Query 034727
Match_columns 86
No_of_seqs 135 out of 1027
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:50:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07238 bifunctional RNase H/ 99.8 2E-18 4.4E-23 123.0 9.5 84 1-86 23-109 (372)
2 PRK13907 rnhA ribonuclease H; 99.8 4.1E-18 9E-23 105.6 9.1 81 1-85 22-103 (128)
3 PRK07708 hypothetical protein; 99.7 6E-17 1.3E-21 109.2 8.9 82 1-84 94-182 (219)
4 COG0328 RnhA Ribonuclease HI [ 99.6 7.5E-16 1.6E-20 98.9 7.2 83 2-85 25-117 (154)
5 PF13456 RVT_3: Reverse transc 99.4 4.4E-13 9.6E-18 76.9 5.7 63 21-86 1-64 (87)
6 cd06222 RnaseH RNase H (RNase 99.4 1.2E-11 2.6E-16 73.5 9.0 82 1-84 20-103 (130)
7 PRK08719 ribonuclease H; Revie 99.2 1.1E-10 2.3E-15 74.6 7.6 75 2-82 29-117 (147)
8 PRK06548 ribonuclease H; Provi 99.1 5.7E-10 1.2E-14 72.3 7.6 68 14-82 35-112 (161)
9 PRK00203 rnhA ribonuclease H; 98.9 8.9E-09 1.9E-13 65.5 6.7 69 12-82 34-112 (150)
10 KOG3752 Ribonuclease H [Replic 98.7 4.5E-08 9.8E-13 70.2 6.0 55 6-60 239-295 (371)
11 PF00075 RNase_H: RNase H; In 98.3 1.7E-06 3.6E-11 52.9 5.0 45 12-59 31-75 (132)
12 KOG1812 Predicted E3 ubiquitin 96.2 0.013 2.8E-07 42.8 5.5 65 19-85 47-113 (384)
13 PRK14840 undecaprenyl pyrophos 81.0 1.5 3.3E-05 30.5 2.4 49 2-50 25-76 (250)
14 KOG1602 Cis-prenyltransferase 80.4 2.3 5E-05 29.9 3.1 39 12-50 52-90 (271)
15 PRK10382 alkyl hydroperoxide r 80.0 4.6 0.0001 26.5 4.4 38 1-39 123-161 (187)
16 PRK13190 putative peroxiredoxi 78.0 6.1 0.00013 26.1 4.5 39 1-40 121-160 (202)
17 PRK13599 putative peroxiredoxi 77.9 6.6 0.00014 26.4 4.7 39 2-41 124-163 (215)
18 PRK15000 peroxidase; Provision 77.6 6 0.00013 26.2 4.4 38 2-40 130-168 (200)
19 COG0450 AhpC Peroxiredoxin [Po 77.4 8.5 0.00018 25.9 5.0 39 2-40 129-167 (194)
20 PRK13191 putative peroxiredoxi 77.3 6.5 0.00014 26.4 4.5 38 2-40 129-167 (215)
21 PRK13189 peroxiredoxin; Provis 75.3 8.2 0.00018 26.0 4.6 39 1-40 130-169 (222)
22 PTZ00137 2-Cys peroxiredoxin; 74.8 6.4 0.00014 27.4 4.1 38 2-40 193-231 (261)
23 PRK14833 undecaprenyl pyrophos 71.3 3.8 8.3E-05 28.1 2.3 39 12-50 20-58 (233)
24 PRK14835 undecaprenyl pyrophos 70.8 3.6 7.7E-05 29.0 2.1 36 15-50 60-95 (275)
25 cd03016 PRX_1cys Peroxiredoxin 70.6 13 0.00029 24.4 4.7 39 2-41 122-161 (203)
26 cd00475 CIS_IPPS Cis (Z)-Isopr 69.0 4.5 9.9E-05 27.5 2.2 48 2-50 7-54 (221)
27 PRK14841 undecaprenyl pyrophos 68.7 4.7 0.0001 27.7 2.2 48 2-50 10-57 (233)
28 PRK14842 undecaprenyl pyrophos 66.7 5.3 0.00011 27.6 2.2 47 3-50 16-62 (241)
29 PRK14828 undecaprenyl pyrophos 66.4 5.1 0.00011 27.9 2.1 35 16-50 46-81 (256)
30 PRK14827 undecaprenyl pyrophos 65.7 5.4 0.00012 28.4 2.1 37 14-50 85-121 (296)
31 PRK14832 undecaprenyl pyrophos 65.5 5.4 0.00012 27.8 2.1 38 13-50 35-72 (253)
32 TIGR00055 uppS undecaprenyl di 65.4 5.8 0.00013 27.2 2.2 48 2-50 6-53 (226)
33 PRK14830 undecaprenyl pyrophos 65.0 5.7 0.00012 27.6 2.1 35 16-50 42-76 (251)
34 PRK14838 undecaprenyl pyrophos 64.7 6 0.00013 27.3 2.2 37 14-50 28-64 (242)
35 PRK14834 undecaprenyl pyrophos 64.5 6 0.00013 27.5 2.2 35 16-50 34-68 (249)
36 PRK14829 undecaprenyl pyrophos 64.2 6.3 0.00014 27.2 2.2 36 15-50 33-68 (243)
37 PRK14837 undecaprenyl pyrophos 63.6 6.2 0.00014 27.1 2.1 48 2-50 13-60 (230)
38 cd03015 PRX_Typ2cys Peroxiredo 63.6 22 0.00048 22.5 4.6 40 1-41 124-164 (173)
39 PRK14831 undecaprenyl pyrophos 63.3 7.1 0.00015 27.1 2.4 36 15-50 39-74 (249)
40 PRK14839 undecaprenyl pyrophos 63.0 6.9 0.00015 27.1 2.2 38 13-50 26-63 (239)
41 PTZ00349 dehydrodolichyl dipho 61.2 6.8 0.00015 28.3 2.0 48 2-50 26-73 (322)
42 COG0020 UppS Undecaprenyl pyro 60.4 7.4 0.00016 27.0 2.0 49 2-51 23-71 (245)
43 TIGR03137 AhpC peroxiredoxin. 59.8 25 0.00055 22.7 4.4 38 2-39 124-161 (187)
44 PRK10240 undecaprenyl pyrophos 59.1 8.4 0.00018 26.4 2.1 38 13-50 10-47 (229)
45 PF00411 Ribosomal_S11: Riboso 58.1 39 0.00084 20.3 4.8 47 2-48 16-68 (110)
46 PTZ00253 tryparedoxin peroxida 56.8 31 0.00068 22.5 4.5 38 2-40 132-170 (199)
47 cd01285 nucleoside_deaminase N 54.3 37 0.00081 20.0 4.2 52 1-52 22-76 (109)
48 cd01284 Riboflavin_deaminase-r 53.2 34 0.00074 20.7 3.9 33 1-34 24-56 (115)
49 PRK14836 undecaprenyl pyrophos 50.7 11 0.00024 26.2 1.6 36 15-50 33-68 (253)
50 cd07353 harmonin_N N-terminal 50.3 9.5 0.00021 21.6 1.0 51 19-80 15-65 (79)
51 CHL00041 rps11 ribosomal prote 48.6 61 0.0013 19.8 6.1 56 2-57 29-95 (116)
52 PRK05309 30S ribosomal protein 48.1 66 0.0014 20.0 6.1 57 2-58 33-100 (128)
53 cd03018 PRX_AhpE_like Peroxire 46.3 21 0.00045 21.6 2.3 31 1-31 118-148 (149)
54 COG0295 Cdd Cytidine deaminase 46.0 62 0.0013 20.5 4.4 48 2-50 32-81 (134)
55 PTZ00090 40S ribosomal protein 45.1 1E+02 0.0022 21.3 5.9 57 2-58 134-202 (233)
56 PHA03326 nuclear egress membra 43.5 33 0.00071 24.2 3.0 17 19-35 151-167 (275)
57 PF00383 dCMP_cyt_deam_1: Cyti 41.2 38 0.00083 19.3 2.8 49 1-50 29-80 (102)
58 COG3341 Predicted double-stran 40.3 54 0.0012 22.6 3.6 51 8-58 95-150 (225)
59 PF01255 Prenyltransf: Putativ 39.8 7.1 0.00015 26.4 -0.6 36 15-50 13-48 (223)
60 TIGR03632 bact_S11 30S ribosom 39.0 87 0.0019 18.8 6.1 47 2-48 16-68 (108)
61 COG3981 Predicted acetyltransf 37.1 56 0.0012 21.6 3.2 26 26-51 116-141 (174)
62 COG0590 CumB Cytosine/adenosin 36.8 90 0.002 19.8 4.2 36 1-36 33-71 (152)
63 cd02955 SSP411 TRX domain, SSP 36.6 64 0.0014 19.7 3.3 35 1-35 85-120 (124)
64 PF05830 NodZ: Nodulation prot 36.5 38 0.00082 24.5 2.5 21 41-61 214-235 (321)
65 PF06006 DUF905: Bacterial pro 33.5 28 0.00061 19.6 1.2 16 1-16 36-52 (70)
66 PF11080 DUF2622: Protein of u 33.4 1.1E+02 0.0024 18.3 4.6 48 2-50 39-89 (96)
67 PF09292 Neil1-DNA_bind: Endon 31.8 51 0.0011 16.4 1.8 16 2-17 20-35 (39)
68 PTZ00129 40S ribosomal protein 31.4 1.5E+02 0.0032 19.2 6.0 47 2-48 44-97 (149)
69 TIGR02530 flg_new flagellar op 30.2 26 0.00057 20.9 0.8 35 21-55 32-67 (96)
70 TIGR01354 cyt_deam_tetra cytid 29.2 99 0.0022 18.9 3.3 47 2-50 27-76 (127)
71 PF08100 Dimerisation: Dimeris 28.4 19 0.00042 18.8 0.0 47 32-80 2-50 (51)
72 PF09827 CRISPR_Cas2: CRISPR a 28.1 84 0.0018 17.2 2.7 39 7-47 27-65 (78)
73 PF09818 ABC_ATPase: Predicted 27.7 1.4E+02 0.0031 22.7 4.4 81 2-83 289-387 (448)
74 TIGR03628 arch_S11P archaeal r 26.7 1.6E+02 0.0035 18.0 5.8 46 2-47 18-70 (114)
75 COG3623 SgaU Putative L-xylulo 25.6 1.3E+02 0.0028 21.3 3.6 35 14-48 81-117 (287)
76 cd02960 AGR Anterior Gradient 24.6 65 0.0014 20.1 1.9 36 1-38 84-124 (130)
77 KOG0854 Alkyl hydroperoxide re 23.8 2.1E+02 0.0046 19.4 4.3 24 18-41 152-175 (224)
78 PRK09607 rps11p 30S ribosomal 23.3 2E+02 0.0044 18.1 6.1 46 2-47 25-77 (132)
79 PF03190 Thioredox_DsbH: Prote 23.2 1.3E+02 0.0028 19.6 3.1 38 1-38 107-145 (163)
80 COG0191 Fba Fructose/tagatose 22.8 1.3E+02 0.0029 21.4 3.4 25 32-56 219-243 (286)
81 PF05171 HemS: Haemin-degradin 22.5 1.5E+02 0.0031 18.1 3.2 29 2-32 100-128 (129)
82 PF02887 PK_C: Pyruvate kinase 22.5 1.6E+02 0.0035 17.3 3.4 22 40-61 38-60 (117)
83 PRK15381 pathogenicity island 22.5 37 0.0008 25.3 0.6 48 1-50 100-151 (408)
84 PRK10860 tRNA-specific adenosi 22.1 1.9E+02 0.0041 18.8 3.8 33 1-34 38-73 (172)
85 COG1225 Bcp Peroxiredoxin [Pos 21.8 2.1E+02 0.0045 18.5 3.9 31 2-33 125-155 (157)
86 cd05017 SIS_PGI_PMI_1 The memb 21.7 1.6E+02 0.0035 17.3 3.2 25 27-51 57-81 (119)
87 cd02969 PRX_like1 Peroxiredoxi 21.4 1.6E+02 0.0035 18.3 3.3 12 1-12 114-125 (171)
88 COG3165 Uncharacterized protei 20.9 81 0.0018 21.4 1.9 46 12-57 60-109 (204)
89 PF10113 Fibrillarin_2: Fibril 20.6 1.4E+02 0.0031 22.8 3.2 26 25-50 231-256 (505)
90 COG4831 Roadblock/LC7 domain [ 20.5 2.1E+02 0.0046 17.3 3.4 31 2-35 19-49 (109)
No 1
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.77 E-value=2e-18 Score=123.00 Aligned_cols=84 Identities=35% Similarity=0.503 Sum_probs=77.5
Q ss_pred CeeCCCCC-EEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHH
Q 034727 1 MLRADDGS-LIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAK 77 (86)
Q Consensus 1 v~~~~~g~-~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~ 77 (86)
||++++|. ++. .+..++..|||.|||.|++.||+.+.++|++++.+++||++|+++++ +|+ ++++.+..|+.+++
T Consensus 23 vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~--~~~~~l~~~~~~i~ 100 (372)
T PRK07238 23 VVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWK--VKHPDMKPLAAQAR 100 (372)
T ss_pred EEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCc--cCChHHHHHHHHHH
Confidence 57888765 555 88889999999999999999999999999999999999999999999 999 99999999999999
Q ss_pred HHhhccCCC
Q 034727 78 RLKDKFLSI 86 (86)
Q Consensus 78 ~l~~~f~~~ 86 (86)
.++++|+++
T Consensus 101 ~l~~~f~~~ 109 (372)
T PRK07238 101 ELASQFGRV 109 (372)
T ss_pred HHHhcCCce
Confidence 999999864
No 2
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.77 E-value=4.1e-18 Score=105.56 Aligned_cols=81 Identities=23% Similarity=0.283 Sum_probs=71.7
Q ss_pred CeeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHH
Q 034727 1 MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRL 79 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l 79 (86)
||++++|.+. .+...+.+|||.|||.|++.||+.+.++|++++.+++||++|+++++ .|. +++.+.+++++++.+
