Query 027772
Match_columns 219
No_of_seqs 207 out of 1318
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 14:56:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03210 Resistant to P. syrin 100.0 4.2E-49 9.1E-54 402.7 18.3 189 13-206 6-218 (1153)
2 PLN03194 putative disease resi 100.0 5.3E-47 1.1E-51 315.5 16.3 155 12-185 19-177 (187)
3 PF01582 TIR: TIR domain; Int 99.9 9.6E-28 2.1E-32 191.2 2.1 134 22-156 1-140 (141)
4 smart00255 TIR Toll - interleu 99.9 2.3E-24 5.1E-29 169.4 12.3 138 19-160 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.7 5.8E-18 1.3E-22 127.0 3.2 87 22-116 1-87 (102)
6 KOG3678 SARM protein (with ste 99.0 1.1E-09 2.4E-14 102.8 7.6 94 15-115 608-709 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.5 2E-07 4.3E-12 73.5 6.2 91 20-116 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 97.5 0.00041 8.8E-09 55.3 7.7 65 21-85 2-70 (150)
9 PF10137 TIR-like: Predicted n 96.4 0.01 2.2E-07 47.0 6.3 78 21-101 1-91 (125)
10 PF13271 DUF4062: Domain of un 90.2 0.98 2.1E-05 32.7 5.6 67 21-88 1-67 (83)
11 COG4916 Uncharacterized protei 86.7 0.74 1.6E-05 41.0 3.5 99 16-121 174-280 (329)
12 PF05014 Nuc_deoxyrib_tr: Nucl 80.9 17 0.00037 27.3 8.6 68 33-101 13-88 (113)
13 COG4271 Predicted nucleotide-b 78.4 6.5 0.00014 33.9 5.9 97 21-125 84-200 (233)
14 cd00860 ThrRS_anticodon ThrRS 72.9 16 0.00035 25.6 6.1 60 20-84 2-61 (91)
15 PF14258 DUF4350: Domain of un 67.4 31 0.00068 23.5 6.4 61 37-111 8-68 (70)
16 cd00738 HGTP_anticodon HGTP an 62.0 32 0.00069 24.1 5.8 60 20-84 2-64 (94)
17 PF03129 HGTP_anticodon: Antic 59.5 26 0.00057 25.0 5.1 48 33-84 15-62 (94)
18 PF01990 ATP-synt_F: ATP synth 59.0 46 0.001 24.3 6.4 68 38-113 8-75 (95)
19 cd02042 ParA ParA and ParB of 53.6 58 0.0012 23.4 6.1 64 22-85 3-73 (104)
20 COG0125 Tmk Thymidylate kinase 53.3 76 0.0017 27.0 7.6 98 22-121 4-140 (208)
21 PF09441 Abp2: ARS binding pro 52.6 3.7 8.1E-05 34.0 -0.5 59 88-157 54-112 (175)
22 cd02426 Pol_gamma_b_Cterm C-te 52.4 13 0.00027 29.2 2.5 32 32-63 42-76 (128)
23 cd00858 GlyRS_anticodon GlyRS 52.4 44 0.00096 25.4 5.5 60 19-84 26-87 (121)
24 PF11074 DUF2779: Domain of un 52.3 10 0.00023 30.0 2.0 32 65-98 62-93 (130)
25 KOG2792 Putative cytochrome C 44.2 19 0.00042 32.1 2.6 32 89-120 153-187 (280)
26 COG0400 Predicted esterase [Ge 43.0 93 0.002 26.5 6.5 58 13-72 140-199 (207)
27 COG1658 Small primase-like pro 40.4 50 0.0011 26.3 4.1 56 19-76 29-84 (127)
28 PF02310 B12-binding: B12 bind 38.7 1.6E+02 0.0034 21.7 7.3 57 36-101 17-74 (121)
29 PF03720 UDPG_MGDP_dh_C: UDP-g 38.5 34 0.00073 25.5 2.8 56 29-84 12-77 (106)
30 cd00861 ProRS_anticodon_short 38.4 85 0.0019 22.0 4.9 47 34-84 18-64 (94)
31 PRK02228 V-type ATP synthase s 38.1 92 0.002 23.3 5.2 64 41-113 13-77 (100)
32 TIGR00418 thrS threonyl-tRNA s 36.0 86 0.0019 30.3 5.9 61 18-83 469-529 (563)
33 PF14359 DUF4406: Domain of un 35.4 1.8E+02 0.0039 21.4 7.1 65 33-101 16-85 (92)
34 PF03709 OKR_DC_1_N: Orn/Lys/A 34.6 1.6E+02 0.0035 22.2 6.2 72 35-120 5-77 (115)
35 COG0276 HemH Protoheme ferro-l 33.8 3.4E+02 0.0073 24.9 9.0 80 34-116 73-161 (320)
36 PRK12325 prolyl-tRNA synthetas 31.4 64 0.0014 30.5 4.1 64 19-86 345-410 (439)
37 cd00859 HisRS_anticodon HisRS 31.4 1.5E+02 0.0032 20.0 5.1 58 21-83 3-60 (91)
38 cd07373 2A5CPDO_A The alpha su 29.5 3.1E+02 0.0067 24.0 7.9 78 33-113 90-172 (271)
39 TIGR00334 5S_RNA_mat_M5 ribonu 28.5 70 0.0015 26.8 3.4 50 33-86 35-84 (174)
40 COG0710 AroD 3-dehydroquinate 28.0 1.4E+02 0.003 26.1 5.2 68 34-106 79-146 (231)
41 PF00875 DNA_photolyase: DNA p 27.6 2.8E+02 0.0061 21.9 6.7 89 37-137 56-148 (165)
42 PRK01189 V-type ATP synthase s 27.2 1.1E+02 0.0024 23.3 4.0 41 42-87 16-57 (104)
43 COG0512 PabA Anthranilate/para 27.0 1.4E+02 0.003 25.4 4.9 46 30-85 8-55 (191)
44 PF10087 DUF2325: Uncharacteri 26.4 1.7E+02 0.0037 21.3 4.9 58 35-94 11-69 (97)
45 TIGR01101 V_ATP_synt_F vacuola 25.1 1.3E+02 0.0028 23.4 4.1 27 61-87 46-72 (115)
46 TIGR00409 proS_fam_II prolyl-t 25.0 52 0.0011 32.4 2.3 33 32-64 488-520 (568)
47 PRK09194 prolyl-tRNA synthetas 24.9 54 0.0012 32.0 2.4 46 18-63 467-514 (565)
48 cd03364 TOPRIM_DnaG_primases T 24.3 88 0.0019 21.8 2.8 39 39-79 35-75 (79)
49 CHL00201 syh histidine-tRNA sy 23.3 1.9E+02 0.0042 27.1 5.7 60 19-83 325-384 (430)
50 PRK03991 threonyl-tRNA synthet 22.6 94 0.002 30.9 3.6 61 19-84 499-559 (613)
51 cd04904 ACT_AAAH ACT domain of 22.5 1.6E+02 0.0036 20.3 3.9 31 13-46 36-66 (74)
52 cd01424 MGS_CPS_II Methylglyox 22.4 3.1E+02 0.0067 20.1 5.7 30 21-52 2-31 (110)
53 PRK14938 Ser-tRNA(Thr) hydrola 22.0 2.2E+02 0.0047 26.9 5.6 59 19-82 274-332 (387)
54 COG4916 Uncharacterized protei 22.0 1E+02 0.0022 27.8 3.3 99 18-119 5-107 (329)
55 cd00862 ProRS_anticodon_zinc P 21.7 90 0.002 26.2 2.9 46 19-64 10-61 (202)
56 cd00138 PLDc Phospholipase D. 21.1 3.5E+02 0.0075 21.1 6.1 43 58-100 17-64 (176)
57 cd00154 Rab Rab family. Rab G 21.1 2.6E+02 0.0056 20.5 5.1 30 59-88 57-87 (159)
58 PRK12305 thrS threonyl-tRNA sy 20.8 2.1E+02 0.0046 27.7 5.6 60 19-83 476-535 (575)
59 PRK14799 thrS threonyl-tRNA sy 20.5 2.2E+02 0.0048 27.9 5.6 59 19-82 438-496 (545)
60 cd01857 HSR1_MMR1 HSR1/MMR1. 20.3 3.5E+02 0.0075 20.6 5.8 35 66-101 4-38 (141)
No 1
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=4.2e-49 Score=402.66 Aligned_cols=189 Identities=38% Similarity=0.637 Sum_probs=171.3
Q ss_pred CCCCCCeeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHH
Q 027772 13 HQILQSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCL 92 (219)
Q Consensus 13 s~~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl 92 (219)
|+++.++|||||||||+|+|++|++||+++|.++||++|+|+ ++++|+.|.+++.+||++|+++|||||++||+|.|||
T Consensus 6 ~~~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl 84 (1153)
T PLN03210 6 SSSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCL 84 (1153)
T ss_pred CCCCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHH
Confidence 344678999999999999999999999999999999999988 6999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccccCCCeEEEEEeeeCCcccccccccchHHHHHHHHHHhccChHHHHHHHHHHHHhhcccceeecCC--c
