Query 046164
Match_columns 202
No_of_seqs 188 out of 1411
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 09:19:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046164hhsearch_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 6.8E-52 1.5E-56 336.6 17.4 183 5-191 4-186 (187)
2 PLN03210 Resistant to P. syrin 100.0 5.4E-40 1.2E-44 328.6 15.3 167 26-197 7-188 (1153)
3 PF01582 TIR: TIR domain; Int 99.9 1E-22 2.2E-27 159.0 3.3 116 34-150 1-140 (141)
4 smart00255 TIR Toll - interleu 99.9 2.7E-21 5.9E-26 149.1 9.9 101 31-133 1-107 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 1.9E-19 4.1E-24 132.5 2.5 87 34-123 1-87 (102)
6 KOG3678 SARM protein (with ste 99.5 2.3E-13 4.9E-18 124.2 12.2 155 15-186 598-760 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.8 7.1E-09 1.5E-13 80.1 6.5 91 32-123 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 97.8 4.4E-05 9.6E-10 59.7 5.6 65 33-97 2-70 (150)
9 PF10137 TIR-like: Predicted n 96.8 0.0047 1E-07 47.8 6.7 86 33-121 1-101 (125)
10 PF05014 Nuc_deoxyrib_tr: Nucl 93.4 0.6 1.3E-05 34.6 7.8 79 44-123 12-98 (113)
11 PF13271 DUF4062: Domain of un 92.9 0.49 1.1E-05 33.5 6.3 67 33-100 1-67 (83)
12 COG4916 Uncharacterized protei 92.4 0.23 5.1E-06 43.0 4.7 99 27-128 173-280 (329)
13 COG4271 Predicted nucleotide-b 87.0 6 0.00013 33.2 8.8 118 9-132 60-200 (233)
14 PF14359 DUF4406: Domain of un 80.4 16 0.00034 26.5 7.8 72 44-118 15-90 (92)
15 cd00860 ThrRS_anticodon ThrRS 74.1 17 0.00036 25.0 6.3 60 32-96 2-61 (91)
16 cd02042 ParA ParA and ParB of 73.6 18 0.0004 25.6 6.6 64 34-97 3-73 (104)
17 PF03129 HGTP_anticodon: Antic 71.7 7.2 0.00016 27.4 4.0 47 45-95 15-61 (94)
18 cd00738 HGTP_anticodon HGTP an 71.1 20 0.00044 24.6 6.2 61 32-96 2-64 (94)
19 COG3613 Nucleoside 2-deoxyribo 68.7 21 0.00045 29.1 6.4 77 46-122 20-106 (172)
20 cd00858 GlyRS_anticodon GlyRS 62.3 39 0.00084 25.1 6.6 61 30-96 25-87 (121)
21 COG0276 HemH Protoheme ferro-l 61.9 62 0.0014 28.9 8.7 64 47-113 74-146 (320)
22 PF14258 DUF4350: Domain of un 59.3 50 0.0011 21.9 6.3 59 49-118 8-67 (70)
23 cd02426 Pol_gamma_b_Cterm C-te 52.4 12 0.00026 28.6 2.3 50 26-75 22-76 (128)
24 PF02310 B12-binding: B12 bind 51.5 61 0.0013 23.4 6.0 70 48-123 17-87 (121)
25 PLN03194 putative disease resi 49.4 66 0.0014 26.6 6.3 66 57-122 24-89 (187)
26 cd00861 ProRS_anticodon_short 49.0 53 0.0011 22.6 5.1 48 45-96 17-64 (94)
27 PF03709 OKR_DC_1_N: Orn/Lys/A 48.5 89 0.0019 23.1 6.5 72 47-127 5-77 (115)
28 PRK08661 prolyl-tRNA synthetas 46.6 40 0.00087 31.5 5.2 59 17-75 273-337 (477)
29 PF07429 Glyco_transf_56: 4-al 46.4 31 0.00068 31.3 4.3 13 141-153 345-357 (360)
30 COG1658 Small primase-like pro 46.3 39 0.00084 26.2 4.2 55 31-87 29-83 (127)
31 TIGR00418 thrS threonyl-tRNA s 44.6 75 0.0016 30.1 6.8 63 29-96 468-530 (563)
32 PF10087 DUF2325: Uncharacteri 44.3 82 0.0018 22.4 5.6 61 47-109 11-72 (97)
33 PF03437 BtpA: BtpA family; I 40.7 1E+02 0.0022 26.6 6.5 80 50-132 132-217 (254)
34 PLN02924 thymidylate kinase 40.3 2.1E+02 0.0047 23.7 12.7 168 22-190 5-213 (220)
35 PRK09194 prolyl-tRNA synthetas 38.9 69 0.0015 30.6 5.6 52 24-75 461-514 (565)
36 COG0400 Predicted esterase [Ge 38.2 89 0.0019 26.0 5.6 55 28-84 143-199 (207)
37 cd00859 HisRS_anticodon HisRS 37.4 1.2E+02 0.0026 20.0 5.8 58 33-95 3-60 (91)
38 cd00862 ProRS_anticodon_zinc P 37.1 57 0.0012 26.8 4.2 49 29-77 8-62 (202)
39 cd04128 Spg1 Spg1p. Spg1p (se 36.8 2E+02 0.0043 22.6 7.3 51 79-130 66-117 (182)
40 PF01990 ATP-synt_F: ATP synth 36.0 65 0.0014 23.0 3.9 67 51-124 9-75 (95)
41 PF03358 FMN_red: NADPH-depend 35.9 78 0.0017 23.9 4.6 56 45-101 17-85 (152)
42 cd03364 TOPRIM_DnaG_primases T 35.1 55 0.0012 22.3 3.3 30 34-63 46-75 (79)
43 PLN03108 Rab family protein; P 34.7 1.5E+02 0.0033 23.8 6.4 108 81-197 74-190 (210)
44 CHL00201 syh histidine-tRNA sy 34.6 1.2E+02 0.0026 27.8 6.3 62 29-95 323-384 (430)
45 TIGR00334 5S_RNA_mat_M5 ribonu 34.0 86 0.0019 25.6 4.7 50 45-98 35-84 (174)
46 PF03720 UDPG_MGDP_dh_C: UDP-g 33.9 32 0.00069 25.1 2.0 54 41-94 12-75 (106)
47 KOG2903 Predicted glutathione 33.4 1.7E+02 0.0037 25.8 6.5 104 11-129 20-135 (319)
48 PF01269 Fibrillarin: Fibrilla 32.6 47 0.001 28.4 3.0 25 99-123 106-130 (229)
49 TIGR01101 V_ATP_synt_F vacuola 32.5 98 0.0021 23.5 4.5 48 73-127 46-93 (115)
50 cd00138 PLDc Phospholipase D. 32.3 97 0.0021 23.8 4.7 39 46-84 21-64 (176)
51 PF00071 Ras: Ras family; Int 31.9 2.1E+02 0.0046 21.2 6.5 52 80-131 66-118 (162)
52 PRK12325 prolyl-tRNA synthetas 31.9 84 0.0018 29.0 4.9 64 29-96 343-408 (439)
53 PF11074 DUF2779: Domain of un 31.7 41 0.00088 26.0 2.3 31 78-110 63-93 (130)
54 PF01915 Glyco_hydro_3_C: Glyc 31.1 2.9E+02 0.0064 22.5 8.6 86 45-131 46-148 (227)
55 PF12146 Hydrolase_4: Putative 30.6 69 0.0015 22.2 3.2 35 31-66 16-50 (79)
56 PF13401 AAA_22: AAA domain; P 30.5 1.8E+02 0.0038 20.9 5.6 87 34-130 41-128 (131)
57 PRK13762 tRNA-modifying enzyme 29.8 1.4E+02 0.0029 26.5 5.6 39 31-69 130-168 (322)
58 PF00762 Ferrochelatase: Ferro 28.9 2.9E+02 0.0062 24.4 7.5 65 46-113 73-144 (316)
59 TIGR00408 proS_fam_I prolyl-tR 28.8 2.7E+02 0.0059 26.0 7.7 68 25-96 276-348 (472)
60 PF09837 DUF2064: Uncharacteri 28.5 2.6E+02 0.0056 21.0 7.6 77 29-114 8-88 (122)
61 COG4916 Uncharacterized protei 28.2 69 0.0015 28.1 3.3 94 29-124 4-105 (329)
62 PF09419 PGP_phosphatase: Mito 28.2 1.4E+02 0.0031 24.0 5.1 68 54-122 35-111 (168)
63 PRK11784 tRNA 2-selenouridine 27.9 4.5E+02 0.0097 23.6 8.8 115 42-188 190-322 (345)
64 PLN02530 histidine-tRNA ligase 27.8 1.8E+02 0.0039 27.2 6.3 61 30-95 400-460 (487)
65 PRK02228 V-type ATP synthase s 27.7 1.1E+02 0.0025 22.2 4.1 64 54-124 14-77 (100)
66 PTZ00099 rab6; Provisional 27.5 2.7E+02 0.0058 21.9 6.6 52 80-131 47-99 (176)
67 cd07373 2A5CPDO_A The alpha su 26.7 2.7E+02 0.0059 23.8 6.9 82 45-129 90-181 (271)
68 PRK00413 thrS threonyl-tRNA sy 26.5 3.6E+02 0.0079 25.9 8.4 61 31-96 539-599 (638)
69 PRK14799 thrS threonyl-tRNA sy 26.4 1.8E+02 0.004 27.8 6.2 60 31-95 438-497 (545)
70 cd04167 Snu114p Snu114p subfam 25.9 3.5E+02 0.0076 21.7 8.7 88 71-158 79-167 (213)
71 PRK14938 Ser-tRNA(Thr) hydrola 25.9 2.5E+02 0.0054 25.9 6.7 62 29-95 272-333 (387)
72 PRK12305 thrS threonyl-tRNA sy 25.9 1.8E+02 0.004 27.5 6.2 60 31-95 476-535 (575)
73 PRK12444 threonyl-tRNA synthet 25.6 4.1E+02 0.0088 25.7 8.5 63 30-96 540-602 (639)
74 cd02067 B12-binding B12 bindin 25.5 2.6E+02 0.0057 20.2 8.0 69 51-124 19-88 (119)
75 KOG2792 Putative cytochrome C 25.4 68 0.0015 28.0 2.8 26 102-127 154-187 (280)
76 cd02071 MM_CoA_mut_B12_BD meth 25.0 2.9E+02 0.0062 20.4 8.6 68 51-123 19-87 (122)
77 PRK10569 NAD(P)H-dependent FMN 24.9 2.5E+02 0.0053 22.8 6.0 54 47-101 19-81 (191)
78 cd01423 MGS_CPS_I_III Methylgl 24.4 1.1E+02 0.0023 22.5 3.4 29 34-64 3-31 (116)
79 PRK15057 UDP-glucose 6-dehydro 24.0 1.4E+02 0.0031 27.1 4.8 56 36-91 304-365 (388)
80 PF11201 DUF2982: Protein of u 24.0 77 0.0017 25.3 2.7 28 29-56 123-151 (152)
81 COG0125 Tmk Thymidylate kinase 23.3 4.3E+02 0.0094 21.9 11.7 144 34-184 4-203 (208)
82 PF09152 DUF1937: Domain of un 23.1 1.2E+02 0.0027 23.1 3.6 69 49-117 30-111 (116)
83 cd00532 MGS-like MGS-like doma 22.7 2.3E+02 0.0049 20.7 5.0 29 34-64 2-30 (112)
84 KOG1610 Corticosteroid 11-beta 22.7 97 0.0021 27.8 3.3 34 29-66 27-60 (322)
85 COG1058 CinA Predicted nucleot 22.0 1.1E+02 0.0023 26.6 3.4 42 48-94 23-67 (255)
86 cd01424 MGS_CPS_II Methylglyox 21.5 2.4E+02 0.0053 20.2 4.9 29 34-64 3-31 (110)
87 PF02829 3H: 3H domain; Inter 21.1 1.1E+02 0.0023 22.5 2.8 77 102-179 9-92 (98)
88 PF13662 Toprim_4: Toprim doma 21.0 79 0.0017 21.6 2.0 25 58-84 47-71 (81)
89 cd04175 Rap1 Rap1 subgroup. T 21.0 3.6E+02 0.0078 20.1 6.8 62 71-132 57-121 (164)
90 COG2342 Predicted extracellula 20.8 1.4E+02 0.0031 26.4 3.9 44 77-122 33-79 (300)
91 COG1180 PflA Pyruvate-formate 20.6 3.6E+02 0.0078 23.0 6.4 62 34-96 87-148 (260)
92 TIGR00409 proS_fam_II prolyl-t 20.5 1.9E+02 0.0041 27.8 5.1 55 22-76 464-520 (568)
93 TIGR02742 TrbC_Ftype type-F co 20.5 3.1E+02 0.0067 21.2 5.4 35 34-73 3-37 (130)
94 cd04110 Rab35 Rab35 subfamily. 20.2 4.4E+02 0.0095 20.8 7.3 57 71-130 63-123 (199)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=6.8e-52 Score=336.62 Aligned_cols=183 Identities=72% Similarity=1.170 Sum_probs=170.8
Q ss_pred chhhHHHHHHhhcCCCCCcCCCCCCCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhh
Q 046164 5 SSTKSLCRKIIHHRPHHQIQLPITRRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIK 84 (202)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~ 84 (202)
|||..+-.+.+-|.++++.. ..+|||||||+|+|+|++|++||+.+|.++||+||+|+.++.+|+.+.+.|.+||+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~----~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIe 79 (187)
T PLN03194 4 SSTAQLNNRLFLHYPSSSSS----AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIR 79 (187)
T ss_pred hHHHHHhhhhhcccccCCCC----CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHH
Confidence 67888888888888766543 67899999999999999999999999999999999999999999999999999999
Q ss_pred hcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEecCCCCccCCCCCccchhhhHHHHHHHHHHHHhcCCcccCCC
Q 046164 85 HCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYDVKPSQLQVPDNGTCSRKELQRFSRALEEAKYTVGLTFDSIN 164 (202)
Q Consensus 85 ~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~v~p~~vr~~~~~~~~~e~~~~W~~AL~~v~~~~G~~~~~~~ 164 (202)
+|+++|+||||+|++|.||++||++|+++++.||||||+|+|++||+|..+.+.++++++|+.||++|++++|++++..+
T Consensus 80 eSri~IvVfS~~Ya~S~WCLdEL~~I~e~~~~ViPIFY~VdPsdVr~q~~~~~~~e~v~~Wr~AL~~va~l~G~~~~~~~ 159 (187)
T PLN03194 80 NCKVGVAVFSPRYCESYFCLHELALIMESKKRVIPIFCDVKPSQLRVVDNGTCPDEEIRRFNWALEEAKYTVGLTFDSLK 159 (187)
T ss_pred hCeEEEEEECCCcccchhHHHHHHHHHHcCCEEEEEEecCCHHHhhccccCCCCHHHHHHHHHHHHHHhccccccCCCCC
Confidence 99999999999999999999999999999999999999999999999877888899999999999999999999987656
Q ss_pred CCHHHHHHHHHHHHHHHhhhhcccccc
Q 046164 165 GDWSEFLTTATDAVINNLIEVEEESTA 191 (202)
Q Consensus 165 ~~e~~~i~~Iv~~v~~~L~~~~~~~~~ 191 (202)
++|+++|++||+.|.++|..+++|..+
T Consensus 160 ~~e~e~i~~iv~~v~k~l~~~~~~~~~ 186 (187)
T PLN03194 160 GNWSEVVTMASDAVIKNLIELEEEKSV 186 (187)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhcccC
Confidence 899999999999999999999987643
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=5.4e-40 Score=328.58 Aligned_cols=167 Identities=23% Similarity=0.409 Sum_probs=150.7
Q ss_pred CCCCCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHH
Q 046164 26 PITRRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLH 105 (202)
Q Consensus 26 ~~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~ 105 (202)
+++.++|||||||||+|+|++|++||+.+|.++||.+|+|+ ++++|+.+.+++.+||++|+++|||||++|++|.||++
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 44689999999999999999999999999999999999987 59999999999999999999999999999999999999
Q ss_pred HHHHHHHhc----CceecEEEecCCCCccCCCCCcc-----------chhhhHHHHHHHHHHHHhcCCcccCCCCCHHHH
Q 046164 106 ELALIMESR----KKVIPIFYDVKPSQLQVPDNGTC-----------SRKELQRFSRALEEAKYTVGLTFDSINGDWSEF 170 (202)
Q Consensus 106 EL~~i~~~~----~~ViPVfy~v~p~~vr~~~~~~~-----------~~e~~~~W~~AL~~v~~~~G~~~~~~~~~e~~~ 170 (202)
||++|++|+ +.|+||||+|+|++||+|. |.| +++++++|+.||++|++++|+++.. +++|+++
T Consensus 86 el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~-g~f~~~f~~~~~~~~~~~~~~w~~al~~~~~~~g~~~~~-~~~E~~~ 163 (1153)
T PLN03210 86 ELLEIVRCKEELGQLVIPVFYGLDPSHVRKQT-GDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQN-WPNEAKM 163 (1153)
T ss_pred HHHHHHHhhhhcCceEEEEEecccHHHHhhcc-chHHHHHHHHhcccchhHHHHHHHHHHHHhCcCceecCC-CCCHHHH
Confidence 999999986 4899999999999999998 443 5678999999999999999999875 7899999
Q ss_pred HHHHHHHHHHHhhhhcccccccccccc
Q 046164 171 LTTATDAVINNLIEVEEESTANREPMG 197 (202)
Q Consensus 171 i~~Iv~~v~~~L~~~~~~~~~~~~~~g 197 (202)
|++||++|+++|...+. ......||
T Consensus 164 i~~Iv~~v~~~l~~~~~--~~~~~~vG 188 (1153)
T PLN03210 164 IEEIANDVLGKLNLTPS--NDFEDFVG 188 (1153)
T ss_pred HHHHHHHHHHhhccccC--cccccccc
Confidence 99999999999976543 23334555
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=99.86 E-value=1e-22 Score=158.98 Aligned_cols=116 Identities=28% Similarity=0.466 Sum_probs=98.1
Q ss_pred EEEeccccccchhHHHHHHHHHhcC--CCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHH
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRL--RLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIM 111 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~--Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~ 111 (202)
|||||++.+++..|+.+|..+|++. |+++|++++|+.+|..+.+++.++|++|+++|+|+|++|++|.||+.||..|+
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 8999998445789999999999999 99999999999999999999999999999999999999999999999999998
Q ss_pred Hh----c--CceecEEEecCCCCcc-CCCCCc----------c-c----hhhhHHHHHHHH
Q 046164 112 ES----R--KKVIPIFYDVKPSQLQ-VPDNGT----------C-S----RKELQRFSRALE 150 (202)
Q Consensus 112 ~~----~--~~ViPVfy~v~p~~vr-~~~~~~----------~-~----~e~~~~W~~AL~ 150 (202)
++ + +.|+|||+++.+.+++ .+. +. . . .+....|+.++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~-~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQS-LRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHH-HHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhh-HHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 74 2 5899999999999999 343 11 1 1 345678988875
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.85 E-value=2.7e-21 Score=149.12 Aligned_cols=101 Identities=36% Similarity=0.617 Sum_probs=86.4
Q ss_pred CccEEEeccc-cccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHH
Q 046164 31 PCDVFINHRG-TDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELAL 109 (202)
Q Consensus 31 ~ydVFISy~~-~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~ 109 (202)
.|||||||++ .+....|+.+|...|...|+.+|.|+..+..| ...+|.++|++|+++|+|+||+|..|.||..|+..
