Query 025787
Match_columns 248
No_of_seqs 260 out of 1527
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:31:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025787hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0566 SpoU rRNA methylases [ 99.9 2.3E-26 4.9E-31 207.9 12.8 135 109-243 43-193 (260)
2 PRK11181 23S rRNA (guanosine-2 99.9 1E-24 2.3E-29 195.2 12.6 118 126-243 49-178 (244)
3 TIGR00186 rRNA_methyl_3 rRNA m 99.9 4.4E-24 9.5E-29 190.2 13.4 120 126-245 44-175 (237)
4 PRK11081 tRNA guanosine-2'-O-m 99.9 1.2E-22 2.6E-27 181.0 12.5 103 143-247 2-104 (229)
5 PRK10864 putative methyltransf 99.9 2.4E-22 5.2E-27 188.4 12.4 117 126-243 154-280 (346)
6 PF00588 SpoU_methylase: SpoU 99.8 3.8E-20 8.3E-25 151.5 6.6 85 160-244 1-86 (142)
7 TIGR00185 rRNA_methyl_2 rRNA m 99.7 1.2E-17 2.7E-22 139.9 7.6 80 161-242 2-81 (153)
8 KOG2506 SpoU rRNA Methylase fa 99.7 1.4E-17 3E-22 153.5 5.1 92 126-217 168-274 (371)
9 PRK10358 putative rRNA methyla 99.7 4.2E-16 9.1E-21 131.5 9.3 80 161-243 2-82 (157)
10 KOG0838 RNA Methylase, SpoU fa 99.6 3.5E-15 7.6E-20 134.4 7.4 127 115-244 66-195 (271)
11 TIGR00050 rRNA_methyl_1 RNA me 99.3 2E-12 4.2E-17 115.5 6.5 77 161-242 4-81 (233)
12 PRK15114 tRNA (cytidine/uridin 99.3 9.2E-12 2E-16 112.1 7.5 79 160-243 4-83 (245)
13 PRK10433 putative RNA methyltr 98.9 3.4E-09 7.3E-14 94.8 7.5 76 161-240 3-79 (228)
14 KOG0839 RNA Methylase, SpoU fa 98.4 2.2E-07 4.8E-12 97.1 5.3 89 158-247 1324-1414(1477)
15 COG0219 CspR Predicted rRNA me 98.4 1.1E-06 2.4E-11 74.3 7.9 83 161-244 3-85 (155)
16 COG0565 LasT rRNA methylase [T 96.5 0.0069 1.5E-07 55.0 6.4 69 160-229 4-73 (242)
17 PF13380 CoA_binding_2: CoA bi 76.2 6 0.00013 31.4 5.0 52 159-238 56-107 (116)
18 PF13407 Peripla_BP_4: Peripla 68.8 20 0.00043 30.7 6.9 70 150-242 20-89 (257)
19 PRK03958 tRNA 2'-O-methylase; 57.5 27 0.00059 30.4 5.5 54 177-234 22-78 (176)
20 PF14044 NETI: NETI protein 53.5 12 0.00027 26.8 2.3 26 213-238 1-26 (57)
21 COG2242 CobL Precorrin-6B meth 48.9 36 0.00079 29.9 5.0 78 159-239 58-159 (187)
22 COG4080 SpoU rRNA Methylase fa 48.4 29 0.00062 29.4 4.0 69 160-232 2-75 (147)
23 cd04906 ACT_ThrD-I_1 First of 45.8 1.2E+02 0.0026 22.4 7.6 67 162-238 3-71 (85)
24 TIGR01656 Histidinol-ppas hist 44.1 34 0.00075 27.6 3.9 50 183-243 4-53 (147)
25 PF06399 GFRP: GTP cyclohydrol 41.4 41 0.0009 25.9 3.6 37 206-243 37-73 (83)
26 cd06281 PBP1_LacI_like_5 Ligan 39.9 1.6E+02 0.0034 25.2 7.7 90 149-239 20-121 (269)
27 cd04882 ACT_Bt0572_2 C-termina 35.5 1.3E+02 0.0029 19.9 6.2 58 169-237 8-65 (65)
28 PRK10076 pyruvate formate lyas 34.8 1.4E+02 0.0031 26.3 6.6 107 127-237 97-210 (213)
29 COG2106 Uncharacterized conser 34.6 39 0.00085 31.4 3.1 26 172-197 26-51 (272)
30 cd04909 ACT_PDH-BS C-terminal 33.8 1.3E+02 0.0028 20.7 5.1 65 164-236 5-69 (69)
31 PF08032 SpoU_sub_bind: RNA 2' 33.2 32 0.0007 24.3 1.9 23 126-148 45-67 (76)
32 PF14871 GHL6: Hypothetical gl 32.7 1.1E+02 0.0025 24.9 5.3 58 175-239 3-63 (132)
33 cd06320 PBP1_allose_binding Pe 32.4 1.9E+02 0.004 24.8 6.9 28 166-193 38-65 (275)
34 PF02638 DUF187: Glycosyl hydr 32.2 54 0.0012 30.5 3.7 68 170-239 17-89 (311)
35 cd01427 HAD_like Haloacid deha 32.1 62 0.0013 23.8 3.4 26 217-242 24-49 (139)
36 cd06299 PBP1_LacI_like_13 Liga 31.8 2.2E+02 0.0048 24.0 7.2 31 164-194 34-64 (265)
37 smart00642 Aamy Alpha-amylase 28.9 1.2E+02 0.0027 25.4 5.1 55 181-238 28-88 (166)
38 cd02165 NMNAT Nicotinamide/nic 28.6 1.4E+02 0.003 25.3 5.4 70 163-232 2-91 (192)
39 PRK09372 ribonuclease activity 27.9 3.8E+02 0.0081 22.7 7.8 46 150-195 48-96 (159)
40 cd06289 PBP1_MalI_like Ligand- 27.8 3.3E+02 0.0071 22.9 7.6 74 165-240 35-123 (268)
41 PRK00071 nadD nicotinic acid m 27.7 2.7E+02 0.0059 23.8 7.1 80 161-240 5-110 (203)
42 cd02922 FCB2_FMN Flavocytochro 27.6 1.3E+02 0.0028 28.6 5.4 67 175-243 84-154 (344)
43 TIGR01261 hisB_Nterm histidino 26.8 95 0.0021 25.9 3.9 24 219-242 31-54 (161)
44 PF07485 DUF1529: Domain of Un 25.8 1.9E+02 0.0042 23.6 5.5 41 202-242 35-90 (123)
45 COG3142 CutC Uncharacterized p 25.4 1.6E+02 0.0035 27.0 5.3 82 145-231 156-237 (241)
46 TIGR02637 RhaS rhamnose ABC tr 25.2 3E+02 0.0066 24.1 7.1 27 168-194 39-65 (302)
47 cd06324 PBP1_ABC_sugar_binding 25.0 4.2E+02 0.0091 23.4 8.1 45 149-194 21-67 (305)
48 TIGR01163 rpe ribulose-phospha 24.8 2.4E+02 0.0052 23.6 6.2 70 170-241 9-87 (210)
49 PRK10014 DNA-binding transcrip 24.5 3.4E+02 0.0074 24.2 7.4 91 149-240 85-188 (342)
50 cd06293 PBP1_LacI_like_11 Liga 24.5 2E+02 0.0044 24.4 5.7 90 150-240 21-122 (269)
51 COG1303 Uncharacterized protei 24.4 79 0.0017 27.5 3.0 53 177-233 23-79 (179)
52 cd06280 PBP1_LacI_like_4 Ligan 24.1 3.3E+02 0.0072 23.1 7.0 90 149-239 20-120 (263)
53 PRK12487 ribonuclease activity 23.9 4.6E+02 0.01 22.4 7.7 48 150-197 48-98 (163)
54 cd06300 PBP1_ABC_sugar_binding 23.6 4E+02 0.0087 22.6 7.5 33 162-194 37-69 (272)
55 cd06311 PBP1_ABC_sugar_binding 23.6 2.7E+02 0.0059 23.8 6.4 33 162-194 37-69 (274)
56 COG4996 Predicted phosphatase 23.4 1.2E+02 0.0027 25.7 3.9 58 184-241 5-65 (164)
57 cd06305 PBP1_methylthioribose_ 23.2 3.6E+02 0.0077 22.8 7.0 29 165-193 35-63 (273)
58 cd04885 ACT_ThrD-I Tandem C-te 22.7 1.4E+02 0.003 20.9 3.6 58 169-236 7-66 (68)
59 cd01538 PBP1_ABC_xylose_bindin 22.7 2.4E+02 0.0052 24.6 6.0 45 149-194 20-64 (288)
60 COG3426 Butyrate kinase [Energ 22.1 72 0.0016 30.4 2.5 34 168-201 103-138 (358)
61 cd01424 MGS_CPS_II Methylglyox 22.0 76 0.0016 24.4 2.3 22 220-241 13-34 (110)
62 cd01540 PBP1_arabinose_binding 21.9 3.2E+02 0.007 23.5 6.6 67 149-240 20-86 (289)
63 cd06310 PBP1_ABC_sugar_binding 21.9 3.9E+02 0.0084 22.7 7.0 27 168-194 40-66 (273)
64 cd06314 PBP1_tmGBP Periplasmic 21.6 3E+02 0.0064 23.6 6.2 46 149-194 19-64 (271)
65 PRK06769 hypothetical protein; 21.5 1.4E+02 0.003 24.9 4.0 25 218-242 29-53 (173)
66 cd06301 PBP1_rhizopine_binding 21.5 4.8E+02 0.01 22.1 7.5 45 149-194 20-65 (272)
67 cd06302 PBP1_LsrB_Quorum_Sensi 21.5 3.4E+02 0.0073 23.9 6.7 45 149-193 20-64 (298)
68 cd06308 PBP1_sensor_kinase_lik 21.4 5E+02 0.011 22.1 7.6 32 163-194 34-65 (270)
69 cd06290 PBP1_LacI_like_9 Ligan 21.1 3.7E+02 0.008 22.7 6.7 91 149-240 20-121 (265)
70 PF13607 Succ_CoA_lig: Succiny 21.0 1.3E+02 0.0028 24.8 3.6 36 158-195 55-90 (138)
71 PRK08224 ligC ATP-dependent DN 20.6 2.2E+02 0.0048 27.1 5.6 65 144-218 135-199 (350)
72 cd06316 PBP1_ABC_sugar_binding 20.5 4.3E+02 0.0093 23.0 7.1 44 150-193 21-64 (294)
73 PRK15447 putative protease; Pr 20.3 1.7E+02 0.0036 27.1 4.6 56 172-242 15-70 (301)
74 PRK10528 multifunctional acyl- 20.1 2.8E+02 0.006 23.2 5.6 45 148-192 61-115 (191)
75 PF13419 HAD_2: Haloacid dehal 20.1 1.8E+02 0.0039 22.5 4.2 27 216-242 76-102 (176)
No 1
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.3e-26 Score=207.90 Aligned_cols=135 Identities=21% Similarity=0.275 Sum_probs=109.8
Q ss_pred EeeccCcCCc-CCCCc----cC-cEEEccHHHHHHcCCCccchhhh---------hHHHHhhcCCCceEEEEeCCCCCCc
Q 025787 109 SLSNKRWFPY-LDRYK----CG-DVYLSSSEVVEALSPYLMEERKE---------RFVNVVKNRSYSVCLVVEGLSDFGN 173 (248)
Q Consensus 109 ~l~~~~~~~~-~~~~~----~~-~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~~r~~~lilVLD~I~DP~N 173 (248)
+|+++.+.+. .+.+. .. +++.++++++++++++.+|++.. ..++++.....+++|+||+|+||||
T Consensus 43 i~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~hqGi~a~~~~~~~~~~~~~~~~~~~~l~lvLd~V~DP~N 122 (260)
T COG0566 43 ILVTEGRLPRFEELLALAAAKGIPVYVVSEAILDKLSGTENHQGIVAVVKKRRYPLLDDLLDAEAQPLLLVLDGVTDPHN 122 (260)
T ss_pred EEEecccchhHHHHHHHHHhcCCeEEEECHHHHHHHhCCCCCCeEEEEEecccccchhhhhhcccCCEEEEEecCcCCcc
Confidence 6677666533 22222 12 79999999999999999887754 2222221113579999999999999
Q ss_pred HHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeC-CHHHHHHHHHHCCceEEEEeeCC
Q 025787 174 VSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWD-APRECFNVLRSRGYRIATTHVGM 243 (248)
Q Consensus 174 lGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~-~l~~~L~~Lk~~G~~ivAt~l~~ 243 (248)
+|||+|||+|||+++||+..+++|+++++++|+|||+++++|+.+.. +..+.++.++++||+|+|+++++
T Consensus 123 lGaIiRtA~a~Gv~~Vi~~~~~~~~~~~~v~r~s~Ga~~~vp~~~~~n~~~~~~~~~~~~G~~v~~t~~~~ 193 (260)
T COG0566 123 LGAIIRTADAFGVDGVILPKRRADPLNPKVIRASAGAAFHVPVIRVTNLARTLLELLKEAGFWVVATSLDG 193 (260)
T ss_pred hhhHHhhHHHhCCCEEEECCCccCCccceeEEecCChheeceeEEEeccHHHHHHHHHHcCeEEEEECCCC
Confidence 99999999999999999999999999999999999999999988877 46667777777999999999987
No 2
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=99.92 E-value=1e-24 Score=195.18 Aligned_cols=118 Identities=19% Similarity=0.222 Sum_probs=105.3
Q ss_pred cEEEccHHHHHHcCCCccchhhh------------hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787 126 DVYLSSSEVVEALSPYLMEERKE------------RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS 193 (248)
Q Consensus 126 ~v~~vs~~vl~~ls~~~~~~R~~------------~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~ 193 (248)
+++.+++++|++++++.+|++.. .++++++.+..++++|||+|+||+|+|||+|||+|||+++|++.+
T Consensus 49 ~~~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~~~~~~~~~~~~~~~~~~lvLd~v~dp~NlGai~Rta~a~G~~~vi~~~ 128 (244)
T PRK11181 49 VIQLANRQTLDEKAEGAVHQGIIARVKPGRQLQENDLPDLLASLEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPK 128 (244)
T ss_pred cEEEeCHHHHhhhhcCCCCceEEEEEecccccchhhHHHHHhcCCCCEEEEEcCCCCcchHHHHHHHHHHcCCCEEEECC
