Query 037050
Match_columns 144
No_of_seqs 145 out of 1099
Neff 9.0
Searched_HMMs 46136
Date Fri Mar 29 08:08:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037050.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037050hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13907 rnhA ribonuclease H; 100.0 3.1E-27 6.7E-32 158.1 12.6 118 1-121 10-127 (128)
2 PF13456 RVT_3: Reverse transc 99.9 1.6E-25 3.5E-30 139.6 8.5 86 35-120 1-86 (87)
3 PRK07238 bifunctional RNase H/ 99.9 3.6E-23 7.7E-28 160.5 13.7 128 1-129 11-140 (372)
4 PRK07708 hypothetical protein; 99.9 1.3E-22 2.7E-27 146.6 13.1 122 1-122 82-209 (219)
5 cd06222 RnaseH RNase H (RNase 99.9 3.1E-20 6.8E-25 121.6 14.7 115 4-119 11-130 (130)
6 COG0328 RnhA Ribonuclease HI [ 99.8 5.1E-20 1.1E-24 125.4 10.9 118 2-122 13-146 (154)
7 PRK08719 ribonuclease H; Revie 99.7 2.5E-16 5.3E-21 107.6 12.1 109 7-120 22-146 (147)
8 PRK00203 rnhA ribonuclease H; 99.7 9.5E-16 2.1E-20 105.1 11.6 114 2-121 13-142 (150)
9 PF00075 RNase_H: RNase H; In 99.7 6.3E-16 1.4E-20 103.3 9.0 109 2-119 13-131 (132)
10 PRK06548 ribonuclease H; Provi 99.6 1.7E-14 3.7E-19 99.6 13.5 112 2-121 15-142 (161)
11 KOG3752 Ribonuclease H [Replic 99.2 4.1E-10 8.9E-15 85.8 12.1 111 6-119 229-363 (371)
12 KOG1812 Predicted E3 ubiquitin 98.1 9.7E-06 2.1E-10 63.5 6.8 117 5-121 16-138 (384)
13 COG0590 CumB Cytosine/adenosin 92.3 0.43 9.3E-06 32.7 5.1 59 5-63 25-84 (152)
14 COG0295 Cdd Cytidine deaminase 89.4 2 4.3E-05 28.9 6.0 55 9-64 27-81 (134)
15 cd01285 nucleoside_deaminase N 88.9 1.5 3.2E-05 28.1 5.1 58 5-62 14-72 (109)
16 cd01284 Riboflavin_deaminase-r 88.5 1.6 3.4E-05 28.5 5.0 41 6-49 17-57 (115)
17 TIGR01354 cyt_deam_tetra cytid 86.0 1.4 3E-05 29.2 3.8 57 7-64 20-76 (127)
18 cd00786 cytidine_deaminase-lik 86.0 4 8.8E-05 25.4 5.7 44 5-48 15-60 (96)
19 PF00336 DNA_pol_viral_C: DNA 82.5 4.3 9.4E-05 29.4 5.1 86 5-109 101-186 (245)
20 cd01283 cytidine_deaminase Cyt 79.6 5 0.00011 25.6 4.4 44 6-49 16-59 (112)
21 TIGR02571 ComEB ComE operon pr 79.5 9.1 0.0002 26.2 5.8 41 7-48 24-80 (151)
22 PRK10860 tRNA-specific adenosi 76.8 6.7 0.00015 27.5 4.7 43 6-49 31-74 (172)
23 PF00383 dCMP_cyt_deam_1: Cyti 74.5 4.6 0.0001 25.1 3.1 46 4-49 20-66 (102)
24 PHA02588 cd deoxycytidylate de 72.8 18 0.00039 25.2 6.0 14 35-48 81-94 (168)
25 cd01286 deoxycytidylate_deamin 71.1 12 0.00026 24.8 4.6 41 7-48 19-81 (131)
26 PF05830 NodZ: Nodulation prot 70.3 11 0.00023 29.1 4.6 63 5-74 165-233 (321)
27 PRK05578 cytidine deaminase; V 61.2 17 0.00037 24.2 3.8 56 8-64 24-79 (131)
28 PRK14828 undecaprenyl pyrophos 60.0 53 0.0012 24.6 6.6 56 7-65 27-82 (256)
29 PRK12411 cytidine deaminase; P 57.7 22 0.00049 23.7 4.0 57 7-64 23-79 (132)
30 PRK06848 hypothetical protein; 52.8 35 0.00075 23.0 4.3 57 6-63 25-81 (139)
31 TIGR00326 eubact_ribD riboflav 50.6 21 0.00045 27.7 3.3 36 9-48 20-55 (344)
32 COG3981 Predicted acetyltransf 50.5 23 0.0005 24.9 3.2 28 40-67 116-143 (174)
33 PRK08298 cytidine deaminase; V 49.2 47 0.001 22.3 4.4 55 9-64 24-78 (136)
34 PRK15000 peroxidase; Provision 46.3 61 0.0013 23.0 5.0 42 11-54 127-168 (200)
35 KOG1018 Cytosine deaminase FCY 46.3 45 0.00097 23.4 4.1 48 7-54 31-79 (169)
36 PF03259 Robl_LC7: Roadblock/L 44.8 36 0.00077 20.2 3.2 17 8-24 14-30 (91)
37 KOG3139 N-acetyltransferase [G 44.7 27 0.00059 24.3 2.8 23 43-65 106-128 (165)
38 PRK14835 undecaprenyl pyrophos 43.9 1.4E+02 0.0031 22.6 6.9 55 7-65 42-96 (275)
39 PRK13191 putative peroxiredoxi 42.8 70 0.0015 23.1 4.9 42 11-54 126-167 (215)
40 PF11080 DUF2622: Protein of u 41.0 92 0.002 19.7 4.5 42 7-48 32-73 (96)
41 COG4097 Predicted ferric reduc 40.1 1.1E+02 0.0023 24.6 5.7 63 79-142 355-419 (438)
42 PRK14827 undecaprenyl pyrophos 39.6 1.6E+02 0.0034 22.7 6.4 54 8-65 69-122 (296)
43 PF05854 MC1: Non-histone chro 39.4 13 0.00027 23.2 0.5 30 12-46 6-35 (93)
44 PRK13190 putative peroxiredoxi 38.8 92 0.002 22.1 4.9 44 10-55 118-161 (202)
45 COG1212 KdsB CMP-2-keto-3-deox 38.5 58 0.0013 24.2 3.8 31 43-73 31-61 (247)
46 cd03016 PRX_1cys Peroxiredoxin 36.1 1.4E+02 0.0031 21.1 5.6 43 11-55 119-161 (203)
47 PRK14834 undecaprenyl pyrophos 35.6 1.9E+02 0.0041 21.6 8.1 58 4-65 12-69 (249)
48 COG0084 TatD Mg-dependent DNas 35.4 20 0.00044 26.8 1.1 46 46-91 188-234 (256)
49 PRK14837 undecaprenyl pyrophos 32.1 77 0.0017 23.4 3.6 56 5-64 5-60 (230)
50 PRK10786 ribD bifunctional dia 32.0 66 0.0014 25.3 3.5 37 9-49 26-62 (367)
51 PRK13599 putative peroxiredoxi 31.8 1.3E+02 0.0029 21.6 4.9 43 11-55 121-163 (215)
52 TIGR00055 uppS undecaprenyl di 31.3 82 0.0018 23.2 3.7 49 13-64 5-53 (226)
53 KOG2882 p-Nitrophenyl phosphat 31.1 69 0.0015 24.7 3.3 46 8-66 20-65 (306)
54 PTZ00137 2-Cys peroxiredoxin; 30.7 1.2E+02 0.0026 22.8 4.6 42 11-54 190-231 (261)
55 PRK14841 undecaprenyl pyrophos 29.8 89 0.0019 23.1 3.7 52 9-64 6-57 (233)
56 COG0117 RibD Pyrimidine deamin 29.7 77 0.0017 21.7 3.1 34 9-46 29-62 (146)
57 PF05903 Peptidase_C97: PPPDE 29.7 43 0.00093 22.8 1.9 32 89-120 92-123 (151)
58 KOG0833 Cytidine deaminase [Nu 29.5 1.4E+02 0.0029 21.1 4.3 39 9-47 43-81 (173)
59 PRK13189 peroxiredoxin; Provis 29.4 1.7E+02 0.0036 21.2 5.1 42 11-54 128-169 (222)
60 PRK14833 undecaprenyl pyrophos 29.3 94 0.002 22.9 3.7 54 7-64 5-58 (233)
61 PLN02807 diaminohydroxyphospho 29.3 75 0.0016 25.2 3.4 36 10-49 56-91 (380)
62 PRK14839 undecaprenyl pyrophos 29.2 88 0.0019 23.2 3.6 54 8-65 11-64 (239)
63 COG0450 AhpC Peroxiredoxin [Po 28.9 2.2E+02 0.0048 20.4 6.0 49 5-55 120-168 (194)
64 PRK14836 undecaprenyl pyrophos 28.8 2.5E+02 0.0054 21.0 6.5 52 7-62 15-66 (253)
65 PF07511 DUF1525: Protein of u 28.7 85 0.0018 20.5 3.0 23 35-57 61-83 (114)
66 KOG3343 Vesicle coat complex C 28.6 2.1E+02 0.0045 20.0 6.7 22 56-77 128-149 (175)
67 PRK14830 undecaprenyl pyrophos 28.3 2.6E+02 0.0055 20.9 6.6 56 6-65 22-77 (251)
68 PLN02182 cytidine deaminase 27.5 1.1E+02 0.0025 23.9 4.0 46 9-58 67-114 (339)
69 PRK09822 lipopolysaccharide co 27.4 70 0.0015 23.8 2.7 20 43-62 173-192 (269)
70 PTZ00349 dehydrodolichyl dipho 27.3 97 0.0021 24.1 3.6 56 5-64 18-73 (322)
71 PRK10382 alkyl hydroperoxide r 27.3 2.3E+02 0.0049 20.0 5.8 41 11-53 121-161 (187)
72 PF12404 DUF3663: Peptidase ; 26.5 1.1E+02 0.0023 18.6 3.0 26 39-64 36-61 (77)
73 cd03015 PRX_Typ2cys Peroxiredo 25.9 2.2E+02 0.0047 19.3 5.3 43 11-55 122-164 (173)
74 COG3693 XynA Beta-1,4-xylanase 25.6 54 0.0012 25.6 2.0 29 109-137 82-115 (345)
75 TIGR02508 type_III_yscG type I 25.3 22 0.00048 22.9 -0.1 19 101-119 18-36 (115)
76 CHL00139 rpl18 ribosomal prote 24.9 2E+02 0.0043 18.5 6.2 51 11-62 29-86 (109)
77 PRK12295 hisZ ATP phosphoribos 24.6 3.5E+02 0.0077 21.3 7.3 65 8-73 86-153 (373)
78 PRK14832 undecaprenyl pyrophos 24.4 1.2E+02 0.0026 22.8 3.5 55 7-65 19-73 (253)
79 PRK09027 cytidine deaminase; P 24.3 1.5E+02 0.0032 22.8 4.1 51 9-60 72-124 (295)
80 COG1519 KdtA 3-deoxy-D-manno-o 24.3 2.1E+02 0.0046 23.2 5.1 41 80-120 243-286 (419)
81 KOG0324 Uncharacterized conser 24.3 2E+02 0.0043 21.0 4.5 31 91-121 97-127 (214)
82 PRK14829 undecaprenyl pyrophos 24.2 1.2E+02 0.0026 22.5 3.6 57 5-65 13-69 (243)
83 TIGR03757 conj_TIGR03757 integ 24.0 1.2E+02 0.0026 19.8 3.1 22 36-57 63-84 (113)
84 KOG1602 Cis-prenyltransferase 23.9 2.7E+02 0.0059 21.1 5.3 54 7-64 37-90 (271)
85 cd00475 CIS_IPPS Cis (Z)-Isopr 23.5 3E+02 0.0065 20.1 6.8 49 13-64 6-54 (221)
86 PLN02402 cytidine deaminase 23.3 1.6E+02 0.0035 22.7 4.1 41 9-49 47-89 (303)
87 TIGR00228 ruvC crossover junct 23.1 2.6E+02 0.0057 19.3 6.5 59 2-61 5-64 (156)
88 PF01614 IclR: Bacterial trans 23.0 2.1E+02 0.0045 18.1 5.4 27 4-30 76-102 (129)
89 PF04954 SIP: Siderophore-inte 22.9 1.2E+02 0.0025 19.5 3.0 34 95-128 47-85 (119)
90 PRK10057 rpsV 30S ribosomal su 21.5 18 0.0004 18.9 -0.8 19 55-73 20-38 (44)
91 PRK14842 undecaprenyl pyrophos 21.3 3.5E+02 0.0076 20.1 6.8 55 7-65 9-63 (241)
92 PRK14831 undecaprenyl pyrophos 21.3 1.6E+02 0.0034 22.0 3.6 54 7-64 21-74 (249)
93 TIGR00060 L18_bact ribosomal p 20.7 2.6E+02 0.0055 18.2 5.7 51 11-62 38-91 (114)
94 PF00925 GTP_cyclohydro2: GTP 20.6 1.6E+02 0.0035 20.3 3.5 36 39-74 124-159 (169)
No 1
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.95 E-value=3.1e-27 Score=158.10 Aligned_cols=118 Identities=17% Similarity=0.098 Sum_probs=105.1
Q ss_pred CCCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchh
Q 037050 1 MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSK 80 (144)
Q Consensus 1 f~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~ 80 (144)
++++++.+|+|+|+||..|.+...+. . +..|+++||++|++.||+.+.++|+++|+++|||+.+++++++.......
