Query psy15410
Match_columns 87
No_of_seqs 108 out of 846
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 20:18:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15410.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15410hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07785 NADH dehydrogenase su 99.5 7.4E-14 1.6E-18 100.1 7.8 70 15-86 66-136 (235)
2 PRK07735 NADH dehydrogenase su 99.4 8.9E-14 1.9E-18 106.0 4.7 68 15-86 277-348 (430)
3 PRK06074 NADH dehydrogenase su 99.3 2.6E-11 5.7E-16 84.4 7.4 71 15-86 3-73 (189)
4 PRK13292 trifunctional NADH de 99.2 2.2E-11 4.7E-16 99.2 6.9 69 17-86 222-295 (788)
5 PRK08491 NADH dehydrogenase su 99.0 1.3E-09 2.8E-14 79.5 6.1 72 9-86 29-100 (263)
6 COG0852 NuoC NADH:ubiquinone o 98.9 8.6E-10 1.9E-14 76.3 3.8 67 16-86 6-72 (176)
7 PRK11742 bifunctional NADH:ubi 98.9 1.9E-09 4E-14 85.5 6.0 66 20-86 2-74 (575)
8 KOG1713|consensus 98.9 1.3E-10 2.9E-15 79.7 -0.9 72 16-87 4-75 (191)
9 CHL00012 ndhJ NADH dehydrogena 98.7 9.1E-09 2E-13 70.2 3.6 54 27-86 14-67 (158)
10 PRK12494 NADH dehydrogenase su 98.3 7.9E-07 1.7E-11 61.3 4.8 63 18-86 18-81 (172)
11 TIGR01961 NuoC_fam NADH (or F4 97.9 1.2E-05 2.6E-10 51.9 3.2 43 42-86 1-43 (121)
12 PF00329 Complex1_30kDa: Respi 97.4 0.00018 3.9E-09 45.3 2.8 30 53-86 1-30 (103)
13 COG3262 HycE Ni,Fe-hydrogenase 86.2 0.72 1.6E-05 31.8 2.5 45 16-60 6-50 (165)
14 PF04446 Thg1: tRNAHis guanyly 82.0 8.2 0.00018 25.6 6.1 44 4-49 40-83 (135)
15 PF02519 Auxin_inducible: Auxi 60.3 8.8 0.00019 24.1 2.2 46 6-58 54-99 (100)
16 TIGR03826 YvyF flagellar opero 60.3 1.6 3.4E-05 29.2 -1.3 37 50-86 31-74 (137)
17 PF03460 NIR_SIR_ferr: Nitrite 57.9 20 0.00042 20.2 3.3 55 4-60 14-68 (69)
18 PF06188 HrpE: HrpE/YscL/FliH 56.2 34 0.00073 23.7 4.8 34 39-72 130-163 (191)
19 PHA01735 hypothetical protein 53.2 12 0.00025 22.6 1.8 25 47-80 31-55 (76)
20 PF02244 Propep_M14: Carboxype 52.5 17 0.00036 20.7 2.4 32 39-71 33-64 (74)
21 smart00591 RWD domain in RING 52.0 45 0.00097 19.8 4.4 58 21-86 3-62 (107)
22 PF02829 3H: 3H domain; Inter 50.8 54 0.0012 20.5 4.7 51 27-77 20-73 (98)
23 PF07288 DUF1447: Protein of u 50.7 22 0.00048 21.2 2.7 47 40-86 18-66 (69)
24 TIGR02491 NrdG anaerobic ribon 50.5 13 0.00028 24.5 1.9 50 9-61 44-93 (154)
25 PLN03183 acetylglucosaminyltra 47.1 13 0.00028 29.1 1.7 23 56-80 166-188 (421)
26 PF05046 Img2: Mitochondrial l 44.3 72 0.0016 19.3 4.7 27 33-60 58-84 (87)
27 COG5503 Uncharacterized conser 43.8 30 0.00065 20.5 2.5 47 40-87 19-67 (69)
28 KOG3054|consensus 40.6 30 0.00064 25.8 2.6 53 7-60 216-271 (299)
29 PF09756 DDRGK: DDRGK domain; 39.4 26 0.00057 24.5 2.1 43 17-61 128-171 (188)
30 PLN03090 auxin-responsive fami 39.2 22 0.00047 22.8 1.6 45 7-58 59-103 (104)
31 COG1334 FlaG Uncharacterized f 36.3 23 0.0005 23.2 1.4 37 27-63 77-113 (120)
32 PF03880 DbpA: DbpA RNA bindin 35.7 89 0.0019 17.9 3.9 41 19-60 18-61 (74)
33 PRK09057 coproporphyrinogen II 34.6 70 0.0015 24.2 3.9 28 31-60 56-83 (380)
34 KOG0537|consensus 34.5 7.8 0.00017 25.3 -1.1 36 39-76 18-53 (124)
35 KOG0799|consensus 34.3 43 0.00092 26.3 2.8 65 13-81 141-207 (439)
36 PRK10597 DNA damage-inducible 34.0 1.1E+02 0.0024 18.6 4.7 46 15-60 21-72 (81)
37 PRK09731 putative general secr 33.0 1.7E+02 0.0037 20.3 6.1 72 13-86 99-170 (178)
38 PF09186 DUF1949: Domain of un 30.3 89 0.0019 16.3 5.3 42 20-61 11-52 (56)
39 COG0023 SUI1 Translation initi 30.2 1.5E+02 0.0033 18.9 4.4 47 12-67 51-97 (104)
40 PRK08898 coproporphyrinogen II 29.3 1.2E+02 0.0027 22.9 4.5 30 30-61 73-102 (394)
41 PRK13347 coproporphyrinogen II 28.3 1.5E+02 0.0032 23.0 4.9 29 31-61 104-132 (453)
42 cd08767 Cdt1_c The C-terminal 28.3 1.6E+02 0.0036 18.9 4.4 43 12-56 80-123 (126)
43 smart00267 GGDEF diguanylate c 27.6 1.4E+02 0.0031 17.8 6.7 37 12-49 57-93 (163)
44 PRK14440 acylphosphatase; Prov 27.5 1.5E+02 0.0032 17.9 4.7 63 20-86 22-89 (90)
45 PF06183 DinI: DinI-like famil 26.5 1.4E+02 0.003 17.2 5.2 30 16-45 10-39 (65)
46 PRK05904 coproporphyrinogen II 26.4 1.5E+02 0.0033 22.3 4.5 28 31-60 57-84 (353)
47 TIGR03365 Bsubt_queE 7-cyano-7 26.3 99 0.0021 21.8 3.4 41 17-61 59-99 (238)
48 PF11387 DUF2795: Protein of u 26.0 22 0.00047 19.0 -0.1 10 72-81 1-10 (44)
49 COG3208 GrsT Predicted thioest 25.7 34 0.00074 25.0 0.9 17 69-85 33-49 (244)
50 PF02682 AHS1: Allophanate hyd 25.2 2.4E+02 0.0052 19.6 7.7 54 6-60 17-72 (202)
51 PRK12338 hypothetical protein; 24.7 1.4E+02 0.003 22.5 4.0 52 27-78 229-289 (319)
52 PRK13667 hypothetical protein; 24.6 99 0.0022 18.4 2.6 47 40-86 19-67 (70)
53 PF05137 PilN: Fimbrial assemb 24.0 1.4E+02 0.0031 16.6 5.5 57 19-76 2-63 (78)
54 PRK06582 coproporphyrinogen II 24.0 2.3E+02 0.005 21.6 5.2 28 31-60 63-90 (390)
55 PLN03219 uncharacterized prote 23.7 47 0.001 21.4 1.2 46 6-57 59-104 (108)
56 PF13394 Fer4_14: 4Fe-4S singl 23.5 14 0.00031 22.6 -1.2 48 12-61 30-77 (119)
57 PF02485 Branch: Core-2/I-Bran 23.5 29 0.00064 24.0 0.2 17 65-81 88-104 (244)
58 COG4866 Uncharacterized conser 23.3 49 0.0011 24.7 1.3 19 45-63 156-174 (294)
59 PRK14424 acylphosphatase; Prov 23.1 1.9E+02 0.0042 17.7 4.7 62 20-86 26-93 (94)
60 PF12993 DUF3877: Domain of un 23.1 2.6E+02 0.0055 19.6 4.7 35 14-51 50-84 (175)
61 PRK06824 translation initiatio 22.4 2.3E+02 0.005 18.4 4.6 44 12-61 66-109 (118)
62 KOG2721|consensus 22.3 2.4E+02 0.0052 20.7 4.6 44 4-49 36-79 (260)
63 PF01037 AsnC_trans_reg: AsnC 22.1 1.5E+02 0.0033 16.1 3.0 22 43-64 2-25 (74)
64 PF08825 E2_bind: E2 binding d 22.0 1.1E+02 0.0023 18.6 2.5 23 45-67 2-25 (84)
65 COG2873 MET17 O-acetylhomoseri 22.0 71 0.0015 25.2 2.0 25 47-79 297-321 (426)
66 PRK05660 HemN family oxidoredu 21.9 2.1E+02 0.0045 21.6 4.5 30 30-61 58-87 (378)
67 PF13647 Glyco_hydro_80: Glyco 21.4 35 0.00077 24.7 0.3 51 12-69 144-194 (308)
68 PF03332 PMM: Eukaryotic phosp 21.0 1.3E+02 0.0028 21.7 3.1 42 17-60 129-172 (220)
No 1
>PRK07785 NADH dehydrogenase subunit C; Provisional
Probab=99.50 E-value=7.4e-14 Score=100.15 Aligned_cols=70 Identities=21% Similarity=0.288 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCC-Cceee
