Query 037694
Match_columns 355
No_of_seqs 218 out of 415
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 03:30:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037694.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037694hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00060 meiotic recombination 100.0 3E-105 7E-110 785.4 31.2 355 1-355 29-384 (384)
2 PRK04342 DNA topoisomerase VI 100.0 5.2E-95 1.1E-99 714.9 31.4 344 1-355 14-366 (367)
3 COG1697 DNA topoisomerase VI, 100.0 9.4E-93 2E-97 677.1 19.1 343 1-353 10-356 (356)
4 KOG2795 Catalytic subunit of t 100.0 4.6E-91 1E-95 668.7 21.7 342 1-355 24-372 (372)
5 cd00223 TOPRIM_TopoIIB_SPO TOP 100.0 8.7E-45 1.9E-49 320.7 15.3 157 183-340 1-160 (160)
6 PF04406 TP6A_N: Type IIB DNA 99.8 2.9E-21 6.2E-26 147.3 5.8 68 62-133 1-68 (68)
7 PF09983 DUF2220: Uncharacteri 99.5 8.6E-14 1.9E-18 125.5 10.2 135 178-334 39-173 (181)
8 PF09664 DUF2399: Protein of u 99.4 1.2E-12 2.7E-17 114.8 6.9 129 179-335 15-146 (152)
9 TIGR02679 conserved hypothetic 98.4 7.3E-07 1.6E-11 89.3 7.8 67 184-255 252-319 (385)
10 cd00188 TOPRIM Topoisomerase-p 96.7 0.0091 2E-07 44.5 7.6 63 183-250 1-63 (83)
11 COG4924 Uncharacterized protei 89.9 0.73 1.6E-05 44.8 5.9 68 178-255 237-304 (386)
12 TIGR00334 5S_RNA_mat_M5 ribonu 89.6 1.8 3.9E-05 39.0 7.9 65 183-255 3-68 (174)
13 smart00493 TOPRIM topoisomeras 86.8 4.8 0.0001 30.1 7.8 65 184-253 2-66 (76)
14 cd01026 TOPRIM_OLD TOPRIM_OLD: 84.8 3.7 8E-05 32.8 6.5 63 182-249 3-70 (97)
15 cd01027 TOPRIM_RNase_M5_like T 80.6 12 0.00027 29.2 7.8 65 183-255 2-66 (81)
16 PRK04017 hypothetical protein; 77.7 9.2 0.0002 32.9 6.8 68 179-255 19-86 (132)
17 PF00072 Response_reg: Respons 75.5 17 0.00037 28.3 7.5 50 207-257 44-93 (112)
18 cd07022 S49_Sppa_36K_type Sign 66.8 45 0.00098 30.5 9.2 101 206-307 43-161 (214)
19 COG3593 Predicted ATP-dependen 62.8 16 0.00036 38.9 6.1 69 182-255 396-469 (581)
20 PF01751 Toprim: Toprim domain 61.7 26 0.00056 27.9 5.8 69 185-255 2-81 (100)
21 KOG4479 Transcription factor e 58.3 8.4 0.00018 30.4 2.2 43 293-342 12-54 (92)
22 COG1658 Small primase-like pro 58.1 55 0.0012 28.0 7.4 67 183-255 10-76 (127)
23 PF03475 3-alpha: 3-alpha doma 55.0 19 0.00041 25.0 3.5 30 296-325 16-45 (47)
24 PF13662 Toprim_4: Toprim doma 50.8 1E+02 0.0023 23.3 7.5 66 184-255 2-67 (81)
25 TIGR00706 SppA_dom signal pept 49.2 1.2E+02 0.0026 27.6 8.8 100 206-307 31-149 (207)
26 PF06490 FleQ: Flagellar regul 46.1 39 0.00086 27.6 4.6 36 208-246 46-81 (109)
27 PRK11778 putative inner membra 46.0 65 0.0014 32.0 6.8 93 212-307 132-242 (330)
28 PF03709 OKR_DC_1_N: Orn/Lys/A 44.7 17 0.00037 30.0 2.3 58 185-244 20-77 (115)
29 PF14421 LmjF365940-deam: A di 43.1 14 0.00031 33.4 1.6 36 216-251 155-190 (193)
30 COG1570 XseA Exonuclease VII, 41.4 1.3E+02 0.0029 31.0 8.4 96 139-256 77-187 (440)
31 PRK04031 DNA primase; Provisio 40.0 79 0.0017 32.3 6.5 63 182-255 169-231 (408)
32 PRK09390 fixJ response regulat 39.6 1.9E+02 0.0042 24.1 8.3 50 207-257 48-97 (202)
33 PRK09468 ompR osmolarity respo 37.7 1.4E+02 0.003 26.6 7.3 42 207-248 50-91 (239)
34 PRK10816 DNA-binding transcrip 37.5 1.5E+02 0.0032 26.0 7.4 50 208-258 46-95 (223)
35 PRK11475 DNA-binding transcrip 35.7 1.7E+02 0.0037 26.7 7.6 47 212-258 46-92 (207)
36 cd07023 S49_Sppa_N_C Signal pe 34.8 2.8E+02 0.0061 25.0 8.9 83 222-307 56-154 (208)
37 KOG2780 Ribosome biogenesis pr 34.2 1.6E+02 0.0034 28.6 7.1 55 207-264 97-155 (302)
38 PF07085 DRTGG: DRTGG domain; 33.6 58 0.0013 26.1 3.7 36 206-247 62-97 (105)
39 TIGR00993 3a0901s04IAP86 chlor 32.7 51 0.0011 36.1 4.0 41 289-329 412-463 (763)
40 cd03364 TOPRIM_DnaG_primases T 32.4 1.8E+02 0.0038 21.9 6.1 57 184-249 2-58 (79)
41 TIGR00315 cdhB CO dehydrogenas 31.1 3.8E+02 0.0082 23.8 8.7 50 188-243 15-64 (162)
42 KOG1527 Uroporphyrin III methy 30.9 33 0.00072 34.5 2.1 61 179-246 279-345 (506)
43 COG0240 GpsA Glycerol-3-phosph 30.5 1.5E+02 0.0032 29.5 6.6 78 163-240 52-132 (329)
44 PRK00933 ribosomal biogenesis 29.9 57 0.0012 29.1 3.3 28 209-237 1-28 (165)
45 COG1537 PelA Predicted RNA-bin 29.0 1.9E+02 0.004 29.1 6.9 54 205-261 191-245 (352)
46 PRK06849 hypothetical protein; 28.0 1.2E+02 0.0027 30.0 5.7 45 206-255 4-48 (389)
47 cd01029 TOPRIM_primases TOPRIM 27.9 2.1E+02 0.0046 21.1 5.8 59 184-251 2-60 (79)
48 PRK10643 DNA-binding transcrip 27.5 1.9E+02 0.004 25.0 6.3 51 207-258 45-95 (222)
49 PF13289 SIR2_2: SIR2-like dom 26.9 2.2E+02 0.0049 23.2 6.4 53 191-245 73-127 (143)
50 KOG3446 NADH:ubiquinone oxidor 26.6 1E+02 0.0022 24.7 3.7 32 208-239 19-54 (97)
51 PRK13856 two-component respons 26.5 3.2E+02 0.0068 24.4 7.8 50 207-257 46-95 (241)
52 TIGR00729 ribonuclease H, mamm 25.9 61 0.0013 29.7 2.9 19 212-230 166-186 (206)
53 COG0794 GutQ Predicted sugar p 23.7 98 0.0021 28.6 3.7 37 208-246 41-82 (202)
54 PF08747 DUF1788: Domain of un 23.0 2.7E+02 0.0057 23.7 6.0 39 206-244 62-102 (126)
55 PF08444 Gly_acyl_tr_C: Aralky 22.8 58 0.0013 26.1 1.8 37 213-251 33-70 (89)
56 PRK03972 ribosomal biogenesis 21.8 1.3E+02 0.0027 28.0 4.0 28 209-236 2-29 (208)
57 PRK08105 flavodoxin; Provision 21.8 2.2E+02 0.0047 24.5 5.4 39 207-245 51-97 (149)
58 PRK09836 DNA-binding transcrip 21.5 3.2E+02 0.0069 23.9 6.7 51 207-258 45-95 (227)
59 cd07018 S49_SppA_67K_type Sign 21.0 2.5E+02 0.0054 25.8 5.9 17 291-307 151-167 (222)
60 cd01748 GATase1_IGP_Synthase T 20.9 1.2E+02 0.0026 27.0 3.8 44 205-254 36-87 (198)
61 COG4069 Uncharacterized protei 20.7 82 0.0018 30.9 2.7 26 234-259 289-314 (367)
62 cd06405 PB1_Mekk2_3 The PB1 do 20.7 83 0.0018 24.6 2.2 27 91-121 36-65 (79)
63 PF10777 YlaC: Inner membrane 20.4 93 0.002 27.4 2.7 31 299-331 113-143 (155)
64 KOG0862 Synaptobrevin/VAMP-lik 20.2 47 0.001 30.9 0.9 59 194-256 61-129 (216)
65 PRK10161 transcriptional regul 20.1 5.8E+02 0.013 22.2 8.1 51 207-258 47-99 (229)
No 1
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=100.00 E-value=3.2e-105 Score=785.39 Aligned_cols=355 Identities=74% Similarity=1.210 Sum_probs=342.2
Q ss_pred ChhHHHHHHHHHHHHHcCCCCCCccccccccCCCCceeccccc-cccceeeecCceeEEeecCchhHHHHHHHHHHHHHH
Q 037694 1 VRARIEVSVINFLKILNSPDPAISDLPLINRKSSNSRVSQGLL-TDVSWIFLSHSFCTRSLTKSNAAKAFVRVWKVMETC 79 (355)
Q Consensus 1 ~~~~Ie~~v~~~l~~L~~~~p~~~~l~~~~R~~~n~~~~~~~~-~~~~~~~~~~~~~~r~~~~~~~~~~f~~~~~vl~~i 79 (355)
|+++||+++++++.+|++|.|+.+++|+|+|+++|+.|+++++ .+...++++++.++|++.+.++|++|+++++||+++
T Consensus 29 ~~~~iE~~~~~~~~~l~~~~~~~~~~~~~~r~~~n~~~~~~~~~~~~~~~~l~~~~~~r~~~~~~~a~kf~~~~~vl~~i 108 (384)
T PLN00060 29 ARARIEVAVLNFLAALNSPDPAISDLPLISRNCSNVLLRRGLLQGDVSSIFLSHLFCKRSLTKAGSAKAFVRVWKVMEMC 108 (384)
T ss_pred HHHHHHHHHHHHHHHHhcCCCccceecccccccccccccccccccccceeeeccceeeEecCCHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999998888999999999999999876 344478899999999999999999999999999999
Q ss_pred HHHHhcCCCccccceeccccCCCccccCchHHHHHHHHHHHHhhccCccccCceecCCeeEEEeeEEecCCCceEecccC
Q 037694 80 FQILSQEKRVTQRELFYKLLCDSPEYFTSQLQVNRTIQDVIALLHCSRFSLGIVASSRGLVAGRLMLQEPNQEVIDCSAC 159 (355)
Q Consensus 80 ~~~l~~~~~~T~RdiYY~~~~~~~~lF~~Q~~~d~~i~di~~~l~~~R~~L~I~a~~KGlv~G~l~i~~~~~~~id~s~~ 159 (355)
|++|.+|+++|+|||||++++|++++|++|++||++|+|||++++++|++|||+|++||+|+|++++.+.+++.+||+..