T Consensus 10 ~~~~~g~~G~G~vi~~~~~~~~~~~~--~-~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~ 86 (128)
T PRK13907 10 SKGNPGPSGAGVFIKGVQPAVQLSLP--L-GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKM 86 (128)
T ss_pred CCCCCCccEEEEEEEECCeeEEEEec--c-cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChh
Confidence 46788999999999999987665432 2 36799999999999999999999999999999999999999987655567
Q ss_pred HHHHHHHHHHHHhcCccEEEEEecCCchHHHHHHHhhhccc
Q 037050 81 IIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQK 121 (144)
Q Consensus 81 ~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~~ 121 (144)
+..++++++.++..|+.+.+.||||++|+.||.||+.+...
T Consensus 87 ~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 87 FAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ 127 (128)
T ss_pred HHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHhc
Confidence 89999999999999999999999999999999999998753
No 2
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.93 E-value=1.6e-25 Score=139.64 Aligned_cols=86 Identities=31% Similarity=0.382 Sum_probs=75.8
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHHHHHHHHHHHHhcCccEEEEEecCCchHHHHHH
Q 037050 35 VAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFL 114 (144)
Q Consensus 35 ~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~L 114 (144)
|++||++|++.||++|+++|+++|++||||+.+++.+++....++.+..++++|+.+++.|+++++.||+|++|++||.|
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~L 80 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADAL 80 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHH
Confidence 68999999999999999999999999999999999999987666689999999999999999999999999999999999
Q ss_pred Hhhhcc
Q 037050 115 AKLVLQ 120 (144)
Q Consensus 115 Ak~a~~ 120 (144)
||.+.+
T Consensus 81 A~~a~~ 86 (87)
T PF13456_consen 81 AKFALS 86 (87)
T ss_dssp HHHHHH
T ss_pred HHHHhh
Confidence 999864
No 3
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.90 E-value=3.6e-23 Score=160.46 Aligned_cols=128 Identities=19% Similarity=0.149 Sum_probs=112.6
Q ss_pred CCCCCCceeEEEEEeCCCCC-eeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCC-Cc
Q 037050 1 MDAKKQVAGLAVVIRDWERN-CVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTN-SM 78 (144)
Q Consensus 1 f~~~~~~~g~G~vird~~g~-~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~-~~ 78 (144)
++.+++.+|+|+|+|+++|. ++...+..++ ..|+++||+.|++.||+.+.++|+++|+|++||+.+++.+++... ..
T Consensus 11 ~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~ 89 (372)
T PRK07238 11 SRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKH 89 (372)
T ss_pred CCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCC
Confidence 35678899999999999764 5556666555 678899999999999999999999999999999999999998754 34
Q ss_pred hhHHHHHHHHHHHHhcCccEEEEEecCCchHHHHHHHhhhcccCCeeeecc
Q 037050 79 SKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLD 129 (144)
Q Consensus 79 ~~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~~~~~~~~~~ 129 (144)
..+..++++++.+.++|+.+++.||+|++|+.||.||+.++......+|.+
T Consensus 90 ~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~~~~~~~~ 140 (372)
T PRK07238 90 PDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAGGEPWG 140 (372)
T ss_pred hHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhhccCCCcc
Confidence 578889999999999999999999999999999999999999777777875
No 4
>PRK07708 hypothetical protein; Validated
Probab=99.90 E-value=1.3e-22 Score=146.57 Aligned_cols=122 Identities=20% Similarity=0.113 Sum_probs=102.9
Q ss_pred CCCCCCceeEEEEEeCCCCCee--eecccccCCCCChHHHHHHHHHHHHHHHHHhCCCc--eEEeccHHHHHHHHhcCCC
Q 037050 1 MDAKKQVAGLAVVIRDWERNCV--AAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYS--VLFESDSHEVVELVNNRTN 76 (144)
Q Consensus 1 f~~~~~~~g~G~vird~~g~~~--~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~--v~~esDs~~vv~~l~~~~~ 76 (144)
|+.+++.+|+|+|++++.|... ......++...|+++||+.|++.||+.|.++|+++ |++++||+.|++++++...
T Consensus 82 ~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk 161 (219)
T PRK07708 82 FDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWP 161 (219)
T ss_pred cCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCce
Confidence 4567889999999998877543 33344566678999999999999999999999976 8999999999999999753
Q ss_pred C-chhHHHHHHHHHHHHhcCcc-EEEEEecCCchHHHHHHHhhhcccC
Q 037050 77 S-MSKIIWVIFEILEKKKNFQN-FKAQHTPRSCNGIAHFLAKLVLQKK 122 (144)
Q Consensus 77 ~-~~~~~~~~~~i~~l~~~~~~-~~~~~v~r~~N~~Ad~LAk~a~~~~ 122 (144)
. ...+..+.+++..+.+.|.. +.+.||+|++|..||.||+.|++..
T Consensus 162 ~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 162 CYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGT 209 (219)
T ss_pred eCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcC
Confidence 3 34677788999888888764 8899999999999999999999843
No 5
>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=99.86 E-value=3.1e-20 Score=121.65 Aligned_cols=115 Identities=21% Similarity=0.162 Sum_probs=102.2
Q ss_pred CCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCC-CchhHH
Q 037050 4 KKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTN-SMSKII 82 (144)
Q Consensus 4 ~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~-~~~~~~ 82 (144)
+.+.+|+|+|+++..+.......... ...+++++|+.|+..||+.+...+.+++.++|||+.+++.+++... ......
T Consensus 11 ~~~~~g~g~v~~~~~~~~~~~~~~~~-~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~ 89 (130)
T cd06222 11 NPGPAGAGVVLRDPGGEVLLSGGLLG-GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNV 89 (130)
T ss_pred CCCceEEEEEEEeCCCeEEEeccccC-CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhH
Confidence 34678999999999998877777654 5789999999999999999999999999999999999999998754 455788
Q ss_pred HHHHHHHHHHhcCccEEEEEecC----CchHHHHHHHhhhc
Q 037050 83 WVIFEILEKKKNFQNFKAQHTPR----SCNGIAHFLAKLVL 119 (144)
Q Consensus 83 ~~~~~i~~l~~~~~~~~~~~v~r----~~N~~Ad~LAk~a~ 119 (144)
.++.+++.+...+..+++.||+| +.|..||.|||.+.
T Consensus 90 ~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 90 DLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 88999999888999999999999 99999999999874
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.83 E-value=5.1e-20 Score=125.38 Aligned_cols=118 Identities=15% Similarity=0.012 Sum_probs=98.0
Q ss_pred CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC---C---
Q 037050 2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR---T--- 75 (144)
Q Consensus 2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~---~--- 75 (144)
..+||++|+|+|++..++..-... ... .+|++.+|++|++.||+.+++.+...|.++|||+.|++.++.- .
T Consensus 13 ~gNpG~gG~g~vl~~~~~~~~~s~--~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~ 89 (154)
T COG0328 13 LGNPGPGGWGAVLRYGDGEKELSG--GEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKN 89 (154)
T ss_pred CCCCCCceEEEEEEcCCceEEEee--eee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhcccc
Confidence 468899999999997666662333 233 6899999999999999999999999999999999999999831 0
Q ss_pred ------CCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhcccC
Q 037050 76 ------NSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQKK 122 (144)
Q Consensus 76 ------~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~~ 122 (144)
..+-.-..+++++..+...+..+.+.||+ +..|+.||.||+.+....
T Consensus 90 ~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 90 GWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred CccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 11223457799999999999999999999 778999999999998743
No 7
>PRK08719 ribonuclease H; Reviewed
Probab=99.71 E-value=2.5e-16 Score=107.62 Aligned_cols=109 Identities=16% Similarity=0.058 Sum_probs=85.7
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------CC---
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN--------RT--- 75 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~--------~~--- 75 (144)
++|+|+++.+..|......+..+....|++.||++|+..||+.+.+. ..|.|||+.+++.++. ..
T Consensus 22 ~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s 97 (147)
T PRK08719 22 RGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKS 97 (147)
T ss_pred CcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccC
Confidence 67999999998887654444445556899999999999999998764 4799999999999952 11
Q ss_pred -CCchhHHHHHHHHHHHHhcCccEEEEEecC----CchHHHHHHHhhhcc
Q 037050 76 -NSMSKIIWVIFEILEKKKNFQNFKAQHTPR----SCNGIAHFLAKLVLQ 120 (144)
Q Consensus 76 -~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r----~~N~~Ad~LAk~a~~ 120 (144)
..+-....+++.|..+.. ...++|.||++ .+|..||.||+.|..
T Consensus 98 ~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 98 DKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 122334677888877766 57799999999 579999999999864
No 8
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.68 E-value=9.5e-16 Score=105.14 Aligned_cols=114 Identities=11% Similarity=-0.014 Sum_probs=86.3
Q ss_pred CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------
Q 037050 2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN-------- 73 (144)
Q Consensus 2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~-------- 73 (144)
+.+++.+|+|+|+...++.....+ ..+ ..|++.||++|+..||+.+.+ ...|.|.|||+.+++.+++
T Consensus 13 ~~n~~~~g~g~v~~~~~~~~~~~~--~~~-~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~ 87 (150)
T PRK00203 13 LGNPGPGGWGAILRYKGHEKELSG--GEA-LTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKN 87 (150)
T ss_pred cCCCCceEEEEEEEECCeeEEEec--CCC-CCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHc
Confidence 456788999999986555433322 233 578999999999999998754 3579999999999999985
Q ss_pred CC--C--CchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhccc
Q 037050 74 RT--N--SMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQK 121 (144)
Q Consensus 74 ~~--~--~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~ 121 (144)
.. . .+-....+++++..++.. ..+.|.||+ ++.|..||.|||.+...
T Consensus 88 ~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 88 GWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred CCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 11 1 122345678888887665 679999999 66799999999998763
No 9
>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=99.66 E-value=6.3e-16 Score=103.27 Aligned_cols=109 Identities=18% Similarity=0.025 Sum_probs=82.1
Q ss_pred CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc-----CCC
Q 037050 2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN-----RTN 76 (144)
Q Consensus 2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~-----~~~ 76 (144)
+.+++.+|+|+|+.+. . ..+..++ ..++..+|++|+..||+ +. .-+++.|+|||+.+++.++. ...