Confidence 58899999999999988775432 344555444457999999999999999999999999999999999
Q ss_pred CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787 194 CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM 243 (248)
Q Consensus 194 ~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~ 243 (248)
+++++++++++|+|||+.+|+++.++.++.++++.||++||+++|++.++
T Consensus 129 ~~~~~~~~~~~r~s~Ga~~~l~~~~~~~~~~~l~~l~~~g~~i~~t~~~~ 178 (244)
T PRK11181 129 DRSAQLNATAKKVACGAAETVPLIRVTNLARTMRMLQEKNIWIVGTAGEA 178 (244)
T ss_pred CCCCCCCCceEEecCCHHHcCeEEEcCCHHHHHHHHHHCCCEEEEEeCCC
Confidence 99999999999999999999999999999999999999999999998764
No 3
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=99.91 E-value=4.4e-24 Score=190.18 Aligned_cols=120 Identities=17% Similarity=0.240 Sum_probs=106.2
Q ss_pred cEEEccHHHHHHcCCCccchhhh---------hHHHHhh---cCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787 126 DVYLSSSEVVEALSPYLMEERKE---------RFVNVVK---NRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS 193 (248)
Q Consensus 126 ~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~---~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~ 193 (248)
+++.+++++|++++++.+|++.. .++++++ +...+++++||+|+||+|+|+|+|||+|||+++|++++
T Consensus 44 ~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~~~~~~~~~~~~~~~~lvLd~v~dp~NlGaI~Rta~afG~~~vil~~ 123 (237)
T TIGR00186 44 NIQLVDRQKLDQLTKGGNHQGIAAKVKPILYKDLNDLYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGVILPK 123 (237)
T ss_pred cEEEeCHHHHHHHhCCCCCCeEEEEEecCCCCCHHHHHHhhhccCCCEEEEEcCCCCCccHHHHHHHHHHcCCCEEEECC
Confidence 58899999999999988775431 4555542 22347899999999999999999999999999999999
Q ss_pred CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCCCc
Q 025787 194 CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMDA 245 (248)
Q Consensus 194 ~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~~A 245 (248)
.+++|++++++|+|||+.+|+++.++.++.++++.|+++||+++|++..+++
T Consensus 124 ~~~~~~~~~~~r~s~Ga~~~l~~~~~~~~~~~l~~l~~~g~~i~~~~~~~~~ 175 (237)
T TIGR00186 124 RRSAPLNSTVVKTSSGAVEYVPLARVTNLSRTITKLKESGFWTVGTDLDAQD 175 (237)
T ss_pred CCcCCCCCceeeeeccccceeEEEEeCCHHHHHHHHHHCCCEEEEEecCCCc
Confidence 9999999999999999999999999999999999999999999999987654
No 4
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=99.89 E-value=1.2e-22 Score=180.97 Aligned_cols=103 Identities=28% Similarity=0.416 Sum_probs=93.7
Q ss_pred cchhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCH
Q 025787 143 MEERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAP 222 (248)
Q Consensus 143 ~~~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l 222 (248)
+++|..+|+++|++++++++||||+|+||+|+|||+|||+|||+++|+++.... ..+...|+|||+.+|+++..+.++
T Consensus 2 ~~~r~~ri~~~l~~r~~~l~vvLd~V~~p~NlGAIiRta~AfGv~~V~~v~~~~--~~~~~~~~s~Ga~~wv~i~~~~~~ 79 (229)
T PRK11081 2 NPERYARICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS--RMRTMGSTAAGSNSWVQVKTHRTI 79 (229)
T ss_pred CchhHHhHHHHHhcCCCCeEEEEeCCCCcchHHHHHHHHHHhCCCeEEEecCCC--ccchhhhhcCCchheEEEEEeCCH
Confidence 578889999999998889999999999999999999999999999999986543 246788999999999999999999
Q ss_pred HHHHHHHHHCCceEEEEeeCCCccc
Q 025787 223 RECFNVLRSRGYRIATTHVGMDACC 247 (248)
Q Consensus 223 ~~~L~~Lk~~G~~ivAt~l~~~Av~ 247 (248)
.++++.||++||+|+|+++++++++
T Consensus 80 ~~~i~~lk~~g~~i~at~~~~~a~~ 104 (229)
T PRK11081 80 GDAVAHLKGQGMQILATHLSDTAVD 104 (229)
T ss_pred HHHHHHHHhCCCEEEEEeCCCCCcc
Confidence 9999999999999999999877653
No 5
>PRK10864 putative methyltransferase; Provisional
Probab=99.88 E-value=2.4e-22 Score=188.36 Aligned_cols=117 Identities=15% Similarity=0.126 Sum_probs=103.2
Q ss_pred cEEEccHHHHHHcCCCccchhhh---------hHHHHhhc-CCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCC
Q 025787 126 DVYLSSSEVVEALSPYLMEERKE---------RFVNVVKN-RSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCD 195 (248)
Q Consensus 126 ~v~~vs~~vl~~ls~~~~~~R~~---------~l~evl~~-r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~ 195 (248)
+++++++++|++++++.+|+++. .++++++. ...+++||||+|+||+|+|+|+|||+|||+++||+.+.
T Consensus 154 ~v~~V~~~~l~kls~~~~hqGV~A~v~~~~~~~l~~~l~~~~~~~~vlvLd~I~DP~NlGaIiRTA~afGv~~Vil~~~- 232 (346)
T PRK10864 154 AYHVVDEAELTKASGTEHHGGVCFLIKKRNGTDVQQWLAQAGAQDCVLALEDVGNPHNLGGIMRSCAHFGVKGVVVQDA- 232 (346)
T ss_pred cEEEeCHHHHHHHhCCCCCCeEEEEEeCCCCCCHHHHhhccccCCeEEEEeCCCCCCcHHHHHHHHHHhCCCEEEECCC-
Confidence 68999999999999998886542 45666552 12458999999999999999999999999999999875
Q ss_pred CCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787 196 SSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM 243 (248)
Q Consensus 196 ~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~ 243 (248)
.++++++++|+|||+.+|+++..+.++.++|+.||++||+|++++..+
T Consensus 233 ~~~~~~kvvRaS~Ga~~~v~i~~~~nl~~~L~~lk~~G~~Iv~t~~~~ 280 (346)
T PRK10864 233 ALLESGAAIRTAEGGAEHVQPITGDSFVDVLDDFRQAGYTIVTTSSHK 280 (346)
T ss_pred CCCCchhHHHHhcChhhcceEEEeCCHHHHHHHHHHCCCEEEEEeCCC
Confidence 477899999999999999999999999999999999999999998754
No 6
>PF00588 SpoU_methylase: SpoU rRNA Methylase family; InterPro: IPR001537 The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases [, ]. The Pet56 protein of Saccharomyces cerevisiae has been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase centre of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The Pet56 protein catalyzes the site-specific formation of 2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and E. coli 23S rRNA providing evidence for an essential modified nucleotide in rRNA [].; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 3N4J_A 3N4K_A 1IPA_A 3ONP_A 3NK6_A 3NK7_A 3IC6_A 1GZ0_D 1MXI_A 1J85_A ....
Probab=99.81 E-value=3.8e-20 Score=151.45 Aligned_cols=85 Identities=29% Similarity=0.396 Sum_probs=79.0
Q ss_pred ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC-CCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEE
Q 025787 160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS-CDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIAT 238 (248)
Q Consensus 160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~-~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivA 238 (248)
++++|||+++||+|+|+|+|||++||+++|++++ ++.|++++++.|+|+|+.+|+++..+.++.++++.+++.||++++
T Consensus 1 ~l~vvl~~~~~p~NlG~i~Rta~afG~~~v~l~~~~~~~~~~~~~~r~s~g~~~~~~~~~~~~~~~~l~~~~~~g~~i~~ 80 (142)
T PF00588_consen 1 MLIVVLDNVQDPGNLGAIIRTAAAFGVDGVILVGPRCADPYNPKVLRASAGAHEHLPIRRVDDLEEALKDLKENGYTIVA 80 (142)
T ss_dssp SEEEEEES-SSHHHHHHHHHHHHHTTESEEEEESSSSSTTTSHHHHHHTTTGHHCSHEEEESSHHHHHHHHHHTTEEEEE
T ss_pred CEEEEEeCCCCcCcHHHHHHHHHHhCCchhheeccccccccccccccccCChhhhhheeeeehhhhhcccccccccccce
Confidence 4789999999999999999999999999999987 777899999999999999999999999999999999999999999
Q ss_pred EeeCCC
Q 025787 239 THVGMD 244 (248)
Q Consensus 239 t~l~~~ 244 (248)
++.+++
T Consensus 81 ~~~~~~ 86 (142)
T PF00588_consen 81 TSPGAT 86 (142)
T ss_dssp ESTTSC
T ss_pred eeeccc
Confidence 998544
No 7
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2. this is part of the trmH (spoU) family of rRNA methylases
Probab=99.72 E-value=1.2e-17 Score=139.87 Aligned_cols=80 Identities=8% Similarity=-0.000 Sum_probs=71.1
Q ss_pred eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEe
Q 025787 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTH 240 (248)
Q Consensus 161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~ 240 (248)
+-+|||++|||+|+|+|+|||+|||++++++.+++.++..++..|++||+.+++++.++.++.+++++||+.| +++++
T Consensus 2 ~~vvL~~v~dP~NlG~iiRta~afGv~~vi~~~~~~~~~~~~~~ra~~~~~~~~~~~~~~~~~~~l~~l~~~g--v~~~~ 79 (153)
T TIGR00185 2 LNIVLYEPEIPPNTGNIARTCAATGTRLHLIEPLGFFLDDKRLKRAGLDYWEFVQLFYHKSWEEFLEAEKPQK--LFALT 79 (153)
T ss_pred eEEEEcCCCCCChHHHHHHHHHHhCCEEEEECCCCCCCccHHHHhhccchHhcCCeEEeCCHHHHHHhCcCCC--EEEEe
Confidence 4589999999999999999999999998988777666666777899999999999999999999999999999 66766
Q ss_pred eC
Q 025787 241 VG 242 (248)
Q Consensus 241 l~ 242 (248)
..
T Consensus 80 ~~ 81 (153)
T TIGR00185 80 KK 81 (153)
T ss_pred CC
Confidence 54
No 8
>KOG2506 consensus SpoU rRNA Methylase family protein [Translation, ribosomal structure and biogenesis]
Probab=99.69 E-value=1.4e-17 Score=153.52 Aligned_cols=92 Identities=20% Similarity=0.128 Sum_probs=79.4
Q ss_pred cEEEccHHHHHHcCCCccchhhhhHH-----HH----------hhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEE
Q 025787 126 DVYLSSSEVVEALSPYLMEERKERFV-----NV----------VKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVH 190 (248)
Q Consensus 126 ~v~~vs~~vl~~ls~~~~~~R~~~l~-----ev----------l~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vi 190 (248)
.++-++..++++.++.++|+...++. +- ......+++||+|+|+||||+|+|+|||+|||+++|+
T Consensus 168 ~i~kVks~d~K~wSsLvSP~svmaIf~~P~d~hl~k~~a~~q~~~s~~lp~~lvcdnirdpgnlgti~rsaaa~~cs~v~ 247 (371)
T KOG2506|consen 168 RIVKVKSLDMKKWSSLVSPESVMAIFLMPIDLHLDKDIATDQNKWSPSLPRVLVCDNIRDPGNLGTIVRSAAAFNCSGVF 247 (371)
T ss_pred eEEeccHHHHHHHhcccCCcchhhhccCcchhchhhhHHHHHhccCCCCCeEEEeccCCCCcchHHHHHHHhhCCCccee
Confidence 46788999999999999986654322 11 1123467999999999999999999999999999999
Q ss_pred EcCCCCCCCCcccccccCCCccceEEE
Q 025787 191 VVSCDSSKRYRENRHVSMGAEKWLDIE 217 (248)
Q Consensus 191 l~~~~~dp~~~k~~R~SmGA~~~v~i~ 217 (248)
++++|+|||.+|+.|++||+.|.+||.