T Consensus 109 ~~~l~~~~~~TkRdiYY~~~~~~~~lF~~Q~~vd~~I~Di~~~l~~~R~~L~I~a~~KGlV~G~l~i~~~~~~~idcs~~ 188 (384)
T PLN00060 109 YQILGEGKLVTQRELFYKLLCDSPEYFSCQRHVNQTVQDVVSLLRCSRYSLGIMASSRGALIGRLVLQEPNEEPVDCSIL 188 (384)
T ss_pred HHHHHcCCccchHHhhcccccCChhhcCCHHHHHHHHHHHHHHHCCCHHHCCeEecCCceEEeeeEEEecCCcEEEeecc
Confidence 99999999999999999999899999999999999999999999999999999999999999999999888889999999
Q ss_pred CCCccccCCChhhhhhhccccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEE
Q 037694 160 GSSGYSISGDLSLLEKLDLKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILA 239 (355)
Q Consensus 160 g~~g~~Ip~~~~~i~~~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~ 239 (355)
|.+|+.||++++.++.+.+.++|+|||||||||||+||++++|+++.||||||||||||++||+||++|++++|++|||+
T Consensus 189 g~~G~~Ip~~~~~i~~~~i~s~a~~VLVVEKeavF~rL~e~~~~~~~~cILITgKGyPD~aTR~fL~~L~~~~p~lPv~~ 268 (384)
T PLN00060 189 GISGHAITGDLNLLSNLILSSDARYIIVVEKDAIFQRLAEDRFFNHIPCILITAKGYPDLATRFILHRLSQTFPNLPILA 268 (384)
T ss_pred CCCceeCCCcHHHhhhcccccCccEEEEEecHHHHHHHHHhhhhhhCCEEEEecCCCCCHHHHHHHHHHHHhcCCCCEEE
Confidence 99999999999888776678999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCChhhHHHHHHhhcCCcccccccccccccceeecccccccccCCCCccCCCCHHHHHHHHHhhhhhhhhHHHHHHHH
Q 037694 240 LVDWNPAGLAILCTFKFGSIGMGMEAYRYACNVKWLGLRGDDVQLIPEQSLLPLKPRDLQIARSLMSSEILQENYKEELS 319 (355)
Q Consensus 240 l~D~DP~Gi~I~~~yk~GS~~~~~~~~~~~~~~~wlGv~~~di~~l~~~~~~pLt~~D~~~l~~ll~~~~~~~~w~~el~ 319 (355)
|||+||||++||++|||||++|+|+++.++|+++|+|++|+|+..+|.++++|||++|++++++||++|++++.|++||+
T Consensus 269 LvD~DP~Gi~I~~tYkyGS~~~a~es~~la~~i~WLGl~~sDi~~l~~~~~i~Lt~rD~~~~~~lL~~~~~~~~w~~EL~ 348 (384)
T PLN00060 269 LVDWNPAGLAILCTYKFGSIGMGLEAYRYACNVKWLGLRGDDLQLIPPEAFVELKPRDLQIAKSLLSSKFLQNRYREELT 348 (384)
T ss_pred EECCCcchHHHHHHhhcCchhhhhcccccccCCeEecCCHHHHhcCCHhhcCCCCHHHHHHHHHHhhChhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999889999999
Q ss_pred HHHHcCCeEeeeehhhcCCchHHHHHHHHHhcCCCC
Q 037694 320 LMVHNGQRAEVEALYFHGYDYLGKYIAKKIVQADYI 355 (355)
Q Consensus 320 ~ml~~~~KaEiEal~~~g~~fl~~Yl~~Ki~~~~~i 355 (355)
+|++.|+|||||||+++|++|+++|||+||.++|||
T Consensus 349 ~Ml~~~~KaEiEAL~~~g~~fl~~Ylp~Ki~~~~~i 384 (384)
T PLN00060 349 LMVQTGKRAEIEALYSHGYDYLGKYVARKIVQGDYI 384 (384)
T ss_pred HHHHhCcchhhHhHHhcChHHHHHHHHHHHhcCCcC
Confidence 999999999999999999999999999999999997
No 2
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=100.00 E-value=5.2e-95 Score=714.94 Aligned_cols=344 Identities=27% Similarity=0.437 Sum_probs=324.9
Q ss_pred ChhHHHHHHHHHHHHHcCCC-CCCccccccccCCCCceeccccccccceeeecCceeEEeecCchhHHHHHHHHHHHHHH
Q 037694 1 VRARIEVSVINFLKILNSPD-PAISDLPLINRKSSNSRVSQGLLTDVSWIFLSHSFCTRSLTKSNAAKAFVRVWKVMETC 79 (355)
Q Consensus 1 ~~~~Ie~~v~~~l~~L~~~~-p~~~~l~~~~R~~~n~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~f~~~~~vl~~i 79 (355)
|+++||++..++++++.+|+ |. +++|+|+++|+.||+. .+.+.+|++.+.|++.++++|++|+++++||+++
T Consensus 14 ~~~~i~~l~~~~~~~~~~g~~p~---~~ip~r~~~n~~~d~~----~~~~~~~~~~~~r~~~~~~~a~~f~~~~~vl~~i 86 (367)
T PRK04342 14 ALKKLRELAEKIYEDIEKGKRPV---LEIPKRTLSNIEYDEK----KGLLVLGDKKSKRSFLNVKQAKKFMQTVLMAEFI 86 (367)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCE---EecccccccceEEccc----cCeEeeCCCceEEecCCHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999 76 8889999999999973 4567799999999999999999999999999999
Q ss_pred HHHHhcCCCccccceeccccCC----CccccCchHHHHHHHHHHHHhhccCccccCceecCCeeEEEeeEEecCCCceEe
Q 037694 80 FQILSQEKRVTQRELFYKLLCD----SPEYFTSQLQVNRTIQDVIALLHCSRFSLGIVASSRGLVAGRLMLQEPNQEVID 155 (355)
Q Consensus 80 ~~~l~~~~~~T~RdiYY~~~~~----~~~lF~~Q~~~d~~i~di~~~l~~~R~~L~I~a~~KGlv~G~l~i~~~~~~~id 155 (355)
|++|.+|+++|+|||||++++| ++++|++|++||++|+|||+++|++|++|||+|++||+|+|++++.+ +++.+|
T Consensus 87 ~~~l~~~~~~T~RdiYY~~~~~~~~~~~~~F~~Q~~~d~~I~dl~~~l~~~R~~L~I~a~~KGlv~G~i~i~~-~~~~id 165 (367)
T PRK04342 87 KELLEENKSSTLRELYYMSKHWIPGLKENTFDDQDESDAVIEDLEVALGVLREELHIRPEEDGSVVGPLRIRD-GTDEID 165 (367)
T ss_pred HHHHHcCCccchhhhcccCcccccccccccCCCHHHHHHHHHHHHHHHCCCHHHCCeeECCCeEEEeceEEEE-CCcEEE
Confidence 9999999999999999998776 78899999999999999999999999999999999999999999998 567999
Q ss_pred cccCCCCccccCCChhhhhhhccccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCC
Q 037694 156 CSACGSSGYSISGDLSLLEKLDLKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDL 235 (355)
Q Consensus 156 ~s~~g~~g~~Ip~~~~~i~~~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~l 235 (355)
|+.+|.+|++||++++.++. +.++|+|||||||+|+|++|++++|+++.||||||||||||++||+||++|++++ ++
T Consensus 166 ~~~~g~~~~~ip~~~~~i~~--i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlItgkG~Pd~~TR~fl~~L~~~~-~l 242 (367)
T PRK04342 166 CSKLGEGGYSIPPNVDNIEF--VDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKGQPARATRRFIKRLNEEL-GL 242 (367)
T ss_pred EeccCCCceeCCCchhhhee--eccCCCEEEEEechHHHHHHHHhCcccccCEEEEECCCCCCHHHHHHHHHHHHhc-CC
Confidence 99999999999999887765 4799999999999999999999999999999999999999999999999999987 89
Q ss_pred CEEEEecCChhhHHHHHHhhcCCccccccccccccc-ceeecccccccccC-CCCccCCCCHHHHHHHHHhhhhhhhhH-
Q 037694 236 PILALVDWNPAGLAILCTFKFGSIGMGMEAYRYACN-VKWLGLRGDDVQLI-PEQSLLPLKPRDLQIARSLMSSEILQE- 312 (355)
Q Consensus 236 pv~~l~D~DP~Gi~I~~~yk~GS~~~~~~~~~~~~~-~~wlGv~~~di~~l-~~~~~~pLt~~D~~~l~~ll~~~~~~~- 312 (355)
|||+|||+||||++||++|||||++++|+++.+++| ++|+|++++|+... |..+++|||++|++++++||++|+++.
T Consensus 243 pv~~l~D~DP~G~~I~~tyk~GS~~~a~~s~~l~~P~~kwlGl~~sDi~~~~~~~~~~~Lt~~D~~~l~~lL~~~~~~~~ 322 (367)
T PRK04342 243 PVYVFTDGDPWGYYIYSVVKYGSIKLAHLSERLATPDAKFIGVTPSDIVEYERDLPTIKLKDSDIKRAKELLNYPWFQTD 322 (367)
T ss_pred CEEEEECCCccHHHHHHHHHhCchhhhhhhhhccCCCCEEecCcHHHHHhhccccccCCCCHHHHHHHHHHhcCccccCH
Confidence 999999999999999999999999999999988776 99999999998764 778899999999999999999999854
Q ss_pred HHHHHHHHHHHcCCeEeeeehhhcCCchHH-HHHHHHHhcCCCC
Q 037694 313 NYKEELSLMVHNGQRAEVEALYFHGYDYLG-KYIAKKIVQADYI 355 (355)
Q Consensus 313 ~w~~el~~ml~~~~KaEiEal~~~g~~fl~-~Yl~~Ki~~~~~i 355 (355)
+|++||++|++.|+|||||||+++|++|++ +|||+||.+++||
T Consensus 323 ~w~~El~~ml~~~~KaEiEal~~~~~~~~~~~Ylp~Ki~~~~~i 366 (367)
T PRK04342 323 FWQKEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL 366 (367)
T ss_pred HHHHHHHHHHHhCCceeeehhhhcChhhhHHHHHHHHHhcCCCC
Confidence 899999999999999999999999999999 7999999999997
No 3
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.4e-93 Score=677.06 Aligned_cols=343 Identities=31% Similarity=0.478 Sum_probs=321.5
Q ss_pred ChhHHHHHHHHHHHHHcCCC-CCCccccccccCCCCceeccccccccceeeecCceeEEeecCchhHHHHHHHHHHHHHH
Q 037694 1 VRARIEVSVINFLKILNSPD-PAISDLPLINRKSSNSRVSQGLLTDVSWIFLSHSFCTRSLTKSNAAKAFVRVWKVMETC 79 (355)
Q Consensus 1 ~~~~Ie~~v~~~l~~L~~~~-p~~~~l~~~~R~~~n~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~f~~~~~vl~~i 79 (355)
|+++|+.....++++|.+|+ |. +.+|+|+.||+.||+ +...+.+|++.+.|+|.++++|++|+++++++.++
T Consensus 10 a~~~l~~~~~~~~~~l~~~~~p~---~~vp~r~~sn~~~d~----~~~~~~lg~r~~~r~~~~v~~a~k~~q~l~~~~~i 82 (356)
T COG1697 10 ALSKLEHFAHKIYEQLEKGQIPI---VEVPTRTKSNIIYDE----ESDHIVLGDRKSERSFLTVKGARKLAQTLLMLDFI 82 (356)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCc---eecccccccccccCc----cccceeccccccchhhhhHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999 55 677899999999997 44577899999999999999999999999999999
Q ss_pred HHHHhcCCCccccceeccccCCCccccCchHHHHHHHHHHHHhhccCccccCceecCCeeEEEeeEEecCCCceEecccC
Q 037694 80 FQILSQEKRVTQRELFYKLLCDSPEYFTSQLQVNRTIQDVIALLHCSRFSLGIVASSRGLVAGRLMLQEPNQEVIDCSAC 159 (355)
Q Consensus 80 ~~~l~~~~~~T~RdiYY~~~~~~~~lF~~Q~~~d~~i~di~~~l~~~R~~L~I~a~~KGlv~G~l~i~~~~~~~id~s~~ 159 (355)
++++..|+++|+|||||.+++|++-.|++|++||++|+||+..+|++|++|||.|++||.|+||+.|++.|+.+|||++.