Q psy15410 15 HLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRP-NRFEV 86 (87)
Q Consensus 15 ~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~-~RFeV 86 (87)
-.+.+.+.| +.|+++|.++.+. .+++++.|+++.+.+++++||++++++|++|+||||||||... .||+|
T Consensus 66 ~~~~l~~~~-~~f~~ai~~~~~~-~~~~~~~V~~e~l~~v~~~Lkd~~~l~F~~l~~vtgVDyp~~~g~~f~v 136 (235)
T PRK07785 66 VADRLEEAL-PEFADAIERVVVD-RGELTLHVRREHLVEVAQTLRDDPALRFELCLGVSGVHYPHDTGRELHA 136 (235)
T ss_pred HHHHHHHHH-HhhhhheeEEEEe-CCeEEEEEcHHHHHHHHHHHHhCccCCcceEeeEEEEecCCCCCCEEEE
Confidence 344556666 7899999999888 7999999999999999999999999999999999999999764 68886
No 2
>PRK07735 NADH dehydrogenase subunit C; Validated
Probab=99.44 E-value=8.9e-14 Score=105.96 Aligned_cols=68 Identities=24% Similarity=0.286 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHhcCCceeEEEE----eeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 15 HLVDFGKYCAEILPKYIEKVQI----TSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 15 ~l~~i~~~L~~~fp~~i~~~~~----~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
+|+.+.+.|.+.||+.|..... . .++++|+|+++.|.+||.|||+++.++|++|+||||||||. ||+|
T Consensus 277 ~l~~l~~~L~e~fg~~i~~~~~i~~~~-~d~lti~V~~e~L~eV~~~Lrd~~~l~Fd~LsdLtGVDy~~---rFeV 348 (430)
T PRK07735 277 YLNKYVEVIKEKLGEDVLEDSYINKLS-KDVPTLVVEPEKYYEVAELLRFHEQLAFDYLSELHGTDFVT---HMEV 348 (430)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhcccc-CCceEEEEcHHHHHHHHHHHHhCcccCCCeeeeEEeEecCC---cEEE
Confidence 5888999999999998876543 3 58999999999999999999999999999999999999984 8987
No 3
>PRK06074 NADH dehydrogenase subunit C; Provisional
Probab=99.25 E-value=2.6e-11 Score=84.44 Aligned_cols=71 Identities=38% Similarity=0.582 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 15 HLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 15 ~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
..+++.+.|+++||+.+.+.... .+.+++.|+++.+.+++.+||++.+++|.+|+++||||||+.+++|+|
T Consensus 3 ~~~~~~~~l~~~f~~~~~~~~~~-~~~~~~~v~~~~l~~v~~~L~~~~~~~f~~L~~l~avD~~~~~~~f~v 73 (189)
T PRK06074 3 KLEELVAKLLEKLPDAIGKVTVA-FGELTLKVPAEKILEVLTFLRDDPELRFEQLIDLTGVDYPERGKRFEV 73 (189)
T ss_pred cHHHHHHHHHHHccccEEEEEEe-CCeEEEEEcHHHHHHHHHHHHhCcccCCCeEEEEEEEecCCCCCcEEE
Confidence 35778999999999999888776 689999999999999999999986689999999999999987778886
No 4
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional
Probab=99.23 E-value=2.2e-11 Score=99.19 Aligned_cols=69 Identities=25% Similarity=0.237 Sum_probs=60.2
Q ss_pred HHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCC-----CCceee
Q psy15410 17 VDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSR-----PNRFEV 86 (87)
Q Consensus 17 ~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~-----~~RFeV 86 (87)
.++.+.|+++||+.+...... .+++++.|+++.+.++++|||++++++|++|+|+||||||.+ .+||+|
T Consensus 222 ~~l~~~l~~~f~~~v~~~~~~-~~~~~~~v~~e~l~~v~~~Lk~~~~~~f~~L~ditaVD~~~~~~~~~~~~f~v 295 (788)
T PRK13292 222 FGLAGELEGAFGDDVRLDEGA-TDMLTYRCPPELVPEVLRHLKKRASSPFRRLEDLAAVDESCRRDREKFPDFTV 295 (788)
T ss_pred HHHHHHHHHHcccceEeeeec-CCcEEEEEcHHHHHHHHHHHHhCcCCCCceeeeEEEEeCCcccccCcCCcEEE
Confidence 347888999999877655555 689999999999999999999999999999999999999863 468987
No 5
>PRK08491 NADH dehydrogenase subunit C; Provisional
Probab=98.97 E-value=1.3e-09 Score=79.47 Aligned_cols=72 Identities=21% Similarity=0.187 Sum_probs=58.0
Q ss_pred CHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 9 DEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 9 ~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
.++..+.+....+.|...+ .|...... .+++++.|+++.+.+++.+|| +++|++|+++|||||+...++|+|
T Consensus 29 ~~~~~~~~~~~l~~l~~~~--~i~~~~~~-~~~~~i~V~~e~l~~V~~~Lk---~~gf~~L~~itaVD~~~~~~~FeV 100 (263)
T PRK08491 29 SYVEGSVFEKDLNHLSYKV--EILESYIE-LDQAVIWIKKDDNFKVLKILK---HLGYECLSEMSAIDFLAKKGGFEV 100 (263)
T ss_pred cccchhHHHHHHHHhcCCe--EEEEEEee-CCcEEEEEcHHHHHHHHHHHH---HcCCCeEEEEEeEecCCCCCcEEE
Confidence 3444556666666666665 35555555 799999999999999999999 488999999999999988889987
No 6
>COG0852 NuoC NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]
Probab=98.93 E-value=8.6e-10 Score=76.33 Aligned_cols=67 Identities=36% Similarity=0.563 Sum_probs=57.9
Q ss_pred HHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 16 LVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 16 l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
+.+....+.+.++..+...... .+++++.+.++.+..+|++||++. |.+|.|+||||||++.+||+|
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~v~~~~~~~~l~~Lk~~~---f~~l~d~~gvD~~~~~~~Fev 72 (176)
T COG0852 6 LAELLERLLAELSTVIETVVVA-EGELTLKVPPDELIDVLKALKDEG---FDHLLDLTGVDYPQETERFEV 72 (176)
T ss_pred hHHHHHhhhhhhhheeeeecee-eeeEEEecCHHHHHHHHHHHhhhh---HHHHHHhhcccccccCCcEEE
Confidence 4556677777888777777665 679999999999999999999975 999999999999999999987
No 7
>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional
Probab=98.93 E-value=1.9e-09 Score=85.53 Aligned_cols=66 Identities=24% Similarity=0.251 Sum_probs=54.8
Q ss_pred HHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCC-------CCceee
Q psy15410 20 GKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSR-------PNRFEV 86 (87)
Q Consensus 20 ~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~-------~~RFeV 86 (87)
++.|+++||+++........++++++|+++.+.+++.+||+ .+++|++|+|+|||||+.+ .+||+|
T Consensus 2 ~~~l~~~f~~~~~~~~~~~~~~~~~~v~~e~l~~v~~~Lk~-~~~~f~~L~~lt~vD~~~~~~~~~~~~~~fev 74 (575)
T PRK11742 2 IGELRNRFGPDAFTVQATRTGIPVVWVKREQLLEVLRFLRK-LPKPYVMLFDLHGIDERLRTHREGLPAADFTV 74 (575)
T ss_pred hHHHHhhcccceeeeEeccCCcEEEEEcHHHHHHHHHHHhc-cCCCCceEEEEEEEecCcccccccCCCCceEE
Confidence 46789999998776554435889999999999999999994 4679999999999999842 457886
No 8
>KOG1713|consensus
Probab=98.91 E-value=1.3e-10 Score=79.73 Aligned_cols=72 Identities=64% Similarity=1.003 Sum_probs=64.2
Q ss_pred HHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceeeC
Q psy15410 16 LVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEVD 87 (87)
Q Consensus 16 l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV~ 87 (87)
+.....+..+.+|+.++++.....+++.+.+++++.++|+.|||.+..++|+.+.||||||-|.+++||||.