T Consensus 248 lt~gccdpwe~kalrag~ga~fr~pi~ 274 (371)
T KOG2506|consen 248 LTPGCCDPWEDKALRAGRGASFRLPIV 274 (371)
T ss_pred ecCCcCCccchhhhhccCCcceeccee
Confidence 999999999999999999999999997
No 9
>PRK10358 putative rRNA methylase; Provisional
Probab=99.65 E-value=4.2e-16 Score=131.54 Aligned_cols=80 Identities=6% Similarity=-0.055 Sum_probs=64.8
Q ss_pred eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCccccccc-CCCccceEEEEeCCHHHHHHHHHHCCceEEEE
Q 025787 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVS-MGAEKWLDIELWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~S-mGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
+.+||++++||||+|||+|||+|||++.|++.+ ++|++++|++|++ +|...|+++..+.++.++++++ .+++++++
T Consensus 2 ~~ivL~~~~dPgNlGti~Rta~a~G~~~viv~~-~~d~~~~k~~raag~~~~~~~~~~~~~~l~~~l~~~--~~~~v~~~ 78 (157)
T PRK10358 2 LNIVLFEPEIPPNTGNIIRLCANTGFRLHIIEP-MGFAWDDKRLRRAGLDYHEFTAVTRHHDYAAFLEAE--NPQRLFAL 78 (157)
T ss_pred eEEEEeCCCCcChHHHHHHHHHHhCCEEEEECC-CCCCCChHHHHhcccccccceeeEEcCCHHHHHHhC--CCceEEEE
Confidence 468999999999999999999999998888755 5699999998874 4444555667778888887743 46899999
Q ss_pred eeCC
Q 025787 240 HVGM 243 (248)
Q Consensus 240 ~l~~ 243 (248)
+..+
T Consensus 79 ~~~~ 82 (157)
T PRK10358 79 TTKG 82 (157)
T ss_pred eCCC
Confidence 8864
No 10
>KOG0838 consensus RNA Methylase, SpoU family [RNA processing and modification]
Probab=99.58 E-value=3.5e-15 Score=134.44 Aligned_cols=127 Identities=25% Similarity=0.254 Sum_probs=98.3
Q ss_pred cCCcCCCCccCcEEEccHHHHHHcCCCccchhhh-hHH--HHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEE
Q 025787 115 WFPYLDRYKCGDVYLSSSEVVEALSPYLMEERKE-RFV--NVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHV 191 (248)
Q Consensus 115 ~~~~~~~~~~~~v~~vs~~vl~~ls~~~~~~R~~-~l~--evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil 191 (248)
|+.+...+....++++.+++++.++......... +.. .++ ...+.++||++.||+|+|||+|+|++||++++++
T Consensus 66 ~~~~~~~~~~~e~~~v~~~~~~~~s~h~L~~~t~~r~h~g~~l---easl~vylde~tDp~n~gaI~rsA~~lg~~~v~l 142 (271)
T KOG0838|consen 66 LLQSATDFRSTEFELVLRRDIEAVSKHDLNSLTDFRPHNGILL---EASLCVYLDEVTDPQNIGAIIRSAYFLGADGVLL 142 (271)
T ss_pred eeccccccCcceeeehhhhhhhccChhhHHHHHhhccccceEE---eeEEEeeccCccCCcchHHHHHhHHHhcCCceEE
Confidence 4444333433356666667776666532221111 000 011 2358899999999999999999999999999999
Q ss_pred cCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCCC
Q 025787 192 VSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGMD 244 (248)
Q Consensus 192 ~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~~ 244 (248)
+.+...+.++.+.++|+|+.+|++|.+|++..++++..+++||+++++....+
T Consensus 143 v~~n~s~lS~~vskss~gale~l~I~q~~~~~efl~vsvaaG~~l~~t~~~~~ 195 (271)
T KOG0838|consen 143 VKGNSSPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVAAGIRLHGTCSWAP 195 (271)
T ss_pred EeccCCCCchhHHHhhhchhheeeHHHcCCHHHHHHHHHhCceEEEEeecCcC
Confidence 99988999999999999999999999999999999999999999999887655
No 11
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen
Probab=99.33 E-value=2e-12 Score=115.47 Aligned_cols=77 Identities=21% Similarity=0.246 Sum_probs=66.4
Q ss_pred eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEE-EeCCHHHHHHHHHHCCceEEEE
Q 025787 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIE-LWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~-~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
+.+||++++||+|+|+|+|+|++||+++++++..+++ +++++.|+|+||.+|++.. .+++++++++. .+ .++|+
T Consensus 4 i~vvL~~~~~p~NiGaiaR~~~~fG~~~l~lv~p~~~-~~~~a~~~a~ga~~~l~~~~v~~~l~eal~~---~~-~vv~t 78 (233)
T TIGR00050 4 IRIVLVEPSHSGNIGSIARAMKNMGLTELCLVNPKSH-LEEEAYALAAGARDILDNAKVVDDLDEALDD---CD-LVVGT 78 (233)
T ss_pred eEEEEECCCCCCCHHHHHHHHHhCCCCEEEEeCCCcC-CCHHHHHHhCChHHhhccCEEECCHHHHHhc---CC-EEEEE
Confidence 7899999999999999999999999999999998877 6889999999999999864 46888887764 34 47777
Q ss_pred eeC
Q 025787 240 HVG 242 (248)
Q Consensus 240 ~l~ 242 (248)
+..
T Consensus 79 t~~ 81 (233)
T TIGR00050 79 SAR 81 (233)
T ss_pred CCC
Confidence 643
No 12
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=99.27 E-value=9.2e-12 Score=112.10 Aligned_cols=79 Identities=15% Similarity=0.174 Sum_probs=63.1
Q ss_pred ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEE-EeCCHHHHHHHHHHCCceEEE
Q 025787 160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIE-LWDAPRECFNVLRSRGYRIAT 238 (248)
Q Consensus 160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~-~~~~l~~~L~~Lk~~G~~ivA 238 (248)
.+.+||++++||||||+|+|+|++||+++++++..++|++++ ++|+|+||.+.+... .+++++++++. ...++|
T Consensus 4 ~i~vVLv~~~~pgNiGaiaRa~~~fG~~~l~lv~p~~~~~~~-a~~~a~GA~~~l~~a~i~~~l~eal~~----~~~vva 78 (245)
T PRK15114 4 NIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQ-AIALAAGASDVIGNATIVDTLDEALAG----CSLVVG 78 (245)
T ss_pred CeEEEEeCCCCCCcHHHHHHHHHhcCCCEEEEeCCCCCCcCH-HHHHcCCchhhcccCeEecCHHHHHhc----CCEEEE
Confidence 378999999999999999999999999999999999888654 899999999533221 24666665543 346999
Q ss_pred EeeCC
Q 025787 239 THVGM 243 (248)
Q Consensus 239 t~l~~ 243 (248)
|+...
T Consensus 79 tt~r~ 83 (245)
T PRK15114 79 TSARS 83 (245)
T ss_pred EcCCc
Confidence 98654
No 13
>PRK10433 putative RNA methyltransferase; Provisional
Probab=98.90 E-value=3.4e-09 Score=94.81 Aligned_cols=76 Identities=21% Similarity=0.341 Sum_probs=63.2
Q ss_pred eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEE-EEeCCHHHHHHHHHHCCceEEEE
Q 025787 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDI-ELWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i-~~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
+.+||.++++|+|||+|.|++.+||++.++++..+..+ ...+.+.++||..|++- ..+++++++++. .+|.+.++
T Consensus 3 i~vVLv~p~~p~NiGaiaRam~nfG~~~L~lV~p~~~~-~~~a~~~A~gA~d~L~~a~v~~tL~eAl~d---~~~vigtt 78 (228)
T PRK10433 3 LTIILVAPARAENVGAAARAMKTMGFSELRIVDSQAHL-EPAARWVAHGSGDILDNAKVFDTLAEALHD---VDFTVATT 78 (228)
T ss_pred eEEEEEcCCCCccHHHHHHHHHHCCCCEEEEeCCCCCC-cHHHHHHhccHHHHhcCceEECCHHHHHHh---CCeEEEEc
Confidence 67999999999999999999999999999999876543 56678999999999984 346898888877 46655544
Q ss_pred e
Q 025787 240 H 240 (248)
Q Consensus 240 ~ 240 (248)
.
T Consensus 79 a 79 (228)
T PRK10433 79 A 79 (228)
T ss_pred c
Confidence 4
No 14
>KOG0839 consensus RNA Methylase, SpoU family [RNA processing and modification]
Probab=98.43 E-value=2.2e-07 Score=97.15 Aligned_cols=89 Identities=19% Similarity=0.273 Sum_probs=75.3
Q ss_pred CCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEe--CCHHHHHHHHHHCCce
Q 025787 158 SYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELW--DAPRECFNVLRSRGYR 235 (248)
Q Consensus 158 ~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~--~~l~~~L~~Lk~~G~~ 235 (248)
...+|||.-=|..|.|+|.|.|||+.||++-+.+.+-.+ ...+...-.||-|..|+|++.+ +++...|++.|.+||+
T Consensus 1324 rssLIVVASLVDKppNLgGicRTcEVFgvs~LvVad~~v-i~DkQFk~lSVtAE~W~pieeVk~~~L~~fLq~kK~EGyT 1402 (1477)
T KOG0839|consen 1324 RSSLIVVASLVDKPPNLGGICRTCEVFGVSLLVVADIKV-INDKQFKNLSVTAERWMPIEEVKLDELASFLQEKKKEGYT 1402 (1477)
T ss_pred ceeEEEEeecccCCCccchhhhhhhhhCcceEEEeeeee-ecchhhhheeeeHHhccchhccChHHHHHHHHHhhhcCcE
Confidence 357999999999999999999999999999877755432 1234456789999999999854 6899999999999999
Q ss_pred EEEEeeCCCccc
Q 025787 236 IATTHVGMDACC 247 (248)
Q Consensus 236 ivAt~l~~~Av~ 247 (248)
|+|++.+++||.
T Consensus 1403 iIglEQTakSV~ 1414 (1477)
T KOG0839|consen 1403 IIGLEQTAKSVK 1414 (1477)
T ss_pred EEeehhcccccc
Confidence 999999999874
No 15
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=98.40 E-value=1.1e-06 Score=74.32 Aligned_cols=83 Identities=10% Similarity=0.018 Sum_probs=69.9
Q ss_pred eEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEe
Q 025787 161 VCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTH 240 (248)
Q Consensus 161 lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~ 240 (248)
+-+||-+-+-|.|.|+|+|+|+++|..=.++=+-.-+.-.++..|+.+-.+..+.+..|+++++++++.+. |-++++.+
T Consensus 3 ~~IvL~~PeIP~NTGNI~R~ca~tga~LhlI~PlGF~l~dk~lkRAGlDY~~~~~l~~h~s~e~fl~~~~~-~~rl~~~t 81 (155)
T COG0219 3 LNIVLYQPEIPPNTGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAGLDYHEKASLTEHDSLEAFLEAEPI-GGRLFALT 81 (155)
T ss_pred cEEEEECCCCCCchhHHHHHHHhcCCeEEEEccCCCccchhhhhhcccchHhhcceEEeCCHHHHHhhccC-CceEEEEE
Confidence 56899999999999999999999999754444444454457789999999999999999999999999988 88888887
Q ss_pred eCCC
Q 025787 241 VGMD 244 (248)
Q Consensus 241 l~~~ 244 (248)
..+.
T Consensus 82 t~~~ 85 (155)
T COG0219 82 TKGT 85 (155)
T ss_pred eccc
Confidence 6543
No 16
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=96.48 E-value=0.0069 Score=54.96 Aligned_cols=69 Identities=20% Similarity=0.301 Sum_probs=56.8
Q ss_pred ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEE-EEeCCHHHHHHHH
Q 025787 160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDI-ELWDAPRECFNVL 229 (248)
Q Consensus 160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i-~~~~~l~~~L~~L 229 (248)
.+.+||=+-+-|+|||++.|...-||++.++++..++. ....+.+.|+||..-+.= ..+++++++|..+
T Consensus 4 ~i~iVLVep~~~gNIG~vARaMKNfGl~eL~LV~Pr~~-~~eeA~a~A~gA~dile~A~i~~tL~eAl~d~ 73 (242)
T COG0565 4 NIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDILENAKIVDTLEEALADC 73 (242)
T ss_pred ccEEEEEcCCCCccHHHHHHHHHhCCcceEEEECCCCC-CCHHHHHHhccchhhhccCeeecCHHHHhcCC
Confidence 36788889999999999999999999999999998866 467899999999855542 2357888887744
No 17
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=76.23 E-value=6 Score=31.43 Aligned_cols=52 Identities=23% Similarity=0.298 Sum_probs=37.3
Q ss_pred CceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEE
Q 025787 159 YSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIAT 238 (248)
Q Consensus 159 ~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivA 238 (248)
.+++++ ...|..+..+++-|.+.|+++||+.++ ..-+++++.++++|+++++
T Consensus 56 iDlavv---~~~~~~~~~~v~~~~~~g~~~v~~~~g-------------------------~~~~~~~~~a~~~gi~vig 107 (116)
T PF13380_consen 56 IDLAVV---CVPPDKVPEIVDEAAALGVKAVWLQPG-------------------------AESEELIEAAREAGIRVIG 107 (116)
T ss_dssp -SEEEE----S-HHHHHHHHHHHHHHT-SEEEE-TT-------------------------S--HHHHHHHHHTT-EEEE
T ss_pred CCEEEE---EcCHHHHHHHHHHHHHcCCCEEEEEcc-------------------------hHHHHHHHHHHHcCCEEEe
Confidence 345555 367899999999999999999999876 3345789999999999885
No 18
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=68.83 E-value=20 Score=30.66 Aligned_cols=70 Identities=19% Similarity=0.230 Sum_probs=52.0
Q ss_pred HHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHH
Q 025787 150 FVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVL 229 (248)
Q Consensus 150 l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~L 229 (248)
+++.++.....+.++.+.-.|+.+.-..++.+-+-|+++|++..... ..+.+.++++
T Consensus 20 ~~~~a~~~g~~~~~~~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~~~-----------------------~~~~~~l~~~ 76 (257)
T PF13407_consen 20 AKAAAKELGYEVEIVFDAQNDPEEQIEQIEQAISQGVDGIIVSPVDP-----------------------DSLAPFLEKA 76 (257)
T ss_dssp HHHHHHHHTCEEEEEEESTTTHHHHHHHHHHHHHTTESEEEEESSST-----------------------TTTHHHHHHH
T ss_pred HHHHHHHcCCEEEEeCCCCCCHHHHHHHHHHHHHhcCCEEEecCCCH-----------------------HHHHHHHHHH
Confidence 34444332333334369999999999999999999999999976532 3455788999
Q ss_pred HHCCceEEEEeeC
Q 025787 230 RSRGYRIATTHVG 242 (248)
Q Consensus 230 k~~G~~ivAt~l~ 242 (248)
+++|+.|+..+..
