~~~~~ViPIFy~v~PsdVr~-q~g---~~f~e~v~~Wr~AL~~v~ 145 (205)
|.|-|.||..-++. .+-+.=.=+-+.++|+|-++.+ |+. ..|.=++++|..|++--|
T Consensus 54 s~~~Lf~LI~k~~~-keikTW~~La~~LGVepp~~ek~qStQKvqQYaVRLKRWM~aMHVDA 114 (175)
T PF09441_consen 54 STFTLFELIRKLES-KEIKTWAQLALELGVEPPDPEKGQSTQKVQQYAVRLKRWMRAMHVDA 114 (175)
T ss_pred hHHHHHHHHHHHhh-hhHhHHHHHHHHhCCCCCCcccccchHHHHHHHHHHHHHHHHhhHHH
Confidence 67888888877665 4333333455567899887654 443 345667889999986433
No 26
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=39.75 E-value=24 Score=31.36 Aligned_cols=32 Identities=28% Similarity=0.406 Sum_probs=23.6
Q ss_pred hhHHHHHHHHHH---hcccCCCCeEEEEEeecCcc
Q 028695 89 PWCLDELAKIVE---CGNKRKDRKVFAVFYGVDPA 120 (205)
Q Consensus 89 ~wCl~EL~~i~~---~~~~~~~~~ViPIFy~v~Ps 120 (205)
.=|-|||.++.. .+....+..++|||.-+||.
T Consensus 153 DICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 153 DICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred CcChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 348899877653 33556677778999999994
No 27
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=38.32 E-value=1.2e+02 Score=22.78 Aligned_cols=72 Identities=18% Similarity=0.183 Sum_probs=44.6
Q ss_pred hHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHh-cCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEE
Q 028695 35 FTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEE-SNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAV 113 (205)
Q Consensus 35 Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~-Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPI 113 (205)
-+..|..+|+++|+.+..-.. .+.....++. ++++-||++=+ ....-...++...++. ...=+||
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~--------~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~-----~~~~iPV 70 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS--------TDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRE-----RNFGIPV 70 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS--------HHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHH-----HSTT-EE
T ss_pred HHHHHHHHHHHCCCEEEEeCC--------hHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHH-----hCCCCCE
Confidence 457899999999998775442 3456666664 89999999866 1111122333333333 3456899
Q ss_pred EeecCcc
Q 028695 114 FYGVDPA 120 (205)
Q Consensus 114 Fy~v~Ps 120 (205)
|.-.++.
T Consensus 71 Fl~~~~~ 77 (115)
T PF03709_consen 71 FLLAERD 77 (115)
T ss_dssp EEEESCC
T ss_pred EEEecCC
Confidence 9876643
No 28
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=38.24 E-value=1e+02 Score=23.12 Aligned_cols=60 Identities=15% Similarity=0.104 Sum_probs=38.6
Q ss_pred eeeEEEeccc--ccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccC
Q 028695 19 KYDVFLSFRG--EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (205)
Q Consensus 19 ~yDVFISfr~--~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~ 84 (205)
.+||+|-.-+ ++ ....+-.|...|.+.|+++-+|.+ ..+...+..|-+.---.++++.++
T Consensus 26 p~~v~Ii~~~~~~~-~~~~a~~la~~LR~~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 26 PIKVAVLPLVKRDE-LVEIAKEISEELRELGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred CcEEEEEecCCcHH-HHHHHHHHHHHHHHCCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcC
Confidence 5788887755 32 234677899999999999999863 244444555533333346666655
No 29
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=36.74 E-value=1.7e+02 Score=21.33 Aligned_cols=71 Identities=20% Similarity=0.177 Sum_probs=44.0
Q ss_pred HHHHHHHHHcCCeEEE-EcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEEE
Q 028695 36 TDNLHTALIRNGFIAF-KDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAVF 114 (205)
Q Consensus 36 v~~L~~aL~~~Gi~vf-~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPIF 114 (205)
...|...|++.|+.+- +|- ... .+++.+++.+.+.-+|.+|-.+. |...++..+.+. .+.....+.-|+
T Consensus 17 l~~la~~l~~~G~~v~~~d~-~~~-----~~~l~~~~~~~~pd~V~iS~~~~---~~~~~~~~l~~~-~k~~~p~~~iv~ 86 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDA-NVP-----PEELVEALRAERPDVVGISVSMT---PNLPEAKRLARA-IKERNPNIPIVV 86 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEES-SB------HHHHHHHHHHTTCSEEEEEESSS---THHHHHHHHHHH-HHTTCTTSEEEE
T ss_pred HHHHHHHHHHCCCeEEEECC-CCC-----HHHHHHHHhcCCCcEEEEEccCc---CcHHHHHHHHHH-HHhcCCCCEEEE
Confidence 3678888999999885 443 221 26788888888888888877543 445555555554 333333344344
Q ss_pred ee
Q 028695 115 YG 116 (205)
Q Consensus 115 y~ 116 (205)
-+
T Consensus 87 GG 88 (121)
T PF02310_consen 87 GG 88 (121)
T ss_dssp EE
T ss_pred EC
Confidence 34
No 30
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=36.32 E-value=2.4e+02 Score=23.81 Aligned_cols=98 Identities=15% Similarity=0.245 Sum_probs=56.9
Q ss_pred EEEecccccC--CcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHH----------------------------H
Q 028695 22 VFLSFRGEDT--RNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKA----------------------------I 71 (205)
Q Consensus 22 VFISfr~~D~--r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~a----------------------------I 71 (205)
.||.+-|-|- ..+-+..|.+.|+.+|++|.+-.+ +.|..+...|.+. |
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~trE--P~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~i 81 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTRE--PGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEVI 81 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC--CCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4788877664 246789999999999998777542 2221111111111 1
Q ss_pred Hh-cCceEEEeccCCcCChhHHH--------HHHHHHHhcccCCCCeEEEEEeecCccc
Q 028695 72 EE-SNVSIVILSKNYASSPWCLD--------ELAKIVECGNKRKDRKVFAVFYGVDPAD 121 (205)
Q Consensus 72 ~~-Sri~IvV~S~~y~~S~wCl~--------EL~~i~~~~~~~~~~~ViPIFy~v~Psd 121 (205)
.- -.-.-+|++..|..|.-+.. +....++.....+-..-+-+|++|+|..