T Consensus 13 ~~~~~~~~~g~v~~~~--~---~~~~~~~-~~s~~~aEl~Ai~~AL~-~~--~~~~v~I~tDS~~v~~~l~~~~~~~~~~ 83 (132)
T PF00075_consen 13 RPNPGKGGAGYVVWGG--R---NFSFRLG-GQSNNRAELQAIIEALK-AL--EHRKVTIYTDSQYVLNALNKWLHGNGWK 83 (132)
T ss_dssp CTTTTEEEEEEEEETT--E---EEEEEEE-SECHHHHHHHHHHHHHH-TH--STSEEEEEES-HHHHHHHHTHHHHTTSB
T ss_pred cCCCCceEEEEEEECC--e---EEEeccc-ccchhhhheehHHHHHH-Hh--hcccccccccHHHHHHHHHHhccccccc
Confidence 3457788999977433 2 3333444 78999999999999999 55 22999999999999998877 332
Q ss_pred CchhHHHHHHHHHHHHhcCccEEEEEecCC-----chHHHHHHHhhhc
Q 037050 77 SMSKIIWVIFEILEKKKNFQNFKAQHTPRS-----CNGIAHFLAKLVL 119 (144)
Q Consensus 77 ~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~-----~N~~Ad~LAk~a~ 119 (144)
.......+..++..++.....+.|.|||.+ +|..||.|||.++
T Consensus 84 ~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 84 KTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp SCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 222222466688887777889999999998 6889999999875
No 10
>PRK06548 ribonuclease H; Provisional
Probab=99.63 E-value=1.7e-14 Score=99.64 Aligned_cols=112 Identities=15% Similarity=0.057 Sum_probs=84.9
Q ss_pred CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------
Q 037050 2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN-------- 73 (144)
Q Consensus 2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~-------- 73 (144)
..+++++|+|+++.+. + .. +... ...|++.||++|++.||+.+. ....+|.|.|||+.+++.+++
T Consensus 15 ~gnpg~~G~g~~~~~~-~-~~---~g~~-~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~ 87 (161)
T PRK06548 15 LANPGPSGWAWYVDEN-T-WD---SGGW-DIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLTKWVYSWKMR 87 (161)
T ss_pred CCCCCceEEEEEEeCC-c-EE---ccCC-CCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHHHHHHHHHHHC
Confidence 4578999999999753 2 21 2212 368999999999999997553 455689999999999999994
Q ss_pred C----CCCchhHHHHHHHHHHHHhcCccEEEEEecCC----chHHHHHHHhhhccc
Q 037050 74 R----TNSMSKIIWVIFEILEKKKNFQNFKAQHTPRS----CNGIAHFLAKLVLQK 121 (144)
Q Consensus 74 ~----~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~----~N~~Ad~LAk~a~~~ 121 (144)
. ...+-.-..++++|..++.. ..++|.||+-+ .|..||.||+.+...
T Consensus 88 gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 88 KWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred CCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 1 11122357888999888766 47999999865 599999999998763
No 11
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]
Probab=99.20 E-value=4.1e-10 Score=85.81 Aligned_cols=111 Identities=14% Similarity=-0.001 Sum_probs=83.8
Q ss_pred CceeEEEEEeCCCCCeeeecccccC-CCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC----------
Q 037050 6 QVAGLAVVIRDWERNCVAAAINTTR-FFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR---------- 74 (144)
Q Consensus 6 ~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~---------- 74 (144)
..+|+|+.+=+ |.-.-.. .++. +..+++.||+.|+.+||+.|++...++|+|.|||..++++++..
T Consensus 229 ~~AGyGvywg~--~~e~N~s-~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k 305 (371)
T KOG3752|consen 229 SRAGYGVYWGP--GHELNVS-GPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWK 305 (371)
T ss_pred CcceeEEeeCC--CCccccc-ccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccc
Confidence 57899998854 3332222 3344 78999999999999999999999999999999999999999850
Q ss_pred CCCc-------hhHHHHHHHHHHHHhc--CccEEEEEecCC----chHHHHHHHhhhc
Q 037050 75 TNSM-------SKIIWVIFEILEKKKN--FQNFKAQHTPRS----CNGIAHFLAKLVL 119 (144)
Q Consensus 75 ~~~~-------~~~~~~~~~i~~l~~~--~~~~~~~~v~r~----~N~~Ad~LAk~a~ 119 (144)
.... -.-...+.++.++.+. ...+++.||+-. +|..||.||+.+.
T Consensus 306 ~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 306 TSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred cccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 0111 1123446666666555 477899999875 6999999999883
No 12
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=9.7e-06 Score=63.51 Aligned_cols=117 Identities=16% Similarity=0.163 Sum_probs=93.5
Q ss_pred CCceeEEEEEeCC-CCCeeeecccccCC--CCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCch--
Q 037050 5 KQVAGLAVVIRDW-ERNCVAAAINTTRF--FGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMS-- 79 (144)
Q Consensus 5 ~~~~g~G~vird~-~g~~~~~~~~~~~~--~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~-- 79 (144)
...+|.|+++.|. +....+........ ..++..||++|+..+|..+.++|+.++.+.+|+..+.+.+.+......
T Consensus 16 ~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~ 95 (384)
T KOG1812|consen 16 ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHR 95 (384)
T ss_pred hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHH
Confidence 4578999999996 66666666655442 378999999999999999999999999999998888887776643322
Q ss_pred hHHHHHHHHHHHHhcCccEEEEEecCC-chHHHHHHHhhhccc
Q 037050 80 KIIWVIFEILEKKKNFQNFKAQHTPRS-CNGIAHFLAKLVLQK 121 (144)
Q Consensus 80 ~~~~~~~~i~~l~~~~~~~~~~~v~r~-~N~~Ad~LAk~a~~~ 121 (144)
.+..++++.+.+...+....-..+++. ..+.|-.||+++...
T Consensus 96 ~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 96 KIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIVS 138 (384)
T ss_pred HHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhcc
Confidence 577888888888888888877788775 557799999998874
No 13
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=92.30 E-value=0.43 Score=32.74 Aligned_cols=59 Identities=12% Similarity=-0.010 Sum_probs=42.9
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCC-CCChHHHHHHHHHHHHHHHHHhCCCceEEecc
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRF-FGNVAMTQAATIEIGMQVALSVGGYSVLFESD 63 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~-~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD 63 (144)
.+...+|.||.+.+|.++..+...... .....+||..||+.|-+......+...++++-
T Consensus 25 ~ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyvT 84 (152)
T COG0590 25 EGEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVT 84 (152)
T ss_pred cCCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEEe
Confidence 345678999999899888866655432 23445899999999998886656666666654
No 14
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=89.38 E-value=2 Score=28.92 Aligned_cols=55 Identities=11% Similarity=0.049 Sum_probs=42.7
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
-+|.++|..+|.+..+..--.....--.-||-.|+..++.. -...+..|.+.+|.
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 36899999999877776644445666778999999999876 45556888898887
No 15
>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=88.88 E-value=1.5 Score=28.12 Aligned_cols=58 Identities=14% Similarity=-0.041 Sum_probs=38.5
Q ss_pred CCceeEEEEEeCCCCCeeeecccccC-CCCChHHHHHHHHHHHHHHHHHhCCCceEEec
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTR-FFGNVAMTQAATIEIGMQVALSVGGYSVLFES 62 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es 62 (144)
.+...+|.+|.|.+|.++..+..... .......||..|+..+.+.-....+....+++
T Consensus 14 ~~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~ 72 (109)
T cd01285 14 EGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYT 72 (109)
T ss_pred cCCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEE
Confidence 34567889999988988776665432 34567899999999887653222244444444
No 16
>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=88.50 E-value=1.6 Score=28.49 Aligned_cols=41 Identities=10% Similarity=0.051 Sum_probs=31.6
Q ss_pred CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHH
Q 037050 6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQV 49 (144)
Q Consensus 6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~ 49 (144)
+...+|.||.+.+|.++..+..... ...+||..|+..+.+.
T Consensus 17 ~~~pvGaviv~~~g~iv~~g~n~~~---~~~HAE~~ai~~a~~~ 57 (115)
T cd01284 17 PNPPVGCVIVDDDGEIVGEGYHRKA---GGPHAEVNALASAGEK 57 (115)
T ss_pred CCCCEEEEEEeCCCeEEEEecCCCC---CcccHHHHHHHHHhhc
Confidence 4557888998888988887665532 6789999999998764
No 17
>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=86.01 E-value=1.4 Score=29.23 Aligned_cols=57 Identities=2% Similarity=-0.049 Sum_probs=39.5
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
...+|.++++.+|.+..+...-.........||..|+..+...-. ..+..+.+-++.
T Consensus 20 ~~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~-~~i~~i~vv~~~ 76 (127)
T TIGR01354 20 NFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGY-RKFVAIAVADSA 76 (127)
T ss_pred CCeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCC-CCeEEEEEEeCC
Confidence 345788999999998775554333455667899999999886532 256677776654
No 18
>cd00786 cytidine_deaminase-like Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. 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.
Probab=85.97 E-value=4 Score=25.42 Aligned_cols=44 Identities=5% Similarity=-0.009 Sum_probs=29.5
Q ss_pred CCceeEEEEEeCC-CCCeeeecccc-cCCCCChHHHHHHHHHHHHH
Q 037050 5 KQVAGLAVVIRDW-ERNCVAAAINT-TRFFGNVAMTQAATIEIGMQ 48 (144)
Q Consensus 5 ~~~~g~G~vird~-~g~~~~~~~~~-~~~~~~~~~aE~~Al~~aL~ 48 (144)
.+...+|.++.+. +|.++..+... .........||..|+..+.+
T Consensus 15 ~~~~pVGaviv~~~~g~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~ 60 (96)
T cd00786 15 ESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS 60 (96)
T ss_pred CCCCCEEEEEEEeCCCCeEeeeEeccCCCCCCeeCHHHHHHHHHHH
Confidence 3566778888875 56666655433 22345678999999988754
No 19
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=82.49 E-value=4.3 Score=29.37 Aligned_cols=86 Identities=12% Similarity=0.006 Sum_probs=53.4
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHHHH
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWV 84 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~~~ 84 (144)
.-..|+|..+ ..|...+.++. .-++..+|++|...|. .+--.++ +-|||..|++.=. ..-++.++..
T Consensus 101 ATpTgwgi~i--~~~~~~~Tfs~----~l~IhtaELlaaClAr----~~~~~r~-l~tDnt~Vlsrky--ts~PW~lac~ 167 (245)
T PF00336_consen 101 ATPTGWGISI--TGQRMRGTFSK----PLPIHTAELLAACLAR----LMSGARC-LGTDNTVVLSRKY--TSFPWLLACA 167 (245)
T ss_pred CCCCcceeee--cCceeeeeecc----cccchHHHHHHHHHHH----hccCCcE-EeecCcEEEeccc--ccCcHHHHHH
Confidence 3456777775 33444444443 4678999999986554 3333344 8899988754211 2345666555
Q ss_pred HHHHHHHHhcCccEEEEEecCCchH
Q 037050 85 IFEILEKKKNFQNFKAQHTPRSCNG 109 (144)
Q Consensus 85 ~~~i~~l~~~~~~~~~~~v~r~~N~ 109 (144)
-+.|. ...++.|||...|-
T Consensus 168 A~wiL------rgts~~yVPS~~NP 186 (245)
T PF00336_consen 168 ANWIL------RGTSFYYVPSKYNP 186 (245)
T ss_pred HHHhh------cCceEEEeccccCc
Confidence 55443 35679999999886
No 20
>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. 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. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.
Probab=79.64 E-value=5 Score=25.65 Aligned_cols=44 Identities=5% Similarity=-0.002 Sum_probs=32.4
Q ss_pred CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHH
Q 037050 6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQV 49 (144)
Q Consensus 6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~ 49 (144)
+...+|.++++.+|.+..+.............||..|+..+...
T Consensus 16 ~~~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~~ 59 (112)
T cd01283 16 SNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSE 59 (112)
T ss_pred CCCeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHHc
Confidence 45678888988889887655544444567788999999888753
No 21
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=79.46 E-value=9.1 Score=26.20 Aligned_cols=41 Identities=7% Similarity=0.003 Sum_probs=27.2
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCC----------------CChHHHHHHHHHHHHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFF----------------GNVAMTQAATIEIGMQ 48 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~----------------~~~~~aE~~Al~~aL~ 48 (144)
...+|.||.+ +|.++..+....+.. ....+||..||..+.+
T Consensus 24 ~~~VGAVIV~-d~~IIs~GyN~~~~g~~~~~~~~~~~~~~~~~~~~HAE~nAI~~a~~ 80 (151)
T TIGR02571 24 RLSVGATIVR-DKRIIAGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQCAK 80 (151)
T ss_pred CCCEEEEEEE-CCEEEEEEECCCCCCCCccccccccccccccCCccCHHHHHHHHHHh
Confidence 3467777764 577888776654321 1346999999998753
No 22
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=76.81 E-value=6.7 Score=27.45 Aligned_cols=43 Identities=12% Similarity=0.117 Sum_probs=29.3
Q ss_pred CceeEEEEEeCCCCCeeeecccccC-CCCChHHHHHHHHHHHHHH
Q 037050 6 QVAGLAVVIRDWERNCVAAAINTTR-FFGNVAMTQAATIEIGMQV 49 (144)
Q Consensus 6 ~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~ 49 (144)
+...+|.||.+ +|.++..+..... ......+||..|+..|.+.