T Consensus 77 ~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 77 KAAGIPVVTVDSD 89 (257)
T ss_dssp HHTTSEEEEESST
T ss_pred hhcCceEEEEecc
Confidence 9999999887655
No 19
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=57.54 E-value=27 Score=30.43 Aligned_cols=54 Identities=15% Similarity=0.137 Sum_probs=37.7
Q ss_pred HHHHHHHHCCCeEEEcCCCCCCCCccc---ccccCCCccceEEEEeCCHHHHHHHHHHCCc
Q 025787 177 TFRSADALGVQSVHVVSCDSSKRYREN---RHVSMGAEKWLDIELWDAPRECFNVLRSRGY 234 (248)
Q Consensus 177 IiRSA~AfGv~~Vil~~~~~dp~~~k~---~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~ 234 (248)
+.|||-|||+++++++.. |+-.... +-.--|+.|.+.+ ..++.++++..++.|-
T Consensus 22 vartARafGa~~~yiv~~--~~~q~~~v~~I~~~WGg~fnv~~--~~s~~~~i~~~k~~G~ 78 (176)
T PRK03958 22 VGLTARALGADKIILASN--DEHVKESVEDIVERWGGPFEVEV--TKSWKKEIREWKDGGI 78 (176)
T ss_pred HHHHHHHcCCceEEEecC--cHHHHHHHHHHHHhcCCceEEEE--cCCHHHHHHHHHhCCc
Confidence 689999999999999864 3321111 1122377777554 5899999999997664
No 20
>PF14044 NETI: NETI protein
Probab=53.54 E-value=12 Score=26.83 Aligned_cols=26 Identities=15% Similarity=0.410 Sum_probs=20.6
Q ss_pred ceEEEEeCCHHHHHHHHHHCCceEEE
Q 025787 213 WLDIELWDAPRECFNVLRSRGYRIAT 238 (248)
Q Consensus 213 ~v~i~~~~~l~~~L~~Lk~~G~~ivA 238 (248)
|..+...+++.+||+.+++.||.-+.
T Consensus 1 kFeV~enETI~~CL~RM~~eGY~Pvr 26 (57)
T PF14044_consen 1 KFEVEENETISDCLARMKKEGYMPVR 26 (57)
T ss_pred CeeccCCCcHHHHHHHHHHcCCCcee
Confidence 34555568899999999999997653
No 21
>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]
Probab=48.88 E-value=36 Score=29.93 Aligned_cols=78 Identities=17% Similarity=0.141 Sum_probs=51.6
Q ss_pred CceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCc-------ccccccCCCc----------------cceE
Q 025787 159 YSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYR-------ENRHVSMGAE----------------KWLD 215 (248)
Q Consensus 159 ~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~-------k~~R~SmGA~----------------~~v~ 215 (248)
...+..+| .|+.=+..|=|+|+.||++.+.++.+.+.-..+ -.+-.+ |.+ --++
T Consensus 58 ~~~v~AIe--~~~~a~~~~~~N~~~fg~~n~~vv~g~Ap~~L~~~~~~daiFIGGg-~~i~~ile~~~~~l~~ggrlV~n 134 (187)
T COG2242 58 SGRVIAIE--RDEEALELIERNAARFGVDNLEVVEGDAPEALPDLPSPDAIFIGGG-GNIEEILEAAWERLKPGGRLVAN 134 (187)
T ss_pred CceEEEEe--cCHHHHHHHHHHHHHhCCCcEEEEeccchHhhcCCCCCCEEEECCC-CCHHHHHHHHHHHcCcCCeEEEE
Confidence 34677777 478889999999999999999999876532211 122222 222 1223
Q ss_pred EEEeCCHHHHHHHHHHCCc-eEEEE
Q 025787 216 IELWDAPRECFNVLRSRGY-RIATT 239 (248)
Q Consensus 216 i~~~~~l~~~L~~Lk~~G~-~ivAt 239 (248)
....++...+++++++.|+ .++-.
T Consensus 135 aitlE~~~~a~~~~~~~g~~ei~~v 159 (187)
T COG2242 135 AITLETLAKALEALEQLGGREIVQV 159 (187)
T ss_pred eecHHHHHHHHHHHHHcCCceEEEE
Confidence 3345777788888888888 44443
No 22
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=48.42 E-value=29 Score=29.42 Aligned_cols=69 Identities=19% Similarity=0.274 Sum_probs=49.8
Q ss_pred ceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCC---Cccccccc--CCCccceEEEEeCCHHHHHHHHHHC
Q 025787 160 SVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKR---YRENRHVS--MGAEKWLDIELWDAPRECFNVLRSR 232 (248)
Q Consensus 160 ~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~---~~k~~R~S--mGA~~~v~i~~~~~l~~~L~~Lk~~ 232 (248)
.+++++.|+..+.-+=-+-|.|..||++.++++.-....- -+.+.|-+ +| .++..++++.++++-|+-.
T Consensus 2 ev~vvlHN~~S~~rv~e~ariaygfg~k~lV~tka~g~AAQsGIp~~~kla~k~G----~~vlvf~dL~DAlevL~P~ 75 (147)
T COG4080 2 EVIVVLHNVSSVQRVLEFARIAYGFGAKRLVLTKAKGSAAQSGIPEVLKLAFKLG----KPVLVFPDLDDALEVLRPD 75 (147)
T ss_pred cEEEEEecCCchHHHHHHHHHHcccCccEEEEEecccHhhhhccHHHHHHHHHhC----CcEEEehhHHHHHHhcCCc
Confidence 3789999999999999999999999999999986432110 01122211 22 4555678999999999743
No 23
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.79 E-value=1.2e+02 Score=22.36 Aligned_cols=67 Identities=13% Similarity=0.083 Sum_probs=36.5
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCc-cceEEEE-eCCHHHHHHHHHHCCceEEE
Q 025787 162 CLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAE-KWLDIEL-WDAPRECFNVLRSRGYRIAT 238 (248)
Q Consensus 162 ilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~-~~v~i~~-~~~l~~~L~~Lk~~G~~ivA 238 (248)
++.++=-..||+++.++..-...++..+.. .+..+ ..|-+ .-+.+.. .++..+.++.|++.||++.-
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~~anI~~~~y---------~~~~~-~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~ 71 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIGPRNITEFNY---------RYADE-KDAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhCCCceeEEEE---------EccCC-CeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEE
Confidence 344444467999999988666333332221 11111 11111 1122212 34488999999999999864
No 24
>TIGR01656 Histidinol-ppas histidinol-phosphate phosphatase family domain. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3.
Probab=44.08 E-value=34 Score=27.60 Aligned_cols=50 Identities=20% Similarity=0.129 Sum_probs=32.5
Q ss_pred HHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787 183 ALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM 243 (248)
Q Consensus 183 AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~ 243 (248)
.|-+++++......+ +.. .|-.+..++...++|+.|+++||+++-++-..
T Consensus 4 ~~d~dgtl~~~~~~~-~~~----------~~~~~~~~~g~~~~l~~Lk~~g~~~~I~Sn~~ 53 (147)
T TIGR01656 4 FLDRDGVINEDTVSD-YPR----------SLDDWQLRPGAVPALLTLRAAGYTVVVVTNQS 53 (147)
T ss_pred EEeCCCceeccCCcc-cCC----------CHHHeEEcCChHHHHHHHHHCCCEEEEEeCCC
Confidence 355666666554322 211 13334456888999999999999998776543
No 25
>PF06399 GFRP: GTP cyclohydrolase I feedback regulatory protein (GFRP); InterPro: IPR009112 GTP cyclohydrolase I feedback regulatory protein (GFRP) in mammals helps regulate the biosynthesis of tetrahydrobiopterin through the feedback inhibition of the rate-limiting enzyme GTP cyclohydrolase I (GTPCHI). Tetrahydrobiopterin is the cofactor required for the hydroxylation of aromatic amino acids. The crystal structure of GFRP reveals that the protein forms a homopentamer []. In the presence of phenylalanine, the stimulatory complex consists of a GTPCHI decamer sandwiched by two GFRP pentamers, which is thought to enhance GTPCHI activity by locking the enzyme in the active state []. The structure of GFRP consists of two alpha/beta layers arranged beta(2)-alpha-beta(2)-alpha-beta(2), with antiparallel beta-sheets in the order 342165.; GO: 0009890 negative regulation of biosynthetic process; PDB: 1IS7_N 1IS8_Q 1WPL_T 1JG5_C.
Probab=41.44 E-value=41 Score=25.89 Aligned_cols=37 Identities=22% Similarity=0.209 Sum_probs=24.7
Q ss_pred ccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeCC
Q 025787 206 VSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVGM 243 (248)
Q Consensus 206 ~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~~ 243 (248)
.-.|..|+..... +.....|++|...||+|+++..-+
T Consensus 37 ~~lgn~f~ey~~~-~~Pr~VLnKLE~~G~kVvsmtgvg 73 (83)
T PF06399_consen 37 TPLGNNFKEYHVD-DPPRVVLNKLEKMGYKVVSMTGVG 73 (83)
T ss_dssp --TT-SS-EEEES-S-HHHHHHHHHHTTEEEEEEEEET
T ss_pred ccccCcceEEEcC-CChHHHHHHHHhcCeEEEEEeccC
Confidence 3456656665543 567789999999999999987644
No 26
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=39.88 E-value=1.6e+02 Score=25.23 Aligned_cols=90 Identities=14% Similarity=0.128 Sum_probs=50.7
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCC--CCCcccccc-----cCC-----CccceEE
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSS--KRYRENRHV-----SMG-----AEKWLDI 216 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~d--p~~~k~~R~-----SmG-----A~~~v~i 216 (248)
.+++.+++.+.. +++.+.-.|+.+...+++....-++++|++.+...+ ++.+...+. ..+ ...++..
T Consensus 20 ~i~~~a~~~g~~-~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~ipvV~i~~~~~~~~~~V~~ 98 (269)
T cd06281 20 GAEDRLRAAGYS-LLIANSLNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASLDLPIVLLDRDMGGGADAVLF 98 (269)
T ss_pred HHHHHHHHcCCE-EEEEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhCCCCEEEEecccCCCCCEEEE
Confidence 445555544333 455566678888999999998889999998765322 111111110 011 1123333
Q ss_pred EEeCCHHHHHHHHHHCCceEEEE
Q 025787 217 ELWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 217 ~~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
.....-..+.++|.+.|++=++.
T Consensus 99 d~~~~g~~a~~~l~~~G~~~i~~ 121 (269)
T cd06281 99 DHAAGMRQAVEYLISLGHRRIAL 121 (269)
T ss_pred CcHHHHHHHHHHHHHCCCcEEEE
Confidence 22233345677888889876654
No 27
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.48 E-value=1.3e+02 Score=19.92 Aligned_cols=58 Identities=16% Similarity=0.177 Sum_probs=35.7
Q ss_pred CCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEE
Q 025787 169 SDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIA 237 (248)
Q Consensus 169 ~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~iv 237 (248)
..||.++.++..-...|+.=+.+........ |. ..+. .+.++....++.|+++||.++
T Consensus 8 d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~---------~~-~~v~-~~ve~~~~~~~~L~~~G~~v~ 65 (65)
T cd04882 8 DKPGGLHEILQILSEEGINIEYMYAFVEKKG---------GK-ALLI-FRTEDIEKAIEVLQERGVELV 65 (65)
T ss_pred CCCcHHHHHHHHHHHCCCChhheEEEccCCC---------Ce-EEEE-EEeCCHHHHHHHHHHCCceEC
Confidence 4599999999888888886432221000000 00 1122 233568899999999999874
No 28
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=34.76 E-value=1.4e+02 Score=26.30 Aligned_cols=107 Identities=9% Similarity=0.126 Sum_probs=60.5
Q ss_pred EEEccHHHHHHcCCCccchhhh-hHHHHhhcCCC--ceEEEEeCCC-CCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcc
Q 025787 127 VYLSSSEVVEALSPYLMEERKE-RFVNVVKNRSY--SVCLVVEGLS-DFGNVSATFRSADALGVQSVHVVSCDSSKRYRE 202 (248)
Q Consensus 127 v~~vs~~vl~~ls~~~~~~R~~-~l~evl~~r~~--~lilVLD~I~-DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k 202 (248)
+.-.+++...+++|..+ ++.. .++.+.+.... -+++|+-+++ ++.|+-+|.+-...+|++.+++.+-+. +. .