Q 027772 93 DELAKIVECGNKRKDRKVFAVFYGVDPADVRKQKGEDFERVFAKYEEEFKENHEKVLKWRAALTTVASLAGWHLQDR--F 170 (219)
Q Consensus 93 ~EL~~i~~~~~~~~~~~ViPVFy~v~psdVr~q~g~~f~~~f~~~~~~~~~~~~~v~~Wr~AL~~va~~~G~~~~~~--~ 170 (219)
+||++|++| +++.+++|+||||+|+|+|||+|+| .||++|.+++++. +++++++||+||++||+++||++.++ +
T Consensus 85 ~el~~i~~~-~~~~~~~v~pvfy~v~p~~v~~~~g-~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~~~~E 160 (1153)
T PLN03210 85 NELLEIVRC-KEELGQLVIPVFYGLDPSHVRKQTG-DFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQNWPNE 160 (1153)
T ss_pred HHHHHHHHh-hhhcCceEEEEEecccHHHHhhccc-hHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCCCCCH
Confidence 999999999 8889999999999999999999999 9999999998754 46899999999999999999999765 4
Q ss_pred hhHHHHHHHhhhhhh----------------------hhhhhccCCCccceeeccCCe
Q 027772 171 FPLIYLLLFNYLFTL----------------------IIFCLFSGDVSPLAFYKHTHV 206 (219)
Q Consensus 171 ~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~i 206 (219)
..++.+|++++...+ .+++..+.+++.+|+|||.||
T Consensus 161 ~~~i~~Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGi 218 (1153)
T PLN03210 161 AKMIEEIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGI 218 (1153)
T ss_pred HHHHHHHHHHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCC
Confidence 556667777765533 446667889999999999996
No 2
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=5.3e-47 Score=315.54 Aligned_cols=155 Identities=24% Similarity=0.420 Sum_probs=135.2
Q ss_pred CCCCCCCeeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhH
Q 027772 12 HHQILQSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWC 91 (219)
Q Consensus 12 ss~~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wC 91 (219)
+|++...+|||||||||+|+|++|++||+.+|+++||+||+|+.++++|+.|.+.|.+||++|+++|+|||++|++|.||
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 HHHHHHHHHhccccCCCeEEEEEeeeCCcccccc-cccchHHHHHHHHHHhccChHHHHHHHHHHHHhhcccceeecCC-
Q 027772 92 LDELAKIVECGNKRKDRKVFAVFYGVDPADVRKQ-KGEDFERVFAKYEEEFKENHEKVLKWRAALTTVASLAGWHLQDR- 169 (219)
Q Consensus 92 l~EL~~i~~~~~~~~~~~ViPVFy~v~psdVr~q-~g~~f~~~f~~~~~~~~~~~~~v~~Wr~AL~~va~~~G~~~~~~- 169 (219)
|+||++|++| ++.||||||+|+|+|||+| .| . .+.+++++||+||++||+++||+++..
T Consensus 99 LdEL~~I~e~-----~~~ViPIFY~VdPsdVr~q~~~-~-------------~~~e~v~~Wr~AL~~va~l~G~~~~~~~ 159 (187)
T PLN03194 99 LHELALIMES-----KKRVIPIFCDVKPSQLRVVDNG-T-------------CPDEEIRRFNWALEEAKYTVGLTFDSLK 159 (187)
T ss_pred HHHHHHHHHc-----CCEEEEEEecCCHHHhhccccC-C-------------CCHHHHHHHHHHHHHHhccccccCCCCC
Confidence 9999999998 3589999999999999997 44 3 135899999999999999999988643
Q ss_pred --chhHHHHHHHhhhhhh
Q 027772 170 --FFPLIYLLLFNYLFTL 185 (219)
Q Consensus 170 --~~~~~~~~~~~~~~~~ 185 (219)
+..++..++..++..+
T Consensus 160 ~~e~e~i~~iv~~v~k~l 177 (187)
T PLN03194 160 GNWSEVVTMASDAVIKNL 177 (187)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 3455555555555443
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=99.94 E-value=9.6e-28 Score=191.19 Aligned_cols=134 Identities=34% Similarity=0.554 Sum_probs=117.1
Q ss_pred EEEecccccCccchHHHHHHHHHcC--CeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHH
Q 027772 22 VFLSFRGEDTRNNFTDNLHTALIRN--GFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIV 99 (219)
Q Consensus 22 VFISfrg~D~r~~Fv~~L~~aL~~~--Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~ 99 (219)
|||||++.+.+..|+++|..+|+++ |+++|++++|+.+|..+.+++.++|++|+++|+|||++|+.|.||+.||..|+
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-CCeEEEEEeeeCCcccc-cccccchHHHHHHHHHHhccC--hHHHHHHHHHHH
Q 027772 100 ECGNKRK-DRKVFAVFYGVDPADVR-KQKGEDFERVFAKYEEEFKEN--HEKVLKWRAALT 156 (219)
Q Consensus 100 ~~~~~~~-~~~ViPVFy~v~psdVr-~q~g~~f~~~f~~~~~~~~~~--~~~v~~Wr~AL~ 156 (219)
+++...+ ..+|+||||++.+++++ .+.+ .|+..|..+.+....+ ..+...|++++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~-~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSL-RFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHH-HHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhH-HHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 9954433 58999999999999999 7899 9999998877655443 468899999875
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.92 E-value=2.3e-24 Score=169.44 Aligned_cols=138 Identities=42% Similarity=0.720 Sum_probs=116.5
Q ss_pred eeeEEEeccc-ccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHH
Q 027772 19 KYDVFLSFRG-EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAK 97 (219)
Q Consensus 19 ~yDVFISfrg-~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~ 97 (219)
.|||||||++ ++....|+.+|...|...|+.+|.|+.. ..|.... +|.++|++|+++|+|+||+|..|.||..|+..
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~-~~~~~~~-~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~ 78 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFE-PGGGDLE-EIDEAIEKSRIAIVVLSPNYAESEWCLDELVA 78 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcc-cccchHH-HHHHHHHHCcEEEEEECcccccChhHHHHHHH
Confidence 4999999999 4566789999999999999999999753 3333333 99999999999999999999999999999999
Q ss_pred HHHhccccCCCeEEEEEeeeCCcccccccccchHHHHHHHHHHhccChHHHHHHHHHHHHhhc
Q 027772 98 IVECGNKRKDRKVFAVFYGVDPADVRKQKGEDFERVFAKYEEEFKENHEKVLKWRAALTTVAS 160 (219)
Q Consensus 98 i~~~~~~~~~~~ViPVFy~v~psdVr~q~g~~f~~~f~~~~~~~~~~~~~v~~Wr~AL~~va~ 160 (219)
++++..+.....||||+++..|+++.++.+ .++..+..+..++.++..+ +.|+.++..+.+
T Consensus 79 a~~~~~~~~~~~iIPI~~~~~~~~~~~~~~-~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 79 ALENALEEGGLRVIPIFYEVIPSDVRKQPG-KFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHHcCCCeEEEEEEecChHHHHhccc-HHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 998833346789999999999999999999 9999998886666543333 789999988764
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.70 E-value=5.8e-18 Score=127.02 Aligned_cols=87 Identities=34% Similarity=0.601 Sum_probs=75.5
Q ss_pred EEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHh
Q 027772 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (219)
Q Consensus 22 VFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~ 101 (219)
|||||+++| ..++..|...|++.|+++|+|. ++.+|+.+.+.+.++|++|+..|+++|++|..|+||..|+..+.+.