T Consensus 31 g~~pvGAVIV~-~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~ 74 (172)
T PRK10860 31 REVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLV 74 (172)
T ss_pred CCCCEEEEEEe-CCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHh
Confidence 34567888876 5888877665433 2334568999999988653
No 23
>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=74.51 E-value=4.6 Score=25.09 Aligned_cols=46 Identities=13% Similarity=-0.010 Sum_probs=31.1
Q ss_pred CCCceeEEEEEeCCCCCeeeecccccC-CCCChHHHHHHHHHHHHHH
Q 037050 4 KKQVAGLAVVIRDWERNCVAAAINTTR-FFGNVAMTQAATIEIGMQV 49 (144)
Q Consensus 4 ~~~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~ 49 (144)
..+...+|.|+.+++|..+..+..... .......||..|+..+-+.
T Consensus 20 ~~~~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~ 66 (102)
T PF00383_consen 20 PCGNFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN 66 (102)
T ss_dssp TTTSSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT
T ss_pred ccCCCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh
Confidence 345678899999977666666654432 2334579999999888765
No 24
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=72.76 E-value=18 Score=25.22 Aligned_cols=14 Identities=7% Similarity=0.024 Sum_probs=11.2
Q ss_pred hHHHHHHHHHHHHH
Q 037050 35 VAMTQAATIEIGMQ 48 (144)
Q Consensus 35 ~~~aE~~Al~~aL~ 48 (144)
..+||..|++.+-+
T Consensus 81 ~~HAE~nAi~~a~~ 94 (168)
T PHA02588 81 EIHAELNAILFAAR 94 (168)
T ss_pred CccHHHHHHHHHhh
Confidence 56899999988753
No 25
>cd01286 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.
Probab=71.06 E-value=12 Score=24.82 Aligned_cols=41 Identities=10% Similarity=0.046 Sum_probs=28.0
Q ss_pred ceeEEEEEeCCCCCeeeecccccC----------------------CCCChHHHHHHHHHHHHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTR----------------------FFGNVAMTQAATIEIGMQ 48 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~----------------------~~~~~~~aE~~Al~~aL~ 48 (144)
...+|.||.+. |.++..+....+ .......||..||..+.+
T Consensus 19 ~~~VGAViv~~-~~iI~~G~N~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HAE~~Ai~~a~~ 81 (131)
T cd01286 19 RRQVGAVIVKD-KRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQKCCRTVHAEQNAILQAAR 81 (131)
T ss_pred CCCEEEEEEEC-CEEEEEeeCCCCCCCCCcccccccccccccccccccCCCCCHHHHHHHHHhH
Confidence 45678888874 667776654432 123567899999998765
No 26
>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=70.29 E-value=11 Score=29.10 Aligned_cols=63 Identities=11% Similarity=0.166 Sum_probs=31.6
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHH---HHHHHHHHHhC---CCceEEeccHHHHHHHHhcC
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATI---EIGMQVALSVG---GYSVLFESDSHEVVELVNNR 74 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al---~~aL~~a~~~g---~~~v~~esDs~~vv~~l~~~ 74 (144)
.+..-+|+-||-.+|.-+..- .....-+..++ +.++..++..- -.+|.+.|||+.|++.+.+.
T Consensus 165 ~g~~~IGVHVRhGngeD~~~h-------~~~~~D~e~~L~~V~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~ 233 (321)
T PF05830_consen 165 AGYSVIGVHVRHGNGEDIMDH-------APYWADEERALRQVCTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKK 233 (321)
T ss_dssp TTSEEEEEEE----------------------HHHHHHHHHHHHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHH
T ss_pred CCCceEEEEEeccCCcchhcc-------CccccCchHHHHHHHHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHH
Confidence 355678999997777422211 22222333344 45555555443 36699999999999999874
No 27
>PRK05578 cytidine deaminase; Validated
Probab=61.22 E-value=17 Score=24.24 Aligned_cols=56 Identities=4% Similarity=-0.042 Sum_probs=38.0
Q ss_pred eeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 8 AGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 8 ~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
-.+|.++++.+|.+..+...-.....-..-||-.|+..++..- +..+..+.+-+|.
T Consensus 24 f~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G-~~~i~~i~vv~~~ 79 (131)
T PRK05578 24 FPVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEG-GGRLVAIACVGET 79 (131)
T ss_pred CceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcC-CCceEEEEEEecC
Confidence 3588999999998877666432233355678999998887432 2346667776665
No 28
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=60.00 E-value=53 Score=24.57 Aligned_cols=56 Identities=14% Similarity=-0.065 Sum_probs=39.1
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
+.-+|+|+ |.+|.+ +....++....-+.+=+.++..-++++.++|++.|.++.=|.
T Consensus 27 P~HvAiIm-DGNrRw--A~~~gl~~~~~GH~~G~~~l~~~~~~~~~~gIk~lTvYaFS~ 82 (256)
T PRK14828 27 PGHVGIIV-DGNRRW--ARKAGFTDVSQGHRAGAAKIGEFLGWCDETDVNVVTLYLLST 82 (256)
T ss_pred CCEEEEEe-cCChHH--HHHcCCCchHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEEh
Confidence 44556544 666654 333333322256778899999999999999999999987653
No 29
>PRK12411 cytidine deaminase; Provisional
Probab=57.68 E-value=22 Score=23.70 Aligned_cols=57 Identities=4% Similarity=-0.007 Sum_probs=38.0
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
.-.+|.+++..+|.+..+...-.....-..-||..|+..++..- +..+..|.+-++.
T Consensus 23 ~~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~g-~~~i~~i~v~~~~ 79 (132)
T PRK12411 23 KFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEG-DKEFVAIAIVADT 79 (132)
T ss_pred CCceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHCC-CCceEEEEEEeCC
Confidence 34688999999998877666433334445678998888876432 2345667777754
No 30
>PRK06848 hypothetical protein; Validated
Probab=52.81 E-value=35 Score=23.03 Aligned_cols=57 Identities=9% Similarity=-0.064 Sum_probs=36.5
Q ss_pred CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEecc
Q 037050 6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESD 63 (144)
Q Consensus 6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD 63 (144)
....+|..++..+|.+..+...-........-||-.|+..++..- +..+..+.+-++
T Consensus 25 s~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~g-~~~i~~i~~v~~ 81 (139)
T PRK06848 25 DWHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEG-DHEIDTIVAVRH 81 (139)
T ss_pred CCCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHcC-CCceEEEEEEec
Confidence 346688999999998776666433334456689999999887431 123444544443
No 31
>TIGR00326 eubact_ribD riboflavin biosynthesis protein RibD. This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model.
Probab=50.63 E-value=21 Score=27.72 Aligned_cols=36 Identities=8% Similarity=0.072 Sum_probs=27.2
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQ 48 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~ 48 (144)
-+|.||.+ +|.++..+..... ...+||..|+..|.+
T Consensus 20 ~vGaviv~-~~~ii~~g~n~~~---~~~HAE~~ai~~a~~ 55 (344)
T TIGR00326 20 LVGCVIVK-NGEIVGEGAHQKA---GEPHAEVHALRQAGE 55 (344)
T ss_pred CEEEEEEe-CCEEEEEeeCCCC---CCCCHHHHHHHHhcc
Confidence 47888887 7888887765432 356999999999855
No 32
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=50.52 E-value=23 Score=24.91 Aligned_cols=28 Identities=18% Similarity=0.336 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHhCCCceEEeccHHHH
Q 037050 40 AATIEIGMQVALSVGGYSVLFESDSHEV 67 (144)
Q Consensus 40 ~~Al~~aL~~a~~~g~~~v~~esDs~~v 67 (144)
-..|+.||+.|+++|+++|.+-+|...+
T Consensus 116 ~emLkl~L~~ar~lgi~~Vlvtcd~dN~ 143 (174)
T COG3981 116 KEMLKLALEKARELGIKKVLVTCDKDNI 143 (174)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEeCCCCc
Confidence 4678999999999999999998886543
No 33
>PRK08298 cytidine deaminase; Validated
Probab=49.24 E-value=47 Score=22.34 Aligned_cols=55 Identities=9% Similarity=-0.003 Sum_probs=35.2
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
.+|..++..+|.+..+...-......-.=||-.|+..++..- ...+..|.+-+|.
T Consensus 24 ~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G-~~~~~~i~v~~~~ 78 (136)
T PRK08298 24 GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQ-KRVTHSICVAREN 78 (136)
T ss_pred ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCC-CceEEEEEEEcCC
Confidence 788999999998876665322334455678999988877432 1123445555554
No 34
>PRK15000 peroxidase; Provisional
Probab=46.32 E-value=61 Score=23.04 Aligned_cols=42 Identities=10% Similarity=0.002 Sum_probs=32.7
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVG 54 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g 54 (144)
+.++.|.+|.+........+ ...+..|++.++.+|+...+.|
T Consensus 127 ~tfiID~~G~I~~~~~~~~~--~gr~~~eilr~l~al~~~~~~~ 168 (200)
T PRK15000 127 GSFLIDANGIVRHQVVNDLP--LGRNIDEMLRMVDALQFHEEHG 168 (200)
T ss_pred EEEEECCCCEEEEEEecCCC--CCCCHHHHHHHHHHhhhHHhcC
Confidence 66788999988887665443 3457889999999999988775
No 35
>KOG1018 consensus Cytosine deaminase FCY1 and related enzymes [Nucleotide transport and metabolism]
Probab=46.29 E-value=45 Score=23.36 Aligned_cols=48 Identities=13% Similarity=0.050 Sum_probs=31.8
Q ss_pred ceeEEEEEeCCCCCeeeecccc-cCCCCChHHHHHHHHHHHHHHHHHhC
Q 037050 7 VAGLAVVIRDWERNCVAAAINT-TRFFGNVAMTQAATIEIGMQVALSVG 54 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~-~~~~~~~~~aE~~Al~~aL~~a~~~g 54 (144)
..-+|+|+.+.+|.++..+-.. .........||..|+..=...+..++
T Consensus 31 ~~pvg~vlV~~~g~v~a~g~n~~~~~~d~t~HaE~~~I~~~~~~~~~~~ 79 (169)
T KOG1018|consen 31 EVPVGAVLVHMDGKVLASGGNMVNEKKDPTAHAEVIAIREEEVMCKSLR 79 (169)
T ss_pred CCceEEEEEeCCCeEEecccceecccCCcchhhHHHHHhhHHHHhhhcC
Confidence 4457888888788887777655 23344556699999998443343433
No 36
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=44.77 E-value=36 Score=20.24 Aligned_cols=17 Identities=18% Similarity=0.126 Sum_probs=13.4
Q ss_pred eeEEEEEeCCCCCeeee
Q 037050 8 AGLAVVIRDWERNCVAA 24 (144)
Q Consensus 8 ~g~G~vird~~g~~~~~ 24 (144)
+--|.++-|.+|.++..
T Consensus 14 gv~~~~l~~~dG~~i~~ 30 (91)
T PF03259_consen 14 GVRGAVLVDKDGLVIAS 30 (91)
T ss_dssp TEEEEEEEETTSEEEEE
T ss_pred CeeEEEEEcCCCCEEEE
Confidence 44578888999988887
No 37
>KOG3139 consensus N-acetyltransferase [General function prediction only]
Probab=44.70 E-value=27 Score=24.29 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhCCCceEEeccHH
Q 037050 43 IEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 43 l~~aL~~a~~~g~~~v~~esDs~ 65 (144)
++.+|+.+.+.|...|++||+-.
T Consensus 106 vr~aId~m~~~g~~eVvLeTe~~ 128 (165)
T KOG3139|consen 106 VRKAIDAMRSRGYSEVVLETEVT 128 (165)
T ss_pred HHHHHHHHHHCCCcEEEEecccc
Confidence 45789999999999999999853
No 38
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=43.90 E-value=1.4e+02 Score=22.63 Aligned_cols=55 Identities=15% Similarity=-0.055 Sum_probs=39.2
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
+.-+|+|+ |.++.+ +....++ ...-+.+-+..+..-++++.++|++.|.++.=|.