T Consensus 4 ~~~fg~ya~e~Lpk~~~k~~~~~~~~lei~~~~~~~i~vl~flk~h~y~r~q~~~Diagvdvp~rk~rfevv 75 (191)
T KOG1713|consen 4 LTLFGKYAAECLPKRVQKVQYQAGDELEILIHPDGVIPVLLFLKGHTYARFQNLYDIAGVDVPTRKNRFEVV 75 (191)
T ss_pred hhHHHHHHHHhhhHHHHhhhhhcccceeeecCCCceeEEEeeeecccceeeeEeEeecCCCcccccceeEEe
Confidence 344567788889998888877656889999999999999999999999999999999999999999999983
No 9
>CHL00012 ndhJ NADH dehydrogenase subunit J
Probab=98.74 E-value=9.1e-09 Score=70.21 Aligned_cols=54 Identities=17% Similarity=0.043 Sum_probs=44.4
Q ss_pred cCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 27 LPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 27 fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
|-..+.+++. .++++++|+++.+.+++.+||+ .+|++|+|+|||||+. ++||+|
T Consensus 14 ~~~~~~~~~~--~~~~~~~V~~~~l~~v~~~Lk~---~gf~~L~~lt~vD~~~-~~~fev 67 (158)
T CHL00012 14 LVHRSLGFDY--QGIETLQIKPEDWHSIAVILYV---YGYNYLRSQCAYDVAP-GGLLAS 67 (158)
T ss_pred CCcccCCCCC--CCCEEEEEcHHHHHHHHHHHHH---cCCCceeEEEEEEcCC-CCeEEE
Confidence 3344555444 4899999999999999999995 6899999999999976 567987
No 10
>PRK12494 NADH dehydrogenase subunit J; Provisional
Probab=98.35 E-value=7.9e-07 Score=61.27 Aligned_cols=63 Identities=13% Similarity=0.040 Sum_probs=54.1
Q ss_pred HHHHHHHHh-cCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 18 DFGKYCAEI-LPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 18 ~i~~~L~~~-fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
.+++.|++. |+..+..... .+...+.|+++.+.+++++||+ .+|++|++++||||+. ++||++
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~V~~~~l~~v~~~L~~---~g~~~l~~~~~vD~~~-~~~~~v 81 (172)
T PRK12494 18 PVSQWLTENGFEHESLGPDH--LGVEIIKVEPDFLLPIATALYA---YGFNYLQCQGGYDEGP-GKELVS 81 (172)
T ss_pred hHHHHHHHcCCCcccccccc--CCCEEEEEcHHHHHHHHHHHHH---CCCCEEEEEEeEccCC-CCEEEE
Confidence 477899999 9998887764 5889999999999999999996 4799999999999975 557765
No 11
>TIGR01961 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C. This model describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This model excludes the NAD(P)H and plastoquinone-dependent form of chloroplasts and
Probab=97.90 E-value=1.2e-05 Score=51.92 Aligned_cols=43 Identities=44% Similarity=0.688 Sum_probs=36.8
Q ss_pred EEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 42 LELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 42 l~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
+++.|+++.+.+++..||++ ..+|.+|++++|+|+|+.. +|++
T Consensus 1 ~~~~v~~~~l~~v~~~l~~~-~~~~~~l~~i~a~D~~~~~-~~~~ 43 (121)
T TIGR01961 1 LVIWIKKEQLLEVLTFLKDP-ALGFELLTDVSGVDYPKEK-RFEV 43 (121)
T ss_pred CEEEEeHHHHHHHHHHHHhc-cCCCCeEeEEEEEecCCCC-eEEE
Confidence 36789999999999999976 6789999999999998654 5765
No 12
>PF00329 Complex1_30kDa: Respiratory-chain NADH dehydrogenase, 30 Kd subunit; InterPro: IPR001268 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. The 30 kDa subunit from NADH:ubiquinone oxidoreductase is found in both eukaryotes and prokaryotes. In mammals and in Neurospora crassa, it is nuclear-encoded as a precursor form with a transit peptide, while in Paramecium (protein P1), in the Dictyostelium discoideum (Slime mold) it is mitochondrial-encoded and it is chloroplast-encoded in various higher plants. It is also present in bacteria.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0055114 oxidation-reduction process; PDB: 2YBB_5 3IAS_E 2FUG_E 3I9V_5 3M9S_E 3IAM_5 3MCR_A.
Probab=97.36 E-value=0.00018 Score=45.25 Aligned_cols=30 Identities=47% Similarity=0.658 Sum_probs=23.6
Q ss_pred HHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 53 PVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 53 ~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
+++++||++ +|..|+++||+|+++++ +|+|
T Consensus 1 e~~~~L~~~---~~~~l~~i~~~D~~~~~-~~~v 30 (103)
T PF00329_consen 1 EVAKFLKDE---GGARLVTITAVDYPEEG-RFEV 30 (103)
T ss_dssp -HHHHHHHT---T--EEEEEEEEE-TTST-SEEE
T ss_pred CHHHHHHHC---CCCeEEEEEEEECCCCC-eEEE
Confidence 589999996 79999999999999987 7886
No 13
>COG3262 HycE Ni,Fe-hydrogenase III component G [Energy production and conversion]
Probab=86.23 E-value=0.72 Score=31.77 Aligned_cols=45 Identities=16% Similarity=0.106 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 16 LVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 16 l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
-+.+...|.++||+.|.+-.-....+++++|..+.+.++++||+.
T Consensus 6 ~e~~~~el~~~fpg~i~~e~~~~~~~~~~~V~~~~l~~~~e~l~~ 50 (165)
T COG3262 6 GEEILAELNERFPGVVLDEERQTRSQLTVTVKREYLPDVVEFLYY 50 (165)
T ss_pred HHHHHHHHHHhCcchhhhhhhhchhheeEEeeHhhhHHHHHHHHH
Confidence 346778899999996654443336899999999999999999995
No 14
>PF04446 Thg1: tRNAHis guanylyltransferase; InterPro: IPR007537 The Thg1 protein from Saccharomyces cerevisiae (Baker's yeast) is responsible for adding a GMP residue to the 5' end of tRNA His [].; PDB: 3OTE_A 3OTC_A 3OTD_A 3OTB_A.
Probab=81.97 E-value=8.2 Score=25.59 Aligned_cols=44 Identities=20% Similarity=0.234 Sum_probs=33.7
Q ss_pred ccCCCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCC
Q psy15410 4 IRKPIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPE 49 (87)
Q Consensus 4 ~~~~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e 49 (87)
..||-|.-..+.+.+.+..|.+.+++.+..... .+|.++...+.
T Consensus 40 f~KP~D~r~~~~M~~aa~~l~~~~~~~~~aY~~--SDEiSfvf~~~ 83 (135)
T PF04446_consen 40 FEKPNDERFLKAMNEAAKALMEEFPDIVLAYGQ--SDEISFVFRKS 83 (135)
T ss_dssp --SS--HHHHHHHHHHHHHHHHHSSSEEEEEEE--TTEEEEEE-TT
T ss_pred CCCCCCHHHHHHHHHHHHHHHHhCCCcEEEEEc--CCeeEEEECCC
Confidence 469999999999999999999999986666665 49999998763
No 15
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=60.31 E-value=8.8 Score=24.14 Aligned_cols=46 Identities=11% Similarity=0.008 Sum_probs=35.8
Q ss_pred CCCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHh
Q psy15410 6 KPIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFL 58 (87)
Q Consensus 6 ~~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fL 58 (87)
-|++++++-.+.++.+.-.+.||-. . .|.++|-++...+..+++.|
T Consensus 54 vp~~~L~hp~f~~LL~~aeeEfG~~------~-~G~l~iPC~~~~Fe~~l~~l 99 (100)
T PF02519_consen 54 VPVSYLNHPLFQELLEQAEEEFGFD------Q-DGPLTIPCDVVLFEHLLWLL 99 (100)
T ss_pred echHHcCchhHHHHHHHHhhhcCcC------C-CCcEEeeCCHHHHHHHHHHh
Confidence 4889999998999888888888731 1 46688888888777777766
No 16
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=60.26 E-value=1.6 Score=29.21 Aligned_cols=37 Identities=24% Similarity=0.453 Sum_probs=27.2
Q ss_pred ChHHHHHHhhcCcc--CCccccccceeeeCCC-----CCCceee
Q psy15410 50 GVVPVLQFLKDHHT--AQFVSLVDIAGMDVPS-----RPNRFEV 86 (87)
Q Consensus 50 ~l~~vl~fLKdd~~--l~F~~L~DItgVDyp~-----~~~RFeV 86 (87)
..-.|-.|||++|+ +.-..+++-|||+... +++|+++
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 45678889999988 7778888888888642 4455554
No 17
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=57.85 E-value=20 Score=20.16 Aligned_cols=55 Identities=16% Similarity=0.130 Sum_probs=35.5
Q ss_pred ccCCCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 4 IRKPIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 4 ~~~~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
++-|--.++.+.+..+++ +.++++.....++.. .+-....|+.+++.++.+.|++
T Consensus 14 ~~~~~G~i~~~~l~~la~-ia~~yg~~~irlT~~-Q~l~l~~v~~~~~~~i~~~L~~ 68 (69)
T PF03460_consen 14 IRIPGGRISAEQLRALAE-IAEKYGDGEIRLTTR-QNLQLRGVPEENLPAIFEELKE 68 (69)
T ss_dssp EB-GGGEEEHHHHHHHHH-HHHHHSTSEEEEETT-SCEEEEEEEGGGHHHHHHHHHH
T ss_pred EeCCCEEECHHHHHHHHH-HHHHhCCCeEEECCC-CeEEEeCCCHHHHHHHHHHHHc
Confidence 444555566666666655 446788544455544 3444446999999999999875
No 18
>PF06188 HrpE: HrpE/YscL/FliH and V-type ATPase subunit E; InterPro: IPR009335 This family consists of several bacterial HrpE proteins, which are believed to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) []. This family also includes V-type proton ATPase subunit E proteins. This subunit appears to form a tight interaction with subunit G in the F0 complex. Subunits E and G may act together as stators to prevent certain subunits from rotating with the central rotary element []. PF01991 from PFAM also contains V-type ATPase subunit E proteins. There is an evolutionary link between type III secretion systems and membrane-associated proton translocating ATPases [].
Probab=56.21 E-value=34 Score=23.72 Aligned_cols=34 Identities=21% Similarity=0.267 Sum_probs=28.7
Q ss_pred CCeEEEEEcCCChHHHHHHhhcCccCCccccccc
Q psy15410 39 GDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDI 72 (87)
Q Consensus 39 ~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DI 72 (87)
.++.+++++|+.+-+|..+|.+++...++.=.|=
T Consensus 130 ~~~~tL~~hP~~~~~V~~~L~~~~~~~w~l~~D~ 163 (191)
T PF06188_consen 130 ESEATLRCHPDQLEEVAAWLAEHPALHWQLQADE 163 (191)
T ss_pred ccceEEEECHHHHHHHHHHHHhCCCcceeeccCC
Confidence 5789999999999999999999987776665543
No 19
>PHA01735 hypothetical protein
Probab=53.20 E-value=12 Score=22.58 Aligned_cols=25 Identities=24% Similarity=0.425 Sum_probs=20.1
Q ss_pred cCCChHHHHHHhhcCccCCccccccceeeeCCCC
Q psy15410 47 IPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSR 80 (87)
Q Consensus 47 ~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~ 80 (87)
....+...+.|||++ |||||=++..