T Consensus 1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~~ 77 (102)
T PF13676_consen 1 VFISYSSED--REFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWKR 77 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHCT
T ss_pred eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHHC
Confidence 899999999 3699999999999999999997 8999999999999999999999999999999999999999998443
Q ss_pred ccccCCCeEEEEEee
Q 027772 102 GNKRKDRKVFAVFYG 116 (219)
Q Consensus 102 ~~~~~~~~ViPVFy~ 116 (219)
++.|+||.++
T Consensus 78 -----~~~iipv~~~ 87 (102)
T PF13676_consen 78 -----GKPIIPVRLD 87 (102)
T ss_dssp -----SESEEEEECS
T ss_pred -----CCEEEEEEEC
Confidence 5699999954
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=98.98 E-value=1.1e-09 Score=102.76 Aligned_cols=94 Identities=28% Similarity=0.454 Sum_probs=80.1
Q ss_pred CCCCeeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccC--------
Q 027772 15 ILQSKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA-------- 86 (219)
Q Consensus 15 ~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~-------- 86 (219)
.-..+.|||||||.. +....++-|...|+.+|++||+|-+.+..|+. .+.+.+.|...+.+|+|++||..
T Consensus 608 ~~skq~DVFISYRRs-tGnQLASLiKV~LQL~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~n 685 (832)
T KOG3678|consen 608 MLSKQIDVFISYRRS-TGNQLASLIKVLLQLRGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDN 685 (832)
T ss_pred cccCCcceEEEeecc-ccHHHHHHHHHHHHhcCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhcccc
Confidence 345689999999875 56789999999999999999999888988865 56899999999999999999965
Q ss_pred CChhHHHHHHHHHHhccccCCCeEEEEEe
Q 027772 87 SSPWCLDELAKIVECGNKRKDRKVFAVFY 115 (219)
Q Consensus 87 ~S~wCl~EL~~i~~~~~~~~~~~ViPVFy 115 (219)
.-.|...||..+++| ++.|||||-
T Consensus 686 CeDWVHKEl~~Afe~-----~KNIiPI~D 709 (832)
T KOG3678|consen 686 CEDWVHKELKCAFEH-----QKNIIPIFD 709 (832)
T ss_pred HHHHHHHHHHHHHHh-----cCCeeeeec
Confidence 346777788888887 789999994
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=98.53 E-value=2e-07 Score=73.48 Aligned_cols=91 Identities=23% Similarity=0.404 Sum_probs=48.8
Q ss_pred eeEEEecccccCccchHHHHHHHHHcC-------Ceee----------EecCCCCcCCccchHHHHHHHHhcCceEEEEe
Q 027772 20 YDVFLSFRGEDTRNNFTDNLHTALIRN-------GFIA----------FKDDETLDRGNEISSELSKAIEESNVSIVILS 82 (219)
Q Consensus 20 yDVFISfrg~D~r~~Fv~~L~~aL~~~-------Gi~v----------f~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S 82 (219)
|.|||||++.|.. ..+..|...+... .+.. +.+..+....+.|...|.++|..|+++||+++
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 6799999999843 3677777777663 2211 11222223445788899999999999999999
Q ss_pred cccCCChhHHHHHHHHHHhccccCCCeEEEEEee
Q 027772 83 KNYASSPWCLDELAKIVECGNKRKDRKVFAVFYG 116 (219)
Q Consensus 83 ~ny~~S~wCl~EL~~i~~~~~~~~~~~ViPVFy~ 116 (219)
++...|.|+..|+..+++. +..||-|.++
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 9999999999999998775 7788888653
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=97.53 E-value=0.00041 Score=55.32 Aligned_cols=65 Identities=20% Similarity=0.339 Sum_probs=52.0
Q ss_pred eEEEecccccCc-cchHHHHHHHHHcC-CeeeEecCCCCcC--CccchHHHHHHHHhcCceEEEEeccc
Q 027772 21 DVFLSFRGEDTR-NNFTDNLHTALIRN-GFIAFKDDETLDR--GNEISSELSKAIEESNVSIVILSKNY 85 (219)
Q Consensus 21 DVFISfrg~D~r-~~Fv~~L~~aL~~~-Gi~vf~D~~~l~~--G~~i~~~i~~aI~~S~~~IvV~S~ny 85 (219)
-|||||+.+... ..-|..|...|++. |+.|.+|.-+... +.....=+.+.+++++..|+|.||.|
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 499999985432 35689999999999 9999999766633 55666677888999999999999543
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=96.40 E-value=0.01 Score=46.98 Aligned_cols=78 Identities=18% Similarity=0.242 Sum_probs=60.8
Q ss_pred eEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEeccc-C------------C
Q 027772 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY-A------------S 87 (219)
Q Consensus 21 DVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny-~------------~ 87 (219)
.|||.|. +|. ..+..+...|+..|+.+.+-.+....|..+.+.+.+...+++.+|++++|+= . .
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 5778888899988887776555678999999999999999999999999952 2 1
Q ss_pred ChhHHHHHHHHHHh
Q 027772 88 SPWCLDELAKIVEC 101 (219)
Q Consensus 88 S~wCl~EL~~i~~~ 101 (219)
-...+.|+-.++..
T Consensus 78 R~NVifE~G~f~g~ 91 (125)
T PF10137_consen 78 RQNVIFELGLFIGK 91 (125)
T ss_pred ccceeehhhHHHhh
Confidence 23456777777654
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=90.18 E-value=0.98 Score=32.66 Aligned_cols=67 Identities=24% Similarity=0.222 Sum_probs=46.9
Q ss_pred eEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCC
Q 027772 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASS 88 (219)
Q Consensus 21 DVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S 88 (219)
.||||-.-.|.. .--..|.+.|.+.|.....-+.--..+....+.+++.|++|+++|.++-..|-..
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 3446777788777765443221112355666788999999999999999999654
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=86.72 E-value=0.74 Score=41.00 Aligned_cols=99 Identities=21% Similarity=0.117 Sum_probs=66.6
Q ss_pred CCCeeeEEEecccccCccchHHHHHHHHH--cCCeeeEecCC---CCcCCccchHHHHHHH--HhcCceEEEEecccCCC
Q 027772 16 LQSKYDVFLSFRGEDTRNNFTDNLHTALI--RNGFIAFKDDE---TLDRGNEISSELSKAI--EESNVSIVILSKNYASS 88 (219)
Q Consensus 16 ~~~~yDVFISfrg~D~r~~Fv~~L~~aL~--~~Gi~vf~D~~---~l~~G~~i~~~i~~aI--~~S~~~IvV~S~ny~~S 88 (219)
..+.||+=+||.|+- | +.|+....+++ ...+..|+|.. .+-+|+ +.+ ++.-+ +.|++.+|.+..||...
T Consensus 174 ~~~~~DiG~SFaGEA-R-~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~~-~L~~~Y~~rC~~~~VF~~~~Y~~K 249 (329)
T COG4916 174 SEKPVDSGISFAGEA-R-NLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LVS-TLDPGYDIRCVVTTVFNTGSYICK 249 (329)
T ss_pred cccccceeeEeehhh-h-hHHHHHHHhhhcccCCceeeeechhhccccCcc-HHH-hcccccCceEEEEEEEeCCceEEe
Confidence 467899999999985 4 79999999998 44578888853 233332 222 22222 25788899999999999
Q ss_pred hhHHHHHHHHHHhccccCCCeEEEEEe-eeCCcc
Q 027772 89 PWCLDELAKIVECGNKRKDRKVFAVFY-GVDPAD 121 (219)
Q Consensus 89 ~wCl~EL~~i~~~~~~~~~~~ViPVFy-~v~psd 121 (219)
.||--|-..+-.. ..-....||-| +++.+.
T Consensus 250 ~~c~~E~~~~r~~---~~~d~~~rI~~~~~d~~a 280 (329)
T COG4916 250 STCHIEGLEGRLN---PILDTGFRIKYLYADNIA 280 (329)
T ss_pred eeeccchhhcccc---ccccccceEEEEecCCcc
Confidence 9999998776443 12234556655 344443
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=80.86 E-value=17 Score=27.30 Aligned_cols=68 Identities=21% Similarity=0.196 Sum_probs=49.4
Q ss_pred cchHHHHHHHHHcCCeeeEecCC-CCc-------CCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHh
Q 027772 33 NNFTDNLHTALIRNGFIAFKDDE-TLD-------RGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (219)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~-~l~-------~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~ 101 (219)
..+...+.+.|++.|+.+|...+ +.. ....|...-.++|++|++.|+++...- .+.=+.-|+-.+...