T Consensus 83 ~e~l~~~~~~TlReiYY~~~~~~~~k~~~Q~esd~lieDie~~~gl~Re~l~i~p~ekG~V~G~l~I~~~g~~~i~~sk~ 162 (356)
T COG1697 83 KELLELGKTSTLREIYYISKHVEVFKFDDQSESDRLIEDIEVTLGLSREDLGIRPEEKGLVYGPLRIREEGEDEIDASKL 162 (356)
T ss_pred HHHHhcCCCccHHHHhhhccCcccccccchhHHHHHHHHHHHHhccCHHHcCCCcccCceEEcceEEEecCCcEEEeeec
Confidence 99999999999999999999877666669999999999999999999999999999999999999999877889999999
Q ss_pred CCCccccCCChhhhhhhccccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEE
Q 037694 160 GSSGYSISGDLSLLEKLDLKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILA 239 (355)
Q Consensus 160 g~~g~~Ip~~~~~i~~~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~ 239 (355)
|.+|++||++++.|+. ++++|+|||||||+|||+||++++||++++|||||||||||++||+||+||++++ ++|||+
T Consensus 163 G~~~y~Ip~~~d~I~f--~~~da~~VlvVEk~avf~rLv~e~~~~k~nailVt~KGqP~raTRrflkrL~eel-~lpv~v 239 (356)
T COG1697 163 GGGGYLIPPDVDVIEF--VDTDAKFVLVVEKDAVFQRLVEEGFWEKENAILVTLKGQPDRATRRFLKRLNEEL-DLPVYV 239 (356)
T ss_pred CCCCCcCCCChhheee--ccccceEEEEEechHHHHHHHHhhhhhhcCeEEEecCCCccHHHHHHHHHHHHHh-CCCEEE
Confidence 9999999999988765 5799999999999999999999999999999999999999999999999999999 999999
Q ss_pred EecCChhhHHHHHHhhcCCccccccccccccc-ceeecccccccccCCCCccCCCCHHHHHHHHHhhhhhhhhH-HHHHH
Q 037694 240 LVDWNPAGLAILCTFKFGSIGMGMEAYRYACN-VKWLGLRGDDVQLIPEQSLLPLKPRDLQIARSLMSSEILQE-NYKEE 317 (355)
Q Consensus 240 l~D~DP~Gi~I~~~yk~GS~~~~~~~~~~~~~-~~wlGv~~~di~~l~~~~~~pLt~~D~~~l~~ll~~~~~~~-~w~~e 317 (355)
|+|+||||++||++|+|||++.||+++.+++| ++++|++|+||..-+.....||+++|++++++++++|+++. .|++|
T Consensus 240 ftDgDPyG~~Iy~~~k~GS~k~ah~se~latp~akflGv~~~DI~~ynl~~t~~l~~~Dik~lk~ll~~~~f~~~~W~~e 319 (356)
T COG1697 240 FTDGDPYGWYIYSVYKYGSIKLAHESERLATPDAKFLGVTMQDIVEYNLPQTDKLKDRDIKRLKELLRDPRFQKEFWKEE 319 (356)
T ss_pred EecCCCCEEEEEEEEEecchhhhhcchhhcCCcceeeeccHHHHhhccccccccchhhhHHHHHHHhccccccchhHHHH
Confidence 99999999999999999999999999988776 99999999999864332568899999999999999999954 89999
Q ss_pred HHHHHHcCCeEeeeehhhcCCchHH-HHHHHHHhcCC
Q 037694 318 LSLMVHNGQRAEVEALYFHGYDYLG-KYIAKKIVQAD 353 (355)
Q Consensus 318 l~~ml~~~~KaEiEal~~~g~~fl~-~Yl~~Ki~~~~ 353 (355)
|+.||+.++|||||||+++|++|++ .|||+||.+++
T Consensus 320 l~~~l~i~kK~E~qAla~kgl~~v~~~ylpeki~e~~ 356 (356)
T COG1697 320 LKLLLKIGKKAEQQALASKGLEFVAKTYLPEKIEELK 356 (356)
T ss_pred HHHHHHHhHHHHHHHHHhcChHHhHHhhhHHHHhccC
Confidence 9999999999999999999999999 69999998764
No 4
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=100.00 E-value=4.6e-91 Score=668.68 Aligned_cols=342 Identities=43% Similarity=0.689 Sum_probs=313.4
Q ss_pred ChhHHHHHHHHHHHHHcCCCCCCccccccccCCCCceeccccccccceeeecCceeEEeecCchhHHHHHHHHHHHHHHH
Q 037694 1 VRARIEVSVINFLKILNSPDPAISDLPLINRKSSNSRVSQGLLTDVSWIFLSHSFCTRSLTKSNAAKAFVRVWKVMETCF 80 (355)
Q Consensus 1 ~~~~Ie~~v~~~l~~L~~~~p~~~~l~~~~R~~~n~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~f~~~~~vl~~i~ 80 (355)
|+++||..|++++.+|+++++. ++..++|..+|..++.++... ...++ .+.|...+.+.+++|++++++|+.||
T Consensus 24 ~la~I~~~v~~~~~~l~r~~~~--sls~~~r~~~n~~~~~~l~~~---~~~~~-~~~~~~~~~~~~~~~~~llrvL~~V~ 97 (372)
T KOG2795|consen 24 VLARIEDFVLSVLVQLARPEGF--SLSVINRKRSNSLSSPDLDTL---VSKSH-NTLRFTFSSKKAKKFAILLRVLEIVH 97 (372)
T ss_pred HHHHHHHHHHHHHHHhhcccCC--cccchhhhhcCCccCcchhhh---hcccc-cccceeeccccchHHHHHHHHHHHHH
Confidence 5899999999999999999833 477889998888877654422 11222 33444444555899999999999999
Q ss_pred HHHhcCCCccccceeccccCCCccccCchHHHHHHHHHHHHhhccCccccCceecCCeeEEEeeEEecCCCceEecccCC
Q 037694 81 QILSQEKRVTQRELFYKLLCDSPEYFTSQLQVNRTIQDVIALLHCSRFSLGIVASSRGLVAGRLMLQEPNQEVIDCSACG 160 (355)
Q Consensus 81 ~~l~~~~~~T~RdiYY~~~~~~~~lF~~Q~~~d~~i~di~~~l~~~R~~L~I~a~~KGlv~G~l~i~~~~~~~id~s~~g 160 (355)
+++..|+++|+|||||+ |+++|++|..||++++|||++|+|+|.+|||.|++||+|+|++.|.+.+|..+||+.+|
T Consensus 98 ell~~~~~~TkRdiyY~----dv~lF~~Qs~Vd~~l~dI~~~l~~SR~sLnI~a~~KGLV~G~l~~~~~ng~~id~~~~~ 173 (372)
T KOG2795|consen 98 ELLELGKRVTKRDIYYM----DVDLFRRQSVVDRLLDDICCLLKCSRYSLNILAASKGLVAGRLRFLEENGDVIDCTESG 173 (372)
T ss_pred HHHHcCCceeeeeeeec----CHHHHhhHHHHHHHHHHHHHHhcCChhcCCeeeecCceEEeeEEEEEcCCcEEEeccCC
Confidence 99999999999999998 89999999999999999999999999999999999999999999999899999999999
Q ss_pred CCccccCCChhhhhhhccccCccEEEEEehhhHHHHHHhccccCCC-CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEE
Q 037694 161 SSGYSISGDLSLLEKLDLKTDARYIIVVEKHAIFQRLTEDFVFNQI-PSILITAKGYPDIATRFLLHRLNRAFPDLPILA 239 (355)
Q Consensus 161 ~~g~~Ip~~~~~i~~~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~-~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~ 239 (355)
.+|.+||++++.+++ +.++|+||||||||||||||+++.|+++. |||+||||||||.+||.||++|.+++ ++||++
T Consensus 174 ~~~~~lp~d~~~i~~--i~tdA~~IlIVEKeavFqrL~~d~~~~~~~~~ilITgKGyPD~~TR~fLkkL~~~~-~lpv~~ 250 (372)
T KOG2795|consen 174 GGPKALPPDIDDISN--ITTDAKFILIVEKEAVFQRLAEDNFFNTFNRCILITGKGYPDIATRLFLKKLEEKL-KLPVYG 250 (372)
T ss_pred CCCccCCCCHHHHhh--hhccceEEEEEehHHHHHHHHHHHHHhhcCCeEEEecCCCCcHHHHHHHHHHHHHh-CCCEEE
Confidence 999999999999887 67999999999999999999999999998 79999999999999999999999999 999999
Q ss_pred EecCChhhHHHHHHhhcCCccccccccccc-ccceeeccccccccc--CCCCccCCCCHHHHHHHHHhhhhhhhhH--HH
Q 037694 240 LVDWNPAGLAILCTFKFGSIGMGMEAYRYA-CNVKWLGLRGDDVQL--IPEQSLLPLKPRDLQIARSLMSSEILQE--NY 314 (355)
Q Consensus 240 l~D~DP~Gi~I~~~yk~GS~~~~~~~~~~~-~~~~wlGv~~~di~~--l~~~~~~pLt~~D~~~l~~ll~~~~~~~--~w 314 (355)
|||+||||++||++|||||++|+||++.++ |+++|+|++|+|+.. .|+++++||+++|.+++++||.+++++. .|
T Consensus 251 LvDaDP~Gi~I~~~Yk~GS~~ms~e~~~~~~p~I~wiGl~psD~~~~n~~k~~~lpL~~~D~k~i~~lL~~~~l~~~p~~ 330 (372)
T KOG2795|consen 251 LVDADPYGIEILLTYKYGSKSMSYESHGLTVPTIRWIGLLPSDLEVKNIPKDQLLPLNKRDIKKIKDLLARLILQKEPVV 330 (372)
T ss_pred EeecCCcceEEEEEeeeCccccccccccccCCcceEEeechhhhhhcCCchheeecccHHHHHHHHHHHhhhhcccChhH
Confidence 999999999999999999999999999887 669999999999986 5667999999999999999999999976 49
Q ss_pred HHHHHHHHHcCCeEeeeehhhcCCchHH-HHHHHHHhcCCCC
Q 037694 315 KEELSLMVHNGQRAEVEALYFHGYDYLG-KYIAKKIVQADYI 355 (355)
Q Consensus 315 ~~el~~ml~~~~KaEiEal~~~g~~fl~-~Yl~~Ki~~~~~i 355 (355)
++|+++|++.++||||||+..+|.+|++ .|+|.|+++++|+
T Consensus 331 r~el~~ml~~~~KaEieal~~~~~~~~~~~yia~k~~~~~~~ 372 (372)
T KOG2795|consen 331 REELERMLKNKVKAEIEALSFFGSDYLSRVYIARKLERISSL 372 (372)
T ss_pred HHHHHHHHhcchhhhhhhhhhcchHHHhhhhhhHHHhhcccC
Confidence 9999999999999999999999999999 6999999999986
No 5
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=100.00 E-value=8.7e-45 Score=320.70 Aligned_cols=157 Identities=45% Similarity=0.765 Sum_probs=146.5
Q ss_pred cEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcCCcccc
Q 037694 183 RYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFGSIGMG 262 (355)
Q Consensus 183 ~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~GS~~~~ 262 (355)
++|+||||+|+|++|++++++...+||+||||||||++||+||++|++++ ++|+|+|+|+||||++|+++|++||.+++
T Consensus 1 ~~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG~P~~~tr~~l~~L~~~~-~~~~~~l~D~DP~Gi~I~~~y~~gs~~~~ 79 (160)
T cd00223 1 DFVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRATRRFLRRLHEEL-DLPVYILVDGDPYGISILLTYKYGSIKLA 79 (160)
T ss_pred CEEEEEecHHHHHHHHHcCccccCCEEEEEcCCcCCHHHHHHHHHHHHhh-CCCEEEEECCCcchhhhhHHHHhCccccc
Confidence 58999999999999999999988899999999999999999999999988 89999999999999999999999999999
Q ss_pred cccccccc-cceeecccccccccCCCCccCCCCHHHHHHHHHhhhhhhh--hHHHHHHHHHHHHcCCeEeeeehhhcCCc
Q 037694 263 MEAYRYAC-NVKWLGLRGDDVQLIPEQSLLPLKPRDLQIARSLMSSEIL--QENYKEELSLMVHNGQRAEVEALYFHGYD 339 (355)
Q Consensus 263 ~~~~~~~~-~~~wlGv~~~di~~l~~~~~~pLt~~D~~~l~~ll~~~~~--~~~w~~el~~ml~~~~KaEiEal~~~g~~ 339 (355)
++...+++ .++|+|++|+|+..++....+|||++|++++++|++++.. ...|++|+++|++.|+|+||||+...|.+
T Consensus 80 ~~~~~~~~~~l~~~G~~~~d~~~~~~~~~~~Ls~~d~~~l~~ll~~~~~~~~~~~~~el~~ml~~~~K~E~Eal~~~~~~ 159 (160)
T cd00223 80 YESESLATPDLRWLGLRPSDIIRLPDLPLLPLSERDLKRAKSLLRRPRFKELPEWKRELQLMLKLGKKAEIEALASCGLE 159 (160)
T ss_pred cccccccCCCcEEccCCHHHHhhccccccCCCCHHHHHHHHHHHhccccccCHHHHHHHHHHHHhCCeeeehhHhhcCCC
Confidence 99877654 5999999999998777788899999999999999999875 34899999999999999999999998876
Q ss_pred h
Q 037694 340 Y 340 (355)
Q Consensus 340 f 340 (355)
|
T Consensus 160 ~ 160 (160)
T cd00223 160 F 160 (160)
T ss_pred C
Confidence 4
No 6
>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]. These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.
Probab=99.84 E-value=2.9e-21 Score=147.31 Aligned_cols=68 Identities=32% Similarity=0.594 Sum_probs=61.2
Q ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCCccccceeccccCCCccccCchHHHHHHHHHHHHhhccCccccCce
Q 037694 62 KSNAAKAFVRVWKVMETCFQILSQEKRVTQRELFYKLLCDSPEYFTSQLQVNRTIQDVIALLHCSRFSLGIV 133 (355)
Q Consensus 62 ~~~~~~~f~~~~~vl~~i~~~l~~~~~~T~RdiYY~~~~~~~~lF~~Q~~~d~~i~di~~~l~~~R~~L~I~ 133 (355)
|++++++|+++++||+.+|++|.+|+++|+|||||+ ++++|++|++||++|+|||.+|+++|++|||+
T Consensus 1 n~~~~~k~a~~l~vl~~i~~~l~~~~~~T~RdiYY~----~~~lF~~Q~~vd~~i~di~~~l~~~R~~L~Iv 68 (68)
T PF04406_consen 1 NVKSARKFAQLLRVLAIIHELLQNNKTSTKRDIYYR----NVSLFKSQREVDRAIDDICCLLGVSREDLNIV 68 (68)
T ss_dssp -TCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHH----CSCS-SSHHHHHHHHHHHHHHHTS-GGGGTEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCccchHHHHHh----chhhccCHHHHHHHHHHHHHHHCCCHHHcCCC
Confidence 468999999999999999999999999999999999 78999999999999999999999999999985
No 7
>PF09983 DUF2220: Uncharacterized protein conserved in bacteria C-term(DUF2220); InterPro: IPR024534 This is a domain of unknown function that is found predominantly in hypothetical bacterial proteins.
Probab=99.50 E-value=8.6e-14 Score=125.53 Aligned_cols=135 Identities=21% Similarity=0.259 Sum_probs=93.9
Q ss_pred cccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcC
Q 037694 178 LKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFG 257 (355)
Q Consensus 178 i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~G 257 (355)
+..+++.|||||+.++|.++.+.. +.++|+|.||+...+++|++.+. ..|+|+|+|.||+|+.|+...+.=
T Consensus 39 ~~~~~~~vliVEN~~tf~~~~~~~-----~~~~Iyg~G~~~~~~~~~~~~~~----~~~~~ywGDiD~~G~~I~~~lr~~ 109 (181)
T PF09983_consen 39 LSLPPRRVLIVENLTTFYSLPELP-----NGLVIYGGGFAISSSRRFLKWLQ----PKPVYYWGDIDPGGLRILERLRRK 109 (181)
T ss_pred ccCCCCEEEEEeCHHHHHHHHhcC-----CeEEEECCCcCcHHHHHHHhhcC----CCceEEeccCCHhHHHHHHHHHHh
Confidence 467899999999999999998432 68999999999999999977443 349999999999999999988741
Q ss_pred CcccccccccccccceeecccccccccCCCCccCCCCHHHHHHHHHhhhhhhhhHHHHHHHHHHHHcCCeEeeeehh
Q 037694 258 SIGMGMEAYRYACNVKWLGLRGDDVQLIPEQSLLPLKPRDLQIARSLMSSEILQENYKEELSLMVHNGQRAEVEALY 334 (355)
Q Consensus 258 S~~~~~~~~~~~~~~~wlGv~~~di~~l~~~~~~pLt~~D~~~l~~ll~~~~~~~~w~~el~~ml~~~~KaEiEal~ 334 (355)
+ ++++=.-+.+..+.........+.+....+++.. |+.+.. ..|+.-++.|+..+++.|||+|.