T Consensus 22 vi~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~---~~~~~~~l~~~~~~l 97 (128)
T PRK13907 22 FIKGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYA---KNKMFAPLLEEALQY 97 (128)
T ss_pred EEEECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHh---cChhHHHHHHHHHHH
Confidence 4677777554 44567889999999999999999999999999999999999999999 884 678899999999999
Q ss_pred hhccCC
Q 034727 80 KDKFLS 85 (86)
Q Consensus 80 ~~~f~~ 85 (86)
+++|+.
T Consensus 98 ~~~f~~ 103 (128)
T PRK13907 98 IKSFDL 103 (128)
T ss_pred HhcCCc
Confidence 999875
No 3
>PRK07708 hypothetical protein; Validated
Probab=99.71 E-value=6e-17 Score=109.17 Aligned_cols=82 Identities=20% Similarity=0.275 Sum_probs=70.6
Q ss_pred CeeCCCCCEEE---eeeccC-CCcchHHHHHHHHHHHHHHHhcCCce--EEEecchHHHHHHHh-hhhhcCCChhHHHHH
Q 034727 1 MLRADDGSLIY---NHNGVG-ITTNNVAKYGSLILGLKYALQKGFFN--FRVRGDSKLVHMQVC-CWLMEDQTPGMAELC 73 (86)
Q Consensus 1 v~~~~~g~~~~---~~~~~g-~~tnn~aEy~Ali~gL~~a~~~~~~~--v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~ 73 (86)
||+++.|.... .+..++ ..|||+|||.|++.||+.|.++|+++ |.+++||++|++|++ .|+ ++++.+++|+
T Consensus 94 VI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk--~~~~~l~~y~ 171 (219)
T PRK07708 94 VIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWP--CYDEHLNHWL 171 (219)
T ss_pred EEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCce--eCChhHHHHH
Confidence 46666665432 334565 68999999999999999999999976 899999999999999 999 9999999999
Q ss_pred HHHHHHhhccC
Q 034727 74 GEAKRLKDKFL 84 (86)
Q Consensus 74 ~~i~~l~~~f~ 84 (86)
+++..++++|.
T Consensus 172 ~~i~~l~~~~~ 182 (219)
T PRK07708 172 DRIEQKLKQLK 182 (219)
T ss_pred HHHHHHHhhCC
Confidence 99999998875
No 4
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.64 E-value=7.5e-16 Score=98.92 Aligned_cols=83 Identities=30% Similarity=0.359 Sum_probs=64.6
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhhhc---------CCCh-hHHH
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLME---------DQTP-GMAE 71 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~~~---------~k~~-~l~~ 71 (86)
|+..+++. ..+...+.+|||.|||.|+|.||+.+.+.+...+.++|||++|+++|+.|..+ .+.| ..+.
T Consensus 25 l~~~~~~~-~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~d 103 (154)
T COG0328 25 LRYGDGEK-ELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKD 103 (154)
T ss_pred EEcCCceE-EEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHH
Confidence 44334443 35555669999999999999999999999999999999999999999866300 1122 4467
Q ss_pred HHHHHHHHhhccCC
Q 034727 72 LCGEAKRLKDKFLS 85 (86)
Q Consensus 72 ~~~~i~~l~~~f~~ 85 (86)
+++++..+.++|..
T Consensus 104 l~~~~~~~~~~~~~ 117 (154)
T COG0328 104 LWEELDELLKRHEL 117 (154)
T ss_pred HHHHHHHHHhhCCe
Confidence 89999999998853
No 5
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.42 E-value=4.4e-13 Score=76.90 Aligned_cols=63 Identities=22% Similarity=0.246 Sum_probs=54.1
Q ss_pred chHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHHhhccCCC
Q 034727 21 NNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRLKDKFLSI 86 (86)
Q Consensus 21 nn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l~~~f~~~ 86 (86)
+++||+.|++.||+.|.++|++++.++|||+.|+++++ .+. .++ .+.++...++.++++|..+
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~--~~~-~~~~~~~~i~~~~~~~~~~ 64 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSS--SRS-ELRPLIQDIRSLLDRFWNV 64 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS-----S-CCHHHHHHHHHHHCCCSCE
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccc--ccc-cccccchhhhhhhccccce
Confidence 57899999999999999999999999999999999999 876 666 7999999999999998753
No 6
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.35 E-value=1.2e-11 Score=73.52 Aligned_cols=82 Identities=26% Similarity=0.234 Sum_probs=69.0
Q ss_pred CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHH
Q 034727 1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKR 78 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~ 78 (86)
|+++++|.... .....+..+++.+|+.|++.||+.+...+.+++.+++||+.++++++ .+. +..+.+.+++..+..
T Consensus 20 v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~--~~~~~~~~~~~~i~~ 97 (130)
T cd06222 20 VLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYE--GKPVKNVDLWQRLLA 97 (130)
T ss_pred EEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcccc--CCChhhHHHHHHHHH
Confidence 35677777776 33333788999999999999999999999999999999999999999 776 677889999999998
Q ss_pred HhhccC
Q 034727 79 LKDKFL 84 (86)
Q Consensus 79 l~~~f~ 84 (86)
+.+++.
T Consensus 98 ~~~~~~ 103 (130)
T cd06222 98 LLKRFH 103 (130)
T ss_pred HHhCCC
Confidence 885554
No 7
>PRK08719 ribonuclease H; Reviewed
Probab=99.20 E-value=1.1e-10 Score=74.59 Aligned_cols=75 Identities=19% Similarity=0.229 Sum_probs=55.3
Q ss_pred eeCCCCCEEE-eeeccC-CCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHH--------h-hhhhcCCCh---
Q 034727 2 LRADDGSLIY-NHNGVG-ITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV--------C-CWLMEDQTP--- 67 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g-~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~--------~-~~~~~~k~~--- 67 (86)
+.+++|..+. .+..++ ..|||.||+.|++.||+.+.+. ..|++||++|++++ + .|+ ..+.
T Consensus 29 v~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~--~s~g~~v 102 (147)
T PRK08719 29 VYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWR--KSDKKPV 102 (147)
T ss_pred EEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcc--cCCCccc
Confidence 4566777664 555554 6899999999999999988754 37999999999999 3 443 2322
Q ss_pred hHHHHHHHHHHHhhc
Q 034727 68 GMAELCGEAKRLKDK 82 (86)
Q Consensus 68 ~l~~~~~~i~~l~~~ 82 (86)
..+.+++++..+.++
T Consensus 103 ~n~dl~~~i~~l~~~ 117 (147)
T PRK08719 103 ANRDLWQQVDELRAR 117 (147)
T ss_pred ccHHHHHHHHHHhCC
Confidence 346778888877653
No 8
>PRK06548 ribonuclease H; Provisional
Probab=99.10 E-value=5.7e-10 Score=72.31 Aligned_cols=68 Identities=25% Similarity=0.235 Sum_probs=51.0
Q ss_pred eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh----h-----hcCCCh-hHHHHHHHHHHHhhc
Q 034727 14 NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW----L-----MEDQTP-GMAELCGEAKRLKDK 82 (86)
Q Consensus 14 ~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~----~-----~~~k~~-~l~~~~~~i~~l~~~ 82 (86)
...+..|||.||+.|++.||+.+ ..+..++.|++||++|+++++.| + .....| ..+.+++++..++++
T Consensus 35 g~~~~~TNnraEl~Aii~aL~~~-~~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~ 112 (161)
T PRK06548 35 GGWDIATNNIAELTAVRELLIAT-RHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN 112 (161)
T ss_pred cCCCCCCHHHHHHHHHHHHHHhh-hcCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc
Confidence 33456999999999999999754 34556899999999999999843 2 001223 458899999888765
No 9
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.88 E-value=8.9e-09 Score=65.53 Aligned_cols=69 Identities=19% Similarity=0.220 Sum_probs=50.7
Q ss_pred eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhhhc--CC-------Ch-hHHHHHHHHHHHhh
Q 034727 12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLME--DQ-------TP-GMAELCGEAKRLKD 81 (86)
Q Consensus 12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~~~--~k-------~~-~l~~~~~~i~~l~~ 81 (86)
++...+..|||.||+.|++.||+.+.+ ...+.|++||++++++++.|... .+ .| ..+.+++++..+++
T Consensus 34 ~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~ 111 (150)
T PRK00203 34 LSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK 111 (150)
T ss_pred EecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc
Confidence 455567899999999999999997754 35799999999999998843200 11 12 34677888887765
Q ss_pred c
Q 034727 82 K 82 (86)
Q Consensus 82 ~ 82 (86)
+
T Consensus 112 ~ 112 (150)
T PRK00203 112 R 112 (150)
T ss_pred c
Confidence 4
No 10
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]
Probab=98.69 E-value=4.5e-08 Score=70.16 Aligned_cols=55 Identities=27% Similarity=0.281 Sum_probs=46.3
Q ss_pred CCCEEEeeecc--CCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh
Q 034727 6 DGSLIYNHNGV--GITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW 60 (86)
Q Consensus 6 ~g~~~~~~~~~--g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~ 60 (86)
+|...-.++++ |..|||.||+.|++.||+.|++.++..++|.|||+++++.|+.|
T Consensus 239 ~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~w 295 (371)
T KOG3752|consen 239 PGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLW 295 (371)
T ss_pred CCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHH
Confidence 34444444444 68999999999999999999999999999999999999998844
No 11
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=98.30 E-value=1.7e-06 Score=52.93 Aligned_cols=45 Identities=27% Similarity=0.210 Sum_probs=37.2
Q ss_pred eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhh
Q 034727 12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC 59 (86)
Q Consensus 12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~ 59 (86)
.+..++..||+.+|+.|++.||+ +.. . +.+.|++||+.+++.++.