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 46889999999999999887542 111 122344455678999999999997755 567788999998765
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=78.37 E-value=6.5 Score=33.86 Aligned_cols=97 Identities=20% Similarity=0.255 Sum_probs=67.6
Q ss_pred eEEEecccccCccchHHHHHHHHHcC-C-eeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccC--------CChh
Q 027772 21 DVFLSFRGEDTRNNFTDNLHTALIRN-G-FIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA--------SSPW 90 (219)
Q Consensus 21 DVFISfrg~D~r~~Fv~~L~~aL~~~-G-i~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~--------~S~w 90 (219)
.|||-|+++ ..+.....+|.+. . ..+|.|. -+..|..+.+.+.+-|.+++.+|++..|+=. +-.|
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 3676777777643 3 4566665 6889999999999999999999999999843 1223
Q ss_pred ------HHHHHHHHHHhccccCCCeEEEEEee----eCCcccccc
Q 027772 91 ------CLDELAKIVECGNKRKDRKVFAVFYG----VDPADVRKQ 125 (219)
Q Consensus 91 ------Cl~EL~~i~~~~~~~~~~~ViPVFy~----v~psdVr~q 125 (219)
.+.||-.+|-+ -++.+|+-+..+ --|||+.-.
T Consensus 159 praRqNVifELGm~mgr---LgRkrv~Il~k~~envelPSDi~Gv 200 (233)
T COG4271 159 PRARQNVIFELGMFMGR---LGRKRVMILMKRDENVELPSDIAGV 200 (233)
T ss_pred ccccccchhhHhhHHhh---cccceEEEEecccccccCccccCce
Confidence 56788888765 344555544331 236665543
No 14
>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=72.88 E-value=16 Score=25.61 Aligned_cols=60 Identities=10% Similarity=0.153 Sum_probs=37.9
Q ss_pred eeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecc
Q 027772 20 YDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 20 yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
+||+|...+++. ...+-.+...|++.|+++-+|... ..+...+..|-+.---.++++.++
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 356788999999999999998743 344455555533332344455443
No 15
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=67.35 E-value=31 Score=23.52 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=37.1
Q ss_pred HHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHhccccCCCeEE
Q 027772 37 DNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVF 111 (219)
Q Consensus 37 ~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~~~~~~~~~Vi 111 (219)
.-|+.-|++.|+.+-.... ...+++..+-+++++++.+.-+. -.++..+.+. .+.++..||
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 12344558889999999965553 3444444444 333444443
No 16
>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=62.02 E-value=32 Score=24.12 Aligned_cols=60 Identities=20% Similarity=0.300 Sum_probs=38.1
Q ss_pred eeEEEecccc---cCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecc
Q 027772 20 YDVFLSFRGE---DTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 20 yDVFISfrg~---D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
++|+|-.-++ . ....+-.+...|++.|+.+-+|.. +..+...+..|-..---.++++.++
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 5766655443 2 235778899999999999999763 3455555555543333466677653
No 17
>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=59.52 E-value=26 Score=24.96 Aligned_cols=48 Identities=17% Similarity=0.244 Sum_probs=32.1
Q ss_pred cchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecc
Q 027772 33 NNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
..++.+|...|++.||++.+|+.+ ..+...+..|-..=--.++|+.++
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~~----~~~~k~~~~a~~~g~p~~iiiG~~ 62 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDSD----KSLGKQIKYADKLGIPFIIIIGEK 62 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESSS----STHHHHHHHHHHTTESEEEEEEHH
T ss_pred HHHHHHHHHHHHHCCCEEEEECCC----CchhHHHHHHhhcCCeEEEEECch
Confidence 357899999999999999999754 344445555544333345555443
No 18
>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=58.98 E-value=46 Score=24.34 Aligned_cols=68 Identities=16% Similarity=0.221 Sum_probs=45.1
Q ss_pred HHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHhccccCCCeEEEE
Q 027772 38 NLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAV 113 (219)
Q Consensus 38 ~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~~~~~~~~~ViPV 113 (219)
.+...++..|+..+... ...+.+...+.+.++...+.|++++++++.. -.+++....+. .....|++|
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 34566788899988875 1234566677777888999999999999874 33444554332 234555555
No 19
>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=53.60 E-value=58 Score=23.44 Aligned_cols=64 Identities=14% Similarity=0.126 Sum_probs=40.7
Q ss_pred EEEecccccCccchHHHHHHHHHcCCeeeEecCCCCc-------CCccchHHHHHHHHhcCceEEEEeccc
Q 027772 22 VFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLD-------RGNEISSELSKAIEESNVSIVILSKNY 85 (219)
Q Consensus 22 VFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~-------~G~~i~~~i~~aI~~S~~~IvV~S~ny 85 (219)
+|.|.+|--.+-.++.+|...|.++|.++..-|-+.. -+-...+....++..|+..|+++.+..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~ 73 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSP 73 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCH
Confidence 4666665544556789999999999988776443322 111223344567777777777776654
No 20
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=53.29 E-value=76 Score=27.04 Aligned_cols=98 Identities=14% Similarity=0.241 Sum_probs=58.5
Q ss_pred EEEecccccC--ccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHH----------------------------
Q 027772 22 VFLSFRGEDT--RNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAI---------------------------- 71 (219)
Q Consensus 22 VFISfrg~D~--r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI---------------------------- 71 (219)
.||.+-|-|- +.+-+..|++.|+.+|+.|.+-.+ +.|..+...|...+
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 5888887774 456789999999999988776431 11212221111111
Q ss_pred Hh-cCceEEEEecccCCChhHHH--------HHHHHHHhccccCCCeEEEEEeeeCCcc
Q 027772 72 EE-SNVSIVILSKNYASSPWCLD--------ELAKIVECGNKRKDRKVFAVFYGVDPAD 121 (219)
Q Consensus 72 ~~-S~~~IvV~S~ny~~S~wCl~--------EL~~i~~~~~~~~~~~ViPVFy~v~psd 121 (219)
.- -.-.-+|++..|..|.-+.. +....+.......-..-+-+|++|+|..
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 11235888999998888766 2333322212222356677888999976
No 21
>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=52.63 E-value=3.7 Score=33.99 Aligned_cols=59 Identities=24% Similarity=0.404 Sum_probs=38.3
Q ss_pred ChhHHHHHHHHHHhccccCCCeEEEEEeeeCCcccccccccchHHHHHHHHHHhccChHHHHHHHHHHHH
Q 027772 88 SPWCLDELAKIVECGNKRKDRKVFAVFYGVDPADVRKQKGEDFERVFAKYEEEFKENHEKVLKWRAALTT 157 (219)
Q Consensus 88 S~wCl~EL~~i~~~~~~~~~~~ViPVFy~v~psdVr~q~g~~f~~~f~~~~~~~~~~~~~v~~Wr~AL~~ 157 (219)
|.|.|.||..-++. .+-+.=.=+-+.++|+|-++.+... .++.+.+.-++++|..|++-
T Consensus 54 s~~~Lf~LI~k~~~-keikTW~~La~~LGVepp~~ek~qS----------tQKvqQYaVRLKRWM~aMHV 112 (175)
T PF09441_consen 54 STFTLFELIRKLES-KEIKTWAQLALELGVEPPDPEKGQS----------TQKVQQYAVRLKRWMRAMHV 112 (175)
T ss_pred hHHHHHHHHHHHhh-hhHhHHHHHHHHhCCCCCCcccccc----------hHHHHHHHHHHHHHHHHhhH
Confidence 57888888887765 4434333445567899888765322 12333445788999999874
No 22
>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=52.42 E-value=13 Score=29.24 Aligned_cols=32 Identities=9% Similarity=0.118 Sum_probs=25.1
Q ss_pred ccchHHHHHHHHHcCCeeeEecCCCC---cCCccc
Q 027772 32 RNNFTDNLHTALIRNGFIAFKDDETL---DRGNEI 63 (219)
Q Consensus 32 r~~Fv~~L~~aL~~~Gi~vf~D~~~l---~~G~~i 63 (219)
-...+..|+..|+..|+.+..|+++- .+|..+
T Consensus 42 ~~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~ 76 (128)
T cd02426 42 LRDLCQGLKNELREAGLSVWPGYLETQHSSLEQLL 76 (128)
T ss_pred HHHHHHHHHHHHHHcCCEEEeccCcccccCHHHHH
Confidence 35678999999999999999998653 455544
No 23
>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=52.38 E-value=44 Score=25.40 Aligned_cols=60 Identities=15% Similarity=0.104 Sum_probs=39.1
Q ss_pred eeeEEEeccc--ccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecc
Q 027772 19 KYDVFLSFRG--EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 19 ~yDVFISfrg--~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
.+||+|-.-+ ++ ....+..|...|++.|++|-+|.. ..+...+..|-+.---.++++.++
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 5788877755 32 235678899999999999999873 244445555544333456666554
No 24
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=52.33 E-value=10 Score=30.02 Aligned_cols=32 Identities=38% Similarity=0.476 Sum_probs=18.6
Q ss_pred HHHHHHHHhcCceEEEEecccCCChhHHHHHHHH
Q 027772 65 SELSKAIEESNVSIVILSKNYASSPWCLDELAKI 98 (219)
Q Consensus 65 ~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i 98 (219)
..+.++|..-..+|+|.+..|-++ |+.||..+
T Consensus 62 ~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 62 EALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 344444444435677776666543 77777765
No 25
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=44.19 E-value=19 Score=32.15 Aligned_cols=32 Identities=28% Similarity=0.437 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHh---ccccCCCeEEEEEeeeCCc
Q 027772 89 PWCLDELAKIVEC---GNKRKDRKVFAVFYGVDPA 120 (219)
Q Consensus 89 ~wCl~EL~~i~~~---~~~~~~~~ViPVFy~v~ps 120 (219)
.=|-|||.++..- +....+..++|||.-|+|.
