Query 029346
Match_columns 194
No_of_seqs 108 out of 352
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 11:27:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029346.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029346hhsearch_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 4.8E-54 1E-58 386.0 11.6 179 6-194 178-384 (384)
2 KOG2795 Catalytic subunit of t 100.0 2.4E-54 5.2E-59 381.4 8.4 186 5-194 161-372 (372)
3 PRK04342 DNA topoisomerase VI 100.0 8.4E-52 1.8E-56 370.9 13.8 179 10-194 163-366 (367)
4 COG1697 DNA topoisomerase VI, 100.0 7E-49 1.5E-53 345.1 5.2 172 12-192 166-356 (356)
5 cd00223 TOPRIM_TopoIIB_SPO TOP 100.0 1.2E-40 2.6E-45 267.4 11.6 141 32-178 1-160 (160)
6 PF09983 DUF2220: Uncharacteri 98.6 4E-08 8.6E-13 80.6 3.0 128 21-173 33-174 (181)
7 PF09664 DUF2399: Protein of u 98.1 2.6E-06 5.6E-11 68.3 4.2 121 22-173 9-146 (152)
8 TIGR02679 conserved hypothetic 93.8 0.085 1.8E-06 48.4 4.4 52 33-85 252-320 (385)
9 cd00188 TOPRIM Topoisomerase-p 93.1 0.24 5.3E-06 32.9 4.9 47 32-78 1-62 (83)
10 COG3593 Predicted ATP-dependen 81.6 2.2 4.7E-05 41.3 4.6 53 31-84 396-469 (581)
11 cd01026 TOPRIM_OLD TOPRIM_OLD: 77.6 4.9 0.00011 29.0 4.4 47 31-78 3-70 (97)
12 smart00493 TOPRIM topoisomeras 69.2 14 0.0003 24.8 4.9 49 33-81 2-65 (76)
13 cd01027 TOPRIM_RNase_M5_like T 64.7 20 0.00043 25.4 5.1 32 52-84 35-66 (81)
14 TIGR00334 5S_RNA_mat_M5 ribonu 50.6 74 0.0016 26.2 6.8 34 52-85 35-69 (174)
15 PF01751 Toprim: Toprim domain 48.3 29 0.00063 24.9 3.7 30 54-83 49-80 (100)
16 PRK04017 hypothetical protein; 45.5 43 0.00092 26.4 4.4 33 52-85 55-87 (132)
17 COG4069 Uncharacterized protei 40.9 16 0.00035 32.8 1.6 28 60-87 286-313 (367)
18 PF13662 Toprim_4: Toprim doma 37.0 85 0.0018 21.5 4.6 22 63-84 46-67 (81)
19 cd03365 TOPRIM_TopoIIA TOPRIM_ 36.7 23 0.0005 27.4 1.7 49 32-81 34-95 (120)
20 COG1658 Small primase-like pro 35.8 99 0.0021 24.1 5.1 54 31-84 9-76 (127)
21 cd01030 TOPRIM_TopoIIA_like TO 35.8 24 0.00053 27.1 1.6 49 32-81 31-91 (115)
22 COG0099 RpsM Ribosomal protein 35.3 33 0.00071 26.7 2.3 16 124-139 47-62 (121)
23 KOG3217 Protein tyrosine phosp 34.7 28 0.0006 28.2 1.9 28 149-176 93-123 (159)
24 KOG3905 Dynein light intermedi 31.1 18 0.00039 33.3 0.3 11 34-44 298-308 (473)
25 COG0052 RpsB Ribosomal protein 30.6 64 0.0014 28.1 3.6 40 24-73 150-189 (252)
26 cd03366 TOPRIM_TopoIIA_GyrB TO 30.1 35 0.00076 26.2 1.7 48 33-81 32-90 (114)
27 PF00072 Response_reg: Respons 26.7 1.6E+02 0.0036 20.1 4.7 50 34-85 1-67 (112)
28 cd03364 TOPRIM_DnaG_primases T 25.0 1.3E+02 0.0028 20.5 3.8 24 54-78 35-58 (79)
29 PF03602 Cons_hypoth95: Conser 22.0 1.1E+02 0.0024 24.8 3.4 55 24-79 58-128 (183)
30 KOG3382 NADH:ubiquinone oxidor 20.3 2.6E+02 0.0057 22.2 4.9 73 48-132 27-117 (151)
No 1
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=100.00 E-value=4.8e-54 Score=386.01 Aligned_cols=179 Identities=30% Similarity=0.452 Sum_probs=163.7
Q ss_pred ccceEEeeecc------cccccccee--eeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHH
Q 029346 6 SNFFIVLCLIS------SAIRICIIT--NTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREI 58 (194)
Q Consensus 6 ~~~~~~~c~ip------~~~~~~~i~--~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L 58 (194)
.|-..++|..+ +|.+++.++ ++.++|+|||||||||||+||++++| |+||++|
T Consensus 178 ~~~~~idcs~~g~~G~~Ip~~~~~i~~~~i~s~a~~VLVVEKeavF~rL~e~~~~~~~~cILITgKGyPD~aTR~fL~~L 257 (384)
T PLN00060 178 PNEEPVDCSILGISGHAITGDLNLLSNLILSSDARYIIVVEKDAIFQRLAEDRFFNHIPCILITAKGYPDLATRFILHRL 257 (384)
T ss_pred cCCcEEEeeccCCCceeCCCcHHHhhhcccccCccEEEEEecHHHHHHHHHhhhhhhCCEEEEecCCCCCHHHHHHHHHH
Confidence 34567888753 455666555 46799999999999999999999987 9999999
Q ss_pred Hhhc-CCcEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHH
Q 029346 59 RCKL-KKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFL 137 (194)
Q Consensus 59 ~~~~-~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll 137 (194)
++++ ++|+|+|||+||||++|++||||||.+++|+++.++|| ++|+|++++|+.. +|.++++|||+||++++++||
T Consensus 258 ~~~~p~lPv~~LvD~DP~Gi~I~~tYkyGS~~~a~es~~la~~-i~WLGl~~sDi~~--l~~~~~i~Lt~rD~~~~~~lL 334 (384)
T PLN00060 258 SQTFPNLPILALVDWNPAGLAILCTYKFGSIGMGLEAYRYACN-VKWLGLRGDDLQL--IPPEAFVELKPRDLQIAKSLL 334 (384)