T Consensus 82 ~pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~ 140 (208)
T COG0125 82 KPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEV 140 (208)
T ss_pred HHhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHH
Confidence 10 11134888999998887765 3333333312222245667788999975
No 31
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=35.68 E-value=44 Score=32.30 Aligned_cols=64 Identities=13% Similarity=0.204 Sum_probs=40.8
Q ss_pred ceeeEEEeccc--ccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCC
Q 028695 18 SKYDVFLSFRG--EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY 85 (205)
Q Consensus 18 ~~yDVFISfr~--~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y 85 (205)
-.++|+|---+ .+.-...+..|+..|++.||.+.+|+++-.+|..+...- ..... .++++.++.
T Consensus 467 aP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~~~ad---~~GiP-~~iiiG~~e 532 (565)
T PRK09194 467 APFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKFADAD---LIGIP-HRIVVGDRG 532 (565)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHHHHHH---hcCCC-EEEEEcCcc
Confidence 35888887543 222346788999999999999999997655555543221 22233 355566553
No 32
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=34.15 E-value=1.9e+02 Score=21.20 Aligned_cols=62 Identities=10% Similarity=0.105 Sum_probs=41.1
Q ss_pred HHHHHHHHcCCeEEEEcCCCC--CCCccchHHH---HHHHHhcCceEEEeccCCcCChhHHHHHHHHHHh
Q 028695 37 DNLHTALIRNGFIAFKDDETL--DRGNEISSEL---SKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (205)
Q Consensus 37 ~~L~~aL~~~Gi~vf~D~~dl--~~G~~i~~~i---~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~ 101 (205)
....+.|..+|..|. ..-.+ ..|.....-+ +..+.+|+. +++=++.-.|+=|.-|+..+.+.
T Consensus 19 ~~~a~~L~~~G~~vv-nPa~~~~~~~~~~~~ym~~~l~~L~~cD~--i~~l~gWe~S~GA~~E~~~A~~l 85 (92)
T PF14359_consen 19 NAAAKRLRAKGYEVV-NPAELGIPEGLSWEEYMRICLAMLSDCDA--IYMLPGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHHHHHHHCCCEEe-CchhhCCCCCCCHHHHHHHHHHHHHhCCE--EEEcCCcccCcchHHHHHHHHHC
Confidence 457778889996655 32233 4555444333 345556663 44459999999999999998765
No 33
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=34.09 E-value=56 Score=30.55 Aligned_cols=64 Identities=14% Similarity=0.074 Sum_probs=39.7
Q ss_pred eeeEEEeccc--ccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCc
Q 028695 19 KYDVFLSFRG--EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (205)
Q Consensus 19 ~yDVFISfr~--~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~ 86 (205)
.++|.|---+ .+.....+..|+..|.+.||.|.+|+++-..|..+. .|-..---.++|+.++-.
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~ki~----~a~~~giP~~iiVG~~e~ 410 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGAKFA----TMDLIGLPWQIIVGPKGL 410 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhHHHH----HHHHcCCCEEEEECCccc
Confidence 3688775432 222345788999999999999999987544454433 332222224566666543
No 34
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=33.62 E-value=1.1e+02 Score=21.19 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=29.8
Q ss_pred chHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccC
Q 028695 34 NFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (205)
Q Consensus 34 ~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~ 84 (205)
..+..|...|.+.|+++.+|.+.-..|. .+..|-..---.++++.++
T Consensus 18 ~~a~~la~~Lr~~g~~v~~d~~~~~l~k----~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 18 ELAEKLYAELQAAGVDVLLDDRNERPGV----KFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHCCCEEEEECCCCCccc----chhHHHhcCCCEEEEECCc
Confidence 4678899999999999999875333333 4444433322345555554
No 35
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=32.58 E-value=60 Score=27.02 Aligned_cols=50 Identities=16% Similarity=0.304 Sum_probs=37.1
Q ss_pred cchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCc
Q 028695 33 NNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (205)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~ 86 (205)
..-...|..+.+.+|+-+|.|.+ .+|+.|...|.+.+-+++.+- +++.++
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD--~~GekIRk~i~~~vp~~khaf--i~~~~a 84 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD--FPGEKIRKKIEQHLPGYENCF--IPKHLA 84 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC--CchHHHHHHHHHHCCCCeEEe--eeHHhc
Confidence 44567788888899999999985 689999888888887666543 344444
No 36
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=31.82 E-value=2.3e+02 Score=22.17 Aligned_cols=95 Identities=20% Similarity=0.258 Sum_probs=49.1
Q ss_pred HHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEEE--
Q 028695 37 DNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAVF-- 114 (205)
Q Consensus 37 ~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPIF-- 114 (205)
..|...|.+.|+...+-. |+ ..+.+.+-+++..+..|++...|..- -...-..+.+. ....+..+.-+-
T Consensus 56 ~~L~~~L~~~g~~L~v~~-----g~-~~~~l~~l~~~~~~~~V~~~~~~~~~--~~~rd~~v~~~-l~~~~i~~~~~~~~ 126 (165)
T PF00875_consen 56 ADLQESLRKLGIPLLVLR-----GD-PEEVLPELAKEYGATAVYFNEEYTPY--ERRRDERVRKA-LKKHGIKVHTFDDH 126 (165)
T ss_dssp HHHHHHHHHTTS-EEEEE-----SS-HHHHHHHHHHHHTESEEEEE---SHH--HHHHHHHHHHH-HHHTTSEEEEE--S
T ss_pred HHHHHHHHhcCcceEEEe-----cc-hHHHHHHHHHhcCcCeeEeccccCHH--HHHHHHHHHHH-HHhcceEEEEECCc
Confidence 677888888999877543 33 23455566788889999999998752 22211222222 111222222111
Q ss_pred eecCccccccccC---cchHHHHHHHHHH
Q 028695 115 YGVDPADVRKQKG---EDFERKVLKWRAA 140 (205)
Q Consensus 115 y~v~PsdVr~q~g---~~f~e~v~~Wr~A 140 (205)
+=+.|.++....| +.|-...++|...