T Consensus 31 TtaDL~AA~d~Lk~N---------dItgv~~~gs 55 (76)
T PHA01735 31 TTADLRAACDWLKSN---------DITGVAVDGS 55 (76)
T ss_pred cHHHHHHHHHHHHHC---------CCceeeCCCC
Confidence 356789999999996 7899988653
No 20
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=52.54 E-value=17 Score=20.71 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=25.9
Q ss_pred CCeEEEEEcCCChHHHHHHhhcCccCCcccccc
Q psy15410 39 GDELELLIIPEGVVPVLQFLKDHHTAQFVSLVD 71 (87)
Q Consensus 39 ~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~D 71 (87)
++..-+.|+++.+..+..+|+.. +..|+.+++
T Consensus 33 ~~~~dv~V~p~~~~~f~~~L~~~-~i~~~v~i~ 64 (74)
T PF02244_consen 33 GRPVDVMVPPEKLEEFEELLKEH-GIEYEVLIE 64 (74)
T ss_dssp TSEEEEEEEGGGHHHHHHHHHHT-T-EEEEEES
T ss_pred CCeEEEEECHHHHHHHHHHHHHC-CCcEEEEeH
Confidence 47789999999999999999976 677776653
No 21
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=51.99 E-value=45 Score=19.77 Aligned_cols=58 Identities=12% Similarity=0.231 Sum_probs=32.2
Q ss_pred HHHHHhcCCceeEEEEeeCC--eEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 21 KYCAEILPKYIEKVQITSGD--ELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 21 ~~L~~~fp~~i~~~~~~~~~--el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
+.|++.||+........ .. ..++.+....- --.+....+.+...... +||...+.+.+
T Consensus 3 eaL~sIy~~~~~~~~~~-~~~~~~~i~l~~~~~------~~~~~~~~~~l~~~~p~-~YP~~~P~i~~ 62 (107)
T smart00591 3 EALESIYPEDFEVIDED-ARIPEITIKLSPSSD------EGEDQYVSLTLQVKLPE-NYPDEAPPISL 62 (107)
T ss_pred HHHHhhccceeEEecCC-CCccEEEEEEecCCC------CCCccceEEEEEEECCC-CCCCCCCCeEE
Confidence 57899999866554443 23 46666654431 01112233444445544 89987776654
No 22
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=50.85 E-value=54 Score=20.54 Aligned_cols=51 Identities=12% Similarity=0.064 Sum_probs=33.3
Q ss_pred cCCceeEEEEe--eCCeEEEEEcCCChHHHHHHhhcCccCCcccccccee-eeC
Q psy15410 27 LPKYIEKVQIT--SGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAG-MDV 77 (87)
Q Consensus 27 fp~~i~~~~~~--~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItg-VDy 77 (87)
.|..|.++.+. ..|+++-.++-.+-.++-+|++.-...+-..|..+|+ |+|
T Consensus 20 ~Gg~V~DV~veHp~YG~i~~~L~i~sr~Dv~~Fi~~l~~~~~~~Ls~LT~GvH~ 73 (98)
T PF02829_consen 20 NGGRVLDVIVEHPVYGEITGNLNISSRRDVDKFIEKLEKSKAKPLSSLTGGVHY 73 (98)
T ss_dssp TT-EEEEEEEEETTTEEEEEEEEE-SHHHHHHHHHHHHH--S--STTGGGGEEE
T ss_pred CCCEEEEEEEeCCCCcEEEEEEecCCHHHHHHHHHHHhccCCcchHHhcCCEee
Confidence 78888887765 2478888887777777777777555556778888887 776
No 23
>PF07288 DUF1447: Protein of unknown function (DUF1447); InterPro: IPR009907 This family consists of several bacterial proteins of around 70 residues in length. The function of this family is unknown.
Probab=50.73 E-value=22 Score=21.20 Aligned_cols=47 Identities=15% Similarity=0.261 Sum_probs=38.4
Q ss_pred CeEEEEEcCCChHHHHHHhhcCccCCccccccceeee--CCCCCCceee
Q psy15410 40 DELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMD--VPSRPNRFEV 86 (87)
Q Consensus 40 ~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVD--yp~~~~RFeV 86 (87)
+..++++.++.-.++-+.|++++...-.+..-++|-+ |-...+-|.|
T Consensus 18 ~T~sLYvEa~s~~evR~~ve~~t~yNIEfI~~L~~~~LeYEk~~~~fkl 66 (69)
T PF07288_consen 18 NTQSLYVEAESEVEVRKLVEDNTPYNIEFIQPLSGKHLEYEKQNPDFKL 66 (69)
T ss_pred cceEEEEEcCCHHHHHHHHHhCCCcCEEEEeeccchHHHHhhcCCCeeE
Confidence 5678999999999999999999888888888888755 5555555665
No 24
>TIGR02491 NrdG anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin ) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer.
Probab=50.49 E-value=13 Score=24.54 Aligned_cols=50 Identities=12% Similarity=0.179 Sum_probs=36.3
Q ss_pred CHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 9 DEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 9 ~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
.+++.+..+++.+.|... + .+..+... +||+.+.-+.+.+.++++.+|..
T Consensus 44 ~~~~~~~~~~i~~~l~~~-~-~~~gVt~s-GGEPllq~~~~~l~~ll~~~k~~ 93 (154)
T TIGR02491 44 KEFTEALEKEIIRDLNDN-P-LIDGLTLS-GGDPLYPRNVEELIELVKKIKAE 93 (154)
T ss_pred CcCCHHHHHHHHHHHHhc-C-CcCeEEEe-ChhhCCCCCHHHHHHHHHHHHHh
Confidence 355666677777777654 3 34567777 99998765558999999999974
No 25
>PLN03183 acetylglucosaminyltransferase family protein; Provisional
Probab=47.10 E-value=13 Score=29.14 Aligned_cols=23 Identities=17% Similarity=0.322 Sum_probs=17.9
Q ss_pred HHhhcCccCCccccccceeeeCCCC
Q psy15410 56 QFLKDHHTAQFVSLVDIAGMDVPSR 80 (87)
Q Consensus 56 ~fLKdd~~l~F~~L~DItgVDyp~~ 80 (87)
.-|+.. ..+++++.++|.|||-.
T Consensus 166 ~LL~~~--~~WDyfinLSGsDyPLk 188 (421)
T PLN03183 166 ILLKRS--KDWDWFINLSASDYPLV 188 (421)
T ss_pred HHHhhC--CCCCEEEEccCCccccc
Confidence 445654 56999999999999943
No 26
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=44.31 E-value=72 Score=19.32 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=20.2
Q ss_pred EEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 33 KVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 33 ~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
.+.+. ...-.|.|.-++..+|-+||.+
T Consensus 58 ~~~V~-~~~g~i~IkG~~~~~Vk~wL~~ 84 (87)
T PF05046_consen 58 DVRVN-ELTGHIEIKGDHVEEVKKWLLE 84 (87)
T ss_pred ceEEe-ecCCEEEEcCccHHHHHHHHHH
Confidence 34444 3456688999999999999975
No 27
>COG5503 Uncharacterized conserved small protein [Function unknown]
Probab=43.79 E-value=30 Score=20.54 Aligned_cols=47 Identities=19% Similarity=0.277 Sum_probs=36.5
Q ss_pred CeEEEEEcCCChHHHHHHhhcCccCCcccccccee--eeCCCCCCceeeC
Q psy15410 40 DELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAG--MDVPSRPNRFEVD 87 (87)
Q Consensus 40 ~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItg--VDyp~~~~RFeV~ 87 (87)
..-+++++.+.-.++=+.|+++ ...-.+..-++| +||-...+-|+|.
T Consensus 19 ~T~sLYle~~se~~vR~ll~e~-~yniEFI~~lsd~~L~YEket~~F~v~ 67 (69)
T COG5503 19 TTDSLYLEADSETKVRQLLKEN-NYNIEFITPLSDAHLDYEKETEVFEVT 67 (69)
T ss_pred ccceEEEechhHHHHHHHHhcc-CcceEEEeecchhhhhhhhhcCceEEE
Confidence 3456788888888899999998 677778777776 4687777778873
No 28
>KOG3054|consensus
Probab=40.62 E-value=30 Score=25.78 Aligned_cols=53 Identities=19% Similarity=0.221 Sum_probs=33.6
Q ss_pred CCCHHHhh-H--HHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 7 PIDEVARS-H--LVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 7 ~~~~~~~~-~--l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
|++.++.+ . -...+.+|+.-+.++...-... ...-.|||..+.+..|++|.|-
T Consensus 216 ~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmD-DRGKfIYIS~eEl~AVAkfIkq 271 (299)
T KOG3054|consen 216 PLEDLASEFGLRTQDSINRIQELLAEGLLTGVMD-DRGKFIYISMEELAAVAKFIKQ 271 (299)
T ss_pred eHHHHHHHhCccHHHHHHHHHHHHHhhhheeeec-CCCceEEecHHHHHHHHHHHHH
Confidence 45555443 1 1334456666666554444444 3456799999999999999985
No 29
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=39.40 E-value=26 Score=24.53 Aligned_cols=43 Identities=19% Similarity=0.122 Sum_probs=14.3
Q ss_pred HHHHHHHHHhcC-CceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 17 VDFGKYCAEILP-KYIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 17 ~~i~~~L~~~fp-~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
.++.++|+.... +.+.++... .| -.|+|.++.+..|+.|++..