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~--~~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~ 78 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGG--DLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVA 78 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccc--hHHHHHHHHHHCcEEEEEECcccccChhHHHHHHH
Confidence 4999999998 45667999999999999999999997643333 33399999999999999999999999999999999
Q ss_pred HHHh-----cCceecEEEecCCCCccCCC
Q 046164 110 IMES-----RKKVIPIFYDVKPSQLQVPD 133 (202)
Q Consensus 110 i~~~-----~~~ViPVfy~v~p~~vr~~~ 133 (202)
+++. .++||||+++..|.++..+.
T Consensus 79 a~~~~~~~~~~~iIPI~~~~~~~~~~~~~ 107 (140)
T smart00255 79 ALENALEEGGLRVIPIFYEVIPSDVRKQP 107 (140)
T ss_pred HHHHHHHcCCCeEEEEEEecChHHHHhcc
Confidence 9874 46999999998887676654
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.76 E-value=1.9e-19 Score=132.50 Aligned_cols=87 Identities=30% Similarity=0.529 Sum_probs=77.7
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHh
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMES 113 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~ 113 (202)
|||||+++|. .++..|...|++.|+++|+|. ++.+|+.+.+.|.++|++|+.+|+++||+|..|+||..|+..+.+.
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 VFISYSSEDR--EFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWKR 77 (102)
T ss_dssp EEEEEEGGGC--CCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHCT
T ss_pred eEEEecCCcH--HHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHHC
Confidence 8999999884 689999999999999999997 8999999999999999999999999999999999999999999888
Q ss_pred cCceecEEEe
Q 046164 114 RKKVIPIFYD 123 (202)
Q Consensus 114 ~~~ViPVfy~ 123 (202)
+++||||.++
T Consensus 78 ~~~iipv~~~ 87 (102)
T PF13676_consen 78 GKPIIPVRLD 87 (102)
T ss_dssp SESEEEEECS
T ss_pred CCEEEEEEEC
Confidence 8899999964
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.50 E-value=2.3e-13 Score=124.16 Aligned_cols=155 Identities=17% Similarity=0.260 Sum_probs=122.3
Q ss_pred hhcCCCCCcCCCCCCCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeC
Q 046164 15 IHHRPHHQIQLPITRRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFS 94 (202)
Q Consensus 15 ~~~~~~~~~~~~~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S 94 (202)
..|+...+.+.. .++.||||||++. +....++.|...|+-+|++||+|.+.+..|. +.+.+.+.|..++.+|+|+|
T Consensus 598 a~H~~~v~~a~~--skq~DVFISYRRs-tGnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLt 673 (832)
T KOG3678|consen 598 AKHPDDVEVAML--SKQIDVFISYRRS-TGNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLT 673 (832)
T ss_pred hcCCCccccccc--cCCcceEEEeecc-ccHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeC
Confidence 345555555543 7889999999965 4678999999999999999999999898886 57789999999999999999
Q ss_pred CCCcC--------ChhhHHHHHHHHHhcCceecEEEecCCCCccCCCCCccchhhhHHHHHHHHHHHHhcCCcccCCCCC
Q 046164 95 PRYCE--------SYFCLHELALIMESRKKVIPIFYDVKPSQLQVPDNGTCSRKELQRFSRALEEAKYTVGLTFDSINGD 166 (202)
Q Consensus 95 ~~y~~--------S~wc~~EL~~i~~~~~~ViPVfy~v~p~~vr~~~~~~~~~e~~~~W~~AL~~v~~~~G~~~~~~~~~ 166 (202)
|+... -+|...||.-++++++.|||||-.. .+. +++-..-.+.+.-+..+.|..|.+ .+
T Consensus 674 P~sLDr~lnD~nCeDWVHKEl~~Afe~~KNIiPI~D~a--FE~---------Pt~ed~iPnDirmi~kyNGvKWvH--dY 740 (832)
T KOG3678|consen 674 PNSLDRLLNDDNCEDWVHKELKCAFEHQKNIIPIFDTA--FEF---------PTKEDQIPNDIRMITKYNGVKWVH--DY 740 (832)
T ss_pred cchHHHHhccccHHHHHHHHHHHHHHhcCCeeeeeccc--ccC---------CCchhcCcHHHHHHHhccCeeeeh--hh
Confidence 98653 4699999999999999999998541 000 011112233445577889998874 68
Q ss_pred HHHHHHHHHHHHHHHhhhhc
Q 046164 167 WSEFLTTATDAVINNLIEVE 186 (202)
Q Consensus 167 e~~~i~~Iv~~v~~~L~~~~ 186 (202)
+..++.|||+-+...|++..
T Consensus 741 QdA~maKvvRFitGe~nRtt 760 (832)
T KOG3678|consen 741 QDACMAKVVRFITGELNRTT 760 (832)
T ss_pred HHHHHHHHHHHHhccccCCC
Confidence 89999999999999998855
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=98.84 E-value=7.1e-09 Score=80.05 Aligned_cols=91 Identities=18% Similarity=0.287 Sum_probs=50.6
Q ss_pred ccEEEeccccccchhHHHHHHHHHhcC-------CCee-E---------ecCCCCCCCCcchHHHHHhhhhcceEEEEeC
Q 046164 32 CDVFINHRGTDTKRTIAGLLHDHLSRL-------RLNP-F---------LDSKNMKPGDRLFDKIDTAIKHCKLGVAVFS 94 (202)
Q Consensus 32 ydVFISy~~~D~r~~fv~~L~~~L~~~-------Gi~v-f---------~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S 94 (202)
|.|||||++.|.. ..+..|...+... .+.. | -+..+......+...|.++|..|.++||+++
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 5799999988753 4677777777662 2221 1 1222223345788999999999999999999
Q ss_pred CCCcCChhhHHHHHHHHHhcCceecEEEe
Q 046164 95 PRYCESYFCLHELALIMESRKKVIPIFYD 123 (202)
Q Consensus 95 ~~y~~S~wc~~EL~~i~~~~~~ViPVfy~ 123 (202)
++...|.|+..|+..+++.+++||.|.+.
T Consensus 80 ~~T~~s~wV~~EI~~A~~~~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALKKGKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTTT---EEEEETT
T ss_pred CCcccCcHHHHHHHHHHHCCCCEEEEECC
Confidence 99999999999999999999999998653
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=97.80 E-value=4.4e-05 Score=59.68 Aligned_cols=65 Identities=18% Similarity=0.239 Sum_probs=53.0
Q ss_pred cEEEeccccccc-hhHHHHHHHHHhcC-CCeeEecCCCCCC--CCcchHHHHHhhhhcceEEEEeCCCC
Q 046164 33 DVFINHRGTDTK-RTIAGLLHDHLSRL-RLNPFLDSKNMKP--GDRLFDKIDTAIKHCKLGVAVFSPRY 97 (202)
Q Consensus 33 dVFISy~~~D~r-~~fv~~L~~~L~~~-Gi~vf~D~~~l~~--G~~i~~~i~~aI~~S~i~IvV~S~~y 97 (202)
-|||||+..... ...|..|...|++. |+.|.+|..+... +..+..=+.+.+++++.+|+|+||.+
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 499999974432 25688999999999 9999999987743 65677778888999999999999544
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=96.82 E-value=0.0047 Score=47.77 Aligned_cols=86 Identities=22% Similarity=0.407 Sum_probs=65.9
Q ss_pred cEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC-CcC------------
Q 046164 33 DVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR-YCE------------ 99 (202)
Q Consensus 33 dVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~-y~~------------ 99 (202)
.|||.|+ .|. ..+..+...|+..|+.+.+-.+....|..+.+.+.+.+.+++.+|++++|+ ...
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 4899998 553 678889999998899876656667899999999999999999999999984 221
Q ss_pred ChhhHHHHHHHHHh-c-CceecEE
Q 046164 100 SYFCLHELALIMES-R-KKVIPIF 121 (202)
Q Consensus 100 S~wc~~EL~~i~~~-~-~~ViPVf 121 (202)
..-.+.|+..++.. + ++++-+.
T Consensus 78 R~NVifE~G~f~g~LGr~rv~~l~ 101 (125)
T PF10137_consen 78 RQNVIFELGLFIGKLGRERVFILV 101 (125)
T ss_pred ccceeehhhHHHhhcCcceEEEEE
Confidence 12356788888764 3 4566554
No 10
>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=93.41 E-value=0.6 Score=34.64 Aligned_cols=79 Identities=15% Similarity=0.130 Sum_probs=56.6
Q ss_pred chhHHHHHHHHHhcCCCeeEecCCC-CC---CCCcchHH----HHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcC
Q 046164 44 KRTIAGLLHDHLSRLRLNPFLDSKN-MK---PGDRLFDK----IDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRK 115 (202)
Q Consensus 44 r~~fv~~L~~~L~~~Gi~vf~D~~~-l~---~G~~i~~~----i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~ 115 (202)
...+...+.+.|++.|+.+|...+. .. .+..+... -.++|++|+++|+++.+.- .+.=+.-|+..+...++
T Consensus 12 ~~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~algk 90 (113)
T PF05014_consen 12 QKARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYALGK 90 (113)
T ss_dssp HHHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHCCC
Confidence 3567889999999999999876531 11 12233333 3468999999999998755 55667889999999998
Q ss_pred ceecEEEe
Q 046164 116 KVIPIFYD 123 (202)
Q Consensus 116 ~ViPVfy~ 123 (202)
+|+-+.-+
T Consensus 91 pv~~~~~d 98 (113)
T PF05014_consen 91 PVILLTED 98 (113)
T ss_dssp EEEEEECC
T ss_pred EEEEEEcC
Confidence 77665433
No 11
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=92.87 E-value=0.49 Score=33.45 Aligned_cols=67 Identities=18% Similarity=0.212 Sum_probs=46.3
Q ss_pred cEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCC
Q 046164 33 DVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCES 100 (202)
Q Consensus 33 dVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S 100 (202)
.||||-.-.|-. .--..|.+.+.+.|.....-+.=-..+....+...+.|++|+++|.++-..|-..
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 389997766642 3456678888877775533221112345556677899999999999999998754
No 12
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=92.35 E-value=0.23 Score=43.00 Aligned_cols=99 Identities=19% Similarity=0.214 Sum_probs=67.8
Q ss_pred CCCCCccEEEeccccccchhHHHHHHHHHhcC--CCeeEecCC---CCCCCCcchHHHHHhh-hhcceEEEEeCCCCcCC
Q 046164 27 ITRRPCDVFINHRGTDTKRTIAGLLHDHLSRL--RLNPFLDSK---NMKPGDRLFDKIDTAI-KHCKLGVAVFSPRYCES 100 (202)
Q Consensus 27 ~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~--Gi~vf~D~~---~l~~G~~i~~~i~~aI-~~S~i~IvV~S~~y~~S 100 (202)
+..+.||+=+||.|+- ++.|..+..+++.. -+..|.|-. -+-+|+ +.+-+...- ..|+..+|....+|...
T Consensus 173 ~~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~~~L~~~Y~~rC~~~~VF~~~~Y~~K 249 (329)
T COG4916 173 SSEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LVSTLDPGYDIRCVVTTVFNTGSYICK 249 (329)
T ss_pred ccccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HHHhcccccCceEEEEEEEeCCceEEe
Confidence 3588999999999975 37899999999843 456777753 233443 222222222 57888899999999999
Q ss_pred hhhHHHHHHHHHhc--CceecEEE-ecCCCC
Q 046164 101 YFCLHELALIMESR--KKVIPIFY-DVKPSQ 128 (202)
Q Consensus 101 ~wc~~EL~~i~~~~--~~ViPVfy-~v~p~~ 128 (202)
.||.-|-..+-+.. +.+.||.| .++-+.