T Consensus 110 -----~------p~~~p~~Md~~~l~~~~~~~~~~~~~~~~~~l~~-L~~~e~-~~~~~l~~~~l~~~~riEQE~I~ 173 (181)
T PF09983_consen 110 -----F------PELKPLLMDEETLERYQDRYGKEPSEPYRRKLPR-LTDEEY-ALFRELIEEMLEEGKRIEQERIP 173 (181)
T ss_pred -----C------CCccccccCHHHHHHHHHhcCCCCCccccccchh-cCHHHH-HHHHHHHHHHHhcCCeeeecccc
Confidence 0 1111111111222211111112234555555655 554332 36888899999999999999985
No 8
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=99.36 E-value=1.2e-12 Score=114.83 Aligned_cols=129 Identities=26% Similarity=0.352 Sum_probs=93.0
Q ss_pred ccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh--c
Q 037694 179 KTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK--F 256 (355)
Q Consensus 179 ~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk--~ 256 (355)
......|.||||-+||.++++. ....++.||++.|+|+.+++.||.+|... +.++++.+|+||.|+.|+..++ |
T Consensus 15 ~~~~~~V~VvENp~Vf~~~~~~--~~~~~~pLVCt~G~p~~A~~~LL~~L~~~--g~~l~y~GDfDp~Gl~IA~~l~~r~ 90 (152)
T PF09664_consen 15 WPPSGRVYVVENPAVFSALADE--LGASCPPLVCTSGQPSAAARRLLDRLAAA--GARLYYSGDFDPEGLRIANRLIQRY 90 (152)
T ss_pred cCCCCEEEEEecHHHHHHHHHh--cCCCCCeEEEcCCcHHHHHHHHHHHHHhC--CCEEEEecCCCHHHHHHHHHHHHHh
Confidence 3445569999999999999988 22245789999999999999999999764 7999999999999999999886 3
Q ss_pred CCcccccccccccccceeeccccccccc-CCCCccCCCCHHHHHHHHHhhhhhhhhHHHHHHHHHHHHcCCeEeeeehhh
Q 037694 257 GSIGMGMEAYRYACNVKWLGLRGDDVQL-IPEQSLLPLKPRDLQIARSLMSSEILQENYKEELSLMVHNGQRAEVEALYF 335 (355)
Q Consensus 257 GS~~~~~~~~~~~~~~~wlGv~~~di~~-l~~~~~~pLt~~D~~~l~~ll~~~~~~~~w~~el~~ml~~~~KaEiEal~~ 335 (355)
|..- --+.+.|... ++. .+++.+..+ +.++ .|+. .+....|.+.|++++||++..
T Consensus 91 ~~~~--------------Wrm~~~dY~~~~~~---~~~~~~~l~-l~~v--~p~~----~~L~~~m~~~~~a~~QE~l~~ 146 (152)
T PF09664_consen 91 GARP--------------WRMDAEDYLAALSA---EPLSGRRLK-LPNV--APWL----PELAEAMRERGRAVYQEALLD 146 (152)
T ss_pred CCcc--------------ccCCHHHHHHhccc---cCCCCCcCC-cccC--Chhc----HHHHHHHHHhCceeeHHHHHH
Confidence 3211 1222233322 221 345555555 4444 4443 345578999999999999864
No 9
>TIGR02679 conserved hypothetical protein TIGR02679. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).
Probab=98.39 E-value=7.3e-07 Score=89.28 Aligned_cols=67 Identities=24% Similarity=0.220 Sum_probs=57.8
Q ss_pred EEEEEehhhHHHHHHhccccCCCCE-EEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 184 YIIVVEKHAIFQRLTEDFVFNQIPS-ILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 184 ~VLvVEK~avF~rL~~~~~~~~~~~-IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
.|.||||-++|+.+++..-. .| .+|++.|||..+++.||++|....+.+ .|+ +|.||.|+.|+...+
T Consensus 252 ~V~vvENp~vf~~~~~~~~~---~~~~lIct~G~p~~a~~~LL~~L~~~g~~l-~Yh-GDfD~~Gi~Ia~~L~ 319 (385)
T TIGR02679 252 RVYVVENPNVLAIALDRLGP---RCAPLVCTDGQPNAAQIKLLDLLAAAGARL-YYH-GDFDWPGLRIANGLI 319 (385)
T ss_pred eEEEEecHHHHHHHHHhcCC---CCceEEECCCcchHHHHHHHHHHHhcCCeE-EEe-cCCChhHHHHHHHHH
Confidence 59999999999999985311 23 799999999999999999999986554 566 999999999999887
No 10
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=96.71 E-value=0.0091 Score=44.50 Aligned_cols=63 Identities=24% Similarity=0.211 Sum_probs=51.9
Q ss_pred cEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHH
Q 037694 183 RYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAI 250 (355)
Q Consensus 183 ~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I 250 (355)
+.|++||..+....+.+.+.. +..++...|.+...+...+.++... ..||+.++|.|+.|..+
T Consensus 1 ~~viivEg~~d~~~l~~~~~~---~~~~~~~~G~~~~~~~~~~~~~~~~--~~~v~i~~D~D~~g~~~ 63 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGY---GGAVVALGGHALNKTRELLKRLLGE--AKEVIIATDADREGEAI 63 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCC---CEEEEEEccEEcHHHHHHHHHHhcC--CCEEEEEcCCChhHHHH
Confidence 358899999999999887644 4778889999888788888888653 48999999999999843
No 11
>COG4924 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.85 E-value=0.73 Score=44.81 Aligned_cols=68 Identities=24% Similarity=0.293 Sum_probs=48.0
Q ss_pred cccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 178 LKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 178 i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
+.-....|++||++-.|..|-+ -...|+|-|.||--. .+++-= .+.+-.+..++|.|-||+-|+.-.+
T Consensus 237 l~lP~srilivENe~sfl~lP~-----~pg~i~i~GaGy~~~---~lvr~~--~l~~~~l~YWGDmDt~Gf~iL~r~R 304 (386)
T COG4924 237 LQLPQSRILIVENEDSFLALPT-----WPGVIIIWGAGYRAV---DLVRGP--YLSNGRLLYWGDMDTDGFKILDRVR 304 (386)
T ss_pred ccCCceeEEEEechhhhhhcCC-----CCCeEEEecCCccHH---Hhhccc--ccccceeeeeccccchHHHHHHHhh
Confidence 3445568999999999998732 124799999999521 222211 1235678999999999999997665
No 12
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=89.57 E-value=1.8 Score=38.98 Aligned_cols=65 Identities=22% Similarity=0.218 Sum_probs=50.7
Q ss_pred cEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCC-ChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 183 RYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYP-DIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 183 ~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyP-d~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
+-|+|||=-.==.+|-+- .+|-.|++.|+. +..|-..++.+++. -.|++|+|.|.-|-.|-....
T Consensus 3 kevIVVEGK~D~~~lk~~-----~d~~~I~T~Gs~i~~~~i~~i~~~~~~---rgVIIfTDpD~~GekIRk~i~ 68 (174)
T TIGR00334 3 KEIIVVEGKDDQARIKQA-----FDVDVIETNGSALKDETINLIKKAQKK---QGVIILTDPDFPGEKIRKKIE 68 (174)
T ss_pred CeEEEEecchHHHHHHHh-----cCceEEEECCCccCHHHHHHHHHHhhc---CCEEEEeCCCCchHHHHHHHH
Confidence 568999855444555322 358888999998 88899999988874 479999999999999987765
No 13
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=86.82 E-value=4.8 Score=30.07 Aligned_cols=65 Identities=20% Similarity=0.180 Sum_probs=43.0
Q ss_pred EEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHH
Q 037694 184 YIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCT 253 (355)
Q Consensus 184 ~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~ 253 (355)
.+++||....-..+.+.++. +...+...|- ..+...+..|.+..+.-.|+.++|.|.-|-.+...
T Consensus 2 ~l~ivEg~~da~~~~~~~~~---~~~~~~~~G~--~~~~~~~~~l~~~~~~~~Iii~~D~D~~G~~~~~~ 66 (76)
T smart00493 2 VLIIVEGPADAIALEKAGGF---GGNVVALGGH--LLKKEIIKLLKRLAKKKEVILATDPDREGEAIAWK 66 (76)
T ss_pred EEEEEcCHHHHHHHHHhcCC---CEEEEEEeee--ecHHHHHHHHHHHhcCCEEEEEcCCChhHHHHHHH
Confidence 47899998888888776642 3333333342 23445666666654334599999999999887643
No 14
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=84.81 E-value=3.7 Score=32.79 Aligned_cols=63 Identities=19% Similarity=0.337 Sum_probs=39.7
Q ss_pred ccEEEEEehhh---HHHHHHhcc--ccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHH
Q 037694 182 ARYIIVVEKHA---IFQRLTEDF--VFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLA 249 (355)
Q Consensus 182 a~~VLvVEK~a---vF~rL~~~~--~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~ 249 (355)
|+.||+||-.+ .++.+.+.- .......-+|-..|- +-..|.+.|.. + ++|+++++|.|..+-.
T Consensus 3 a~~vIlVEG~tE~~~l~~~~~~~~~~~~~~~i~ii~~gG~---~~~~~~~ll~~-~-~i~~~vi~D~D~~~~~ 70 (97)
T cd01026 3 ADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGK---NFKPFIKLLNA-L-GIPVAVLTDLDAKRNE 70 (97)
T ss_pred CCeEEEEecHHHHHHHHHHHHHhCCCHHHCCEEEEEeCCc---chHHHHHHHHH-c-CCCEEEEEeCCCCCCc
Confidence 57899999754 355555431 112224455555553 44555666655 4 7999999999998765
No 15
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=80.55 E-value=12 Score=29.16 Aligned_cols=65 Identities=17% Similarity=0.050 Sum_probs=39.7
Q ss_pred cEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 183 RYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 183 ~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
+.++|||=..=-.+|-+.++. .+.|...|...++ ....++++. .-.|+.|+|+|..|-.|.....
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~--~~~i~t~Gt~~~~-~~~~~l~~~-----~~~VIiltD~D~aG~~i~~~~~ 66 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIE--AEIIETNGSIINK-ETIELIKKA-----YRGVIILTDPDRKGEKIRKKLS 66 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCC--ccEEEECCCcCCH-HHHHHHHHh-----CCEEEEEECCCHHHHHHHHHHH
Confidence 458889876655667666542 1233333333332 344444444 2358999999999999975553
No 16
>PRK04017 hypothetical protein; Provisional
Probab=77.65 E-value=9.2 Score=32.94 Aligned_cols=68 Identities=18% Similarity=0.154 Sum_probs=42.1
Q ss_pred ccCccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 179 KTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 179 ~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
.+....|+|||=-.--.+|-+-|+. .+.|..+|.+..+.. .++... .--|++|+|+|..|-.|....+
T Consensus 19 ~s~~g~vIVVEGk~D~~~L~~lGv~--~~iI~t~g~~~~~~~-----e~ia~~--~r~VIILTD~D~~GekIr~~l~ 86 (132)
T PRK04017 19 FSEAGAPIIVEGKRDVESLRKLGVE--GEIIKVSRTPLAEIA-----ELIASR--GKEVIILTDFDRKGEELAKKLS 86 (132)
T ss_pred hcCCCCEEEEeCccHHHHHHHcCCC--ccEEEECCeecchHH-----HHHHhc--CCeEEEEECCCcchHHHHHHHH
Confidence 3455578999865555666655543 234444444443333 223332 3469999999999999976654
No 17
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=75.51 E-value=17 Score=28.33 Aligned_cols=50 Identities=22% Similarity=0.422 Sum_probs=34.5
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcC
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFG 257 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~G 257 (355)
|-+++..-..|+..--.+++.|....|+.|+.++++-+-.. .....++.|
T Consensus 44 ~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t~~~~~~-~~~~~~~~g 93 (112)
T PF00072_consen 44 PDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVTDEDDSD-EVQEALRAG 93 (112)
T ss_dssp ESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEESSTSHH-HHHHHHHTT
T ss_pred ceEEEEEeeeccccccccccccccccccccEEEecCCCCHH-HHHHHHHCC
Confidence 45777788888888888888888877788888888533322 233334554
No 18
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=66.76 E-value=45 Score=30.50 Aligned_cols=101 Identities=18% Similarity=0.129 Sum_probs=50.0
Q ss_pred CCEEEEEcC--CCCChHHHHHHHHHHhhCCCCCEEEEecC--ChhhHHHHHHhh--c-------CCcccccccccccccc
Q 037694 206 IPSILITAK--GYPDIATRFLLHRLNRAFPDLPILALVDW--NPAGLAILCTFK--F-------GSIGMGMEAYRYACNV 272 (355)
Q Consensus 206 ~~~IlITgk--GyPd~~TR~fL~~L~~~~~~lpv~~l~D~--DP~Gi~I~~~yk--~-------GS~~~~~~~~~~~~~~ 272 (355)
..+|+++.. |-.......+.+.|...-.+.||++.+++ .-.|+.+++.-- + ||+........+..-+
T Consensus 43 i~~Vvl~~~s~gg~~~~~~~l~~~l~~~~~~KpViA~v~g~a~s~gy~lA~~aD~i~a~~~a~~g~iG~~~~~~~~~~ll 122 (214)
T cd07022 43 VRAIVLDIDSPGGEVAGVFELADAIRAARAGKPIVAFVNGLAASAAYWIASAADRIVVTPTAGVGSIGVVASHVDQSKAL 122 (214)
T ss_pred CcEEEEEEeCCCCcHHHHHHHHHHHHHHhcCCCEEEEECCchhhHHHHHHhcCCEEEEcCCCeEEeeeEEEecCCHHHHH
Confidence 345555432 22222334444444432115899999995 556777765322 1 1111111111000002
Q ss_pred eeeccccccccc-----CCCCccCCCCHHHHHHHHHhhhh
Q 037694 273 KWLGLRGDDVQL-----IPEQSLLPLKPRDLQIARSLMSS 307 (355)
Q Consensus 273 ~wlGv~~~di~~-----l~~~~~~pLt~~D~~~l~~ll~~ 307 (355)
.-+|+.+..+.. .+ +.+.++|+.++..+++++..