T Consensus 127 ~L~~~~~i~~~~~~~~~vFtpf~k~~~~~ 155 (165)
T PF00875_consen 127 TLVPPDDIPKKDGEPYKVFTPFRKKWEKQ 155 (165)
T ss_dssp SSS-HHHCHSTTSSSHSSHHHHHHHHHCH
T ss_pred EEEeccccccCCCCCcccHHHHHHHHHhc
Confidence 1266888877666 4445555556443
No 37
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=31.10 E-value=1.8e+02 Score=21.24 Aligned_cols=30 Identities=23% Similarity=0.291 Sum_probs=21.5
Q ss_pred eEEEecccccCCcchHHHHHHHHHcCCeEEEE
Q 028695 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFK 52 (205)
Q Consensus 21 DVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~ 52 (205)
.||+|.+..|. .-...+.+.|.+.|+++|-
T Consensus 2 ~vl~s~~~~~k--~~~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 2 TVFISVADRDK--PEAVEIAKRLAELGFKLVA 31 (110)
T ss_pred eEEEEEEcCcH--hHHHHHHHHHHHCCCEEEE
Confidence 37899877662 3344777788888988875
No 38
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=30.78 E-value=1.7e+02 Score=21.60 Aligned_cols=63 Identities=11% Similarity=0.238 Sum_probs=35.8
Q ss_pred HHHcCCeEEEE-cCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEE
Q 028695 42 ALIRNGFIAFK-DDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAV 113 (205)
Q Consensus 42 aL~~~Gi~vf~-D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPI 113 (205)
.+...|+..+. .++ -+++...+.+.+.+-++.|++++++++.. +-+++...++. ...-.|+||
T Consensus 14 GFrLaGi~~~~~~~~----~ee~~~~l~~l~~~~d~gII~Ite~~~~~--i~e~i~~~~~~---~~~P~ii~I 77 (100)
T PRK02228 14 GFRLAGIRKVYEVPD----DEKLDEAVEEVLEDDDVGILVMHDDDLEK--LPRRLRRTLEE---SVEPTVVTL 77 (100)
T ss_pred HHHHcCCceEEeeCC----HHHHHHHHHHHhhCCCEEEEEEehhHhHh--hHHHHHHHHhc---CCCCEEEEE
Confidence 45567886443 221 13455555556677789999999997652 33444443332 223345555
No 39
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=29.28 E-value=1e+02 Score=26.71 Aligned_cols=76 Identities=20% Similarity=0.154 Sum_probs=45.6
Q ss_pred chHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCC-CCeEEE
Q 028695 34 NFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRK-DRKVFA 112 (205)
Q Consensus 34 ~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~-~~~ViP 112 (205)
.....|.+..+.+| .-|+|= ++..++....++.+.-.+-+ +|+|-+..++.+.++|+..++..|...+ ...-|+
T Consensus 79 ~~i~ll~~la~~~~-~d~iDi-El~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~aDivKiA 153 (231)
T COG0710 79 EYIELLKKLAELNG-PDYIDI-ELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLGADIVKIA 153 (231)
T ss_pred HHHHHHHHHHhhcC-CCEEEE-EccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhCCCeEEEE
Confidence 45566666666666 456665 34333322222222222222 8889999999999999999998865555 334444
Q ss_pred EE
Q 028695 113 VF 114 (205)
Q Consensus 113 IF 114 (205)
+.
T Consensus 154 vm 155 (231)
T COG0710 154 VM 155 (231)
T ss_pred ec
Confidence 44
No 40
>PF08902 DUF1848: Domain of unknown function (DUF1848); InterPro: IPR014998 This group of proteins are functionally uncharacterised. The C terminus contains a cluster of cysteines that are similar to the iron-sulphur cluster found at the N terminus of IPR007197 from INTERPRO.
