Query psy3458
Match_columns 151
No_of_seqs 150 out of 1089
Neff 9.7
Searched_HMMs 46136
Date Fri Aug 16 17:13:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3458.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3458hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 100.0 3.1E-42 6.7E-47 228.3 14.7 141 5-150 2-144 (154)
2 PRK06548 ribonuclease H; Provi 100.0 4.1E-41 8.8E-46 226.5 16.7 138 5-150 4-141 (161)
3 PRK08719 ribonuclease H; Revie 100.0 6.3E-40 1.4E-44 219.0 16.5 142 4-150 2-146 (147)
4 PRK00203 rnhA ribonuclease H; 100.0 2.2E-38 4.7E-43 213.1 16.0 138 6-150 3-141 (150)
5 KOG3752|consensus 100.0 8.9E-36 1.9E-40 218.8 14.4 147 2-149 208-363 (371)
6 PF00075 RNase_H: RNase H; In 100.0 6.4E-29 1.4E-33 163.6 11.8 130 5-150 2-132 (132)
7 PRK13907 rnhA ribonuclease H; 100.0 3.8E-28 8.2E-33 159.4 12.3 123 6-149 1-125 (128)
8 PRK07708 hypothetical protein; 99.9 7E-25 1.5E-29 154.9 13.0 129 3-150 70-207 (219)
9 cd06222 RnaseH RNase H (RNase 99.9 9.5E-24 2.1E-28 136.7 14.2 128 8-149 1-130 (130)
10 PRK07238 bifunctional RNase H/ 99.9 4.1E-23 8.9E-28 157.3 13.4 126 6-150 2-131 (372)
11 PF13456 RVT_3: Reverse transc 99.7 2.6E-17 5.6E-22 100.6 9.9 86 49-150 1-86 (87)
12 KOG1812|consensus 93.7 0.19 4E-06 39.1 5.5 42 46-87 46-87 (384)
13 PF05380 Peptidase_A17: Pao re 92.6 0.57 1.2E-05 31.6 6.0 55 5-66 80-143 (159)
14 PF00336 DNA_pol_viral_C: DNA 82.2 1.4 3.1E-05 31.1 2.6 59 6-82 94-153 (245)
15 PF05830 NodZ: Nodulation prot 73.8 26 0.00055 26.6 7.1 62 25-87 168-232 (321)
16 COG3341 Predicted double-stran 73.6 9.5 0.0002 27.3 4.6 76 8-87 67-151 (225)
17 PRK14828 undecaprenyl pyrophos 69.2 19 0.00042 26.5 5.6 52 26-78 29-81 (256)
18 PRK14827 undecaprenyl pyrophos 54.7 35 0.00077 25.7 4.9 52 27-79 71-122 (296)
19 COG1902 NemA NADH:flavin oxido 45.8 67 0.0015 25.0 5.3 94 51-148 141-250 (363)
20 COG3981 Predicted acetyltransf 43.8 37 0.0008 23.4 3.3 25 55-79 117-141 (174)
21 TIGR01354 cyt_deam_tetra cytid 41.3 87 0.0019 20.2 4.7 52 25-78 23-76 (127)
22 PF10298 WhiA_N: WhiA N-termin 40.6 38 0.00082 20.2 2.7 39 49-87 3-42 (86)
23 PRK14841 undecaprenyl pyrophos 40.5 74 0.0016 23.1 4.6 52 27-79 7-58 (233)
24 PRK14833 undecaprenyl pyrophos 40.4 76 0.0016 23.0 4.6 52 27-79 8-59 (233)
25 KOG1602|consensus 40.4 86 0.0019 23.2 4.9 51 27-78 40-90 (271)
26 COG1212 KdsB CMP-2-keto-3-deox 39.6 73 0.0016 23.2 4.3 31 57-87 31-61 (247)
27 TIGR00055 uppS undecaprenyl di 39.0 84 0.0018 22.7 4.6 51 28-79 4-54 (226)
28 PRK14834 undecaprenyl pyrophos 37.7 94 0.002 22.8 4.8 53 26-79 17-69 (249)
29 PRK14837 undecaprenyl pyrophos 37.4 89 0.0019 22.7 4.6 52 27-79 10-61 (230)
30 PRK14832 undecaprenyl pyrophos 36.3 95 0.0021 22.9 4.6 52 27-79 22-73 (253)
31 PRK14842 undecaprenyl pyrophos 36.3 94 0.002 22.7 4.6 52 27-79 12-63 (241)
32 PRK14835 undecaprenyl pyrophos 35.7 1E+02 0.0023 23.0 4.8 53 26-79 44-96 (275)
33 cd00475 CIS_IPPS Cis (Z)-Isopr 35.5 97 0.0021 22.3 4.5 51 27-78 4-54 (221)
34 PRK14839 undecaprenyl pyrophos 34.8 1.1E+02 0.0023 22.4 4.7 53 26-79 12-64 (239)
35 COG1519 KdtA 3-deoxy-D-manno-o 33.9 2.2E+02 0.0047 22.8 6.4 41 108-149 244-285 (419)
36 PRK14838 undecaprenyl pyrophos 32.9 1.2E+02 0.0025 22.3 4.6 52 27-79 14-65 (242)
37 PTZ00349 dehydrodolichyl dipho 32.4 1.2E+02 0.0026 23.3 4.7 51 27-78 23-73 (322)
38 PRK14829 undecaprenyl pyrophos 30.4 1.3E+02 0.0029 21.9 4.6 53 26-79 17-69 (243)
39 cd01285 nucleoside_deaminase N 30.3 1.4E+02 0.003 18.5 4.4 40 48-87 44-83 (109)
40 cd01284 Riboflavin_deaminase-r 30.3 1.2E+02 0.0026 19.3 3.9 28 48-79 42-69 (115)
41 COG0295 Cdd Cytidine deaminase 29.9 1.7E+02 0.0036 19.4 4.6 52 26-78 29-81 (134)
42 PF00289 CPSase_L_chain: Carba 29.5 60 0.0013 20.5 2.4 29 57-85 14-42 (110)
43 PRK14830 undecaprenyl pyrophos 28.5 1.5E+02 0.0033 21.8 4.7 53 26-79 25-77 (251)
44 PF07131 DUF1382: Protein of u 27.8 36 0.00078 19.0 1.0 15 137-151 12-26 (61)
45 KOG1817|consensus 26.9 2.8E+02 0.006 22.5 5.9 55 5-66 449-503 (533)
46 PRK14831 undecaprenyl pyrophos 26.5 1.6E+02 0.0035 21.6 4.5 52 26-78 23-74 (249)
47 cd04733 OYE_like_2_FMN Old yel 26.3 1.3E+02 0.0027 23.0 4.1 69 56-128 150-223 (338)
48 PRK10708 hypothetical protein; 26.2 68 0.0015 17.7 1.9 19 1-19 1-19 (62)
49 COG2100 Predicted Fe-S oxidore 25.4 3.3E+02 0.0072 21.3 8.5 76 51-149 140-215 (414)
50 PRK14840 undecaprenyl pyrophos 25.3 2.2E+02 0.0048 21.0 5.0 34 46-79 44-77 (250)
51 PF10781 DSRB: Dextransucrase 24.7 74 0.0016 17.6 1.9 19 1-19 1-19 (62)
52 PF04566 RNA_pol_Rpb2_4: RNA p 24.3 64 0.0014 18.1 1.7 12 3-14 41-52 (63)
53 COG3051 CitF Citrate lyase, al 23.5 1.8E+02 0.0039 23.0 4.3 42 108-149 47-93 (513)
54 PF07228 SpoIIE: Stage II spor 23.3 30 0.00065 23.4 0.2 18 1-18 121-138 (193)
55 PF11821 DUF3341: Protein of u 22.9 1.1E+02 0.0024 21.1 2.9 24 55-78 13-36 (173)
56 PRK05728 DNA polymerase III su 22.5 1.9E+02 0.0042 19.0 4.0 37 61-98 22-58 (142)
57 KOG1393|consensus 22.4 1.4E+02 0.003 23.7 3.6 28 6-36 154-181 (462)
58 PF12404 DUF3663: Peptidase ; 22.0 1.6E+02 0.0034 17.5 3.0 27 53-79 36-62 (77)
59 COG0117 RibD Pyrimidine deamin 21.9 82 0.0018 21.1 2.0 45 13-64 22-66 (146)
60 PRK14836 undecaprenyl pyrophos 20.9 1.7E+02 0.0037 21.6 3.7 49 27-76 18-66 (253)
61 PF11208 DUF2992: Protein of u 20.0 97 0.0021 20.4 2.1 10 7-16 1-10 (132)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.1e-42 Score=228.33 Aligned_cols=141 Identities=37% Similarity=0.651 Sum_probs=127.8
Q ss_pred CcEEEEEccCCCCCCCCCCceEEEEEEcCCC-ccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHH
Q psy3458 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENN-PLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIK 83 (151)
Q Consensus 5 ~~~~iytDGs~~~~~~~~~~ag~gv~~~~~~-~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~ 83 (151)
..+.|||||||.++|++ +|||+++..+. ....+.... .+|||+|||+|+++||+.+++.+++.|.|+|||++|++
T Consensus 2 ~~v~if~DGa~~gNpG~---gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~ 77 (154)
T COG0328 2 KKVEIFTDGACLGNPGP---GGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVE 77 (154)
T ss_pred CceEEEecCccCCCCCC---ceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHH
Confidence 46899999999999987 48888776443 334555554 89999999999999999999988999999999999999
Q ss_pred HHHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCC-ceEEEEecCCCCCcchHHHHHHHHhhhc
Q psy3458 84 CVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQME-SVKWEFVPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 84 ~l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~-~v~~~~v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
+|+.|+.+|++++|+++.++|++|.+||+++.+++. ++ .|.++|||+|+|+++|++||+||+.|++
T Consensus 78 ~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~-~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~ 144 (154)
T COG0328 78 GITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLK-RHELVFWEWVKGHAGHPENERADQLAREAAR 144 (154)
T ss_pred HHHHHHhhccccCccccccCccccHHHHHHHHHHHh-hCCeEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999 66 7999999999999999999999999864
No 2
>PRK06548 ribonuclease H; Provisional
Probab=100.00 E-value=4.1e-41 Score=226.52 Aligned_cols=138 Identities=33% Similarity=0.497 Sum_probs=120.4
Q ss_pred CcEEEEEccCCCCCCCCCCceEEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHH
Q psy3458 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKC 84 (151)
Q Consensus 5 ~~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~ 84 (151)
..+.|||||+|.+++++ +|+|+++..... .++.. +.+|||+|||+|+++||+.+.. ....|.|+|||++++++
T Consensus 4 ~~~~IytDGa~~gnpg~---~G~g~~~~~~~~--~~g~~-~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~ 76 (161)
T PRK06548 4 NEIIAATDGSSLANPGP---SGWAWYVDENTW--DSGGW-DIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINS 76 (161)
T ss_pred CEEEEEEeeccCCCCCc---eEEEEEEeCCcE--EccCC-CCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHH
Confidence 34999999999999876 589988764332 23322 3789999999999999987653 33579999999999999
Q ss_pred HHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEecCCCCCcchHHHHHHHHhhhc
Q psy3458 85 VQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 85 l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
++.|+++|++++|+++.|+|+.|.+||++|.+++. ...|+|.|||+|+|+++|+.||+||++|+.