T Consensus 123 ~k~Gi~~~~~~~g~~K~~~-~~~~~~s~~~re~~~~~l~~ 161 (214)
T cd07022 123 EKAGLKVTLIFAGAHKVDG-NPDEPLSDEARARLQAEVDA 161 (214)
T ss_pred HhCCCeEEEEEcCCCccCC-CCCCCCCHHHHHHHHHHHHH
Confidence 334555544321 22 24468999999999999875
No 19
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=62.85 E-value=16 Score=38.89 Aligned_cols=69 Identities=20% Similarity=0.274 Sum_probs=48.5
Q ss_pred ccEEEEEehhh---HHHHHHhccccCCC-C-EEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 182 ARYIIVVEKHA---IFQRLTEDFVFNQI-P-SILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 182 a~~VLvVEK~a---vF~rL~~~~~~~~~-~-~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
|+.||.||=+| +.+.|++....+-. . ..+|-.. ......|++ +.+.. ++|+++++|+||.|...-.+-+
T Consensus 396 Ar~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~---gs~~k~f~k-f~~~~-gI~~~vitD~D~~g~~~~~~~~ 469 (581)
T COG3593 396 ARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFA---GSGLKPFIK-FAEAM-GIRVHVITDGDEAGKKYEATVR 469 (581)
T ss_pred hceeEEEeccchhhhHHHHHHHhccccccCcEEEEeec---ccCcHHHHH-Hhhcc-CceEEEEecCCcccchhhhhhh
Confidence 78899999877 36667665444322 2 3444322 246678888 77776 6999999999999998776665
No 20
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=61.70 E-value=26 Score=27.91 Aligned_cols=69 Identities=17% Similarity=0.189 Sum_probs=43.7
Q ss_pred EEEEehhhHHHHHHhccccCCCCEEEEEcCCCC------C----hHHHHHHHHHHhhCC-CCCEEEEecCChhhHHHHHH
Q 037694 185 IIVVEKHAIFQRLTEDFVFNQIPSILITAKGYP------D----IATRFLLHRLNRAFP-DLPILALVDWNPAGLAILCT 253 (355)
Q Consensus 185 VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyP------d----~~TR~fL~~L~~~~~-~lpv~~l~D~DP~Gi~I~~~ 253 (355)
++||||.+.-..+.+... .....++.+.|-- + ......++.|.+.++ -=.|+..+|+|.-|=.|+..
T Consensus 2 liIvE~ps~a~~i~~~l~--~~~~~v~~~~Ghl~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~ 79 (100)
T PF01751_consen 2 LIIVEKPSDAKAIAKALG--GEEYIVIATSGHLLELAKPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWE 79 (100)
T ss_dssp EEEESSHHHHHHHHHHSS--TTTEEEEEESSSSEESTTSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHH
T ss_pred EEEEeCHHHHHHHHHHcC--CCCEEEEEeCCcccccccccccccccccccchhhHHHhhhccEeeecCCCChHHHHHHHH
Confidence 689999999888877543 2346677666654 1 122333444443311 24699999999999998865
Q ss_pred hh
Q 037694 254 FK 255 (355)
Q Consensus 254 yk 255 (355)
..
T Consensus 80 i~ 81 (100)
T PF01751_consen 80 II 81 (100)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 21
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=58.26 E-value=8.4 Score=30.39 Aligned_cols=43 Identities=16% Similarity=0.382 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHhhhhhhhhHHHHHHHHHHHHcCCeEeeeehhhcCCchHH
Q 037694 293 LKPRDLQIARSLMSSEILQENYKEELSLMVHNGQRAEVEALYFHGYDYLG 342 (355)
Q Consensus 293 Lt~~D~~~l~~ll~~~~~~~~w~~el~~ml~~~~KaEiEal~~~g~~fl~ 342 (355)
+-..|+.++++||...-.++-|+.++..|.++ .+-.+|.+.++
T Consensus 12 ~~tgdr~~lKeLL~trLvECGW~d~ik~mcrn-------iimEkG~~n~t 54 (92)
T KOG4479|consen 12 LRTGDRAALKELLHTRLVECGWHDDIKEMCRN-------IIMEKGVDNIT 54 (92)
T ss_pred hhcccHHHHHHHHHHHHHHcccHHHHHHHHHH-------HHHHhcccccc
Confidence 34459999999999888888999999999884 46667766544
No 22
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=58.08 E-value=55 Score=28.00 Aligned_cols=67 Identities=19% Similarity=0.134 Sum_probs=40.9
Q ss_pred cEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 183 RYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 183 ~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
+.|+|||=-.==.+|-+-+.. +.|.+.|.|-=...|-..+++.+. .=.|+.|+|+|-.|=.|-....
T Consensus 10 ~~vIVVEGK~D~~~l~~~~~~---~~i~~~g~~i~~~~~ie~i~~~~~---~k~VIILTD~D~~Ge~Irk~l~ 76 (127)
T COG1658 10 KEVIVVEGKDDTASLKRLGDA---GVIITNGSAINSLETIELIKKAQK---YKGVIILTDPDRKGERIRKKLK 76 (127)
T ss_pred CceEEEeCCcHHHHHHHhcCC---ceEEEcCCccchHHHHHHHHHhhc---cCCEEEEeCCCcchHHHHHHHH
Confidence 678999953333333222211 234444444322666666666554 4579999999999998876654
No 23
>PF03475 3-alpha: 3-alpha domain; InterPro: IPR005163 This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C terminus of proteins related to the YiiM protein (P32157 from SWISSPROT) from Escherichia coli.; PDB: 1O67_C 1O65_C.
Probab=54.96 E-value=19 Score=24.95 Aligned_cols=30 Identities=13% Similarity=0.297 Sum_probs=23.3
Q ss_pred HHHHHHHHhhhhhhhhHHHHHHHHHHHHcC
Q 037694 296 RDLQIARSLMSSEILQENYKEELSLMVHNG 325 (355)
Q Consensus 296 ~D~~~l~~ll~~~~~~~~w~~el~~ml~~~ 325 (355)
.|...+..+++-|.+.+.|++.++..+..+
T Consensus 16 ~n~~~l~~ll~~~~La~~Wr~~~~kRL~~~ 45 (47)
T PF03475_consen 16 LNPEALERLLALPALAESWRKSFEKRLEKG 45 (47)
T ss_dssp --HHHHHHHHTSTT--HHHHHHHHHHHHHS
T ss_pred CCHHHHHHHHcCCcccHHHHHHHHHHHHcC
Confidence 467888899999999889999999999865
No 24
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=50.77 E-value=1e+02 Score=23.30 Aligned_cols=66 Identities=14% Similarity=-0.010 Sum_probs=36.7
Q ss_pred EEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 184 YIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 184 ~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
.+++||-+.-=-.|.+.++. +++.+.| |-- .+..-+.+.......-+|+.++|.|.-|...+....
T Consensus 2 ~viIvEG~~D~~~l~~~g~~---~~v~~~g-~~~--~~~~~~~~~~~~~~~~~Vii~~D~D~~G~~~a~~i~ 67 (81)
T PF13662_consen 2 EVIIVEGEFDAIALEQAGYK---NVVAVLG-GNL--SPLDQILREKLEKKVKEVIIAFDNDKAGEKAAQKIA 67 (81)
T ss_dssp -EEEESSHHHHHHHHHTT-T---TEEEESS-SS-----HHHHHHHHHH---SEEEEEEESSHHHHHHHHHHH
T ss_pred EEEEECCHHHHHHHHHhCCC---eEEEECC-CCC--ChHHHhChHhhhccCceEEEEeCcCHHHHHHHHHHH
Confidence 47889987777777666433 3454444 322 233333322221102579999999999987765443
No 25
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=49.20 E-value=1.2e+02 Score=27.56 Aligned_cols=100 Identities=21% Similarity=0.285 Sum_probs=51.1
Q ss_pred CCEEEEEc---CCCCChHHHHHHHHHHhhCCCCCEEEEecCChh--hHHHHHHhh--c-------CCccccccccccccc
Q 037694 206 IPSILITA---KGYPDIATRFLLHRLNRAFPDLPILALVDWNPA--GLAILCTFK--F-------GSIGMGMEAYRYACN 271 (355)
Q Consensus 206 ~~~IlITg---kGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~--Gi~I~~~yk--~-------GS~~~~~~~~~~~~~ 271 (355)
..+|++++ .|.+ .....+...|.+.-.+.||++++++-.. |+.|++.-- + ||+........+..-
T Consensus 31 i~~vvl~~~s~Gg~~-~~~~~l~~~i~~~~~~kpvia~v~g~a~s~g~~la~aaD~i~a~p~a~vg~iGv~~~~~~~~~~ 109 (207)
T TIGR00706 31 IKALLLRINSPGGTV-VASEEIYEKLKKLKAKKPVVASMGGVAASGGYYIAMAADEIVANPGTITGSIGVILQGANVEKL 109 (207)
T ss_pred ccEEEEEecCCCCCH-HHHHHHHHHHHHhcCCCCEEEEECCccchHHHHHHhcCCEEEECCCCeEEeeeEEEecCCHHHH
Confidence 35666665 3333 2345556666543115899999988664 666664321 1 111111111000001
Q ss_pred ceeecccccccc-----cCCCCccCCCCHHHHHHHHHhhhh
Q 037694 272 VKWLGLRGDDVQ-----LIPEQSLLPLKPRDLQIARSLMSS 307 (355)
Q Consensus 272 ~~wlGv~~~di~-----~l~~~~~~pLt~~D~~~l~~ll~~ 307 (355)
+.-+|+.+..+. ..+ +.+.++|+.++..+++++..
T Consensus 110 l~k~Gv~~~~~~~g~~K~~~-~~~~~~s~~~~e~~~~~l~~ 149 (207)
T TIGR00706 110 YEKLGIEFEVIKSGEYKDIG-SPTRELTPEERDILQNLVNE 149 (207)
T ss_pred HHhCCceEEEEEcCCCcCCC-CCCCCCCHHHHHHHHHHHHH
Confidence 222444443322 122 24468999999999998875
No 26
>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).
Probab=46.10 E-value=39 Score=27.65 Aligned_cols=36 Identities=22% Similarity=0.288 Sum_probs=30.4
Q ss_pred EEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChh
Q 037694 208 SILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPA 246 (355)
Q Consensus 208 ~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~ 246 (355)
|+++.|.+- .+..+++.|....|.+||+.++|.+..
T Consensus 46 ~~v~~g~~~---~~~~~l~~l~~~~~~~Pvlllg~~~~~ 81 (109)
T PF06490_consen 46 CAVILGSCS---KLAELLKELLKWAPHIPVLLLGEHDSP 81 (109)
T ss_pred EEEEecCch---hHHHHHHHHHhhCCCCCEEEECCCCcc
Confidence 666666555 888999999999999999999998876
No 27
>PRK11778 putative inner membrane peptidase; Provisional
Probab=46.00 E-value=65 Score=32.02 Aligned_cols=93 Identities=17% Similarity=0.139 Sum_probs=53.1
Q ss_pred EcCCCCChH--HHHHHHHHHhhCCCCCEEEEecCCh--hhHHHHHHhh---------cCCcccccccccccccceeeccc
Q 037694 212 TAKGYPDIA--TRFLLHRLNRAFPDLPILALVDWNP--AGLAILCTFK---------FGSIGMGMEAYRYACNVKWLGLR 278 (355)
Q Consensus 212 TgkGyPd~~--TR~fL~~L~~~~~~lpv~~l~D~DP--~Gi~I~~~yk---------~GS~~~~~~~~~~~~~~~wlGv~ 278 (355)
++.|.++-+ ...-+.++.+. +.||++++|.-. .|+.|+|.=- .||+........+..-+.-+|+.
T Consensus 132 SpGG~v~~s~~a~~~l~~lr~~--~kpVva~v~~~AASggY~iAsaAD~I~A~P~a~vGSIGVi~~~~~~~~lLeKlGI~ 209 (330)
T PRK11778 132 SPGGVVHGYGLAASQLQRLRDA--GIPLTVAVDKVAASGGYMMACVADKIIAAPFAIVGSIGVVAQIPNFHRLLKKHDID 209 (330)
T ss_pred CCCCchhHHHHHHHHHHHHHhc--CCCEEEEECCchhhHHHHHHHhCCEEEECCCCeEEeeeeeeeccCHHHHHHHCCCc
Confidence 366766432 33336667653 689999998554 7888887432 34443322221111113445555
Q ss_pred ccccc-----cCCCCccCCCCHHHHHHHHHhhhh
Q 037694 279 GDDVQ-----LIPEQSLLPLKPRDLQIARSLMSS 307 (355)
Q Consensus 279 ~~di~-----~l~~~~~~pLt~~D~~~l~~ll~~ 307 (355)
..-+. ... +.+.|+|+.++..+++++..