T Consensus 97 iK~~d~~~~~~~tG~~~-~~il~nl~~l~~~g~~v~iR~~vIPg~nd~~e~i~~ia~~l~~l~~~~~~llpyh~--~g-~ 172 (213)
T PRK10076 97 LKIMDATQARDVVKMNL-PRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALDVLIPLGIKQIHLLPFHQ--YG-E 172 (213)
T ss_pred eccCCHHHHHHHHCCCH-HHHHHHHHHHHhCCCcEEEEEEEECCCCCCHHHHHHHHHHHHHcCCceEEEecCCc--cc-h
Confidence 44456777778777433 3333 44444432111 2578899986 689999999999989999998876432 10 0
Q ss_pred cccccCCCc-c--ceEEEEeCCHHHHHHHHHHCCceEE
Q 025787 203 NRHVSMGAE-K--WLDIELWDAPRECFNVLRSRGYRIA 237 (248)
Q Consensus 203 ~~R~SmGA~-~--~v~i~~~~~l~~~L~~Lk~~G~~iv 237 (248)
..=-.+|-. + -.+...-+.++++.+.+++.|+.+.
T Consensus 173 ~Ky~~lg~~y~~~~~~~~~~~~l~~~~~~~~~~gl~~~ 210 (213)
T PRK10076 173 PKYRLLGKTWSMKEVPAPSSADVATMREMAERAGFQVT 210 (213)
T ss_pred hHHHHcCCcCccCCCCCcCHHHHHHHHHHHHHcCCeEE
Confidence 000011111 0 0111112345556667778888874
No 29
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=34.57 E-value=39 Score=31.44 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=22.4
Q ss_pred CcHHHHHHHHHHHCCCeEEEcCCCCC
Q 025787 172 GNVSATFRSADALGVQSVHVVSCDSS 197 (248)
Q Consensus 172 ~NlGAIiRSA~AfGv~~Vil~~~~~d 197 (248)
.=+|-|.|.|+-|||+.|++.+...+
T Consensus 26 ~Kvg~IARaaaiF~V~eIii~~D~~~ 51 (272)
T COG2106 26 YKVGQIARAAAIFRVDEIIIYEDGDD 51 (272)
T ss_pred HHHHHHHHHHHhhcccEEEEEeCCCC
Confidence 45899999999999999999886543
No 30
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=33.79 E-value=1.3e+02 Score=20.68 Aligned_cols=65 Identities=11% Similarity=0.159 Sum_probs=38.8
Q ss_pred EEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceE
Q 025787 164 VVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRI 236 (248)
Q Consensus 164 VLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~i 236 (248)
.++--..||++..+.+.-+..|+.=.-+.... ... . ..|.. .+.+..-.+.+.+++.|+++||.+
T Consensus 5 ~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~---~~~---~-~~~~~-~i~v~~~~~~~~~~~~L~~~G~~v 69 (69)
T cd04909 5 YVDVPDEPGVIAEVTQILGDAGISIKNIEILE---IRE---G-IGGIL-RISFKTQEDRERAKEILKEAGYEV 69 (69)
T ss_pred EEEcCCCCCHHHHHHHHHHHcCCCceeeEeEE---eec---C-CcEEE-EEEECCHHHHHHHHHHHHHcCCcC
Confidence 34445679999999999999999744332111 000 0 11111 222211146789999999999974
No 31
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=33.19 E-value=32 Score=24.33 Aligned_cols=23 Identities=26% Similarity=0.202 Sum_probs=18.4
Q ss_pred cEEEccHHHHHHcCCCccchhhh
Q 025787 126 DVYLSSSEVVEALSPYLMEERKE 148 (248)
Q Consensus 126 ~v~~vs~~vl~~ls~~~~~~R~~ 148 (248)
+++.+++++|++++++.+|++..
T Consensus 45 ~v~~v~~~~l~~ls~~~~hQGv~ 67 (76)
T PF08032_consen 45 PVYEVSKKVLDKLSDTENHQGVV 67 (76)
T ss_dssp EEEEE-HHHHHHCTTTSS-TTEE
T ss_pred eEEEeCHHHHHHHcCCCCCCeEE
Confidence 79999999999999998887643
No 32
>PF14871 GHL6: Hypothetical glycosyl hydrolase 6
Probab=32.66 E-value=1.1e+02 Score=24.94 Aligned_cols=58 Identities=17% Similarity=0.170 Sum_probs=40.6
Q ss_pred HHHHHHHHHHCCCeEEEcCCCC--CCCCcccccccCCC-ccceEEEEeCCHHHHHHHHHHCCceEEEE
Q 025787 175 SATFRSADALGVQSVHVVSCDS--SKRYRENRHVSMGA-EKWLDIELWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 175 GAIiRSA~AfGv~~Vil~~~~~--dp~~~k~~R~SmGA-~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
...+++...+|++.|.+-.+|. -.||+.-+ |. .+++. .+=+.+.++.++++|+++++=
T Consensus 3 ~~~~~~lk~~~v~si~i~a~~h~g~ayYPt~~----~~~hp~L~---~Dllge~v~a~h~~Girv~ay 63 (132)
T PF14871_consen 3 EQFVDTLKEAHVNSITIFAKCHGGYAYYPTKV----GPRHPGLK---RDLLGEQVEACHERGIRVPAY 63 (132)
T ss_pred HHHHHHHHHhCCCEEEEEcccccEEEEccCCC----CcCCCCCC---cCHHHHHHHHHHHCCCEEEEE
Confidence 4567888899999999955432 23455433 33 35554 255689999999999999874
No 33
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=32.39 E-value=1.9e+02 Score=24.78 Aligned_cols=28 Identities=7% Similarity=-0.059 Sum_probs=18.2
Q ss_pred eCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787 166 EGLSDFGNVSATFRSADALGVQSVHVVS 193 (248)
Q Consensus 166 D~I~DP~NlGAIiRSA~AfGv~~Vil~~ 193 (248)
++-.|+.+.-..++....-++++|++.+
T Consensus 38 ~~~~~~~~~~~~i~~l~~~~vdgiIi~~ 65 (275)
T cd06320 38 PSEGDQQGQLSIAENMINKGYKGLLFSP 65 (275)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCEEEECC
Confidence 3334555566677777777777777754
No 34
>PF02638 DUF187: Glycosyl hydrolase like GH101; InterPro: IPR003790 This entry describes proteins of unknown function.
Probab=32.23 E-value=54 Score=30.52 Aligned_cols=68 Identities=12% Similarity=0.092 Sum_probs=45.7
Q ss_pred CCCcHHHHHHHHHHHCCCeEEEc-CCCCCCCCccccccc----CCCccceEEEEeCCHHHHHHHHHHCCceEEEE
Q 025787 170 DFGNVSATFRSADALGVQSVHVV-SCDSSKRYRENRHVS----MGAEKWLDIELWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 170 DP~NlGAIiRSA~AfGv~~Vil~-~~~~dp~~~k~~R~S----mGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
++..+-.++..++..|+..|++- ....|.+|+..+-.- .|....- ..++-|+.++++.|++|..|.|-
T Consensus 17 ~~~~~~~~l~~l~~~~~N~V~~qVr~~gda~Y~S~~~p~s~~~~g~~~~~--pg~DpL~~~I~eaHkrGlevHAW 89 (311)
T PF02638_consen 17 SKEQIDEMLDDLKSAGFNAVFVQVRPRGDALYPSDIEPWSGYLTGKQGKD--PGFDPLEFMIEEAHKRGLEVHAW 89 (311)
T ss_pred CHHHHHHHHHHHHHcCCCEEEEEEEeCcEEEecccccccccccCCCCCCC--CCccHHHHHHHHHHHcCCEEEEE
Confidence 67788999999999999999983 334555544321111 1111110 12577899999999999999875
No 35
>cd01427 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
Probab=32.09 E-value=62 Score=23.85 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=20.7
Q ss_pred EEeCCHHHHHHHHHHCCceEEEEeeC
Q 025787 217 ELWDAPRECFNVLRSRGYRIATTHVG 242 (248)
Q Consensus 217 ~~~~~l~~~L~~Lk~~G~~ivAt~l~ 242 (248)
...+...+.|+.|+++|+.++-++..
T Consensus 24 ~~~~~~~~~l~~l~~~g~~i~ivS~~ 49 (139)
T cd01427 24 ELYPGVKEALKELKEKGIKLALATNK 49 (139)
T ss_pred CcCcCHHHHHHHHHHCCCeEEEEeCc
Confidence 33578889999999999998877643
No 36
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=31.84 E-value=2.2e+02 Score=24.03 Aligned_cols=31 Identities=10% Similarity=-0.005 Sum_probs=20.5
Q ss_pred EEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 164 VVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 164 VLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
+.+.-.|+...-.+++....-|+++||+.+.
T Consensus 34 ~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~ 64 (265)
T cd06299 34 IGNSDENPETENRYLDNLLSQRVDGIIVVPH 64 (265)
T ss_pred EEeCCCCHHHHHHHHHHHHhcCCCEEEEcCC
Confidence 3344456666667777777777888777653
No 37
>smart00642 Aamy Alpha-amylase domain.
Probab=28.95 E-value=1.2e+02 Score=25.41 Aligned_cols=55 Identities=15% Similarity=0.225 Sum_probs=31.0
Q ss_pred HHHHCCCeEEEcCCCCCCCCcccccccCCCc--cc--e--EEEEeCCHHHHHHHHHHCCceEEE
Q 025787 181 ADALGVQSVHVVSCDSSKRYRENRHVSMGAE--KW--L--DIELWDAPRECFNVLRSRGYRIAT 238 (248)
Q Consensus 181 A~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~--~~--v--~i~~~~~l~~~L~~Lk~~G~~ivA 238 (248)
-..+|+++|++.+-...+.. -....|-. .+ + .+-..+++.+.+++++++|.+|+.
T Consensus 28 l~~lG~~~I~l~Pi~~~~~~---~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vil 88 (166)
T smart00642 28 LKDLGVTAIWLSPIFESPQG---YPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVIL 88 (166)
T ss_pred HHHCCCCEEEECcceeCCCC---CCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEEE
Confidence 45679999999774322110 00111111 00 0 111236788899999999999874
No 38
>cd02165 NMNAT Nicotinamide/nicotinate mononucleotide adenylyltransferase. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis.
Probab=28.61 E-value=1.4e+02 Score=25.27 Aligned_cols=70 Identities=16% Similarity=0.202 Sum_probs=43.7
Q ss_pred EEEeCCCCCCcHH--HHHHHH-HHHCCCeEEEcCCCCCCCCc----------ccccccCCCccceEEEEe-------CCH
Q 025787 163 LVVEGLSDFGNVS--ATFRSA-DALGVQSVHVVSCDSSKRYR----------ENRHVSMGAEKWLDIELW-------DAP 222 (248)
Q Consensus 163 lVLD~I~DP~NlG--AIiRSA-~AfGv~~Vil~~~~~dp~~~----------k~~R~SmGA~~~v~i~~~-------~~l 222 (248)
.|+-|--||-..| .+++.| .-++.+.|+++.....+... +.++.+....+++.+..+ .-.
T Consensus 2 ~i~gGsFdP~H~GH~~~~~~a~~~~~~d~v~~~~~~~~~~k~~~~~~~~~R~~m~~~~~~~~~~i~v~~~e~~~~~~~~t 81 (192)
T cd02165 2 ALFGGSFDPPHLGHLAIAEEALEELGLDRVLLLPSANPPHKPPKPASFEHRLEMLKLAIEDNPKFEVSDIEIKRDGPSYT 81 (192)
T ss_pred eEEeeCCCCCCHHHHHHHHHHHHHcCCCEEEEEeCCCCCCCCCCCCCHHHHHHHHHHHHcCCCCEEEeHHHHhCCCCCCH
Confidence 4677888888887 445555 55667899988765333210 123444555677777532 345
Q ss_pred HHHHHHHHHC
Q 025787 223 RECFNVLRSR 232 (248)
Q Consensus 223 ~~~L~~Lk~~ 232 (248)
.++|+.|++.
T Consensus 82 ~~tl~~l~~~ 91 (192)
T cd02165 82 IDTLEELRER 91 (192)
T ss_pred HHHHHHHHHh
Confidence 5788888875
No 39
>PRK09372 ribonuclease activity regulator protein RraA; Provisional
Probab=27.88 E-value=3.8e+02 Score=22.73 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=31.8
Q ss_pred HHHHhhcCCCceEEEEeCCC--CCCcHHHHHHH-HHHHCCCeEEEcCCC
Q 025787 150 FVNVVKNRSYSVCLVVEGLS--DFGNVSATFRS-ADALGVQSVHVVSCD 195 (248)
Q Consensus 150 l~evl~~r~~~lilVLD~I~--DP~NlGAIiRS-A~AfGv~~Vil~~~~ 195 (248)
+.+.++.-++.-++|+|+-. +-.-.|.++=+ |.+.|+.++++-+..