T Consensus 153 DICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 153 DICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred CcChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 4488999876653 2455667777999999995
No 26
>COG0400 Predicted esterase [General function prediction only]
Probab=43.04 E-value=93 Score=26.50 Aligned_cols=58 Identities=21% Similarity=0.094 Sum_probs=43.0
Q ss_pred CCCCCCeeeEEEecccccC--ccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHH
Q 027772 13 HQILQSKYDVFLSFRGEDT--RNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIE 72 (219)
Q Consensus 13 s~~~~~~yDVFISfrg~D~--r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~ 72 (219)
+.......-|||++-..|. -.....+|.+.|+..|..|.... ..-|-.|.++-.++++
T Consensus 140 ~~~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~--~~~GH~i~~e~~~~~~ 199 (207)
T COG0400 140 LLPDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRW--HEGGHEIPPEELEAAR 199 (207)
T ss_pred cccccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEE--ecCCCcCCHHHHHHHH
Confidence 3445677889999988886 35677999999999999998875 3467777665544443
No 27
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=40.37 E-value=50 Score=26.25 Aligned_cols=56 Identities=14% Similarity=0.200 Sum_probs=41.2
Q ss_pred eeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCc
Q 027772 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNV 76 (219)
Q Consensus 19 ~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~ 76 (219)
..++|+-..+.=....+++.|..++..+|+-++.|.+ .+|+.|...+.+.+..+..
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 3566666644322256888999999999999999974 5899988888888777544
No 28
>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=38.69 E-value=1.6e+02 Score=21.65 Aligned_cols=57 Identities=19% Similarity=0.160 Sum_probs=38.6
Q ss_pred HHHHHHHHHcCCeeeE-ecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHh
Q 027772 36 TDNLHTALIRNGFIAF-KDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (219)
Q Consensus 36 v~~L~~aL~~~Gi~vf-~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~ 101 (219)
...|...|++.|+.+- +|- ... .+++.+++.+.+.-+|.+|-.+. |...++..+.+.
T Consensus 17 l~~la~~l~~~G~~v~~~d~-~~~-----~~~l~~~~~~~~pd~V~iS~~~~---~~~~~~~~l~~~ 74 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDA-NVP-----PEELVEALRAERPDVVGISVSMT---PNLPEAKRLARA 74 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEES-SB------HHHHHHHHHHTTCSEEEEEESSS---THHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCeEEEECC-CCC-----HHHHHHHHhcCCCcEEEEEccCc---CcHHHHHHHHHH
Confidence 3678888999999885 443 222 16788888888888888876543 445555555554
No 29
>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=38.46 E-value=34 Score=25.54 Aligned_cols=56 Identities=20% Similarity=0.292 Sum_probs=34.5
Q ss_pred ccCccchHHHHHHHHHcCCeeeEecCCCCc----------CCccchHHHHHHHHhcCceEEEEecc
Q 027772 29 EDTRNNFTDNLHTALIRNGFIAFKDDETLD----------RGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 29 ~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~----------~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
.|+|.+=+-.|.+.|.++|+.+.+.|--+. .|-...+.+.++++.++..|+.-..+
T Consensus 12 ~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h~ 77 (106)
T PF03720_consen 12 DDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDHD 77 (106)
T ss_dssp S--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--G
T ss_pred cccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecCH
Confidence 578999999999999999999887653221 12223345678888888776655444
No 30
>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=38.41 E-value=85 Score=22.03 Aligned_cols=47 Identities=15% Similarity=0.144 Sum_probs=30.1
Q ss_pred chHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecc
Q 027772 34 NFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 34 ~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
..+..|...|++.|+++.+|.+.- .+...+..|-..---.++++.++
T Consensus 18 ~~a~~la~~Lr~~g~~v~~d~~~~----~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 18 ELAEKLYAELQAAGVDVLLDDRNE----RPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHCCCEEEEECCCC----CcccchhHHHhcCCCEEEEECCc
Confidence 577889999999999999987532 33334444533333345555544
No 31
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=38.10 E-value=92 Score=23.28 Aligned_cols=64 Identities=13% Similarity=0.248 Sum_probs=37.8
Q ss_pred HHHHcCCeeeEe-cCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHhccccCCCeEEEE
Q 027772 41 TALIRNGFIAFK-DDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAV 113 (219)
Q Consensus 41 ~aL~~~Gi~vf~-D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~~~~~~~~~ViPV 113 (219)
-.++..|+..+. .++ .+.+...+.+.+.+-+++|++++++++.. +-+++...++. .....|+||
T Consensus 13 ~GFrLaGi~~~~~~~~----~ee~~~~l~~l~~~~d~gII~Ite~~~~~--i~e~i~~~~~~---~~~P~ii~I 77 (100)
T PRK02228 13 TGFRLAGIRKVYEVPD----DEKLDEAVEEVLEDDDVGILVMHDDDLEK--LPRRLRRTLEE---SVEPTVVTL 77 (100)
T ss_pred HHHHHcCCceEEeeCC----HHHHHHHHHHHhhCCCEEEEEEehhHhHh--hHHHHHHHHhc---CCCCEEEEE
Confidence 345677886443 221 13445556666677789999999998763 34455554432 234455555
No 32
>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=35.95 E-value=86 Score=30.32 Aligned_cols=61 Identities=11% Similarity=0.212 Sum_probs=42.0
Q ss_pred CeeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEec
Q 027772 18 SKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (219)
Q Consensus 18 ~~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ 83 (219)
...||+|-.-+++. ...+..|...|+++|++|-+|.+ +..+...+..|-+.---.++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEch
Confidence 45788887666543 46789999999999999999874 445666666664433345555554
No 33
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=35.37 E-value=1.8e+02 Score=21.42 Aligned_cols=65 Identities=11% Similarity=0.124 Sum_probs=41.8
Q ss_pred cchHHHHHHHHHcCCeeeEecCCCC--cCCccchHHHH---HHHHhcCceEEEEecccCCChhHHHHHHHHHHh
Q 027772 33 NNFTDNLHTALIRNGFIAFKDDETL--DRGNEISSELS---KAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (219)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~~l--~~G~~i~~~i~---~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~ 101 (219)
..|. ...+.|+.+|..|.- .-.+ ..|.....-+. ..+..|+. +++=|+.-.|.=|.-|...+.+.