Probab=28.48 E-value=4.2e+02 Score=23.49 Aligned_cols=132 Identities=17% Similarity=0.228 Sum_probs=80.9
Q ss_pred eeeEEEecccccCCcchHHHHHHHHHcCCeEEEEc------CCCCCCCccchHHHHHHHHh-------cCce----EEEe
Q 028695 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKD------DETLDRGNEISSELSKAIEE-------SNVS----IVIL 81 (205)
Q Consensus 19 ~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D------~~dl~~G~~i~~~i~~aI~~-------Sri~----IvV~ 81 (205)
..|.++ |-.++.. .|..+|. .|.+.|++.++. .++++|+-.-..++.+++++ -|+. =|++
T Consensus 47 ~Vd~iV-FWTKnp~-P~l~~L~-~l~~~gy~~yfq~Tit~Y~~~lEp~vP~~~~~i~~f~~Ls~~iG~~rViWRYDPIil 123 (266)
T PF08902_consen 47 DVDCIV-FWTKNPA-PFLPYLD-ELDERGYPYYFQFTITGYGKDLEPNVPPKDERIETFRELSERIGPERVIWRYDPIIL 123 (266)
T ss_pred cceEEE-EecCCcH-HHHhhHH-HHHhCCCceEEEEEeCCCCccccCCCCCHHHHHHHHHHHHHHHCCCcEEEecCCEeE
Confidence 344444 5456653 5777775 578889988874 44688876544444443332 2222 1567
Q ss_pred ccCCcCChhHHHHHHHHHHhcccCCCCeEEEEEeecCccccccccC-----cch-HHHHHHHHHHHHHhhcccceeecCC
Q 028695 82 SKNYASSPWCLDELAKIVECGNKRKDRKVFAVFYGVDPADVRKQKG-----EDF-ERKVLKWRAALTTVASLAGWHLQDR 155 (205)
Q Consensus 82 S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPIFy~v~PsdVr~q~g-----~~f-~e~v~~Wr~AL~~v~~~~G~~~~~~ 155 (205)
+..|.- .|-++.+..+.+. .+.....++-=|.+..+.--++... ... .+....--..|.++|.-.|..+..-
T Consensus 124 ~~~~~~-~~h~~~F~~la~~-L~g~t~~~viSF~D~Y~k~~~~l~~~~~~~~~~~~~~~~~l~~~l~~ia~~~g~~l~tC 201 (266)
T PF08902_consen 124 TDKYTV-DYHLEAFERLAEA-LAGYTDRCVISFLDLYRKVRRNLARLGFRIREPSEEEKRELAKRLAEIAKKYGMTLYTC 201 (266)
T ss_pred CCCCCH-HHHHHHHHHHHHH-HhccCCEEEEEeeeccHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHcCCEEEeC
Confidence 777543 7888888888877 5555667777787776643333222 111 4556666778899998888776543
No 41
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=28.05 E-value=1.4e+02 Score=28.52 Aligned_cols=62 Identities=11% Similarity=0.213 Sum_probs=41.7
Q ss_pred ceeeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccC
Q 028695 18 SKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (205)
Q Consensus 18 ~~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~ 84 (205)
...||+|-.-+++. ...+..|...|.+.|++|-+|.+ +..+...+..|-+.---.++|+.++
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~~ 530 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGDK 530 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEchh
Confidence 35788887655543 46788999999999999999874 4455555655543333345555554
No 42
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=27.66 E-value=45 Score=32.48 Aligned_cols=34 Identities=18% Similarity=0.364 Sum_probs=27.8
Q ss_pred CcchHHHHHHHHHcCCeEEEEcCCCCCCCccchH
Q 028695 32 RNNFTDNLHTALIRNGFIAFKDDETLDRGNEISS 65 (205)
Q Consensus 32 r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~ 65 (205)
....+..|++.|+..|+.+.+|+++-.+|..+.+
T Consensus 488 ~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~d 521 (568)
T TIGR00409 488 QQQLAEELYSELLAQGVDVLLDDRNERAGVKFAD 521 (568)
T ss_pred HHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHHh
Confidence 3467899999999999999999987667766543
No 43
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=27.40 E-value=1.9e+02 Score=19.22 Aligned_cols=34 Identities=26% Similarity=0.172 Sum_probs=23.6
Q ss_pred eEEEecccccCCcchHHHHHHHHHcCCeEEEEcCC
Q 028695 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDE 55 (205)
Q Consensus 21 DVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~ 55 (205)
||+|...+++. ..-+-.+...|.+.|+++.++..
T Consensus 3 ~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~ 36 (91)
T cd00859 3 DVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYG 36 (91)
T ss_pred cEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecC
Confidence 67666544432 23467788999999999988653
No 44
>cd07373 2A5CPDO_A The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO) catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the alpha subunit, which does not contain a potential metal binding site and may not possess catalytic activity.
Probab=26.63 E-value=3.3e+02 Score=23.61 Aligned_cols=78 Identities=21% Similarity=0.236 Sum_probs=52.0
Q ss_pred cchHHHHHHHHHcCCeEEE-EcCCC--CCCCccchHHHHHHH-H-hcCceEEEeccCCcCChhHHHHHHHHHHhcccCCC
Q 028695 33 NNFTDNLHTALIRNGFIAF-KDDET--LDRGNEISSELSKAI-E-ESNVSIVILSKNYASSPWCLDELAKIVECGNKRKD 107 (205)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf-~D~~d--l~~G~~i~~~i~~aI-~-~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~ 107 (205)
..++..+.+.|.+.||.+- +|... +--|--+. +.-+ . ..++-||.+|-+..-+.....+|-+++....+..+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 5689999999999999886 66632 44444332 2333 2 46777888999886677777789888873223334
Q ss_pred CeEEEE
Q 028695 108 RKVFAV 113 (205)
Q Consensus 108 ~~ViPI 113 (205)
++|+-|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 566644
No 45
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=26.61 E-value=1.8e+02 Score=21.50 Aligned_cols=61 Identities=25% Similarity=0.360 Sum_probs=34.2
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEEcCC--------CC-----CCCcc-chHHHHHHHHh-cCceEEEeccC
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDE--------TL-----DRGNE-ISSELSKAIEE-SNVSIVILSKN 84 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~--------dl-----~~G~~-i~~~i~~aI~~-Sri~IvV~S~~ 84 (205)
||||-+..| +.-...+.+.|...|++++--.. .+ .++.. -.+++.+.|.+ -++.+||..|+
T Consensus 2 i~isv~d~~--K~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn~~~ 77 (112)
T cd00532 2 VFLSVSDHV--KAMLVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEccc--HHHHHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 688876665 23344777777788887764321 11 11100 12456666766 66666666554
No 46
>PF03437 BtpA: BtpA family; InterPro: IPR005137 Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A [], which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA [], Ycf3 [, ], and Ycf4 (IPR003359 from INTERPRO) []. Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation []. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane [, ]. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain []. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids []. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners []. Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions.
Probab=25.26 E-value=3e+02 Score=24.17 Aligned_cols=78 Identities=17% Similarity=0.236 Sum_probs=48.4
Q ss_pred HHHHcCCeEEEEcCC---C-CCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEEEe-
Q 028695 41 TALIRNGFIAFKDDE---T-LDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAVFY- 115 (205)
Q Consensus 41 ~aL~~~Gi~vf~D~~---d-l~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPIFy- 115 (205)
+.|... +++|-|=+ . -..+..+.+....+++....=-+++|-.-...+=-+++|..+-+. -. +|||.