T Consensus 31 ~~~~~~~~s~~~aEl~Ai~~AL~-~~~-~-~~v~I~tDS~~v~~~l~~ 75 (132)
T PF00075_consen 31 FSFRLGGQSNNRAELQAIIEALK-ALE-H-RKVTIYTDSQYVLNALNK 75 (132)
T ss_dssp EEEEEESECHHHHHHHHHHHHHH-THS-T-SEEEEEES-HHHHHHHHT
T ss_pred EEecccccchhhhheehHHHHHH-Hhh-c-ccccccccHHHHHHHHHH
Confidence 44555699999999999999999 552 2 999999999999998874
No 12
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.013 Score=42.76 Aligned_cols=65 Identities=22% Similarity=0.200 Sum_probs=53.6
Q ss_pred CcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCCh-hHHHHHHHHHHHhhccCC
Q 034727 19 TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTP-GMAELCGEAKRLKDKFLS 85 (86)
Q Consensus 19 ~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~-~l~~~~~~i~~l~~~f~~ 85 (86)
.|--.||+.|++.||..+..+|+.++.++.|+..++..+. ... .+.. .+..+.+.+....++|.+
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~--~~~~~~~~~l~~~v~~~r~~l~~ 113 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREK--PEQHRKIVLLVELVQRIREQLTS 113 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhh--HHHHHHHHHHHHHHHHHHHHhhc
Confidence 5677999999999999999999999999999988888777 765 4444 577788888777776653
No 13
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=81.03 E-value=1.5 Score=30.45 Aligned_cols=49 Identities=12% Similarity=-0.050 Sum_probs=37.3
Q ss_pred eeCCCCCEEE-ee--eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIY-NH--NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~-~~--~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
|.|.||++-. .. ..+.....+.+.+.++..-++.|.++|++.+.+|.=|
T Consensus 25 ImDGNrRwAk~~~~~~gl~~~~GH~~G~~~l~~v~~~c~~~GIk~lTvYaFS 76 (250)
T PRK14840 25 IMDGNRRWYRKHEQFCQKRAISGHYYGAKSLPQIVDTALHLGIEVLTLFAFS 76 (250)
T ss_pred EcCCChHHHhhCCCccCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 4455555533 11 1245667899999999999999999999999999877
No 14
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=80.44 E-value=2.3 Score=29.87 Aligned_cols=39 Identities=18% Similarity=0.154 Sum_probs=34.0
Q ss_pred eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
....++....+.|.+.+|..=|++|.++|++.|.+|.=|
T Consensus 52 Kk~~L~~~~GH~aGf~~l~~ile~C~~lGI~~vT~fAFS 90 (271)
T KOG1602|consen 52 KKRGLETSEGHEAGFEALKEILELCKELGIKEVTVFAFS 90 (271)
T ss_pred HhcCCCcccchHHHHHHHHHHHHHHHHcCCcEEEEEEEe
Confidence 444566788899999999999999999999999998766
No 15
>PRK10382 alkyl hydroperoxide reductase subunit C; Provisional
Probab=79.98 E-value=4.6 Score=26.54 Aligned_cols=38 Identities=11% Similarity=0.137 Sum_probs=28.8
Q ss_pred CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhc
Q 034727 1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQK 39 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~ 39 (86)
+|.|++|.++. .....+ ...|..|..+.+.+|+...++
T Consensus 123 fIID~~G~I~~~~~~~~~-~~~~~~eil~~l~alq~~~~~ 161 (187)
T PRK10382 123 FVVDPQGIIQAIEVTAEG-IGRDASDLLRKIKAAQYVASH 161 (187)
T ss_pred EEECCCCEEEEEEEeCCC-CCCCHHHHHHHHHhhhhHhhc
Confidence 37899999998 443333 335899999999999987766
No 16
>PRK13190 putative peroxiredoxin; Provisional
Probab=78.00 E-value=6.1 Score=26.08 Aligned_cols=39 Identities=8% Similarity=0.041 Sum_probs=29.0
Q ss_pred CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
+|.|++|.+.. ..... ..--|..|...++.+|+...++|
T Consensus 121 fiId~~G~I~~~~~~~~-~~gr~~~ellr~l~~l~~~~~~~ 160 (202)
T PRK13190 121 FIIDPNQIVRWMIYYPA-ETGRNIDEIIRITKALQVNWKRK 160 (202)
T ss_pred EEECCCCEEEEEEEeCC-CCCCCHHHHHHHHHHhhhHHhcC
Confidence 37889998887 43333 33358999999999999887765
No 17
>PRK13599 putative peroxiredoxin; Provisional
Probab=77.85 E-value=6.6 Score=26.36 Aligned_cols=39 Identities=21% Similarity=0.121 Sum_probs=29.4
Q ss_pred eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727 2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGF 41 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~ 41 (86)
|.|++|.+.. ..... ....|..|...++.+|+...+.++
T Consensus 124 IID~dG~Ir~~~~~p~-~~gr~~~eilr~l~~lq~~~~~~~ 163 (215)
T PRK13599 124 IVDDKGTIRLIMYYPQ-EVGRNVDEILRALKALQTADQYGV 163 (215)
T ss_pred EECCCCEEEEEEEcCC-CCCCCHHHHHHHHHHhhhhhhcCC
Confidence 7899999987 43333 333588999999999999887764
No 18
>PRK15000 peroxidase; Provisional
Probab=77.65 E-value=6 Score=26.18 Aligned_cols=38 Identities=16% Similarity=0.251 Sum_probs=29.1
Q ss_pred eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
|.||+|.+.. ....++.. .|..|...++.+|+...++|
T Consensus 130 iID~~G~I~~~~~~~~~~g-r~~~eilr~l~al~~~~~~~ 168 (200)
T PRK15000 130 LIDANGIVRHQVVNDLPLG-RNIDEMLRMVDALQFHEEHG 168 (200)
T ss_pred EECCCCEEEEEEecCCCCC-CCHHHHHHHHHHhhhHHhcC
Confidence 7899999988 44444333 48889999999999888775
No 19
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=77.41 E-value=8.5 Score=25.87 Aligned_cols=39 Identities=18% Similarity=0.143 Sum_probs=31.0
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
|.||+|.+....-+-....-|.-|...++++|+...++|
T Consensus 129 IIDp~g~ir~~~v~~~~iGRn~dEilR~idAlq~~~~hg 167 (194)
T COG0450 129 IIDPDGVIRHILVNPLTIGRNVDEILRVIDALQFVAKHG 167 (194)
T ss_pred EECCCCeEEEEEEecCCCCcCHHHHHHHHHHHHHHHHhC
Confidence 788999887744444456678999999999999987776
No 20
>PRK13191 putative peroxiredoxin; Provisional
Probab=77.28 E-value=6.5 Score=26.37 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=29.5
Q ss_pred eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
|.|++|.+.. ....++.. .|..|...++.+|+...++|
T Consensus 129 IID~~G~Ir~~~~~~~~~g-r~~~eilr~l~alq~~~~~~ 167 (215)
T PRK13191 129 IVDDKGTVRLILYYPMEIG-RNIDEILRAIRALQLVDKAG 167 (215)
T ss_pred EECCCCEEEEEEecCCCCC-CCHHHHHHHHHHhhhhhhcC
Confidence 7899999988 45555433 48999999999999877765
No 21
>PRK13189 peroxiredoxin; Provisional
Probab=75.28 E-value=8.2 Score=25.96 Aligned_cols=39 Identities=15% Similarity=0.088 Sum_probs=28.5
Q ss_pred CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
.|.|++|.+.+ ....+ ....|..|...++.+|+...++|
T Consensus 130 fIID~~G~Ir~~~~~~~-~~gr~~~eilr~l~alq~~~~~~ 169 (222)
T PRK13189 130 FIIDPKGIIRAILYYPQ-EVGRNMDEILRLVKALQTSDEKG 169 (222)
T ss_pred EEECCCCeEEEEEecCC-CCCCCHHHHHHHHHHhhhHhhcC
Confidence 37899998887 33333 33336889999999999888775
No 22
>PTZ00137 2-Cys peroxiredoxin; Provisional
Probab=74.80 E-value=6.4 Score=27.43 Aligned_cols=38 Identities=18% Similarity=0.245 Sum_probs=29.9
Q ss_pred eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
|.|++|.+.. ....++... |..|...++++|+...+.|
T Consensus 193 IID~dG~I~~~~~~~~~~gr-~v~eiLr~l~alq~~~~~g 231 (261)
T PTZ00137 193 LVDKAGVVKHVAVYDLGLGR-SVDETLRLFDAVQFAEKTG 231 (261)
T ss_pred EECCCCEEEEEEEeCCCCCC-CHHHHHHHHHHhchhhhcC
Confidence 7899999998 545554443 8999999999999887775
No 23
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=71.31 E-value=3.8 Score=28.14 Aligned_cols=39 Identities=8% Similarity=-0.067 Sum_probs=33.6
Q ss_pred eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
....+.....+.+.+.++..-++.|.++|++.+.+|.=|
T Consensus 20 ~~~gl~~~~GH~~G~~~l~~~~~~c~~~gI~~lTvyaFS 58 (233)
T PRK14833 20 KLRGKARAAGHKKGVKTLREITIWCANHKLECLTLYAFS 58 (233)
T ss_pred HHCCCChhhhHHHHHHHHHHHHHHHHHcCCCEEEEeecc
Confidence 344555677899999999999999999999999999877
No 24
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=70.84 E-value=3.6 Score=29.00 Aligned_cols=36 Identities=14% Similarity=0.040 Sum_probs=31.3
Q ss_pred ccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 15 GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 15 ~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.+.....+.+.+.++..-+++|.++|++.+.+|.-|
T Consensus 60 g~~~~~GH~~G~~~l~~i~~~c~~lGIk~lTvYaFS 95 (275)
T PRK14835 60 GLQREMGHEFGVQKAYEVLEWCLELGIPTVTIWVFS 95 (275)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEE
Confidence 345566789999999999999999999999999877
No 25
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=70.63 E-value=13 Score=24.42 Aligned_cols=39 Identities=8% Similarity=-0.023 Sum_probs=28.5
Q ss_pred eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727 2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGF 41 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~ 41 (86)
|.|++|.+.. ....+... .|..|...++.+|+...+.|.