T Consensus 77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~-~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~ 141 (161)
T PRK06548 77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME-NRNIRMSWVNAHTGHPLNEAADSLARQAAN 141 (161)
T ss_pred HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh-cCceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998 678999999999999999999999999873
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=100.00 E-value=6.3e-40 Score=218.98 Aligned_cols=142 Identities=30% Similarity=0.466 Sum_probs=122.4
Q ss_pred CCcEEEEEccCCCCCCCCCCceEEEEEEcC--CCcc-ccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHH
Q psy3458 4 DNHVVVFTDGACPRNGKVGASAGYGVYFGE--NNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQF 80 (151)
Q Consensus 4 ~~~~~iytDGs~~~~~~~~~~ag~gv~~~~--~~~~-~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~ 80 (151)
.+.++|||||||..+++..+.+|+|+++.. +... ..+..+.+..||++|||+|++.||+.+.+. ..|+|||++
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y 77 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY 77 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence 357899999999988765445788887533 3322 234445556899999999999999999764 379999999
Q ss_pred HHHHHHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEecCCCCCcchHHHHHHHHhhhc
Q psy3458 81 MIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 81 vi~~l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
++++++.|+++|++++|+++.+.+++|.++|++|..+++ ..+|+|.|||+|+|+++|+.||+||+.|++
T Consensus 78 vi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 78 CVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 999999999999999999999999999999999999998 778999999999999999999999999976
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=100.00 E-value=2.2e-38 Score=213.13 Aligned_cols=138 Identities=35% Similarity=0.630 Sum_probs=120.6
Q ss_pred cEEEEEccCCCCCCCCCCceEEEEEEc-CCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHH
Q psy3458 6 HVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKC 84 (151)
Q Consensus 6 ~~~iytDGs~~~~~~~~~~ag~gv~~~-~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~ 84 (151)
.++|||||||.++++. +|+|+++. ++.....++.. +..||++|||+|++.||+.+.+. ..|.|+|||++++++
T Consensus 3 ~v~iytDGs~~~n~~~---~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~--~~v~I~tDS~yvi~~ 76 (150)
T PRK00203 3 QVEIYTDGACLGNPGP---GGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP--CEVTLYTDSQYVRQG 76 (150)
T ss_pred eEEEEEEecccCCCCc---eEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC--CeEEEEECHHHHHHH
Confidence 4899999999988776 57877764 33333344433 37899999999999999988753 689999999999999
Q ss_pred HHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEecCCCCCcchHHHHHHHHhhhc
Q psy3458 85 VQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 85 l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
|+.|+++|++++|+++.|++++|.++|+++.+++. ...|.|.|||+|+|+++|+.||+||+.|+.
T Consensus 77 i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~ 141 (150)
T PRK00203 77 ITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAE 141 (150)
T ss_pred HHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998 788999999999999999999999999863
No 5
>KOG3752|consensus
Probab=100.00 E-value=8.9e-36 Score=218.80 Aligned_cols=147 Identities=41% Similarity=0.730 Sum_probs=138.9
Q ss_pred CCCCcEEEEEccCCCCCCCCCCceEEEEEEcCCCccccccccC-CcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHH
Q psy3458 2 DPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVT-GRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQF 80 (151)
Q Consensus 2 ~~~~~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~~~~~~~~~-~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~ 80 (151)
++.+.++|||||||..++..++.|||||||++++..+.++++. +..|||+|||.|+.+||+.+++....+|+|.|||.+
T Consensus 208 e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~ 287 (371)
T KOG3752|consen 208 EEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEY 287 (371)
T ss_pred ccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHH
Confidence 3456689999999999998888999999999999999999998 699999999999999999999988889999999999
Q ss_pred HHHHHHhhHHHHHHcCccccCCCc-----cCCHHHHHHHHHHhcCC---CceEEEEecCCCCCcchHHHHHHHHhhh
Q psy3458 81 MIKCVQEWMPKWQSNGWRKADGKP-----VQNKEELQELLHQIGQM---ESVKWEFVPGHGNSHGNMKADEMARDAA 149 (151)
Q Consensus 81 vi~~l~~~~~~w~~~~~~~~~~~~-----~~~~~l~~~i~~~~~~~---~~v~~~~v~~h~~~~~N~~AD~lA~~a~ 149 (151)
+++.|+.|+++|+.++|+++.+.+ +.+.+.+.++.++.+ + .+|++.||++|+|+++|+.||.||+++.
T Consensus 288 ~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q-~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 288 FINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQ-EISNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred HHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHh-hhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 999999999999999999999999 999999999999998 5 6799999999999999999999999984
No 6
>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=99.96 E-value=6.4e-29 Score=163.63 Aligned_cols=130 Identities=32% Similarity=0.601 Sum_probs=97.8
Q ss_pred CcEEEEEccCCCCCCCCCCceEEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHH
Q psy3458 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKC 84 (151)
Q Consensus 5 ~~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~ 84 (151)
+.+.||||||+.++++.+ |+|+++..++ ..+..++ ..|++++||+|+++||+.+ .. +.++|+|||+++++.