T Consensus 135 ~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~----~~---~PVlvG 206 (254)
T PF03437_consen 135 KRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREA----VP---VPVLVG 206 (254)
T ss_pred HHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhc----CC---CCEEEe
Confidence 344444 99998732 1 123445666767788887776666676654433345555555332 22 99999
Q ss_pred -ecCcccccccc
Q 028695 116 -GVDPADVRKQK 126 (205)
Q Consensus 116 -~v~PsdVr~q~ 126 (205)
.+.+.++.++.
T Consensus 207 SGvt~~Ni~~~l 218 (254)
T PF03437_consen 207 SGVTPENIAEYL 218 (254)
T ss_pred cCCCHHHHHHHH
Confidence 48898887764
No 47
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=25.07 E-value=3.2e+02 Score=24.86 Aligned_cols=80 Identities=19% Similarity=0.272 Sum_probs=52.0
Q ss_pred chHHHHHHHHHcC----CeEEEEcCCCCCCCccchHHHHHHHHhcC---ceEEEeccCCcCCh--hHHHHHHHHHHhccc
Q 028695 34 NFTDNLHTALIRN----GFIAFKDDETLDRGNEISSELSKAIEESN---VSIVILSKNYASSP--WCLDELAKIVECGNK 104 (205)
Q Consensus 34 ~Fv~~L~~aL~~~----Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sr---i~IvV~S~~y~~S~--wCl~EL~~i~~~~~~ 104 (205)
..+..+.++|+++ .++|++- ++-|.+..++..+++.+.. +.++.+.|.|..+. --.+++..+++..+.
T Consensus 73 ~~T~~q~~~L~~~L~~~~~~V~~a---mry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~~~~ 149 (320)
T COG0276 73 VITRAQAAALEERLDLPDFKVYLA---MRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRG 149 (320)
T ss_pred HHHHHHHHHHHHHhCCCCccEEEe---ecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHhcCC
Confidence 3455666666654 5677763 4567776667777776644 57788888887543 357788888866232
Q ss_pred CCCCeEEEEEee
Q 028695 105 RKDRKVFAVFYG 116 (205)
Q Consensus 105 ~~~~~ViPIFy~ 116 (205)
......||-||+
T Consensus 150 ~~~i~~I~~~~~ 161 (320)
T COG0276 150 QPKISTIPDYYD 161 (320)
T ss_pred CCceEEecCccC
Confidence 234578888876
No 48
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=25.05 E-value=1.2e+02 Score=22.93 Aligned_cols=41 Identities=5% Similarity=0.167 Sum_probs=30.5
Q ss_pred HHHcCCeE-EEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcC
Q 028695 42 ALIRNGFI-AFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (205)
Q Consensus 42 aL~~~Gi~-vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~ 87 (205)
.++..|+. +|...++ + -...+.+.+.+-++.|++++++++.
T Consensus 16 GFrlaGi~~v~~~~~~----e-~~~~~~~~l~~~~~gII~iTE~~a~ 57 (104)
T PRK01189 16 GFRLLGIGDTIEAEGK----D-LVKKFLEIFNNPKCKYIFVSESTKN 57 (104)
T ss_pred HHHHcCCceEEEcCCH----H-HHHHHHHHHhcCCeEEEEEEHHHHh
Confidence 46677996 8865432 2 2367788888999999999999775
No 49
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=24.69 E-value=86 Score=21.64 Aligned_cols=37 Identities=14% Similarity=0.187 Sum_probs=21.0
Q ss_pred HHHHHc--CCeEEEEcCCCCCCCccchHHHHHHHHhcCceE
Q 028695 40 HTALIR--NGFIAFKDDETLDRGNEISSELSKAIEESNVSI 78 (205)
Q Consensus 40 ~~aL~~--~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~I 78 (205)
...|.+ +.+.+|.|.+ .+|......+.+....-...+
T Consensus 36 ~~~L~~~~~~vii~~D~D--~aG~~a~~~~~~~l~~~g~~~ 74 (79)
T cd03364 36 AELLKRLAKEVILAFDGD--EAGQKAALRALELLLKLGLNV 74 (79)
T ss_pred HHHHHhcCCeEEEEECCC--HHHHHHHHHHHHHHHHCCCeE
Confidence 444444 5677777764 466666555555555544433
No 50
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=24.63 E-value=4e+02 Score=22.57 Aligned_cols=59 Identities=17% Similarity=0.136 Sum_probs=31.5
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEe
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVIL 81 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~ 81 (205)
|.+-+...+.....+..|.++|+..|+++-... .+.+|..=...+...|++++.-+|++
T Consensus 138 v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~d~~~~l~~i~~~~~~~vi~ 196 (334)
T cd06342 138 VAIIDDKTAYGQGLADEFKKALKAAGGKVVARE-GTTDGATDFSAILTKIKAANPDAVFF 196 (334)
T ss_pred EEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEe-cCCCCCccHHHHHHHHHhcCCCEEEE
Confidence 444343333334566777788887887765433 35555322234455566665555544
No 51
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=24.54 E-value=2.5e+02 Score=21.24 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCCeEEEEEeecC
Q 028695 65 SELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAVFYGVD 118 (205)
Q Consensus 65 ~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~~ViPIFy~v~ 118 (205)
.++.++|+++++.++|+.-.-..+.+. .++...+.. .. .+..++-|+=+.|
T Consensus 3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~-~~l~~~l~~-~~-~~k~~iivlNK~D 53 (141)
T cd01857 3 RQLWRVVERSDIVVQIVDARNPLLFRP-PDLERYVKE-VD-PRKKNILLLNKAD 53 (141)
T ss_pred HHHHHHHhhCCEEEEEEEccCCcccCC-HHHHHHHHh-cc-CCCcEEEEEechh
Confidence 356677888888777777654444332 244444443 11 2344454444433
No 52
>TIGR01093 aroD 3-dehydroquinate dehydratase, type I. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by TIGR01088.