T Consensus 122 iID~~G~I~~~~~~~~~~g-r~~~ell~~l~~lq~~~~~~~ 161 (203)
T cd03016 122 IIDPDKKIRLILYYPATTG-RNFDEILRVVDALQLTDKHKV 161 (203)
T ss_pred EECCCCeEEEEEecCCCCC-CCHHHHHHHHHHHhhHhhcCc
Confidence 7889998887 44444332 368899999999998877653
No 26
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=69.04 E-value=4.5 Score=27.51 Aligned_cols=48 Identities=15% Similarity=0.117 Sum_probs=37.0
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
|.|.||++- ....+.....+.+.+..+..-++.|.++|++.+.+|.=|
T Consensus 7 ImDGNrRwA-~~~gl~~~~GH~~G~~~~~~i~~~~~~~gI~~lTvyaFS 54 (221)
T cd00475 7 IMDGNRRWA-KQRGMDRIEGHKAGAEKLRDILRWCLELGVKEVTLYAFS 54 (221)
T ss_pred ecCCCHHHH-HHCCCChhHhHHHHHHHHHHHHHHHHHcCCCEEEEEeec
Confidence 344444442 344556777899999999999999999999999999766
No 27
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=68.67 E-value=4.7 Score=27.72 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=37.0
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
|.|.||++- ....+.....+.+.+.++..-++.|.++|++.+.+|.=|
T Consensus 10 ImDGNrRwA-k~~g~~~~~GH~~G~~~l~~i~~~~~~lgIk~lTvYaFS 57 (233)
T PRK14841 10 IMDGNGRWA-KKRGLPRIKGHQRGAEVLHNTVKWSLELGIKYLTAFSFS 57 (233)
T ss_pred EccCCHHHH-HHCCCchhhhHHHHHHHHHHHHHHHHHcCCCEEEEEeee
Confidence 344444442 333455677899999999999999999999999999877
No 28
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=66.73 E-value=5.3 Score=27.63 Aligned_cols=47 Identities=13% Similarity=0.098 Sum_probs=36.4
Q ss_pred eCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 3 RADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 3 ~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.|.||++- ....+.....+.+.+..+..-++.|.++|++.+.+|.=|
T Consensus 16 mDGNrRwA-k~~gl~~~~GH~~G~~~l~~i~~~c~~lgI~~vTvYaFS 62 (241)
T PRK14842 16 MDGNGRWA-ESQGKKRSEGHREGANAIDRLMDASLEYGLKNISLYAFS 62 (241)
T ss_pred cCCCHHHH-HHCCCChhHhHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 33344432 333456677899999999999999999999999999877
No 29
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=66.39 E-value=5.1 Score=27.90 Aligned_cols=35 Identities=9% Similarity=-0.200 Sum_probs=30.2
Q ss_pred cCCC-cchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 16 VGIT-TNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 16 ~g~~-tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
+... ..+.+.+.++..-+++|.++|++.+.+|.-|
T Consensus 46 l~~~~~GH~~G~~~l~~~~~~~~~~gIk~lTvYaFS 81 (256)
T PRK14828 46 FTDVSQGHRAGAAKIGEFLGWCDETDVNVVTLYLLS 81 (256)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEE
Confidence 3444 6688999999999999999999999999875
No 30
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=65.66 E-value=5.4 Score=28.43 Aligned_cols=37 Identities=16% Similarity=-0.007 Sum_probs=32.3
Q ss_pred eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 14 NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 14 ~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
..+.....+.+.+.++..-++.|.++|++.|.+|.=|
T Consensus 85 ~gl~~~~GH~~G~~~l~~v~~~c~~lGI~~lTvYaFS 121 (296)
T PRK14827 85 RGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFS 121 (296)
T ss_pred CCCCHhHHHHHHHHHHHHHHHHHHHcCCCEEEEeeec
Confidence 3455677789999999999999999999999999876
No 31
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=65.50 E-value=5.4 Score=27.79 Aligned_cols=38 Identities=13% Similarity=0.007 Sum_probs=32.9
Q ss_pred eeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 13 HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 13 ~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
...+.....+.+.+.++..-++.|.++|++.+.+|.=|
T Consensus 35 ~~gl~~~~GH~~G~~~l~~i~~~c~~~gI~~lTvyaFS 72 (253)
T PRK14832 35 SQGLPRIAGHRQGARTLKELLRCCKDWGIKALTAYAFS 72 (253)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 33455677899999999999999999999999999877
No 32
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=65.43 E-value=5.8 Score=27.17 Aligned_cols=48 Identities=17% Similarity=0.110 Sum_probs=37.8
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
|.|.||++- ....+.....+.+...++..-++.|.++|++.+.+|.=|
T Consensus 6 ImDGNrRwA-k~~gl~~~~GH~~G~~~~~~v~~~c~~~GI~~lT~yaFS 53 (226)
T TIGR00055 6 IMDGNGRWA-KKKGKPRAYGHKAGVKSLRRILRWCANLGVECLTLYAFS 53 (226)
T ss_pred EcCCCHHHH-HHCCCChhHhHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 445555553 333456677899999999999999999999999999877
No 33
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=64.95 E-value=5.7 Score=27.57 Aligned_cols=35 Identities=14% Similarity=-0.052 Sum_probs=30.0
Q ss_pred cCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 16 VGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 16 ~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
+.....+.+-+..+..-+++|.++|++.+.+|.-|
T Consensus 42 l~~~~Gh~~G~~~l~~~l~~c~~~GI~~vTvYaFS 76 (251)
T PRK14830 42 LPRIAGHKAGMDTVKKITKAASELGVKVLTLYAFS 76 (251)
T ss_pred CchhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEEe
Confidence 33455688999999999999999999999999865
No 34
>PRK14838 undecaprenyl pyrophosphate synthase; Provisional
Probab=64.70 E-value=6 Score=27.34 Aligned_cols=37 Identities=14% Similarity=-0.037 Sum_probs=32.0
Q ss_pred eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 14 NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 14 ~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
..+.....+.+.+..+..-++.|.++|++.+.+|.=|
T Consensus 28 ~gl~~~~GH~~G~~~l~~i~~~~~~~gI~~lT~YaFS 64 (242)
T PRK14838 28 RGKERSFGHQAGAETVHIITEEAARLGVKFLTLYTFS 64 (242)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeec
Confidence 3455667889999999999999999999999999877
No 35
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=64.49 E-value=6 Score=27.46 Aligned_cols=35 Identities=14% Similarity=-0.048 Sum_probs=30.8
Q ss_pred cCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 16 VGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 16 ~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
+.....+.+.+..+..-+++|.++|++.+.+|.-|
T Consensus 34 ~~~~~GH~~G~~~l~~i~~~c~~lgI~~lTvYaFS 68 (249)
T PRK14834 34 LPRAAGHRAGVEALRRVVRAAGELGIGYLTLFAFS 68 (249)
T ss_pred CchhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEEe
Confidence 44566789999999999999999999999999865
No 36
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=64.15 E-value=6.3 Score=27.22 Aligned_cols=36 Identities=19% Similarity=0.046 Sum_probs=31.7
Q ss_pred ccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 15 GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 15 ~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.+.....+.+.+.++..-+++|.++|++.+.+|.=|
T Consensus 33 g~~~~~GH~~G~~~l~~iv~~c~~~gI~~vTvYaFS 68 (243)
T PRK14829 33 GLKRTEGHKAGEPVLFDVVAGAIEAGVPYLSLYTFS 68 (243)
T ss_pred CCChhHHHHHHHHHHHHHHHHHHHcCCCEEEEeeec
Confidence 445667789999999999999999999999999876
No 37
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=63.61 E-value=6.2 Score=27.10 Aligned_cols=48 Identities=10% Similarity=-0.000 Sum_probs=37.2
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
|.|.||++- ....+.....+.+...++..-++.|.++|++.+.+|.=|
T Consensus 13 ImDGNrRwA-k~~gl~~~~GH~~G~~~~~~i~~~c~~~GI~~lT~YaFS 60 (230)
T PRK14837 13 IMDGNRRWA-LKKGLSFFEGHKEGLKRAKEIVKHSLKLGIKYLSLYVFS 60 (230)
T ss_pred EccCCHHHH-HHCCCchhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 444455542 233455677899999999999999999999999999877
No 38
>cd03015 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric
Probab=63.59 E-value=22 Score=22.45 Aligned_cols=40 Identities=13% Similarity=0.170 Sum_probs=27.2
Q ss_pred CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727 1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGF 41 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~ 41 (86)
+|.|++|.++. ..... +...+..|....+..+..+.++|.
T Consensus 124 ~lID~~G~I~~~~~~~~-~~~~~~~~il~~l~~~~~~~~~~~ 164 (173)
T cd03015 124 FIIDPEGIIRHITVNDL-PVGRSVDETLRVLDALQFVEEHGE 164 (173)
T ss_pred EEECCCCeEEEEEecCC-CCCCCHHHHHHHHHHhhhhhhcCC
Confidence 37889999887 43332 223356778888888888777764
No 39
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=63.35 E-value=7.1 Score=27.06 Aligned_cols=36 Identities=14% Similarity=-0.024 Sum_probs=31.9
Q ss_pred ccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 15 GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 15 ~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.+.....+.+.+.++..-+++|.++|++.+.+|.=|
T Consensus 39 gl~~~~GH~~G~~~l~~i~~~c~~~GI~~vT~yaFS 74 (249)
T PRK14831 39 GLPRIMGHRRGVDALKDLLRCCKDWGIGALTAYAFS 74 (249)
T ss_pred CCchhhhHHHHHHHHHHHHHHHHHcCCCEEEEeecc
Confidence 445667789999999999999999999999999888
No 40
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=62.96 E-value=6.9 Score=27.05 Aligned_cols=38 Identities=13% Similarity=0.009 Sum_probs=32.4
Q ss_pred eeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 13 HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 13 ~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
...+.....+.+.+.++..-++.|.++|++.+.+|.=|
T Consensus 26 ~~gl~~~~GH~~G~~~l~~i~~~c~~~GI~~lTvYaFS 63 (239)
T PRK14839 26 ARGLPRLAGHRAGVEAIRRVVEAAPDLGIGTLTLYAFS 63 (239)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEec
Confidence 33455667789999999999999999999999999877
No 41
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=61.16 E-value=6.8 Score=28.30 Aligned_cols=48 Identities=10% Similarity=0.072 Sum_probs=37.2
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
|.|.||++- ....+.....+.+...++..-++.|.++|++.+.+|.=|
T Consensus 26 IMDGNrRwA-k~~gl~~~~GH~~G~~~l~~il~~c~~lGIk~lTlYAFS 73 (322)
T PTZ00349 26 IMDGNRRFA-KEKGLHSAIGHFMGSKALIQIIEICIKLKIKILSVFSFS 73 (322)
T ss_pred EcCCCHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 444455543 233455667899999999999999999999999999877
No 42
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=60.41 E-value=7.4 Score=26.98 Aligned_cols=49 Identities=14% Similarity=0.088 Sum_probs=36.3
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchH
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSK 51 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~ 51 (86)
|.|.+|++-. ...+.....+.+-..++-.-++.|.++|++.+.+|..|-
T Consensus 23 ImDGN~RwAk-~~~~~r~~Gh~~G~~~~~~i~~~~~~lgik~ltlyafSt 71 (245)
T COG0020 23 IMDGNRRWAK-KRGLPRIEGHKAGAKALREILEWCLELGIKYLTLYAFST 71 (245)
T ss_pred EecCChHHHH-hCCCChhHHHHHhHHHHHHHHHHHHHcCCCEEEEEEEeh
Confidence 3444444422 224556777888889999999999999999999999884
No 43
>TIGR03137 AhpC peroxiredoxin. This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue.