T Consensus 128 ~~~i~ri~~L~~~g~ltGv~Dd-rG-kfIyIs~eE~~~va~fi~~r 171 (188)
T PF09756_consen 128 QDVINRIQELEAEGRLTGVIDD-RG-KFIYISEEEMEAVAKFIKQR 171 (188)
T ss_dssp HHHHHHHHHHHHHSSS-EEE-T-T---EEE----------------
T ss_pred HHHHHHHHHHHHCCCceeeEcC-CC-CeEEecHHHHHHHHHHHHHc
Confidence 445566666665 445666655 45 77999999999999999975
No 30
>PLN03090 auxin-responsive family protein; Provisional
Probab=39.17 E-value=22 Score=22.77 Aligned_cols=45 Identities=9% Similarity=0.007 Sum_probs=34.1
Q ss_pred CCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHh
Q psy15410 7 PIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFL 58 (87)
Q Consensus 7 ~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fL 58 (87)
|++++++-.+.++.+.-.+.||-. . .|.++|-++.+.+..++..+
T Consensus 59 p~~~L~hP~F~~LL~~aeeEfGf~------~-~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 59 PISFLTHPEFQSLLQQAEEEFGFD------H-DMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred EHHHcCCHHHHHHHHHHHHHhCCC------C-CCcEEEeCCHHHHHHHHHHh
Confidence 788888888888888888888731 2 35688878887777777665
No 31
>COG1334 FlaG Uncharacterized flagellar protein FlaG [Cell motility and secretion]
Probab=36.33 E-value=23 Score=23.23 Aligned_cols=37 Identities=19% Similarity=0.175 Sum_probs=25.6
Q ss_pred cCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCcc
Q psy15410 27 LPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHT 63 (87)
Q Consensus 27 fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~ 63 (87)
++..+.++.....|+..=.|+++.+.++++.|++.-+
T Consensus 77 lg~~vVkI~d~~TgeVIRqIPpee~L~l~~r~~d~~g 113 (120)
T COG1334 77 LGELVVKIIDKDTGEVIRQIPPEEALELAARMRDVIG 113 (120)
T ss_pred cCcEEEEEEECCCCcchhhCChHHHHHHHHHHHHhhh
Confidence 4444555444435666667899999999999997544
No 32
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=35.66 E-value=89 Score=17.94 Aligned_cols=41 Identities=15% Similarity=0.017 Sum_probs=28.8
Q ss_pred HHHHHHHhc---CCceeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 19 FGKYCAEIL---PKYIEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 19 i~~~L~~~f---p~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
+...|.+.. ++.|-.+.+. ...-.+.|+++....++..|+.
T Consensus 18 iv~~i~~~~gi~~~~IG~I~I~-~~~S~vev~~~~a~~v~~~l~~ 61 (74)
T PF03880_consen 18 IVGAICNEAGIPGRDIGRIDIF-DNFSFVEVPEEVAEKVLEALNG 61 (74)
T ss_dssp HHHHHHTCTTB-GGGEEEEEE--SS-EEEEE-TT-HHHHHHHHTT
T ss_pred HHHHHHhccCCCHHhEEEEEEe-eeEEEEEECHHHHHHHHHHhcC
Confidence 444555553 3678888888 6889999999999999999985
No 33
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=34.55 E-value=70 Score=24.15 Aligned_cols=28 Identities=21% Similarity=0.391 Sum_probs=14.8
Q ss_pred eeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 31 IEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 31 i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
+..+... +|.++ .++++.+..++..++.
T Consensus 56 i~tiy~G-GGTPs-~l~~~~L~~ll~~i~~ 83 (380)
T PRK09057 56 LTSIFFG-GGTPS-LMQPETVAALLDAIAR 83 (380)
T ss_pred cCeEEeC-CCccc-cCCHHHHHHHHHHHHH
Confidence 4444443 34443 3556666666666665
No 34
>KOG0537|consensus
Probab=34.49 E-value=7.8 Score=25.31 Aligned_cols=36 Identities=31% Similarity=0.413 Sum_probs=29.9
Q ss_pred CCeEEEEEcCCChHHHHHHhhcCccCCccccccceeee
Q psy15410 39 GDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMD 76 (87)
Q Consensus 39 ~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVD 76 (87)
.+..+|.|+- ++.+|-.||.+||+-. +.|.+..|-|
T Consensus 18 ~~d~Wvii~g-kVYDvT~Fl~eHPGG~-~vLl~~AGkD 53 (124)
T KOG0537|consen 18 KDDCWVIIHG-KVYDVTSFLDEHPGGE-DVLLEYAGKD 53 (124)
T ss_pred CCCeEEEECC-EEEeccchhhhCCChH-HHHHHHhchh
Confidence 4678888877 9999999999999854 8888777766
No 35
>KOG0799|consensus
Probab=34.32 E-value=43 Score=26.26 Aligned_cols=65 Identities=14% Similarity=0.064 Sum_probs=39.6
Q ss_pred hhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCcc--CCccccccceeeeCCCCC
Q psy15410 13 RSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHT--AQFVSLVDIAGMDVPSRP 81 (87)
Q Consensus 13 ~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~--l~F~~L~DItgVDyp~~~ 81 (87)
........+.|.+.||..+... ..+.+.+-.++.+...+.-|++--+ ..-++++.++|.|||-+.
T Consensus 141 ~~~fk~~~~~L~~cf~NV~v~~----k~~~v~~~G~s~l~a~l~c~~~Ll~~~~~W~yfinLs~~D~PlkT 207 (439)
T KOG0799|consen 141 PPEFRVAMQQLASCFPNVIVLP----KRESVTYGGHSILAAHLNCLADLLKLSGDWDYFINLSNSDYPLKT 207 (439)
T ss_pred CHHHHHHHHHHHhcCCceEEec----cccceecCCchhhHHHHHHHHHHHhcCCCCceeeeccCCCcccCC
Confidence 3334455667888888643211 3445555555555555555444322 348999999999999654
No 36
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=34.04 E-value=1.1e+02 Score=18.59 Aligned_cols=46 Identities=11% Similarity=0.089 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCce--eEEEEeeCCeEEE-EE---cCCChHHHHHHhhc
Q psy15410 15 HLVDFGKYCAEILPKYI--EKVQITSGDELEL-LI---IPEGVVPVLQFLKD 60 (87)
Q Consensus 15 ~l~~i~~~L~~~fp~~i--~~~~~~~~~el~i-~i---~~e~l~~vl~fLKd 60 (87)
...++..+|..+||+.. ..+.....+.+++ -. +++.+-++++-.-+
T Consensus 21 L~~EL~kRl~~~fPd~~~~v~Vr~~s~n~lsv~g~~k~dK~~i~eiLqE~we 72 (81)
T PRK10597 21 LAGELSRRIQYAFPDNEGHVSVRYAAANNLSVIGATKEDKDRISEILQETWE 72 (81)
T ss_pred HHHHHHHHHHhhCCCCCccEEEeecCCCceEecCCCcchHHHHHHHHHHHHh
Confidence 34778999999999975 3333221344544 11 33455555554443
No 37
>PRK09731 putative general secretion pathway protein YghD; Provisional
Probab=32.97 E-value=1.7e+02 Score=20.32 Aligned_cols=72 Identities=14% Similarity=0.229 Sum_probs=52.2
Q ss_pred hhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCccccccceeeeCCCCCCceee
Q psy15410 13 RSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86 (87)
Q Consensus 13 ~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~~~~RFeV 86 (87)
..+|..+...=.+.++-.+.-+... ++.+.+.+++-.+-.++.+|-+= +-++..-+.-..||..+.++.-+|
T Consensus 99 ~~sL~~~V~~SA~~~gL~i~R~QP~-Ge~vQVwld~v~F~~ll~WL~~L-~~q~GV~V~~ldl~~~~~pG~V~V 170 (178)
T PRK09731 99 PAQVSRVISDSASAHSVVIKRIAER-GENIQVWIEPVVFNDLLNWLNAL-DEKYALRVTQIDVSAAEKPGMVNV 170 (178)
T ss_pred CccHHHHHHHHHHHCCCeEEEecCC-CCEEEEEECCCCHHHHHHHHHHH-HHhcCceEEEEeeecCCCCCEEEE
Confidence 4567777788888888777777765 66799999999999999999863 234556666666667666654443
No 38
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=30.27 E-value=89 Score=16.30 Aligned_cols=42 Identities=19% Similarity=-0.020 Sum_probs=30.6
Q ss_pred HHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 20 GKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 20 ~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
.+++.+.++-.|.+......-.+++.|+++.+-.+...|.+-
T Consensus 11 v~~~l~~~~~~i~~~~y~~~V~~~v~v~~~~~~~f~~~l~~~ 52 (56)
T PF09186_consen 11 VERLLEQNGIEIVDEDYTDDVTLTVAVPEEEVEEFKAQLTDL 52 (56)
T ss_dssp HHHHHHHTTTEEEEEEECTTEEEEEEEECCCHHHHHHHHHHH
T ss_pred HHHHHHHCCCEEEcceecceEEEEEEECHHHHHHHHHHHHHH
Confidence 455666788777666655344577788999999999998763
No 39
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=30.15 E-value=1.5e+02 Score=18.90 Aligned_cols=47 Identities=15% Similarity=0.053 Sum_probs=34.9
Q ss_pred HhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCcc
Q psy15410 12 ARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFV 67 (87)
Q Consensus 12 ~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~ 67 (87)
+.-.|+.++..|+++|+- +-.+. .+ .|.+--++-..+..||-+ .+|+
T Consensus 51 ~~~dlk~Lak~LKk~cac---GGtvk-~~--~IeiQGdhr~~v~~~L~~---~G~k 97 (104)
T COG0023 51 KDIDLKKLAKELKKKCAC---GGTVK-DG--EIEIQGDHRDKVKELLIK---KGFK 97 (104)
T ss_pred chhhHHHHHHHHHHHcCC---Cceec-CC--EEEEeChHHHHHHHHHHH---cCCc
Confidence 344688999999999983 22344 34 688999999999999976 5554
No 40
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=29.29 E-value=1.2e+02 Score=22.94 Aligned_cols=30 Identities=20% Similarity=0.266 Sum_probs=16.3
Q ss_pred ceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 30 YIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 30 ~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
.+..+... +|.++ .++++.|..++..++..