T Consensus 210 ~evi~aG~yK~a~-~pf~~~see~Re~~q~~Ld~ 242 (330)
T PRK11778 210 VELHTAGEYKRTL-TLFGENTEEGREKFREELEE 242 (330)
T ss_pred eEEEEecCccCCC-CCCCCCCHHHHHHHHHHHHH
Confidence 44332 222 35578899999999998874
No 28
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=44.73 E-value=17 Score=30.00 Aligned_cols=58 Identities=16% Similarity=0.312 Sum_probs=37.2
Q ss_pred EEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCC
Q 037694 185 IIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWN 244 (355)
Q Consensus 185 VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~D 244 (355)
|+.+.+-.---+++++. ...-|++|+--+-..-....++..+.....++|||.++|-+
T Consensus 20 vv~~~~~dd~~~~i~~~--~~i~avvi~~d~~~~~~~~~ll~~i~~~~~~iPVFl~~~~~ 77 (115)
T PF03709_consen 20 VVDADSTDDALAIIESF--TDIAAVVISWDGEEEDEAQELLDKIRERNFGIPVFLLAERD 77 (115)
T ss_dssp EEEESSHHHHHHHHHCT--TTEEEEEEECHHHHHHHHHHHHHHHHHHSTT-EEEEEESCC
T ss_pred EEEeCChHHHHHHHHhC--CCeeEEEEEcccccchhHHHHHHHHHHhCCCCCEEEEecCC
Confidence 44444443334444431 12347888754333356789999999998899999999977
No 29
>PF14421 LmjF365940-deam: A distinct subfamily of CDD/CDA-like deaminases
Probab=43.08 E-value=14 Score=33.43 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHH
Q 037694 216 YPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAIL 251 (355)
Q Consensus 216 yPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~ 251 (355)
+|+=+--.+|+|+.+..|+..+|-|.|.+|.+++|.
T Consensus 155 ~PCGaC~ewL~KIAe~np~f~v~mFd~t~c~~vy~~ 190 (193)
T PF14421_consen 155 FPCGACKEWLRKIAEANPDFRVYMFDDTRCRNVYIL 190 (193)
T ss_pred CcchHHHHHHHHHHHhCCCeEEEEecCCCcceEEEe
Confidence 678899999999999999999999999999988663
No 30
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=41.42 E-value=1.3e+02 Score=31.04 Aligned_cols=96 Identities=27% Similarity=0.421 Sum_probs=65.1
Q ss_pred eEEEeeEEecCCCc-eEecccCCCCccccCCChh-hhhhhccccCccEEEEEehhhHHHHHHhccccCC--------C-C
Q 037694 139 LVAGRLMLQEPNQE-VIDCSACGSSGYSISGDLS-LLEKLDLKTDARYIIVVEKHAIFQRLTEDFVFNQ--------I-P 207 (355)
Q Consensus 139 lv~G~l~i~~~~~~-~id~s~~g~~g~~Ip~~~~-~i~~~~i~~~a~~VLvVEK~avF~rL~~~~~~~~--------~-~ 207 (355)
+|.|.+++.++.|+ .+-|..+.+.|.+ .+. .++ ..=.+|..+|.++. + +
T Consensus 77 ~v~G~is~Y~~rG~YQi~~~~~~p~G~G---~L~~~~E-----------------~lK~kL~aEGlFd~~~KkpLP~~p~ 136 (440)
T COG1570 77 LVRGKISLYEPRGDYQIVAESMEPAGLG---ALYLAFE-----------------QLKAKLAAEGLFDPERKKPLPFFPK 136 (440)
T ss_pred EEEEEEEEEcCCCceEEEEecCCcCChh---HHHHHHH-----------------HHHHHHHhCCCcChhhcCCCCCCCC
Confidence 58899999988766 4666655444432 111 111 22356677776642 2 2
Q ss_pred EE-EEEcCCCCChHHHHHHHHHHhhCCCCCEEEE---ecCChhhHHHHHHhhc
Q 037694 208 SI-LITAKGYPDIATRFLLHRLNRAFPDLPILAL---VDWNPAGLAILCTFKF 256 (355)
Q Consensus 208 ~I-lITgkGyPd~~TR~fL~~L~~~~~~lpv~~l---~D~DP~Gi~I~~~yk~ 256 (355)
|| +||+.. .-+-|.+++.++..+|.++|+++ |-||-.+-+|......
T Consensus 137 ~IGVITS~t--gAairDIl~~~~rR~P~~~viv~pt~VQG~~A~~eIv~aI~~ 187 (440)
T COG1570 137 KIGVITSPT--GAALRDILHTLSRRFPSVEVIVYPTLVQGEGAAEEIVEAIER 187 (440)
T ss_pred eEEEEcCCc--hHHHHHHHHHHHhhCCCCeEEEEeccccCCCcHHHHHHHHHH
Confidence 44 888764 45789999999999999998865 7888888888877764
No 31
>PRK04031 DNA primase; Provisional
Probab=40.03 E-value=79 Score=32.28 Aligned_cols=63 Identities=24% Similarity=0.264 Sum_probs=44.3
Q ss_pred ccEEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 182 ARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 182 a~~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
.++|+|||=-+=--+|.+.|+. |.|-.-|-..|+. +.+|.. .-.|..|+|+|..|-.|.....
T Consensus 169 ~~~iIVVEG~~DVi~L~~aGi~---nvVAt~GT~l~~~-----i~~l~k---~~~Vil~~DgD~aGe~I~k~l~ 231 (408)
T PRK04031 169 SDAIIVVEGRADVLNLLRYGIK---NAIAVEGTNVPET-----IIELSK---KKTVTAFLDGDRGGELILKELL 231 (408)
T ss_pred CCeEEEEeCHHHHHHHHhcccc---eEEEeCCcccHHH-----HHHHhc---CCCEEEEECCCHHHHHHHHHHH
Confidence 4789999987777778877755 3555555544443 445544 2368999999999999976554
No 32
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=39.63 E-value=1.9e+02 Score=24.13 Aligned_cols=50 Identities=22% Similarity=0.266 Sum_probs=35.8
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcC
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFG 257 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~G 257 (355)
+-++|..-..|+...-.++..+....+++|++.++..+- .-.....++.|
T Consensus 48 ~d~ii~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~~-~~~~~~~~~~g 97 (202)
T PRK09390 48 FGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGD-VPLAVEAMKLG 97 (202)
T ss_pred CCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCC-HHHHHHHHHcC
Confidence 456677778999999999999988777899998875433 23333445555
No 33
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=37.69 E-value=1.4e+02 Score=26.60 Aligned_cols=42 Identities=14% Similarity=0.059 Sum_probs=32.9
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhH
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGL 248 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi 248 (355)
+-++|..-..|+.....+++.+....+++|++.+++.+....
T Consensus 50 ~dlvild~~l~~~~g~~~~~~lr~~~~~~pii~ls~~~~~~~ 91 (239)
T PRK09468 50 FHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLTAKGEEVD 91 (239)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCcHHH
Confidence 346677788899888899999987767899999987655443
No 34
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=37.51 E-value=1.5e+02 Score=25.97 Aligned_cols=50 Identities=26% Similarity=0.280 Sum_probs=36.8
Q ss_pred EEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcCC
Q 037694 208 SILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFGS 258 (355)
Q Consensus 208 ~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~GS 258 (355)
-++|..-..|+.....+++.+....|++|+..+++.+-....+ ..+..|.
T Consensus 46 dlvild~~l~~~~g~~l~~~lr~~~~~~pii~ls~~~~~~~~~-~~l~~Ga 95 (223)
T PRK10816 46 DIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKV-EVLSAGA 95 (223)
T ss_pred CEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHH-HHHHcCC
Confidence 3556677899999999999998876789999998766554433 4455553
No 35
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=35.66 E-value=1.7e+02 Score=26.66 Aligned_cols=47 Identities=17% Similarity=-0.002 Sum_probs=34.4
Q ss_pred EcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcCC
Q 037694 212 TAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFGS 258 (355)
Q Consensus 212 TgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~GS 258 (355)
.--+.|+..--.+++.|....|++||.+++..|..-..+....+.|-
T Consensus 46 ~d~~mp~~~Gl~~~~~l~~~~p~~~iIvlt~~~~~~~~~~~~~~~Ga 92 (207)
T PRK11475 46 SAMRSERREGLSCLTELAIKFPRMRRLVIADDDIEARLIGSLSPSPL 92 (207)
T ss_pred cccCCCCCCHHHHHHHHHHHCCCCCEEEEeCCCCHHHHHHHHHHcCC
Confidence 56677888888999999998999999999875544434433335563
No 36
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=34.76 E-value=2.8e+02 Score=24.97 Aligned_cols=83 Identities=23% Similarity=0.243 Sum_probs=42.4
Q ss_pred HHHHHHHHhhCCCCCEEEEecCChh--hHHHHHHhh---------cCCcccccccccccccceeeccccccc-----ccC
Q 037694 222 RFLLHRLNRAFPDLPILALVDWNPA--GLAILCTFK---------FGSIGMGMEAYRYACNVKWLGLRGDDV-----QLI 285 (355)
Q Consensus 222 R~fL~~L~~~~~~lpv~~l~D~DP~--Gi~I~~~yk---------~GS~~~~~~~~~~~~~~~wlGv~~~di-----~~l 285 (355)
+..++.+... +.||++++++-.. |+.|++.-- +||+........+..-+.-+|+.+.-+ +..
T Consensus 56 ~~~i~~~~~~--~kpvia~v~g~~~s~g~~lA~aaD~i~a~~~s~~g~iG~~~~~~~~~~~l~k~Gi~~~~~~~g~~K~~ 133 (208)
T cd07023 56 YREIRRLRKA--KKPVVASMGDVAASGGYYIAAAADKIVANPTTITGSIGVIGQGPNLEELLDKLGIERDTIKSGPGKDK 133 (208)
T ss_pred HHHHHHHHhc--CCcEEEEECCcchhHHHHHHhhCCEEEECCCCeEEeCcEEEecCCHHHHHHhcCCceEEEecCCCccC
Confidence 3344444332 5799999997653 566665422 122222111111110022244444433 222
Q ss_pred CCCccCCCCHHHHHHHHHhhhh
Q 037694 286 PEQSLLPLKPRDLQIARSLMSS 307 (355)
Q Consensus 286 ~~~~~~pLt~~D~~~l~~ll~~ 307 (355)
+ +...++|+.++..++++|..
T Consensus 134 ~-~~~~~~s~~~~e~~~~~l~~ 154 (208)
T cd07023 134 G-SPDRPLTEEERAILQALVDD 154 (208)
T ss_pred C-CCCCCCCHHHHHHHHHHHHH
Confidence 2 23567999999999888875
No 37
>KOG2780 consensus Ribosome biogenesis protein RPF1, contains IMP4 domain [RNA processing and modification]
Probab=34.20 E-value=1.6e+02 Score=28.57 Aligned_cols=55 Identities=20% Similarity=0.219 Sum_probs=37.9
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCC---hh-hHHHHHHhhcCCcccccc
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWN---PA-GLAILCTFKFGSIGMGME 264 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~D---P~-Gi~I~~~yk~GS~~~~~~ 264 (355)
|-||||++-.|...|..|.+-|.+-.|+.-+ .+-| -. +++|+..--++..-.-++
T Consensus 97 pKvlITt~~~~~~~t~~~~~eL~~iiPNs~~---~~R~~~~vk~i~~~a~~~eftdlvvV~e 155 (302)
T KOG2780|consen 97 PKVLITTSKNPKRTTYKFASELLDIIPNSTV---KKRDNYTVKSIVEIAIKREFTDLVVVNE 155 (302)
T ss_pred ccEEEEcCCCCcccHHHHHHHHHHhCCCceE---EecCCchHHHHHHHHHHhcCCceEEEec
Confidence 7899999999999999999999998776544 4555 33 224444444554433333
No 38
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=33.60 E-value=58 Score=26.08 Aligned_cols=36 Identities=19% Similarity=0.305 Sum_probs=22.0
Q ss_pred CCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhh
Q 037694 206 IPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAG 247 (355)
Q Consensus 206 ~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~G 247 (355)
..||++||...|+-.+..+.+.. ++|++ .++.|-|-
T Consensus 62 i~~iIltg~~~~~~~v~~la~~~-----~i~vi-~t~~dtf~ 97 (105)
T PF07085_consen 62 IACIILTGGLEPSEEVLELAKEL-----GIPVI-STPYDTFE 97 (105)
T ss_dssp ECEEEEETT----HHHHHHHHHH-----T-EEE-E-SS-HHH
T ss_pred CCEEEEeCCCCCCHHHHHHHHHC-----CCEEE-EECCCHHH
Confidence 57999999999999998888766 47764 55665543
No 39
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=32.67 E-value=51 Score=36.05 Aligned_cols=41 Identities=17% Similarity=0.226 Sum_probs=32.1
Q ss_pred ccCCCCHHHHHHHHHhhhhhhh-----------hHHHHHHHHHHHHcCCeEe
Q 037694 289 SLLPLKPRDLQIARSLMSSEIL-----------QENYKEELSLMVHNGQRAE 329 (355)
Q Consensus 289 ~~~pLt~~D~~~l~~ll~~~~~-----------~~~w~~el~~ml~~~~KaE 329 (355)
.+.||++....++..-.+..++ +..|++|++++.+.+++.+
T Consensus 412 pf~~l~ksq~~kl~k~q~k~y~de~dyr~kl~~kkq~ke~~~r~k~~k~~~~ 463 (763)
T TIGR00993 412 PFKPLTKAQMAKLSKEQRKAYLEEYDYRVKLLQKKQWREELKRMKMMKKFGK 463 (763)
T ss_pred CCccccHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4678999999888777665443 3389999999999988865
No 40
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=32.40 E-value=1.8e+02 Score=21.92 Aligned_cols=57 Identities=16% Similarity=0.091 Sum_probs=33.0
Q ss_pred EEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHH
Q 037694 184 YIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLA 249 (355)
Q Consensus 184 ~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~ 249 (355)
.|+++|=.--.-.+.+.++ .+++-..|....+ ..+..|... .-.|+.++|.|+.|..