Probab=59.81 E-value=25 Score=22.73 Aligned_cols=38 Identities=8% Similarity=-0.006 Sum_probs=27.6
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhc
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQK 39 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~ 39 (86)
|.|++|.++..........-+..|..+.+.+++.+.+.
T Consensus 124 iID~~G~I~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~ 161 (187)
T TIGR03137 124 VIDPEGVIQAVEITDNGIGRDASELLRKIKAAQYVAAH 161 (187)
T ss_pred EECCCCEEEEEEEeCCCCCCCHHHHHHHHHHhhhHHhc
Confidence 78899999873333233334788888988999988876
No 44
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=59.06 E-value=8.4 Score=26.39 Aligned_cols=38 Identities=16% Similarity=0.078 Sum_probs=32.5
Q ss_pred eeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 13 HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 13 ~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
...+.....+.+.+..+..-++.|.++|++.+.+|.=|
T Consensus 10 ~~g~~~~~GH~~G~~~l~~i~~~c~~~GI~~lT~yaFS 47 (229)
T PRK10240 10 KQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS 47 (229)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeee
Confidence 33455667789999999999999999999999999877
No 45
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 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 [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=58.10 E-value=39 Score=20.31 Aligned_cols=47 Identities=19% Similarity=0.179 Sum_probs=32.1
Q ss_pred eeCCCCCEEE-eee-ccC----CCcchHHHHHHHHHHHHHHHhcCCceEEEec
Q 034727 2 LRADDGSLIY-NHN-GVG----ITTNNVAKYGSLILGLKYALQKGFFNFRVRG 48 (86)
Q Consensus 2 ~~~~~g~~~~-~~~-~~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~ 48 (86)
+.|.+|.++. .+. .+| ......|-+.+....++.+.++|++.+.+.-
T Consensus 16 lTd~~G~~~~~~S~G~~gfK~~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i 68 (110)
T PF00411_consen 16 LTDLKGNVLFWSSAGSLGFKGARKSTPYAAQQAAEKIAKKAKELGIKTVRVKI 68 (110)
T ss_dssp EEETTSEEEEEEETTTSSTTTTCGSSHHHHHHHHHHHHHHHHCTTEEEEEEEE
T ss_pred EECCCCCEEEEEeccccccccccccCHHHHHHHHHHHHHHHHHcCCeEEEEEE
Confidence 4578888886 333 334 2344566667777888899999998776653
No 46
>PTZ00253 tryparedoxin peroxidase; Provisional
Probab=56.80 E-value=31 Score=22.47 Aligned_cols=38 Identities=18% Similarity=0.251 Sum_probs=27.5
Q ss_pred eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727 2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG 40 (86)
Q Consensus 2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~ 40 (86)
|.|++|.++. ...... ...|..|....+.+++.....+
T Consensus 132 iID~~G~i~~~~~~~~~-~~r~~~e~l~~l~a~~~~~~~~ 170 (199)
T PTZ00253 132 IIDPKGMLRQITVNDMP-VGRNVEEVLRLLEAFQFVEKHG 170 (199)
T ss_pred EECCCCEEEEEEecCCC-CCCCHHHHHHHHHhhhhHHhcC
Confidence 6899999887 333333 4457888888889998876643
No 47
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=54.33 E-value=37 Score=19.99 Aligned_cols=52 Identities=10% Similarity=-0.040 Sum_probs=28.7
Q ss_pred CeeCCCCCEEEeeeccCC---CcchHHHHHHHHHHHHHHHhcCCceEEEecchHH
Q 034727 1 MLRADDGSLIYNHNGVGI---TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKL 52 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~---~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~l 52 (86)
||.+++|+++..+..-.. ....-||..|+..+.+.--....+...+|+.-+-
T Consensus 22 viv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~EP 76 (109)
T cd01285 22 VIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEP 76 (109)
T ss_pred EEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCCC
Confidence 477888888863322211 2334688888877654322122455666665443
No 48
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=53.18 E-value=34 Score=20.71 Aligned_cols=33 Identities=15% Similarity=0.121 Sum_probs=21.3
Q ss_pred CeeCCCCCEEEeeeccCCCcchHHHHHHHHHHHH
Q 034727 1 MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLK 34 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~ 34 (86)
||.+++|+++..+..-.. ...-||..|+..+.+
T Consensus 24 viv~~~g~iv~~g~n~~~-~~~HAE~~ai~~a~~ 56 (115)
T cd01284 24 VIVDDDGEIVGEGYHRKA-GGPHAEVNALASAGE 56 (115)
T ss_pred EEEeCCCeEEEEecCCCC-CcccHHHHHHHHHhh
Confidence 467777888863222222 456789988877765
No 49
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=50.72 E-value=11 Score=26.19 Aligned_cols=36 Identities=17% Similarity=0.145 Sum_probs=30.5
Q ss_pred ccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 15 GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 15 ~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.+.....+.+-+.++..-+++|.++|++.+.+|.=|
T Consensus 33 gl~~~~GH~~G~~~~~~iv~~c~~~gI~~lTvYaFS 68 (253)
T PRK14836 33 GKPRVEGHRAGVRAVRRTIEFCLEKGIEMLTLFAFS 68 (253)
T ss_pred CCchhhhHHHHHHHHHHHHHHHHHcCCCEEehhHhh
Confidence 345566788999999999999999999999998744
No 50
>cd07353 harmonin_N N-terminal protein-binding module of harmonin. Harmonin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. Harmonin contains a single copy of this domain, which is found at the N-terminus of all three harmonin isoform classes (a, b and c), and which preceeds the first PDZ protein-binding domain, PDZ1. This harmonin_N domain binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network.
Probab=50.29 E-value=9.5 Score=21.64 Aligned_cols=51 Identities=25% Similarity=0.091 Sum_probs=32.6
Q ss_pred CcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhhhcCCChhHHHHHHHHHHHh
Q 034727 19 TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLK 80 (86)
Q Consensus 19 ~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~~~~k~~~l~~~~~~i~~l~ 80 (86)
.-.|++|-.++...|+.-.+-+. --.+.||-++||| .|.=-|+++.|+.+.
T Consensus 15 ~ie~EaEkd~lY~~Lr~YHqSm~-lp~li~Dlk~VIN----------~P~R~pLfd~IR~li 65 (79)
T cd07353 15 LIDNEAEKDYLYDVLRMYHQSMN-LPVLVGDLKLVIN----------EPSRLPLFDAIRPLI 65 (79)
T ss_pred hhccHHHHHHHHHHHHHHHhccC-HHHHHHHHHHHhC----------CccccchHHHHHhhc
Confidence 34588999999999986655331 1234466666654 444456777777654
No 51
>CHL00041 rps11 ribosomal protein S11
Probab=48.57 E-value=61 Score=19.75 Aligned_cols=56 Identities=11% Similarity=0.086 Sum_probs=35.5
Q ss_pred eeCCCCCEEE-eee-ccC----CCcchHHHHHHHHHHHHHHHhcCCceEEEec-----chHHHHHHH
Q 034727 2 LRADDGSLIY-NHN-GVG----ITTNNVAKYGSLILGLKYALQKGFFNFRVRG-----DSKLVHMQV 57 (86)
Q Consensus 2 ~~~~~g~~~~-~~~-~~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~-----DS~lvi~q~ 57 (86)
|.|+.|.++. .+. .+| ......|-..|.-...+.+.++|++.+.++- ..+.+++.+
T Consensus 29 lTd~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG~G~Gr~~~ir~l 95 (116)
T CHL00041 29 VTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKGPGLGRDTALRAI 95 (116)
T ss_pred EEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcHHHHHHHH
Confidence 5678899886 443 233 2233566666666778889999998776654 334555544
No 52
>PRK05309 30S ribosomal protein S11; Validated
Probab=48.09 E-value=66 Score=20.00 Aligned_cols=57 Identities=16% Similarity=0.099 Sum_probs=36.0
Q ss_pred eeCCCCCEEE-eee-ccC----CCcchHHHHHHHHHHHHHHHhcCCceEEEec-----chHHHHHHHh
Q 034727 2 LRADDGSLIY-NHN-GVG----ITTNNVAKYGSLILGLKYALQKGFFNFRVRG-----DSKLVHMQVC 58 (86)
Q Consensus 2 ~~~~~g~~~~-~~~-~~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~-----DS~lvi~q~~ 58 (86)
+.|..|.++. .+. .+| .-....|-+.|.....+.+.++|++.+.++- ..+.++..+.
T Consensus 33 lTd~~G~~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr~~air~L~ 100 (128)
T PRK05309 33 ITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQ 100 (128)
T ss_pred EEcCCCCEEEEEecCccEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcHHHHHHHHH
Confidence 5678888886 443 233 2333556666667778889999998776654 2345555543
No 53
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=46.30 E-value=21 Score=21.58 Aligned_cols=31 Identities=13% Similarity=0.203 Sum_probs=18.8
Q ss_pred CeeCCCCCEEEeeeccCCCcchHHHHHHHHH
Q 034727 1 MLRADDGSLIYNHNGVGITTNNVAKYGSLIL 31 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~ 31 (86)
+|.|++|+++...........+..++.+++.
T Consensus 118 ~lid~~G~v~~~~~~~~~~~~~~~~~~~~~~ 148 (149)
T cd03018 118 FVIDRDGIIRYAWVSDDGEPRDLPDYDEALD 148 (149)
T ss_pred EEECCCCEEEEEEecCCcccccchhHHHHhh
Confidence 3678899877522222222667778877765
No 54
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=46.00 E-value=62 Score=20.45 Aligned_cols=48 Identities=19% Similarity=0.229 Sum_probs=31.8
Q ss_pred eeCCCCCEEE--eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIY--NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~--~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
++..+|+++. --+..--.-.+.||-.|+..++.. -...+..+.+++|+
T Consensus 32 ~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 32 LRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred EEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 6677887775 223333344578999999888754 22345678888886
No 55
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=45.11 E-value=1e+02 Score=21.32 Aligned_cols=57 Identities=12% Similarity=0.072 Sum_probs=36.0
Q ss_pred eeCCCCCE--E-E-eeeccC----CCcchHHHHHHHHHHHHHHHhcCCceEEEe----cchHHHHHHHh
Q 034727 2 LRADDGSL--I-Y-NHNGVG----ITTNNVAKYGSLILGLKYALQKGFFNFRVR----GDSKLVHMQVC 58 (86)
Q Consensus 2 ~~~~~g~~--~-~-~~~~~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~----~DS~lvi~q~~ 58 (86)
|.|..|.. + | .+..+| ......|-+.|.-.+.+.|.++|++.+.|+ |-.+-+++++.