T Consensus 250 ~~c~~E~~~~r~~~~~d~~~rI~~~~~d~~a 280 (329)
T COG4916 250 STCHIEGLEGRLNPILDTGFRIKYLYADNIA 280 (329)
T ss_pred eeeccchhhccccccccccceEEEEecCCcc
Confidence 99999976664432 36777766 344433
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=87.05 E-value=6 Score=33.17 Aligned_cols=118 Identities=20% Similarity=0.287 Sum_probs=73.5
Q ss_pred HHHHHHhhcCCC-CCcCCCCCCCCccEEEeccccccchhHHHHHHHHHhc-CCC-eeEecCCCCCCCCcchHHHHHhhhh
Q 046164 9 SLCRKIIHHRPH-HQIQLPITRRPCDVFINHRGTDTKRTIAGLLHDHLSR-LRL-NPFLDSKNMKPGDRLFDKIDTAIKH 85 (202)
Q Consensus 9 ~~~~~~~~~~~~-~~~~~~~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~-~Gi-~vf~D~~~l~~G~~i~~~i~~aI~~ 85 (202)
-+++++.+.... .+-+.+-|..+ .|||-|+++. .+.....+|.+ .-. .+|.|.- ...|..+.+.+.+-|.+
T Consensus 60 ~i~~~~a~~a~~~~qna~t~p~~k-kvFvv~ghd~----iArael~allrd~~l~~vi~d~~-~~~g~~ile~lek~i~~ 133 (233)
T COG4271 60 CLGVQPANAAAPAPQNAATMPNLK-KVFVVSGHDA----IARAELEALLRDWKLEPVILDGL-FSEGQTILESLEKYIAE 133 (233)
T ss_pred chhhhhhhhcCcCcccccccCCce-eEEEEeccHH----HHHHHHHHHhhccccceEEecCc-ccccHHHHHHHHHHhhh
Confidence 344555443222 22244446666 9999987532 56555566654 333 4666653 66888999999999999
Q ss_pred cceEEEEeCCCCc-----C---Chh------hHHHHHHHHHh-c-CceecEEEe---c-CCCCccCC
Q 046164 86 CKLGVAVFSPRYC-----E---SYF------CLHELALIMES-R-KKVIPIFYD---V-KPSQLQVP 132 (202)
Q Consensus 86 S~i~IvV~S~~y~-----~---S~w------c~~EL~~i~~~-~-~~ViPVfy~---v-~p~~vr~~ 132 (202)
++.+|++.+|+=. . ..| ...||...+.. + ++|+-+..+ | -|||+...
T Consensus 134 v~FAi~latPDDkgy~~~~~~~k~~praRqNVifELGm~mgrLgRkrv~Il~k~~envelPSDi~Gv 200 (233)
T COG4271 134 VKFAIVLATPDDKGYRAVHSREKAFPRARQNVIFELGMFMGRLGRKRVMILMKRDENVELPSDIAGV 200 (233)
T ss_pred ceEEEEEecCcccccccccchhhccccccccchhhHhhHHhhcccceEEEEecccccccCccccCce
Confidence 9999999999743 1 224 56688887764 3 455544432 1 36666543
No 14
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=80.43 E-value=16 Score=26.54 Aligned_cols=72 Identities=13% Similarity=0.059 Sum_probs=49.2
Q ss_pred chhHHHHHHHHHhcCCCeeEecCCC-CCCCCcchHHHH---HhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCcee
Q 046164 44 KRTIAGLLHDHLSRLRLNPFLDSKN-MKPGDRLFDKID---TAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVI 118 (202)
Q Consensus 44 r~~fv~~L~~~L~~~Gi~vf~D~~~-l~~G~~i~~~i~---~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~Vi 118 (202)
+..|. .....|+..|+.|.--... ...|..+..-+. ..+..|+..+ +=|++-.|.=|.-|...+.+.+..|+
T Consensus 15 ~~~f~-~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~--~l~gWe~S~GA~~E~~~A~~lGl~V~ 90 (92)
T PF14359_consen 15 RPAFN-AAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIY--MLPGWENSRGARLEHELAKKLGLPVI 90 (92)
T ss_pred HHHHH-HHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEE--EcCCcccCcchHHHHHHHHHCCCeEe
Confidence 34454 5778899999776543322 255555554443 4467777543 44999999999999999988876553
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=74.12 E-value=17 Score=24.95 Aligned_cols=60 Identities=18% Similarity=0.115 Sum_probs=38.2
Q ss_pred ccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 32 CDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 32 ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
++|+|...+.+. ...+..+...|++.|++|-+|... ..+...+..|-..---.++++.++
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 677776654432 456888999999999999998643 345556655543333344444443
No 16
>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=73.57 E-value=18 Score=25.59 Aligned_cols=64 Identities=20% Similarity=0.086 Sum_probs=40.8
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCC-------CCCcchHHHHHhhhhcceEEEEeCCCC
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMK-------PGDRLFDKIDTAIKHCKLGVAVFSPRY 97 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~-------~G~~i~~~i~~aI~~S~i~IvV~S~~y 97 (202)
+|.|..|.--+..++.+|...|.++|.++.+-+-+.. .+-.+......++..|+..|+++.++.
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 4667766554567888999999999988766433221 111223444566777777777776653
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=71.74 E-value=7.2 Score=27.35 Aligned_cols=47 Identities=19% Similarity=0.080 Sum_probs=31.7
Q ss_pred hhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 45 RTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 45 ~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
..++.+|...|.+.||++.+|..+. .+...+..|-..=--.++|+.+
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~~~----~~~k~~~~a~~~g~p~~iiiG~ 61 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDSDK----SLGKQIKYADKLGIPFIIIIGE 61 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESSSS----THHHHHHHHHHTTESEEEEEEH
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCC----chhHHHHHHhhcCCeEEEEECc
Confidence 4678999999999999999997443 4455666664333334444443
No 18
>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=71.14 E-value=20 Score=24.60 Aligned_cols=61 Identities=18% Similarity=0.050 Sum_probs=39.1
Q ss_pred ccEEEeccccc--cchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 32 CDVFINHRGTD--TKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 32 ydVFISy~~~D--~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
++|+|-.-+.+ .....+..+...|++.|+.+.+|.. +..+...+..|-..---.++++.++
T Consensus 2 ~~v~ii~~~~~~~~~~~~a~~~~~~Lr~~g~~v~~~~~----~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVEAREYAQKLLNALLANGIRVLYDDR----ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHHHHHHHHHHHHHHHHCCCEEEecCC----CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 56666654330 2246788899999999999998764 3455566666544433466666654
No 19
>COG3613 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]
Probab=68.71 E-value=21 Score=29.13 Aligned_cols=77 Identities=13% Similarity=0.095 Sum_probs=54.6
Q ss_pred hHHHHHHHHHhcCCCeeEecCC------CCCCC---CcchHHHHHhhhhcceEEEEeCCCC-cCChhhHHHHHHHHHhcC
Q 046164 46 TIAGLLHDHLSRLRLNPFLDSK------NMKPG---DRLFDKIDTAIKHCKLGVAVFSPRY-CESYFCLHELALIMESRK 115 (202)
Q Consensus 46 ~fv~~L~~~L~~~Gi~vf~D~~------~l~~G---~~i~~~i~~aI~~S~i~IvV~S~~y-~~S~wc~~EL~~i~~~~~ 115 (202)
...+.|...|.+.|+.++.-.+ +..++ ..|.+.=.+.|.+|+++|.++.+-= ...+=...|+..+...++
T Consensus 20 ~~~d~lkall~~~gf~~~~P~d~~~~~~~~~p~~~a~~i~e~d~~~i~~aD~vla~ld~fr~~~DsGTa~E~GYa~AlgK 99 (172)
T COG3613 20 ELRDELKALLLEAGFEVLSPFDEAEPIAETGPNETAEKIYEADIKLIDQADIVLANLDPFRPDPDSGTAFELGYAIALGK 99 (172)
T ss_pred HHHHHHHHHHHHcCCeeeCcchhccCccccCccHHHHHHHHHHHHHHhhcCEEEEecCCCCCCCCCcchHHHHHHHHcCC
Confidence 4577889999999999887522 22232 2333344467999999999998754 112235679999999999
Q ss_pred ceecEEE
Q 046164 116 KVIPIFY 122 (202)
Q Consensus 116 ~ViPVfy 122 (202)
+|++.+-
T Consensus 100 Pv~~~~~ 106 (172)
T COG3613 100 PVYAYRK 106 (172)
T ss_pred ceEEEee
Confidence 9999864
No 20
>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=62.27 E-value=39 Score=25.12 Aligned_cols=61 Identities=11% Similarity=-0.003 Sum_probs=41.3
Q ss_pred CCccEEEeccc--cccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 30 RPCDVFINHRG--TDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 30 ~~ydVFISy~~--~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
..++|||-.-+ .+ ....+..|...|++.|++|-+|.. ..+...+..|-+.---.++++.++
T Consensus 25 ap~~v~Ii~~~~~~~-~~~~a~~la~~LR~~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 25 APIKVAVLPLVKRDE-LVEIAKEISEELRELGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred CCcEEEEEecCCcHH-HHHHHHHHHHHHHHCCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcC
Confidence 45888887765 32 245677899999999999999863 345566666644444456666655
No 21
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=61.85 E-value=62 Score=28.94 Aligned_cols=64 Identities=20% Similarity=0.296 Sum_probs=36.7
Q ss_pred HHHHHHHHHhcC----CCeeEecCCCCCCCCcchHHHHHhhhhc---ceEEEEeCCCCcCCh--hhHHHHHHHHHh
Q 046164 47 IAGLLHDHLSRL----RLNPFLDSKNMKPGDRLFDKIDTAIKHC---KLGVAVFSPRYCESY--FCLHELALIMES 113 (202)
Q Consensus 47 fv~~L~~~L~~~----Gi~vf~D~~~l~~G~~i~~~i~~aI~~S---~i~IvV~S~~y~~S~--wc~~EL~~i~~~ 113 (202)
....+.++|+++ .+.|++. +.-|.++.++...++... +++++.+.|.|..|. -..+++..+++.
T Consensus 74 ~T~~q~~~L~~~L~~~~~~V~~a---mry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~ 146 (320)
T COG0276 74 ITRAQAAALEERLDLPDFKVYLA---MRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKE 146 (320)
T ss_pred HHHHHHHHHHHHhCCCCccEEEe---ecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHh
Confidence 344455555443 5777764 456666666666666443 346667778777543 344555555543
No 22
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=59.26 E-value=50 Score=21.93 Aligned_cols=59 Identities=15% Similarity=-0.049 Sum_probs=39.2
Q ss_pred HHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCCh-hhHHHHHHHHHhcCcee
Q 046164 49 GLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESY-FCLHELALIMESRKKVI 118 (202)
Q Consensus 49 ~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~-wc~~EL~~i~~~~~~Vi 118 (202)
.-++..|++.|++|-.... ...++.....++++++|.+.-+. --.++|...++.|..++
T Consensus 8 ~a~~~~L~~~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~~~~~~~l~~~v~~G~~lv 67 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSEPEEAEALLEWVEAGNTLV 67 (70)
T ss_pred HHHHHHHHHCCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCchHHHHHHHHHHHcCCEEE
Confidence 4577888888998854332 11244558889999999966553 55567777777765443
No 23
>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=52.38 E-value=12 Score=28.61 Aligned_cols=50 Identities=18% Similarity=0.122 Sum_probs=32.5
Q ss_pred CCCCCCccEEEecc--ccccchhHHHHHHHHHhcCCCeeEecCCCC---CCCCcc
Q 046164 26 PITRRPCDVFINHR--GTDTKRTIAGLLHDHLSRLRLNPFLDSKNM---KPGDRL 75 (202)
Q Consensus 26 ~~~~~~ydVFISy~--~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l---~~G~~i 75 (202)
|..-..|+|=|--- ..+.-...+..|+..|...|+.|+.|+++- .+|..+
T Consensus 22 P~~iAP~qV~Iipi~~~~~~~~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~ 76 (128)
T cd02426 22 HPCLAPYKVAIDCGKGDTAELRDLCQGLKNELREAGLSVWPGYLETQHSSLEQLL 76 (128)
T ss_pred CCCCCCeEEEEEeccCChHHHHHHHHHHHHHHHHcCCEEEeccCcccccCHHHHH
Confidence 33455677654422 122234678899999999999999998753 455443
No 24
>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=51.49 E-value=61 Score=23.43 Aligned_cols=70 Identities=19% Similarity=0.131 Sum_probs=44.0
Q ss_pred HHHHHHHHhcCCCeeE-ecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEe
Q 046164 48 AGLLHDHLSRLRLNPF-LDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYD 123 (202)
Q Consensus 48 v~~L~~~L~~~Gi~vf-~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~ 123 (202)
...|...|++.|+.|- +|.. .. .+++.+++.+.+.-+|.+|-.+.....-..++....+...+=+||..+
T Consensus 17 l~~la~~l~~~G~~v~~~d~~-~~-----~~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv~G 87 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDAN-VP-----PEELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKERNPNIPIVVG 87 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESS-B------HHHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCC-CC-----HHHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEEEE
Confidence 4468899999999984 4442 22 267778888777777888765444443444555555554444555554
No 25
>PLN03194 putative disease resistance protein; Provisional
Probab=49.45 E-value=66 Score=26.60 Aligned_cols=66 Identities=6% Similarity=0.067 Sum_probs=51.3
Q ss_pred cCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEE
Q 046164 57 RLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFY 122 (202)
Q Consensus 57 ~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy 122 (202)
+..+.||+.-++-.....|..-|.++++...+.+.+-........--..+|.++++..+..|.||=
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS 89 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFS 89 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEEC
Confidence 468999998765555557888999999999988877665555555556688999998888888874
No 26
>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=49.01 E-value=53 Score=22.62 Aligned_cols=48 Identities=21% Similarity=0.073 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 45 RTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 45 ~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
...+..|...|++.|++|.+|...- .+...+..|-..---.++++.++
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~~~----~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDRNE----RPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCC----CcccchhHHHhcCCCEEEEECCc
Confidence 3578889999999999999987533 34445555533333345555544
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=48.52 E-value=89 Score=23.14 Aligned_cols=72 Identities=18% Similarity=0.085 Sum_probs=47.1
Q ss_pred HHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhh-hcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEecC
Q 046164 47 IAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIK-HCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYDVK 125 (202)
Q Consensus 47 fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~-~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~v~ 125 (202)
....|..+|++.|+.+..-.. .+.....++ .+++..||+|=+ ....-...++...++.+..=+|||.-.+
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~--------~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~~~~iPVFl~~~ 75 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS--------TDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRERNFGIPVFLLAE 75 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS--------HHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHHHSTT-EEEEEES
T ss_pred HHHHHHHHHHHCCCEEEEeCC--------hHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHHhCCCCCEEEEec
Confidence 467899999999998765432 244445554 599999999866 2211233455555666678899999766
Q ss_pred CC
Q 046164 126 PS 127 (202)
Q Consensus 126 p~ 127 (202)
+.