T Consensus 48 ~~~~i~~~~~GdVlVid~~g~~~~a~~G~~~~~~a~~~G~~G~VidG~v 96 (159)
T PRK09372 48 VKELLEEPGEGRVLVVDGGGSLRRALVGDNLAELAVDNGWEGIVVYGCV 96 (159)
T ss_pred HHHHHhcCCCCeEEEEECCCCcCcEeehHHHHHHHHHcCCeEEEecccc
Confidence 33455544566788898654 45677877665 778899999886654
No 40
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=27.75 E-value=3.3e+02 Score=22.88 Aligned_cols=74 Identities=11% Similarity=0.022 Sum_probs=38.0
Q ss_pred EeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCccccc-c--------cC------CCccceEEEEeCCHHHHHHHH
Q 025787 165 VEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRH-V--------SM------GAEKWLDIELWDAPRECFNVL 229 (248)
Q Consensus 165 LD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R-~--------Sm------GA~~~v~i~~~~~l~~~L~~L 229 (248)
.+.=.|+.....+++.+.+-|+++|++.+...+. .. .++ . .. +...++..-.+.....+.+.|
T Consensus 35 ~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~-~~-~~~~~~~~~ipvV~~~~~~~~~~~~~v~~d~~~~~~~~~~~l 112 (268)
T cd06289 35 ANSGEDVERQEQLLSTMLEHGVAGIILCPAAGTS-PD-LLKRLAESGIPVVLVAREVAGAPFDYVGPDNAAGARLATEHL 112 (268)
T ss_pred ecCCCChHHHHHHHHHHHHcCCCEEEEeCCCCcc-HH-HHHHHHhcCCCEEEEeccCCCCCCCEEeecchHHHHHHHHHH
Confidence 3444456666666677666677777666532111 00 111 0 00 112233333334456677888
Q ss_pred HHCCceEEEEe
Q 025787 230 RSRGYRIATTH 240 (248)
Q Consensus 230 k~~G~~ivAt~ 240 (248)
.++|++-++.-
T Consensus 113 ~~~g~~~i~~l 123 (268)
T cd06289 113 ISLGHRRIAFI 123 (268)
T ss_pred HHCCCCCEEEe
Confidence 88898766653
No 41
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=27.68 E-value=2.7e+02 Score=23.81 Aligned_cols=80 Identities=13% Similarity=0.079 Sum_probs=50.1
Q ss_pred eEEEEeCCCCCCcHHHH--HHHH-HHHCCCeEEEcCCCCCCCCc-----------ccccccCCCccceEEEEe-------
Q 025787 161 VCLVVEGLSDFGNVSAT--FRSA-DALGVQSVHVVSCDSSKRYR-----------ENRHVSMGAEKWLDIELW------- 219 (248)
Q Consensus 161 lilVLD~I~DP~NlGAI--iRSA-~AfGv~~Vil~~~~~dp~~~-----------k~~R~SmGA~~~v~i~~~------- 219 (248)
.+.++-|--||-..|=+ ++.| +.+|.+.|++......+... ..++.+.....++.+..+
T Consensus 5 ~i~i~gGsFdP~H~GH~~l~~~a~~~~~~d~v~~~p~~~~~~k~~~~~~~~~~R~~m~~~a~~~~~~~~v~~~E~~~~~~ 84 (203)
T PRK00071 5 RIGLFGGTFDPPHYGHLAIAEEAAERLGLDEVWFLPNPGPPHKPQKPLAPLEHRLAMLELAIADNPRFSVSDIELERPGP 84 (203)
T ss_pred EEEEEeeCCCccCHHHHHHHHHHHHHcCCCEEEEEeCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCceEEeHHHHhCCCC
Confidence 47889999999999854 5555 45888999887764433221 123334445566766522
Q ss_pred CCHHHHHHHHHHCC-----ceEEEEe
Q 025787 220 DAPRECFNVLRSRG-----YRIATTH 240 (248)
Q Consensus 220 ~~l~~~L~~Lk~~G-----~~ivAt~ 240 (248)
.-..+.|+.|++.. |.|+|.|
T Consensus 85 syT~~tl~~l~~~~p~~~~~fiiG~D 110 (203)
T PRK00071 85 SYTIDTLRELRARYPDVELVFIIGAD 110 (203)
T ss_pred CCHHHHHHHHHHHCCCCcEEEEEcHH
Confidence 23457888888753 5566655
No 42
>cd02922 FCB2_FMN Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.
Probab=27.58 E-value=1.3e+02 Score=28.61 Aligned_cols=67 Identities=10% Similarity=0.068 Sum_probs=45.2
Q ss_pred HHHHHHHHHHCCCeEEEcCCCCCCCCcccccc-cCCCccceEEEEe---CCHHHHHHHHHHCCceEEEEeeCC
Q 025787 175 SATFRSADALGVQSVHVVSCDSSKRYRENRHV-SMGAEKWLDIELW---DAPRECFNVLRSRGYRIATTHVGM 243 (248)
Q Consensus 175 GAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~-SmGA~~~v~i~~~---~~l~~~L~~Lk~~G~~ivAt~l~~ 243 (248)
=++.|-|...|+-.++=+..+. + ...+.+. .-++..|+.++.+ .-+.+.++..++.||..+.++++.
T Consensus 84 ~~~AraA~~~gi~~~lss~s~~-s-~e~v~~~~~~~~~~w~Qly~~~d~~~~~~l~~ra~~ag~~alvltvD~ 154 (344)
T cd02922 84 LNLARAAGKHGILQMISTNASC-S-LEEIVDARPPDQPLFFQLYVNKDRTKTEELLKRAEKLGAKAIFLTVDA 154 (344)
T ss_pred HHHHHHHHHcCCCEEecCcccC-C-HHHHHHhcCCCCcEEEEEeecCCHHHHHHHHHHHHHcCCCEEEEECCC
Confidence 3778888888887555333332 2 2334454 3356788888765 455677888889999999998763
No 43
>TIGR01261 hisB_Nterm histidinol-phosphatase. This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis.
Probab=26.79 E-value=95 Score=25.92 Aligned_cols=24 Identities=13% Similarity=0.142 Sum_probs=20.9
Q ss_pred eCCHHHHHHHHHHCCceEEEEeeC
Q 025787 219 WDAPRECFNVLRSRGYRIATTHVG 242 (248)
Q Consensus 219 ~~~l~~~L~~Lk~~G~~ivAt~l~ 242 (248)
+++..+.|++|+++||+++.++-.
T Consensus 31 ~pgv~e~L~~L~~~g~~l~IvSN~ 54 (161)
T TIGR01261 31 EKGVIPALLKLKKAGYKFVMVTNQ 54 (161)
T ss_pred CCCHHHHHHHHHHCCCeEEEEeCC
Confidence 588999999999999999887653
No 44
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=25.81 E-value=1.9e+02 Score=23.59 Aligned_cols=41 Identities=22% Similarity=0.367 Sum_probs=31.6
Q ss_pred ccccccCCCccceEEEEe---------------CCHHHHHHHHHHCCceEEEEeeC
Q 025787 202 ENRHVSMGAEKWLDIELW---------------DAPRECFNVLRSRGYRIATTHVG 242 (248)
Q Consensus 202 k~~R~SmGA~~~v~i~~~---------------~~l~~~L~~Lk~~G~~ivAt~l~ 242 (248)
+.++.+||---|+.+... +.+..+++.|+++|+.|.|.+-+
T Consensus 35 ~~~~~~~~l~~~~aF~~~~~G~A~~~Gd~vll~~EV~pvi~aL~~~GI~vtAlHNH 90 (123)
T PF07485_consen 35 RRLPPPMGLTSWIAFEPDGDGKAMVMGDFVLLEDEVNPVISALRKNGIEVTALHNH 90 (123)
T ss_pred EEcCCccccceeEEEEECCCCcEEEeecEEecHHHHHHHHHHHHHCCceEEEEecc
Confidence 346777787888887653 23667999999999999999854
No 45
>COG3142 CutC Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]
Probab=25.40 E-value=1.6e+02 Score=26.96 Aligned_cols=82 Identities=16% Similarity=0.197 Sum_probs=0.0
Q ss_pred hhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHH
Q 025787 145 ERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRE 224 (248)
Q Consensus 145 ~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~ 224 (248)
++...+.+++++...++.++.-+=-+++|+-.+.+. .|+..+|.+....-+|+ ..+++||+.-...-+.+..-.+
T Consensus 156 eg~~~l~~li~~a~gri~Im~GaGV~~~N~~~l~~~---tg~~e~H~s~~~~~~~~--~~~~~m~~~~~~~~~~~~td~~ 230 (241)
T COG3142 156 EGLDLLKRLIEQAKGRIIIMAGAGVRAENIAELVLL---TGVTEVHGSAGVEMRYR--NPGSSMGADDFADEYIYDTDGA 230 (241)
T ss_pred hhHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHh---cCchhhhhccccccccc--CccCccccccccccccccCcHH
Q ss_pred HHHHHHH
Q 025787 225 CFNVLRS 231 (248)
Q Consensus 225 ~L~~Lk~ 231 (248)
.+.++|.
T Consensus 231 ~v~~~~~ 237 (241)
T COG3142 231 AVAEMKA 237 (241)
T ss_pred HHHHHHH
No 46
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.
Probab=25.20 E-value=3e+02 Score=24.12 Aligned_cols=27 Identities=11% Similarity=-0.028 Sum_probs=22.2
Q ss_pred CCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 168 LSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 168 I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
-.|+...-..++++..-|+++|++.+.
T Consensus 39 ~~d~~~q~~~i~~l~~~~vdgiIi~~~ 65 (302)
T TIGR02637 39 GTTAEGQIEVVNSLIAQKVDAIAISAN 65 (302)
T ss_pred CCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 357777788999999999999999753
No 47
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=25.00 E-value=4.2e+02 Score=23.42 Aligned_cols=45 Identities=7% Similarity=-0.153 Sum_probs=30.4
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHH--CCCeEEEcCC
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADAL--GVQSVHVVSC 194 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~Af--Gv~~Vil~~~ 194 (248)
.+++.+.+.... +++.+.=.|+...-.+++....- |+++|++.+.
T Consensus 21 gi~~~~~~~g~~-v~~~~~~~~~~~~~~~i~~~~~~~~~vdgiIi~~~ 67 (305)
T cd06324 21 FMQAAADDLGIE-LEVLYAERDRFLMLQQARTILQRPDKPDALIFTNE 67 (305)
T ss_pred HHHHHHHhcCCe-EEEEeCCCCHHHHHHHHHHHHHhccCCCEEEEcCC
Confidence 355555443333 34445445777788999999999 9999999653
No 48
>TIGR01163 rpe ribulose-phosphate 3-epimerase. This family consists of Ribulose-phosphate 3-epimerase, also known as pentose-5-phosphate 3-epimerase (PPE). PPE converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. It has been found in a wide range of bacteria, archebacteria, fungi and plants.
Probab=24.77 E-value=2.4e+02 Score=23.62 Aligned_cols=70 Identities=16% Similarity=0.204 Sum_probs=39.6
Q ss_pred CCCcHHHHHHHHHHHCCCeEEEc--CCCCCC---CCc---ccccccCCCccc-eEEEEeCCHHHHHHHHHHCCceEEEEe
Q 025787 170 DFGNVSATFRSADALGVQSVHVV--SCDSSK---RYR---ENRHVSMGAEKW-LDIELWDAPRECFNVLRSRGYRIATTH 240 (248)
Q Consensus 170 DP~NlGAIiRSA~AfGv~~Vil~--~~~~dp---~~~---k~~R~SmGA~~~-v~i~~~~~l~~~L~~Lk~~G~~ivAt~ 240 (248)
|+.|+...++.+...|++.|++. ++..-+ ... +.+|. ....+- +.+ ...+..+.++.+++.|...+..+
T Consensus 9 ~~~~~~~~~~~~~~~g~d~i~~~~~Dg~~~~~~~~~~~~v~~i~~-~~~~~v~v~l-m~~~~~~~~~~~~~~gadgv~vh 86 (210)
T TIGR01163 9 DFARLGEEVKAVEEAGADWIHVDVMDGHFVPNLTFGPPVLEALRK-YTDLPIDVHL-MVENPDRYIEDFAEAGADIITVH 86 (210)
T ss_pred CHHHHHHHHHHHHHcCCCEEEEcCCCCCCCCCcccCHHHHHHHHh-cCCCcEEEEe-eeCCHHHHHHHHHHcCCCEEEEc
Confidence 67789999999999999999985 110000 111 11221 111121 222 23466677888888877665555
Q ss_pred e
Q 025787 241 V 241 (248)
Q Consensus 241 l 241 (248)
.
T Consensus 87 ~ 87 (210)
T TIGR01163 87 P 87 (210)
T ss_pred c
Confidence 4
No 49
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=24.53 E-value=3.4e+02 Score=24.19 Aligned_cols=91 Identities=12% Similarity=0.088 Sum_probs=47.5
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCC--CCCccccc-----ccCC------CccceE
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSS--KRYRENRH-----VSMG------AEKWLD 215 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~d--p~~~k~~R-----~SmG------A~~~v~ 215 (248)
.+++.+.+.+. .+++.+.-.|+......++....-++++||+.+.... +...+..+ +..+ ...++.