T ss_pred HHhcCCCCEEEEECCCcchHHHHHHhhcCchhhhhcccccccC-CeEecCCHHHHhc--CCHhhcCCCCHHHHHHHHHHh
Confidence 9996 89999999999999999999999999999999999986 9999999999984 888899999999999999999
Q ss_pred hcCCcchhccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346 138 EKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL 194 (194)
Q Consensus 138 ~~~~~~~~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~ 194 (194)
++ |+++ ..|++||++|++.++|||||||++.|.+|+++ |||+||.++||+
T Consensus 335 ~~----~~~~--~~w~~EL~~Ml~~~~KaEiEAL~~~g~~fl~~-Ylp~Ki~~~~~i 384 (384)
T PLN00060 335 SS----KFLQ--NRYREELTLMVQTGKRAEIEALYSHGYDYLGK-YVARKIVQGDYI 384 (384)
T ss_pred hC----hhHH--HHHHHHHHHHHHhCcchhhHhHHhcChHHHHH-HHHHHHhcCCcC
Confidence 99 7885 39999999999999999999999999999995 999999999997
No 2
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=100.00 E-value=2.4e-54 Score=381.39 Aligned_cols=186 Identities=35% Similarity=0.545 Sum_probs=178.8
Q ss_pred cccceEEeee------ccccccccceeeeeccccEEEEEccchhhhhhchhHH--------------------HHHHHHH
Q 029346 5 ESNFFIVLCL------ISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI--------------------VILLREI 58 (194)
Q Consensus 5 ~~~~~~~~c~------ip~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f--------------------R~fl~~L 58 (194)
|-|-..++|+ -|+|+|++.|..+.++|+||||||||||||||+++.| |.|||+|
T Consensus 161 ~~ng~~id~~~~~~~~~~lp~d~~~i~~i~tdA~~IlIVEKeavFqrL~~d~~~~~~~~~ilITgKGyPD~~TR~fLkkL 240 (372)
T KOG2795|consen 161 EENGDVIDCTESGGGPKALPPDIDDISNITTDAKFILIVEKEAVFQRLAEDNFFNTFNRCILITGKGYPDIATRLFLKKL 240 (372)
T ss_pred EcCCcEEEeccCCCCCccCCCCHHHHhhhhccceEEEEEehHHHHHHHHHHHHHhhcCCeEEEecCCCCcHHHHHHHHHH
Confidence 5577889999 7899999999999999999999999999999999977 9999999
Q ss_pred HhhcCCcEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHh
Q 029346 59 RCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLE 138 (194)
Q Consensus 59 ~~~~~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~ 138 (194)
.+++++|++||||||||||+|+++|||||.+|+|+++++++|+++|+|++|+|+..++.|+++++||+++|.+++++||+
T Consensus 241 ~~~~~lpv~~LvDaDP~Gi~I~~~Yk~GS~~ms~e~~~~~~p~I~wiGl~psD~~~~n~~k~~~lpL~~~D~k~i~~lL~ 320 (372)
T KOG2795|consen 241 EEKLKLPVYGLVDADPYGIEILLTYKYGSKSMSYESHGLTVPTIRWIGLLPSDLEVKNIPKDQLLPLNKRDIKKIKDLLA 320 (372)
T ss_pred HHHhCCCEEEEeecCCcceEEEEEeeeCccccccccccccCCcceEEeechhhhhhcCCchheeecccHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcchhccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346 139 KGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL 194 (194)
Q Consensus 139 ~~~~~~~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~ 194 (194)
+ ..++.++.|++||++|++.++||||||+..+|.+|+.+.|+|.|+..++|+
T Consensus 321 ~----~~l~~~p~~r~el~~ml~~~~KaEieal~~~~~~~~~~~yia~k~~~~~~~ 372 (372)
T KOG2795|consen 321 R----LILQKEPVVREELERMLKNKVKAEIEALSFFGSDYLSRVYIARKLERISSL 372 (372)
T ss_pred h----hhcccChhHHHHHHHHHhcchhhhhhhhhhcchHHHhhhhhhHHHhhcccC
Confidence 9 577778899999999999999999999999999999999999999999985
No 3
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=100.00 E-value=8.4e-52 Score=370.92 Aligned_cols=179 Identities=28% Similarity=0.443 Sum_probs=168.2
Q ss_pred EEeeec------cccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCC
Q 029346 10 IVLCLI------SSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKK 64 (194)
Q Consensus 10 ~~~c~i------p~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~l 64 (194)
.++|.- .+|.+++.|+++.++|++||||||+|+|++|++++| |+||++|++++++
T Consensus 163 ~id~~~~g~~~~~ip~~~~~i~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlItgkG~Pd~~TR~fl~~L~~~~~l 242 (367)
T PRK04342 163 EIDCSKLGEGGYSIPPNVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKGQPARATRRFIKRLNEELGL 242 (367)
T ss_pred EEEEeccCCCceeCCCchhhheeeccCCCEEEEEechHHHHHHHHhCcccccCEEEEECCCCCCHHHHHHHHHHHHhcCC
Confidence 567754 556678889989999999999999999999999866 9999999999999
Q ss_pred cEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcch
Q 029346 65 SVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVA 144 (194)
Q Consensus 65 pi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~ 144 (194)
|+|+|+|+||||++|+++|++||.+++|+++.++||+++|+|++++|+.++ +|..+.+|||++|++++++||++ |