T Consensus 2 ~~~~iytDgS~~~~~~~~---~~g~v~~~~~--~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~~--~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKG---GAGYVVWGGR--NFSFRLG-GQSNNRAELQAIIEALKAL-EH--RKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEE---EEEEEEETTE--EEEEEEE-SECHHHHHHHHHHHHHHTH-ST--SEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCce---EEEEEEECCe--EEEeccc-ccchhhhheehHHHHHHHh-hc--ccccccccHHHHHHH
Confidence 568999999999876653 4555444442 4555555 8899999999999999944 33 899999999999999
Q ss_pred HHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEecCCCCC-cchHHHHHHHHhhhc
Q psy3458 85 VQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVPGHGNS-HGNMKADEMARDAAG 150 (151)
Q Consensus 85 l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~~h~~~-~~N~~AD~lA~~a~~ 150 (151)
++.|+++ ++|...... .+++.++.+++..+.+|.|+|||+|+|+ .+|+.||+|||.|++
T Consensus 73 l~~~~~~---~~~~~~~~~----~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 73 LNKWLHG---NGWKKTSNG----RPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp HHTHHHH---TTSBSCTSS----SBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred HHHhccc---ccccccccc----ccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence 9998776 555442211 1244455555544778999999999999 599999999999974
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.96 E-value=3.8e-28 Score=159.45 Aligned_cols=123 Identities=28% Similarity=0.387 Sum_probs=101.3
Q ss_pred cEEEEEccCCCCCCCCCCceEEEEEEcCCCcc-ccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHH
Q psy3458 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKC 84 (151)
Q Consensus 6 ~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~~-~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~ 84 (151)
+++||||||++.+++. +|+|+++.+.... ..++. .+..||+.||++|++.||+.+.+.+.++|.|+|||++++++
T Consensus 1 ~~~iy~DGa~~~~~g~---~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~ 76 (128)
T PRK13907 1 MIEVYIDGASKGNPGP---SGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERA 76 (128)
T ss_pred CEEEEEeeCCCCCCCc---cEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHH
Confidence 4789999999998876 5888888654332 22222 34789999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCc-eEEEEecCCCCCcchHHHHHHHHhhh
Q psy3458 85 VQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMES-VKWEFVPGHGNSHGNMKADEMARDAA 149 (151)
Q Consensus 85 l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~-v~~~~v~~h~~~~~N~~AD~lA~~a~ 149 (151)
+++ .|. ....+.++++++..+++ .++ +.|.||||+ +|+.||.||+.|+
T Consensus 77 ~~~--------~~~----~~~~~~~l~~~~~~l~~-~f~~~~~~~v~r~----~N~~Ad~LA~~a~ 125 (128)
T PRK13907 77 VEK--------EYA----KNKMFAPLLEEALQYIK-SFDLFFIKWIPSS----QNKVADELARKAI 125 (128)
T ss_pred HhH--------HHh----cChhHHHHHHHHHHHHh-cCCceEEEEcCch----hchhHHHHHHHHH
Confidence 998 232 12345889999999998 665 777999999 9999999999986
No 8
>PRK07708 hypothetical protein; Validated
Probab=99.93 E-value=7e-25 Score=154.88 Aligned_cols=129 Identities=21% Similarity=0.332 Sum_probs=99.5
Q ss_pred CCCcEEEEEccCCCCCCCCCCceEEEEEE--cCCCcc---ccccccCCcchHHHHHHHHHHHHHHHcHhcCCce--EEEE
Q psy3458 3 PDNHVVVFTDGACPRNGKVGASAGYGVYF--GENNPL---NVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDR--VCIK 75 (151)
Q Consensus 3 ~~~~~~iytDGs~~~~~~~~~~ag~gv~~--~~~~~~---~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~--v~i~ 75 (151)
+.+.+++|||||+..+++. +|+|+++ .++... ..+..+.+..|||.||+.|++.||+.+.++|.++ |+|+
T Consensus 70 ep~~~~vY~DGs~~~n~g~---aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~ 146 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKL---AGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFR 146 (219)
T ss_pred CCCcEEEEEeeccCCCCCC---cEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEE
Confidence 4567999999999877765 4666654 333221 2223455468999999999999999999998865 8999
Q ss_pred cCcHHHHHHHHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCc--eEEEEecCCCCCcchHHHHHHHHhhhc
Q psy3458 76 SDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMES--VKWEFVPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 76 tDs~~vi~~l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~--v~~~~v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
+||++|++++++ .|+..... ...+..++..+++ ++. +.|.||||. .|+.||+||+.|++
T Consensus 147 ~DSqlVi~qi~g--------~wk~~~~~---l~~y~~~i~~l~~-~~~l~~~~~~VpR~----~N~~AD~LAk~Al~ 207 (219)
T PRK07708 147 GDSQVVLNQLAG--------EWPCYDEH---LNHWLDRIEQKLK-QLKLTPVYEPISRK----QNKEADQLATQALE 207 (219)
T ss_pred eccHHHHHHhCC--------CceeCChh---HHHHHHHHHHHHh-hCCceEEEEECCch----hhhHHHHHHHHHHh
Confidence 999999999998 56554322 2456777777777 554 778999999 99999999999986
No 9
>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=99.92 E-value=9.5e-24 Score=136.70 Aligned_cols=128 Identities=39% Similarity=0.647 Sum_probs=101.5
Q ss_pred EEEEccCCCCCCCCCCceEEEEEEcCCCc--cccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHHH
Q psy3458 8 VVFTDGACPRNGKVGASAGYGVYFGENNP--LNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCV 85 (151)
Q Consensus 8 ~iytDGs~~~~~~~~~~ag~gv~~~~~~~--~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~l 85 (151)
++|||||+..+.+. +|+|+++..... ...........+++.+|+.|++.||+.+...+.+++.|+|||+.+++.+
T Consensus 1 ~~~~Dgs~~~~~~~---~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~ 77 (130)
T cd06222 1 VIYTDGSCRGNPGP---AGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINAL 77 (130)
T ss_pred CEEecccCCCCCCc---eEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHh
Confidence 48999999876543 688888754332 2222222147899999999999999999988889999999999999999
Q ss_pred HhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEecCCCCCcchHHHHHHHHhhh
Q psy3458 86 QEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVPGHGNSHGNMKADEMARDAA 149 (151)
Q Consensus 86 ~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~~h~~~~~N~~AD~lA~~a~ 149 (151)
+++ .. ..+.....+++.+.+++.+...++|.|||+|+++.+|..||.||+.++
T Consensus 78 ~~~--------~~---~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 78 TGW--------YE---GKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred hcc--------cc---CCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 982 11 233456788888888885477899999999999999999999999874
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.90 E-value=4.1e-23 Score=157.26 Aligned_cols=126 Identities=27% Similarity=0.376 Sum_probs=100.2
Q ss_pred cEEEEEccCCCCCCCCCCceEEEEEEcCC--C-c-cccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHH
Q psy3458 6 HVVVFTDGACPRNGKVGASAGYGVYFGEN--N-P-LNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81 (151)
Q Consensus 6 ~~~iytDGs~~~~~~~~~~ag~gv~~~~~--~-~-~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~v 81 (151)
.+.||||||+.++++. +|+|+++.+. . . ...+..+. ..||+.||++|++.||+.+.+.++++|+|++||++|
T Consensus 2 ~~~i~~DGa~~~n~g~---aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lv 77 (372)
T PRK07238 2 KVVVEADGGSRGNPGP---AGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLV 77 (372)
T ss_pred eEEEEecCCCCCCCCc---eEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHH
Confidence 4789999999999876 5888877543 2 2 13344433 789999999999999999999999999999999999
Q ss_pred HHHHHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEecCCCCCcchHHHHHHHHhhhc
Q psy3458 82 IKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 82 i~~l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
++++++ +|+.+.. ....++.++..++++...++|.||||+ +|+.||.||+.|+.
T Consensus 78 i~~i~~--------~~~~~~~---~l~~~~~~i~~l~~~f~~~~i~~v~r~----~N~~AD~LA~~a~~ 131 (372)
T PRK07238 78 VEQMSG--------RWKVKHP---DMKPLAAQARELASQFGRVTYTWIPRA----RNAHADRLANEAMD 131 (372)
T ss_pred HHHhCC--------CCccCCh---HHHHHHHHHHHHHhcCCceEEEECCch----hhhHHHHHHHHHHH
Confidence 999997 5543211 225566777888873345999999998 99999999999864
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.74 E-value=2.6e-17 Score=100.56 Aligned_cols=86 Identities=21% Similarity=0.281 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHHHHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEE
Q psy3458 49 NNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEF 128 (151)
Q Consensus 49 ~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~ 128 (151)
+..||+.|++.||+.+.+.|.++|.|+|||+.+++.+++ ++.. .. ....++.+|..+++....+.|.|
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~--------~~~~---~~-~~~~~~~~i~~~~~~~~~~~~~~ 68 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAING--------RSSS---RS-ELRPLIQDIRSLLDRFWNVSVSH 68 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTT--------SS------S-CCHHHHHHHHHHHCCCSCEEEEE
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccc--------cccc---cc-cccccchhhhhhhccccceEEEE
Confidence 468999999999999999999999999999999999998 2211 12 55889999999999545699999
Q ss_pred ecCCCCCcchHHHHHHHHhhhc
Q psy3458 129 VPGHGNSHGNMKADEMARDAAG 150 (151)
Q Consensus 129 v~~h~~~~~N~~AD~lA~~a~~ 150 (151)
|||. .|..||.|||.|++
T Consensus 69 i~r~----~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 69 IPRE----QNKVADALAKFALS 86 (87)
T ss_dssp --GG----GSHHHHHHHHHHHH
T ss_pred EChH----HhHHHHHHHHHHhh
Confidence 9999 99999999999874
No 12
>KOG1812|consensus
Probab=93.73 E-value=0.19 Score=39.06 Aligned_cols=42 Identities=19% Similarity=0.312 Sum_probs=37.0
Q ss_pred cchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHHHHh
Q psy3458 46 RVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQE 87 (151)
Q Consensus 46 ~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~l~~ 87 (151)
..+...+|+.|+..+|..+...+..++.++.|+....+.+.+
T Consensus 46 ~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~ 87 (384)
T KOG1812|consen 46 SITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAG 87 (384)
T ss_pred ccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhh
Confidence 478999999999999999999999999999998777775554
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=92.62 E-value=0.57 Score=31.64 Aligned_cols=55 Identities=24% Similarity=0.262 Sum_probs=34.2
Q ss_pred CcEEEEEccCCCCCCCCCCceEEEEEEcC---CCcc---ccc-cccCC--cchHHHHHHHHHHHHHHHcHh
Q psy3458 5 NHVVVFTDGACPRNGKVGASAGYGVYFGE---NNPL---NVA-GKVTG--RVTNNNAEIQGAIHALKQAKS 66 (151)
Q Consensus 5 ~~~~iytDGs~~~~~~~~~~ag~gv~~~~---~~~~---~~~-~~~~~--~~t~~~aEl~Al~~aL~~~~~ 66 (151)
-.+.+|+|+|-.. .|..+|.+. +... -.+ .++.+ ..|.-+.||.|++.|.+.+..