T Consensus 85 gi~~~a~~~g~-~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~~~~~~~~~~V~ 163 (342)
T PRK10014 85 GLTEALEAQGR-MVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAEEKGIPVVFASRASYLDDVDTVR 163 (342)
T ss_pred HHHHHHHHcCC-EEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEecCCCCCCCCEEE
Confidence 34444443333 2333444456667778888888888999888764311 11010000 0011 112233
Q ss_pred EEEeCCHHHHHHHHHHCCceEEEEe
Q 025787 216 IELWDAPRECFNVLRSRGYRIATTH 240 (248)
Q Consensus 216 i~~~~~l~~~L~~Lk~~G~~ivAt~ 240 (248)
.-.+.....+.++|.++|++-++.-
T Consensus 164 ~D~~~~~~~a~~~L~~~G~~~I~~i 188 (342)
T PRK10014 164 PDNMQAAQLLTEHLIRNGHQRIAWL 188 (342)
T ss_pred eCCHHHHHHHHHHHHHCCCCEEEEE
Confidence 2222334567788889998777654
No 50
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=24.48 E-value=2e+02 Score=24.44 Aligned_cols=90 Identities=11% Similarity=-0.030 Sum_probs=45.2
Q ss_pred HHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCC-CCCcccccc-----cC------CCccceEEE
Q 025787 150 FVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSS-KRYRENRHV-----SM------GAEKWLDIE 217 (248)
Q Consensus 150 l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~d-p~~~k~~R~-----Sm------GA~~~v~i~ 217 (248)
+++.+.+.+..+ ++...=.|+...-.+++.....++++|++.....+ .......+. .. ....++..-
T Consensus 21 i~~~~~~~gy~v-~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~~pvV~i~~~~~~~~~~~V~~d 99 (269)
T cd06293 21 VEEEADARGLSL-VLCATRNRPERELTYLRWLDTNHVDGLIFVTNRPDDGALAKLINSYGNIVLVDEDVPGAKVPKVFCD 99 (269)
T ss_pred HHHHHHHCCCEE-EEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCCHHHHHHHHhcCCCEEEECCCCCCCCCCEEEEC
Confidence 444444333333 33333346667777788888888888887653211 111111110 00 112344433
Q ss_pred EeCCHHHHHHHHHHCCceEEEEe
Q 025787 218 LWDAPRECFNVLRSRGYRIATTH 240 (248)
Q Consensus 218 ~~~~l~~~L~~Lk~~G~~ivAt~ 240 (248)
....-..+.+.|.++|++-++.-
T Consensus 100 ~~~~~~~~~~~L~~~G~~~i~~i 122 (269)
T cd06293 100 NEQGGRLATRHLARAGHRRIAFV 122 (269)
T ss_pred CHHHHHHHHHHHHHCCCceEEEE
Confidence 33334567778888888776654
No 51
>COG1303 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.45 E-value=79 Score=27.51 Aligned_cols=53 Identities=11% Similarity=0.160 Sum_probs=31.1
Q ss_pred HHHHHHHHCCCeEEEcCCCCCCCC----cccccccCCCccceEEEEeCCHHHHHHHHHHCC
Q 025787 177 TFRSADALGVQSVHVVSCDSSKRY----RENRHVSMGAEKWLDIELWDAPRECFNVLRSRG 233 (248)
Q Consensus 177 IiRSA~AfGv~~Vil~~~~~dp~~----~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G 233 (248)
+.-||-|||+++|++.+.+ |.-- ++++ ..-|.-|.+... .|....++..|+-|
T Consensus 23 V~LtARAfGA~gil~~~e~-De~v~esv~dVv-~rwGG~F~v~~~--~nw~~~i~~wk~gG 79 (179)
T COG1303 23 VALTARAFGADGILLDGEE-DEKVVESVEDVV-ERWGGPFFVKFG--VNWRKVIREWKEGG 79 (179)
T ss_pred hhhhhHhhCCceEEEcCcc-cHHHHHHHHHHH-HhcCCCEEEEEc--ccHHHHHHHhhcCC
Confidence 3458999999999998664 3211 1122 234444544442 45667777777633
No 52
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=24.06 E-value=3.3e+02 Score=23.06 Aligned_cols=90 Identities=12% Similarity=0.090 Sum_probs=47.8
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCccc-------ccc----cCCCccceEEE
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYREN-------RHV----SMGAEKWLDIE 217 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~-------~R~----SmGA~~~v~i~ 217 (248)
.+++.+++.+.. ++++..-.|+...-.+++....-++++|++.+...+...... +-. ..+...++..-
T Consensus 20 ~i~~~~~~~g~~-~~~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~~~~~~~~~~iPvV~~~~~~~~~~~~~v~~d 98 (263)
T cd06280 20 AVEDAAYRAGLR-VILCNTDEDPEKEAMYLELMEEERVTGVIFAPTRATLRRLAELRLSFPVVLIDRAGPAGRVDAVVLD 98 (263)
T ss_pred HHHHHHHHCCCE-EEEEeCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCchHHHHHhcCCCEEEECCCCCCCCCCEEEEC
Confidence 344444444333 344555566767777888888888999988765322211110 000 01112333332
Q ss_pred EeCCHHHHHHHHHHCCceEEEE
Q 025787 218 LWDAPRECFNVLRSRGYRIATT 239 (248)
Q Consensus 218 ~~~~l~~~L~~Lk~~G~~ivAt 239 (248)
....-..+.+.|.++|++-++.
T Consensus 99 ~~~~g~~a~~~L~~~g~~~i~~ 120 (263)
T cd06280 99 NRAAARTLVEHLVAQGYRRIGG 120 (263)
T ss_pred cHHHHHHHHHHHHHCCCceEEE
Confidence 2233355677888899875554
No 53
>PRK12487 ribonuclease activity regulator protein RraA; Reviewed
Probab=23.93 E-value=4.6e+02 Score=22.40 Aligned_cols=48 Identities=17% Similarity=0.185 Sum_probs=33.0
Q ss_pred HHHHhhcCCCceEEEEeCC--CCCCcHHHHHHH-HHHHCCCeEEEcCCCCC
Q 025787 150 FVNVVKNRSYSVCLVVEGL--SDFGNVSATFRS-ADALGVQSVHVVSCDSS 197 (248)
Q Consensus 150 l~evl~~r~~~lilVLD~I--~DP~NlGAIiRS-A~AfGv~~Vil~~~~~d 197 (248)
+.+.++.-++.-++|+|.= .+-...|.++=+ |.+.|+.++++-+..-|
T Consensus 48 ~~~al~~~~~GdVlVid~~g~~~~a~~G~~~a~~a~~~G~aG~VidG~vRD 98 (163)
T PRK12487 48 VKEVLAQDGKGKVLVVDGGGSCRRALLGDQIAQSALDNGWEGIVINGCVRD 98 (163)
T ss_pred HHHHHhcCCCCeEEEEECCCCCCcEeehHHHHHHHHHCCCeEEEEeecccC
Confidence 4455554445677788854 456788887766 77889999998765433
No 54
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=23.63 E-value=4e+02 Score=22.62 Aligned_cols=33 Identities=21% Similarity=0.251 Sum_probs=21.8
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 162 CLVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 162 ilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
+++.+.=.|+.-.-..++.+..-++++|++...
T Consensus 37 l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~ 69 (272)
T cd06300 37 FIVTSADGDVAQQIADIRNLIAQGVDAIIINPA 69 (272)
T ss_pred EEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 444555556666677777777777777777653
No 55
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=23.57 E-value=2.7e+02 Score=23.79 Aligned_cols=33 Identities=9% Similarity=0.067 Sum_probs=22.7
Q ss_pred EEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 162 CLVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 162 ilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
+++.+.=.|+.+.-.+++...+-|+++|++.+.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~vDgiii~~~ 69 (274)
T cd06311 37 FILVTASNDTEQQNAQQDLLINRKIDALVILPF 69 (274)
T ss_pred EEEEcCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 444454456666777788888888888888653
No 56
>COG4996 Predicted phosphatase [General function prediction only]
Probab=23.37 E-value=1.2e+02 Score=25.75 Aligned_cols=58 Identities=17% Similarity=0.148 Sum_probs=37.3
Q ss_pred HCCCeEEEcCCCCCCCCcccccccCCCc---cceEEEEeCCHHHHHHHHHHCCceEEEEee
Q 025787 184 LGVQSVHVVSCDSSKRYRENRHVSMGAE---KWLDIELWDAPRECFNVLRSRGYRIATTHV 241 (248)
Q Consensus 184 fGv~~Vil~~~~~dp~~~k~~R~SmGA~---~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l 241 (248)
|.+++-+-..+.-..+++...|+|..++ .-..+..+.+..+.+++++..||-+-.++-
T Consensus 5 ~d~d~t~wdhh~iSsl~pPf~rVs~n~i~Ds~G~ev~L~~~v~~~l~warnsG~i~~~~sW 65 (164)
T COG4996 5 FDADKTLWDHHNISSLEPPFRRVSSNTIEDSKGREVHLFPDVKETLKWARNSGYILGLASW 65 (164)
T ss_pred EeCCCcccccccchhcCCcceecCccceecCCCeEEEEcHHHHHHHHHHHhCCcEEEEeec
Confidence 3344444444433345566677777666 444555568889999999999998765554
No 57
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=23.19 E-value=3.6e+02 Score=22.84 Aligned_cols=29 Identities=14% Similarity=0.069 Sum_probs=17.6
Q ss_pred EeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787 165 VEGLSDFGNVSATFRSADALGVQSVHVVS 193 (248)
Q Consensus 165 LD~I~DP~NlGAIiRSA~AfGv~~Vil~~ 193 (248)
.+.-.|+...-..+++...-++++|++..
T Consensus 35 ~~~~~~~~~~~~~l~~~~~~~vdgii~~~ 63 (273)
T cd06305 35 YDAGGDDAKQADQIDQAIAQKVDAIIIQH 63 (273)
T ss_pred ECCCCCHHHHHHHHHHHHHcCCCEEEEec
Confidence 34444555555666666666777777654
No 58
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.71 E-value=1.4e+02 Score=20.92 Aligned_cols=58 Identities=10% Similarity=0.012 Sum_probs=31.5
Q ss_pred CCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEE--EeCCHHHHHHHHHHCCceE
Q 025787 169 SDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIE--LWDAPRECFNVLRSRGYRI 236 (248)
Q Consensus 169 ~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~--~~~~l~~~L~~Lk~~G~~i 236 (248)
..||.+..+++.-.- |+.=+-+...... ...+. -.+-++ ..+...+.++.|++.||.+
T Consensus 7 dkPG~l~~~~~~i~~-~~nI~~~~~~~~~--------~~~~~-v~v~ie~~~~~~~~~i~~~L~~~G~~~ 66 (68)
T cd04885 7 ERPGALKKFLELLGP-PRNITEFHYRNQG--------GDEAR-VLVGIQVPDREDLAELKERLEALGYPY 66 (68)
T ss_pred CCCCHHHHHHHHhCC-CCcEEEEEEEcCC--------CCceE-EEEEEEeCCHHHHHHHHHHHHHcCCCc
Confidence 457777777665554 5543333222211 11111 122222 2357788999999999975
No 59
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=22.69 E-value=2.4e+02 Score=24.63 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=30.7
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
.+++.++..+ -.+++.+.-.|+...-.+++.+.+.++++|++.+.
T Consensus 20 gi~~~a~~~g-~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~ 64 (288)
T cd01538 20 NFEAALKELG-AEVIVQNANGDPAKQISQIENMIAKGVDVLVIAPV 64 (288)
T ss_pred HHHHHHHHcC-CEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 3444444333 23455566567777888999999999999998763
No 60
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=22.11 E-value=72 Score=30.40 Aligned_cols=34 Identities=26% Similarity=0.168 Sum_probs=28.4
Q ss_pred CCCCCcHHHHH--HHHHHHCCCeEEEcCCCCCCCCc
Q 025787 168 LSDFGNVSATF--RSADALGVQSVHVVSCDSSKRYR 201 (248)
Q Consensus 168 I~DP~NlGAIi--RSA~AfGv~~Vil~~~~~dp~~~ 201 (248)
-+.+.|+|+|+ |.|+++||-+-|+.+-.+|-..+
T Consensus 103 G~haSnLGaiiA~~ia~~~gvPayIVDPvvVDEm~~ 138 (358)
T COG3426 103 GEHASNLGAIIANRIAKALGVPAYIVDPVVVDEMED 138 (358)
T ss_pred CcchhhhhHHHHHHHhhhcCCCeeeeCceehhhcch
Confidence 45678999997 88999999999998888875544
No 61
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=22.03 E-value=76 Score=24.37 Aligned_cols=22 Identities=18% Similarity=0.237 Sum_probs=17.3
Q ss_pred CCHHHHHHHHHHCCceEEEEee
Q 025787 220 DAPRECFNVLRSRGYRIATTHV 241 (248)
Q Consensus 220 ~~l~~~L~~Lk~~G~~ivAt~l 241 (248)
+.+.+..+.|.+.||.++|+..
T Consensus 13 ~~~~~~~~~l~~~G~~l~aT~g 34 (110)
T cd01424 13 PEAVEIAKRLAELGFKLVATEG 34 (110)
T ss_pred hHHHHHHHHHHHCCCEEEEchH
Confidence 3556778888999999999853
No 62
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=21.94 E-value=3.2e+02 Score=23.47 Aligned_cols=67 Identities=10% Similarity=0.147 Sum_probs=40.4
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHH
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNV 228 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~ 228 (248)
.+++.+++....++ ++ +.+|+...-..++.+-..++++|++.....+ ...+.++.