T Consensus 16 ~~f~-~~a~~L~~~G~~vvn-Pa~~~~~~~~~~~~ym~~~l~~L~~cD~--i~~l~gWe~S~GA~~E~~~A~~l 85 (92)
T PF14359_consen 16 PAFN-AAAKRLRAKGYEVVN-PAELGIPEGLSWEEYMRICLAMLSDCDA--IYMLPGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHH-HHHHHHHHCCCEEeC-chhhCCCCCCCHHHHHHHHHHHHHhCCE--EEEcCCcccCcchHHHHHHHHHC
Confidence 3443 477788999966553 2223 45554444333 34556663 34449999999999999998765
No 34
>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=34.63 E-value=1.6e+02 Score=22.21 Aligned_cols=72 Identities=18% Similarity=0.183 Sum_probs=44.2
Q ss_pred hHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHh-cCceEEEEecccCCChhHHHHHHHHHHhccccCCCeEEEE
Q 027772 35 FTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEE-SNVSIVILSKNYASSPWCLDELAKIVECGNKRKDRKVFAV 113 (219)
Q Consensus 35 Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~-S~~~IvV~S~ny~~S~wCl~EL~~i~~~~~~~~~~~ViPV 113 (219)
-+..|..+|++.|+.+..-.. .+.....++. ++++-||+|-+ ....-...+|...++. ...=+||
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 467899999999988765432 3456666664 89999999876 1111122333333333 3455899
Q ss_pred EeeeCCc
Q 027772 114 FYGVDPA 120 (219)
Q Consensus 114 Fy~v~ps 120 (219)
|.-+++.
T Consensus 71 Fl~~~~~ 77 (115)
T PF03709_consen 71 FLLAERD 77 (115)
T ss_dssp EEEESCC
T ss_pred EEEecCC
Confidence 9866633
No 35
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=33.78 E-value=3.4e+02 Score=24.92 Aligned_cols=80 Identities=19% Similarity=0.272 Sum_probs=53.3
Q ss_pred chHHHHHHHHHcC----CeeeEecCCCCcCCccchHHHHHHHHhcC---ceEEEEecccCCCh--hHHHHHHHHHHhccc
Q 027772 34 NFTDNLHTALIRN----GFIAFKDDETLDRGNEISSELSKAIEESN---VSIVILSKNYASSP--WCLDELAKIVECGNK 104 (219)
Q Consensus 34 ~Fv~~L~~aL~~~----Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~---~~IvV~S~ny~~S~--wCl~EL~~i~~~~~~ 104 (219)
..+..+.++|+++ .+.|++- ++-|.+..++..+++.+.. +.++.+.|.|..++ --.+++..+++....
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 3555666666654 5677764 4567777777777777644 57888889987554 357888888876232
Q ss_pred cCCCeEEEEEee
Q 027772 105 RKDRKVFAVFYG 116 (219)
Q Consensus 105 ~~~~~ViPVFy~ 116 (219)
......||-||+
T Consensus 150 ~~~i~~I~~~~~ 161 (320)
T COG0276 150 QPKISTIPDYYD 161 (320)
T ss_pred CCceEEecCccC
Confidence 335578888876
No 36
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=31.44 E-value=64 Score=30.48 Aligned_cols=64 Identities=14% Similarity=0.079 Sum_probs=39.7
Q ss_pred eeeEEEeccc--ccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccC
Q 027772 19 KYDVFLSFRG--EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (219)
Q Consensus 19 ~yDVFISfrg--~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~ 86 (219)
.++|.|---+ .+.....+..|+..|++.||+|.+|+++-..|.. +..|-..---.+||+.++-.
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~k----i~~a~~~giP~~iiVG~~e~ 410 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGAK----FATMDLIGLPWQIIVGPKGL 410 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhHH----HHHHHHcCCCEEEEECCccc
Confidence 4688765432 2223467899999999999999999865444443 33332222235666665543
No 37
>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=31.41 E-value=1.5e+02 Score=20.01 Aligned_cols=58 Identities=22% Similarity=0.169 Sum_probs=33.2
Q ss_pred eEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEec
Q 027772 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (219)
Q Consensus 21 DVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ 83 (219)
||+|-..+++. ..-+-.+...|++.|+++.++... ..+...+..|-..---.++++.+
T Consensus 3 ~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~~----~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 3 DVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYGG----RKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred cEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecCC----CCHHHHHHHHHHcCCCEEEEEcH
Confidence 67666544432 234678899999999999887532 22333344443222234555554
No 38
>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=29.47 E-value=3.1e+02 Score=24.03 Aligned_cols=78 Identities=21% Similarity=0.236 Sum_probs=52.8
Q ss_pred cchHHHHHHHHHcCCeeeE-ecCCC--CcCCccchHHHHHHH-H-hcCceEEEEecccCCChhHHHHHHHHHHhccccCC
Q 027772 33 NNFTDNLHTALIRNGFIAF-KDDET--LDRGNEISSELSKAI-E-ESNVSIVILSKNYASSPWCLDELAKIVECGNKRKD 107 (219)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf-~D~~~--l~~G~~i~~~i~~aI-~-~S~~~IvV~S~ny~~S~wCl~EL~~i~~~~~~~~~ 107 (219)
..++..+.+.|.+.||.+- +|.+. +--|--+. +.-+ . ..++-||.+|-+..-+.....+|-+++...-+..+
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 4799999999999999886 66532 44444333 2233 2 46777888999886677777889888873123334
Q ss_pred CeEEEE
Q 027772 108 RKVFAV 113 (219)
Q Consensus 108 ~~ViPV 113 (219)
++|+-|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 566644
No 39
>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=28.55 E-value=70 Score=26.81 Aligned_cols=50 Identities=16% Similarity=0.304 Sum_probs=35.8
Q ss_pred cchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccC
Q 027772 33 NNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (219)
Q Consensus 33 ~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~ 86 (219)
..-...|..+.+.+||-+|.|.+ .+|+.|...|.+.+-++..+- +++.++
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 34567777888889999999974 578888888888776666433 344444
No 40
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=27.99 E-value=1.4e+02 Score=26.10 Aligned_cols=68 Identities=18% Similarity=0.136 Sum_probs=42.0
Q ss_pred chHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHhccccC
Q 027772 34 NFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRK 106 (219)
Q Consensus 34 ~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~~~~~~ 106 (219)
.....|.+..+.+| .-|+|= ++..++....++.+.-.+-+ +|+|-+..++++.++|+..++..+...+
T Consensus 79 ~~i~ll~~la~~~~-~d~iDi-El~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~ 146 (231)
T COG0710 79 EYIELLKKLAELNG-PDYIDI-ELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLG 146 (231)
T ss_pred HHHHHHHHHHhhcC-CCEEEE-EccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhC
Confidence 45556666666666 567775 34333322222222222222 8899999999999999999998844444
No 41
>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=27.59 E-value=2.8e+02 Score=21.86 Aligned_cols=89 Identities=22% Similarity=0.362 Sum_probs=47.7
Q ss_pred HHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCCChhHHH-HHHHHHHhccccCCCeEEEEEe
Q 027772 37 DNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLD-ELAKIVECGNKRKDRKVFAVFY 115 (219)
Q Consensus 37 ~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~-EL~~i~~~~~~~~~~~ViPVFy 115 (219)
..|...|.+.|+...+-. |+ ..+.+.+-+++..+.-|++...|..-.-=.+ ++.+.+. ..+-.+. -+.
T Consensus 56 ~~L~~~L~~~g~~L~v~~-----g~-~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~----~~~i~~~-~~~ 124 (165)
T PF00875_consen 56 ADLQESLRKLGIPLLVLR-----GD-PEEVLPELAKEYGATAVYFNEEYTPYERRRDERVRKALK----KHGIKVH-TFD 124 (165)
T ss_dssp HHHHHHHHHTTS-EEEEE-----SS-HHHHHHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHH----HTTSEEE-EE-
T ss_pred HHHHHHHHhcCcceEEEe-----cc-hHHHHHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHH----hcceEEE-EEC
Confidence 568888888999877533 33 2345666778888999999999876222111 2233332 1222222 121
Q ss_pred e---eCCcccccccccchHHHHHHH
Q 027772 116 G---VDPADVRKQKGEDFERVFAKY 137 (219)
Q Consensus 116 ~---v~psdVr~q~g~~f~~~f~~~ 137 (219)
+ +.|.++....| .....|...