T Consensus 76 ~~ 77 (115)
T PF03709_consen 76 RD 77 (115)
T ss_dssp CC
T ss_pred CC
Confidence 44
No 28
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=46.58 E-value=40 Score=31.52 Aligned_cols=59 Identities=22% Similarity=0.256 Sum_probs=37.3
Q ss_pred cCCCCCcCCCCCCCCccEEEeccc-----cccchhHHHHHHHHHhcCCCeeEecC-CCCCCCCcc
Q 046164 17 HRPHHQIQLPITRRPCDVFINHRG-----TDTKRTIAGLLHDHLSRLRLNPFLDS-KNMKPGDRL 75 (202)
Q Consensus 17 ~~~~~~~~~~~~~~~ydVFISy~~-----~D~r~~fv~~L~~~L~~~Gi~vf~D~-~~l~~G~~i 75 (202)
|....+...|.....++|+|---. .+.-...+..|...|++.|++|.+|+ .+..+|..+
T Consensus 273 ~~D~~Gl~lP~~iAP~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~gkK~ 337 (477)
T PRK08661 273 HGDDKGLVLPPKIAPIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPGWKF 337 (477)
T ss_pred hCccCCCccCcccCCCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHH
Confidence 333333344434456898876431 12224678899999999999999998 444555433
No 29
>PF07429 Glyco_transf_56: 4-alpha-L-fucosyltransferase glycosyl transferase group 56; InterPro: IPR009993 This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc [].; GO: 0008417 fucosyltransferase activity, 0009246 enterobacterial common antigen biosynthetic process, 0009276 Gram-negative-bacterium-type cell wall
Probab=46.42 E-value=31 Score=31.30 Aligned_cols=13 Identities=38% Similarity=0.358 Sum_probs=9.7
Q ss_pred hhHHHHHHHHHHH
Q 046164 141 ELQRFSRALEEAK 153 (202)
Q Consensus 141 ~~~~W~~AL~~v~ 153 (202)
=.+.|+.||+.++
T Consensus 345 y~~~w~~~l~~~~ 357 (360)
T PF07429_consen 345 YLQGWRQALRLAA 357 (360)
T ss_pred hHHHHHHHHHHHh
Confidence 3568999988665
No 30
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=46.31 E-value=39 Score=26.18 Aligned_cols=55 Identities=15% Similarity=0.187 Sum_probs=41.8
Q ss_pred CccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcc
Q 046164 31 PCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCK 87 (202)
Q Consensus 31 ~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~ 87 (202)
-.++|+-..+.-....+...|..++..+|+-++.|.+ .+|+.+...|.+.+.++.
T Consensus 29 ~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D--~~Ge~Irk~l~~~l~~~~ 83 (127)
T COG1658 29 DAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD--RKGERIRKKLKEYLPGAK 83 (127)
T ss_pred CCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC--cchHHHHHHHHHHhcccc
Confidence 3567776654322256788899999999999999986 689999888888887743
No 31
>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=44.55 E-value=75 Score=30.08 Aligned_cols=63 Identities=19% Similarity=0.165 Sum_probs=43.9
Q ss_pred CCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 29 RRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 29 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
....+|+|-.-+++ ....+..|...|++.|++|-+|.. +..+...+..|-..---.++|+.++
T Consensus 468 ~~p~~v~vi~~~~~-~~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~~ 530 (563)
T TIGR00418 468 LAPVQVVVIPVNER-HLDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGDK 530 (563)
T ss_pred CCCceEEEEEccch-HHHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEchh
Confidence 35678888776544 346788999999999999999864 4456667776654444455566543
No 32
>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=44.27 E-value=82 Score=22.44 Aligned_cols=61 Identities=11% Similarity=0.065 Sum_probs=39.4
Q ss_pred HHHHHHHHHhcCCCeeEecCCCCCCCCc-chHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHH
Q 046164 47 IAGLLHDHLSRLRLNPFLDSKNMKPGDR-LFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELAL 109 (202)
Q Consensus 47 fv~~L~~~L~~~Gi~vf~D~~~l~~G~~-i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~ 109 (202)
....+...+++.|...-+.. -..|.. -...|...|.+++++|++.+---....|...+..+
T Consensus 11 ~~~~~~~~~~~~G~~~~~hg--~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~~ak 72 (97)
T PF10087_consen 11 RERRYKRILEKYGGKLIHHG--RDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKKAAK 72 (97)
T ss_pred cHHHHHHHHHHcCCEEEEEe--cCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHHHHH
Confidence 46688889999999865541 112221 12247888999999888876665566666555433
No 33
>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=40.71 E-value=1e+02 Score=26.59 Aligned_cols=80 Identities=11% Similarity=0.097 Sum_probs=50.2
Q ss_pred HHHHHHhcCCCeeEecCCC----CCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEe--
Q 046164 50 LLHDHLSRLRLNPFLDSKN----MKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYD-- 123 (202)
Q Consensus 50 ~L~~~L~~~Gi~vf~D~~~----l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~-- 123 (202)
..++.|... +++|.|-.. -..+..+.+....+++.+..=-+++|-.-...+=-+.+|..+-+.-. +|||.+
T Consensus 132 r~R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~~~--~PVlvGSG 208 (254)
T PF03437_consen 132 RYRKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREAVP--VPVLVGSG 208 (254)
T ss_pred HHHHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhcCC--CCEEEecC
Confidence 344555555 999988642 12344566666677777777677777665544444566666544333 999995
Q ss_pred cCCCCccCC
Q 046164 124 VKPSQLQVP 132 (202)
Q Consensus 124 v~p~~vr~~ 132 (202)
+.|.++..+
T Consensus 209 vt~~Ni~~~ 217 (254)
T PF03437_consen 209 VTPENIAEY 217 (254)
T ss_pred CCHHHHHHH
Confidence 777776654
No 34
>PLN02924 thymidylate kinase
Probab=40.35 E-value=2.1e+02 Score=23.69 Aligned_cols=168 Identities=12% Similarity=0.114 Sum_probs=84.8
Q ss_pred CcCCCCCCCCccEEEecccccc--chhHHHHHHHHHhcCCCeeEecCC---CCCCCCcchH-------------HHHHh-
Q 046164 22 QIQLPITRRPCDVFINHRGTDT--KRTIAGLLHDHLSRLRLNPFLDSK---NMKPGDRLFD-------------KIDTA- 82 (202)
Q Consensus 22 ~~~~~~~~~~ydVFISy~~~D~--r~~fv~~L~~~L~~~Gi~vf~D~~---~l~~G~~i~~-------------~i~~a- 82 (202)
+|..++...+--.||.+-|-|- +.+-+..|.+.|..+|+.+..-.+ +-..|+.+.+ .+.-+
T Consensus 5 ~~~~~~~~~~~g~~IviEGiDGsGKsTq~~~L~~~l~~~g~~v~~~~ep~~~~~~g~~ir~~l~~~~~~~~~~~~llf~a 84 (220)
T PLN02924 5 GMETESSVESRGALIVLEGLDRSGKSTQCAKLVSFLKGLGVAAELWRFPDRTTSVGQMISAYLSNKSQLDDRAIHLLFSA 84 (220)
T ss_pred ccCCCCCcCCCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCCceeeeCCCCCChHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence 3444444444557999988774 357788899999999998632110 0001111111 10000
Q ss_pred --------hhhc-ceEEEEeCCCCcCChhhHHH-------HHHHHHhc--CceecEEEecCCCCccCCC--C-Ccc-chh
Q 046164 83 --------IKHC-KLGVAVFSPRYCESYFCLHE-------LALIMESR--KKVIPIFYDVKPSQLQVPD--N-GTC-SRK 140 (202)
Q Consensus 83 --------I~~S-~i~IvV~S~~y~~S~wc~~E-------L~~i~~~~--~~ViPVfy~v~p~~vr~~~--~-~~~-~~e 140 (202)
|... ...-+|++..|.-|.....- ....++.+ .+=+-|+++++|.....-. . .++ ..+
T Consensus 85 dR~~~~~~I~pal~~g~vVI~DRy~~S~~ayq~~~g~~~~~~~~~~~~~~~PDlvi~Ld~~~~~a~~R~~~~~~~~E~~~ 164 (220)
T PLN02924 85 NRWEKRSLMERKLKSGTTLVVDRYSYSGVAFSAAKGLDLEWCKAPEVGLPAPDLVLYLDISPEEAAERGGYGGERYEKLE 164 (220)
T ss_pred HHHHHHHHHHHHHHCCCEEEEccchhHHHHHHHhcCCCHHHHHHHHhCCCCCCEEEEEeCCHHHHHHHhccCccccccHH
Confidence 1100 01235778888887765531 11222222 1223367788776532211 0 112 223
Q ss_pred hhHHHHHHHHHHHHhcCCcccCCCCCHHHHHHHHHHHHHHHhhhhccccc
Q 046164 141 ELQRFSRALEEAKYTVGLTFDSINGDWSEFLTTATDAVINNLIEVEEEST 190 (202)
Q Consensus 141 ~~~~W~~AL~~v~~~~G~~~~~~~~~e~~~i~~Iv~~v~~~L~~~~~~~~ 190 (202)
-.++=+.+..+++. ..+..-+...+-.+..++|.+.|.+.+..+..+.|
T Consensus 165 ~~~rv~~~Y~~la~-~~~~vIDa~~sieeV~~~I~~~I~~~l~~~~~~~~ 213 (220)
T PLN02924 165 FQKKVAKRFQTLRD-SSWKIIDASQSIEEVEKKIREVVLDTVQRCLAGKP 213 (220)
T ss_pred HHHHHHHHHHHHhh-cCEEEECCCCCHHHHHHHHHHHHHHHHHhccccCc
Confidence 34455566666655 34443233556666777777777776765554433
No 35
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=38.92 E-value=69 Score=30.57 Aligned_cols=52 Identities=23% Similarity=0.365 Sum_probs=36.7
Q ss_pred CCCCCCCCccEEEeccc--cccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcc
Q 046164 24 QLPITRRPCDVFINHRG--TDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRL 75 (202)
Q Consensus 24 ~~~~~~~~ydVFISy~~--~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i 75 (202)
.-|.....++|+|---+ .+.-...+..|+..|++.|+++.+|+++-.+|..+
T Consensus 461 ~~P~~iaP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~ 514 (565)
T PRK09194 461 IWPKAIAPFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKF 514 (565)
T ss_pred cCCCccCCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHH
Confidence 33444667999887553 12234678899999999999999998765555433
No 36
>COG0400 Predicted esterase [General function prediction only]
Probab=38.17 E-value=89 Score=25.97 Aligned_cols=55 Identities=13% Similarity=0.102 Sum_probs=41.8
Q ss_pred CCCCccEEEecccccc--chhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhh
Q 046164 28 TRRPCDVFINHRGTDT--KRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIK 84 (202)
Q Consensus 28 ~~~~ydVFISy~~~D~--r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~ 84 (202)
.....-|||++-..|. -...+.+|.+.|+..|..|..... ..|-.+.++-.++++
T Consensus 143 ~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~--~~GH~i~~e~~~~~~ 199 (207)
T COG0400 143 DLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWH--EGGHEIPPEELEAAR 199 (207)
T ss_pred ccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEEe--cCCCcCCHHHHHHHH
Confidence 4677889999988875 356788999999999999988764 366667665555544
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=37.35 E-value=1.2e+02 Score=19.97 Aligned_cols=58 Identities=16% Similarity=0.136 Sum_probs=33.8
Q ss_pred cEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 33 DVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 33 dVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
||||-..+.+ ...-+..+...|.+.|++|.++... ..+...+..|-..--..++++.+
T Consensus 3 ~v~i~~~~~~-~~~~a~~i~~~Lr~~g~~v~~~~~~----~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 3 DVYVVPLGEG-ALSEALELAEQLRDAGIKAEIDYGG----RKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred cEEEEEcChH-HHHHHHHHHHHHHHCCCEEEEecCC----CCHHHHHHHHHHcCCCEEEEEcH
Confidence 6776654433 2344778899999999999886532 22344444443332234455544
No 38
>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=37.07 E-value=57 Score=26.78 Aligned_cols=49 Identities=22% Similarity=0.287 Sum_probs=33.9
Q ss_pred CCCccEEEeccccc-----cchhHHHHHHHHHhcCCCeeEecCCCC-CCCCcchH
Q 046164 29 RRPCDVFINHRGTD-----TKRTIAGLLHDHLSRLRLNPFLDSKNM-KPGDRLFD 77 (202)
Q Consensus 29 ~~~ydVFISy~~~D-----~r~~fv~~L~~~L~~~Gi~vf~D~~~l-~~G~~i~~ 77 (202)
...++|+|---+.+ .-...+..|...|...||++.+|+++- .+|..+..
T Consensus 8 iAP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~~ 62 (202)
T cd00862 8 VAPIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFND 62 (202)
T ss_pred hcCceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHHH
Confidence 34577777643322 023578899999999999999998654 67765543
No 39
>cd04128 Spg1 Spg1p. Spg1p (septum-promoting GTPase) was first identified in the fission yeast S. pombe, where it regulates septum formation in the septation initiation network (SIN) through the cdc7 protein kinase. Spg1p is an essential gene that localizes to the spindle pole bodies. When GTP-bound, it binds cdc7 and causes it to translocate to spindle poles. Sid4p (septation initiation defective) is required for localization of Spg1p to the spindle pole body, and the ability of Spg1p to promote septum formation from any point in the cell cycle depends on Sid4p. Spg1p is negatively regulated by Byr4 and cdc16, which form a two-component GTPase activating protein (GAP) for Spg1p. The existence of a SIN-related pathway in plants has been proposed. 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
Probab=36.80 E-value=2e+02 Score=22.63 Aligned_cols=51 Identities=14% Similarity=0.066 Sum_probs=25.8
Q ss_pred HHHhhhhcceEEEEeCCCCcCChhhHHH-HHHHHHhcCceecEEEecCCCCcc
Q 046164 79 IDTAIKHCKLGVAVFSPRYCESYFCLHE-LALIMESRKKVIPIFYDVKPSQLQ 130 (202)
Q Consensus 79 i~~aI~~S~i~IvV~S~~y~~S~wc~~E-L~~i~~~~~~ViPVfy~v~p~~vr 130 (202)
....+++++.+|+|++-.-..|---+.+ +..+.+....-+||+. ....|+.
T Consensus 66 ~~~~~~~a~~iilv~D~t~~~s~~~i~~~~~~~~~~~~~~~pilV-gnK~Dl~ 117 (182)
T cd04128 66 LPLVCNDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIPILV-GTKYDLF 117 (182)
T ss_pred hHHHCcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEE-EEchhcc
Confidence 3346789999999998543333111111 2222222233456655 3456654
No 40
>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=36.04 E-value=65 Score=22.97 Aligned_cols=67 Identities=10% Similarity=0.169 Sum_probs=44.2
Q ss_pred HHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEec
Q 046164 51 LHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYDV 124 (202)
Q Consensus 51 L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~v 124 (202)
+...|+-.|+..+... ...+.....+.+.+++..+.|++++++++.. -.+++....+ +...|++..+
T Consensus 9 ~v~gFrLaGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~--~~~~l~~~~~--~~~~P~iv~I 75 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAEK--IRDELDEYRE--ESSLPLIVEI 75 (95)
T ss_dssp HHHHHHHTTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT--HHHHHHHHHH--TSSSSEEEEE
T ss_pred HHHHHHHcCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH--HHHHHHHHHh--ccCCceEEEc
Confidence 4456778899988865 1234556677777889999999999998764 2344444433 2355665543
No 41
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=35.87 E-value=78 Score=23.93 Aligned_cols=56 Identities=20% Similarity=0.286 Sum_probs=36.7
Q ss_pred hhHHHHHHHHHhcCCCee-EecCCCCC-C-----------CCcchHHHHHhhhhcceEEEEeCCCCcCCh
Q 046164 45 RTIAGLLHDHLSRLRLNP-FLDSKNMK-P-----------GDRLFDKIDTAIKHCKLGVAVFSPRYCESY 101 (202)
Q Consensus 45 ~~fv~~L~~~L~~~Gi~v-f~D~~~l~-~-----------G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~ 101 (202)
...+..+.+.|++.|+.+ .+|-.+.. | -..-..++.+.+.+++ .||+.||.|..+.