T Consensus 42 P~HVAiIm-DGNrRw--Ak~~g~~-~~~GH~~G~~~l~~i~~~c~~lGIk~lTvYaFS~ 96 (275)
T PRK14835 42 PRHLGLIL-DGNRRF--ARALGLQ-REMGHEFGVQKAYEVLEWCLELGIPTVTIWVFST 96 (275)
T ss_pred CCEEEEEe-cCchHH--HHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEEc
Confidence 34556544 666654 3333333 3456788888999999999999999999987664
No 39
>PRK13191 putative peroxiredoxin; Provisional
Probab=42.75 E-value=70 Score=23.07 Aligned_cols=42 Identities=14% Similarity=0.011 Sum_probs=32.1
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVG 54 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g 54 (144)
+.+|.|.+|.+.......++ ...+.-|++.++.+|+.....|
T Consensus 126 ~tfIID~~G~Ir~~~~~~~~--~gr~~~eilr~l~alq~~~~~~ 167 (215)
T PRK13191 126 AVFIVDDKGTVRLILYYPME--IGRNIDEILRAIRALQLVDKAG 167 (215)
T ss_pred EEEEECCCCEEEEEEecCCC--CCCCHHHHHHHHHHhhhhhhcC
Confidence 56788999988776655443 3458899999999999877764
No 40
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=41.04 E-value=92 Score=19.71 Aligned_cols=42 Identities=19% Similarity=0.274 Sum_probs=30.5
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQ 48 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~ 48 (144)
.+|+--.+.|.+|.+..-++..+...+.-..-|..++..+|-
T Consensus 32 ~~GF~~tl~D~~G~~HeLgtntfgl~S~l~~~eV~~la~~la 73 (96)
T PF11080_consen 32 RAGFSTTLTDEDGNPHELGTNTFGLISALSAEEVAQLARGLA 73 (96)
T ss_pred hcCceeEEecCCCCEeecCCCeEEEEecCCHHHHHHHHHHHh
Confidence 467777899999998888887777555555556777766663
No 41
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=40.05 E-value=1.1e+02 Score=24.64 Aligned_cols=63 Identities=10% Similarity=0.029 Sum_probs=42.0
Q ss_pred hhHHHHHHHHHHHHhcCccEEEEEecCCchH--HHHHHHhhhcccCCeeeeccCCChHHHHHHhcc
Q 037050 79 SKIIWVIFEILEKKKNFQNFKAQHTPRSCNG--IAHFLAKLVLQKKEIVIWLDEIPTDILYLISSS 142 (144)
Q Consensus 79 ~~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~--~Ad~LAk~a~~~~~~~~~~~~~P~~i~~~l~~D 142 (144)
++-+...++++.+.++.+++.+.=+....|- -++.++|....+..+.+|++ -|..+++.+.+|
T Consensus 355 ~e~~~y~~eLr~~~qkl~~~~lHiiDSs~~g~l~~e~ler~~~~~~~~sv~fC-GP~~m~dsL~r~ 419 (438)
T COG4097 355 WEEALYAEELRALAQKLPNVVLHIIDSSKDGYLDQEDLERYPDRPRTRSVFFC-GPIKMMDSLRRD 419 (438)
T ss_pred CchhHHHHHHHHHHhcCCCeEEEEecCCCCCccCHHHhhccccccCcceEEEE-cCHHHHHHHHHH
Confidence 3345668899999999999988666665554 35666776333334468887 566666666655
No 42
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=39.57 E-value=1.6e+02 Score=22.71 Aligned_cols=54 Identities=13% Similarity=-0.094 Sum_probs=39.4
Q ss_pred eeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 8 AGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 8 ~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
--+|+ |-|.+|.+ +....++ ...-+.+-+.++..-++++.++|++.|.++.=|.
T Consensus 69 ~HVAi-IMDGNrRw--Ak~~gl~-~~~GH~~G~~~l~~v~~~c~~lGI~~lTvYaFSt 122 (296)
T PRK14827 69 NHVAI-VMDGNGRW--ATQRGLA-RTEGHKMGEAVVIDIACGAIELGIKWLSLYAFST 122 (296)
T ss_pred CeEEE-eccCchHH--HHHCCCC-HhHHHHHHHHHHHHHHHHHHHcCCCEEEEeeecc
Confidence 34555 44767755 3333344 4567888889999999999999999999986553
No 43
>PF05854 MC1: Non-histone chromosomal protein MC1; InterPro: IPR008674 This family consists of archaeal chromosomal protein MC1 sequences which protect DNA against thermal denaturation [].; GO: 0042262 DNA protection; PDB: 1T23_A 2KHL_A.
Probab=39.41 E-value=13 Score=23.24 Aligned_cols=30 Identities=13% Similarity=0.145 Sum_probs=21.3
Q ss_pred EEEeCCCCCeeeecccccCCCCChHHHHHHHHHHH
Q 037050 12 VVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIG 46 (144)
Q Consensus 12 ~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~a 46 (144)
+++||.+|.-+..|+.. +|-+|-+-|...|
T Consensus 6 F~Lr~~~G~E~gvFtG~-----~PrqAAlKAA~Rg 35 (93)
T PF05854_consen 6 FALRDEDGNEIGVFTGA-----QPRQAALKAARRG 35 (93)
T ss_dssp EEEETTTTSEEEEEEES-----SCCHHHHHHHCCT
T ss_pred EEEEcCCCccccEEeCC-----CHHHHHHHHhhcC
Confidence 78999999988888764 4555655555544
No 44
>PRK13190 putative peroxiredoxin; Provisional
Probab=38.79 E-value=92 Score=22.09 Aligned_cols=44 Identities=14% Similarity=-0.046 Sum_probs=32.6
Q ss_pred EEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCC
Q 037050 10 LAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGG 55 (144)
Q Consensus 10 ~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~ 55 (144)
=+.++.|.+|.+........ ....+..|++.++.+|+...+.|.
T Consensus 118 p~~fiId~~G~I~~~~~~~~--~~gr~~~ellr~l~~l~~~~~~~~ 161 (202)
T PRK13190 118 RGVFIIDPNQIVRWMIYYPA--ETGRNIDEIIRITKALQVNWKRKV 161 (202)
T ss_pred eEEEEECCCCEEEEEEEeCC--CCCCCHHHHHHHHHHhhhHHhcCC
Confidence 36688899998776554433 334578899999999999887753
No 45
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=38.46 E-value=58 Score=24.15 Aligned_cols=31 Identities=26% Similarity=0.294 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhCCCceEEeccHHHHHHHHhc
Q 037050 43 IEIGMQVALSVGGYSVLFESDSHEVVELVNN 73 (144)
Q Consensus 43 l~~aL~~a~~~g~~~v~~esDs~~vv~~l~~ 73 (144)
+.+-.+-|.+-|..+|++.||+..+.+.+.+
T Consensus 31 I~rV~e~a~~s~~~rvvVATDde~I~~av~~ 61 (247)
T COG1212 31 IVRVAERALKSGADRVVVATDDERIAEAVQA 61 (247)
T ss_pred HHHHHHHHHHcCCCeEEEEcCCHHHHHHHHH
Confidence 3455667777799999999999999999976
No 46
>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=36.11 E-value=1.4e+02 Score=21.09 Aligned_cols=43 Identities=12% Similarity=-0.004 Sum_probs=31.3
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGG 55 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~ 55 (144)
+.++.|.+|.+......... ......|++.++.+|+.....|.
T Consensus 119 ~~fiID~~G~I~~~~~~~~~--~gr~~~ell~~l~~lq~~~~~~~ 161 (203)
T cd03016 119 AVFIIDPDKKIRLILYYPAT--TGRNFDEILRVVDALQLTDKHKV 161 (203)
T ss_pred EEEEECCCCeEEEEEecCCC--CCCCHHHHHHHHHHHhhHhhcCc
Confidence 46888999988776654433 23457899999999998876653
No 47
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=35.57 E-value=1.9e+02 Score=21.62 Aligned_cols=58 Identities=10% Similarity=-0.055 Sum_probs=41.7
Q ss_pred CCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 4 KKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 4 ~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
.+-+.-+|+|+ |.++.+ +....++ ...-+.+=+..+..-++++.++|++.|.++.=|.
T Consensus 12 ~~~P~HVAiIm-DGNrRw--Ak~~g~~-~~~GH~~G~~~l~~i~~~c~~lgI~~lTvYaFS~ 69 (249)
T PRK14834 12 MSVPRHVAIIM-DGNGRW--AKARGLP-RAAGHRAGVEALRRVVRAAGELGIGYLTLFAFSS 69 (249)
T ss_pred CCCCCeEEEEe-cCchHH--HHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEEec
Confidence 34455666654 766655 3333333 4567888899999999999999999999998554
No 48
>COG0084 TatD Mg-dependent DNase [DNA replication, recombination, and repair]
Probab=35.36 E-value=20 Score=26.75 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=29.0
Q ss_pred HHHHHHHhCCCceEEeccHHHHHHH-HhcCCCCchhHHHHHHHHHHH
Q 037050 46 GMQVALSVGGYSVLFESDSHEVVEL-VNNRTNSMSKIIWVIFEILEK 91 (144)
Q Consensus 46 aL~~a~~~g~~~v~~esDs~~vv~~-l~~~~~~~~~~~~~~~~i~~l 91 (144)
.-+.+..+-..++.+||||..+.-. ..++...+......++.+..+
T Consensus 188 ~~ev~~~iPldrLL~ETDsPyl~P~p~rGkrNeP~~v~~v~~~iAel 234 (256)
T COG0084 188 LREVARELPLDRLLLETDAPYLAPVPYRGKRNEPAYVRHVAEKLAEL 234 (256)
T ss_pred HHHHHHhCCHhHeEeccCCCCCCCcCCCCCCCCchHHHHHHHHHHHH
Confidence 3455667788999999999987654 333333344455555555444
No 49
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=32.10 E-value=77 Score=23.39 Aligned_cols=56 Identities=14% Similarity=-0.019 Sum_probs=41.3
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
+-+--+|+ |-|.+|.+ +....++ ...-+.+=+.++..-++++.++|++.|.++.=|
T Consensus 5 ~~P~HVAi-ImDGNrRw--Ak~~gl~-~~~GH~~G~~~~~~i~~~c~~~GI~~lT~YaFS 60 (230)
T PRK14837 5 SLPSHVGI-IMDGNRRW--ALKKGLS-FFEGHKEGLKRAKEIVKHSLKLGIKYLSLYVFS 60 (230)
T ss_pred CCCCeEEE-EccCCHHH--HHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 34455665 44777766 3333344 456788999999999999999999999998655
No 50
>PRK10786 ribD bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=32.03 E-value=66 Score=25.30 Aligned_cols=37 Identities=8% Similarity=0.152 Sum_probs=25.6
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQV 49 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~ 49 (144)
-+|.||-+ +|.++..+..... ...+||..|+..+-+.
T Consensus 26 ~vGaviv~-~g~ii~~g~n~~~---g~~HAE~~ai~~a~~~ 62 (367)
T PRK10786 26 NVGCVIVK-DGEIVGEGYHQRA---GEPHAEVHALRMAGEK 62 (367)
T ss_pred CEEEEEEe-CCEEEEEEeCCCC---CCCCHHHHHHHHHhhh
Confidence 36777765 5888877765322 2369999999988653
No 51
>PRK13599 putative peroxiredoxin; Provisional
Probab=31.80 E-value=1.3e+02 Score=21.61 Aligned_cols=43 Identities=16% Similarity=-0.048 Sum_probs=31.3
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGG 55 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~ 55 (144)
..+|.|.+|.+........ ....+..|++..+.+|+.+...+.
T Consensus 121 ~tfIID~dG~Ir~~~~~p~--~~gr~~~eilr~l~~lq~~~~~~~ 163 (215)
T PRK13599 121 AVFIVDDKGTIRLIMYYPQ--EVGRNVDEILRALKALQTADQYGV 163 (215)
T ss_pred EEEEECCCCEEEEEEEcCC--CCCCCHHHHHHHHHHhhhhhhcCC
Confidence 4577899998877754332 344678899999999988877643
No 52
>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=31.33 E-value=82 Score=23.16 Aligned_cols=49 Identities=10% Similarity=-0.034 Sum_probs=37.6
Q ss_pred EEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 13 VIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 13 vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
+|-|.+|.+ +....++ ...-+.+=+.++..-++++.++|++.|.++.=|
T Consensus 5 iImDGNrRw--Ak~~gl~-~~~GH~~G~~~~~~v~~~c~~~GI~~lT~yaFS 53 (226)
T TIGR00055 5 IIMDGNGRW--AKKKGKP-RAYGHKAGVKSLRRILRWCANLGVECLTLYAFS 53 (226)
T ss_pred EEcCCCHHH--HHHCCCC-hhHhHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 455777765 3333344 456888899999999999999999999998655
No 53
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=31.05 E-value=69 Score=24.69 Aligned_cols=46 Identities=11% Similarity=0.101 Sum_probs=31.9
Q ss_pred eeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHH
Q 037050 8 AGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHE 66 (144)
Q Consensus 8 ~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~ 66 (144)
.++-.++-|.+|.... +...+++. + ++|..+.++| ++++|-|++..