T Consensus 80 ~~L~~F~DAS~~a-------ygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASESA-------YGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeecccccc-------eeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 3578999999653 344555433 2211 111 12222 458899999999999988753
No 14
>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=82.16 E-value=1.4 Score=31.10 Aligned_cols=59 Identities=20% Similarity=0.339 Sum_probs=37.3
Q ss_pred cEEEEEccCCCCCCCCCCceEEEEEEcCCCcc-ccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHH
Q psy3458 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMI 82 (151)
Q Consensus 6 ~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~~-~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi 82 (151)
...||+|+.-. |+|+.++.+... ..+. .-....+||.|...|.-+... + .|-|||.+|+
T Consensus 94 lc~VfaDATpT---------gwgi~i~~~~~~~Tfs~----~l~IhtaELlaaClAr~~~~~----r-~l~tDnt~Vl 153 (245)
T PF00336_consen 94 LCQVFADATPT---------GWGISITGQRMRGTFSK----PLPIHTAELLAACLARLMSGA----R-CLGTDNTVVL 153 (245)
T ss_pred CCceeccCCCC---------cceeeecCceeeeeecc----cccchHHHHHHHHHHHhccCC----c-EEeecCcEEE
Confidence 34567776433 455556554432 2222 456889999999888766543 3 4899999876
No 15
>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=73.83 E-value=26 Score=26.61 Aligned_cols=62 Identities=16% Similarity=0.202 Sum_probs=31.9
Q ss_pred eEEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcC---CceEEEEcCcHHHHHHHHh
Q psy3458 25 AGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSAN---IDRVCIKSDSQFMIKCVQE 87 (151)
Q Consensus 25 ag~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~---~~~v~i~tDs~~vi~~l~~ 87 (151)
.-+||.++.|........ ....+....-|.-++.+++.++.+. ..+|.+.|||+-|++.+++
T Consensus 168 ~~IGVHVRhGngeD~~~h-~~~~~D~e~~L~~V~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~ 232 (321)
T PF05830_consen 168 SVIGVHVRHGNGEDIMDH-APYWADEERALRQVCTAIDKAKALAPPKPVRIFLATDSAEVIDQFRK 232 (321)
T ss_dssp EEEEEEE----------------HHHHHHHHHHHHHHHHHHTS--SS-EEEEEEES-HHHHHHHHH
T ss_pred ceEEEEEeccCCcchhcc-CccccCchHHHHHHHHHHHHHHhccCCCCeeEEEecCcHHHHHHHHH
Confidence 367887765433221111 1133333444666677777665542 2478889999999999998
No 16
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=73.55 E-value=9.5 Score=27.27 Aligned_cols=76 Identities=13% Similarity=0.199 Sum_probs=48.8
Q ss_pred EEEEccCCCCCCCCCCceEEEEEEcC----CCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceE-EEE----cCc
Q psy3458 8 VVFTDGACPRNGKVGASAGYGVYFGE----NNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRV-CIK----SDS 78 (151)
Q Consensus 8 ~iytDGs~~~~~~~~~~ag~gv~~~~----~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v-~i~----tDs 78 (151)
.-+.+|+....|+.+ ++-++.+. ...+..+..++ ..+|..+|.+|.+.+|+.+...+.++. ++| .||
T Consensus 67 i~~~~G~y~~~p~t~---~~k~yr~k~~~~~~~lt~~~~~~-~~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds 142 (225)
T COG3341 67 ISWAKGDYDAKPGTQ---EFKEYRGKCTIEYSWLTESSEFS-IKSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDS 142 (225)
T ss_pred ceeccCCccccCCCc---ceeEEeccccccceeeeeecccc-cccCchHHHHHHhccccccccccCccceeeccCCcchh
Confidence 445667777666543 44444432 12223333333 778999999999999998877655544 447 688
Q ss_pred HHHHHHHHh
Q psy3458 79 QFMIKCVQE 87 (151)
Q Consensus 79 ~~vi~~l~~ 87 (151)
+..+..+.+
T Consensus 143 ~a~~k~~k~ 151 (225)
T COG3341 143 WAYFKYVKD 151 (225)
T ss_pred HHHHHHHhh
Confidence 888877766
No 17
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=69.21 E-value=19 Score=26.47 Aligned_cols=52 Identities=15% Similarity=0.081 Sum_probs=36.0
Q ss_pred EEEEEEcCCCccccccccCCcc-hHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRV-TNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~-t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
=+|+++..+..+.....++ .. .-+.+=..++...++++.+.|++.|++|.=|
T Consensus 29 HvAiImDGNrRwA~~~gl~-~~~~GH~~G~~~l~~~~~~~~~~gIk~lTvYaFS 81 (256)
T PRK14828 29 HVGIIVDGNRRWARKAGFT-DVSQGHRAGAAKIGEFLGWCDETDVNVVTLYLLS 81 (256)
T ss_pred EEEEEecCChHHHHHcCCC-chHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEE
Confidence 3566665444433333333 33 5567888999999999999999999998664
No 18
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=54.69 E-value=35 Score=25.70 Aligned_cols=52 Identities=12% Similarity=0.045 Sum_probs=34.6
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+|+++..+..+.....++ ...-+.+=..++...++++.+.|++.|++|.=|.
T Consensus 71 VAiIMDGNrRwAk~~gl~-~~~GH~~G~~~l~~v~~~c~~lGI~~lTvYaFSt 122 (296)
T PRK14827 71 VAIVMDGNGRWATQRGLA-RTEGHKMGEAVVIDIACGAIELGIKWLSLYAFST 122 (296)
T ss_pred EEEeccCchHHHHHCCCC-HhHHHHHHHHHHHHHHHHHHHcCCCEEEEeeecc
Confidence 344443333333333333 4556677788999999999999999999996553
No 19
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=45.77 E-value=67 Score=24.97 Aligned_cols=94 Identities=17% Similarity=0.236 Sum_probs=56.4
Q ss_pred HHHHHHHHHH----HHHcHhcCCceEEEEcCcHHHHHHHHhhHHHHHHcCccccCCCccCC-----HHHHHHHHHHhcCC
Q psy3458 51 NAEIQGAIHA----LKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQN-----KEELQELLHQIGQM 121 (151)
Q Consensus 51 ~aEl~Al~~a----L~~~~~~~~~~v~i~tDs~~vi~~l~~~~~~w~~~~~~~~~~~~~~~-----~~l~~~i~~~~~~~ 121 (151)
..|+..++.. -+.+++-|..-|.|+.=.-|+++++-.....-+...| |....| .++++.+.+.....
T Consensus 141 ~~eI~~ii~~f~~AA~rA~~AGFDgVEIH~AhGYLi~qFlsp~tN~RtD~Y----GGSlENR~Rf~~EVv~aVr~~vg~~ 216 (363)
T COG1902 141 EEEIEEVIEDFARAARRAKEAGFDGVEIHGAHGYLLSQFLSPLTNKRTDEY----GGSLENRARFLLEVVDAVREAVGAD 216 (363)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCEEEEeeccchHHHHhcCCccCCCCCcc----CCcHHHHHHHHHHHHHHHHHHhCCC
Confidence 5566555554 4555667899999999999999988762222222222 222333 44555666666545
Q ss_pred CceEEEEecCCC----CC---cchHHHHHHHHhh
Q psy3458 122 ESVKWEFVPGHG----NS---HGNMKADEMARDA 148 (151)
Q Consensus 122 ~~v~~~~v~~h~----~~---~~N~~AD~lA~~a 148 (151)
+.|-++--+... |. ...+.|+.|.+.+
T Consensus 217 ~~vg~Rls~~d~~~~~g~~~~e~~~la~~L~~~G 250 (363)
T COG1902 217 FPVGVRLSPDDFFDGGGLTIEEAVELAKALEEAG 250 (363)
T ss_pred ceEEEEECccccCCCCCCCHHHHHHHHHHHHhcC
Confidence 456666666443 11 3467777777776
No 20
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=43.78 E-value=37 Score=23.44 Aligned_cols=25 Identities=24% Similarity=0.331 Sum_probs=22.6
Q ss_pred HHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 55 QGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 55 ~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+.+..||+.++++++++|.|..|..