T Consensus 243 pv~~l~D~DP~G~~I~~tyk~GS~~~a~~s~~l~~P~~kwlGl~~sDi~~~-~~~~~~~~Lt~~D~~~l~~lL~~----~ 317 (367)
T PRK04342 243 PVYVFTDGDPWGYYIYSVVKYGSIKLAHLSERLATPDAKFIGVTPSDIVEY-ERDLPTIKLKDSDIKRAKELLNY----P 317 (367)
T ss_pred CEEEEECCCccHHHHHHHHHhCchhhhhhhhhccCCCCEEecCcHHHHHhh-ccccccCCCCHHHHHHHHHHhcC----c
Confidence 999999999999999999999999999999999999999999999999987 67788999999999999999999 7
Q ss_pred hccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346 145 FVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL 194 (194)
Q Consensus 145 ~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~ 194 (194)
+++ .++|++||++|++.|+|||||||++.|.+|++++|||+||.+++|+
T Consensus 318 ~~~-~~~w~~El~~ml~~~~KaEiEal~~~~~~~~~~~Ylp~Ki~~~~~i 366 (367)
T PRK04342 318 WFQ-TDFWQKEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL 366 (367)
T ss_pred ccc-CHHHHHHHHHHHHhCCceeeehhhhcChhhhHHHHHHHHHhcCCCC
Confidence 774 6899999999999999999999999999999999999999999997
No 4
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=100.00 E-value=7e-49 Score=345.06 Aligned_cols=172 Identities=30% Similarity=0.460 Sum_probs=163.5
Q ss_pred eeeccccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCCcEEEEecC
Q 029346 12 LCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKKSVLGSFDC 72 (194)
Q Consensus 12 ~c~ip~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~lpi~~L~D~ 72 (194)
+|+|| ++++.|+++.++|+|||||||+||||||++++| |+||++|.+++++||++|+|+
T Consensus 166 ~y~Ip--~~~d~I~f~~~da~~VlvVEk~avf~rLv~e~~~~k~nailVt~KGqP~raTRrflkrL~eel~lpv~vftDg 243 (356)
T COG1697 166 GYLIP--PDVDVIEFVDTDAKFVLVVEKDAVFQRLVEEGFWEKENAILVTLKGQPDRATRRFLKRLNEELDLPVYVFTDG 243 (356)
T ss_pred CCcCC--CChhheeeccccceEEEEEechHHHHHHHHhhhhhhcCeEEEecCCCccHHHHHHHHHHHHHhCCCEEEEecC
Confidence 46776 789999999999999999999999999999988 999999999999999999999
Q ss_pred CcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHH
Q 029346 73 NPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASW 152 (194)
Q Consensus 73 DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~ 152 (194)
||||++||++|+|||.+.||+++.+++|.++++||+++|+..++.| +..+|+++|+++++++++. |+++.+. |
T Consensus 244 DPyG~~Iy~~~k~GS~k~ah~se~latp~akflGv~~~DI~~ynl~--~t~~l~~~Dik~lk~ll~~----~~f~~~~-W 316 (356)
T COG1697 244 DPYGWYIYSVYKYGSIKLAHESERLATPDAKFLGVTMQDIVEYNLP--QTDKLKDRDIKRLKELLRD----PRFQKEF-W 316 (356)
T ss_pred CCCEEEEEEEEEecchhhhhcchhhcCCcceeeeccHHHHhhcccc--ccccchhhhHHHHHHHhcc----ccccchh-H
Confidence 9999999999999999999999999999999999999999999987 5669999999999999999 8997555 9
Q ss_pred HHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCC
Q 029346 153 EKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAED 192 (194)
Q Consensus 153 ~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~ 192 (194)
++||+.|++.++||||||++++|.+|++..|||+||.+.+
T Consensus 317 ~~el~~~l~i~kK~E~qAla~kgl~~v~~~ylpeki~e~~ 356 (356)
T COG1697 317 KEELKLLLKIGKKAEQQALASKGLEFVAKTYLPEKIEELK 356 (356)
T ss_pred HHHHHHHHHHhHHHHHHHHHhcChHHhHHhhhHHHHhccC
Confidence 9999999999999999999999999999999999998753
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=1.2e-40 Score=267.37 Aligned_cols=141 Identities=35% Similarity=0.560 Sum_probs=129.9
Q ss_pred cEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhhCCccccc
Q 029346 32 FIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAG 92 (194)
Q Consensus 32 ~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~ 92 (194)
++||||||+|||++|+++++ |.||++|+++.++|+|+++|+||||++|+++|++||.+++|
T Consensus 1 ~~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG~P~~~tr~~l~~L~~~~~~~~~~l~D~DP~Gi~I~~~y~~gs~~~~~ 80 (160)
T cd00223 1 DFVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRATRRFLRRLHEELDLPVYILVDGDPYGISILLTYKYGSIKLAY 80 (160)
T ss_pred CEEEEEecHHHHHHHHHcCccccCCEEEEEcCCcCCHHHHHHHHHHHHhhCCCEEEEECCCcchhhhhHHHHhCcccccc
Confidence 58999999999999999754 99999999988999999999999999999999999999999
Q ss_pred ccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHHHHHHhCCeeeEeeec
Q 029346 93 RNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALD 172 (194)
Q Consensus 93 ~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~~ml~~~~KaEieal~ 172 (194)
+...+++|+++|+|++++|+.+ ++..+.+|||++|++++++++++ +....+++|++|+++|++.|+|+||||+.