T Consensus 17 ~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD-~iI~~sP~y~~~~ 85 (152)
T PF03358_consen 17 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEAD-GIIFASPVYNGSV 85 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSS-EEEEEEEEBTTBE
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCC-eEEEeecEEcCcC
Confidence 467788888888888865 44554431 1 1222356677888888 5667889888653
No 42
>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=35.14 E-value=55 Score=22.30 Aligned_cols=30 Identities=23% Similarity=0.224 Sum_probs=13.0
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeE
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPF 63 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf 63 (202)
|+|.|-+.+.....+..+.+.|...|+.++
T Consensus 46 vii~~D~D~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 46 VILAFDGDEAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred EEEEECCCHHHHHHHHHHHHHHHHCCCeEE
Confidence 444443333333344444444444444443
No 43
>PLN03108 Rab family protein; Provisional
Probab=34.69 E-value=1.5e+02 Score=23.83 Aligned_cols=108 Identities=16% Similarity=0.190 Sum_probs=50.6
Q ss_pred HhhhhcceEEEEeCCCCcCChhhHHH-HHHHHHhcCceecEEEecCCCCccCCCCCccchhhhHHHHHHHHHHHHhcCCc
Q 046164 81 TAIKHCKLGVAVFSPRYCESYFCLHE-LALIMESRKKVIPIFYDVKPSQLQVPDNGTCSRKELQRFSRALEEAKYTVGLT 159 (202)
Q Consensus 81 ~aI~~S~i~IvV~S~~y~~S~wc~~E-L~~i~~~~~~ViPVfy~v~p~~vr~~~~~~~~~e~~~~W~~AL~~v~~~~G~~ 159 (202)
..+..++..|+|++..-..|---+.+ +..+.+....-+|++.-....|+.+.. ....+..+++... .|+.
T Consensus 74 ~~~~~ad~~vlv~D~~~~~s~~~l~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~--~~~~~~~~~~~~~-------~~~~ 144 (210)
T PLN03108 74 SYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRR--AVSTEEGEQFAKE-------HGLI 144 (210)
T ss_pred HHhccCCEEEEEEECCcHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCcccc--CCCHHHHHHHHHH-------cCCE
Confidence 44677888999998764433221212 222222222345655544455554322 1123334444322 2332
Q ss_pred cc---C-CCCCHHHHHHHHHHHHHHHh----hhhcccccccccccc
Q 046164 160 FD---S-INGDWSEFLTTATDAVINNL----IEVEEESTANREPMG 197 (202)
Q Consensus 160 ~~---~-~~~~e~~~i~~Iv~~v~~~L----~~~~~~~~~~~~~~g 197 (202)
+- . ...+=.+..+.+++.+.+++ .....+...+.+|+|
T Consensus 145 ~~e~Sa~~~~~v~e~f~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (210)
T PLN03108 145 FMEASAKTAQNVEEAFIKTAAKIYKKIQDGVFDVSNESYGIKVGYG 190 (210)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHHHHHhhhccccccccccccccccC
Confidence 21 1 12344555666666666554 233334556666666
No 44
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=34.56 E-value=1.2e+02 Score=27.84 Aligned_cols=62 Identities=16% Similarity=0.227 Sum_probs=41.8
Q ss_pred CCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 29 RRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 29 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
....||+|-+-+.+. ...+-.+...|.++|++|-+|.. +..+...+..|-+.--..++|+.+
T Consensus 323 ~~~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 323 KQSIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 345789998754432 45677899999999999988653 244566666665544445666655
No 45
>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=34.05 E-value=86 Score=25.61 Aligned_cols=50 Identities=12% Similarity=0.209 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCc
Q 046164 45 RTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYC 98 (202)
Q Consensus 45 ~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~ 98 (202)
..-...|..+.+.+|+-+|.|.+ .+|+.|...|.+.+-++..+- ++..++
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 34567788888999999999986 699999999988887776443 444443
No 46
>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=33.89 E-value=32 Score=25.09 Aligned_cols=54 Identities=17% Similarity=0.135 Sum_probs=33.0
Q ss_pred cccchhHHHHHHHHHhcCCCeeEecCCCCC----------CCCcchHHHHHhhhhcceEEEEeC
Q 046164 41 TDTKRTIAGLLHDHLSRLRLNPFLDSKNMK----------PGDRLFDKIDTAIKHCKLGVAVFS 94 (202)
Q Consensus 41 ~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~----------~G~~i~~~i~~aI~~S~i~IvV~S 94 (202)
.|.|.+=+-.|.+.|.+.|+.|.+.+--+. .|-.+.+.+.++++.+++.|+.-.
T Consensus 12 ~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~ 75 (106)
T PF03720_consen 12 DDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATD 75 (106)
T ss_dssp S--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS-
T ss_pred cccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEec
Confidence 578888899999999999999877553221 122233456778888887665544
No 47
>KOG2903 consensus Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]
Probab=33.36 E-value=1.7e+02 Score=25.82 Aligned_cols=104 Identities=18% Similarity=0.252 Sum_probs=58.1
Q ss_pred HHHHhhcCCCCCcCCCCCCCCccEEEeccccccchhHHHH--HHHHHhc----CCCee--E-ecCCCCCCCCcchHHHHH
Q 046164 11 CRKIIHHRPHHQIQLPITRRPCDVFINHRGTDTKRTIAGL--LHDHLSR----LRLNP--F-LDSKNMKPGDRLFDKIDT 81 (202)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~ydVFISy~~~D~r~~fv~~--L~~~L~~----~Gi~v--f-~D~~~l~~G~~i~~~i~~ 81 (202)
+|+.++..+....-+ ...|..|+||... |+.. +..+|+- -|+++ | .|+. |=.+.++ ..
T Consensus 20 fr~~iSkd~~~~~pa---kgryhLYvslaCP-----WAhRtLi~r~LKGL~~~i~~s~v~~~~d~~----gW~F~~~-~~ 86 (319)
T KOG2903|consen 20 FRETISKDHPIFKPA---KGRYHLYVSLACP-----WAHRTLIVRALKGLEPAIGVSVVHWHLDDK----GWRFLDE-HI 86 (319)
T ss_pred cccccCCCCCccCCC---CceEEEEEeccCc-----HHHHHHHHHHHcCccccceeEEeccccCCC----cccCCCc-cc
Confidence 344555544444433 5789999999743 3433 3334431 24433 4 2322 2222221 01
Q ss_pred hhhhcceEEEEeCCCCcCChhhHHHHHHHHHh---cCceecEEEecCCCCc
Q 046164 82 AIKHCKLGVAVFSPRYCESYFCLHELALIMES---RKKVIPIFYDVKPSQL 129 (202)
Q Consensus 82 aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~---~~~ViPVfy~v~p~~v 129 (202)
.+.++.+.++ +++.+...--+.||-.+..- ++--+||+.+..-..|
T Consensus 87 ~~nDs~~l~~--~~d~~~g~k~l~elY~~~~p~Y~grfTVPVLWD~k~ktI 135 (319)
T KOG2903|consen 87 IINDSERLGV--TPDPLNGAKRLRELYYIASPNYTGRFTVPVLWDLKTKTI 135 (319)
T ss_pred CCCchhcccC--CCcccccchhHHHHHhhcCCCCCceEEEEEEEcccccee
Confidence 2356666665 77777766678898887653 4778999998654443
No 48
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [, ]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [] and is similar to the yeast NOP1 protein []. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0008168 methyltransferase activity, 0006364 rRNA processing, 0008033 tRNA processing; PDB: 3PLA_E 3ID6_C 3ID5_B 1NT2_A 3NVK_J 2NNW_B 3NVM_B 3NMU_J 1PRY_A 1G8A_A ....
Probab=32.62 E-value=47 Score=28.36 Aligned_cols=25 Identities=28% Similarity=0.388 Sum_probs=22.1
Q ss_pred CChhhHHHHHHHHHhcCceecEEEe
Q 046164 99 ESYFCLHELALIMESRKKVIPIFYD 123 (202)
Q Consensus 99 ~S~wc~~EL~~i~~~~~~ViPVfy~ 123 (202)
-|+|+..+|....+.+.+|+||+-+
T Consensus 106 fs~r~~rdL~~la~~R~NIiPIl~D 130 (229)
T PF01269_consen 106 FSPRSMRDLLNLAKKRPNIIPILED 130 (229)
T ss_dssp SSHHHHHHHHHHHHHSTTEEEEES-
T ss_pred ecchhHHHHHHHhccCCceeeeecc
Confidence 5889999999999999999999865
No 49
>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=32.48 E-value=98 Score=23.47 Aligned_cols=48 Identities=15% Similarity=0.357 Sum_probs=33.0
Q ss_pred CcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEecCCC
Q 046164 73 DRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYDVKPS 127 (202)
Q Consensus 73 ~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~v~p~ 127 (202)
+.+...+.+.+.+.++.|++++++++. ++...++.-+.++|.+..+ |+
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~------~i~~~I~~~~~~~PaIieI-P~ 93 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE------MIRHAVDAHTRSIPAVLEI-PS 93 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH------HhHHHHHhcCCcCCEEEEE-CC
Confidence 445566666688899999999998664 3444444444788887765 44
No 50
>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=32.34 E-value=97 Score=23.83 Aligned_cols=39 Identities=18% Similarity=0.298 Sum_probs=19.1
Q ss_pred hHHHHHHHHHhcCCCeeEecCCCCCC-----CCcchHHHHHhhh
Q 046164 46 TIAGLLHDHLSRLRLNPFLDSKNMKP-----GDRLFDKIDTAIK 84 (202)
Q Consensus 46 ~fv~~L~~~L~~~Gi~vf~D~~~l~~-----G~~i~~~i~~aI~ 84 (202)
.+...+.+.+.+..-++++-...+.+ +..+.+.|.+|.+
T Consensus 21 ~~~~~i~~~I~~A~~~I~i~~~~~~~~~~~~~~~l~~~L~~a~~ 64 (176)
T cd00138 21 SDLDALLEAISNAKKSIYIASFYLSPLITEYGPVILDALLAAAR 64 (176)
T ss_pred hHHHHHHHHHHhhheEEEEEEeEecccccccchHHHHHHHHHHH
Confidence 34445556665544444443333333 4455556655554
No 51
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=31.92 E-value=2.1e+02 Score=21.21 Aligned_cols=52 Identities=23% Similarity=0.174 Sum_probs=31.4
Q ss_pred HHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcC-ceecEEEecCCCCccC
Q 046164 80 DTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRK-KVIPIFYDVKPSQLQV 131 (202)
Q Consensus 80 ~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~-~ViPVfy~v~p~~vr~ 131 (202)
...+++++.+|+++|.+-..|---+..+...+.... .-+|++.-....|+..
T Consensus 66 ~~~~~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~D~~~ 118 (162)
T PF00071_consen 66 DIFYRNSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKSDLSD 118 (162)
T ss_dssp HHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG
T ss_pred cccccccccccccccccccccccccccccccccccccccccceeeeccccccc
Confidence 345899999999999776555433334444333333 2456666555566554
No 52
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=31.90 E-value=84 Score=29.01 Aligned_cols=64 Identities=19% Similarity=0.157 Sum_probs=40.1
Q ss_pred CCCccEEEeccc--cccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 29 RRPCDVFINHRG--TDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 29 ~~~ydVFISy~~--~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
...++|+|---+ .+.....+..|...|.+.|++|.+|+++-..| ..+..|-..---.++|+.++
T Consensus 343 iaP~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg----~ki~~a~~~giP~~iiVG~~ 408 (439)
T PRK12325 343 VAPFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPG----AKFATMDLIGLPWQIIVGPK 408 (439)
T ss_pred cCCeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHh----HHHHHHHHcCCCEEEEECCc
Confidence 345899876442 22234678899999999999999998754444 44444422222245555554
No 53
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=31.74 E-value=41 Score=25.98 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=17.6
Q ss_pred HHHHhhhhcceEEEEeCCCCcCChhhHHHHHHH
Q 046164 78 KIDTAIKHCKLGVAVFSPRYCESYFCLHELALI 110 (202)
Q Consensus 78 ~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i 110 (202)
.|.++|..-...|+|.+..|-.+ |+.||...
T Consensus 63 ~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 63 ALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 33333333335677777666544 77777665
No 54
>PF01915 Glyco_hydro_3_C: Glycosyl hydrolase family 3 C-terminal domain; InterPro: IPR002772 Glycoside hydrolase family 3 GH3 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-xylosidase (3.2.1.37 from EC); N-acetyl beta-glucosaminidase (3.2.1.52 from EC); glucan beta-1,3-glucosidase (3.2.1.58 from EC); cellodextrinase(3.2.1.74 from EC); exo-1,3-1,4-glucanase (3.2.1 from EC). These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often C-terminal to the glycoside hydrolase family 3, N-terminal domain IPR001764 from INTERPRO.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3LK6_D 3NVD_B 3BMX_B 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A 1J8V_A 1IEX_A ....
Probab=31.06 E-value=2.9e+02 Score=22.49 Aligned_cols=86 Identities=15% Similarity=0.063 Sum_probs=54.8
Q ss_pred hhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCc----------------CChhhHHHHH
Q 046164 45 RTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYC----------------ESYFCLHELA 108 (202)
Q Consensus 45 ~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~----------------~S~wc~~EL~ 108 (202)
.++.+.|.+.+...++.+..+....... ....+..+...+++.+|+++.+.+. .-+++..||.
T Consensus 46 ~t~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~li 124 (227)
T PF01915_consen 46 VTPLDALKQRFGNAGVVVPEGGDAVDDD-EGIDEAVAAAKEADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQELI 124 (227)
T ss_dssp BHHHHHHHHHHHTTSEEEECCCCCCCCC-SCHHHHHHHHHCSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHHH
T ss_pred ccHHhhhccccCCCceEEeeeccccccc-cchHHHHHHhhcCCEEEEeccccccccccccccccCCcccccchhhHHHHH
Confidence 4677778888888887765433222222 3345677888999999999884332 3346777887
Q ss_pred HHHH-hcCceecEEEecCCCCccC
Q 046164 109 LIME-SRKKVIPIFYDVKPSQLQV 131 (202)
Q Consensus 109 ~i~~-~~~~ViPVfy~v~p~~vr~ 131 (202)
..+. .++++|-|+....|-++..