T Consensus 117 emLkl~L~~ar~lgi~~Vlvtcd~d 141 (174)
T COG3981 117 EMLKLALEKARELGIKKVLVTCDKD 141 (174)
T ss_pred HHHHHHHHHHHHcCCCeEEEEeCCC
Confidence 6789999999999999999998864
No 21
>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=41.32 E-value=87 Score=20.21 Aligned_cols=52 Identities=10% Similarity=0.056 Sum_probs=32.9
Q ss_pred eEEEEEEcCCCccccccccC--CcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 25 AGYGVYFGENNPLNVAGKVT--GRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 25 ag~gv~~~~~~~~~~~~~~~--~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
.|.+++..+|..+...- .. ...-...||..|+..+...-.+ .+..+.+.++.
T Consensus 23 vgAa~~~~~G~i~~G~n-~e~~~~~~s~~AE~~Ai~~a~~~g~~-~i~~i~vv~~~ 76 (127)
T TIGR01354 23 VGAALLTKDGRIFTGVN-VENASYPLTICAERSAIGKAISAGYR-KFVAIAVADSA 76 (127)
T ss_pred EEEEEEeCCCCEEEEEe-ecccCCCCCcCHHHHHHHHHHHcCCC-CeEEEEEEeCC
Confidence 46666667776644211 11 1334568999999999876433 56788888765
No 22
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=40.56 E-value=38 Score=20.15 Aligned_cols=39 Identities=10% Similarity=0.020 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHcHh-cCCceEEEEcCcHHHHHHHHh
Q psy3458 49 NNNAEIQGAIHALKQAKS-ANIDRVCIKSDSQFMIKCVQE 87 (151)
Q Consensus 49 ~~~aEl~Al~~aL~~~~~-~~~~~v~i~tDs~~vi~~l~~ 87 (151)
.+.|||.|++.---.+.- .+--.+.+.|++..+.+.+-.
T Consensus 3 c~~AELaAlir~~G~l~~~~~~~~l~~~ten~~vARri~~ 42 (86)
T PF10298_consen 3 CRIAELAALIRFSGSLSISNGRISLEISTENAAVARRIYS 42 (86)
T ss_dssp HHHHHHHHHHHHHEEECTTTTEEEE--EES-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCEEEEECCEEEEEEEeCCHHHHHHHHH
Confidence 467999999876543322 222378889999987755554
No 23
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=40.52 E-value=74 Score=23.10 Aligned_cols=52 Identities=12% Similarity=0.054 Sum_probs=36.2
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+|+++..+..+.....++ ...-+.+=..++...++++.+.|++.|++|.=|.
T Consensus 7 VaiImDGNrRwAk~~g~~-~~~GH~~G~~~l~~i~~~~~~lgIk~lTvYaFS~ 58 (233)
T PRK14841 7 VAIIMDGNGRWAKKRGLP-RIKGHQRGAEVLHNTVKWSLELGIKYLTAFSFST 58 (233)
T ss_pred EEEEccCCHHHHHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEeeeH
Confidence 455554444433333333 5566788889999999999999999999996553
No 24
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=40.40 E-value=76 Score=23.04 Aligned_cols=52 Identities=6% Similarity=0.035 Sum_probs=36.8
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+|+++..+..+.....++ ...-+++=..++...++++.+.|++.|++|.=|.
T Consensus 8 VaiImDGNrRwA~~~gl~-~~~GH~~G~~~l~~~~~~c~~~gI~~lTvyaFS~ 59 (233)
T PRK14833 8 LAIIMDGNGRWAKLRGKA-RAAGHKKGVKTLREITIWCANHKLECLTLYAFST 59 (233)
T ss_pred EEEEccCCHHHHHHCCCC-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEeecch
Confidence 455554444443334443 5566788889999999999999999999996553
No 25
>KOG1602|consensus
Probab=40.38 E-value=86 Score=23.23 Aligned_cols=51 Identities=14% Similarity=0.104 Sum_probs=38.2
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
++++...+..+.-...++ ...-.+|=..++..-|++..+.|++.|++|.=|
T Consensus 40 VaFIMDGNRR~AKk~~L~-~~~GH~aGf~~l~~ile~C~~lGI~~vT~fAFS 90 (271)
T KOG1602|consen 40 VAFIMDGNRRYAKKRGLE-TSEGHEAGFEALKEILELCKELGIKEVTVFAFS 90 (271)
T ss_pred eEEEecCchHHHHhcCCC-cccchHHHHHHHHHHHHHHHHcCCcEEEEEEEe
Confidence 455555555544444555 466778999999999999999999999998644
No 26
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=39.59 E-value=73 Score=23.24 Aligned_cols=31 Identities=23% Similarity=0.386 Sum_probs=25.1
Q ss_pred HHHHHHHcHhcCCceEEEEcCcHHHHHHHHh
Q psy3458 57 AIHALKQAKSANIDRVCIKSDSQFMIKCVQE 87 (151)
Q Consensus 57 l~~aL~~~~~~~~~~v~i~tDs~~vi~~l~~ 87 (151)
+....+.+.+-+..+|++-||++-+.+.+++
T Consensus 31 I~rV~e~a~~s~~~rvvVATDde~I~~av~~ 61 (247)
T COG1212 31 IVRVAERALKSGADRVVVATDDERIAEAVQA 61 (247)
T ss_pred HHHHHHHHHHcCCCeEEEEcCCHHHHHHHHH
Confidence 4455566666677899999999999999987
No 27
>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=38.96 E-value=84 Score=22.72 Aligned_cols=51 Identities=10% Similarity=0.113 Sum_probs=34.7
Q ss_pred EEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 28 GVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 28 gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
++++..+..+.....++ ...-+.+=..++...++++.+.|++.|++|.=|.
T Consensus 4 AiImDGNrRwAk~~gl~-~~~GH~~G~~~~~~v~~~c~~~GI~~lT~yaFSt 54 (226)
T TIGR00055 4 AIIMDGNGRWAKKKGKP-RAYGHKAGVKSLRRILRWCANLGVECLTLYAFST 54 (226)
T ss_pred EEEcCCCHHHHHHCCCC-hhHhHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 44444333333333333 4556777888999999999999999999997553
No 28
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=37.70 E-value=94 Score=22.83 Aligned_cols=53 Identities=13% Similarity=0.144 Sum_probs=36.9
Q ss_pred EEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
=+++++..+..+.....++ ...-..+=+..+...++++.+.|++.|++|.=|.
T Consensus 17 HVAiImDGNrRwAk~~g~~-~~~GH~~G~~~l~~i~~~c~~lgI~~lTvYaFS~ 69 (249)
T PRK14834 17 HVAIIMDGNGRWAKARGLP-RAAGHRAGVEALRRVVRAAGELGIGYLTLFAFSS 69 (249)
T ss_pred eEEEEecCchHHHHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEEec
Confidence 3566665554433333333 4556677788899999999999999999997554
No 29
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=37.43 E-value=89 Score=22.67 Aligned_cols=52 Identities=12% Similarity=0.141 Sum_probs=36.2
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+++++..+..+.....++ ...-+.+=..++...++++.+.|++.|++|.=|.
T Consensus 10 VAiImDGNrRwAk~~gl~-~~~GH~~G~~~~~~i~~~c~~~GI~~lT~YaFS~ 61 (230)
T PRK14837 10 VGIIMDGNRRWALKKGLS-FFEGHKEGLKRAKEIVKHSLKLGIKYLSLYVFST 61 (230)
T ss_pred EEEEccCCHHHHHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 555554444433333333 4556778889999999999999999999997554
No 30
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.30 E-value=95 Score=22.89 Aligned_cols=52 Identities=13% Similarity=0.116 Sum_probs=36.8
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+|++...+..+.....++ ...-+.+=..++...++++.+.|++.|++|.=|.
T Consensus 22 VAiImDGNrRwAk~~gl~-~~~GH~~G~~~l~~i~~~c~~~gI~~lTvyaFS~ 73 (253)
T PRK14832 22 IAVIMDGNGRWATSQGLP-RIAGHRQGARTLKELLRCCKDWGIKALTAYAFST 73 (253)
T ss_pred EEEECCCCHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 555554444433333333 5667788889999999999999999999997554
No 31
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.27 E-value=94 Score=22.72 Aligned_cols=52 Identities=8% Similarity=0.053 Sum_probs=36.6
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+|+++..+..+.....++ ...-+++=...+..-++++.+.|++.|++|.=|.
T Consensus 12 VaiImDGNrRwAk~~gl~-~~~GH~~G~~~l~~i~~~c~~lgI~~vTvYaFS~ 63 (241)
T PRK14842 12 IAVIMDGNGRWAESQGKK-RSEGHREGANAIDRLMDASLEYGLKNISLYAFST 63 (241)
T ss_pred EEEEcCCCHHHHHHCCCC-hhHhHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 556554444433333333 5556778889999999999999999999997554
No 32
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=35.75 E-value=1e+02 Score=22.97 Aligned_cols=53 Identities=21% Similarity=0.135 Sum_probs=35.8
Q ss_pred EEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
=+|+++..+..+.....++ ...-..+=...+..-++++.+.|++.|++|.=|.