T Consensus 81 ~~~~~~~~~l~~~G~~~~d~~~--~~~~~~~~Ls~~d~~~l~~ll~~----~~~~~~~~~~~el~~ml~~~~K~E~Eal~ 154 (160)
T cd00223 81 ESESLATPDLRWLGLRPSDIIR--LPDLPLLPLSERDLKRAKSLLRR----PRFKELPEWKRELQLMLKLGKKAEIEALA 154 (160)
T ss_pred ccccccCCCcEEccCCHHHHhh--ccccccCCCCHHHHHHHHHHHhc----cccccCHHHHHHHHHHHHhCCeeeehhHh
Confidence 9999999999999999999975 45678899999999999999999 45445789999999999999999999999
Q ss_pred cccccc
Q 029346 173 MYEYKY 178 (194)
Q Consensus 173 ~~g~~~ 178 (194)
+.|.+|
T Consensus 155 ~~~~~~ 160 (160)
T cd00223 155 SCGLEF 160 (160)
T ss_pred hcCCCC
Confidence 887653
No 6
>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=98.56 E-value=4e-08 Score=80.57 Aligned_cols=128 Identities=20% Similarity=0.113 Sum_probs=85.5
Q ss_pred ccceeeeeccccEEEEEccchhhhhhchh---------HH-----HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhhC
Q 029346 21 ICIITNTVSNFFIVIRLIREGAANRTCEN---------KI-----VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFG 86 (194)
Q Consensus 21 ~~~i~~i~~~a~~VLVVEKdavF~~L~~~---------~f-----R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~G 86 (194)
++.+..+...++.|||||..+.|.++.+. || +.|++.+.. .|++.++|-||+|+.|+...+.-
T Consensus 33 ~~~l~~~~~~~~~vliVEN~~tf~~~~~~~~~~~Iyg~G~~~~~~~~~~~~~~~---~~~~ywGDiD~~G~~I~~~lr~~ 109 (181)
T PF09983_consen 33 LEELEILSLPPRRVLIVENLTTFYSLPELPNGLVIYGGGFAISSSRRFLKWLQP---KPVYYWGDIDPGGLRILERLRRK 109 (181)
T ss_pred HHHHHhccCCCCEEEEEeCHHHHHHHHhcCCeEEEECCCcCcHHHHHHHhhcCC---CceEEeccCCHhHHHHHHHHHHh
Confidence 45566667789999999999999999853 33 666664433 39999999999999999988762
Q ss_pred CcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHHHHHHhCCee
Q 029346 87 SKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKA 166 (194)
Q Consensus 87 S~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~~ml~~~~Ka 166 (194)
+|.++-.-+....+.++ .. ....+.+....+.+.. |+. + ....|+.=++.|+..+++.
T Consensus 110 ------------~p~~~p~~Md~~~l~~~-~~-~~~~~~~~~~~~~l~~-L~~----~---e~~~~~~l~~~~l~~~~ri 167 (181)
T PF09983_consen 110 ------------FPELKPLLMDEETLERY-QD-RYGKEPSEPYRRKLPR-LTD----E---EYALFRELIEEMLEEGKRI 167 (181)
T ss_pred ------------CCCccccccCHHHHHHH-HH-hcCCCCCccccccchh-cCH----H---HHHHHHHHHHHHHhcCCee
Confidence 24444455555555543 11 1111224444444444 333 1 1345665666689999999
Q ss_pred eEeeecc
Q 029346 167 EIEALDM 173 (194)
Q Consensus 167 Eieal~~ 173 (194)
|+|++..
T Consensus 168 EQE~I~~ 174 (181)
T PF09983_consen 168 EQERIPW 174 (181)
T ss_pred eeccccH
Confidence 9999973
No 7
>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=98.13 E-value=2.6e-06 Score=68.33 Aligned_cols=121 Identities=17% Similarity=0.131 Sum_probs=80.9
Q ss_pred cceeeeeccccEEEEEccchhhhhhchh-HH----------------HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHh
Q 029346 22 CIITNTVSNFFIVIRLIREGAANRTCEN-KI----------------VILLREIRCKLKKSVLGSFDCNPYGIHILTVYM 84 (194)
Q Consensus 22 ~~i~~i~~~a~~VLVVEKdavF~~L~~~-~f----------------R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk 84 (194)
..+..+.+....|.|||+-+||.++++. +. +.||.+|.. .+.++++-+|+||.|+.|+...+
T Consensus 9 ~~~~~~~~~~~~V~VvENp~Vf~~~~~~~~~~~~pLVCt~G~p~~A~~~LL~~L~~-~g~~l~y~GDfDp~Gl~IA~~l~ 87 (152)
T PF09664_consen 9 SRVPRIWPPSGRVYVVENPAVFSALADELGASCPPLVCTSGQPSAAARRLLDRLAA-AGARLYYSGDFDPEGLRIANRLI 87 (152)
T ss_pred hccccccCCCCEEEEEecHHHHHHHHHhcCCCCCeEEEcCCcHHHHHHHHHHHHHh-CCCEEEEecCCCHHHHHHHHHHH
Confidence 3344455666679999999999999987 11 999999954 58999999999999999999987
Q ss_pred hCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHHHHHHhCC
Q 029346 85 FGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGE 164 (194)
Q Consensus 85 ~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~~ml~~~~ 164 (194)
.- +. +.| | -+.+.|+... + ...+++.+..+ +.++ . |+. +.=...|.+.|+
T Consensus 88 ~r-----~~----~~~---W-rm~~~dY~~~-~---~~~~~~~~~l~-l~~v--~----p~~------~~L~~~m~~~~~ 137 (152)
T PF09664_consen 88 QR-----YG----ARP---W-RMDAEDYLAA-L---SAEPLSGRRLK-LPNV--A----PWL------PELAEAMRERGR 137 (152)
T ss_pred HH-----hC----Ccc---c-cCCHHHHHHh-c---cccCCCCCcCC-cccC--C----hhc------HHHHHHHHHhCc
Confidence 41 00 122 2 3445555321 1 22255555544 3333 1 222 233346999999
Q ss_pred eeeEeeecc
Q 029346 165 KAEIEALDM 173 (194)
Q Consensus 165 KaEieal~~ 173 (194)
+++.|++..