T Consensus 73 ~i~siy~G-GGTPs-~L~~~~L~~ll~~i~~~ 102 (394)
T PRK08898 73 QVHTVFIG-GGTPS-LLSAAGLDRLLSDVRAL 102 (394)
T ss_pred ceeEEEEC-CCCcC-CCCHHHHHHHHHHHHHh
Confidence 34455543 34442 35666667777766653
No 41
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=28.35 E-value=1.5e+02 Score=22.97 Aligned_cols=29 Identities=14% Similarity=0.360 Sum_probs=16.4
Q ss_pred eeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 31 IEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 31 i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
|..+... +|.++ .++++.+.+++..++..
T Consensus 104 v~~i~fg-GGTPs-~l~~~~l~~ll~~i~~~ 132 (453)
T PRK13347 104 VSQLHWG-GGTPT-ILNPDQFERLMAALRDA 132 (453)
T ss_pred EEEEEEc-Ccccc-cCCHHHHHHHHHHHHHh
Confidence 4444443 34432 25677777777777764
No 42
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=28.30 E-value=1.6e+02 Score=18.91 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=28.5
Q ss_pred HhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcC-CChHHHHH
Q psy15410 12 ARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIP-EGVVPVLQ 56 (87)
Q Consensus 12 ~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~-e~l~~vl~ 56 (87)
+..-+++-...|.+..|+|+...... +++ .+.+++ ..+-.|..
T Consensus 80 s~~E~E~~l~LL~el~P~Wis~~~~~-~~~-~lk~~k~~~~~~V~~ 123 (126)
T cd08767 80 SRGEVEEHLRLLAELAPDWISEKSLR-KGD-YLKIDKKVDLEKVRK 123 (126)
T ss_pred CHHHHHHHHHHHHHhChHHheeeeeC-Cce-EEEECccccHHHHHH
Confidence 34556677788889999999888885 444 455544 44444443
No 43
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=27.60 E-value=1.4e+02 Score=17.79 Aligned_cols=37 Identities=19% Similarity=0.185 Sum_probs=26.0
Q ss_pred HhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCC
Q psy15410 12 ARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPE 49 (87)
Q Consensus 12 ~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e 49 (87)
..+.+..+++.|+..+++...-.... .+++.+.++..
T Consensus 57 ~~~~l~~i~~~l~~~~~~~~~~~r~~-~~~f~ii~~~~ 93 (163)
T smart00267 57 GDELLQEVAQRLSSCLRPGDLLARLG-GDEFALLLPET 93 (163)
T ss_pred HHHHHHHHHHHHHHhcCCCCEEEEec-CceEEEEecCC
Confidence 45667889999999998643334445 67888877655
No 44
>PRK14440 acylphosphatase; Provisional
Probab=27.48 E-value=1.5e+02 Score=17.95 Aligned_cols=63 Identities=14% Similarity=0.117 Sum_probs=34.7
Q ss_pred HHHHHHhcCCceeEEEEe-eCCeEEEEE--cCCChHHHHHHhhcCccCCcccccccee--eeCCCCCCceee
Q psy15410 20 GKYCAEILPKYIEKVQIT-SGDELELLI--IPEGVVPVLQFLKDHHTAQFVSLVDIAG--MDVPSRPNRFEV 86 (87)
Q Consensus 20 ~~~L~~~fp~~i~~~~~~-~~~el~i~i--~~e~l~~vl~fLKdd~~l~F~~L~DItg--VDyp~~~~RFeV 86 (87)
...+..+++ +.+...+ ..|...+.+ +.+.+-+++++|+..|. +-...++.. .|+...-..|++
T Consensus 22 v~~~A~~~g--l~G~V~N~~dG~Vei~~~G~~~~v~~f~~~l~~gp~--~a~V~~i~~~~~~~~~~~~~F~i 89 (90)
T PRK14440 22 VQIHAIRLG--IKGYAKNLPDGSVEVVAEGYEEALSKLLERIKQGPP--AAEVEKVDFSFSEYKGEFEDFET 89 (90)
T ss_pred HHHHHHHcC--CEEEEEECCCCCEEEEEEcCHHHHHHHHHHHhhCCC--CcEEEEEEEEEeCCCCCCCCeEE
Confidence 344555666 2333322 134344444 56779999999998775 444444433 344333356775
No 45
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=26.49 E-value=1.4e+02 Score=17.24 Aligned_cols=30 Identities=17% Similarity=0.120 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhcCCceeEEEEeeCCeEEEE
Q psy15410 16 LVDFGKYCAEILPKYIEKVQITSGDELELL 45 (87)
Q Consensus 16 l~~i~~~L~~~fp~~i~~~~~~~~~el~i~ 45 (87)
..++..+|...||+....+.....+.+++.
T Consensus 10 ~~EL~kRl~~~yPd~~v~Vr~~s~~~l~v~ 39 (65)
T PF06183_consen 10 ESELTKRLHRQYPDAEVRVRPGSANGLSVS 39 (65)
T ss_dssp HHHHHHHHHHH-SS-EEEEEEESS-EEEEE
T ss_pred HHHHHHHHHHHCCCceEeeeecccCccccC
Confidence 466889999999997666654433455554
No 46
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=26.39 E-value=1.5e+02 Score=22.27 Aligned_cols=28 Identities=11% Similarity=0.134 Sum_probs=14.4
Q ss_pred eeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 31 IEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 31 i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
+..+..- +|.+++ ++++.+..++..++.
T Consensus 57 ~~tiy~G-GGTPs~-L~~~~l~~ll~~i~~ 84 (353)
T PRK05904 57 FKTIYLG-GGTPNC-LNDQLLDILLSTIKP 84 (353)
T ss_pred eEEEEEC-CCcccc-CCHHHHHHHHHHHHH
Confidence 4444443 344432 456666666666655
No 47
>TIGR03365 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine.
Probab=26.26 E-value=99 Score=21.83 Aligned_cols=41 Identities=10% Similarity=0.024 Sum_probs=27.3
Q ss_pred HHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 17 VDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 17 ~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
+++.+.+.+.-+..+..+... +||+.+. ..+.++++.|++.
T Consensus 59 ~ei~~~i~~~~~~~~~~V~lT-GGEPll~---~~l~~li~~l~~~ 99 (238)
T TIGR03365 59 EEVWQELKALGGGTPLHVSLS-GGNPALQ---KPLGELIDLGKAK 99 (238)
T ss_pred HHHHHHHHHHhCCCCCeEEEe-CCchhhh---HhHHHHHHHHHHC
Confidence 444444544333334566777 8999886 3799999999864
No 48
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=25.98 E-value=22 Score=18.96 Aligned_cols=10 Identities=30% Similarity=0.733 Sum_probs=7.3
Q ss_pred ceeeeCCCCC
Q psy15410 72 IAGMDVPSRP 81 (87)
Q Consensus 72 ItgVDyp~~~ 81 (87)
+.|||||-.+
T Consensus 1 L~~~dyPa~k 10 (44)
T PF11387_consen 1 LKGVDYPADK 10 (44)
T ss_pred CCCCCCCCCH
Confidence 4689999653
No 49
>COG3208 GrsT Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=25.69 E-value=34 Score=25.04 Aligned_cols=17 Identities=24% Similarity=0.636 Sum_probs=14.6
Q ss_pred cccceeeeCCCCCCcee
Q psy15410 69 LVDIAGMDVPSRPNRFE 85 (87)
Q Consensus 69 L~DItgVDyp~~~~RFe 85 (87)
=+++++|.||.|..||.
T Consensus 33 ~iel~avqlPGR~~r~~ 49 (244)
T COG3208 33 DIELLAVQLPGRGDRFG 49 (244)
T ss_pred hhheeeecCCCcccccC
Confidence 36789999999999975
No 50
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=25.17 E-value=2.4e+02 Score=19.60 Aligned_cols=54 Identities=13% Similarity=0.063 Sum_probs=41.8
Q ss_pred CCCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCCh--HHHHHHhhc
Q psy15410 6 KPIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGV--VPVLQFLKD 60 (87)
Q Consensus 6 ~~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l--~~vl~fLKd 60 (87)
..++.-....+..+.+.|++.....|.++.-. ...+.|.-++..+ ..+..+|+.