T Consensus 125 ~~v~~~~~~~Ivvv~~~~P~~l~~ 148 (227)
T PF01915_consen 125 KAVAAAGKKVIVVVNSGNPYDLDP 148 (227)
T ss_dssp HHHHHHHSCEEEEEE-SSGGCGHC
T ss_pred HHHHHhcCCeEEEEecCCccccHH
Confidence 7654 3467776666666766643
No 55
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=30.59 E-value=69 Score=22.16 Aligned_cols=35 Identities=17% Similarity=0.064 Sum_probs=26.1
Q ss_pred CccEEEeccccccchhHHHHHHHHHhcCCCeeEecC
Q 046164 31 PCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDS 66 (202)
Q Consensus 31 ~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~ 66 (202)
+--|+|.+--.+.. ..-.+|.+.|.++|+.||.-+
T Consensus 16 k~~v~i~HG~~eh~-~ry~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 16 KAVVVIVHGFGEHS-GRYAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred CEEEEEeCCcHHHH-HHHHHHHHHHHhCCCEEEEEC
Confidence 55689998655433 345689999999999998754
No 56
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=30.45 E-value=1.8e+02 Score=20.91 Aligned_cols=87 Identities=17% Similarity=0.168 Sum_probs=50.1
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC-CcCChhhHHHHHHHHH
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR-YCESYFCLHELALIME 112 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~-y~~S~wc~~EL~~i~~ 112 (202)
+++......+...|...|..+|...... -...+.+.+.+.+.+++.+..++|+-+- +..+.-.++.|..+.+
T Consensus 41 ~~~~~~~~~~~~~~~~~i~~~l~~~~~~-------~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~ 113 (131)
T PF13401_consen 41 IYVNCPSSRTPRDFAQEILEALGLPLKS-------RQTSDELRSLLIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN 113 (131)
T ss_dssp EEEEHHHHSSHHHHHHHHHHHHT-SSSS-------TS-HHHHHHHHHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC
T ss_pred EEEEeCCCCCHHHHHHHHHHHhCccccc-------cCCHHHHHHHHHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh
Confidence 4666665555678888898888765444 1233445577888888888866666543 3213333444433333
Q ss_pred hcCceecEEEecCCCCcc
Q 046164 113 SRKKVIPIFYDVKPSQLQ 130 (202)
Q Consensus 113 ~~~~ViPVfy~v~p~~vr 130 (202)
..-++|.+-..| .++
T Consensus 114 --~~~~~vvl~G~~-~l~ 128 (131)
T PF13401_consen 114 --ESNIKVVLVGTP-ELE 128 (131)
T ss_dssp --SCBEEEEEEESS-TTT
T ss_pred --CCCCeEEEEECh-hhH
Confidence 455566655445 443
No 57
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=29.79 E-value=1.4e+02 Score=26.51 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=32.1
Q ss_pred CccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCC
Q 046164 31 PCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNM 69 (202)
Q Consensus 31 ~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l 69 (202)
.-+|-||..|+-+-+.++..|...+.+.|++++++....
T Consensus 130 ~~~v~iSl~GEPlL~p~l~eli~~~k~~Gi~~~L~TNG~ 168 (322)
T PRK13762 130 PKHVAISLSGEPTLYPYLPELIEEFHKRGFTTFLVTNGT 168 (322)
T ss_pred CCEEEEeCCccccchhhHHHHHHHHHHcCCCEEEECCCC
Confidence 357889988988766678889999999999999987654
No 58
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=28.95 E-value=2.9e+02 Score=24.41 Aligned_cols=65 Identities=18% Similarity=0.243 Sum_probs=38.8
Q ss_pred hHHHHHHHHHhcCC--CeeEecCCCCCCCCcchHHHHHhhh---hcceEEEEeCCCCcCCh--hhHHHHHHHHHh
Q 046164 46 TIAGLLHDHLSRLR--LNPFLDSKNMKPGDRLFDKIDTAIK---HCKLGVAVFSPRYCESY--FCLHELALIMES 113 (202)
Q Consensus 46 ~fv~~L~~~L~~~G--i~vf~D~~~l~~G~~i~~~i~~aI~---~S~i~IvV~S~~y~~S~--wc~~EL~~i~~~ 113 (202)
..+..|.+.|...| +.|++. +.-|....++..+.+. -.++.++.+.|.|..+. -+.+++..++..
T Consensus 73 ~qa~~l~~~L~~~~~~~~V~~a---mry~~P~i~~~l~~l~~~g~~~ivvlPLyPqyS~~ttgs~~~~~~~~~~~ 144 (316)
T PF00762_consen 73 RQAEALQQRLDERGVDVEVYYA---MRYGPPSIEDALEELKADGVDRIVVLPLYPQYSSSTTGSYLDEVERALKK 144 (316)
T ss_dssp HHHHHHHHHHHHH-EEEEEEEE---ESSSSSBHHHHHHHHHHTT-SEEEEEESSSS--TTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCeeEEEE---eccCCCCHHHHHHHHHHcCCCeEEEEeCCCchhHhhHHHHHHHHHHHHHh
Confidence 45666777777663 455553 5667666666655554 44667788889888544 466666666654
No 59
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. 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 families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=28.83 E-value=2.7e+02 Score=26.00 Aligned_cols=68 Identities=18% Similarity=0.190 Sum_probs=41.3
Q ss_pred CCCCCCCccEEEec---ccc--ccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 25 LPITRRPCDVFINH---RGT--DTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 25 ~~~~~~~ydVFISy---~~~--D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
.|.....++|+|-- ... +.-...+..|...|++.|++|.+|.++-.+| ..+..|-..---.++++.++
T Consensus 276 ~P~~iaP~qV~Iipi~~~~~~~~~~~~~A~~l~~~Lr~~girv~lD~r~~s~g----kk~k~Ae~~GvP~~IiIG~~ 348 (472)
T TIGR00408 276 LPPRVAPIQVVIIPIIFKKKENEKVMEAAREVRSRLKKAGFRVHIDDRDNRPG----RKFYQWEIKGIPLRIEVGPN 348 (472)
T ss_pred eChhhCcceEEEEEccCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHH----HHHHHHHHCCCCEEEEECcc
Confidence 33345568888764 221 1234678899999999999999998643444 44444432222244455544
No 60
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=28.49 E-value=2.6e+02 Score=21.02 Aligned_cols=77 Identities=12% Similarity=0.050 Sum_probs=37.1
Q ss_pred CCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhc---ceEEEEeCCCCc-CChhhH
Q 046164 29 RRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHC---KLGVAVFSPRYC-ESYFCL 104 (202)
Q Consensus 29 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S---~i~IvV~S~~y~-~S~wc~ 104 (202)
...+|++|.|.+.+.+ .....+ ....++.++. +.|..+.+.+.+|++.. .-.|+++.-+.. -...-+
T Consensus 8 ~~~~~~~l~~~~~~~~-~~~~~~---~~~~~~~~~~-----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~l~~~~l 78 (122)
T PF09837_consen 8 ADGADVVLAYTPDGDH-AAFRQL---WLPSGFSFFP-----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPDLTPDDL 78 (122)
T ss_dssp TSSSEEEEEE----TT-HHHHHH---HH-TTSEEEE-------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHH
T ss_pred CCCcCEEEEEcCCccH-HHHhcc---ccCCCCEEee-----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCCCCHHHH
Confidence 4568999999976643 333233 4456677664 46777888888777665 224555544433 333333
Q ss_pred HHHHHHHHhc
Q 046164 105 HELALIMESR 114 (202)
Q Consensus 105 ~EL~~i~~~~ 114 (202)
.+....++..
T Consensus 79 ~~A~~~L~~~ 88 (122)
T PF09837_consen 79 EQAFEALQRH 88 (122)
T ss_dssp HHHHHHTTT-
T ss_pred HHHHHHhccC
Confidence 3433444433
No 61
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=28.20 E-value=69 Score=28.10 Aligned_cols=94 Identities=15% Similarity=0.259 Sum_probs=63.9
Q ss_pred CCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCC--CCCCCcchHHHHHhh-hhcceEEEEeCCCCcCChhhHH
Q 046164 29 RRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKN--MKPGDRLFDKIDTAI-KHCKLGVAVFSPRYCESYFCLH 105 (202)
Q Consensus 29 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~--l~~G~~i~~~i~~aI-~~S~i~IvV~S~~y~~S~wc~~ 105 (202)
+.++.+=+||.++|. .+++....-|..+|+.+|.|-.+ -.-|..+.+-+.+.- +..-+++...|.+|-...|...
T Consensus 4 ~~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~~~~e~~q~~~~~~~~f~~~~~~r~~~~~~ 81 (329)
T COG4916 4 NVQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYDYLSEIYQDKALFTIMFISEHYSRKMWTNH 81 (329)
T ss_pred chheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHHHHHHHHhhhhHHHhhhhhccccCcCCCcH
Confidence 445777899999884 68999999999999999987532 112333332222211 3455678889999999999999
Q ss_pred HHHHHHHhc-----CceecEEEec
Q 046164 106 ELALIMESR-----KKVIPIFYDV 124 (202)
Q Consensus 106 EL~~i~~~~-----~~ViPVfy~v 124 (202)
|+...+... ..++|-.++.
T Consensus 82 ~~~~~~a~~~~~~~~~~~~~~~~~ 105 (329)
T COG4916 82 ERQAMQARAFQEHQEYILPARFDE 105 (329)
T ss_pred HHHHHHHHHhhhccEEehhhhhcc
Confidence 887765422 2566666653
No 62
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=28.20 E-value=1.4e+02 Score=24.02 Aligned_cols=68 Identities=21% Similarity=0.177 Sum_probs=42.2
Q ss_pred HHhcCCCeeEe-cCCC-CC--CCCcchHHHHHhhhhcce-----EEEEeCCCCcCChhhHHHHHHHHHhcCceecEEE
Q 046164 54 HLSRLRLNPFL-DSKN-MK--PGDRLFDKIDTAIKHCKL-----GVAVFSPRYCESYFCLHELALIMESRKKVIPIFY 122 (202)
Q Consensus 54 ~L~~~Gi~vf~-D~~~-l~--~G~~i~~~i~~aI~~S~i-----~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy 122 (202)
.|.+.||+..+ |.++ |. .-+.+.+++.+.+++++. .|+|+|-+--++.--..+-+..++..-. ||||.
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~lg-Ipvl~ 111 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKALG-IPVLR 111 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHHhhC-CcEEE
Confidence 48999999655 5443 32 335677888888887773 3889998865554322333444443322 78764
No 63
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=27.90 E-value=4.5e+02 Score=23.59 Aligned_cols=115 Identities=13% Similarity=0.178 Sum_probs=69.1
Q ss_pred ccchhHHHHHHHHHhcCCC--eeEecCCCCCCCC-cchHHHHHhhhhcceEEEEeCC---------CCcCChh------h
Q 046164 42 DTKRTIAGLLHDHLSRLRL--NPFLDSKNMKPGD-RLFDKIDTAIKHCKLGVAVFSP---------RYCESYF------C 103 (202)
Q Consensus 42 D~r~~fv~~L~~~L~~~Gi--~vf~D~~~l~~G~-~i~~~i~~aI~~S~i~IvV~S~---------~y~~S~w------c 103 (202)
.+...|-+.|..+|.+..- .+|+-++.-.-|. .+.+.+.++++.+.++++-.|. +|..-.+ -
T Consensus 190 psQ~~Fe~~l~~~l~~~~~~~~i~vE~Es~~IG~~~lP~~l~~~m~~~~~v~i~~~~e~Rv~~l~~~Y~~~~~~~~~~~~ 269 (345)
T PRK11784 190 PSQKDFENLLAEALLKLDPARPIVVEDESRRIGRVHLPEALYEAMQQAPIVVVEAPLEERVERLLEDYVLRMHAAGFQAY 269 (345)
T ss_pred cchHHHHHHHHHHHHcCCCCCeEEEEeccccccCccCCHHHHHHHhhCCEEEEECCHHHHHHHHHHHhhhhhhhhhhhcc
Confidence 3567899999999976543 6788776666665 5677889999998777655442 2221110 0
Q ss_pred HHHHHHHHHhcCceecEEEecCCCCccCCCCCccchhhhHHHHHHHHHHHHhcCCcccCCCCCHHHHHHHHHHHHHHHhh
Q 046164 104 LHELALIMESRKKVIPIFYDVKPSQLQVPDNGTCSRKELQRFSRALEEAKYTVGLTFDSINGDWSEFLTTATDAVINNLI 183 (202)
Q Consensus 104 ~~EL~~i~~~~~~ViPVfy~v~p~~vr~~~~~~~~~e~~~~W~~AL~~v~~~~G~~~~~~~~~e~~~i~~Iv~~v~~~L~ 183 (202)
.++|..++.. ++ .+...++++.|..++.. ++..++++.+..+-++.++
T Consensus 270 ~~~l~~~l~~---------------i~----k~lg~~~~~~~~~~~~~-------------~~~~~~~~~ll~~yYDp~Y 317 (345)
T PRK11784 270 PEYLAEALQR---------------IR----KRLGGERYQELLALLDA-------------GGHLAWIEELLLEYYDPMY 317 (345)
T ss_pred HHHHHHHHHH---------------HH----HhcCHHHHHHHHHHHHc-------------CCHHHHHHHHHHHhCChhh
Confidence 0111111110 00 12234566666666653 5678888888888888888
Q ss_pred hhccc
Q 046164 184 EVEEE 188 (202)
Q Consensus 184 ~~~~~ 188 (202)
....+
T Consensus 318 ~~~~~ 322 (345)
T PRK11784 318 RYQLE 322 (345)
T ss_pred hhhhh
Confidence 65543
No 64
>PLN02530 histidine-tRNA ligase
Probab=27.78 E-value=1.8e+02 Score=27.24 Aligned_cols=61 Identities=11% Similarity=-0.039 Sum_probs=42.3
Q ss_pred CCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 30 RPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 30 ~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
...||+|.+-+++ ....+..+...|.++|++|-+|..+ ..+...+..|-+.---.|+++.+
T Consensus 400 ~~~dVlVi~~~~~-~~~~A~~ia~~LR~~Gi~vevd~~~----~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 400 HQVDDVVFALDED-LQGAAAGVASRLREKGRSVDLVLEP----KKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCCcEEEEEcChH-HHHHHHHHHHHHHHCCCeEEEecCC----CCHHHHHHHHHHCCCCEEEEEch
Confidence 4578999875544 3457888999999999999887542 34566666665544445666664
No 65
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=27.68 E-value=1.1e+02 Score=22.19 Aligned_cols=64 Identities=13% Similarity=0.217 Sum_probs=36.9
Q ss_pred HHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEec
Q 046164 54 HLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYDV 124 (202)
Q Consensus 54 ~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~v 124 (202)
.++-.|+..+.... ..+.....+.+.+.+-++.|++++++++.. +.+++...++ +...|++.-+
T Consensus 14 GFrLaGi~~~~~~~---~~ee~~~~l~~l~~~~d~gII~Ite~~~~~--i~e~i~~~~~--~~~~P~ii~I 77 (100)
T PRK02228 14 GFRLAGIRKVYEVP---DDEKLDEAVEEVLEDDDVGILVMHDDDLEK--LPRRLRRTLE--ESVEPTVVTL 77 (100)
T ss_pred HHHHcCCceEEeeC---CHHHHHHHHHHHhhCCCEEEEEEehhHhHh--hHHHHHHHHh--cCCCCEEEEE
Confidence 45668987543211 113355566666678889999999997653 2333443333 3455555544
No 66
>PTZ00099 rab6; Provisional
Probab=27.47 E-value=2.7e+02 Score=21.93 Aligned_cols=52 Identities=15% Similarity=0.130 Sum_probs=27.1
Q ss_pred HHhhhhcceEEEEeCCCCcCCh-hhHHHHHHHHHhcCceecEEEecCCCCccC
Q 046164 80 DTAIKHCKLGVAVFSPRYCESY-FCLHELALIMESRKKVIPIFYDVKPSQLQV 131 (202)
Q Consensus 80 ~~aI~~S~i~IvV~S~~y~~S~-wc~~EL~~i~~~~~~ViPVfy~v~p~~vr~ 131 (202)
...++.++++|+|++-.-..|- -+...+..+++....-+||++-....|+..