T Consensus 138 a~~QE~l~~ 146 (152)
T PF09664_consen 138 AVYQEALLD 146 (152)
T ss_pred eeeHHHHHH
Confidence 999999874
No 8
>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=93.79 E-value=0.085 Score=48.35 Aligned_cols=52 Identities=12% Similarity=-0.003 Sum_probs=43.5
Q ss_pred EEEEEccchhhhhhchh------------HH-----HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhh
Q 029346 33 IVIRLIREGAANRTCEN------------KI-----VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMF 85 (194)
Q Consensus 33 ~VLVVEKdavF~~L~~~------------~f-----R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~ 85 (194)
.|.|||-=+||..+++. |+ +.||.+|... +.++++=.|.||-||.|+..-+.
T Consensus 252 ~V~vvENp~vf~~~~~~~~~~~~~lIct~G~p~~a~~~LL~~L~~~-g~~l~YhGDfD~~Gi~Ia~~L~~ 320 (385)
T TIGR02679 252 RVYVVENPNVLAIALDRLGPRCAPLVCTDGQPNAAQIKLLDLLAAA-GARLYYHGDFDWPGLRIANGLIR 320 (385)
T ss_pred eEEEEecHHHHHHHHHhcCCCCceEEECCCcchHHHHHHHHHHHhc-CCeEEEecCCChhHHHHHHHHHH
Confidence 59999999999999884 33 9999999875 45566669999999999988763
No 9
>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=93.10 E-value=0.24 Score=32.88 Aligned_cols=47 Identities=15% Similarity=-0.033 Sum_probs=32.7
Q ss_pred cEEEEEccchhhhhhchhHH-------------HHHHHHHHhhc--CCcEEEEecCCcchhH
Q 029346 32 FIVIRLIREGAANRTCENKI-------------VILLREIRCKL--KKSVLGSFDCNPYGIH 78 (194)
Q Consensus 32 ~~VLVVEKdavF~~L~~~~f-------------R~fl~~L~~~~--~lpi~~L~D~DP~Gi~ 78 (194)
+.|++||.++....|.+.++ ......+.... ..+++.++|.|+.|..
T Consensus 1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~v~i~~D~D~~g~~ 62 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEA 62 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCCCEEEEEEccEEcHHHHHHHHHHhcCCCEEEEEcCCChhHHH
Confidence 36889999998887776533 21233333322 4899999999999983
No 10
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=81.63 E-value=2.2 Score=41.29 Aligned_cols=53 Identities=11% Similarity=-0.059 Sum_probs=41.6
Q ss_pred ccEEEEEccch---hhhhhchhH------------------HHHHHHHHHhhcCCcEEEEecCCcchhHHHHHHh
Q 029346 31 FFIVIRLIREG---AANRTCENK------------------IVILLREIRCKLKKSVLGSFDCNPYGIHILTVYM 84 (194)
Q Consensus 31 a~~VLVVEKda---vF~~L~~~~------------------fR~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk 84 (194)
|+.||.||=+| +.+.|+... |..|++ +.+..++++++++|+||.|...-.+-+
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 ARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGSGLKPFIK-FAEAMGIRVHVITDGDEAGKKYEATVR 469 (581)
T ss_pred hceeEEEeccchhhhHHHHHHHhccccccCcEEEEeecccCcHHHHH-HhhccCceEEEEecCCcccchhhhhhh
Confidence 67899999876 356555431 189998 888889999999999999998776655
No 11
>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=77.55 E-value=4.9 Score=29.03 Aligned_cols=47 Identities=11% Similarity=-0.041 Sum_probs=33.0
Q ss_pred ccEEEEEccch---hhhhhchh--------H----------HHHHHHHHHhhcCCcEEEEecCCcchhH
Q 029346 31 FFIVIRLIREG---AANRTCEN--------K----------IVILLREIRCKLKKSVLGSFDCNPYGIH 78 (194)
Q Consensus 31 a~~VLVVEKda---vF~~L~~~--------~----------fR~fl~~L~~~~~lpi~~L~D~DP~Gi~ 78 (194)
|+.||+||-++ +++.+.+. + +..|.+.|. .+++|+++++|.|.-+-.
T Consensus 3 a~~vIlVEG~tE~~~l~~~~~~~~~~~~~~~i~ii~~gG~~~~~~~~ll~-~~~i~~~vi~D~D~~~~~ 70 (97)
T cd01026 3 ADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGKNFKPFIKLLN-ALGIPVAVLTDLDAKRNE 70 (97)
T ss_pred CCeEEEEecHHHHHHHHHHHHHhCCCHHHCCEEEEEeCCcchHHHHHHHH-HcCCCEEEEEeCCCCCCc
Confidence 57788898754 34444432 1 266766665 468999999999998876
No 12
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=69.19 E-value=14 Score=24.81 Aligned_cols=49 Identities=16% Similarity=0.038 Sum_probs=31.5
Q ss_pred EEEEEccchhhhhhchhHH--------------HHHHHHHHhhcC-CcEEEEecCCcchhHHHH
Q 029346 33 IVIRLIREGAANRTCENKI--------------VILLREIRCKLK-KSVLGSFDCNPYGIHILT 81 (194)
Q Consensus 33 ~VLVVEKdavF~~L~~~~f--------------R~fl~~L~~~~~-lpi~~L~D~DP~Gi~I~~ 81 (194)
.++|||....--++.+.++ ...+..|.+... -.|+..+|.|+-|-.+..
T Consensus 2 ~l~ivEg~~da~~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~~~~~Iii~~D~D~~G~~~~~ 65 (76)
T smart00493 2 VLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEIIKLLKRLAKKKEVILATDPDREGEAIAW 65 (76)
T ss_pred EEEEEcCHHHHHHHHHhcCCCEEEEEEeeeecHHHHHHHHHHHhcCCEEEEEcCCChhHHHHHH
Confidence 3667776655555444322 345555555433 469999999999988764
No 13
>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=64.73 E-value=20 Score=25.43 Aligned_cols=32 Identities=16% Similarity=0.010 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHh
Q 029346 52 VILLREIRCKLKKSVLGSFDCNPYGIHILTVYM 84 (194)
Q Consensus 52 R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk 84 (194)
...+..|.+. .-.++.|+|+|.-|-.|.....