Probab=24.42 E-value=2.3e+02 Score=23.81 Aligned_cols=69 Identities=17% Similarity=0.123 Sum_probs=38.7
Q ss_pred HHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCChhHHHHHHHHHHhcccCCCC
Q 028695 37 DNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDR 108 (205)
Q Consensus 37 ~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~ 108 (205)
..|..+..+.+. -++|= |+..++....++.+++...+ .-+|.|-+.....|-.+|+..+++.+.+.+..
T Consensus 82 ~ll~~~~~~~~~-d~vDi-El~~~~~~~~~l~~~~~~~~-~kvI~S~H~f~~tp~~~~l~~~~~~~~~~gaD 150 (228)
T TIGR01093 82 EELKRAADSPGP-DFVDI-ELFLPDDAVKELINIAKKGG-TKIIMSYHDFQKTPSWEEIVERLEKALSYGAD 150 (228)
T ss_pred HHHHHHHHhCCC-CEEEE-EccCCHHHHHHHHHHHHHCC-CEEEEeccCCCCCCCHHHHHHHHHHHHHhCCC
Confidence 333333334443 44454 34444444444555444444 45666887778888889988888774444333
No 53
>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.20 E-value=5.3e+02 Score=24.20 Aligned_cols=112 Identities=17% Similarity=0.119 Sum_probs=60.0
Q ss_pred eEEEeccCCcCChhHHHHHHHHHHhcc---cCCCCeEEEEEeecCc-cccccccC-----------cchHHHHHHHHHHH
Q 028695 77 SIVILSKNYASSPWCLDELAKIVECGN---KRKDRKVFAVFYGVDP-ADVRKQKG-----------EDFERKVLKWRAAL 141 (205)
Q Consensus 77 ~IvV~S~~y~~S~wCl~EL~~i~~~~~---~~~~~~ViPIFy~v~P-sdVr~q~g-----------~~f~e~v~~Wr~AL 141 (205)
.+++-+..+..+..|-+++..+.+.+. +......+|+.|..+. .++.+... .........|+.|.
T Consensus 156 ~~~ISTag~~~~~~~~~~~~~~~~iL~g~~~~~d~~~f~~i~~~d~~~d~~D~~~W~kANP~Lg~~~~~~~l~~~~~~a~ 235 (477)
T PF03354_consen 156 IIIISTAGDDRSGPCDEEYDYARKILDGRGEIEDDRYFPFIYEADDDDDWDDPENWIKANPSLGVSVSLEYLREEAEKAR 235 (477)
T ss_pred EEEEeCCCCCCCcHHHHHHHHHHHHHHhccCccCCceEEEEecCCccccccChhhHhhcCCCCCCCccHHHHHHHHHHHH
Confidence 344444556778888877776665422 3455789999998765 33444322 11123344555555
Q ss_pred HHhhcccce---eecCC-------cchhHHHHhHhhHhhhhhhhhhcCCCCcceeeccCceeeeeecccc
Q 028695 142 TTVASLAGW---HLQDR-------FFPLIYLLLFNYLFTLIIFCLFSGDVSPLAFYKHTHVTSLEISSSN 201 (205)
Q Consensus 142 ~~v~~~~G~---~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (205)
..-+....| +++-+ |.+.. .+.-+..+....+.|.+-++|++.|+.+
T Consensus 236 ~~~~~~~~f~~k~lN~w~~~~~~~~i~~~-------------~w~~~~~~~~~~~~g~~~~~G~DlS~~~ 292 (477)
T PF03354_consen 236 RSPSKEAEFLTKRLNIWVQASEDSWIDME-------------DWDACCDVDLEDLRGRPCYIGLDLSSTT 292 (477)
T ss_pred hhhhhHHHHHHHhcCeeeeccccccCCHH-------------HHHhcCCCChHHhCCCEEEEEEeeCCCC
Confidence 443333332 11111 11111 1111244555567788889999999865
No 54
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=24.13 E-value=3.9e+02 Score=23.79 Aligned_cols=66 Identities=15% Similarity=0.100 Sum_probs=33.9
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCcCC
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASS 88 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~~S 88 (205)
|+|-++...-.+++...+.+.|+.+|.++-.++ ...+++.-...+...|..++.-+|++...+...
T Consensus 151 v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~-~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~ 216 (366)
T COG0683 151 VAIIGDDYAYGEGLADAFKAALKALGGEVVVEE-VYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDA 216 (366)
T ss_pred EEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEE-eeCCCCCChHHHHHHHHhcCCCEEEECCCCccc
Confidence 444444443345566666666666766522222 344444334445555555555555555554443
No 55
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=23.67 E-value=1.8e+02 Score=27.28 Aligned_cols=57 Identities=23% Similarity=0.441 Sum_probs=38.8
Q ss_pred CCCCCccchHHHHHHHHhcCceEEEeccCCc----CChhHHH-H-HHHHHHhcccCCCCeEEEEEee
Q 028695 56 TLDRGNEISSELSKAIEESNVSIVILSKNYA----SSPWCLD-E-LAKIVECGNKRKDRKVFAVFYG 116 (205)
Q Consensus 56 dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~----~S~wCl~-E-L~~i~~~~~~~~~~~ViPIFy~ 116 (205)
++.|...+.. .-|..+|--++|--..|+ .|+.|.+ | |.+..+| ...+++.+||||--
T Consensus 180 nmTpDrHLGa---A~id~~rpdlLIsESTYattiRdskr~rERdFLk~Vhec-Va~GGkvlIPvFAL 242 (501)
T KOG1136|consen 180 NMTPDRHLGA---AWIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHEC-VARGGKVLIPVFAL 242 (501)
T ss_pred cCCcccccch---hhhccccCceEEeeccceeeeccccchhHHHHHHHHHHH-HhcCCeEEEEeeec
Confidence 4444444432 236677777776666677 5888876 4 5566789 77789999999953
No 56
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=22.70 E-value=2.9e+02 Score=21.36 Aligned_cols=29 Identities=28% Similarity=0.176 Sum_probs=18.9
Q ss_pred CCCccchHHHHHHHHhcCceEEEeccCCc
Q 028695 58 DRGNEISSELSKAIEESNVSIVILSKNYA 86 (205)
Q Consensus 58 ~~G~~i~~~i~~aI~~Sri~IvV~S~~y~ 86 (205)
..++.+.+.+.++|.+++..|.+.+..+.