T Consensus 2 ~v~i~EG~~D~ls~~~~g~---~~~va~~G~~~~~----~~~~~L~~~--~~~vii~~D~D~aG~~ 58 (79)
T cd03364 2 KVILVEGYMDVIALHQAGI---KNVVASLGTALTE----EQAELLKRL--AKEVILAFDGDEAGQK 58 (79)
T ss_pred eEEEEeCHHHHHHHHHcCC---CCEEECCCccCcH----HHHHHHHhc--CCeEEEEECCCHHHHH
Confidence 4677875554555555542 2455554555532 223333321 2358999999999974
No 41
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=31.08 E-value=3.8e+02 Score=23.79 Aligned_cols=50 Identities=18% Similarity=0.315 Sum_probs=29.1
Q ss_pred EehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecC
Q 037694 188 VEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDW 243 (355)
Q Consensus 188 VEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~ 243 (355)
|..+...+.|.+. +.|.|++ |.|-=....+.-+.++.+.+ ++||+.=.-+
T Consensus 15 ~~p~~aa~lLk~A----KRPvIiv-G~ga~~~~a~e~l~~laEkl-giPVvtT~~~ 64 (162)
T TIGR00315 15 VSPKLVAMMIKRA----KRPLLIV-GPENLEDEEKELIVKFIEKF-DLPVVATADT 64 (162)
T ss_pred cCHHHHHHHHHcC----CCcEEEE-CCCcCcccHHHHHHHHHHHH-CCCEEEcCcc
Confidence 3566666666433 3355555 54443224566666777766 8999876654
No 42
>KOG1527 consensus Uroporphyrin III methyltransferase [Coenzyme transport and metabolism]
Probab=30.92 E-value=33 Score=34.47 Aligned_cols=61 Identities=21% Similarity=0.298 Sum_probs=39.9
Q ss_pred ccCccEEEEEehhhHHHHHHhccccCCCC---EEEEEcC--CCCChHHHHHHHHHHhhC-CCCCEEEEecCChh
Q 037694 179 KTDARYIIVVEKHAIFQRLTEDFVFNQIP---SILITAK--GYPDIATRFLLHRLNRAF-PDLPILALVDWNPA 246 (355)
Q Consensus 179 ~~~a~~VLvVEK~avF~rL~~~~~~~~~~---~IlITgk--GyPd~~TR~fL~~L~~~~-~~lpv~~l~D~DP~ 246 (355)
-..|+++| +.+|+-+...+-.| -++|.+| |+.+++-..+...+-+.+ .+.-|+-|--+|||
T Consensus 279 I~sAD~~L-------aDkLVp~avL~Lipp~t~lfia~KfpGna~raQ~Elh~~~l~~l~~G~~VVRLKqGDPy 345 (506)
T KOG1527|consen 279 IQSADLLL-------ADKLVPNAVLELIPPDTRLFIAGKFPGNASRAQEELHELLLNFLEAGATVVRLKQGDPY 345 (506)
T ss_pred Hhhcceeh-------hhhcccHHHHhhcCCCCceEEeecCCCchhHHHHHHHHHHHHHHhCCCEEEEecCCCce
Confidence 36678887 56777665444332 3555554 666666666766665543 26889999999997
No 43
>COG0240 GpsA Glycerol-3-phosphate dehydrogenase [Energy production and conversion]
Probab=30.53 E-value=1.5e+02 Score=29.50 Aligned_cols=78 Identities=19% Similarity=0.276 Sum_probs=48.7
Q ss_pred ccccCCChhhhhhhc-cccCccEEEEEehhhHHHHHHhc--cccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEE
Q 037694 163 GYSISGDLSLLEKLD-LKTDARYIIVVEKHAIFQRLTED--FVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILA 239 (355)
Q Consensus 163 g~~Ip~~~~~i~~~~-i~~~a~~VLvVEK~avF~rL~~~--~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~ 239 (355)
|..+|+++....++. .-.++++|+++=.-..+...++. .+-.+...|+..+||+-.-..+++=..+.+.+|.-|+.+
T Consensus 52 ~i~lp~~l~at~Dl~~a~~~ad~iv~avPs~~~r~v~~~l~~~l~~~~~iv~~sKGie~~t~~l~seii~e~l~~~~~~v 131 (329)
T COG0240 52 GILLPPNLKATTDLAEALDGADIIVIAVPSQALREVLRQLKPLLLKDAIIVSATKGLEPETGRLLSEIIEEELPDNPIAV 131 (329)
T ss_pred CccCCcccccccCHHHHHhcCCEEEEECChHHHHHHHHHHhhhccCCCeEEEEeccccCCCcchHHHHHHHHcCCCeEEE
Confidence 455565543322221 23458888777665555555544 334445678889999998877777777788777666444
Q ss_pred E
Q 037694 240 L 240 (355)
Q Consensus 240 l 240 (355)
|
T Consensus 132 L 132 (329)
T COG0240 132 L 132 (329)
T ss_pred E
Confidence 3
No 44
>PRK00933 ribosomal biogenesis protein; Validated
Probab=29.90 E-value=57 Score=29.10 Aligned_cols=28 Identities=29% Similarity=0.394 Sum_probs=24.4
Q ss_pred EEEEcCCCCChHHHHHHHHHHhhCCCCCE
Q 037694 209 ILITAKGYPDIATRFLLHRLNRAFPDLPI 237 (355)
Q Consensus 209 IlITgkGyPd~~TR~fL~~L~~~~~~lpv 237 (355)
++||+...|+..||.|.+.|...+ +++.
T Consensus 1 mIITTSrkPs~~t~~fAkeLa~~l-n~~y 28 (165)
T PRK00933 1 MIITTSRKPSQRTRSLVKDLARFL-NCKY 28 (165)
T ss_pred CEEECCCCCCHHHHHHHHHHHHHh-CCEE
Confidence 479999999999999999999887 6553
No 45
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=28.96 E-value=1.9e+02 Score=29.09 Aligned_cols=54 Identities=19% Similarity=0.335 Sum_probs=40.0
Q ss_pred CCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEec-CChhhHHHHHHhhcCCccc
Q 037694 205 QIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVD-WNPAGLAILCTFKFGSIGM 261 (355)
Q Consensus 205 ~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D-~DP~Gi~I~~~yk~GS~~~ 261 (355)
..+.|+|+|.|| .-..|...+.+..|++|-++..| ++-+.--|+.+.|.|...-
T Consensus 191 ~~~~iIvaGPGF---~k~~~~~~~~~~~p~~~~~~~~~~s~~g~~gi~EvLkr~~v~k 245 (352)
T COG1537 191 NLDIIIVAGPGF---AKEDFYDFLRERYPELANIVIEDTSTGGRAGINEVLKRGAVDK 245 (352)
T ss_pred CCCeEEEeCCch---HHHHHHHHHHHhcccccceEEEeccCcchHHHHHHHhhhhHHh
Confidence 457899999887 77889999999999888444555 4444346888888887653
No 46
>PRK06849 hypothetical protein; Provisional
Probab=28.01 E-value=1.2e+02 Score=30.03 Aligned_cols=45 Identities=22% Similarity=0.178 Sum_probs=33.5
Q ss_pred CCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhh
Q 037694 206 IPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFK 255 (355)
Q Consensus 206 ~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk 255 (355)
.+.|||||.|.| .+..+.+.|.+. +..|+ ++|.+|+.+...+.|-
T Consensus 4 ~~~VLI~G~~~~--~~l~iar~l~~~--G~~Vi-~~d~~~~~~~~~s~~~ 48 (389)
T PRK06849 4 KKTVLITGARAP--AALELARLFHNA--GHTVI-LADSLKYPLSRFSRAV 48 (389)
T ss_pred CCEEEEeCCCcH--HHHHHHHHHHHC--CCEEE-EEeCCchHHHHHHHhh
Confidence 357999999988 577778888775 67765 6699988876555544
No 47
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=27.93 E-value=2.1e+02 Score=21.12 Aligned_cols=59 Identities=17% Similarity=0.107 Sum_probs=33.8
Q ss_pred EEEEEehhhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHH
Q 037694 184 YIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAIL 251 (355)
Q Consensus 184 ~VLvVEK~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~ 251 (355)
.++++|=.----.+.+.++ .+++...|.+... .-+..+... .-.|+.+.|.|.-|..-.
T Consensus 2 ~v~i~EG~~Dals~~~~~~---~~~~~~~g~~~~~----~~~~~l~~~--~~~vii~~D~D~~G~~~~ 60 (79)
T cd01029 2 EVIIVEGYMDVLALHQAGI---KNVVAALGTANTE----EQLRLLKRF--ARTVILAFDNDEAGKKAA 60 (79)
T ss_pred EEEEEeCHHHHHHHHHcCC---CCEEECCCccCcH----HHHHHHHhc--CCEEEEEECCCHHHHHHH
Confidence 4677875555556666554 2455444554443 222223221 257999999999996433
No 48
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=27.54 E-value=1.9e+02 Score=25.02 Aligned_cols=51 Identities=24% Similarity=0.343 Sum_probs=35.8
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcCC
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFGS 258 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~GS 258 (355)
+-+++..-..|+.....+++.+....+..|+..+++.+-.. .....+..|.
T Consensus 45 ~d~illd~~~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~-~~~~~~~~ga 95 (222)
T PRK10643 45 YSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARDTLE-DRVAGLDVGA 95 (222)
T ss_pred CCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHH-HHHHHHhcCC
Confidence 34566677889998899999998876789999988654332 2334455553
No 49
>PF13289 SIR2_2: SIR2-like domain
Probab=26.86 E-value=2.2e+02 Score=23.21 Aligned_cols=53 Identities=11% Similarity=0.110 Sum_probs=35.3
Q ss_pred hhHHHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhCCC--CCEEEEecCCh
Q 037694 191 HAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPD--LPILALVDWNP 245 (355)
Q Consensus 191 ~avF~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~~~--lpv~~l~D~DP 245 (355)
...|.+.++.-+ ... .+|+-|-|+.|..-+.+++.+.+..+. -+.|+++-.++
T Consensus 73 ~~~~~~~l~~~l-~~~-~~lfiGys~~D~~i~~~l~~~~~~~~~~~~~~~~v~~~~~ 127 (143)
T PF13289_consen 73 NPWFPNFLRSLL-RSK-TLLFIGYSFNDPDIRQLLRSALENSGKSRPRHYIVIPDPD 127 (143)
T ss_pred HHHHHHHHHHHH-cCC-CEEEEEECCCCHHHHHHHHHHHHhccCCCccEEEEEcCCc
Confidence 344555555444 223 444449999999999999999887643 46776666555
No 50
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=26.56 E-value=1e+02 Score=24.73 Aligned_cols=32 Identities=31% Similarity=0.484 Sum_probs=25.9
Q ss_pred EEEEEcCCCCChHHHHHHHHHH----hhCCCCCEEE
Q 037694 208 SILITAKGYPDIATRFLLHRLN----RAFPDLPILA 239 (355)
Q Consensus 208 ~IlITgkGyPd~~TR~fL~~L~----~~~~~lpv~~ 239 (355)
-|+++-|+-..-.+|.|+.+-. ..+|++||++
T Consensus 19 RI~lcqkspaSagvR~fvEk~Y~~lKkaNP~lPILI 54 (97)
T KOG3446|consen 19 RIHLCQKSPASAGVREFVEKFYVNLKKANPDLPILI 54 (97)
T ss_pred eeeecCCCCcchhHHHHHHHhhhhhhhcCCCCcEee
Confidence 4788889988999999998754 3468999865
No 51
>PRK13856 two-component response regulator VirG; Provisional
Probab=26.53 E-value=3.2e+02 Score=24.45 Aligned_cols=50 Identities=10% Similarity=0.173 Sum_probs=35.2
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcC
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFG 257 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~G 257 (355)
+-++|..-..|+...-.+++.+... +.+|+..+++..+..-.....+..|
T Consensus 46 ~dlvi~d~~l~~~~g~~l~~~i~~~-~~~pii~lt~~~~~~~~~~~~l~~G 95 (241)
T PRK13856 46 VDVVVVDLNLGREDGLEIVRSLATK-SDVPIIIISGDRLEEADKVVALELG 95 (241)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhc-CCCcEEEEECCCCcHHHHHHHHhcC
Confidence 4577778888998888999999865 4799999987433333344445555
No 52
>TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit.
Probab=25.91 E-value=61 Score=29.67 Aligned_cols=19 Identities=37% Similarity=0.560 Sum_probs=15.8
Q ss_pred EcCCCC-ChHHHHHHHH-HHh
Q 037694 212 TAKGYP-DIATRFLLHR-LNR 230 (355)
Q Consensus 212 TgkGyP-d~~TR~fL~~-L~~ 230 (355)
.|+||| |..|+.|++. +..