T Consensus 125 ~~~L~~~~~i~~~~~-~~~~vFtpf 148 (165)
T PF00875_consen 125 DHTLVPPDDIPKKDG-EPYKVFTPF 148 (165)
T ss_dssp -SSSS-HHHCHSTTS-SSHSSHHHH
T ss_pred CcEEEeccccccCCC-CCcccHHHH
Confidence 1 67888877777 555555433
No 42
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=27.17 E-value=1.1e+02 Score=23.26 Aligned_cols=41 Identities=5% Similarity=0.122 Sum_probs=30.7
Q ss_pred HHHcCCee-eEecCCCCcCCccchHHHHHHHHhcCceEEEEecccCC
Q 027772 42 ALIRNGFI-AFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (219)
Q Consensus 42 aL~~~Gi~-vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~ 87 (219)
.++..|+. +|...++ +. ..++.+.+.+-++.|++++++++.
T Consensus 16 GFrlaGi~~v~~~~~~----e~-~~~~~~~l~~~~~gII~iTE~~a~ 57 (104)
T PRK01189 16 GFRLLGIGDTIEAEGK----DL-VKKFLEIFNNPKCKYIFVSESTKN 57 (104)
T ss_pred HHHHcCCceEEEcCCH----HH-HHHHHHHHhcCCeEEEEEEHHHHh
Confidence 56778996 8865432 22 357788888999999999999876
No 43
>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=27.04 E-value=1.4e+02 Score=25.44 Aligned_cols=46 Identities=26% Similarity=0.340 Sum_probs=33.0
Q ss_pred cCccchHHHHHHHHHcCC--eeeEecCCCCcCCccchHHHHHHHHhcCceEEEEeccc
Q 027772 30 DTRNNFTDNLHTALIRNG--FIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY 85 (219)
Q Consensus 30 D~r~~Fv~~L~~aL~~~G--i~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ny 85 (219)
|...+|+-.|++.|++.| +.|+.++ ++ .. ..++..+--.+|+||.=
T Consensus 8 DNyDSFtyNLv~yl~~lg~~v~V~rnd-~~------~~---~~~~~~~pd~iviSPGP 55 (191)
T COG0512 8 DNYDSFTYNLVQYLRELGAEVTVVRND-DI------SL---ELIEALKPDAIVISPGP 55 (191)
T ss_pred ECccchHHHHHHHHHHcCCceEEEECC-cc------CH---HHHhhcCCCEEEEcCCC
Confidence 444589999999999987 6666665 22 11 15677777889999874
No 44
>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=26.41 E-value=1.7e+02 Score=21.26 Aligned_cols=58 Identities=17% Similarity=0.243 Sum_probs=35.2
Q ss_pred hHHHHHHHHHcCCeeeEecCCCCcCCc-cchHHHHHHHHhcCceEEEEecccCCChhHHHH
Q 027772 35 FTDNLHTALIRNGFIAFKDDETLDRGN-EISSELSKAIEESNVSIVILSKNYASSPWCLDE 94 (219)
Q Consensus 35 Fv~~L~~aL~~~Gi~vf~D~~~l~~G~-~i~~~i~~aI~~S~~~IvV~S~ny~~S~wCl~E 94 (219)
...++...+++.|...-... -..|. .-...+...|.++++.|++.+----...|...+
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 46678888999998766551 11121 222247788899998887764444444444444
No 45
>TIGR01101 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit
Probab=25.10 E-value=1.3e+02 Score=23.38 Aligned_cols=27 Identities=15% Similarity=0.482 Sum_probs=20.5
Q ss_pred ccchHHHHHHHHhcCceEEEEecccCC
Q 027772 61 NEISSELSKAIEESNVSIVILSKNYAS 87 (219)
Q Consensus 61 ~~i~~~i~~aI~~S~~~IvV~S~ny~~ 87 (219)
+.+...+.+.+...+++|+++++++++
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~ 72 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE 72 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH
Confidence 345556666677899999999988765
No 46
>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=25.00 E-value=52 Score=32.36 Aligned_cols=33 Identities=18% Similarity=0.370 Sum_probs=27.0
Q ss_pred ccchHHHHHHHHHcCCeeeEecCCCCcCCccch
Q 027772 32 RNNFTDNLHTALIRNGFIAFKDDETLDRGNEIS 64 (219)
Q Consensus 32 r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~ 64 (219)
-...+..|+..|+..|+.+.+|+++-.+|..+.
T Consensus 488 ~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~ 520 (568)
T TIGR00409 488 QQQLAEELYSELLAQGVDVLLDDRNERAGVKFA 520 (568)
T ss_pred HHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHH
Confidence 346889999999999999999998766666554
No 47
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=24.88 E-value=54 Score=32.02 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=33.2
Q ss_pred CeeeEEEeccc--ccCccchHHHHHHHHHcCCeeeEecCCCCcCCccc
Q 027772 18 SKYDVFLSFRG--EDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEI 63 (219)
Q Consensus 18 ~~yDVFISfrg--~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i 63 (219)
-.|||+|---+ .+.-...+..|+..|+..||++.+|+++-..|..+
T Consensus 467 aP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~ 514 (565)
T PRK09194 467 APFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKF 514 (565)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHH
Confidence 45888886543 12234678899999999999999998754555444
No 48
>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=24.27 E-value=88 Score=21.77 Aligned_cols=39 Identities=13% Similarity=0.147 Sum_probs=21.8
Q ss_pred HHHHHHc--CCeeeEecCCCCcCCccchHHHHHHHHhcCceEE
Q 027772 39 LHTALIR--NGFIAFKDDETLDRGNEISSELSKAIEESNVSIV 79 (219)
Q Consensus 39 L~~aL~~--~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~Iv 79 (219)
....|.+ +.+.+|+|.+ .+|..-...+.+....-...+-
T Consensus 35 ~~~~L~~~~~~vii~~D~D--~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 35 QAELLKRLAKEVILAFDGD--EAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred HHHHHHhcCCeEEEEECCC--HHHHHHHHHHHHHHHHCCCeEE
Confidence 3444444 5677777764 4666655555555555444433
No 49
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=23.31 E-value=1.9e+02 Score=27.07 Aligned_cols=60 Identities=13% Similarity=0.156 Sum_probs=40.0
Q ss_pred eeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEec
Q 027772 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (219)
Q Consensus 19 ~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ 83 (219)
..||+|-+-+++. ...+-.+...|+++|++|-+|.. +..+...+..|-+.--..++|+.+
T Consensus 325 ~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 325 SIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 4689998755433 35677899999999999988753 244555566665544445666655
No 50
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=22.62 E-value=94 Score=30.93 Aligned_cols=61 Identities=15% Similarity=0.152 Sum_probs=38.3
Q ss_pred eeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEecc
Q 027772 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (219)
Q Consensus 19 ~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~n 84 (219)
.++|+|---+++ ....+..|+..|++.|++|.+|+++- .+...+.+|-..---.++|+-++
T Consensus 499 P~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~----slgkKir~A~~~GiP~iIVIG~k 559 (613)
T PRK03991 499 PTQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDE----SLGKKIRDAGKEWIPYVVVIGDK 559 (613)
T ss_pred CceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCC----CHHHHHHHHHHcCCCEEEEECcc
Confidence 368776654443 34688999999999999999998643 33334444432222345555433
No 51
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=22.51 E-value=1.6e+02 Score=20.27 Aligned_cols=31 Identities=23% Similarity=0.330 Sum_probs=22.0
Q ss_pred CCCCCCeeeEEEecccccCccchHHHHHHHHHcC
Q 027772 13 HQILQSKYDVFLSFRGEDTRNNFTDNLHTALIRN 46 (219)
Q Consensus 13 s~~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~ 46 (219)
+....++|.+||-+.+.|. . +.++.+.|++.