T Consensus 44 HVAiImDGNrRwAk~~g~~-~~~GH~~G~~~l~~i~~~c~~lGIk~lTvYaFS~ 96 (275)
T PRK14835 44 HLGLILDGNRRFARALGLQ-REMGHEFGVQKAYEVLEWCLELGIPTVTIWVFST 96 (275)
T ss_pred EEEEEecCchHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEEc
Confidence 3556665444433333333 3445677788999999999999999999986553
No 33
>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=35.52 E-value=97 Score=22.29 Aligned_cols=51 Identities=12% Similarity=0.102 Sum_probs=34.5
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
+|+++..+..+.....++ ...-.++=...+..-++++.+.|++.+++|.=|
T Consensus 4 vaiImDGNrRwA~~~gl~-~~~GH~~G~~~~~~i~~~~~~~gI~~lTvyaFS 54 (221)
T cd00475 4 VAFIMDGNRRWAKQRGMD-RIEGHKAGAEKLRDILRWCLELGVKEVTLYAFS 54 (221)
T ss_pred EEEecCCCHHHHHHCCCC-hhHhHHHHHHHHHHHHHHHHHcCCCEEEEEeec
Confidence 345554433333333333 556677888899999999999999999999544
No 34
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=34.83 E-value=1.1e+02 Score=22.43 Aligned_cols=53 Identities=13% Similarity=0.181 Sum_probs=36.8
Q ss_pred EEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
=+|+++..+..+.....++ ...-..+=..++..-++++.+.|++.|++|.=|.
T Consensus 12 HVAiImDGNrRwAk~~gl~-~~~GH~~G~~~l~~i~~~c~~~GI~~lTvYaFS~ 64 (239)
T PRK14839 12 HVAIIMDGNGRWATARGLP-RLAGHRAGVEAIRRVVEAAPDLGIGTLTLYAFSS 64 (239)
T ss_pred EEEEEcCCCHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEech
Confidence 3556654444433333333 4556777888999999999999999999997554
No 35
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=33.87 E-value=2.2e+02 Score=22.79 Aligned_cols=41 Identities=12% Similarity=0.133 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhcCCC-ceEEEEecCCCCCcchHHHHHHHHhhh
Q psy3458 108 KEELQELLHQIGQME-SVKWEFVPGHGNSHGNMKADEMARDAA 149 (151)
Q Consensus 108 ~~l~~~i~~~~~~~~-~v~~~~v~~h~~~~~N~~AD~lA~~a~ 149 (151)
.+++-++...+...+ ...+.+||||= .-.+..++.+.+.++
T Consensus 244 eei~l~~~~~l~~~~~~~llIlVPRHp-ERf~~v~~l~~~~gl 285 (419)
T COG1519 244 EEIILDAHQALKKQFPNLLLILVPRHP-ERFKAVENLLKRKGL 285 (419)
T ss_pred HHHHHHHHHHHHhhCCCceEEEecCCh-hhHHHHHHHHHHcCC
Confidence 355555444443244 58899999991 113444444444433
No 36
>PRK14838 undecaprenyl pyrophosphate synthase; Provisional
Probab=32.93 E-value=1.2e+02 Score=22.26 Aligned_cols=52 Identities=10% Similarity=0.029 Sum_probs=36.3
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+++++..+..+.....++ ...-..+=...+...++++.+.|++.|++|.=|.
T Consensus 14 VAiImDGNrRwA~~~gl~-~~~GH~~G~~~l~~i~~~~~~~gI~~lT~YaFS~ 65 (242)
T PRK14838 14 IAIIMDGNGRWAKERGKE-RSFGHQAGAETVHIITEEAARLGVKFLTLYTFST 65 (242)
T ss_pred EEEeccCCHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeech
Confidence 555554444433333333 5567788889999999999999999999996553
No 37
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=32.44 E-value=1.2e+02 Score=23.28 Aligned_cols=51 Identities=10% Similarity=0.062 Sum_probs=35.6
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
+++++..+..+.....++ ...-+.+=..++..-|+.+.+.|++.|++|.=|
T Consensus 23 VAiIMDGNrRwAk~~gl~-~~~GH~~G~~~l~~il~~c~~lGIk~lTlYAFS 73 (322)
T PTZ00349 23 ISIIMDGNRRFAKEKGLH-SAIGHFMGSKALIQIIEICIKLKIKILSVFSFS 73 (322)
T ss_pred EEEEcCCCHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence 455654444433333333 445677788899999999999999999998654
No 38
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=30.42 E-value=1.3e+02 Score=21.93 Aligned_cols=53 Identities=13% Similarity=0.080 Sum_probs=36.9
Q ss_pred EEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
=+|+++..+..+.....++ ...-+.+=..++..-++++.+.|++.|++|.=|.
T Consensus 17 HvaiImDGNrRwAk~~g~~-~~~GH~~G~~~l~~iv~~c~~~gI~~vTvYaFS~ 69 (243)
T PRK14829 17 HIAVVMDGNGRWATQRGLK-RTEGHKAGEPVLFDVVAGAIEAGVPYLSLYTFST 69 (243)
T ss_pred eEEEecCCCHHHHHHCCCC-hhHHHHHHHHHHHHHHHHHHHcCCCEEEEeeecc
Confidence 3556554444433333333 5566788889999999999999999999997653
No 39
>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=30.31 E-value=1.4e+02 Score=18.48 Aligned_cols=40 Identities=15% Similarity=0.120 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHHHHh
Q psy3458 48 TNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQE 87 (151)
Q Consensus 48 t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~l~~ 87 (151)
....||..|+..+.+..........++|+..+....+..-
T Consensus 44 ~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~EPC~mC~~a 83 (109)
T cd01285 44 PTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPMCAGA 83 (109)
T ss_pred CcccHHHHHHHHHHHHhCCCccCCeEEEEeCCChHHHHHH
Confidence 4568999999999887654345678888877666555443
No 40
>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=30.26 E-value=1.2e+02 Score=19.26 Aligned_cols=28 Identities=11% Similarity=0.029 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 48 TNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 48 t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
....||..|+..+.+. .....++|+--+
T Consensus 42 ~~~HAE~~ai~~a~~~----~l~g~tly~TlE 69 (115)
T cd01284 42 GGPHAEVNALASAGEK----LARGATLYVTLE 69 (115)
T ss_pred CcccHHHHHHHHHhhc----CCCCeEEEEeCC
Confidence 5678999999999875 234566776544
No 41
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=29.95 E-value=1.7e+02 Score=19.36 Aligned_cols=52 Identities=15% Similarity=0.137 Sum_probs=32.5
Q ss_pred EEEEEEcCCCcccccc-ccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 26 GYGVYFGENNPLNVAG-KVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~-~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
|..+...+|..+...- ......-...||-.||..|+.. -......|.+++|+
T Consensus 29 GAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 29 GAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred EEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 5555556665432111 1111445679999999999887 33445689998887
No 42
>PF00289 CPSase_L_chain: Carbamoyl-phosphate synthase L chain, N-terminal domain; InterPro: IPR005481 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the large subunit of carbamoyl phosphate synthase. This domain can also be found in certain other related proteins. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VA7_A 3OUU_A 3OUZ_B 1W96_B 1W93_A 1ULZ_A 3HB9_C 3HO8_A 3BG5_C 3HBL_A ....
Probab=29.49 E-value=60 Score=20.45 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=22.7
Q ss_pred HHHHHHHcHhcCCceEEEEcCcHHHHHHH
Q psy3458 57 AIHALKQAKSANIDRVCIKSDSQFMIKCV 85 (151)
Q Consensus 57 l~~aL~~~~~~~~~~v~i~tDs~~vi~~l 85 (151)
...+++.++++|++.|.|+++...+-...
T Consensus 14 a~r~~ra~r~~Gi~tv~v~s~~d~~s~~~ 42 (110)
T PF00289_consen 14 AVRIIRALRELGIETVAVNSNPDTVSTHV 42 (110)
T ss_dssp HHHHHHHHHHTTSEEEEEEEGGGTTGHHH
T ss_pred HHHHHHHHHHhCCcceeccCchhcccccc
Confidence 67888899999999999999875543333
No 43
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=28.48 E-value=1.5e+02 Score=21.75 Aligned_cols=53 Identities=11% Similarity=0.127 Sum_probs=35.5
Q ss_pred EEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
=+|+++..+..+.....++ ...-.++=...+...++++.+.|++.|++|.=|.