T Consensus 20 ~~~DtfifDcDGVlW~-g~~~ipGs-----~------e~l~~L~~~g-K~i~fvTNNSt 65 (306)
T KOG2882|consen 20 DSFDTFIFDCDGVLWL-GEKPIPGS-----P------EALNLLKSLG-KQIIFVTNNST 65 (306)
T ss_pred hhcCEEEEcCCcceee-cCCCCCCh-----H------HHHHHHHHcC-CcEEEEeCCCc
Confidence 4566789999996544 66566642 2 5566677778 88999888754
No 54
>PTZ00137 2-Cys peroxiredoxin; Provisional
Probab=30.69 E-value=1.2e+02 Score=22.77 Aligned_cols=42 Identities=17% Similarity=0.057 Sum_probs=32.3
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVG 54 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g 54 (144)
+.+|.|.+|.+........+ ......|++.++.|||...+.|
T Consensus 190 ~tFIID~dG~I~~~~~~~~~--~gr~v~eiLr~l~alq~~~~~g 231 (261)
T PTZ00137 190 ASVLVDKAGVVKHVAVYDLG--LGRSVDETLRLFDAVQFAEKTG 231 (261)
T ss_pred EEEEECCCCEEEEEEEeCCC--CCCCHHHHHHHHHHhchhhhcC
Confidence 55788999988877654443 3457899999999999987775
No 55
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.82 E-value=89 Score=23.06 Aligned_cols=52 Identities=17% Similarity=-0.040 Sum_probs=38.7
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
-+|+ |-|.++.+ +....++ ...-+.+=+.++..-++++.++|++.|.++.=|
T Consensus 6 HVai-ImDGNrRw--Ak~~g~~-~~~GH~~G~~~l~~i~~~~~~lgIk~lTvYaFS 57 (233)
T PRK14841 6 HVAI-IMDGNGRW--AKKRGLP-RIKGHQRGAEVLHNTVKWSLELGIKYLTAFSFS 57 (233)
T ss_pred EEEE-EccCCHHH--HHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEeee
Confidence 3444 44766655 3333344 566888999999999999999999999998644
No 56
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=29.74 E-value=77 Score=21.66 Aligned_cols=34 Identities=9% Similarity=0.136 Sum_probs=23.2
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIG 46 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~a 46 (144)
-+|.||.+.. .++..+...- .-.-.||..||..|
T Consensus 29 ~VG~VIV~~~-~Ivg~G~h~~---aG~pHAEv~Al~~a 62 (146)
T COG0117 29 SVGCVIVKDG-EIVGEGYHEK---AGGPHAEVCALRMA 62 (146)
T ss_pred ceeEEEEECC-EEEeeeecCC---CCCCcHHHHHHHHc
Confidence 3577776644 7777666432 34557999999888
No 57
>PF05903 Peptidase_C97: PPPDE putative peptidase domain; InterPro: IPR008580 This domain consists of the N-terminal portion of several eukaryotic sequences. The function of this domain is unknown.; PDB: 2WP7_A 3EBQ_A.
Probab=29.68 E-value=43 Score=22.77 Aligned_cols=32 Identities=16% Similarity=0.259 Sum_probs=23.6
Q ss_pred HHHHhcCccEEEEEecCCchHHHHHHHhhhcc
Q 037050 89 LEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQ 120 (144)
Q Consensus 89 ~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~ 120 (144)
.++...|..-+-.-+.|+||..++.|++.-..
T Consensus 92 ~~l~~~~~~~~Y~Ll~~NCNhFs~~l~~~L~g 123 (151)
T PF05903_consen 92 RSLSREFTGDSYHLLNRNCNHFSDALCQFLTG 123 (151)
T ss_dssp HHHHTT-SGGG-BTTTBSHHHHHHHHHHHHHS
T ss_pred HHHHhhccCCcchhhhhhhhHHHHHHHHHhCC
Confidence 34555677777778899999999999998544
No 58
>KOG0833 consensus Cytidine deaminase [Nucleotide transport and metabolism]
Probab=29.47 E-value=1.4e+02 Score=21.11 Aligned_cols=39 Identities=5% Similarity=-0.115 Sum_probs=28.1
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGM 47 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL 47 (144)
-+|.++|-++|.+..+...-.-......-||-.|+..++
T Consensus 43 kVGA~~r~ssGrif~G~NVEn~~~~~sIcAEr~ai~~l~ 81 (173)
T KOG0833|consen 43 KVGAAGRASSGRIFLGVNVENASYHHSICAERFAIANLA 81 (173)
T ss_pred ceEEEEEecCCcEEEeeeecccCCCCcccHHHHHHHHHH
Confidence 468999999998766655444446666778888877666
No 59
>PRK13189 peroxiredoxin; Provisional
Probab=29.39 E-value=1.7e+02 Score=21.20 Aligned_cols=42 Identities=19% Similarity=0.049 Sum_probs=30.4
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVG 54 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g 54 (144)
+.+|.|.+|.+......... ...+..|++.++.+|+...+.|
T Consensus 128 ~tfIID~~G~Ir~~~~~~~~--~gr~~~eilr~l~alq~~~~~~ 169 (222)
T PRK13189 128 AVFIIDPKGIIRAILYYPQE--VGRNMDEILRLVKALQTSDEKG 169 (222)
T ss_pred EEEEECCCCeEEEEEecCCC--CCCCHHHHHHHHHHhhhHhhcC
Confidence 56888999987665543332 3345679999999999887775
No 60
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.33 E-value=94 Score=22.95 Aligned_cols=54 Identities=11% Similarity=-0.079 Sum_probs=40.2
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
+.-+|+| -|.++.+ +....++ ...-+.+=+.++..-++++.++|++.|.++.=|
T Consensus 5 P~HVaiI-mDGNrRw--A~~~gl~-~~~GH~~G~~~l~~~~~~c~~~gI~~lTvyaFS 58 (233)
T PRK14833 5 LKHLAII-MDGNGRW--AKLRGKA-RAAGHKKGVKTLREITIWCANHKLECLTLYAFS 58 (233)
T ss_pred CCeEEEE-ccCCHHH--HHHCCCC-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEeecc
Confidence 3445554 4766655 4444444 466888999999999999999999999998655
No 61
>PLN02807 diaminohydroxyphosphoribosylaminopyrimidine deaminase
Probab=29.28 E-value=75 Score=25.23 Aligned_cols=36 Identities=11% Similarity=0.180 Sum_probs=24.7
Q ss_pred EEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHH
Q 037050 10 LAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQV 49 (144)
Q Consensus 10 ~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~ 49 (144)
+|.||.+ +|.++..+..... . ..+||..|+..|-+.
T Consensus 56 VGaViV~-~g~Ii~~g~n~~~--g-~~HAEi~Ai~~a~~~ 91 (380)
T PLN02807 56 VGCVIVK-DGRIVGEGFHPKA--G-QPHAEVFALRDAGDL 91 (380)
T ss_pred EEEEEEE-CCEEEEEEeCCCC--C-CcCHHHHHHHHhhhh
Confidence 5666654 3888877765432 2 369999999988653
No 62
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.22 E-value=88 Score=23.24 Aligned_cols=54 Identities=15% Similarity=-0.027 Sum_probs=40.0
Q ss_pred eeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 8 AGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 8 ~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
.-+|+ |-|.+|.+ +....++ ...-..+-+.++..-++++.++|++.|.++.=|.
T Consensus 11 ~HVAi-ImDGNrRw--Ak~~gl~-~~~GH~~G~~~l~~i~~~c~~~GI~~lTvYaFS~ 64 (239)
T PRK14839 11 LHVAI-IMDGNGRW--ATARGLP-RLAGHRAGVEAIRRVVEAAPDLGIGTLTLYAFSS 64 (239)
T ss_pred CEEEE-EcCCCHHH--HHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEech
Confidence 44555 44777765 4443344 4568888999999999999999999999986553
No 63
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=28.89 E-value=2.2e+02 Score=20.45 Aligned_cols=49 Identities=12% Similarity=-0.018 Sum_probs=35.6
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCC
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGG 55 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~ 55 (144)
.+.+-=|.+|.|++|.+........ ...-+.-|.+.++.|||+..++|.
T Consensus 120 ~g~a~R~~FIIDp~g~ir~~~v~~~--~iGRn~dEilR~idAlq~~~~hg~ 168 (194)
T COG0450 120 EGLALRGTFIIDPDGVIRHILVNPL--TIGRNVDEILRVIDALQFVAKHGE 168 (194)
T ss_pred CCcceeEEEEECCCCeEEEEEEecC--CCCcCHHHHHHHHHHHHHHHHhCC
Confidence 3444458889999997765554332 345677899999999999888763
No 64
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=28.81 E-value=2.5e+02 Score=21.00 Aligned_cols=52 Identities=10% Similarity=0.011 Sum_probs=38.3
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEec
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFES 62 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es 62 (144)
+.-+|+|+ |.+|.+ +....++ ...-..+=+.++..-++++.++|++.|.++.
T Consensus 15 P~HVAiIm-DGNrRw--A~~~gl~-~~~GH~~G~~~~~~iv~~c~~~gI~~lTvYa 66 (253)
T PRK14836 15 PRHIAIIM-DGNGRW--AKRRGKP-RVEGHRAGVRAVRRTIEFCLEKGIEMLTLFA 66 (253)
T ss_pred CCeEEEec-CCcHHH--HHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEehhH
Confidence 44556544 666654 3333344 4667888889999999999999999999987
No 65
>PF07511 DUF1525: Protein of unknown function (DUF1525); InterPro: IPR011090 This family of proteins is restricted to the Gammaproteobacteria. Members belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=28.68 E-value=85 Score=20.50 Aligned_cols=23 Identities=26% Similarity=0.069 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCc
Q 037050 35 VAMTQAATIEIGMQVALSVGGYS 57 (144)
Q Consensus 35 ~~~aE~~Al~~aL~~a~~~g~~~ 57 (144)
-++.++...+.|+-.||.+|+++
T Consensus 61 ~~q~~L~~Ayqgv~~Aw~lgi~k 83 (114)
T PF07511_consen 61 QLQQQLAQAYQGVVDAWSLGITK 83 (114)
T ss_pred HHHHHHHHHHHHHHHHHHhCccc
Confidence 34566677788999999999866
No 66
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.65 E-value=2.1e+02 Score=20.02 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=18.0
Q ss_pred CceEEeccHHHHHHHHhcCCCC
Q 037050 56 YSVLFESDSHEVVELVNNRTNS 77 (144)
Q Consensus 56 ~~v~~esDs~~vv~~l~~~~~~ 77 (144)
.-|++|||...+++.+..+...
T Consensus 128 ~GvILEtdp~~ia~rv~~~~~~ 149 (175)
T KOG3343|consen 128 GGVILETDPNQIAQRVALRPTD 149 (175)
T ss_pred CceEEecCHHHHHHHhccCCCC
Confidence 3489999999999999876543
No 67
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=28.28 E-value=2.6e+02 Score=20.92 Aligned_cols=56 Identities=13% Similarity=-0.040 Sum_probs=39.0
Q ss_pred CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
-+--+|+|+ |.++.+ +....++ ...-..+=+..+..-++++.++|++.|.++.=|.