T Consensus 35 ~~~~~~l~~~-~~~VIiltD~D~aG~~i~~~~~ 66 (81)
T cd01027 35 KETIELIKKA-YRGVIILTDPDRKGEKIRKKLS 66 (81)
T ss_pred HHHHHHHHHh-CCEEEEEECCCHHHHHHHHHHH
Confidence 4566666554 5689999999999999966554
No 14
>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=50.56 E-value=74 Score=26.20 Aligned_cols=34 Identities=18% Similarity=-0.055 Sum_probs=24.5
Q ss_pred HHHHHHHHhhc-CCcEEEEecCCcchhHHHHHHhh
Q 029346 52 VILLREIRCKL-KKSVLGSFDCNPYGIHILTVYMF 85 (194)
Q Consensus 52 R~fl~~L~~~~-~lpi~~L~D~DP~Gi~I~~tYk~ 85 (194)
..-+.++.+.. .-.|++|+|.|--|-.|-.....
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD~~GekIRk~i~~ 69 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQ 69 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCCCchHHHHHHHHH
Confidence 34444444432 46899999999999998877764
No 15
>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=48.29 E-value=29 Score=24.93 Aligned_cols=30 Identities=13% Similarity=0.101 Sum_probs=21.4
Q ss_pred HHHHHHhhc--CCcEEEEecCCcchhHHHHHH
Q 029346 54 LLREIRCKL--KKSVLGSFDCNPYGIHILTVY 83 (194)
Q Consensus 54 fl~~L~~~~--~lpi~~L~D~DP~Gi~I~~tY 83 (194)
.++.|.+.. --.++..+|+|.-|=.|+.--
T Consensus 49 ~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i 80 (100)
T PF01751_consen 49 QIKNLKKLLKKADEIIIATDPDREGELIAWEI 80 (100)
T ss_dssp HHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHH
T ss_pred cchhhHHHhhhccEeeecCCCChHHHHHHHHH
Confidence 366666542 358999999999999887644
No 16
>PRK04017 hypothetical protein; Provisional
Probab=45.53 E-value=43 Score=26.37 Aligned_cols=33 Identities=15% Similarity=-0.000 Sum_probs=23.7
Q ss_pred HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhh
Q 029346 52 VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMF 85 (194)
Q Consensus 52 R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~ 85 (194)
..+..++.. ..--|++|+|+|..|-.|......
T Consensus 55 ~~~~e~ia~-~~r~VIILTD~D~~GekIr~~l~~ 87 (132)
T PRK04017 55 AEIAELIAS-RGKEVIILTDFDRKGEELAKKLSE 87 (132)
T ss_pred chHHHHHHh-cCCeEEEEECCCcchHHHHHHHHH
Confidence 444444532 345899999999999999766643
No 17
>COG4069 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.87 E-value=16 Score=32.81 Aligned_cols=28 Identities=14% Similarity=0.087 Sum_probs=19.3
Q ss_pred hhcCCcEEEEecCCcchhHHHHHHhhCC
Q 029346 60 CKLKKSVLGSFDCNPYGIHILTVYMFGS 87 (194)
Q Consensus 60 ~~~~lpi~~L~D~DP~Gi~I~~tYk~GS 87 (194)
..+++|++|++|+||.-+-=...|.-||
T Consensus 286 ~RfgipiiGItDgD~D~~~~~~~~~~gs 313 (367)
T COG4069 286 YRFGIPIIGITDGDCDEVTREVNIAPGS 313 (367)
T ss_pred HhcCCcEEecccCChHHhhhhcccCCCc
Confidence 3469999999999999444333444443
No 18
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=37.03 E-value=85 Score=21.54 Aligned_cols=22 Identities=23% Similarity=0.202 Sum_probs=17.2
Q ss_pred CCcEEEEecCCcchhHHHHHHh
Q 029346 63 KKSVLGSFDCNPYGIHILTVYM 84 (194)
Q Consensus 63 ~lpi~~L~D~DP~Gi~I~~tYk 84 (194)
.-+++.++|.|.-|...+..-.
T Consensus 46 ~~~Vii~~D~D~~G~~~a~~i~ 67 (81)
T PF13662_consen 46 VKEVIIAFDNDKAGEKAAQKIA 67 (81)
T ss_dssp -SEEEEEEESSHHHHHHHHHHH
T ss_pred CceEEEEeCcCHHHHHHHHHHH
Confidence 4789999999999987665443
No 19
>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofact
Probab=36.68 E-value=23 Score=27.45 Aligned_cols=49 Identities=12% Similarity=0.014 Sum_probs=33.3
Q ss_pred cEEEEEccchhhhhhch-hHHHHHHHHHH------hhc------CCcEEEEecCCcchhHHHH
Q 029346 32 FIVIRLIREGAANRTCE-NKIVILLREIR------CKL------KKSVLGSFDCNPYGIHILT 81 (194)
Q Consensus 32 ~~VLVVEKdavF~~L~~-~~fR~fl~~L~------~~~------~lpi~~L~D~DP~Gi~I~~ 81 (194)
-.||=|||-. +.++.+ +-++.++.-|- +.. .=.+.+++|+|+.|.+|..