T Consensus 17 ~~~~~~~~~~v~al~~~l~~~~~~gi~e~vp~-~~sllV~fdp~~~~~~~l~~~l~~ 72 (202)
T PF02682_consen 17 EEIDLEINARVLALARALRAAPLPGIVEVVPA-YRSLLVHFDPLRIDRAALRAALEE 72 (202)
T ss_dssp SSS-HHHHHHHHHHHHHHHHHT-TTEEEEEEE-SSEEEEEESTTTSHHHHHHHHHHH
T ss_pred CcCCHHHHHHHHHHHHHHhcCCCCCeEEeecc-ccEEEEEEcCCcCCHHHHHHHHHH
Confidence 45677777788889999999988889888887 7899999988874 567777764
No 51
>PRK12338 hypothetical protein; Provisional
Probab=24.70 E-value=1.4e+02 Score=22.55 Aligned_cols=52 Identities=10% Similarity=0.057 Sum_probs=38.9
Q ss_pred cCCceeEEEEeeCC---eEEEEEcCCChHHHHHHhhcCccCC-----cccccccee-eeCC
Q psy15410 27 LPKYIEKVQITSGD---ELELLIIPEGVVPVLQFLKDHHTAQ-----FVSLVDIAG-MDVP 78 (87)
Q Consensus 27 fp~~i~~~~~~~~~---el~i~i~~e~l~~vl~fLKdd~~l~-----F~~L~DItg-VDyp 78 (87)
.|..|.++...-+| +++-.++-..-.++-+|++.=...+ +..|..+|+ |+|-
T Consensus 229 ~Gg~v~dV~h~iyG~~~~i~~~l~i~s~~dv~~Fi~~~~~~~~~~~~~~~L~~lT~gvH~H 289 (319)
T PRK12338 229 HGGRITDISYPIPGFKDPLKREVNVSDPDEAEKFIKRLNENPKKKEDLKRLYSLSNNVHSH 289 (319)
T ss_pred CCCEEEEecccCCCCCceeEEEEccCCHHHHHHHHHHHhhCCccccchhhHHHHhCCeeEE
Confidence 45666666533356 7999999999999999998655566 889999987 8763
No 52
>PRK13667 hypothetical protein; Provisional
Probab=24.65 E-value=99 Score=18.44 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=35.4
Q ss_pred CeEEEEEcCCChHHHHHHhhcCccCCccccccceeee--CCCCCCceee
Q psy15410 40 DELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMD--VPSRPNRFEV 86 (87)
Q Consensus 40 ~el~i~i~~e~l~~vl~fLKdd~~l~F~~L~DItgVD--yp~~~~RFeV 86 (87)
..-++++.++...++-+.|+++....-.+..-++|-+ |-...+-|.+
T Consensus 19 ~T~sLYlEa~s~~e~R~~v~~~t~yNIEfI~~L~~~~LeYEk~~~~fkl 67 (70)
T PRK13667 19 TTQTLYLEADSEVEVRGRLKDRTAYNIEFIQLLSGAHLEYEKENGDFKL 67 (70)
T ss_pred ccceEEEEcCCHHHHHHHHhhCCCcCEEEEEecchhHHHHhhcCCCeEE
Confidence 5578999999999999999998777666766666643 6555555665
No 53
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=24.02 E-value=1.4e+02 Score=16.57 Aligned_cols=57 Identities=23% Similarity=0.253 Sum_probs=34.5
Q ss_pred HHHHHHHhcCCc--eeEEEEeeCCeEEEEEcCCC---hHHHHHHhhcCccCCccccccceeee
Q psy15410 19 FGKYCAEILPKY--IEKVQITSGDELELLIIPEG---VVPVLQFLKDHHTAQFVSLVDIAGMD 76 (87)
Q Consensus 19 i~~~L~~~fp~~--i~~~~~~~~~el~i~i~~e~---l~~vl~fLKdd~~l~F~~L~DItgVD 76 (87)
+.+.|....|+. +..+... ++.+.|.-.+.. +..++.-|+..|.+.=-.+..+...+
T Consensus 2 ll~~L~~~~P~~v~l~~l~~~-~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~~~~ 63 (78)
T PF05137_consen 2 LLDELARALPEGVWLTSLSIN-GNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSISRQE 63 (78)
T ss_pred hHHHHHhhCCCCEEEEEEEEe-CCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEEeec
Confidence 456788888864 5667776 788888776654 45555555565554433344444444
No 54
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=23.96 E-value=2.3e+02 Score=21.57 Aligned_cols=28 Identities=18% Similarity=0.280 Sum_probs=13.1
Q ss_pred eeEEEEeeCCeEEEEEcCCChHHHHHHhhc
Q psy15410 31 IEKVQITSGDELELLIIPEGVVPVLQFLKD 60 (87)
Q Consensus 31 i~~~~~~~~~el~i~i~~e~l~~vl~fLKd 60 (87)
+..+... +|.++ .++++.+..++..++.
T Consensus 63 i~tiy~G-GGTPs-~l~~~~l~~ll~~i~~ 90 (390)
T PRK06582 63 IKSIFFG-GGTPS-LMNPVIVEGIINKISN 90 (390)
T ss_pred eeEEEEC-CCccc-cCCHHHHHHHHHHHHH
Confidence 4444443 33332 2445555555555554
No 55
>PLN03219 uncharacterized protein; Provisional
Probab=23.71 E-value=47 Score=21.43 Aligned_cols=46 Identities=13% Similarity=0.057 Sum_probs=35.3
Q ss_pred CCCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHH
Q psy15410 6 KPIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQF 57 (87)
Q Consensus 6 ~~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~f 57 (87)
-|++++++-.+.++.+.-.+.||-. -. .|.++|-++.+.+..++.+
T Consensus 59 VPi~yL~hP~F~~LL~~AeEEfGf~-----~~-~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 59 VPISYLNHPLFREFLNRAEEECGFH-----HS-MGGLTIPCREESFLHLITS 104 (108)
T ss_pred EEHHHcCChHHHHHHHHHHHHhCCC-----CC-CCCEEEeCCHHHHHHHHHh
Confidence 3888999999999999999999831 11 3668888888887777654
No 56
>PF13394 Fer4_14: 4Fe-4S single cluster domain; PDB: 1TV8_B 1TV7_A 2FB2_A 2FB3_A.
Probab=23.49 E-value=14 Score=22.55 Aligned_cols=48 Identities=23% Similarity=0.296 Sum_probs=29.0
Q ss_pred HhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 12 ARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 12 ~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
+.+.+.++++.+...-.. ...+... +||+.+..+.+.+.++++.++..
T Consensus 30 ~~~~~~~~i~~~~~~~~~-~~~v~~~-GGEPll~~~~~~l~~~i~~~~~~ 77 (119)
T PF13394_consen 30 SIEELEEIIDELKEKGFR-PSTVVFT-GGEPLLYLNPEDLIELIEYLKER 77 (119)
T ss_dssp -HHHHHHHHHHHHHTT-----EEEEE-SSSGGGSTTHHHHHHHHCTSTT-
T ss_pred cHhHHHHHHHHHHhcCCc-eEEEEEE-CCCCccccCHHHHHHHHHHHHhh
Confidence 334444444433333321 2346677 89998888888899999999876
No 57
>PF02485 Branch: Core-2/I-Branching enzyme; InterPro: IPR003406 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. This is the glycosyltransferase family 14 GT14 from CAZY, a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme (2.4.1.150 from EC) and core-2 branching enzyme (2.4.1.102 from EC). I-branching enzyme, an integral membrane protein, converts linear into branched poly-N-acetyllactosaminoglycans in the glycosylation pathway, and is responsible for the production of the blood group I-antigen during embryonic development []. Core-2 branching enzyme, also an integral membrane protein, forms crucial side-chain branches in O-glycans in the glycosylation pathway [].; GO: 0008375 acetylglucosaminyltransferase activity, 0016020 membrane; PDB: 3OTK_D 2GAM_A 2GAK_B.
Probab=23.47 E-value=29 Score=23.99 Aligned_cols=17 Identities=18% Similarity=0.442 Sum_probs=11.9
Q ss_pred CccccccceeeeCCCCC
Q psy15410 65 QFVSLVDIAGMDVPSRP 81 (87)
Q Consensus 65 ~F~~L~DItgVDyp~~~ 81 (87)
+++++..|+|-|||-+.
T Consensus 88 ~~~y~~llSg~D~Pl~s 104 (244)
T PF02485_consen 88 DWDYFILLSGQDYPLKS 104 (244)
T ss_dssp ---EEEEEETTEEESS-
T ss_pred CCcEEEEcccccccccc
Confidence 69999999999999543
No 58
>COG4866 Uncharacterized conserved protein [Function unknown]
Probab=23.31 E-value=49 Score=24.75 Aligned_cols=19 Identities=37% Similarity=0.566 Sum_probs=15.8
Q ss_pred EEcCCChHHHHHHhhcCcc
Q psy15410 45 LIIPEGVVPVLQFLKDHHT 63 (87)
Q Consensus 45 ~i~~e~l~~vl~fLKdd~~ 63 (87)
.|.++++.+||+|||.=.+
T Consensus 156 ~Is~~nl~EV~~FlKkW~e 174 (294)
T COG4866 156 KISPQNLKEVLEFLKKWFE 174 (294)
T ss_pred ecCcccHHHHHHHHHHHHH
Confidence 4789999999999997433
No 59
>PRK14424 acylphosphatase; Provisional
Probab=23.13 E-value=1.9e+02 Score=17.72 Aligned_cols=62 Identities=15% Similarity=0.231 Sum_probs=35.1
Q ss_pred HHHHHHhcC--CceeEEEEeeCCeEEEEE--cCCChHHHHHHhhcCccCCccccccceeee--CCCCCCceee
Q psy15410 20 GKYCAEILP--KYIEKVQITSGDELELLI--IPEGVVPVLQFLKDHHTAQFVSLVDIAGMD--VPSRPNRFEV 86 (87)
Q Consensus 20 ~~~L~~~fp--~~i~~~~~~~~~el~i~i--~~e~l~~vl~fLKdd~~l~F~~L~DItgVD--yp~~~~RFeV 86 (87)
...+..+++ .+|.+.. .|...+.+ +.+.+-.++++|+..|. +-....+..-+ |.+.-.+|++
T Consensus 26 v~~~A~~~gl~G~V~N~~---dG~Vei~~qG~~~~v~~f~~~l~~gp~--~a~V~~v~~~~~~~~~~~~~F~~ 93 (94)
T PRK14424 26 TVREAHALGLRGWVANLE---DGTVEAMIQGPAAQIDRMLAWLRHGPP--AARVTEVTFEERRTEKRFERFQQ 93 (94)
T ss_pred HHHHHHHcCCeEEEEECC---CCCEEEEEEECHHHHHHHHHHHHhCCC--CcEEEEEEEEEeCCCCCCCCcEE
Confidence 344555555 4443221 34445554 67779999999998765 44444444433 3343456775
No 60
>PF12993 DUF3877: Domain of unknown function, E. rectale Gene description (DUF3877); InterPro: IPR024539 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=23.10 E-value=2.6e+02 Score=19.58 Aligned_cols=35 Identities=26% Similarity=0.399 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCCh
Q psy15410 14 SHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGV 51 (87)
Q Consensus 14 ~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l 51 (87)
+.|..+...+..+||+ ..+..+ ++...+.|+++.-
T Consensus 50 ~~L~~f~~~~~~~lG~--v~vs~k-~eRFCf~IP~~g~ 84 (175)
T PF12993_consen 50 EALEEFPEYVKDRLGE--VEVSHK-GERFCFHIPEEGS 84 (175)
T ss_pred HHHHHhHHHHHhhhcc--EEEEec-CcEEEEEcCcHHH
Confidence 4567788899999997 455666 7889999987743
No 61
>PRK06824 translation initiation factor Sui1; Validated
Probab=22.44 E-value=2.3e+02 Score=18.40 Aligned_cols=44 Identities=16% Similarity=0.049 Sum_probs=33.1
Q ss_pred HhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 12 ARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 12 ~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
....+..++..|+.+++- .-.+. .+ .|.|.-++--.+..||.+.