T Consensus 17 ~~~~~~~~~i~~~I~~A~~~I~i~~~~~~ 45 (176)
T cd00138 17 VGGRSDLDALLEAISNAKKSIYIASFYLS 45 (176)
T ss_pred cCcchHHHHHHHHHHhhheEEEEEEeEec
Confidence 34556666677777777777777776544
No 57
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=22.53 E-value=3.1e+02 Score=20.64 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=12.9
Q ss_pred eeEEEecccccCCcchHHHHHHHHHcCCeEEEE
Q 028695 20 YDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFK 52 (205)
Q Consensus 20 yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~ 52 (205)
.||-|-|+..+ ....++..+++. |+++-+
T Consensus 68 ~DVvIDfT~p~---~~~~~~~~~~~~-g~~~Vi 96 (124)
T PF01113_consen 68 ADVVIDFTNPD---AVYDNLEYALKH-GVPLVI 96 (124)
T ss_dssp -SEEEEES-HH---HHHHHHHHHHHH-T-EEEE
T ss_pred CCEEEEcCChH---HhHHHHHHHHhC-CCCEEE
Confidence 66666666443 233444444433 555444
No 58
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=22.44 E-value=3.2e+02 Score=20.10 Aligned_cols=29 Identities=10% Similarity=0.146 Sum_probs=21.8
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEE
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFK 52 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~ 52 (205)
||+|....| +. -...+.+.|...|+++|-
T Consensus 3 vlisv~~~d-k~-~~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYS-KP-ELLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCccc-ch-hHHHHHHHHHHCCCEEEE
Confidence 799998776 33 345777888888998875
No 59
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=22.31 E-value=1e+02 Score=30.34 Aligned_cols=43 Identities=16% Similarity=0.154 Sum_probs=31.1
Q ss_pred eeeEEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCcc
Q 028695 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNE 62 (205)
Q Consensus 19 ~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~ 62 (205)
.++|+|---+++ ....+..|...|.+.||+|.+|+++-..|..
T Consensus 499 P~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~slgkK 541 (613)
T PRK03991 499 PTQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDESLGKK 541 (613)
T ss_pred CceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCCCHHHH
Confidence 368776654443 3467899999999999999999864444433
No 60
>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=22.31 E-value=1.6e+02 Score=24.94 Aligned_cols=47 Identities=28% Similarity=0.345 Sum_probs=33.7
Q ss_pred cCCcchHHHHHHHHHcCC--eEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCCc
Q 028695 30 DTRNNFTDNLHTALIRNG--FIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (205)
Q Consensus 30 D~r~~Fv~~L~~aL~~~G--i~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y~ 86 (205)
|...+|+-.|+..|.+.| +.|+.++ + +. ...++..+--.+|+||.=-
T Consensus 8 DNyDSFtyNLv~yl~~lg~~v~V~rnd-~------~~---~~~~~~~~pd~iviSPGPG 56 (191)
T COG0512 8 DNYDSFTYNLVQYLRELGAEVTVVRND-D------IS---LELIEALKPDAIVISPGPG 56 (191)
T ss_pred ECccchHHHHHHHHHHcCCceEEEECC-c------cC---HHHHhhcCCCEEEEcCCCC
Confidence 344589999999999877 6677665 2 12 1267777778899999743
No 61
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di
Probab=22.11 E-value=2.4e+02 Score=20.44 Aligned_cols=29 Identities=14% Similarity=0.147 Sum_probs=19.9
Q ss_pred CCcc-chHHHHHHHHhcCceEEEeccCCcC
Q 028695 59 RGNE-ISSELSKAIEESNVSIVILSKNYAS 87 (205)
Q Consensus 59 ~G~~-i~~~i~~aI~~Sri~IvV~S~~y~~ 87 (205)
+|.. ........+++++..|+|++..-..
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~ 86 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRE 86 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHH
Confidence 4433 3344566788999999999986533
No 62
>PF08132 AdoMetDC_leader: S-adenosyl-l-methionine decarboxylase leader peptide; InterPro: IPR012511 This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism [].
Probab=21.97 E-value=87 Score=20.86 Aligned_cols=24 Identities=29% Similarity=0.283 Sum_probs=17.6
Q ss_pred CCCCCCCCCceeeEEEecccccCC
Q 028695 9 SSTHHQILQSKYDVFLSFRGEDTR 32 (205)
Q Consensus 9 sssss~~~~~~yDVFISfr~~D~r 32 (205)
||+|++.....|.+=|-|+-+|.|
T Consensus 10 ssssss~~s~~yeaPLgYsIEDvR 33 (54)
T PF08132_consen 10 SSSSSSSNSLFYEAPLGYSIEDVR 33 (54)
T ss_pred ccccccccceEEeccccceeeecc
Confidence 334445555679999999999987
No 63
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=21.45 E-value=4e+02 Score=23.12 Aligned_cols=63 Identities=10% Similarity=0.096 Sum_probs=33.9
Q ss_pred EEEecccccCCcchHHHHHHHHHcCCeEEEEcCCCCCCCccchHHHHHHHHhcCceEEEeccCC
Q 028695 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY 85 (205)
Q Consensus 22 VFISfr~~D~r~~Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~i~~~i~~aI~~Sri~IvV~S~~y 85 (205)
|.+-+...+-....+..+..+|++.|+.+-... .+.+++.=.......|.+++.-+|++.-..