T Consensus 20 gi~~~~~~~g~~~~-~~-~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~-----------------------~~~~~~~~ 74 (289)
T cd01540 20 FAKKAAKEKGFTVV-KI-DVPDGEKVLSAIDNLGAQGAKGFVICVPDVK-----------------------LGPAIVAK 74 (289)
T ss_pred HHHHHHHHcCCEEE-Ec-cCCCHHHHHHHHHHHHHcCCCEEEEccCchh-----------------------hhHHHHHH
Confidence 45555554333333 33 3336666777888888899999998653110 11245677
Q ss_pred HHHCCceEEEEe
Q 025787 229 LRSRGYRIATTH 240 (248)
Q Consensus 229 Lk~~G~~ivAt~ 240 (248)
+++.|+.++..+
T Consensus 75 ~~~~~iPvV~~~ 86 (289)
T cd01540 75 AKAYNMKVVAVD 86 (289)
T ss_pred HHhCCCeEEEec
Confidence 777777777665
No 63
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.89 E-value=3.9e+02 Score=22.69 Aligned_cols=27 Identities=15% Similarity=0.153 Sum_probs=20.0
Q ss_pred CCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 168 LSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 168 I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
-.|+...-.+++....-++++|++.+.
T Consensus 40 ~~~~~~~~~~i~~l~~~~vdgvii~~~ 66 (273)
T cd06310 40 ETDVAGQVNLLENAIARGPDAILLAPT 66 (273)
T ss_pred CCCHHHHHHHHHHHHHhCCCEEEEcCC
Confidence 357777777888777778888888654
No 64
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=21.58 E-value=3e+02 Score=23.56 Aligned_cols=46 Identities=15% Similarity=0.075 Sum_probs=29.7
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
.+++.+.+.+..+.++...-.|+......++....-++++|++.+.
T Consensus 19 gi~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~ 64 (271)
T cd06314 19 GVKAAGKELGVDVEFVVPQQGTVNAQLRMLEDLIAEGVDGIAISPI 64 (271)
T ss_pred HHHHHHHHcCCeEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 3444444433333333334457777888888888889999998764
No 65
>PRK06769 hypothetical protein; Validated
Probab=21.53 E-value=1.4e+02 Score=24.90 Aligned_cols=25 Identities=12% Similarity=0.198 Sum_probs=21.4
Q ss_pred EeCCHHHHHHHHHHCCceEEEEeeC
Q 025787 218 LWDAPRECFNVLRSRGYRIATTHVG 242 (248)
Q Consensus 218 ~~~~l~~~L~~Lk~~G~~ivAt~l~ 242 (248)
.++...+.|++||++||+++.++-.
T Consensus 29 ~~pgv~e~L~~Lk~~G~~l~I~Tn~ 53 (173)
T PRK06769 29 LFPFTKASLQKLKANHIKIFSFTNQ 53 (173)
T ss_pred ECCCHHHHHHHHHHCCCEEEEEECC
Confidence 3588999999999999999888754
No 66
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=21.53 E-value=4.8e+02 Score=22.09 Aligned_cols=45 Identities=16% Similarity=0.094 Sum_probs=30.1
Q ss_pred hHHHHhhc-CCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 149 RFVNVVKN-RSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 149 ~l~evl~~-r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
.+++.++. .. --+++.+.-.|+.+.=..++.+...+++++++.+.
T Consensus 20 gi~~~~~~~~~-~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~ 65 (272)
T cd06301 20 AMKEHAKVLGG-VELQFEDAKNDVATQLSQVENFIAQGVDAIIVVPV 65 (272)
T ss_pred HHHHHHHHcCC-cEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 34555543 22 23444455567777878888888889999998664
No 67
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=21.46 E-value=3.4e+02 Score=23.93 Aligned_cols=45 Identities=18% Similarity=0.108 Sum_probs=27.1
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS 193 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~ 193 (248)
.+++.+++....++++...-.|+...-..++.+..-++++|++.+
T Consensus 20 gi~~~a~~~g~~v~~~~~~~~d~~~~~~~i~~~~~~~~DgiIi~~ 64 (298)
T cd06302 20 GAKEAAKELGVDAIYVGPTTADAAGQVQIIEDLIAQGVDAIAVVP 64 (298)
T ss_pred HHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 344444433333333334445777777788888788888888864
No 68
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=21.36 E-value=5e+02 Score=22.08 Aligned_cols=32 Identities=13% Similarity=0.151 Sum_probs=22.4
Q ss_pred EEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCC
Q 025787 163 LVVEGLSDFGNVSATFRSADALGVQSVHVVSC 194 (248)
Q Consensus 163 lVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~ 194 (248)
++.+.-.|+.+.-..++.+-+.++++|++.+.
T Consensus 34 ~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~ 65 (270)
T cd06308 34 IIADAADDNSKQVADIENFIRQGVDLLIISPN 65 (270)
T ss_pred EEEcCCCCHHHHHHHHHHHHHhCCCEEEEecC
Confidence 33444456777777888888888888888654
No 69
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.09 E-value=3.7e+02 Score=22.68 Aligned_cols=91 Identities=10% Similarity=0.070 Sum_probs=45.7
Q ss_pred hHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccc-----cCC------CccceEEE
Q 025787 149 RFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHV-----SMG------AEKWLDIE 217 (248)
Q Consensus 149 ~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~-----SmG------A~~~v~i~ 217 (248)
.+++.+++.+..+ ++...=.|+...-.+++....-|+++|++.+...+...-...+. ..| ...++...
T Consensus 20 gi~~~~~~~gy~~-~~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~~~~~~~~~~iPvV~i~~~~~~~~~~~V~~d 98 (265)
T cd06290 20 GMERGLNGSGYSP-IIATGHWNQSRELEALELLKSRRVDALILLGGDLPEEEILALAEEIPVLAVGRRVPGPGAASIAVD 98 (265)
T ss_pred HHHHHHHHCCCEE-EEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCChHHHHHHhcCCCEEEECCCcCCCCCCEEEEC
Confidence 3444444443333 33333345555667777888888888888754321100000110 011 01233332
Q ss_pred EeCCHHHHHHHHHHCCceEEEEe
Q 025787 218 LWDAPRECFNVLRSRGYRIATTH 240 (248)
Q Consensus 218 ~~~~l~~~L~~Lk~~G~~ivAt~ 240 (248)
.......+.++|.++|++-++.-
T Consensus 99 ~~~a~~~~~~~l~~~g~~~i~~i 121 (265)
T cd06290 99 NFQGGYLATQHLIDLGHRRIAHI 121 (265)
T ss_pred cHHHHHHHHHHHHHCCCCeEEEE
Confidence 33334567778888898777654
No 70
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=21.00 E-value=1.3e+02 Score=24.76 Aligned_cols=36 Identities=22% Similarity=0.261 Sum_probs=20.6
Q ss_pred CCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCC
Q 025787 158 SYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCD 195 (248)
Q Consensus 158 ~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~ 195 (248)
+.-+.+.+|++.||..+=..+|-+..- +-|++....
T Consensus 55 t~~I~ly~E~~~d~~~f~~~~~~a~~~--KPVv~lk~G 90 (138)
T PF13607_consen 55 TRVIVLYLEGIGDGRRFLEAARRAARR--KPVVVLKAG 90 (138)
T ss_dssp --EEEEEES--S-HHHHHHHHHHHCCC--S-EEEEE--
T ss_pred CCEEEEEccCCCCHHHHHHHHHHHhcC--CCEEEEeCC
Confidence 445789999999997777777766555 666665544
No 71
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=20.63 E-value=2.2e+02 Score=27.10 Aligned_cols=65 Identities=11% Similarity=0.184 Sum_probs=42.7
Q ss_pred chhhhhHHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEE
Q 025787 144 EERKERFVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIEL 218 (248)
Q Consensus 144 ~~R~~~l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~ 218 (248)
.+|...|++++.. .+.+-+.+.+.+..+.-.+++.+...|.+||++=.. |-.|..-.|+ |+.+..
T Consensus 135 ~eRr~~L~~l~~~--~~~i~~~~~~~~~~~~~~~~~~a~~~G~EGIV~Kr~--dS~Y~~Grr~------WlKiK~ 199 (350)
T PRK08224 135 AERRAALEAAAAG--SGPVHLTPATTDPATARRWFEEFEGAGLDGVIAKPL--DGPYQPGKRA------MFKVKH 199 (350)
T ss_pred HHHHHHHHHhcCC--CCcEEEecccCCHHHHHHHHHHHHhCCCcEEEEeCC--CCCcCCCCcC------EEEEcc
Confidence 3777788888753 233555666666667778999999999999987332 3334333332 887754
No 72
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.50 E-value=4.3e+02 Score=22.98 Aligned_cols=44 Identities=7% Similarity=-0.025 Sum_probs=25.5
Q ss_pred HHHHhhcCCCceEEEEeCCCCCCcHHHHHHHHHHHCCCeEEEcC
Q 025787 150 FVNVVKNRSYSVCLVVEGLSDFGNVSATFRSADALGVQSVHVVS 193 (248)
Q Consensus 150 l~evl~~r~~~lilVLD~I~DP~NlGAIiRSA~AfGv~~Vil~~ 193 (248)
+++.+.+.+..++++.+.-.++.-.-..++.+-+-++++|++.+
T Consensus 21 i~~~a~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~dgiii~~ 64 (294)
T cd06316 21 AKDEFAKLGIEVVATTDAQFDPAKQVADIETTISQKPDIIISIP 64 (294)
T ss_pred HHHHHHHcCCEEEEecCCCCCHHHHHHHHHHHHHhCCCEEEEcC
Confidence 44445444333333334434444445677778888899998865
No 73
>PRK15447 putative protease; Provisional
Probab=20.28 E-value=1.7e+02 Score=27.07 Aligned_cols=56 Identities=13% Similarity=0.046 Sum_probs=39.1
Q ss_pred CcHHHHHHHHHHHCCCeEEEcCCCCCCCCcccccccCCCccceEEEEeCCHHHHHHHHHHCCceEEEEeeC
Q 025787 172 GNVSATFRSADALGVQSVHVVSCDSSKRYRENRHVSMGAEKWLDIELWDAPRECFNVLRSRGYRIATTHVG 242 (248)
Q Consensus 172 ~NlGAIiRSA~AfGv~~Vil~~~~~dp~~~k~~R~SmGA~~~v~i~~~~~l~~~L~~Lk~~G~~ivAt~l~ 242 (248)
+|+=+...-.++.|+|+|++.... ++. |. ++ ..+++.+.++.++++|.+||.+.+.
T Consensus 15 ~~~~~~~~~~~~~gaDaVY~g~~~---~~~---R~--------~f-~~~~l~e~v~~~~~~gkkvyva~p~ 70 (301)
T PRK15447 15 ETVRDFYQRAADSPVDIVYLGETV---CSK---RR--------EL-KVGDWLELAERLAAAGKEVVLSTLA 70 (301)
T ss_pred CCHHHHHHHHHcCCCCEEEECCcc---CCC---cc--------CC-CHHHHHHHHHHHHHcCCEEEEEecc
Confidence 566666666777899999997532 222 22 11 2368889999999999999886643
No 74
>PRK10528 multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1; Provisional
Probab=20.13 E-value=2.8e+02 Score=23.23 Aligned_cols=45 Identities=18% Similarity=0.158 Sum_probs=34.0
Q ss_pred hhHHHHhhcCCCceEEEEeCCCCC----------CcHHHHHHHHHHHCCCeEEEc
Q 025787 148 ERFVNVVKNRSYSVCLVVEGLSDF----------GNVSATFRSADALGVQSVHVV 192 (248)
Q Consensus 148 ~~l~evl~~r~~~lilVLD~I~DP----------~NlGAIiRSA~AfGv~~Vil~ 192 (248)
.++++.+...++++++++=|+.|. .|+-.|+.-+.+.|++-+++.
T Consensus 61 ~rl~~~l~~~~pd~Vii~~GtND~~~~~~~~~~~~~l~~li~~~~~~~~~~ill~ 115 (191)
T PRK10528 61 ARLPALLKQHQPRWVLVELGGNDGLRGFPPQQTEQTLRQIIQDVKAANAQPLLMQ 115 (191)
T ss_pred HHHHHHHHhcCCCEEEEEeccCcCccCCCHHHHHHHHHHHHHHHHHcCCCEEEEE
Confidence 355565544356889999999996 688889988888898877663
No 75
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=20.09 E-value=1.8e+02 Score=22.54 Aligned_cols=27 Identities=19% Similarity=0.421 Sum_probs=22.2
Q ss_pred EEEeCCHHHHHHHHHHCCceEEEEeeC
Q 025787 216 IELWDAPRECFNVLRSRGYRIATTHVG 242 (248)
Q Consensus 216 i~~~~~l~~~L~~Lk~~G~~ivAt~l~ 242 (248)
...+++..+.|+.|+++|++++.++-.
T Consensus 76 ~~~~~~~~~~L~~l~~~~~~~~i~Sn~ 102 (176)
T PF13419_consen 76 LQPYPGVRELLERLKAKGIPLVIVSNG 102 (176)
T ss_dssp EEESTTHHHHHHHHHHTTSEEEEEESS
T ss_pred cchhhhhhhhhhhcccccceeEEeecC
Confidence 344689999999999999999887654
Done!