T Consensus 134 lTD~~GNv~tl~WSSAG~~GFKGsKKsTpfAAQ~aae~aakka~~~GIk~V~V~vKGpGgREtALRaL~ 202 (233)
T PTZ00090 134 VVNKSKNYKTVFGSFAGNVGFRKKLQQSERCAYRIGENIAKKCRRLGIFAVDIKFRRIMRVETVLQAFY 202 (233)
T ss_pred EEeCCCCEEEEEEEcccccCcccCccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeCCChHHHHHHHHH
Confidence 56788884 4 4 444555 223345555566677888999999877664 33456666654
No 56
>PHA03326 nuclear egress membrane protein; Provisional
Probab=43.45 E-value=33 Score=24.19 Aligned_cols=17 Identities=18% Similarity=0.214 Sum_probs=13.7
Q ss_pred CcchHHHHHHHHHHHHH
Q 034727 19 TTNNVAKYGSLILGLKY 35 (86)
Q Consensus 19 ~tnn~aEy~Ali~gL~~ 35 (86)
.-.|+.||.+|+..|-+
T Consensus 151 GPenE~EY~~LLReiy~ 167 (275)
T PHA03326 151 GPENESEYIALLREIYA 167 (275)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 44699999999998743
No 57
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=41.19 E-value=38 Score=19.26 Aligned_cols=49 Identities=8% Similarity=-0.029 Sum_probs=25.9
Q ss_pred CeeCCCCCEEEeeeccCCCcc---hHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 1 MLRADDGSLIYNHNGVGITTN---NVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~tn---n~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
||++++|..+..+......++ --||..|+..+-+. -....+...+|+-.
T Consensus 29 viv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~-~~~~~~~~~lyvt~ 80 (102)
T PF00383_consen 29 VIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN-GGSSLKGCTLYVTL 80 (102)
T ss_dssp EEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT-TSSGETTEEEEEEE
T ss_pred EEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh-ccccccCcccccCC
Confidence 467777777763333222333 38899998876654 11112335555533
No 58
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=40.34 E-value=54 Score=22.59 Aligned_cols=51 Identities=18% Similarity=0.147 Sum_probs=38.4
Q ss_pred CEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEE-e----cchHHHHHHHh
Q 034727 8 SLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRV-R----GDSKLVHMQVC 58 (86)
Q Consensus 8 ~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i-~----~DS~lvi~q~~ 58 (86)
.++..+...+..+|+.+|..|.+.|++....++.+...| + -||+--++-+.
T Consensus 95 ~~lt~~~~~~~~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k 150 (225)
T COG3341 95 SWLTESSEFSIKSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVK 150 (225)
T ss_pred eeeeeecccccccCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHh
Confidence 344455566789999999999999999988887766655 5 57776666554
No 59
>PF01255 Prenyltransf: Putative undecaprenyl diphosphate synthase; InterPro: IPR001441 Synonym(s): Di-trans-poly-cis-undecaprenyl-diphosphate synthase, Undecaprenyl pyrophosphate synthetase, Undecaprenyl pyrophosphate synthase, UPP synthetase Di-trans-poly-cis-decaprenylcistransferase (2.5.1.31 from EC) (UPP synthetase) generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) []. This bacterial enzyme is also found in archaebacteria and in a number of uncharacterised proteins including some from yeasts. This entry also matches related enzymes that transfer alkyl groups, such as dehydrodolichyl diphosphate synthase.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 2D2R_B 2DTN_B 1F75_B 1X07_A 2E9D_A 1JP3_A 3QAS_A 1X09_A 1V7U_B 2E9A_A ....
Probab=39.76 E-value=7.1 Score=26.37 Aligned_cols=36 Identities=19% Similarity=0.133 Sum_probs=29.0
Q ss_pred ccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 15 GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 15 ~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.++....+.+.+..+..-++.|.++|++.+.+|.=|
T Consensus 13 g~~~~~Gh~~G~~~l~~i~~~~~~~gI~~lTvYaFS 48 (223)
T PF01255_consen 13 GLPRSEGHRAGAEKLKEIVEWCLELGIKYLTVYAFS 48 (223)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHCT-SEEEEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEec
Confidence 344556678889999999999999999999999755
No 60
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=38.97 E-value=87 Score=18.77 Aligned_cols=47 Identities=17% Similarity=0.088 Sum_probs=29.6
Q ss_pred eeCCCCCEEE-eee-ccC----CCcchHHHHHHHHHHHHHHHhcCCceEEEec
Q 034727 2 LRADDGSLIY-NHN-GVG----ITTNNVAKYGSLILGLKYALQKGFFNFRVRG 48 (86)
Q Consensus 2 ~~~~~g~~~~-~~~-~~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~ 48 (86)
+.|+.|.++. .+. .+| ......|-..|.....+.+.++|++.+.++-
T Consensus 16 lTd~~g~~~~~~S~G~~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~ 68 (108)
T TIGR03632 16 ITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYV 68 (108)
T ss_pred EEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE
Confidence 5678888876 443 233 2233455455555667888899998776654
No 61
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=37.11 E-value=56 Score=21.63 Aligned_cols=26 Identities=27% Similarity=0.188 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHhcCCceEEEecchH
Q 034727 26 YGSLILGLKYALQKGFFNFRVRGDSK 51 (86)
Q Consensus 26 y~Ali~gL~~a~~~~~~~v~i~~DS~ 51 (86)
-+.|-.||+.|.++|++.|.+-.|+.
T Consensus 116 ~emLkl~L~~ar~lgi~~Vlvtcd~d 141 (174)
T COG3981 116 KEMLKLALEKARELGIKKVLVTCDKD 141 (174)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEeCCC
Confidence 35677899999999999999988864
No 62
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=36.83 E-value=90 Score=19.80 Aligned_cols=36 Identities=14% Similarity=0.098 Sum_probs=21.2
Q ss_pred CeeCCCCCEEEeeeccCCCcc---hHHHHHHHHHHHHHH
Q 034727 1 MLRADDGSLIYNHNGVGITTN---NVAKYGSLILGLKYA 36 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~tn---n~aEy~Ali~gL~~a 36 (86)
||++++|.++..+......++ .-||..|+-.+-+..
T Consensus 33 viV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~ 71 (152)
T COG0590 33 VIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETL 71 (152)
T ss_pred EEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhh
Confidence 577788888873333322222 257777776665544
No 63
>cd02955 SSP411 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein, called SSP411, is specifically expressed in the testis in an age-dependent manner. The SSP411 mRNA is increased during spermiogenesis and is localized in round and elongated spermatids, suggesting a function in fertility regulation.
Probab=36.58 E-value=64 Score=19.73 Aligned_cols=35 Identities=3% Similarity=0.020 Sum_probs=21.0
Q ss_pred CeeCCCCCEEEeeeccCCC-cchHHHHHHHHHHHHH
Q 034727 1 MLRADDGSLIYNHNGVGIT-TNNVAKYGSLILGLKY 35 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~-tnn~aEy~Ali~gL~~ 35 (86)
|+.+|+|+++..+.+++.. .-+...+.-++..++.
T Consensus 85 vfl~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 (124)
T cd02955 85 VFLTPDLKPFFGGTYFPPEDRYGRPGFKTVLEKIRE 120 (124)
T ss_pred EEECCCCCEEeeeeecCCCCcCCCcCHHHHHHHHHH
Confidence 4789999999855555332 2234555555555543
No 64
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=36.53 E-value=38 Score=24.54 Aligned_cols=21 Identities=19% Similarity=-0.069 Sum_probs=16.9
Q ss_pred CceEEEecchHHHHHHHh-hhh
Q 034727 41 FFNFRVRGDSKLVHMQVC-CWL 61 (86)
Q Consensus 41 ~~~v~i~~DS~lvi~q~~-~~~ 61 (86)
..+|.+-|||+-|++++. .+.
T Consensus 214 ~~~IFLATDSaeVid~fr~~FP 235 (321)
T PF05830_consen 214 PVRIFLATDSAEVIDQFRKKFP 235 (321)
T ss_dssp -EEEEEEES-HHHHHHHHHHST
T ss_pred CeeEEEecCcHHHHHHHHHHCC
Confidence 357999999999999998 874
No 65
>PF06006 DUF905: Bacterial protein of unknown function (DUF905); InterPro: IPR009253 This family consists of several short hypothetical proteobacterial proteins of unknown function.; PDB: 2HJJ_A.