T Consensus 36 ~~~~~~~y~Ffvd~~~~~~--~-~~~~l~~L~~~ 66 (74)
T cd04904 36 SRRNGSEYEFFVDCEVDRG--D-LDQLISSLRRV 66 (74)
T ss_pred CCCCCceEEEEEEEEcChH--H-HHHHHHHHHHh
Confidence 3446789999999998653 2 56666777654
No 52
>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=22.39 E-value=3.1e+02 Score=20.13 Aligned_cols=30 Identities=23% Similarity=0.320 Sum_probs=21.3
Q ss_pred eEEEecccccCccchHHHHHHHHHcCCeeeEe
Q 027772 21 DVFLSFRGEDTRNNFTDNLHTALIRNGFIAFK 52 (219)
Q Consensus 21 DVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~ 52 (219)
.||+|.+..| +. -...+.+.|.+.|+++|-
T Consensus 2 ~vl~s~~~~~-k~-~~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 2 TVFISVADRD-KP-EAVEIAKRLAELGFKLVA 31 (110)
T ss_pred eEEEEEEcCc-Hh-HHHHHHHHHHHCCCEEEE
Confidence 3789988766 33 344777788888888874
No 53
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=22.00 E-value=2.2e+02 Score=26.91 Aligned_cols=59 Identities=17% Similarity=0.181 Sum_probs=38.2
Q ss_pred eeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEe
Q 027772 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILS 82 (219)
Q Consensus 19 ~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S 82 (219)
.++|+|-.-+++. ...+..|...|++.|+++.+|.. +..+...+.+|-+.---.++++.
T Consensus 274 P~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIIIG 332 (387)
T PRK14938 274 PIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIIIG 332 (387)
T ss_pred cceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEC
Confidence 4677665545543 35678899999999999999873 34555566666443333444443
No 54
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=21.99 E-value=1e+02 Score=27.80 Aligned_cols=99 Identities=19% Similarity=0.347 Sum_probs=68.8
Q ss_pred CeeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCC--CcCCccchHHHHHHHHh--cCceEEEEecccCCChhHHH
Q 027772 18 SKYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDET--LDRGNEISSELSKAIEE--SNVSIVILSKNYASSPWCLD 93 (219)
Q Consensus 18 ~~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~--l~~G~~i~~~i~~aI~~--S~~~IvV~S~ny~~S~wCl~ 93 (219)
-++.+=+||.++|. .+++..-.-|...|+.+|+|-.+ -..|.++.. ++.-|.+ .-+++...|.+|-...|...
T Consensus 5 ~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~-~~~e~~q~~~~~~~~f~~~~~~r~~~~~~ 81 (329)
T COG4916 5 VQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYD-YLSEIYQDKALFTIMFISEHYSRKMWTNH 81 (329)
T ss_pred hheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHH-HHHHHHhhhhHHHhhhhhccccCcCCCcH
Confidence 35667789999984 58888888899999999987321 234555543 2333333 44678889999999999999
Q ss_pred HHHHHHHhccccCCCeEEEEEeeeCC
Q 027772 94 ELAKIVECGNKRKDRKVFAVFYGVDP 119 (219)
Q Consensus 94 EL~~i~~~~~~~~~~~ViPVFy~v~p 119 (219)
|++.++..........++|-.++..|
T Consensus 82 ~~~~~~a~~~~~~~~~~~~~~~~~~~ 107 (329)
T COG4916 82 ERQAMQARAFQEHQEYILPARFDETP 107 (329)
T ss_pred HHHHHHHHHhhhccEEehhhhhccCC
Confidence 99887754244455577787776443
No 55
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. 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, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=21.75 E-value=90 Score=26.19 Aligned_cols=46 Identities=20% Similarity=0.161 Sum_probs=32.2
Q ss_pred eeeEEEecccccC-----ccchHHHHHHHHHcCCeeeEecCCCC-cCCccch
Q 027772 19 KYDVFLSFRGEDT-----RNNFTDNLHTALIRNGFIAFKDDETL-DRGNEIS 64 (219)
Q Consensus 19 ~yDVFISfrg~D~-----r~~Fv~~L~~aL~~~Gi~vf~D~~~l-~~G~~i~ 64 (219)
.++|+|---+.+. -...+..|...|+..||++-+|+++- .+|..+.
T Consensus 10 P~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~ 61 (202)
T cd00862 10 PIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFN 61 (202)
T ss_pred CceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHH
Confidence 4677665433220 23578999999999999999998654 6666654
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=21.08 E-value=3.5e+02 Score=21.09 Aligned_cols=43 Identities=28% Similarity=0.239 Sum_probs=27.0
Q ss_pred cCCccchHHHHHHHHhcCceEEEEecccCC-----ChhHHHHHHHHHH
Q 027772 58 DRGNEISSELSKAIEESNVSIVILSKNYAS-----SPWCLDELAKIVE 100 (219)
Q Consensus 58 ~~G~~i~~~i~~aI~~S~~~IvV~S~ny~~-----S~wCl~EL~~i~~ 100 (219)
..++.+.+.+.++|.+++..|.+.+..+.. .+.-+++|..+.+
T Consensus 17 ~~~~~~~~~i~~~I~~A~~~I~i~~~~~~~~~~~~~~~l~~~L~~a~~ 64 (176)
T cd00138 17 VGGRSDLDALLEAISNAKKSIYIASFYLSPLITEYGPVILDALLAAAR 64 (176)
T ss_pred cCcchHHHHHHHHHHhhheEEEEEEeEecccccccchHHHHHHHHHHH
Confidence 455666777778888888888877775553 3333445544443
No 57
>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=21.06 E-value=2.6e+02 Score=20.51 Aligned_cols=30 Identities=13% Similarity=0.131 Sum_probs=20.4
Q ss_pred CCc-cchHHHHHHHHhcCceEEEEecccCCC
Q 027772 59 RGN-EISSELSKAIEESNVSIVILSKNYASS 88 (219)
Q Consensus 59 ~G~-~i~~~i~~aI~~S~~~IvV~S~ny~~S 88 (219)
+|. .........+++++..|+|++..-..+
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~~ 87 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRES 87 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHHH
Confidence 443 334455667888999999999865443
No 58
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=20.76 E-value=2.1e+02 Score=27.75 Aligned_cols=60 Identities=10% Similarity=0.211 Sum_probs=39.7
Q ss_pred eeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEec
Q 027772 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (219)
Q Consensus 19 ~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S~ 83 (219)
.+||+|---+++. ...+..|...|++.||+|-+|.+ +..+...+..|-..---.++|+.+
T Consensus 476 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 476 PVQVVIIPVADAH-NEYAEEVAKKLRAAGIRVEVDTS----NERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CccEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEec
Confidence 4588887655442 45788999999999999999875 334555555554433334555544
No 59
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=20.47 E-value=2.2e+02 Score=27.92 Aligned_cols=59 Identities=15% Similarity=0.219 Sum_probs=38.5
Q ss_pred eeeEEEecccccCccchHHHHHHHHHcCCeeeEecCCCCcCCccchHHHHHHHHhcCceEEEEe
Q 027772 19 KYDVFLSFRGEDTRNNFTDNLHTALIRNGFIAFKDDETLDRGNEISSELSKAIEESNVSIVILS 82 (219)
Q Consensus 19 ~yDVFISfrg~D~r~~Fv~~L~~aL~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~~~IvV~S 82 (219)
..||+|-.-+++ -...+..+...|+++|++|-+|.+ +..+...+..|-..---.++|+.
T Consensus 438 P~qV~Iipi~e~-~~~~A~~Ia~~LR~~GirVelD~~----~~~lgkkir~A~k~gip~viIIG 496 (545)
T PRK14799 438 SVQVRVLPITDE-VNEYAEKVLNDMRKRRIRAEIDYA----GETLSKRIKNAYDQGVPYILIVG 496 (545)
T ss_pred CceEEEEEcCHH-HHHHHHHHHHHHHhCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEC
Confidence 458877665544 346788999999999999999874 34555555555332223444444
No 60
>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=20.28 E-value=3.5e+02 Score=20.62 Aligned_cols=35 Identities=17% Similarity=0.215 Sum_probs=21.2
Q ss_pred HHHHHHHhcCceEEEEecccCCChhHHHHHHHHHHh
Q 027772 66 ELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (219)
Q Consensus 66 ~i~~aI~~S~~~IvV~S~ny~~S~wCl~EL~~i~~~ 101 (219)
++.++|+++++.++|++-.-..+.+. .++...+..
T Consensus 4 ~~~~~i~~aD~vl~ViD~~~p~~~~~-~~l~~~l~~ 38 (141)
T cd01857 4 QLWRVVERSDIVVQIVDARNPLLFRP-PDLERYVKE 38 (141)
T ss_pred HHHHHHhhCCEEEEEEEccCCcccCC-HHHHHHHHh
Confidence 56777888888888887655444432 244454443
Done!