T Consensus 34 GKiLNv~ka~-~~ki~~n~Ei~~li~alG~g~~~~~~~~~~~lrY~kiiimtDaD~DG~hI~~ 95 (120)
T cd03365 34 GKLLNVREAS-HKQIMENAEIQNIKKILGLQHGKSDYESTKSLRYGRLMIMTDQDHDGSHIKG 95 (120)
T ss_pred CccchhhcCC-HHHHhcCHHHHHHHHHhCCCCCcccccccccCCcCeEEEEeCCCCCccHHHH
Confidence 3577788865 555543 44577777764 111 1368999999999999864
No 20
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=35.78 E-value=99 Score=24.13 Aligned_cols=54 Identities=17% Similarity=0.067 Sum_probs=36.2
Q ss_pred ccEEEEEccch---hhhhhchhHH----------HHHHHHHHhhc-CCcEEEEecCCcchhHHHHHHh
Q 029346 31 FFIVIRLIREG---AANRTCENKI----------VILLREIRCKL-KKSVLGSFDCNPYGIHILTVYM 84 (194)
Q Consensus 31 a~~VLVVEKda---vF~~L~~~~f----------R~fl~~L~~~~-~lpi~~L~D~DP~Gi~I~~tYk 84 (194)
.+.|+|||=-. --+++...+- -.++.+|.... .-.|++|+|+|-.|=.|....+
T Consensus 9 ~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~~Ge~Irk~l~ 76 (127)
T COG1658 9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDRKGERIRKKLK 76 (127)
T ss_pred cCceEEEeCCcHHHHHHHhcCCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCCcchHHHHHHHH
Confidence 36788998422 2344433321 46777777644 4679999999999998876654
No 21
>cd01030 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=35.76 E-value=24 Score=27.11 Aligned_cols=49 Identities=12% Similarity=0.179 Sum_probs=33.3
Q ss_pred cEEEEEccchhhhhhc-hhHHHHHHHHHHhh-----c------CCcEEEEecCCcchhHHHH
Q 029346 32 FIVIRLIREGAANRTC-ENKIVILLREIRCK-----L------KKSVLGSFDCNPYGIHILT 81 (194)
Q Consensus 32 ~~VLVVEKdavF~~L~-~~~fR~fl~~L~~~-----~------~lpi~~L~D~DP~Gi~I~~ 81 (194)
-.+|=|||-. +.++. ++-++.++.-|-.. . -=.+.+++|+|+.|.+|..
T Consensus 31 GKiLNv~ka~-~~k~~~n~Ei~~l~~alG~~~~~~~~~~~~lrY~kiiimtDaD~DG~hI~~ 91 (115)
T cd01030 31 GKILNVEKAS-LKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMTDADVDGSHIRT 91 (115)
T ss_pred CeeccHhcCC-HHHHhcChHHHHHHHHhCCCCCcccCChhhcCcCeEEEEeCCCCCccHhHH
Confidence 3577788865 45544 44557777766521 1 1368999999999999864
No 22
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=35.31 E-value=33 Score=26.70 Aligned_cols=16 Identities=19% Similarity=0.542 Sum_probs=14.8
Q ss_pred cCCHHHHHHHHHHHhc
Q 029346 124 ILSKDDISKLKTFLEK 139 (194)
Q Consensus 124 ~Lt~rD~~~~~~ll~~ 139 (194)
.||+.++.++.+.+++
T Consensus 47 eLteeei~~ir~~i~~ 62 (121)
T COG0099 47 ELTEEEIERLRDAIQN 62 (121)
T ss_pred cCCHHHHHHHHHHHHh
Confidence 6999999999999995
No 23
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=34.72 E-value=28 Score=28.17 Aligned_cols=28 Identities=25% Similarity=0.369 Sum_probs=19.3
Q ss_pred cHHHHHHHHH---HHHhCCeeeEeeeccccc
Q 029346 149 NASWEKELQK---MSKEGEKAEIEALDMYEY 176 (194)
Q Consensus 149 ~~~~~~EL~~---ml~~~~KaEieal~~~g~ 176 (194)
.+.-.++|++ -...|.||++.-|.+.+.
T Consensus 93 DesN~~dL~~~a~~~~~~~kakV~Llgsy~~ 123 (159)
T KOG3217|consen 93 DESNLRDLLRKASNQPKGSKAKVLLLGSYDK 123 (159)
T ss_pred cHHHHHHHHHHhccCCCCcceEEEEeeccCC
Confidence 3444556666 466789999999987654
No 24
>KOG3905 consensus Dynein light intermediate chain [Cell motility]
Probab=31.12 E-value=18 Score=33.28 Aligned_cols=11 Identities=0% Similarity=0.030 Sum_probs=9.7
Q ss_pred EEEEccchhhh
Q 029346 34 VIRLIREGAAN 44 (194)
Q Consensus 34 VLVVEKdavF~ 44 (194)
.+||||||||-
T Consensus 298 AlVVEkdaVfI 308 (473)
T KOG3905|consen 298 ALVVEKDAVFI 308 (473)
T ss_pred ceEeecceeEe
Confidence 58999999993
No 25
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=30.57 E-value=64 Score=28.13 Aligned_cols=40 Identities=18% Similarity=0.045 Sum_probs=23.2
Q ss_pred eeeeeccccEEEEEccchhhhhhchhHHHHHHHHHHhhcCCcEEEEecCC
Q 029346 24 ITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCN 73 (194)
Q Consensus 24 i~~i~~~a~~VLVVEKdavF~~L~~~~fR~fl~~L~~~~~lpi~~L~D~D 73 (194)
|..+..-.+.++||....=-+-..| +..+++||++++|.|
T Consensus 150 Ik~m~~~Pd~l~ViDp~~e~iAv~E----------A~klgIPVvAlvDTn 189 (252)
T COG0052 150 IKDMKGLPDVLFVIDPRKEKIAVKE----------ANKLGIPVVALVDTN 189 (252)
T ss_pred hhhccCCCCEEEEeCCcHhHHHHHH----------HHHcCCCEEEEecCC
Confidence 3334444667777755433332222 224699999999865
No 26
>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. 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 strand joining and as a general acid in strand cleava
Probab=30.14 E-value=35 Score=26.21 Aligned_cols=48 Identities=15% Similarity=0.257 Sum_probs=32.6
Q ss_pred EEEEEccchhhhhhch-hHHHHHHHHHHh----hc------CCcEEEEecCCcchhHHHH
Q 029346 33 IVIRLIREGAANRTCE-NKIVILLREIRC----KL------KKSVLGSFDCNPYGIHILT 81 (194)
Q Consensus 33 ~VLVVEKdavF~~L~~-~~fR~fl~~L~~----~~------~lpi~~L~D~DP~Gi~I~~ 81 (194)
.||=|||-. |.++.+ +-++.++.-|-. +. -=.+.+++|+|+.|.+|..