T Consensus 47 ~~~~~~ad~~ilv~D~t~~~sf~~~~~w~~~i~~~~~~~~piilVgNK~DL~~ 99 (176)
T PTZ00099 47 PSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGD 99 (176)
T ss_pred HHHhCCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECccccc
Confidence 3457899999999985433221 111222333332223456555445566543
No 67
>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=26.71 E-value=2.7e+02 Score=23.80 Aligned_cols=82 Identities=16% Similarity=0.062 Sum_probs=52.9
Q ss_pred hhHHHHHHHHHhcCCCeeE-ecCC--CCCCCCcchHHHHHhh--hhcceEEEEeCCCCcCChhhHHHHHHHHHh-----c
Q 046164 45 RTIAGLLHDHLSRLRLNPF-LDSK--NMKPGDRLFDKIDTAI--KHCKLGVAVFSPRYCESYFCLHELALIMES-----R 114 (202)
Q Consensus 45 ~~fv~~L~~~L~~~Gi~vf-~D~~--~l~~G~~i~~~i~~aI--~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~-----~ 114 (202)
..++..+.+.|.+.|+.+- +|.. .+.-|.-. + + .-+ ...++-||.+|.+...+.....+|.+++.. .
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~v-P-L-~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTIT-A-C-TLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHH-H-H-HHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 4789999999999999986 6663 35555422 1 1 223 246777888998886677777788887652 2
Q ss_pred CceecEEEecCCCCc
Q 046164 115 KKVIPIFYDVKPSQL 129 (202)
Q Consensus 115 ~~ViPVfy~v~p~~v 129 (202)
++|+-|-=+.--..+
T Consensus 167 ~rV~iIgSG~lSH~L 181 (271)
T cd07373 167 KRVAVVGVGGLSGSL 181 (271)
T ss_pred CeEEEEEecccccCc
Confidence 566644333333334
No 68
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=26.52 E-value=3.6e+02 Score=25.85 Aligned_cols=61 Identities=15% Similarity=0.091 Sum_probs=41.8
Q ss_pred CccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 31 PCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 31 ~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
..+|+|-.-+.. ....+..|...|.+.|++|-+|.. +..+...+..|-..---.++|+.++
T Consensus 539 p~~v~Ii~~~~~-~~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kki~~A~~~g~~~~iiiG~~ 599 (638)
T PRK00413 539 PVQVVVLPITDK-HADYAKEVAKKLKAAGIRVEVDLR----NEKIGYKIREAQLQKVPYMLVVGDK 599 (638)
T ss_pred cceEEEEEeChh-HHHHHHHHHHHHHhCCCEEEEECC----CCCHhHHHHHhhccCCCEEEEEcch
Confidence 468888765543 346788999999999999999874 3445566666644434456666554
No 69
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=26.38 E-value=1.8e+02 Score=27.84 Aligned_cols=60 Identities=13% Similarity=0.162 Sum_probs=39.6
Q ss_pred CccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 31 PCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 31 ~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
..+|+|-.-+++ -...+..+...|+++|++|-+|.. +..+...+..|-..---.++|+.+
T Consensus 438 P~qV~Iipi~e~-~~~~A~~Ia~~LR~~GirVelD~~----~~~lgkkir~A~k~gip~viIIG~ 497 (545)
T PRK14799 438 SVQVRVLPITDE-VNEYAEKVLNDMRKRRIRAEIDYA----GETLSKRIKNAYDQGVPYILIVGK 497 (545)
T ss_pred CceEEEEEcCHH-HHHHHHHHHHHHHhCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECh
Confidence 468887765443 346788999999999999999874 345566666653332334445544
No 70
>cd04167 Snu114p Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
Probab=25.93 E-value=3.5e+02 Score=21.71 Aligned_cols=88 Identities=9% Similarity=0.056 Sum_probs=42.9
Q ss_pred CCC-cchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCceecEEEecCCCCccCCCCCccchhhhHHHHHHH
Q 046164 71 PGD-RLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKKVIPIFYDVKPSQLQVPDNGTCSRKELQRFSRAL 149 (202)
Q Consensus 71 ~G~-~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~ViPVfy~v~p~~vr~~~~~~~~~e~~~~W~~AL 149 (202)
||. .+......++..++.+|+|++-.-..+.+...-+..+...+.+++.|.=+.|-.............+++.+....+
T Consensus 79 pG~~~f~~~~~~~~~~aD~~llVvD~~~~~~~~~~~~~~~~~~~~~p~iiviNK~D~~~~~~~l~~~~~~~~l~~~i~~~ 158 (213)
T cd04167 79 PGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILEGLPIVLVINKIDRLILELKLPPNDAYFKLRHIIDEV 158 (213)
T ss_pred CCCcchHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECcccCcccccCCHHHHHHHHHHHHHHH
Confidence 553 3556677889999999999986544444332222222223334444433333221111110111124556666666
Q ss_pred HHHHHhcCC
Q 046164 150 EEAKYTVGL 158 (202)
Q Consensus 150 ~~v~~~~G~ 158 (202)
...+...+.
T Consensus 159 n~~~~~~~~ 167 (213)
T cd04167 159 NNIIASFST 167 (213)
T ss_pred HHHHHHhcC
Confidence 665554443
No 71
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=25.92 E-value=2.5e+02 Score=25.90 Aligned_cols=62 Identities=19% Similarity=0.081 Sum_probs=40.9
Q ss_pred CCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 29 RRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 29 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
-..++|+|-.-+.+ -...+..|...|++.|+++.+|.. +..+...+..|-+.---.++++.+
T Consensus 272 LAP~qV~IIpl~ee-l~e~AlkLA~eLR~aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIIIGe 333 (387)
T PRK14938 272 LNPIQVRILPVKKD-FLDFSIQVAERLRKEGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIIIGE 333 (387)
T ss_pred cCcceEEEEEeChH-HHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECc
Confidence 34578777665544 345678899999999999999863 345666776665433334444443
No 72
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=25.86 E-value=1.8e+02 Score=27.55 Aligned_cols=60 Identities=23% Similarity=0.197 Sum_probs=40.0
Q ss_pred CccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCC
Q 046164 31 PCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSP 95 (202)
Q Consensus 31 ~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~ 95 (202)
.++|+|---+++ -...+..|...|.+.||+|-+|.++ ..+...+..|-..---.++|+.+
T Consensus 476 p~~v~Ii~~~~~-~~~~a~~i~~~Lr~~gi~v~~d~~~----~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 476 PVQVVIIPVADA-HNEYAEEVAKKLRAAGIRVEVDTSN----ERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CccEEEEEeChH-HHHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHhcCCCEEEEEec
Confidence 468888765443 2457889999999999999998753 34556666664433334555544
No 73
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=25.57 E-value=4.1e+02 Score=25.71 Aligned_cols=63 Identities=19% Similarity=0.125 Sum_probs=42.8
Q ss_pred CCccEEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 30 RPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 30 ~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
...+|+|-.-+++.-...+..|...|++.|++|-+|.. +..+...+..|-..---.++|+.++
T Consensus 540 ap~qV~Ii~~~~~~~~~~a~~la~~LR~~Gi~veid~~----~~sl~kq~k~A~k~g~~~~iiiG~~ 602 (639)
T PRK12444 540 APVQVKVIPVSNAVHVQYADEVADKLAQAGIRVERDER----DEKLGYKIREAQMQKIPYVLVIGDK 602 (639)
T ss_pred CCceEEEEEcccHHHHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEcch
Confidence 46788877655411246788999999999999999864 3456667766654444455566554
No 74
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=25.50 E-value=2.6e+02 Score=20.17 Aligned_cols=69 Identities=12% Similarity=0.014 Sum_probs=42.0
Q ss_pred HHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcCc-eecEEEec
Q 046164 51 LHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRKK-VIPIFYDV 124 (202)
Q Consensus 51 L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~~-ViPVfy~v 124 (202)
+...|+..|+.|..-..++ -.+++.+++.+.+.-+|.+|-......--..++...++...+ =++|+..-
T Consensus 19 ~~~~l~~~G~~V~~lg~~~-----~~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vGG 88 (119)
T cd02067 19 VARALRDAGFEVIDLGVDV-----PPEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVGG 88 (119)
T ss_pred HHHHHHHCCCEEEECCCCC-----CHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEEC
Confidence 5567789999995422222 245778888888888888886633333233455555544433 46676654
No 75
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=25.42 E-value=68 Score=28.05 Aligned_cols=26 Identities=27% Similarity=0.575 Sum_probs=19.5
Q ss_pred hhHHHHHHHHH------h--cCceecEEEecCCC
Q 046164 102 FCLHELALIME------S--RKKVIPIFYDVKPS 127 (202)
Q Consensus 102 wc~~EL~~i~~------~--~~~ViPVfy~v~p~ 127 (202)
=|-+||.+... . +.+++|||.-++|.
T Consensus 154 ICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 154 ICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred cChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 59999988643 1 23677999999994
No 76
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=24.96 E-value=2.9e+02 Score=20.40 Aligned_cols=68 Identities=10% Similarity=-0.009 Sum_probs=42.9
Q ss_pred HHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhc-CceecEEEe
Q 046164 51 LHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESR-KKVIPIFYD 123 (202)
Q Consensus 51 L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~-~~ViPVfy~ 123 (202)
+...|+..|+.|..=. .+.-.+++..++.+.+.-++++|-......--..++...++.. ..-++|+..
T Consensus 19 ~~~~l~~~G~~vi~lG-----~~vp~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~G 87 (122)
T cd02071 19 IARALRDAGFEVIYTG-----LRQTPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGAGDILVVGG 87 (122)
T ss_pred HHHHHHHCCCEEEECC-----CCCCHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCCCCCEEEEE
Confidence 3455788999986522 1223457778888888888888765444433456666666544 346777776
No 77
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=24.89 E-value=2.5e+02 Score=22.78 Aligned_cols=54 Identities=19% Similarity=0.378 Sum_probs=34.0
Q ss_pred HHHHHHHHHhcCCCee-EecCCCCCCCC--------cchHHHHHhhhhcceEEEEeCCCCcCCh
Q 046164 47 IAGLLHDHLSRLRLNP-FLDSKNMKPGD--------RLFDKIDTAIKHCKLGVAVFSPRYCESY 101 (202)
Q Consensus 47 fv~~L~~~L~~~Gi~v-f~D~~~l~~G~--------~i~~~i~~aI~~S~i~IvV~S~~y~~S~ 101 (202)
.+..+.+.|.+.|..+ .+|-.++..++ .-...+.+.|.+++ .||+.||-|..|-
T Consensus 19 l~~~~~~~l~~~g~ev~~idL~~l~~~~~~~~~~~~~~~~~~~~~i~~AD-~iIi~tP~Y~~s~ 81 (191)
T PRK10569 19 LLEYAREWLNGLGVEVYHWNLQNFAPEDLLYARFDSPALKTFTEQLAQAD-GLIVATPVYKASF 81 (191)
T ss_pred HHHHHHHHHHhCCCEEEEEEccCCChHHHHhccCCCHHHHHHHHHHHHCC-EEEEECCccCCCC
Confidence 4455666667778776 45655554321 12335567788888 5678899998764
No 78
>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=24.43 E-value=1.1e+02 Score=22.48 Aligned_cols=29 Identities=17% Similarity=0.206 Sum_probs=22.3
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEe
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFL 64 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~ 64 (202)
||||....| +..+ ..+...|...|++++-
T Consensus 3 vlisv~~~d-k~~~-~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYS-KPEL-LPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCccc-chhH-HHHHHHHHHCCCEEEE
Confidence 799998765 3444 4888889999999874
No 79
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=24.01 E-value=1.4e+02 Score=27.11 Aligned_cols=56 Identities=9% Similarity=0.104 Sum_probs=39.3
Q ss_pred Eeccc--cccchhHHHHHHHHHhcCCCeeEecCCCCCC----CCcchHHHHHhhhhcceEEE
Q 046164 36 INHRG--TDTKRTIAGLLHDHLSRLRLNPFLDSKNMKP----GDRLFDKIDTAIKHCKLGVA 91 (202)
Q Consensus 36 ISy~~--~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~----G~~i~~~i~~aI~~S~i~Iv 91 (202)
++|.. .|.|++=+..|.+.|..+|..|...|--+.. |-.+.+++..+++.++..|+
T Consensus 304 lafK~~t~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 304 LIMKSGSDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred ceeCCCCCccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 45653 4788888889999999999987664432222 34466677788888887653
No 80
>PF11201 DUF2982: Protein of unknown function (DUF2982); InterPro: IPR021367 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=24.00 E-value=77 Score=25.32 Aligned_cols=28 Identities=25% Similarity=0.304 Sum_probs=20.5
Q ss_pred CCCccEEEecccccc-chhHHHHHHHHHh
Q 046164 29 RRPCDVFINHRGTDT-KRTIAGLLHDHLS 56 (202)
Q Consensus 29 ~~~ydVFISy~~~D~-r~~fv~~L~~~L~ 56 (202)
...||+|||-+.-|. -..|+..|++.+.
T Consensus 123 ~lGYdlfi~~~~LDR~~~eFv~Llr~~~a 151 (152)
T PF11201_consen 123 LLGYDLFIPASDLDRDPEEFVGLLRRYQA 151 (152)
T ss_pred hcCceEEeEhhhccCCHHHHHHHHHHHHh
Confidence 457999999986552 2578888877653
No 81
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=23.26 E-value=4.3e+02 Score=21.86 Aligned_cols=144 Identities=22% Similarity=0.344 Sum_probs=76.2
Q ss_pred EEEecccccc--chhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhh------------------c-------
Q 046164 34 VFINHRGTDT--KRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKH------------------C------- 86 (202)
Q Consensus 34 VFISy~~~D~--r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~------------------S------- 86 (202)
.||.+-|-|- +.+-+..|++.|+.+|+.|.+-.+ +.|..+...|.+.+-+ .
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 5888877663 356788899999999998876542 2222333333222211 0
Q ss_pred ----ceEEEEeCCCCcCChhhHHH--------HHHHHHh--c---CceecEEEecCCCC-ccCCC---C--Cccchhh--
Q 046164 87 ----KLGVAVFSPRYCESYFCLHE--------LALIMES--R---KKVIPIFYDVKPSQ-LQVPD---N--GTCSRKE-- 141 (202)
Q Consensus 87 ----~i~IvV~S~~y~~S~wc~~E--------L~~i~~~--~---~~ViPVfy~v~p~~-vr~~~---~--~~~~~e~-- 141 (202)
.-.-+|++..|.-|.-+-+- ....+.. . ++-+-+|++++|.. ++... . .++..+.
T Consensus 82 ~pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~al~R~~~r~~~~~r~E~~~~~ 161 (208)
T COG0125 82 KPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVALERIRKRGELRDRFEKEDDE 161 (208)
T ss_pred HHhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHHHHHHHhcCCccchhhhHHHH
Confidence 11247889999988866552 2222211 1 35566788998864 11111 0 1222111
Q ss_pred -hHHHHHHHHHHHHhcC--C-cccCCCCCHHHHHHHHHHHHHHHhhh
Q 046164 142 -LQRFSRALEEAKYTVG--L-TFDSINGDWSEFLTTATDAVINNLIE 184 (202)
Q Consensus 142 -~~~W~~AL~~v~~~~G--~-~~~~~~~~e~~~i~~Iv~~v~~~L~~ 184 (202)
.++=+....+++.... + ..+ .+.+ ++++.++|...|.+
T Consensus 162 f~~kvr~~Y~~la~~~~~r~~vId-a~~~----~e~v~~~i~~~l~~ 203 (208)
T COG0125 162 FLEKVREGYLELAAKFPERIIVID-ASRP----LEEVHEEILKILKE 203 (208)
T ss_pred HHHHHHHHHHHHHhhCCCeEEEEE-CCCC----HHHHHHHHHHHHHH
Confidence 4455555556666554 2 233 2344 55555555555443
No 82
>PF09152 DUF1937: Domain of unknown function (DUF1937); InterPro: IPR015235 This entry is represented by Bacteriophage N15, Gp57. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a set of hypothetical bacterial and phage proteins whose exact function has not, as yet, been described. ; PDB: 1T1J_A.