T Consensus 66 ~~~dlk~l~K~LKkk~gc---GGtvk-d~--~IeiQGD~r~~v~~~L~~~ 109 (118)
T PRK06824 66 AEDALKELAKELKRRCGT---GGTLK-DG--VIEIQGDHVELLLAELLKR 109 (118)
T ss_pred CHHHHHHHHHHHHHHhcC---CceEe-cC--EEEEcCcHHHHHHHHHHHC
Confidence 445689999999999983 22333 23 5889999999999999863
No 62
>KOG2721|consensus
Probab=22.27 E-value=2.4e+02 Score=20.70 Aligned_cols=44 Identities=20% Similarity=0.252 Sum_probs=35.8
Q ss_pred ccCCCCHHHhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCC
Q psy15410 4 IRKPIDEVARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPE 49 (87)
Q Consensus 4 ~~~~~~~~~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e 49 (87)
..||=|+-+-+.+..-+..+.+.||+.|.+...+ +|-++...+.
T Consensus 36 FeKPNDe~aLnLMnscA~~Vl~ef~DIv~AyG~S--DEYSFV~kk~ 79 (260)
T KOG2721|consen 36 FEKPNDETALNLMNSCASAVLEEFPDIVFAYGYS--DEYSFVFKKS 79 (260)
T ss_pred ccCCChHHHHHHHHHHHHHHHHhccceEEEeccC--cceeeeeccc
Confidence 4689999888889999999999999988877664 7777766544
No 63
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=22.06 E-value=1.5e+02 Score=16.10 Aligned_cols=22 Identities=9% Similarity=-0.005 Sum_probs=17.9
Q ss_pred EEEEcCCC--hHHHHHHhhcCccC
Q psy15410 43 ELLIIPEG--VVPVLQFLKDHHTA 64 (87)
Q Consensus 43 ~i~i~~e~--l~~vl~fLKdd~~l 64 (87)
.+.+++.. ..++.++|+..|+.
T Consensus 2 ~V~~~~~~~~~~~~~~~l~~~p~V 25 (74)
T PF01037_consen 2 LVKVEPGHDAYDEFAEALAEIPEV 25 (74)
T ss_dssp EEEESTTGTHHHHHHHHHHTSTTE
T ss_pred EEEEcCCCchHHHHHHHHHcCCCE
Confidence 46777777 99999999998873
No 64
>PF08825 E2_bind: E2 binding domain; InterPro: IPR014929 E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains []. ; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0045116 protein neddylation; PDB: 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H 1YOV_B 3FN1_A ....
Probab=22.05 E-value=1.1e+02 Score=18.58 Aligned_cols=23 Identities=13% Similarity=0.169 Sum_probs=15.5
Q ss_pred EEcCC-ChHHHHHHhhcCccCCcc
Q psy15410 45 LIIPE-GVVPVLQFLKDHHTAQFV 67 (87)
Q Consensus 45 ~i~~e-~l~~vl~fLKdd~~l~F~ 67 (87)
.++++ -+-+++..|+++|+++++
T Consensus 2 ~v~~~~TL~~lid~L~~~~~~qlk 25 (84)
T PF08825_consen 2 EVSPSWTLQDLIDSLCEKPEFQLK 25 (84)
T ss_dssp EESTTSBSHHHHHHHHHSTTT--S
T ss_pred CcCccchHHHHHHHHHhChhhhcC
Confidence 44444 477899999999887665
No 65
>COG2873 MET17 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]
Probab=21.99 E-value=71 Score=25.21 Aligned_cols=25 Identities=28% Similarity=0.474 Sum_probs=21.8
Q ss_pred cCCChHHHHHHhhcCccCCccccccceeeeCCC
Q psy15410 47 IPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPS 79 (87)
Q Consensus 47 ~~e~l~~vl~fLKdd~~l~F~~L~DItgVDyp~ 79 (87)
+.++...|.+||+.||. +..|-||.
T Consensus 297 H~~NA~~vA~~L~~Hpk--------V~~V~Ypg 321 (426)
T COG2873 297 HCENALKVAEFLENHPK--------VAWVNYPG 321 (426)
T ss_pred HHHhHHHHHHHHhcCCC--------eeeeecCC
Confidence 55689999999999997 88999984
No 66
>PRK05660 HemN family oxidoreductase; Provisional
Probab=21.93 E-value=2.1e+02 Score=21.63 Aligned_cols=30 Identities=17% Similarity=0.262 Sum_probs=17.2
Q ss_pred ceeEEEEeeCCeEEEEEcCCChHHHHHHhhcC
Q psy15410 30 YIEKVQITSGDELELLIIPEGVVPVLQFLKDH 61 (87)
Q Consensus 30 ~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd 61 (87)
.+..+... +|++++ ++++.+..++..++..
T Consensus 58 ~v~ti~~G-GGtPs~-l~~~~l~~ll~~l~~~ 87 (378)
T PRK05660 58 EVHSIFIG-GGTPSL-FSAEAIQRLLDGVRAR 87 (378)
T ss_pred ceeEEEeC-CCcccc-CCHHHHHHHHHHHHHh
Confidence 35555554 455533 4566777777777653
No 67
>PF13647 Glyco_hydro_80: Glycosyl hydrolase family 80 of chitosanase A
Probab=21.38 E-value=35 Score=24.71 Aligned_cols=51 Identities=22% Similarity=0.191 Sum_probs=35.4
Q ss_pred HhhHHHHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHHHHHHhhcCccCCcccc
Q psy15410 12 ARSHLVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSL 69 (87)
Q Consensus 12 ~~~~l~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~vl~fLKdd~~l~F~~L 69 (87)
+...|..|.+.|++.|-..-.... ..-...|+.+.+.+|+..||. ++|..+
T Consensus 144 kraaltkic~alqs~fd~~q~~yv----mshyahid~dkl~pvl~alk~---~gft~f 194 (308)
T PF13647_consen 144 KRAALTKICQALQSDFDNQQDQYV----MSHYAHIDQDKLVPVLNALKK---IGFTSF 194 (308)
T ss_pred hHHHHHHHHHHHHhhhhhhhhHHH----HHhhhhccccchhHHHHHHhh---cCccee
Confidence 446788999999999974211111 223357899999999999996 555443
No 68
>PF03332 PMM: Eukaryotic phosphomannomutase; InterPro: IPR005002 This enzyme (5.4.2.8 from EC) is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.; GO: 0004615 phosphomannomutase activity, 0019307 mannose biosynthetic process, 0005737 cytoplasm; PDB: 2I55_B 2I54_C 3F9R_A 2FUE_A 2FUC_A 2AMY_A 2Q4R_A.
Probab=20.95 E-value=1.3e+02 Score=21.71 Aligned_cols=42 Identities=19% Similarity=0.351 Sum_probs=29.7
Q ss_pred HHHHHHHHHhcCCceeEEEEeeCCeEEEEEcCCChHH--HHHHhhc
Q psy15410 17 VDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVP--VLQFLKD 60 (87)
Q Consensus 17 ~~i~~~L~~~fp~~i~~~~~~~~~el~i~i~~e~l~~--vl~fLKd 60 (87)
..+++.|+++||+.-..+.+ +|+.++-|-+..|-+ -|++|.+
T Consensus 129 ~~~v~~L~~~f~d~~L~~si--GGqiSiDvfp~GwDKty~Lr~l~~ 172 (220)
T PF03332_consen 129 EKLVEALKKEFPDFGLTFSI--GGQISIDVFPKGWDKTYCLRHLED 172 (220)
T ss_dssp HHHHHHHHHHTCCCSEEEEE--ETTTEEEEEETT-SGGGGGGGTTT
T ss_pred HHHHHHHHHHCCCCceEEec--CCceEEccccCCccHHHHHHHHHh
Confidence 56889999999986555555 799999998776643 2444443
Done!