T Consensus 32 KiLNv~ka~-~~ki~~n~Ei~~li~alG~g~~~~~~~~~lrY~kiiimtDaD~DG~hI~~ 90 (114)
T cd03366 32 KILNVEKAR-LDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTDADVDGAHIRT 90 (114)
T ss_pred ccchHhhcc-HHHHhcChHHHHHHHHhCCCCCCCCChhhCCcCeEEEEeCCCCCchHHHH
Confidence 577788865 555543 345666666652 11 1368999999999999864
No 27
>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=26.70 E-value=1.6e+02 Score=20.14 Aligned_cols=50 Identities=12% Similarity=0.057 Sum_probs=34.1
Q ss_pred EEEEccchhhhhhchhHH--------------HHHHHHHHhhcCCcEEEEecCCc---chhHHHHHHhh
Q 029346 34 VIRLIREGAANRTCENKI--------------VILLREIRCKLKKSVLGSFDCNP---YGIHILTVYMF 85 (194)
Q Consensus 34 VLVVEKdavF~~L~~~~f--------------R~fl~~L~~~~~lpi~~L~D~DP---~Gi~I~~tYk~ 85 (194)
|||||.+..+.++.+..+ ..++..+.+. -|=++++|.+. .|++++...+.
T Consensus 1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~--~~d~iiid~~~~~~~~~~~~~~i~~ 67 (112)
T PF00072_consen 1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKH--PPDLIIIDLELPDGDGLELLEQIRQ 67 (112)
T ss_dssp EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHS--TESEEEEESSSSSSBHHHHHHHHHH
T ss_pred cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhccc--CceEEEEEeeecccccccccccccc
Confidence 789999999888877644 6667777543 37778888554 45555555543
No 28
>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=24.99 E-value=1.3e+02 Score=20.47 Aligned_cols=24 Identities=21% Similarity=0.230 Sum_probs=16.9
Q ss_pred HHHHHHhhcCCcEEEEecCCcchhH
Q 029346 54 LLREIRCKLKKSVLGSFDCNPYGIH 78 (194)
Q Consensus 54 fl~~L~~~~~lpi~~L~D~DP~Gi~ 78 (194)
.+..|... .-.++.++|.|+-|..
T Consensus 35 ~~~~L~~~-~~~vii~~D~D~aG~~ 58 (79)
T cd03364 35 QAELLKRL-AKEVILAFDGDEAGQK 58 (79)
T ss_pred HHHHHHhc-CCeEEEEECCCHHHHH
Confidence 34444432 3579999999999974
No 29
>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH. They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.
Probab=22.02 E-value=1.1e+02 Score=24.78 Aligned_cols=55 Identities=15% Similarity=0.124 Sum_probs=32.4
Q ss_pred eeeeeccccEEEEEccchhhhhhchhHH----------------HHHHHHHHhhcCCcEEEEecCCcchhHH
Q 029346 24 ITNTVSNFFIVIRLIREGAANRTCENKI----------------VILLREIRCKLKKSVLGSFDCNPYGIHI 79 (194)
Q Consensus 24 i~~i~~~a~~VLVVEKdavF~~L~~~~f----------------R~fl~~L~~~~~lpi~~L~D~DP~Gi~I 79 (194)
++-++..|+.|+.||++.---+.++... ..++.++.....--=++|.| -||....
T Consensus 58 lEALSRGA~~v~fVE~~~~a~~~i~~N~~~l~~~~~~~v~~~d~~~~l~~~~~~~~~fDiIflD-PPY~~~~ 128 (183)
T PF03602_consen 58 LEALSRGAKSVVFVEKNRKAIKIIKKNLEKLGLEDKIRVIKGDAFKFLLKLAKKGEKFDIIFLD-PPYAKGL 128 (183)
T ss_dssp HHHHHTT-SEEEEEES-HHHHHHHHHHHHHHT-GGGEEEEESSHHHHHHHHHHCTS-EEEEEE---STTSCH
T ss_pred HHHHhcCCCeEEEEECCHHHHHHHHHHHHHhCCCcceeeeccCHHHHHHhhcccCCCceEEEEC-CCcccch
Confidence 3445678999999999977665665533 56666664322223377888 6788764
No 30
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=20.28 E-value=2.6e+02 Score=22.25 Aligned_cols=73 Identities=12% Similarity=0.032 Sum_probs=47.2
Q ss_pred hhHH-HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCcccccccc----------
Q 029346 48 ENKI-VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYN---------- 116 (194)
Q Consensus 48 ~~~f-R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~---------- 116 (194)
+.|+ |..+..|-..-...|--||-.|-||=. - +|+..+..++=+|+-.-+.+-.+++
T Consensus 27 e~Gglr~~~~k~yrtd~~kiGTLVG~DkfGNk----------Y--yen~~~fygRhRWVeya~kv~~Dyd~S~VP~EWh~ 94 (151)
T KOG3382|consen 27 EEGGLRCLLDKLYRTDDHKIGTLVGVDKFGNK----------Y--YENNDYFYGRHRWVEYASKVNWDYDASQVPAEWHG 94 (151)
T ss_pred hhccHHHHHHHHHhcccccceeeeeecccccc----------h--hcccceecccceeEEecccccccccccCCCHHHHh
Confidence 3454 888877776656788899988877632 2 5555666778888876665544432
Q ss_pred -------CCccccccCCHHHHHH
Q 029346 117 -------IPKLCRQILSKDDISK 132 (194)
Q Consensus 117 -------~~~~~~~~Lt~rD~~~ 132 (194)
.|.+..+|+.+++.-.
T Consensus 95 WlH~iTD~~p~~~~~~~~~k~i~ 117 (151)
T KOG3382|consen 95 WLHFITDDPPDEKLPLPPKKWIL 117 (151)
T ss_pred HhHhhccCCccccCCCCHHHHhH
Confidence 2445566777776543
Done!