Probab=23.13 E-value=1.2e+02 Score=23.07 Aligned_cols=69 Identities=16% Similarity=0.049 Sum_probs=40.3
Q ss_pred HHHHHHHhcCCCeeEecC--------CCCCCCCc-----chHHHHHhhhhcceEEEEeCCCCcCChhhHHHHHHHHHhcC
Q 046164 49 GLLHDHLSRLRLNPFLDS--------KNMKPGDR-----LFDKIDTAIKHCKLGVAVFSPRYCESYFCLHELALIMESRK 115 (202)
Q Consensus 49 ~~L~~~L~~~Gi~vf~D~--------~~l~~G~~-----i~~~i~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~~~~~ 115 (202)
.+-...|-+.|+.+|--. .-+...+. |.+--..-++.|+.+||.-.|.+..|.=...|+..+.+.+.
T Consensus 30 ~r~aa~l~~~G~~~fSpv~~sH~~~~~~~~~~~~~~~~~W~~~d~~~L~~c~~lvV~~i~GW~~S~Gi~~Ei~~a~~~~~ 109 (116)
T PF09152_consen 30 NRVAAELLKAGHAAFSPVVMSHPINFELLGDDDPLIQKLWEDWDRPFLDACDELVVLDIPGWDDSEGIWAEIEAAEEMGM 109 (116)
T ss_dssp HHHHHHHHHTT-EEEEHHHHHHHHHCCGTTS-HHHHHHHHHHHHHHHHHH-SEEEE---TTGGG-HHHHHHHHHHHHTT-
T ss_pred HHHHHHHHhcCCeeEeccccccccchhcccccCcchhHHHHHHhHHHHHhcceeEEecCCCccccccHHHHHHHHHHcCC
Confidence 344455667999988651 11112222 22222234688999999999999999999999999998876
Q ss_pred ce
Q 046164 116 KV 117 (202)
Q Consensus 116 ~V 117 (202)
+|
T Consensus 110 ~V 111 (116)
T PF09152_consen 110 PV 111 (116)
T ss_dssp EE
T ss_pred eE
Confidence 54
No 83
>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=22.72 E-value=2.3e+02 Score=20.65 Aligned_cols=29 Identities=24% Similarity=0.213 Sum_probs=19.6
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEe
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFL 64 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~ 64 (202)
||||-+..| +..++ .+...|...|+.++-
T Consensus 2 i~isv~d~~-K~~~~-~~a~~l~~~G~~i~A 30 (112)
T cd00532 2 VFLSVSDHV-KAMLV-DLAPKLSSDGFPLFA 30 (112)
T ss_pred EEEEEEccc-HHHHH-HHHHHHHHCCCEEEE
Confidence 688877555 33344 777777788888753
No 84
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=22.67 E-value=97 Score=27.78 Aligned_cols=34 Identities=24% Similarity=0.338 Sum_probs=27.7
Q ss_pred CCCccEEEeccccccchhHHHHHHHHHhcCCCeeEecC
Q 046164 29 RRPCDVFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDS 66 (202)
Q Consensus 29 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~ 66 (202)
....=|||. |.|+ +|-..|...|.++|++||---
T Consensus 27 ~~~k~VlIT--GCDS--GfG~~LA~~L~~~Gf~V~Agc 60 (322)
T KOG1610|consen 27 LSDKAVLIT--GCDS--GFGRLLAKKLDKKGFRVFAGC 60 (322)
T ss_pred cCCcEEEEe--cCCc--HHHHHHHHHHHhcCCEEEEEe
Confidence 344669995 7786 899999999999999998754
No 85
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=22.00 E-value=1.1e+02 Score=26.60 Aligned_cols=42 Identities=21% Similarity=0.349 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCCeeEecCCCCCCCCc---chHHHHHhhhhcceEEEEeC
Q 046164 48 AGLLHDHLSRLRLNPFLDSKNMKPGDR---LFDKIDTAIKHCKLGVAVFS 94 (202)
Q Consensus 48 v~~L~~~L~~~Gi~vf~D~~~l~~G~~---i~~~i~~aI~~S~i~IvV~S 94 (202)
+.+|.+.|...|+.+..-. -.||. |.+.+..++++++ +||+|
T Consensus 23 a~~la~~L~~~G~~v~~~~---~VgD~~~~I~~~l~~a~~r~D--~vI~t 67 (255)
T COG1058 23 AAFLADELTELGVDLARIT---TVGDNPDRIVEALREASERAD--VVITT 67 (255)
T ss_pred HHHHHHHHHhcCceEEEEE---ecCCCHHHHHHHHHHHHhCCC--EEEEC
Confidence 6689999999999987643 34553 4445555666644 45566
No 86
>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=21.47 E-value=2.4e+02 Score=20.21 Aligned_cols=29 Identities=28% Similarity=0.310 Sum_probs=21.3
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEe
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFL 64 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~ 64 (202)
||+|.+..| +.. ...+...|.+.|++++-
T Consensus 3 vl~s~~~~~-k~~-~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 3 VFISVADRD-KPE-AVEIAKRLAELGFKLVA 31 (110)
T ss_pred EEEEEEcCc-HhH-HHHHHHHHHHCCCEEEE
Confidence 789988665 333 44777888888998874
No 87
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=21.13 E-value=1.1e+02 Score=22.54 Aligned_cols=77 Identities=18% Similarity=0.285 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHhcCceecEEEecCCC-CccCCCCCccchhhhHHHHHHHHHH-----HHhc-CCcccCCCCCHHHHHHHH
Q 046164 102 FCLHELALIMESRKKVIPIFYDVKPS-QLQVPDNGTCSRKELQRFSRALEEA-----KYTV-GLTFDSINGDWSEFLTTA 174 (202)
Q Consensus 102 wc~~EL~~i~~~~~~ViPVfy~v~p~-~vr~~~~~~~~~e~~~~W~~AL~~v-----~~~~-G~~~~~~~~~e~~~i~~I 174 (202)
--.+||..++++|-+|.=|++....- .++... .-.+...+++|.+.+.+- ++++ |.|+=.......+-+++|
T Consensus 9 ~~~~EL~~IVd~Gg~V~DV~veHp~YG~i~~~L-~i~sr~Dv~~Fi~~l~~~~~~~Ls~LT~GvH~HtI~a~~~e~l~~I 87 (98)
T PF02829_consen 9 EIEDELEIIVDNGGRVLDVIVEHPVYGEITGNL-NISSRRDVDKFIEKLEKSKAKPLSSLTGGVHYHTIEAPDEEDLDKI 87 (98)
T ss_dssp GHHHHHHHHHHTT-EEEEEEEEETTTEEEEEEE-EE-SHHHHHHHHHHHHH--S--STTGGGGEEEEEEEESSHHHHHHH
T ss_pred HHHHHHHHHHHCCCEEEEEEEeCCCCcEEEEEE-ecCCHHHHHHHHHHHhccCCcchHHhcCCEeeEEEEECCHHHHHHH
Confidence 35689999999999998888864321 222211 123567888888888652 3333 455433223445556666
Q ss_pred HHHHH
Q 046164 175 TDAVI 179 (202)
Q Consensus 175 v~~v~ 179 (202)
.+...
T Consensus 88 ~~~L~ 92 (98)
T PF02829_consen 88 EEALK 92 (98)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 65544
No 88
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=21.05 E-value=79 Score=21.59 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=13.0
Q ss_pred CCCeeEecCCCCCCCCcchHHHHHhhh
Q 046164 58 LRLNPFLDSKNMKPGDRLFDKIDTAIK 84 (202)
Q Consensus 58 ~Gi~vf~D~~~l~~G~~i~~~i~~aI~ 84 (202)
..+-+++|.+ .+|......+.+.+.
T Consensus 47 ~~Vii~~D~D--~~G~~~a~~i~~~l~ 71 (81)
T PF13662_consen 47 KEVIIAFDND--KAGEKAAQKIAKKLL 71 (81)
T ss_dssp SEEEEEEESS--HHHHHHHHHHHHHHG
T ss_pred ceEEEEeCcC--HHHHHHHHHHHHHHH
Confidence 4455566654 355555555555443
No 89
>cd04175 Rap1 Rap1 subgroup. The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n
Probab=20.99 E-value=3.6e+02 Score=20.05 Aligned_cols=62 Identities=19% Similarity=0.243 Sum_probs=29.8
Q ss_pred CCCcchHHH-HHhhhhcceEEEEeCCCCcCChhhHHHH-HHHHHh-cCceecEEEecCCCCccCC
Q 046164 71 PGDRLFDKI-DTAIKHCKLGVAVFSPRYCESYFCLHEL-ALIMES-RKKVIPIFYDVKPSQLQVP 132 (202)
Q Consensus 71 ~G~~i~~~i-~~aI~~S~i~IvV~S~~y~~S~wc~~EL-~~i~~~-~~~ViPVfy~v~p~~vr~~ 132 (202)
+|..-...+ ....+.++..|+|++-.-..|--.+.++ ..+.+. ...=+|++.-....|+..+
T Consensus 57 ~G~~~~~~~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~ 121 (164)
T cd04175 57 AGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDE 121 (164)
T ss_pred CCcccchhHHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcchhc
Confidence 454333333 3357888999999975433322111111 222221 1122566665556666543
No 90
>COG2342 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]
Probab=20.84 E-value=1.4e+02 Score=26.41 Aligned_cols=44 Identities=27% Similarity=0.495 Sum_probs=35.6
Q ss_pred HHHHHhhhhcceEEEEeCCCCc---CChhhHHHHHHHHHhcCceecEEE
Q 046164 77 DKIDTAIKHCKLGVAVFSPRYC---ESYFCLHELALIMESRKKVIPIFY 122 (202)
Q Consensus 77 ~~i~~aI~~S~i~IvV~S~~y~---~S~wc~~EL~~i~~~~~~ViPVfy 122 (202)
+.-..+|.+++--++|+-|.|. .++|..+||.+..+.+ ++||=|
T Consensus 33 d~~~~~i~~~~f~llVVDps~~g~~~~~~~~eelr~~~~gg--~~pIAY 79 (300)
T COG2342 33 DAYINEILNSPFDLLVVDPSYCGPFNTPWTIEELRTKADGG--VKPIAY 79 (300)
T ss_pred cchHHHHhcCCCcEEEEeccccCCCCCcCcHHHHHHHhcCC--eeEEEE
Confidence 3445789999999999999665 6789999999887776 777766
No 91
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=20.65 E-value=3.6e+02 Score=23.04 Aligned_cols=62 Identities=16% Similarity=0.166 Sum_probs=38.2
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCCcchHHHHHhhhhcceEEEEeCCC
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLFDKIDTAIKHCKLGVAVFSPR 96 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~~~i~~aI~~S~i~IvV~S~~ 96 (202)
|-+|+...-....|+..+..+.++.|+++.+|.....+.... ..+...++.-.+=|=-++++
T Consensus 87 vt~SGGEP~~q~e~~~~~~~~ake~Gl~~~l~TnG~~~~~~~-~~l~~~~D~v~~DlK~~~~~ 148 (260)
T COG1180 87 VTFSGGEPTLQAEFALDLLRAAKERGLHVALDTNGFLPPEAL-EELLPLLDAVLLDLKAFDDE 148 (260)
T ss_pred EEEECCcchhhHHHHHHHHHHHHHCCCcEEEEcCCCCCHHHH-HHHHhhcCeEEEeeccCChH
Confidence 555554333467889999999999999999998766554433 33433333333334344444
No 92
>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=20.52 E-value=1.9e+02 Score=27.81 Aligned_cols=55 Identities=25% Similarity=0.335 Sum_probs=37.7
Q ss_pred CcCCCCCCCCccEEEeccc-cc-cchhHHHHHHHHHhcCCCeeEecCCCCCCCCcch
Q 046164 22 QIQLPITRRPCDVFINHRG-TD-TKRTIAGLLHDHLSRLRLNPFLDSKNMKPGDRLF 76 (202)
Q Consensus 22 ~~~~~~~~~~ydVFISy~~-~D-~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~~i~ 76 (202)
+..-|..-..|+|=|---. .| .-..++..|++.|+..|+.|.+|+++-.+|..+.
T Consensus 464 Gl~wP~~iAP~qV~Iip~~~~~~~~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~ 520 (568)
T TIGR00409 464 GIIWPKAIAPYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFA 520 (568)
T ss_pred CCcCChhhCCeEEEEEEcCCChHHHHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHH
Confidence 3344444567888665321 22 2346789999999999999999998766675443
No 93
>TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC. This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model.
Probab=20.49 E-value=3.1e+02 Score=21.16 Aligned_cols=35 Identities=14% Similarity=0.162 Sum_probs=24.0
Q ss_pred EEEeccccccchhHHHHHHHHHhcCCCeeEecCCCCCCCC
Q 046164 34 VFINHRGTDTKRTIAGLLHDHLSRLRLNPFLDSKNMKPGD 73 (202)
Q Consensus 34 VFISy~~~D~r~~fv~~L~~~L~~~Gi~vf~D~~~l~~G~ 73 (202)
||+||+-.+. . ...|....++.|+.+.+- ++..|+
T Consensus 3 vFvS~SMP~~--~-Lk~l~~~a~~~g~~~VlR--G~~~~~ 37 (130)
T TIGR02742 3 VFVSFSMPEP--L-LKQLLDQAEALGAPLVIR--GLLDNG 37 (130)
T ss_pred EEEEcCCCHH--H-HHHHHHHHHHhCCeEEEe--CCCCCC
Confidence 7999998763 3 446666677788876653 466654
No 94
>cd04110 Rab35 Rab35 subfamily. Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. 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 dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is
Probab=20.16 E-value=4.4e+02 Score=20.76 Aligned_cols=57 Identities=14% Similarity=0.077 Sum_probs=29.7
Q ss_pred CCCcchHHH-HHhhhhcceEEEEeCCCCcCChhhHHHHHHHH---HhcCceecEEEecCCCCcc
Q 046164 71 PGDRLFDKI-DTAIKHCKLGVAVFSPRYCESYFCLHELALIM---ESRKKVIPIFYDVKPSQLQ 130 (202)
Q Consensus 71 ~G~~i~~~i-~~aI~~S~i~IvV~S~~y~~S~wc~~EL~~i~---~~~~~ViPVfy~v~p~~vr 130 (202)
+|......+ ...+..++.+|+|++..-..| ..++...+ ......+|++.-....|+.
T Consensus 63 ~G~~~~~~~~~~~~~~a~~iilv~D~~~~~s---~~~~~~~~~~i~~~~~~~piivVgNK~Dl~ 123 (199)
T cd04110 63 AGQERFRTITSTYYRGTHGVIVVYDVTNGES---FVNVKRWLQEIEQNCDDVCKVLVGNKNDDP 123 (199)
T ss_pred CCchhHHHHHHHHhCCCcEEEEEEECCCHHH---HHHHHHHHHHHHHhCCCCCEEEEEECcccc
Confidence 554332333 445778888999998754333 33333322 2223445655544455554
Done!