Probab=33.51 E-value=28 Score=19.59 Aligned_cols=16 Identities=19% Similarity=0.478 Sum_probs=9.1
Q ss_pred CeeCCCCCEEE-eeecc
Q 034727 1 MLRADDGSLIY-NHNGV 16 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~ 16 (86)
||||++|+.++ ...+-
T Consensus 36 vvRd~~g~mvWRaWNFE 52 (70)
T PF06006_consen 36 VVRDTEGQMVWRAWNFE 52 (70)
T ss_dssp EEE-SS--EEEEEESSS
T ss_pred EEEcCCCcEEEEeeccC
Confidence 58888999998 54444
No 66
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=33.38 E-value=1.1e+02 Score=18.28 Aligned_cols=48 Identities=21% Similarity=0.088 Sum_probs=31.3
Q ss_pred eeCCCCCEEE-eee-ccCCCcchHHHHHHHHHHHHHHHhcCC-ceEEEecch
Q 034727 2 LRADDGSLIY-NHN-GVGITTNNVAKYGSLILGLKYALQKGF-FNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~-~~~-~~g~~tnn~aEy~Ali~gL~~a~~~~~-~~v~i~~DS 50 (86)
|.|++|.+.. ... +....++...|..+++.||-.. .+|. -.|.+.+-+
T Consensus 39 l~D~~G~~HeLgtntfgl~S~l~~~eV~~la~~lae~-algk~p~V~V~t~~ 89 (96)
T PF11080_consen 39 LTDEDGNPHELGTNTFGLISALSAEEVAQLARGLAES-ALGKTPEVEVTTWE 89 (96)
T ss_pred EecCCCCEeecCCCeEEEEecCCHHHHHHHHHHHhhh-hcCCCCceEEEEHH
Confidence 6789999987 433 4456777888999999988532 2232 345554443
No 67
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=31.79 E-value=51 Score=16.36 Aligned_cols=16 Identities=31% Similarity=0.561 Sum_probs=8.6
Q ss_pred eeCCCCCEEEeeeccC
Q 034727 2 LRADDGSLIYNHNGVG 17 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g 17 (86)
++|.+|+.++|..--|
T Consensus 20 l~D~~gRTiWFqGdPG 35 (39)
T PF09292_consen 20 LRDRNGRTIWFQGDPG 35 (39)
T ss_dssp EE-TTS-EEEESS---
T ss_pred ccccCCCEEEeeCCCC
Confidence 6888999998554433
No 68
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=31.43 E-value=1.5e+02 Score=19.16 Aligned_cols=47 Identities=9% Similarity=-0.029 Sum_probs=31.6
Q ss_pred eeCCCCCEEE--eeeccC----C-CcchHHHHHHHHHHHHHHHhcCCceEEEec
Q 034727 2 LRADDGSLIY--NHNGVG----I-TTNNVAKYGSLILGLKYALQKGFFNFRVRG 48 (86)
Q Consensus 2 ~~~~~g~~~~--~~~~~g----~-~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~ 48 (86)
|.|..|.++. .+..+| . .....|-..|.....+.+.++|++.+.|.-
T Consensus 44 iTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~v 97 (149)
T PTZ00129 44 VTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGINALHIKL 97 (149)
T ss_pred EEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCeEEEEEE
Confidence 4577788775 333444 1 344566666777888889999998876655
No 69
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=30.21 E-value=26 Score=20.95 Aligned_cols=35 Identities=23% Similarity=0.231 Sum_probs=29.2
Q ss_pred chHHHHHHHHHHHHHHHhcCCc-eEEEecchHHHHH
Q 034727 21 NNVAKYGSLILGLKYALQKGFF-NFRVRGDSKLVHM 55 (86)
Q Consensus 21 nn~aEy~Ali~gL~~a~~~~~~-~v~i~~DS~lvi~ 55 (86)
=...++.-+-.|...|.+.|.+ .+.++.|..+|++
T Consensus 32 l~~~~~~~i~~av~~A~~KG~kesLvl~~d~AlVvs 67 (96)
T TIGR02530 32 INPDDWKKLLEAVEEAESKGVKDSLILMNDAALVVS 67 (96)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCceEEEeCCEEEEEE
Confidence 3567888899999999999984 6888888888876
No 70
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=29.22 E-value=99 Score=18.89 Aligned_cols=47 Identities=15% Similarity=0.192 Sum_probs=28.4
Q ss_pred eeCCCCCEEEeeeccCCCc---chHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 2 LRADDGSLIYNHNGVGITT---NNVAKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~t---nn~aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
+++.+|+++. +......+ .-.||-.|+..+...-. ..++.+.+.+++
T Consensus 27 ~~~~~G~i~~-G~n~e~~~~~~s~~AE~~Ai~~a~~~g~-~~i~~i~vv~~~ 76 (127)
T TIGR01354 27 LLTKDGRIFT-GVNVENASYPLTICAERSAIGKAISAGY-RKFVAIAVADSA 76 (127)
T ss_pred EEeCCCCEEE-EEeecccCCCCCcCHHHHHHHHHHHcCC-CCeEEEEEEeCC
Confidence 5667788776 33333332 23688888877764422 256778777665
No 71
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=28.37 E-value=19 Score=18.79 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=26.5
Q ss_pred HHHHHHhcCCce-EEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHHh
Q 034727 32 GLKYALQKGFFN-FRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRLK 80 (86)
Q Consensus 32 gL~~a~~~~~~~-v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l~ 80 (86)
+|+.|.++|+-. +.-.||+.+-..++. .-. +.+|.-..+.+++.+++
T Consensus 2 aLk~aveLgI~dii~~~g~~~ls~~eia~~l~--~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 2 ALKCAVELGIPDIIHNAGGGPLSLSEIAARLP--TSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp HHHHHHHTTHHHHHHHHTTS-BEHHHHHHTST--CT-TTHHHHHHHHHHHH
T ss_pred cHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcC--CCCcchHHHHHHHHHHh
Confidence 466677777633 233334555556665 444 45666677777777654
No 72
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=28.14 E-value=84 Score=17.18 Aligned_cols=39 Identities=21% Similarity=0.077 Sum_probs=23.5
Q ss_pred CCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEe
Q 034727 7 GSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVR 47 (86)
Q Consensus 7 g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~ 47 (86)
|..+..|-+.|..|++... .+...|+.....+..++.++
T Consensus 27 g~~iQ~SVf~~~~~~~~~~--~l~~~l~~~i~~~~d~i~i~ 65 (78)
T PF09827_consen 27 GTRIQYSVFEGNLTNAELR--KLRRELEKLIDPDEDSIRIY 65 (78)
T ss_dssp TEEEETTEEEEEE-HHHHH--HHHHHHHHHSCTTTCEEEEE
T ss_pred CccccceEEEEEcCHHHHH--HHHHHHHhhCCCCCCEEEEE
Confidence 5455567777766655444 77777777666554555554
No 73
>PF09818 ABC_ATPase: Predicted ATPase of the ABC class; InterPro: IPR019195 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry consists of various predicted ABC transporter class ATPases.
Probab=27.69 E-value=1.4e+02 Score=22.72 Aligned_cols=81 Identities=16% Similarity=0.216 Sum_probs=49.0
Q ss_pred eeCCCCCEEE---eeeccC----------CCcchHHHHHHHHHHHHHHHhcCCceEEEecch---HHHHHH--Hhhhhhc
Q 034727 2 LRADDGSLIY---NHNGVG----------ITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS---KLVHMQ--VCCWLME 63 (86)
Q Consensus 2 ~~~~~g~~~~---~~~~~g----------~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS---~lvi~q--~~~~~~~ 63 (86)
||..||+.+. .+-++. ..|-|..-.......+..|++.|.+.+.|.-|. ++.++- |+..-.
T Consensus 289 irAEDGR~V~~vDISpFI~~LP~g~dT~~FsT~~ASGSTSqAAnI~EAlE~Ga~~LLiDEDtsATNfmiRD~rMq~Lv~- 367 (448)
T PF09818_consen 289 IRAEDGRSVEGVDISPFINNLPGGKDTTCFSTENASGSTSQAANIMEALEAGARLLLIDEDTSATNFMIRDERMQALVS- 367 (448)
T ss_pred EEecCCceEeCccchHHHhhCCCCCCCCcccccCCCchHHHHHHHHHHHHcCCCEEEEcCcccchheeehhHHHHHhhc-
Confidence 4556777775 333332 134455566666677777889999999999987 444421 111100
Q ss_pred CCChhHHHHHHHHHHHhhcc
Q 034727 64 DQTPGMAELCGEAKRLKDKF 83 (86)
Q Consensus 64 ~k~~~l~~~~~~i~~l~~~f 83 (86)
.....+.|+.+.++.|.+++
T Consensus 368 k~kEPITPfidrvr~l~~~~ 387 (448)
T PF09818_consen 368 KEKEPITPFIDRVRSLYEKL 387 (448)
T ss_pred cCCCCcchHHHHHHHHHHHc
Confidence 01223778888898887664
No 74
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=26.67 E-value=1.6e+02 Score=18.04 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=28.7
Q ss_pred eeCCCCC-EEE-eeec-cC----CCcchHHHHHHHHHHHHHHHhcCCceEEEe
Q 034727 2 LRADDGS-LIY-NHNG-VG----ITTNNVAKYGSLILGLKYALQKGFFNFRVR 47 (86)
Q Consensus 2 ~~~~~g~-~~~-~~~~-~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~ 47 (86)
|.|..|. .+. .+.. .| ......|-..|.-...+.|.++|++.+.+.
T Consensus 18 vTD~~G~~~~~~~S~G~~g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ 70 (114)
T TIGR03628 18 ITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIK 70 (114)
T ss_pred EEcCCCCEEEEEecCcceEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEE
Confidence 4577884 344 3332 23 244455666666688889999999876554
No 75
>COG3623 SgaU Putative L-xylulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=25.56 E-value=1.3e+02 Score=21.28 Aligned_cols=35 Identities=11% Similarity=0.141 Sum_probs=24.5
Q ss_pred eccCCC--cchHHHHHHHHHHHHHHHhcCCceEEEec
Q 034727 14 NGVGIT--TNNVAKYGSLILGLKYALQKGFFNFRVRG 48 (86)
Q Consensus 14 ~~~g~~--tnn~aEy~Ali~gL~~a~~~~~~~v~i~~ 48 (86)
.++|+. ++-.--+.=+.+++++|.++|++.|.+-|
T Consensus 81 fPfGS~D~~~r~~aleiM~KaI~LA~dLGIRtIQLAG 117 (287)
T COG3623 81 FPFGSKDEATRQQALEIMEKAIQLAQDLGIRTIQLAG 117 (287)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhCceeEeecc
Confidence 345533 33444566677899999999999987754
No 76
>cd02960 AGR Anterior Gradient (AGR) family; members of this family are similar to secreted proteins encoded by the cement gland-specific genes XAG-1 and XAG-2, expressed in the anterior region of dorsal ectoderm of Xenopus. They are implicated in the formation of the cement gland and the induction of forebrain fate. The human homologs, hAG-2 and hAG-3, are secreted proteins associated with estrogen-positive breast tumors. Yeast two-hybrid studies identified the metastasis-associated C4.4a protein and dystroglycan as binding partners, indicating possible roles in the development and progression of breast cancer. hAG-2 has also been implicated in prostate cancer. Its gene was cloned as an androgen-inducible gene and it was shown to be overexpressed in prostate cancer cells at the mRNA and protein levels. AGR proteins contain one conserved cysteine corresponding to the first cysteine in the CXXC motif of TRX. They show high sequence similarity to ERp19.
Probab=24.64 E-value=65 Score=20.11 Aligned_cols=36 Identities=25% Similarity=0.167 Sum_probs=21.6
Q ss_pred CeeCCCCCEEEeeeccCCCcch-----HHHHHHHHHHHHHHHh
Q 034727 1 MLRADDGSLIYNHNGVGITTNN-----VAKYGSLILGLKYALQ 38 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~tnn-----~aEy~Ali~gL~~a~~ 38 (86)
++.|++|+++. ...|..+|+ .++..-++.+++.|..
T Consensus 84 vFld~~g~vi~--~i~Gy~~~~~~~y~~~~~~~~~~~m~~a~~ 124 (130)
T cd02960 84 MFVDPSLTVRA--DITGRYSNRLYTYEPADIPLLIENMKKALK 124 (130)
T ss_pred EEECCCCCCcc--cccccccCccceeCcCcHHHHHHHHHHHHH
Confidence 46788998875 223444443 3455566677776665
No 77
>KOG0854 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=23.77 E-value=2.1e+02 Score=19.36 Aligned_cols=24 Identities=25% Similarity=0.228 Sum_probs=19.8
Q ss_pred CCcchHHHHHHHHHHHHHHHhcCC
Q 034727 18 ITTNNVAKYGSLILGLKYALQKGF 41 (86)
Q Consensus 18 ~~tnn~aEy~Ali~gL~~a~~~~~ 41 (86)
..-.|..|..-+|++|+++.+.++
T Consensus 152 ttGRN~dEiLRvidsLqlt~~k~V 175 (224)
T KOG0854|consen 152 TTGRNFDEILRVIDSLQLTDKKGV 175 (224)
T ss_pred ccCcCHHHHHHHHHHHhhhccccc
Confidence 445589999999999999988664
No 78
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=23.33 E-value=2e+02 Score=18.08 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=28.1
Q ss_pred eeCCCCC-EEE-eeec-cC----CCcchHHHHHHHHHHHHHHHhcCCceEEEe
Q 034727 2 LRADDGS-LIY-NHNG-VG----ITTNNVAKYGSLILGLKYALQKGFFNFRVR 47 (86)
Q Consensus 2 ~~~~~g~-~~~-~~~~-~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~ 47 (86)
+.|..|. ++. .+.. .| ......|-..|.-...+.|.++|++.+.|.