T Consensus 147 v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~-~~~~~~~d~~~~i~~l~~~~~d~v~~~~~~ 209 (347)
T cd06340 147 VALVHEDTEFGTSVAEAIKKFAKERGFEIVEDI-SYPANARDLTSEVLKLKAANPDAILPASYT 209 (347)
T ss_pred EEEEecCchHhHHHHHHHHHHHHHcCCEEEEee-ccCCCCcchHHHHHHHHhcCCCEEEEcccc
Confidence 444443222224456667777777887765433 355554323344556666666666665444
No 64
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.16 E-value=2.7e+02 Score=19.96 Aligned_cols=58 Identities=19% Similarity=0.256 Sum_probs=34.3
Q ss_pred hHHHHHHHHHcCCeEEEEcCCCCCCCcc-chHHHHHHHHhcCceEEEeccCCcCChhHHHH
Q 028695 35 FTDNLHTALIRNGFIAFKDDETLDRGNE-ISSELSKAIEESNVSIVILSKNYASSPWCLDE 94 (205)
Q Consensus 35 Fv~~L~~aL~~~Gi~vf~D~~dl~~G~~-i~~~i~~aI~~Sri~IvV~S~~y~~S~wCl~E 94 (205)
...++...+++.|.+.-... -..|.. -...+...|.++++.|++..----...|...+
T Consensus 11 ~~~~~~~~~~~~G~~~~~hg--~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 11 RERRYKRILEKYGGKLIHHG--RDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred cHHHHHHHHHHcCCEEEEEe--cCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 46678888899998765551 111221 12247778888998777655443344444333
No 65
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=20.27 E-value=1.2e+02 Score=28.69 Aligned_cols=61 Identities=11% Similarity=0.071 Sum_probs=37.9
Q ss_pred eeeEEEeccc-----ccCCcchHHHHHHHHHcCCeEEEEcC-CCCCCCccchHHHHHHH-HhcCceEEEeccC
Q 028695 19 KYDVFLSFRG-----EDTRNNFTDNLHTALIRNGFIAFKDD-ETLDRGNEISSELSKAI-EESNVSIVILSKN 84 (205)
Q Consensus 19 ~yDVFISfr~-----~D~r~~Fv~~L~~aL~~~Gi~vf~D~-~dl~~G~~i~~~i~~aI-~~Sri~IvV~S~~ 84 (205)
.++|+|---. .+.-...+..|...|.+.||+|-+|+ ++-.+|..+. +|- .+.. .++++.++
T Consensus 287 P~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~gkK~~----~ae~~GvP-~~IiIG~~ 354 (477)
T PRK08661 287 PIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPGWKFN----EWELKGVP-LRIEIGPR 354 (477)
T ss_pred CCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHH----HHHHCCCC-EEEEECcc
Confidence 4788776431 12224578899999999999999998 4445555443 332 2333 45555655
No 66
>PRK08350 hypothetical protein; Provisional
Probab=20.27 E-value=90 Score=28.71 Aligned_cols=33 Identities=9% Similarity=0.094 Sum_probs=29.4
Q ss_pred CceeeEEEecccccCCcchHHHHHHHHHcCCeE
Q 028695 17 QSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFI 49 (205)
Q Consensus 17 ~~~yDVFISfr~~D~r~~Fv~~L~~aL~~~Gi~ 49 (205)
...|.+.+|||+-+|..+|+.||.-+|...-|+
T Consensus 279 ~~g~~~vvSHRSGETeD~~IAdLaVa~~agqIK 311 (341)
T PRK08350 279 SERITPILAEAKYESADEALPHLAVGLRCPAML 311 (341)
T ss_pred HcCCeEEeecCCCCCcchhHHHHHHHhCCCccc
Confidence 346899999999999999999999999988886
No 67
>cd03411 Ferrochelatase_N Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=20.08 E-value=4.4e+02 Score=20.76 Aligned_cols=78 Identities=19% Similarity=0.296 Sum_probs=43.5
Q ss_pred hHHHHHHHHHcCC--eEEEEcCCCCCCCccchHHHHHHHHh---cCceEEEeccCCcCC--hhHHHHHHHHHHhcccCCC
Q 028695 35 FTDNLHTALIRNG--FIAFKDDETLDRGNEISSELSKAIEE---SNVSIVILSKNYASS--PWCLDELAKIVECGNKRKD 107 (205)
Q Consensus 35 Fv~~L~~aL~~~G--i~vf~D~~dl~~G~~i~~~i~~aI~~---Sri~IvV~S~~y~~S--~wCl~EL~~i~~~~~~~~~ 107 (205)
.+..|.+.|.+.+ +.++.- ++-|+...++..+.+.+ .++.++-+.|.|..+ .-+++++...+........
T Consensus 73 q~~~l~~~L~~~~~~~~v~~a---mry~~P~i~~~l~~l~~~g~~~iivlPl~P~~S~~Tt~s~~~~~~~~~~~~~~~~~ 149 (159)
T cd03411 73 QAEALEKALDERGIDVKVYLA---MRYGPPSIEEALEELKADGVDRIVVLPLYPQYSASTTGSYLDEVERALKKLRPAPE 149 (159)
T ss_pred HHHHHHHHHhccCCCcEEEeh---HhcCCCCHHHHHHHHHHcCCCEEEEEECCcccccccHHHHHHHHHHHHHhcCCCCc
Confidence 4566666676543 444442 44555554554444443 556788888888644 4477777777654122233
Q ss_pred CeEEEEEe
Q 028695 108 RKVFAVFY 115 (205)
Q Consensus 108 ~~ViPIFy 115 (205)
..+|+-||
T Consensus 150 ~~~i~~~~ 157 (159)
T cd03411 150 LRVIRSFY 157 (159)
T ss_pred EEEeCccc
Confidence 45555444
Done!