T Consensus 166 ~GsGY~sd~~t~~~l~~~~~~ 186 (206)
T TIGR00729 166 FGSGYPSDPRTREWLEEYFKS 186 (206)
T ss_pred CCCcCCCCHHHHHHHHHHHHh
Confidence 599999 6889999997 443
No 53
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=23.66 E-value=98 Score=28.61 Aligned_cols=37 Identities=14% Similarity=0.221 Sum_probs=32.9
Q ss_pred EEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEe-----cCChh
Q 037694 208 SILITAKGYPDIATRFLLHRLNRAFPDLPILALV-----DWNPA 246 (355)
Q Consensus 208 ~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~-----D~DP~ 246 (355)
-|+|+|-|--..-.|.|..+|... +.|.|.+. ++|-.
T Consensus 41 kv~V~G~GkSG~Igkk~Aa~L~s~--G~~a~fv~p~ea~hgdlg 82 (202)
T COG0794 41 KVFVTGVGKSGLIGKKFAARLAST--GTPAFFVGPAEALHGDLG 82 (202)
T ss_pred cEEEEcCChhHHHHHHHHHHHHcc--CCceEEecCchhccCCcc
Confidence 599999999999999999999985 78999999 76643
No 54
>PF08747 DUF1788: Domain of unknown function (DUF1788); InterPro: IPR014858 This entry represents a putative uncharacterised protein of length around 200 amino acids.
Probab=22.96 E-value=2.7e+02 Score=23.66 Aligned_cols=39 Identities=23% Similarity=0.456 Sum_probs=32.2
Q ss_pred CCEEEEEcCC--CCChHHHHHHHHHHhhCCCCCEEEEecCC
Q 037694 206 IPSILITAKG--YPDIATRFLLHRLNRAFPDLPILALVDWN 244 (355)
Q Consensus 206 ~~~IlITgkG--yPd~~TR~fL~~L~~~~~~lpv~~l~D~D 244 (355)
.+.++|||-| ||=.-+-.+|+.|+....+.|+..|.=|.
T Consensus 62 ~~vv~ltGvG~l~P~~R~h~lL~~l~~~~~~~plv~FyPG~ 102 (126)
T PF08747_consen 62 RDVVFLTGVGSLFPFIRSHELLNNLQPKFGNVPLVVFYPGE 102 (126)
T ss_pred CcEEEEeCcchhcchhhHHHHHHHHHHHhcCCeEEEECCce
Confidence 4679999777 89888889999999987689998886544
No 55
>PF08444 Gly_acyl_tr_C: Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region; InterPro: IPR013652 This entry represents mammalian-specific glycine N-acyltransferase (also called aralkyl acyl-CoA:amino acid N-acyltransferase; 2.3.1.13 from EC). Mitochondrial acyltransferases catalyse the transfer of an acyl group from acyl-CoA to the N terminus of glycine to produce N-acylglycine. These enzymes can conjugate a multitude of substrates to form a variety of N-acylglycines. The CoA derivatives of a number of aliphatic and aromatic acids, but not phenylacetyl-CoA or (indol-3-yl)acetyl-CoA, can act as donor [, ].
Probab=22.76 E-value=58 Score=26.13 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=29.3
Q ss_pred cCCCCChHHHHHHHHHHhhCCCCCEEEEecCC-hhhHHHH
Q 037694 213 AKGYPDIATRFLLHRLNRAFPDLPILALVDWN-PAGLAIL 251 (355)
Q Consensus 213 gkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~D-P~Gi~I~ 251 (355)
+||+-......+.+.|+.. ++|+|+.||-| -......
T Consensus 33 ~~G~~~~v~~~~~~~L~~~--g~P~Y~hv~~~N~~~~r~~ 70 (89)
T PF08444_consen 33 GQGLMSQVMYHLAQYLHKL--GFPFYGHVDEDNEASQRLS 70 (89)
T ss_pred cCCHHHHHHHHHHHHHHHC--CCCeEeehHhccHHHHHHH
Confidence 7888888999999999885 89999999854 3344444
No 56
>PRK03972 ribosomal biogenesis protein; Validated
Probab=21.83 E-value=1.3e+02 Score=28.04 Aligned_cols=28 Identities=39% Similarity=0.535 Sum_probs=25.2
Q ss_pred EEEEcCCCCChHHHHHHHHHHhhCCCCC
Q 037694 209 ILITAKGYPDIATRFLLHRLNRAFPDLP 236 (355)
Q Consensus 209 IlITgkGyPd~~TR~fL~~L~~~~~~lp 236 (355)
||||+.=.|..-||.|++-|..-+|+.-
T Consensus 2 iLITTSr~PS~rtr~F~keL~~v~Pns~ 29 (208)
T PRK03972 2 MLITTSHRPTRRTRSFGHDLERVFPNSL 29 (208)
T ss_pred EEEECCCCccHHHHHHHHHHHHhCCCCE
Confidence 8999999999999999999999887653
No 57
>PRK08105 flavodoxin; Provisional
Probab=21.80 E-value=2.2e+02 Score=24.49 Aligned_cols=39 Identities=18% Similarity=0.149 Sum_probs=27.9
Q ss_pred CEEEEE---cCCCCChHHHHHHHHHHhhCC---C--CCEEEEecCCh
Q 037694 207 PSILIT---AKGYPDIATRFLLHRLNRAFP---D--LPILALVDWNP 245 (355)
Q Consensus 207 ~~IlIT---gkGyPd~~TR~fL~~L~~~~~---~--lpv~~l~D~DP 245 (355)
.+|+|| |-|-|.-+...|+..|.+..+ + .-|++|+|...
T Consensus 51 ~vi~~~sT~G~Ge~p~~~~~f~~~l~~~~~~l~~~~~avfGlGds~Y 97 (149)
T PRK08105 51 LVLVVTSTTGQGDLPDSIVPLFQALKDTAGYQPNLRYGVIALGDSSY 97 (149)
T ss_pred eEEEEECCCCCCCCChhHHHHHHHHHhcCcccCCCEEEEEeeecCCH
Confidence 466665 778888888999999887422 2 33788888763
No 58
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=21.54 E-value=3.2e+02 Score=23.90 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=35.4
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHhhcCC
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRAFPDLPILALVDWNPAGLAILCTFKFGS 258 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~yk~GS 258 (355)
+-++|..-..|+...-.+++.+....|++|+..+++.+ ..-.....+..|.
T Consensus 45 ~dlvild~~~~~~~g~~~~~~lr~~~~~~pii~ls~~~-~~~~~~~~~~~Ga 95 (227)
T PRK09836 45 YDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALG-TIEHRVKGLELGA 95 (227)
T ss_pred CCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCC-CHHHHHHHHhCCC
Confidence 34566677889888889999998776789998887543 3333444555554
No 59
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=20.95 E-value=2.5e+02 Score=25.76 Aligned_cols=17 Identities=18% Similarity=0.319 Sum_probs=13.9
Q ss_pred CCCCHHHHHHHHHhhhh
Q 037694 291 LPLKPRDLQIARSLMSS 307 (355)
Q Consensus 291 ~pLt~~D~~~l~~ll~~ 307 (355)
.++|+.+++.+++++..
T Consensus 151 ~~~s~~~r~~~~~~l~~ 167 (222)
T cd07018 151 DDMSPEAREQTQALLDS 167 (222)
T ss_pred ccCCHHHHHHHHHHHHH
Confidence 36899999999888875
No 60
>cd01748 GATase1_IGP_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS). Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS). IGPS incorporates ammonia derived from glutamine into N1-[(5'-phosphoribulosyl)-formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to form 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR) and imidazole glycerol phosphate (IGP). The glutamine amidotransferase domain generates the ammonia nucleophile which is channeled from the glutaminase active site to the PRFAR active site. IGPS belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site.
Probab=20.95 E-value=1.2e+02 Score=27.05 Aligned_cols=44 Identities=16% Similarity=0.177 Sum_probs=31.2
Q ss_pred CCCEEEEEcCCCCChH--------HHHHHHHHHhhCCCCCEEEEecCChhhHHHHHHh
Q 037694 205 QIPSILITAKGYPDIA--------TRFLLHRLNRAFPDLPILALVDWNPAGLAILCTF 254 (355)
Q Consensus 205 ~~~~IlITgkGyPd~~--------TR~fL~~L~~~~~~lpv~~l~D~DP~Gi~I~~~y 254 (355)
..+.|+|+|.|.|+.+ ...+++...+. +.|+++.+ +|+.+++.+
T Consensus 36 ~~d~iiipG~~~~~~~~~~~~~~~~~~~i~~~~~~--~~pilGiC----~G~q~l~~~ 87 (198)
T cd01748 36 SADKLILPGVGAFGDAMANLRERGLIEALKEAIAS--GKPFLGIC----LGMQLLFES 87 (198)
T ss_pred cCCEEEECCCCcHHHHHHHHHHcChHHHHHHHHHC--CCcEEEEC----HHHHHhccc
Confidence 4678999998887643 34555555443 78999887 788887665
No 61
>COG4069 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.70 E-value=82 Score=30.95 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=20.0
Q ss_pred CCCEEEEecCChhhHHHHHHhhcCCc
Q 037694 234 DLPILALVDWNPAGLAILCTFKFGSI 259 (355)
Q Consensus 234 ~lpv~~l~D~DP~Gi~I~~~yk~GS~ 259 (355)
++||.+++|+|+.-+.-...|.-||+
T Consensus 289 gipiiGItDgD~D~~~~~~~~~~gsv 314 (367)
T COG4069 289 GIPIIGITDGDCDEVTREVNIAPGSV 314 (367)
T ss_pred CCcEEecccCChHHhhhhcccCCCcE
Confidence 89999999999996555555555554
No 62
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=20.67 E-value=83 Score=24.58 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=20.6
Q ss_pred ccceeccccCCCcccc---CchHHHHHHHHHHHH
Q 037694 91 QRELFYKLLCDSPEYF---TSQLQVNRTIQDVIA 121 (355)
Q Consensus 91 ~RdiYY~~~~~~~~lF---~~Q~~~d~~i~di~~ 121 (355)
+=|+||++ .++- .+|.+.|++|+-+..
T Consensus 36 ~mdl~ytn----~eL~iPl~~Q~DLDkAie~ld~ 65 (79)
T cd06405 36 PMDLHYTN----NELLIPLKNQEDLDRAIELLDR 65 (79)
T ss_pred eeeEEEec----ccEEEeccCHHHHHHHHHHHcc
Confidence 45899994 3333 899999999987753
No 63
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=20.41 E-value=93 Score=27.44 Aligned_cols=31 Identities=13% Similarity=0.344 Sum_probs=25.5
Q ss_pred HHHHHhhhhhhhhHHHHHHHHHHHHcCCeEeee
Q 037694 299 QIARSLMSSEILQENYKEELSLMVHNGQRAEVE 331 (355)
Q Consensus 299 ~~l~~ll~~~~~~~~w~~el~~ml~~~~KaEiE 331 (355)
+.+.++|++|.+.+.-+.+|++|+.. |.|+-
T Consensus 113 ~ai~~iL~~p~V~~~~K~~i~~i~~~--Kgei~ 143 (155)
T PF10777_consen 113 QAIDKILQSPQVPDEIKQGIQRIIST--KGEIS 143 (155)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHh--CCcee
Confidence 45667899999998999999999985 66653
No 64
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.19 E-value=47 Score=30.94 Aligned_cols=59 Identities=22% Similarity=0.266 Sum_probs=43.6
Q ss_pred HHHHHhccccCCCCEEEEEcCCCCChHHHHHHHHHHhhC----------CCCCEEEEecCChhhHHHHHHhhc
Q 037694 194 FQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAF----------PDLPILALVDWNPAGLAILCTFKF 256 (355)
Q Consensus 194 F~rL~~~~~~~~~~~IlITgkGyPd~~TR~fL~~L~~~~----------~~lpv~~l~D~DP~Gi~I~~~yk~ 256 (355)
||-+++.+++ ++.|+-++||....=.+|.-|++|+ |-..-|+|.-.|++==.+=..|..
T Consensus 61 fHfli~~~Vc----ylvicd~~yP~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~FieFD~~IQk~Kk~ynd 129 (216)
T KOG0862|consen 61 FHFLIESGVC----YLVICDKSYPRKLAFSYLEDLAQEFDKSYGKNIIQPASRPYAFIEFDTFIQKTKKRYND 129 (216)
T ss_pred EEEEecCCEE----EEEEecCCCcHHHHHHHHHHHHHHHHHhcccccCCccCCCeeEEehhHHHHHHHHHhcC
Confidence 4555555544 7999999999999999999999875 234568999999875555555543
No 65
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=20.09 E-value=5.8e+02 Score=22.20 Aligned_cols=51 Identities=16% Similarity=0.286 Sum_probs=34.9
Q ss_pred CEEEEEcCCCCChHHHHHHHHHHhh--CCCCCEEEEecCChhhHHHHHHhhcCC
Q 037694 207 PSILITAKGYPDIATRFLLHRLNRA--FPDLPILALVDWNPAGLAILCTFKFGS 258 (355)
Q Consensus 207 ~~IlITgkGyPd~~TR~fL~~L~~~--~~~lpv~~l~D~DP~Gi~I~~~yk~GS 258 (355)
+-++|..-..|+.....+++.+... .|.+|+..+++.+-.. .+...++.|.
T Consensus 47 ~dlvild~~l~~~~g~~~~~~l~~~~~~~~~pvi~ls~~~~~~-~~~~~~~~Ga 99 (229)
T PRK10161 47 PDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEE-DRVRGLETGA 99 (229)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhccccCCCCEEEEECCCCHH-HHHHHHHcCC
Confidence 3455666778888888999999764 3679999998765333 3444455553
Done!