T Consensus 25 vTD~~G~~~~~~~S~G~~g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~ 77 (132)
T PRK09607 25 ITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIK 77 (132)
T ss_pred EEcCCCCEEEEEecCcceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEE
Confidence 4677885 554 3332 22 234445555555677788999999866554
No 79
>PF03190 Thioredox_DsbH: Protein of unknown function, DUF255; InterPro: IPR004879 This is a group of uncharacterised proteins.; PDB: 3IRA_A.
Probab=23.22 E-value=1.3e+02 Score=19.60 Aligned_cols=38 Identities=8% Similarity=0.064 Sum_probs=19.9
Q ss_pred CeeCCCCCEEEeeeccC-CCcchHHHHHHHHHHHHHHHh
Q 034727 1 MLRADDGSLIYNHNGVG-ITTNNVAKYGSLILGLKYALQ 38 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g-~~tnn~aEy~Ali~gL~~a~~ 38 (86)
|+.+|+|+++..+.+++ ..+.....+..++..+...+.
T Consensus 107 vfltPdg~p~~~~tY~P~~~~~g~~~f~~~l~~i~~~w~ 145 (163)
T PF03190_consen 107 VFLTPDGKPFFGGTYFPPEDRYGRPGFLQLLERIAELWK 145 (163)
T ss_dssp EEE-TTS-EEEEESS--SS-BTTB--HHHHHHHHHHHHH
T ss_pred EEECCCCCeeeeeeecCCCCCCCCccHHHHHHHHHHHHH
Confidence 46789999999666664 445555556666555544443
No 80
>COG0191 Fba Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism]
Probab=22.78 E-value=1.3e+02 Score=21.42 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=21.1
Q ss_pred HHHHHHhcCCceEEEecchHHHHHH
Q 034727 32 GLKYALQKGFFNFRVRGDSKLVHMQ 56 (86)
Q Consensus 32 gL~~a~~~~~~~v~i~~DS~lvi~q 56 (86)
-++.+.++|+.++-|.||-++..-.
T Consensus 219 eI~~aI~~GV~KvNi~Td~~~A~~~ 243 (286)
T COG0191 219 EIREAIKLGVAKVNIDTDLQLAFTA 243 (286)
T ss_pred HHHHHHHhCceEEeeCcHHHHHHHH
Confidence 3667889999999999999888754
No 81
>PF05171 HemS: Haemin-degrading HemS.ChuX domain; InterPro: IPR007845 The Yersinia enterocolitica O:8 periplasmic binding protein-dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS. The structure for HemS has been solved and consists of a tandem repeat of the domain represented in this entry[].; GO: 0006826 iron ion transport; PDB: 2HQ2_A 2J0R_A 2J0P_A 1U9T_A.
Probab=22.54 E-value=1.5e+02 Score=18.09 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=16.8
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHH
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILG 32 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~g 32 (86)
++|.+|+.+..- .+....+.++|.+|+..
T Consensus 100 ~fD~~G~~i~ki--~~~~~~~~~~W~~Lv~~ 128 (129)
T PF05171_consen 100 FFDAQGEAIHKI--FGTRDSESAAWRALVEE 128 (129)
T ss_dssp EEETTS-EEEEE--EESTTS-HHHHHHHHHC
T ss_pred EECCCCCEEEEE--ECCCCCCHHHHHHHHHh
Confidence 467788887521 22223778888888764
No 82
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=22.52 E-value=1.6e+02 Score=17.30 Aligned_cols=22 Identities=14% Similarity=0.063 Sum_probs=15.2
Q ss_pred CCceEEEecchHHHHHHHh-hhh
Q 034727 40 GFFNFRVRGDSKLVHMQVC-CWL 61 (86)
Q Consensus 40 ~~~~v~i~~DS~lvi~q~~-~~~ 61 (86)
..-+|...++++-+.++++ -|.
T Consensus 38 P~~pIiavt~~~~~~r~l~l~~G 60 (117)
T PF02887_consen 38 PKVPIIAVTPNESVARQLSLYWG 60 (117)
T ss_dssp TSSEEEEEESSHHHHHHGGGSTT
T ss_pred CCCeEEEEcCcHHHHhhhhcccc
Confidence 4456777777777777777 665
No 83
>PRK15381 pathogenicity island 2 effector protein SseJ; Provisional
Probab=22.49 E-value=37 Score=25.26 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=24.9
Q ss_pred CeeCCCCCEEE-eeeccCCCcchH---HHHHHHHHHHHHHHhcCCceEEEecch
Q 034727 1 MLRADDGSLIY-NHNGVGITTNNV---AKYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 1 v~~~~~g~~~~-~~~~~g~~tnn~---aEy~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
+|+|.||+.|. ...-. .++.. -|..-+.-+.+-+.-.++..+.++|||
T Consensus 100 ~i~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ai~vFGDS 151 (408)
T PRK15381 100 IIKDDNGENILSIEVEC--HPEAFGLAKEINKSHPKPKNISLGDITRLVFFGDS 151 (408)
T ss_pred EEecCCCceEEEEEEec--CHHHHHHHHHhcccCCCCCccccCCCCeEEEeCCc
Confidence 36778888775 33322 22221 122222222222333467889999999
No 84
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=22.06 E-value=1.9e+02 Score=18.77 Aligned_cols=33 Identities=18% Similarity=0.015 Sum_probs=18.0
Q ss_pred CeeCCCCCEEEeeeccCCCc---chHHHHHHHHHHHH
Q 034727 1 MLRADDGSLIYNHNGVGITT---NNVAKYGSLILGLK 34 (86)
Q Consensus 1 v~~~~~g~~~~~~~~~g~~t---nn~aEy~Ali~gL~ 34 (86)
||++ +|++|..+..-...+ ..-||..|+..+.+
T Consensus 38 VIV~-~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~ 73 (172)
T PRK10860 38 VLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGL 73 (172)
T ss_pred EEEe-CCEEEEEeeCCCCCCCCCccCHHHHHHHHHHH
Confidence 4554 677776222211111 24689998877654
No 85
>COG1225 Bcp Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=21.80 E-value=2.1e+02 Score=18.53 Aligned_cols=31 Identities=13% Similarity=0.084 Sum_probs=22.2
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHH
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGL 33 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL 33 (86)
|.|++|.+.... .-....++..|-.+.+..+
T Consensus 125 vId~dG~I~~~~-~~v~~~~h~~~vl~~l~~l 155 (157)
T COG1225 125 VIDPDGKIRYVW-RKVKVKGHADEVLAALKKL 155 (157)
T ss_pred EECCCCeEEEEe-cCCCCcccHHHHHHHHHHh
Confidence 678899888744 5567777877777666554
No 86
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=21.67 E-value=1.6e+02 Score=17.28 Aligned_cols=25 Identities=12% Similarity=0.135 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhcCCceEEEecchH
Q 034727 27 GSLILGLKYALQKGFFNFRVRGDSK 51 (86)
Q Consensus 27 ~Ali~gL~~a~~~~~~~v~i~~DS~ 51 (86)
.-++.+++.|.+.|++.+.+-++++
T Consensus 57 ~e~i~~~~~a~~~g~~iI~IT~~~~ 81 (119)
T cd05017 57 EETLSAVEQAKERGAKIVAITSGGK 81 (119)
T ss_pred HHHHHHHHHHHHCCCEEEEEeCCch
Confidence 3455777788899998888888885
No 87
>cd02969 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.
Probab=21.38 E-value=1.6e+02 Score=18.26 Aligned_cols=12 Identities=42% Similarity=0.778 Sum_probs=9.5
Q ss_pred CeeCCCCCEEEe
Q 034727 1 MLRADDGSLIYN 12 (86)
Q Consensus 1 v~~~~~g~~~~~ 12 (86)
+|.|++|+++..
T Consensus 114 ~lid~~G~v~~~ 125 (171)
T cd02969 114 FLFDPDGKLVYR 125 (171)
T ss_pred EEECCCCeEEEe
Confidence 478999998863
No 88
>COG3165 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.93 E-value=81 Score=21.42 Aligned_cols=46 Identities=24% Similarity=0.166 Sum_probs=29.9
Q ss_pred eeeccCCCcchHHHHHHHHHHHHHHHhcC--C--ceEEEecchHHHHHHH
Q 034727 12 NHNGVGITTNNVAKYGSLILGLKYALQKG--F--FNFRVRGDSKLVHMQV 57 (86)
Q Consensus 12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~--~--~~v~i~~DS~lvi~q~ 57 (86)
.+.+-|..+.-..-+.+++..|......| + .++.+.||++++.+-+
T Consensus 60 ls~~eg~~Dc~v~~~~s~L~~L~~~~~~~~~~~~g~l~veGD~q~~q~l~ 109 (204)
T COG3165 60 LSAWEGEADCTVRARASVLPKLRDRQQLGQLARSGELEVEGDIQLAQNLV 109 (204)
T ss_pred hhcccCCCCeeeeechhhhHHHHhhccchhhccCCceeecchHHHHHHHH
Confidence 33444444555555566666666555555 3 7899999999988754
No 89
>PF10113 Fibrillarin_2: Fibrillarin-like archaeal protein; InterPro: IPR016760 Members of this protein family are HmdC, whose gene regularly occurs in the context of genes for HmdA (5,10-methenyltetrahydromethanopterin hydrogenase) and the radical SAM protein HmdB involved in biosynthesis of the HmdA cofactor. Bioinformatics suggests this protein, a homologue of eukaryotic fibrillarin, may be involved in biosynthesis of the guanylyl pyridinol cofactor in HmdA.
Probab=20.56 E-value=1.4e+02 Score=22.82 Aligned_cols=26 Identities=38% Similarity=0.569 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHhcCCceEEEecch
Q 034727 25 KYGSLILGLKYALQKGFFNFRVRGDS 50 (86)
Q Consensus 25 Ey~Ali~gL~~a~~~~~~~v~i~~DS 50 (86)
.|.-||.||+.|.++++.-+.++|--
T Consensus 231 GyddLI~G~~a~id~~vDvfVvEGgP 256 (505)
T PF10113_consen 231 GYDDLITGLKACIDMGVDVFVVEGGP 256 (505)
T ss_pred ChHHHHHHHHHHHhcCCcEEEEeCCC
Confidence 47789999999999999999998864
No 90
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=20.53 E-value=2.1e+02 Score=17.27 Aligned_cols=31 Identities=16% Similarity=0.139 Sum_probs=22.3
Q ss_pred eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHH
Q 034727 2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKY 35 (86)
Q Consensus 2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~ 35 (86)
..+|||..+. +-|+.+--.||..|.+.|-..
T Consensus 19 efs~DGkLv~---Ykgdm~k~~A~maAkmcaAnn 49 (109)
T COG4831 19 EFSPDGKLVE---YKGDMPKEMAEMAAKMCAANN 49 (109)
T ss_pred eeCCCCceEE---eeCCCCHHHHHHHHHHHHHHH
Confidence 3578898875 345778888888888776543
Done!