T Consensus 25 HVAiImDGNrRwAk~~gl~-~~~Gh~~G~~~l~~~l~~c~~~GI~~vTvYaFS~ 77 (251)
T PRK14830 25 HIAIIMDGNGRWAKKRMLP-RIAGHKAGMDTVKKITKAASELGVKVLTLYAFST 77 (251)
T ss_pred eEEEEecCchHHHHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEEEEeh
Confidence 3566665544433333332 3445566677889999999999999999997553
No 44
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=27.82 E-value=36 Score=19.00 Aligned_cols=15 Identities=13% Similarity=0.034 Sum_probs=10.7
Q ss_pred chHHHHHHHHhhhcC
Q psy3458 137 GNMKADEMARDAAGW 151 (151)
Q Consensus 137 ~N~~AD~lA~~a~~~ 151 (151)
.-+.|+.||+.|++|
T Consensus 12 ~lE~A~~La~~GIRF 26 (61)
T PF07131_consen 12 ALEMAHSLAHIGIRF 26 (61)
T ss_pred HHHHHHHHHHcCcee
Confidence 346788888887764
No 45
>KOG1817|consensus
Probab=26.92 E-value=2.8e+02 Score=22.49 Aligned_cols=55 Identities=25% Similarity=0.228 Sum_probs=33.7
Q ss_pred CcEEEEEccCCCCCCCCCCceEEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHh
Q psy3458 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66 (151)
Q Consensus 5 ~~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~ 66 (151)
+...-+++|..-+.... ..-++||+++. .+ .... ..+.+.||+.|...||+....
T Consensus 449 dip~y~V~~~~gpa~~r--~y~Vavyf~gk-rl--at~~--G~nik~Ae~rAA~~ALe~~~~ 503 (533)
T KOG1817|consen 449 DIPLYKVLGAKGPANDR--NYKVAVYFKGK-RL--ATGV--GSNIKQAEMRAAMQALENLKM 503 (533)
T ss_pred CCceEEEecccCCCCCC--ceEEEEEECCE-EE--eecc--CchHhHHHHHHHHHHHHHHHh
Confidence 34455677655433222 24677788662 21 1111 467889999999999988763
No 46
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.53 E-value=1.6e+02 Score=21.63 Aligned_cols=52 Identities=13% Similarity=0.102 Sum_probs=36.0
Q ss_pred EEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 26 GYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 26 g~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
=+|+++..+..+.....++ ...-+++=..++..-++++.+.|++.|++|.=|
T Consensus 23 HVaiImDGNrRwA~~~gl~-~~~GH~~G~~~l~~i~~~c~~~GI~~vT~yaFS 74 (249)
T PRK14831 23 HVAVIMDGNGRWAKRRGLP-RIMGHRRGVDALKDLLRCCKDWGIGALTAYAFS 74 (249)
T ss_pred eEEEecCCcHHHHHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEEEeecc
Confidence 3555554444433333333 455677788899999999999999999999766
No 47
>cd04733 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=26.27 E-value=1.3e+02 Score=22.97 Aligned_cols=69 Identities=17% Similarity=0.246 Sum_probs=39.5
Q ss_pred HHHHHHHHcHhcCCceEEEEcCcHHHHHHHHhhHHHHHHcCccccCCCccCC-----HHHHHHHHHHhcCCCceEEEE
Q psy3458 56 GAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQN-----KEELQELLHQIGQMESVKWEF 128 (151)
Q Consensus 56 Al~~aL~~~~~~~~~~v~i~tDs~~vi~~l~~~~~~w~~~~~~~~~~~~~~~-----~~l~~~i~~~~~~~~~v~~~~ 128 (151)
....|-+.+.+-|..-|.|..-+-|+++++-......+...| |..+.| .++++.|.+.+...+.|.++.
T Consensus 150 ~~~~aA~ra~~aGfDgVeih~a~gyLl~qFlsp~~N~R~D~y----GGslenR~rf~~EiI~aIR~avG~d~~v~vri 223 (338)
T cd04733 150 RFAHAARLAQEAGFDGVQIHAAHGYLLSQFLSPLTNKRTDEY----GGSLENRARLLLEIYDAIRAAVGPGFPVGIKL 223 (338)
T ss_pred HHHHHHHHHHHcCCCEEEEchhhhhHHHHhcCCcCCCCCccC----CCCHHHHHHHHHHHHHHHHHHcCCCCeEEEEE
Confidence 344455666677889999999999988888762211111112 222223 345555666654355665554
No 48
>PRK10708 hypothetical protein; Provisional
Probab=26.17 E-value=68 Score=17.75 Aligned_cols=19 Identities=42% Similarity=0.566 Sum_probs=15.3
Q ss_pred CCCCCcEEEEEccCCCCCC
Q psy3458 1 MDPDNHVVVFTDGACPRNG 19 (151)
Q Consensus 1 ~~~~~~~~iytDGs~~~~~ 19 (151)
|+-++.+.+-|||.-+..+
T Consensus 1 MkvnD~VtVKTDG~~rR~G 19 (62)
T PRK10708 1 MKVNDRVTVKTDGGPRRPG 19 (62)
T ss_pred CccccEEEEecCCCccccc
Confidence 5667899999999887653
No 49
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=25.43 E-value=3.3e+02 Score=21.26 Aligned_cols=76 Identities=11% Similarity=0.046 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHcHhcCCceEEEEcCcHHHHHHHHhhHHHHHHcCccccCCCccCCHHHHHHHHHHhcCCCceEEEEec
Q psy3458 51 NAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFVP 130 (151)
Q Consensus 51 ~aEl~Al~~aL~~~~~~~~~~v~i~tDs~~vi~~l~~~~~~w~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~v~~~~v~ 130 (151)
..|..-++..++.+.+..-+-+..+.|-| |+|..+..+-+.++.+.. --.+.+.-..
T Consensus 140 ~Vd~eyLl~w~~kVa~~KgkglEaHlDGq----------------------GEP~lYP~l~~lVqalk~-~~~v~vVSmQ 196 (414)
T COG2100 140 VVDPEYLLEWFEKVARFKGKGLEAHLDGQ----------------------GEPLLYPHLVDLVQALKE-HKGVEVVSMQ 196 (414)
T ss_pred EecHHHHHHHHHHHHhhhCCCeEEEecCC----------------------CCCccchhHHHHHHHHhc-CCCceEEEEe
Confidence 34555566666555544334555555544 677766655555555544 2236666667
Q ss_pred CCCCCcchHHHHHHHHhhh
Q psy3458 131 GHGNSHGNMKADEMARDAA 149 (151)
Q Consensus 131 ~h~~~~~N~~AD~lA~~a~ 149 (151)
.|-....-+.+|+|++.++
T Consensus 197 Tng~~L~~~lv~eLeeAGL 215 (414)
T COG2100 197 TNGVLLSKKLVDELEEAGL 215 (414)
T ss_pred eCceeccHHHHHHHHHhCC
Confidence 7766666788888887765
No 50
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=25.31 E-value=2.2e+02 Score=20.96 Aligned_cols=34 Identities=9% Similarity=0.049 Sum_probs=28.5
Q ss_pred cchHHHHHHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 46 RVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 46 ~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
...-+.+=+.++...++++.+.|++.|++|.=|.
T Consensus 44 ~~~GH~~G~~~l~~v~~~c~~~GIk~lTvYaFS~ 77 (250)
T PRK14840 44 AISGHYYGAKSLPQIVDTALHLGIEVLTLFAFST 77 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEeeh
Confidence 4556788889999999999999999999996553
No 51
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=24.72 E-value=74 Score=17.61 Aligned_cols=19 Identities=42% Similarity=0.597 Sum_probs=15.3
Q ss_pred CCCCCcEEEEEccCCCCCC
Q psy3458 1 MDPDNHVVVFTDGACPRNG 19 (151)
Q Consensus 1 ~~~~~~~~iytDGs~~~~~ 19 (151)
|+-++.+.+-|||.-+..+
T Consensus 1 MkvnD~VtVKTDG~~rR~G 19 (62)
T PF10781_consen 1 MKVNDRVTVKTDGGPRREG 19 (62)
T ss_pred CccccEEEEecCCcccccc
Confidence 5667899999999887653
No 52
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=24.35 E-value=64 Score=18.15 Aligned_cols=12 Identities=17% Similarity=0.343 Sum_probs=8.0
Q ss_pred CCCcEEEEEccC
Q psy3458 3 PDNHVVVFTDGA 14 (151)
Q Consensus 3 ~~~~~~iytDGs 14 (151)
....+.||||++
T Consensus 41 ~~~ei~I~tD~G 52 (63)
T PF04566_consen 41 REKEIRINTDAG 52 (63)
T ss_dssp TTTEEEEE-SSC
T ss_pred cCCEEEEEccCC
Confidence 356788888876
No 53
>COG3051 CitF Citrate lyase, alpha subunit [Energy production and conversion]
Probab=23.47 E-value=1.8e+02 Score=23.01 Aligned_cols=42 Identities=17% Similarity=0.118 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhc-----CCCceEEEEecCCCCCcchHHHHHHHHhhh
Q psy3458 108 KEELQELLHQIG-----QMESVKWEFVPGHGNSHGNMKADEMARDAA 149 (151)
Q Consensus 108 ~~l~~~i~~~~~-----~~~~v~~~~v~~h~~~~~N~~AD~lA~~a~ 149 (151)
..+...+.+.+. .++.|.|+|--|.-+..-|..-+.+|+.+.