T Consensus 22 ~P~HVAiIm-DGNrRw--Ak~~gl~-~~~Gh~~G~~~l~~~l~~c~~~GI~~vTvYaFS~ 77 (251)
T PRK14830 22 IPKHIAIIM-DGNGRW--AKKRMLP-RIAGHKAGMDTVKKITKAASELGVKVLTLYAFST 77 (251)
T ss_pred CCCeEEEEe-cCchHH--HHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEEeh
Confidence 345566554 555543 3333333 3457778888999999999999999999998553
No 68
>PLN02182 cytidine deaminase
Probab=27.54 E-value=1.1e+02 Score=23.91 Aligned_cols=46 Identities=4% Similarity=-0.220 Sum_probs=31.2
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCC--hHHHHHHHHHHHHHHHHHhCCCce
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGN--VAMTQAATIEIGMQVALSVGGYSV 58 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~--~~~aE~~Al~~aL~~a~~~g~~~v 58 (144)
-+|.+++..+|.+..+...-..+..- ..-||-.|+-.++ ..|.+++
T Consensus 67 ~VGAa~l~~sG~iy~GvNVEnas~pl~~tICAEr~AI~~A~----~~Ge~~i 114 (339)
T PLN02182 67 KVGAVGRASSGRVYLGVNVDFPGLPLHHSIHAEQFLVTNLA----LNSEKDL 114 (339)
T ss_pred eeeEEEEeCCCCEEEEEEeecCCCccCCccCHHHHHHHHHH----HCCCCce
Confidence 46889999999887777644333222 4589999888876 4455443
No 69
>PRK09822 lipopolysaccharide core biosynthesis protein; Provisional
Probab=27.38 E-value=70 Score=23.84 Aligned_cols=20 Identities=20% Similarity=0.132 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCCceEEec
Q 037050 43 IEIGMQVALSVGGYSVLFES 62 (144)
Q Consensus 43 l~~aL~~a~~~g~~~v~~es 62 (144)
.++|||++..+|+++|.+.+
T Consensus 173 aY~ALQIaY~LGF~~I~iaG 192 (269)
T PRK09822 173 AYTAIQVAYSLKYGRIICSG 192 (269)
T ss_pred HHHHHHHHHHcCCCEEEEEe
Confidence 56899999999999999876
No 70
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=27.33 E-value=97 Score=24.12 Aligned_cols=56 Identities=9% Similarity=0.010 Sum_probs=40.5
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
+-+--+|+|+ |.+|.+ +....++ ...-+.+-+.++..-++++.++|++.|.++.=|
T Consensus 18 ~iP~HVAiIM-DGNrRw--Ak~~gl~-~~~GH~~G~~~l~~il~~c~~lGIk~lTlYAFS 73 (322)
T PTZ00349 18 INIKHISIIM-DGNRRF--AKEKGLH-SAIGHFMGSKALIQIIEICIKLKIKILSVFSFS 73 (322)
T ss_pred CCCCcEEEEc-CCCHHH--HHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 3344556544 777765 4444444 455788899999999999999999999988644
No 71
>PRK10382 alkyl hydroperoxide reductase subunit C; Provisional
Probab=27.28 E-value=2.3e+02 Score=19.96 Aligned_cols=41 Identities=12% Similarity=-0.116 Sum_probs=31.5
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHh
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSV 53 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~ 53 (144)
+.++.|.+|.+........ .......|+++.+.+||.....
T Consensus 121 ~tfIID~~G~I~~~~~~~~--~~~~~~~eil~~l~alq~~~~~ 161 (187)
T PRK10382 121 ATFVVDPQGIIQAIEVTAE--GIGRDASDLLRKIKAAQYVASH 161 (187)
T ss_pred EEEEECCCCEEEEEEEeCC--CCCCCHHHHHHHHHhhhhHhhc
Confidence 4578899998877765432 3446789999999999998776
No 72
>PF12404 DUF3663: Peptidase ; InterPro: IPR008330 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family represents the peptidase B group of leucyl aminopeptidases, which are restricted to the gammaproteobacteria. They contain a C-terminal aminopeptidase catalytic domain and an N-terminal domain of unknown function. They are zinc-dependent exopeptidases (3.4.11.1 from EC) and belong to MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF). They selectively release N-terminal amino acid residues from polypeptides and proteins and are involved in the processing, catabolism and degradation of intracellular proteins [, , ]. Leucyl aminopeptidase forms a homohexamer containing two trimers stacked on top of one another []. Each monomer binds two zinc ions. The zinc-binding and catalytic sites are located within the C-terminal catalytic domain []. The same catalytic aminopeptidase domain is found in the other M17 peptidases IPR011356 from INTERPRO. These two groups of aminopeptidases differ by their N-terminal domains. The N-terminal domain in members of IPR011356 from INTERPRO has been implicated in DNA binding [, ] and it is not associated with members of this family which have a different N-terminal domain and therefore are not expected to bind DNA or be involved in transcriptional regulation. In addition, there are related proteins with the same catalytic domain and unique N-terminal sequences unrelated to any of the two N-terminal domains discussed above. For additional information please see [, , , ]. ; GO: 0004177 aminopeptidase activity, 0008235 metalloexopeptidase activity, 0030145 manganese ion binding, 0005737 cytoplasm
Probab=26.46 E-value=1.1e+02 Score=18.55 Aligned_cols=26 Identities=12% Similarity=0.065 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 39 QAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 39 E~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
++.++..|-+.....|++.|.+.+|.
T Consensus 36 ~l~~IQrAaRkLd~qGI~~V~L~G~~ 61 (77)
T PF12404_consen 36 DLRAIQRAARKLDGQGIKNVALAGEG 61 (77)
T ss_pred chHHHHHHHHHHhhCCCceEEEecCC
Confidence 47888899999999999999999984
No 73
>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=25.92 E-value=2.2e+02 Score=19.33 Aligned_cols=43 Identities=14% Similarity=0.067 Sum_probs=30.7
Q ss_pred EEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCC
Q 037050 11 AVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGG 55 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~ 55 (144)
..++.|.+|.+........+. .....|++..+..++.+.++|.
T Consensus 122 ~~~lID~~G~I~~~~~~~~~~--~~~~~~il~~l~~~~~~~~~~~ 164 (173)
T cd03015 122 GTFIIDPEGIIRHITVNDLPV--GRSVDETLRVLDALQFVEEHGE 164 (173)
T ss_pred EEEEECCCCeEEEEEecCCCC--CCCHHHHHHHHHHhhhhhhcCC
Confidence 578889999888877544332 2345778888888888887764
No 74
>COG3693 XynA Beta-1,4-xylanase [Carbohydrate transport and metabolism]
Probab=25.65 E-value=54 Score=25.59 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=23.6
Q ss_pred HHHHHHHhhhcccC-----CeeeeccCCChHHHH
Q 037050 109 GIAHFLAKLVLQKK-----EIVIWLDEIPTDILY 137 (144)
Q Consensus 109 ~~Ad~LAk~a~~~~-----~~~~~~~~~P~~i~~ 137 (144)
..||++|..|...+ ++.+|+...|+++..
T Consensus 82 e~AD~ia~FAr~h~m~lhGHtLvW~~q~P~W~~~ 115 (345)
T COG3693 82 EAADAIANFARKHNMPLHGHTLVWHSQVPDWLFG 115 (345)
T ss_pred cchHHHHHHHHHcCCeeccceeeecccCCchhhc
Confidence 46999999998844 567999999999854
No 75
>TIGR02508 type_III_yscG type III secretion protein, YscG family. YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.
Probab=25.32 E-value=22 Score=22.95 Aligned_cols=19 Identities=26% Similarity=0.244 Sum_probs=16.1
Q ss_pred EEecCCchHHHHHHHhhhc
Q 037050 101 QHTPRSCNGIAHFLAKLVL 119 (144)
Q Consensus 101 ~~v~r~~N~~Ad~LAk~a~ 119 (144)
.|...|.|.+||+|+..+.
T Consensus 18 ~HcHqEA~tIAdwL~~~~~ 36 (115)
T TIGR02508 18 HHCHQEANTIADWLHLKGE 36 (115)
T ss_pred chHHHHHHHHHHHHhcCCc
Confidence 4888999999999988763
No 76
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=24.91 E-value=2e+02 Score=18.54 Aligned_cols=51 Identities=16% Similarity=0.164 Sum_probs=32.0
Q ss_pred EEEEeCCCCCeeeecccc---c----CCCCChHHHHHHHHHHHHHHHHHhCCCceEEec
Q 037050 11 AVVIRDWERNCVAAAINT---T----RFFGNVAMTQAATIEIGMQVALSVGGYSVLFES 62 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~---~----~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es 62 (144)
.=||.|..|..+.+.+.. + ....+...|...+.+.|- .|.+.|+..|+|.-
T Consensus 29 aQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~-ra~~~gi~~vvfDr 86 (109)
T CHL00139 29 AQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAK-KSLKKGITKVVFDR 86 (109)
T ss_pred EEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHH-HHHHCCCCEEEEcC
Confidence 346778888888877742 1 123444455555555553 46688999988863
No 77
>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=24.63 E-value=3.5e+02 Score=21.33 Aligned_cols=65 Identities=14% Similarity=0.158 Sum_probs=42.6
Q ss_pred eeEEEEEeCCCCC---eeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc
Q 037050 8 AGLAVVIRDWERN---CVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN 73 (144)
Q Consensus 8 ~g~G~vird~~g~---~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~ 73 (144)
.=+|=|+|...|. +.-.+...++ ..+...||+..+..+.+....+|+.++.++--+..+++.+-.
T Consensus 86 ~Y~g~VfR~~~gr~rEf~Q~GvEiiG-~~~~~~aDaEvi~l~~~~L~~lgl~~~~i~ig~~~il~~ll~ 153 (373)
T PRK12295 86 AYLGEVFRQRRDRASEFLQAGIESFG-RADPAAADAEVLALALEALAALGPGDLEVRLGDVGLFAALVD 153 (373)
T ss_pred EEEccEEECCCCCCCcceEeeEEeeC-CCCCccchHHHHHHHHHHHHHcCCCceEEEeCCHHHHHHHHH
Confidence 3457788876553 2233333343 334455666667777788889999999888777777777754
No 78
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=24.38 E-value=1.2e+02 Score=22.75 Aligned_cols=55 Identities=16% Similarity=-0.069 Sum_probs=40.4
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
+--+|+ |-|.++.+ +....++ ...-+.+-+.++..-++++.++|++.|.++.=|.
T Consensus 19 P~HVAi-ImDGNrRw--Ak~~gl~-~~~GH~~G~~~l~~i~~~c~~~gI~~lTvyaFS~ 73 (253)
T PRK14832 19 PQHIAV-IMDGNGRW--ATSQGLP-RIAGHRQGARTLKELLRCCKDWGIKALTAYAFST 73 (253)
T ss_pred CCEEEE-ECCCCHHH--HHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 344555 44766665 3443344 5668888999999999999999999999987553
No 79
>PRK09027 cytidine deaminase; Provisional
Probab=24.33 E-value=1.5e+02 Score=22.79 Aligned_cols=51 Identities=8% Similarity=-0.022 Sum_probs=33.5
Q ss_pred eEEEEEeCCCCCeeeecccccC--CCCChHHHHHHHHHHHHHHHHHhCCCceEE
Q 037050 9 GLAVVIRDWERNCVAAAINTTR--FFGNVAMTQAATIEIGMQVALSVGGYSVLF 60 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~--~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~ 60 (144)
-+|.+++..+|.+..+...-.. ...-..-||-.|+..++..- +.++..|.+
T Consensus 72 ~VGAa~~~~sG~iy~GvNvE~~~~s~~~tiCAEr~Ai~~a~~~G-e~~i~~I~v 124 (295)
T PRK09027 72 NVGAIARGVSGNFYFGANMEFAGAALQQTVHAEQSAISHAWLRG-EKAIADITV 124 (295)
T ss_pred cEEEEEEeCCCCEEEEEeeccCCCCCCCCcCHHHHHHHHHHHCC-CCceEEEEE
Confidence 4688899999988777664332 23456789999998877421 234444444
No 80
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=24.32 E-value=2.1e+02 Score=23.18 Aligned_cols=41 Identities=20% Similarity=0.214 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHHHhcCccEEEEEecCC---chHHHHHHHhhhcc
Q 037050 80 KIIWVIFEILEKKKNFQNFKAQHTPRS---CNGIAHFLAKLVLQ 120 (144)
Q Consensus 80 ~~~~~~~~i~~l~~~~~~~~~~~v~r~---~N~~Ad~LAk~a~~ 120 (144)
+-..+++-.+.+.+++++..+.+|||+ .+.+++.+.+.+++
T Consensus 243 Eeei~l~~~~~l~~~~~~~llIlVPRHpERf~~v~~l~~~~gl~ 286 (419)
T COG1519 243 EEEIILDAHQALKKQFPNLLLILVPRHPERFKAVENLLKRKGLS 286 (419)
T ss_pred hHHHHHHHHHHHHhhCCCceEEEecCChhhHHHHHHHHHHcCCe
Confidence 333456666679999999999999998 46777777777666
No 81
>KOG0324 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.31 E-value=2e+02 Score=21.05 Aligned_cols=31 Identities=16% Similarity=0.242 Sum_probs=24.0
Q ss_pred HHhcCccEEEEEecCCchHHHHHHHhhhccc
Q 037050 91 KKKNFQNFKAQHTPRSCNGIAHFLAKLVLQK 121 (144)
Q Consensus 91 l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~~ 121 (144)
|...|..-+..-+.+++|..-+.||.+-...
T Consensus 97 L~~ey~G~~YhL~~kNCNHFsn~la~~Ltgk 127 (214)
T KOG0324|consen 97 LSEEYRGNSYHLLTKNCNHFSNELALQLTGK 127 (214)
T ss_pred HHhhcCCceehhhhhccchhHHHHHHHHcCC
Confidence 5567777788888999998888888765554
No 82
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=24.22 E-value=1.2e+02 Score=22.50 Aligned_cols=57 Identities=16% Similarity=-0.018 Sum_probs=41.8
Q ss_pred CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
+-+.-+|+|. |.++.+ +....++ ...-+.+=+.++..-++++.++|++.|.++.=|.