T Consensus 47 ~Kl~~SleEaI~~sGlkdGMTiSFHH~fR~GD~vvN~Vm~~Ia~mGf 93 (513)
T COG3051 47 RKLCASLEEAIRRSGLKDGMTISFHHAFRGGDLVVNMVMDVIAKMGF 93 (513)
T ss_pred hhHHHHHHHHHHHhCccCCeEEEeeehhcCCceeHHHHHHHHHHhCc
Confidence 344444444432 478899999999977778999999999875
No 54
>PF07228 SpoIIE: Stage II sporulation protein E (SpoIIE); InterPro: IPR001932 This domain is found in protein phosphatase 2C, as well as other proteins eg. pyruvate dehydrogenase (lipoamide)-phosphatase (3.1.3.43 from EC), adenylate cyclase (4.6.1.1 from EC) and some bacterial stage II sporulation E proteins (3.1.3.16 from EC). Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases (3.1.3.16 from EC). PP2C [] is a monomeric enzyme of about 42 Kd which shows broad substrate specificity and is dependent on divalent cations (mainly manganese and magnesium) for its activity. Its exact physiological role is still unclear. Three isozymes are currently known in mammals: PP2C-alpha, -beta and -gamma. In yeast, there are at least four PP2C homologs: phosphatase PTC1 [], which has weak tyrosine phosphatase activity in addition to its activity on serines, phosphatases PTC2 and PTC3, and hypothetical protein YBR125c. Isozymes of PP2C are also known from Arabidopsis thaliana (ABI1, PPH1), Caenorhabditis elegans (FEM-2, F42G9.1, T23F11.1), Leishmania chagasi and Paramecium tetraurelia. In A. thaliana, the kinase associated protein phosphatase (KAPP) [] is an enzyme that dephosphorylates the Ser/Thr receptor-like kinase RLK5 and which contains a C-terminal PP2C domain. PP2C does not seem to be evolutionary related to the main family of serine/ threonine phosphatases: PP1, PP2A and PP2B. However, it is significantly similar to the catalytic subunit of pyruvate dehydrogenase phosphatase 3.1.3.43 from EC (PDPC) [], which catalyzes dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. PDPC is a mitochondrial enzyme and, like PP2C, is magnesium-dependent.; GO: 0003824 catalytic activity; PDB: 3KE6_B 3ZT9_A 3RNR_A 3EQ2_A 3F7A_B 3F79_A 3ES2_B 3PU9_B 3T91_B 3T9Q_B ....
Probab=23.33 E-value=30 Score=23.44 Aligned_cols=18 Identities=22% Similarity=0.634 Sum_probs=13.3
Q ss_pred CCCCCcEEEEEccCCCCC
Q psy3458 1 MDPDNHVVVFTDGACPRN 18 (151)
Q Consensus 1 ~~~~~~~~iytDGs~~~~ 18 (151)
+++.+.+.+||||-....
T Consensus 121 l~~gd~l~l~TDGl~e~~ 138 (193)
T PF07228_consen 121 LEPGDRLLLYTDGLFEAL 138 (193)
T ss_dssp --TTEEEEEECHHHCTTT
T ss_pred eccccEEEEeCCChhhcc
Confidence 357888999999988754
No 55
>PF11821 DUF3341: Protein of unknown function (DUF3341); InterPro: IPR021776 This family of proteins are functionally uncharacterised. This family is found in bacteria. Proteins in this family are about 170 amino acids in length.
Probab=22.89 E-value=1.1e+02 Score=21.09 Aligned_cols=24 Identities=13% Similarity=0.138 Sum_probs=20.9
Q ss_pred HHHHHHHHHcHhcCCceEEEEcCc
Q psy3458 55 QGAIHALKQAKSANIDRVCIKSDS 78 (151)
Q Consensus 55 ~Al~~aL~~~~~~~~~~v~i~tDs 78 (151)
.+++.|++.+++.|++...+||--
T Consensus 13 ~~l~~A~~~~r~~G~~~~d~ytPf 36 (173)
T PF11821_consen 13 EALLHAARKLRDAGYRIWDVYTPF 36 (173)
T ss_pred HHHHHHHHHHHHcCCceeEEeCCC
Confidence 678999999999999999988864
No 56
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=22.52 E-value=1.9e+02 Score=19.01 Aligned_cols=37 Identities=14% Similarity=0.185 Sum_probs=26.0
Q ss_pred HHHcHhcCCceEEEEcCcHHHHHHHHhhHHHHHHcCcc
Q psy3458 61 LKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWR 98 (151)
Q Consensus 61 L~~~~~~~~~~v~i~tDs~~vi~~l~~~~~~w~~~~~~ 98 (151)
++.+...| .+|.|++++....+.|...+..+....+.
T Consensus 22 ~~ka~~~g-~rv~I~~~d~~~a~~lD~~LW~~~~~sFl 58 (142)
T PRK05728 22 AEKALRAG-WRVLVQCEDEEQAEALDEALWTFRDESFL 58 (142)
T ss_pred HHHHHHCC-CEEEEEcCCHHHHHHHHHHhcCCCCCcCC
Confidence 34445554 68999998888899999977665555543
No 57
>KOG1393|consensus
Probab=22.44 E-value=1.4e+02 Score=23.68 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=19.0
Q ss_pred cEEEEEccCCCCCCCCCCceEEEEEEcCCCc
Q psy3458 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNP 36 (151)
Q Consensus 6 ~~~iytDGs~~~~~~~~~~ag~gv~~~~~~~ 36 (151)
.+.||-+|.+++.++.| .+++.++++-+
T Consensus 154 DIAvY~~G~aRpTGGAg---AVAmLIgPnAp 181 (462)
T KOG1393|consen 154 DIAVYAKGNARPTGGAG---AVAMLIGPNAP 181 (462)
T ss_pred eEEEecCCCCCCCCCcc---eEEEEEcCCCc
Confidence 46789999999877653 45556666543
No 58
>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=21.95 E-value=1.6e+02 Score=17.46 Aligned_cols=27 Identities=11% Similarity=0.281 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHcHhcCCceEEEEcCcH
Q psy3458 53 EIQGAIHALKQAKSANIDRVCIKSDSQ 79 (151)
Q Consensus 53 El~Al~~aL~~~~~~~~~~v~i~tDs~ 79 (151)
+|.+|-.|-+.+..+|++.|.+..|.-
T Consensus 36 ~l~~IQrAaRkLd~qGI~~V~L~G~~W 62 (77)
T PF12404_consen 36 DLRAIQRAARKLDGQGIKNVALAGEGW 62 (77)
T ss_pred chHHHHHHHHHHhhCCCceEEEecCCc
Confidence 478899999999999999999999954
No 59
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=21.89 E-value=82 Score=21.14 Aligned_cols=45 Identities=22% Similarity=0.202 Sum_probs=24.7
Q ss_pred cCCCCCCCCCCceEEEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHc
Q psy3458 13 GACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64 (151)
Q Consensus 13 Gs~~~~~~~~~~ag~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~ 64 (151)
|...+||.. |. |+.+++.. +...+....-...||..|+..|=+.+
T Consensus 22 g~T~pNP~V----G~-VIV~~~~I--vg~G~h~~aG~pHAEv~Al~~ag~~a 66 (146)
T COG0117 22 GTTSPNPSV----GC-VIVKDGEI--VGEGYHEKAGGPHAEVCALRMAGEAA 66 (146)
T ss_pred CcCCCCCce----eE-EEEECCEE--EeeeecCCCCCCcHHHHHHHHcCccc
Confidence 344566665 43 34455533 22222224556789999998884444
No 60
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.85 E-value=1.7e+02 Score=21.56 Aligned_cols=49 Identities=10% Similarity=0.150 Sum_probs=33.3
Q ss_pred EEEEEcCCCccccccccCCcchHHHHHHHHHHHHHHHcHhcCCceEEEEc
Q psy3458 27 YGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKS 76 (151)
Q Consensus 27 ~gv~~~~~~~~~~~~~~~~~~t~~~aEl~Al~~aL~~~~~~~~~~v~i~t 76 (151)
+|+++..+..+.....++ ...-.++=..++..-++++.+.|++.|++|.
T Consensus 18 VAiImDGNrRwA~~~gl~-~~~GH~~G~~~~~~iv~~c~~~gI~~lTvYa 66 (253)
T PRK14836 18 IAIIMDGNGRWAKRRGKP-RVEGHRAGVRAVRRTIEFCLEKGIEMLTLFA 66 (253)
T ss_pred EEEecCCcHHHHHHCCCc-hhhhHHHHHHHHHHHHHHHHHcCCCEEehhH
Confidence 555554443333333333 4455667778899999999999999999997
No 61
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.04 E-value=97 Score=20.38 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=7.8
Q ss_pred EEEEEccCCC
Q psy3458 7 VVVFTDGACP 16 (151)
Q Consensus 7 ~~iytDGs~~ 16 (151)
++||+||.+-
T Consensus 1 LTV~Fdg~FW 10 (132)
T PF11208_consen 1 LTVYFDGPFW 10 (132)
T ss_pred CeEEecCCcE
Confidence 5799999764
Done!