T Consensus 13 ~~P~HvaiIm-DGNrRw--Ak~~g~~-~~~GH~~G~~~l~~iv~~c~~~gI~~vTvYaFS~ 69 (243)
T PRK14829 13 KLPRHIAVVM-DGNGRW--ATQRGLK-RTEGHKAGEPVLFDVVAGAIEAGVPYLSLYTFST 69 (243)
T ss_pred CCCCeEEEec-CCCHHH--HHHCCCC-hhHHHHHHHHHHHHHHHHHHHcCCCEEEEeeecc
Confidence 3345566644 766655 4444344 5668888999999999999999999999987653
No 83
>TIGR03757 conj_TIGR03757 integrating conjugative element protein, PFL_4709 family. Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer.
Probab=23.99 E-value=1.2e+02 Score=19.81 Aligned_cols=22 Identities=18% Similarity=0.081 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHhCCCc
Q 037050 36 AMTQAATIEIGMQVALSVGGYS 57 (144)
Q Consensus 36 ~~aE~~Al~~aL~~a~~~g~~~ 57 (144)
.+-++...+.|+-.||.+|+++
T Consensus 63 ~q~~l~~Ayqgv~~Aw~lGi~k 84 (113)
T TIGR03757 63 LQRRLAQAYQGVADAWQLGVTK 84 (113)
T ss_pred HHHHHHHHHHHHHHHHHcCCcc
Confidence 4445566778888899999866
No 84
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=23.87 E-value=2.7e+02 Score=21.07 Aligned_cols=54 Identities=13% Similarity=-0.015 Sum_probs=41.2
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
+--+++|+ | |.--.+....++ ...-++|-+.++..=|+++.++|++.|.++.=|
T Consensus 37 P~HVaFIM-D--GNRR~AKk~~L~-~~~GH~aGf~~l~~ile~C~~lGI~~vT~fAFS 90 (271)
T KOG1602|consen 37 PRHVAFIM-D--GNRRYAKKRGLE-TSEGHEAGFEALKEILELCKELGIKEVTVFAFS 90 (271)
T ss_pred cceeEEEe-c--CchHHHHhcCCC-cccchHHHHHHHHHHHHHHHHcCCcEEEEEEEe
Confidence 44566655 5 443446666676 488999999999999999999999999887543
No 85
>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=23.54 E-value=3e+02 Score=20.10 Aligned_cols=49 Identities=18% Similarity=0.009 Sum_probs=36.8
Q ss_pred EEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 13 VIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 13 vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
||-|.++.+ +....++ ...-..+-+..+..-++++.++|++.+.++.=|
T Consensus 6 iImDGNrRw--A~~~gl~-~~~GH~~G~~~~~~i~~~~~~~gI~~lTvyaFS 54 (221)
T cd00475 6 FIMDGNRRW--AKQRGMD-RIEGHKAGAEKLRDILRWCLELGVKEVTLYAFS 54 (221)
T ss_pred EecCCCHHH--HHHCCCC-hhHhHHHHHHHHHHHHHHHHHcCCCEEEEEeec
Confidence 455766655 3333343 466888899999999999999999999998544
No 86
>PLN02402 cytidine deaminase
Probab=23.29 E-value=1.6e+02 Score=22.72 Aligned_cols=41 Identities=5% Similarity=-0.288 Sum_probs=28.4
Q ss_pred eEEEEEeCCCCCeeeecccccCCCCC--hHHHHHHHHHHHHHH
Q 037050 9 GLAVVIRDWERNCVAAAINTTRFFGN--VAMTQAATIEIGMQV 49 (144)
Q Consensus 9 g~G~vird~~g~~~~~~~~~~~~~~~--~~~aE~~Al~~aL~~ 49 (144)
-+|.+++..+|.+..+...-..+... ..-||-.|+..++..
T Consensus 47 ~VGAa~l~~~G~i~~GvNVEnasy~l~~tiCAEr~Ai~~av~~ 89 (303)
T PLN02402 47 HVGAVGLGSSGRIFLGVNLEFPGLPLHHSVHAEQFLITNLTLN 89 (303)
T ss_pred eeeEEEEeCCCCEEEEEeeecCCCCCCCcccHHHHHHHHHHHc
Confidence 46889999999877766643332222 568999999887743
No 87
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=23.11 E-value=2.6e+02 Score=19.27 Aligned_cols=59 Identities=15% Similarity=0.084 Sum_probs=31.5
Q ss_pred CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHH-HhCCCceEEe
Q 037050 2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVAL-SVGGYSVLFE 61 (144)
Q Consensus 2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~-~~g~~~v~~e 61 (144)
|+.....|||+|=.. .+....-..+.+.....++..-+..+..+|+... +.....+.+|
T Consensus 5 DPGl~~tG~gvi~~~-~~~~~~v~~G~I~t~~~~~~~RL~~I~~~l~~~i~~y~P~~~aiE 64 (156)
T TIGR00228 5 DPGSRVTGYGVIRQV-GRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPNYFAIE 64 (156)
T ss_pred CcccccccEEEEEec-CCeEEEEEeeEEECCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEe
Confidence 566777888876543 2333333333333223456666677777776554 3344444444
No 88
>PF01614 IclR: Bacterial transcriptional regulator This Pfam family contains some of the members of the iclR family; InterPro: IPR014757 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; PDB: 3MQ0_A 2IA2_D 3OBF_B 2G7U_C 3R4K_A 1TF1_D 1MKM_A 1YSP_A 3BJN_A 1TD5_A ....
Probab=23.02 E-value=2.1e+02 Score=18.13 Aligned_cols=27 Identities=33% Similarity=0.203 Sum_probs=22.0
Q ss_pred CCCceeEEEEEeCCCCCeeeecccccC
Q 037050 4 KKQVAGLAVVIRDWERNCVAAAINTTR 30 (144)
Q Consensus 4 ~~~~~g~G~vird~~g~~~~~~~~~~~ 30 (144)
.++..++++-|+|.+|..+.+.+...+
T Consensus 76 ~~gv~~iA~Pi~~~~g~~~~alsv~~~ 102 (129)
T PF01614_consen 76 EPGVAAIAVPIFDPNGQVVAALSVSGP 102 (129)
T ss_dssp STTEEEEEEEEEETTSCEEEEEEEEEE
T ss_pred ccccceEEEEEECCCCCEEEEEEEeeE
Confidence 457889999999999999888876544
No 89
>PF04954 SIP: Siderophore-interacting protein; InterPro: IPR007037 This entry includes the vibriobactin utilization protein viuB, which is involved in the removal of iron from iron-vibriobactin complexes, as well as several hypothetical proteins.; PDB: 2GPJ_A.
Probab=22.85 E-value=1.2e+02 Score=19.52 Aligned_cols=34 Identities=21% Similarity=0.347 Sum_probs=19.5
Q ss_pred CccEEEEEecCCch-----HHHHHHHhhhcccCCeeeec
Q 037050 95 FQNFKAQHTPRSCN-----GIAHFLAKLVLQKKEIVIWL 128 (144)
Q Consensus 95 ~~~~~~~~v~r~~N-----~~Ad~LAk~a~~~~~~~~~~ 128 (144)
-..+++.|+.|... .+++.|+..........+|.
T Consensus 47 ~~~~~v~wv~r~~~~~~~~~l~~al~~~~~~~~~~~vW~ 85 (119)
T PF04954_consen 47 PAGVEVTWVPRDGPAAQGSALADALRDLPLPAGDGYVWV 85 (119)
T ss_dssp -TEEEEEEEE-SS--TT-HHHHHHHTTS---SS-EEEEE
T ss_pred CCCCEEEEEeCCCCCchHHHHHHHHHHhhccCCCeEEEE
Confidence 46789999999887 55666665555444566776
No 90
>PRK10057 rpsV 30S ribosomal subunit S22; Reviewed
Probab=21.54 E-value=18 Score=18.88 Aligned_cols=19 Identities=26% Similarity=0.228 Sum_probs=14.9
Q ss_pred CCceEEeccHHHHHHHHhc
Q 037050 55 GYSVLFESDSHEVVELVNN 73 (144)
Q Consensus 55 ~~~v~~esDs~~vv~~l~~ 73 (144)
-++|++|+|...+|+.-.+
T Consensus 20 qrKvV~Egd~~t~vn~~tG 38 (44)
T PRK10057 20 QRKVVTEGDKSSVVNNPTG 38 (44)
T ss_pred ceeEEeeCCcceeEecccc
Confidence 3789999999998874443
No 91
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.31 E-value=3.5e+02 Score=20.09 Aligned_cols=55 Identities=20% Similarity=0.094 Sum_probs=40.2
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~ 65 (144)
+.-+|+| -|.++.+ +....++ ...-+.+=+..+..-++++.++|++.|.++.=|.
T Consensus 9 P~HVaiI-mDGNrRw--Ak~~gl~-~~~GH~~G~~~l~~i~~~c~~lgI~~vTvYaFS~ 63 (241)
T PRK14842 9 PAHIAVI-MDGNGRW--AESQGKK-RSEGHREGANAIDRLMDASLEYGLKNISLYAFST 63 (241)
T ss_pred CCeEEEE-cCCCHHH--HHHCCCC-hhHhHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 4455654 4766655 3333344 4567888999999999999999999999987553
No 92
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.26 E-value=1.6e+02 Score=22.02 Aligned_cols=54 Identities=11% Similarity=-0.149 Sum_probs=40.1
Q ss_pred ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050 7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64 (144)
Q Consensus 7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs 64 (144)
+--+|+| -|.++.+ +....++ ...-+.+-+.++..-++++.++|++.|.++.=|
T Consensus 21 P~HVaiI-mDGNrRw--A~~~gl~-~~~GH~~G~~~l~~i~~~c~~~GI~~vT~yaFS 74 (249)
T PRK14831 21 PKHVAVI-MDGNGRW--AKRRGLP-RIMGHRRGVDALKDLLRCCKDWGIGALTAYAFS 74 (249)
T ss_pred CCeEEEe-cCCcHHH--HHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEeecc
Confidence 3455654 4766655 3333344 467888899999999999999999999998766
No 93
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=20.68 E-value=2.6e+02 Score=18.24 Aligned_cols=51 Identities=22% Similarity=0.233 Sum_probs=32.5
Q ss_pred EEEEeCCCCCeeeecccccC---CCCChHHHHHHHHHHHHHHHHHhCCCceEEec
Q 037050 11 AVVIRDWERNCVAAAINTTR---FFGNVAMTQAATIEIGMQVALSVGGYSVLFES 62 (144)
Q Consensus 11 G~vird~~g~~~~~~~~~~~---~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es 62 (144)
.=+|-|..|..+.+.+..-. ...+...|...+...|- .|.+.|+..|+|.-
T Consensus 38 aQiIdd~~~~tlasaST~ek~~~~~~n~~aA~~vG~~la~-ra~~~gi~~vvfDr 91 (114)
T TIGR00060 38 AQVIDDSKSEVLASASTLEKKLKYTGNKDAAKKVGKLVAE-RLKEKGIKDVVFDR 91 (114)
T ss_pred EEEEECCCCEEEEEEecchhhhcCCCCHHHHHHHHHHHHH-HHHHCCCCEEEEeC
Confidence 45677777777777774211 23445556666665554 46678999998764
No 94
>PF00925 GTP_cyclohydro2: GTP cyclohydrolase II; InterPro: IPR000926 GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin. The enzyme converts GTP and water to formate, 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)- pyrimidine and pyrophosphate, and requires magnesium as a cofactor. It is sometimes found as a bifunctional enzyme with 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP_synthase) IPR000422 from INTERPRO. ; GO: 0003935 GTP cyclohydrolase II activity, 0009231 riboflavin biosynthetic process; PDB: 2BZ0_B 2BZ1_A.
Probab=20.59 E-value=1.6e+02 Score=20.30 Aligned_cols=36 Identities=11% Similarity=0.095 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC
Q 037050 39 QAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR 74 (144)
Q Consensus 39 E~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~ 74 (144)
.+.-.-.|.+...++|++++.+-|.+..=+..+.+-
T Consensus 124 d~R~ygigaqIL~dLGV~~~rLLtnnp~k~~~L~g~ 159 (169)
T PF00925_consen 124 DLRDYGIGAQILRDLGVKKMRLLTNNPRKYVALEGF 159 (169)
T ss_dssp ----THHHHHHHHHTT--SEEEE-S-HHHHHHHHHT
T ss_pred ccccHHHHHHHHHHcCCCEEEECCCChhHHHHHhcC
Confidence 445666889999999999999999988777777653
Done!