Query 040782
Match_columns 435
No_of_seqs 211 out of 434
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 11:45:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040782.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040782hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04342 DNA topoisomerase VI 100.0 8.9E-95 1.9E-99 737.8 33.3 351 83-435 8-366 (367)
2 PLN00060 meiotic recombination 100.0 3E-94 6.4E-99 732.7 29.3 349 81-435 21-384 (384)
3 KOG2795 Catalytic subunit of t 100.0 8.3E-92 1.8E-96 698.2 23.7 361 64-435 10-372 (372)
4 COG1697 DNA topoisomerase VI, 100.0 5.1E-90 1.1E-94 682.2 21.2 345 86-433 7-356 (356)
5 cd00223 TOPRIM_TopoIIB_SPO TOP 100.0 8E-45 1.7E-49 331.7 15.9 160 258-419 1-160 (160)
6 PF04406 TP6A_N: Type IIB DNA 99.8 2.9E-20 6.3E-25 147.0 5.4 68 144-211 1-68 (68)
7 PF09983 DUF2220: Uncharacteri 99.6 4.5E-16 9.8E-21 145.3 9.2 163 223-413 10-173 (181)
8 PF09664 DUF2399: Protein of u 99.4 8.3E-13 1.8E-17 120.2 8.0 133 253-414 14-146 (152)
9 TIGR02679 conserved hypothetic 98.7 2.5E-08 5.4E-13 103.3 6.9 126 259-414 252-379 (385)
10 cd00188 TOPRIM Topoisomerase-p 96.6 0.011 2.3E-07 45.7 7.8 64 258-325 1-64 (83)
11 COG4924 Uncharacterized protei 91.9 0.36 7.8E-06 48.7 6.1 68 252-330 236-305 (386)
12 TIGR00334 5S_RNA_mat_M5 ribonu 88.0 2.8 6.1E-05 39.3 8.4 81 258-345 3-86 (174)
13 cd01026 TOPRIM_OLD TOPRIM_OLD: 82.6 4.9 0.00011 33.4 6.6 63 257-323 3-70 (97)
14 cd01027 TOPRIM_RNase_M5_like T 79.1 14 0.0003 30.2 7.9 66 258-330 2-67 (81)
15 smart00493 TOPRIM topoisomeras 78.9 12 0.00027 28.9 7.5 65 259-328 2-67 (76)
16 PRK04017 hypothetical protein; 75.1 8.1 0.00018 34.7 5.9 67 256-330 21-87 (132)
17 COG3593 Predicted ATP-dependen 73.7 7.6 0.00016 42.9 6.5 102 224-329 356-469 (581)
18 PF13662 Toprim_4: Toprim doma 54.1 77 0.0017 25.1 7.4 66 259-330 2-68 (81)
19 PF01751 Toprim: Toprim domain 53.6 44 0.00095 27.6 6.1 68 260-329 2-81 (100)
20 COG1658 Small primase-like pro 52.0 83 0.0018 28.1 7.8 67 258-329 10-76 (127)
21 cd07022 S49_Sppa_36K_type Sign 49.5 1.5E+02 0.0032 28.1 9.8 105 280-384 42-161 (214)
22 PF00072 Response_reg: Respons 45.2 1.2E+02 0.0025 24.3 7.4 32 284-315 46-78 (112)
23 PRK04031 DNA primase; Provisio 36.6 98 0.0021 32.9 6.7 65 256-330 168-232 (408)
24 PRK11517 transcriptional regul 36.1 2.6E+02 0.0057 25.1 9.0 49 283-332 46-94 (223)
25 cd03364 TOPRIM_DnaG_primases T 34.7 1.3E+02 0.0029 23.6 6.0 57 259-323 2-58 (79)
26 PRK08252 enoyl-CoA hydratase; 32.0 1.5E+02 0.0032 28.9 6.9 45 306-356 89-137 (254)
27 PRK13856 two-component respons 31.0 2.4E+02 0.0052 26.2 8.0 50 282-331 46-95 (241)
28 cd01029 TOPRIM_primases TOPRIM 27.6 2.9E+02 0.0062 21.3 6.8 59 259-325 2-60 (79)
29 PRK00933 ribosomal biogenesis 25.9 71 0.0015 29.7 3.3 28 284-311 1-28 (165)
30 COG0052 RpsB Ribosomal protein 25.4 40 0.00086 33.5 1.6 17 306-322 177-195 (252)
31 PF07085 DRTGG: DRTGG domain; 24.7 93 0.002 25.9 3.6 35 281-320 62-96 (105)
32 PF03709 OKR_DC_1_N: Orn/Lys/A 22.3 1.4E+02 0.003 25.6 4.2 57 260-318 20-77 (115)
33 TIGR00729 ribonuclease H, mamm 22.3 71 0.0015 30.5 2.6 19 287-305 166-186 (206)
34 TIGR00987 himA integration hos 21.2 1.8E+02 0.0039 24.0 4.6 37 73-109 6-42 (96)
35 cd07023 S49_Sppa_N_C Signal pe 20.9 6.9E+02 0.015 23.3 9.3 78 307-384 65-154 (208)
36 PRK07511 enoyl-CoA hydratase; 20.8 3.7E+02 0.008 26.1 7.4 43 307-355 97-143 (260)
37 PRK00285 ihfA integration host 20.5 1.8E+02 0.004 24.0 4.5 41 69-109 3-43 (99)
No 1
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=100.00 E-value=8.9e-95 Score=737.79 Aligned_cols=351 Identities=37% Similarity=0.617 Sum_probs=341.1
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHcCCCceEEeccCCCCCcccccCCCeEEecCCccccccCChhhHHHHHHHHHHHHHHH
Q 040782 83 DLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIH 162 (435)
Q Consensus 83 ~~~~~ev~~rIe~~~~~i~~~i~~g~~~~~~ip~R~~~n~~~~~~~~~~~l~~~~~~r~~~~~~~~~k~a~~~~vl~~i~ 162 (435)
..++++++++||++++++++++.+|+.|++++|+|+.+|..||++.+.+++|++.+.|+|.|++++++|+++++|++++|
T Consensus 8 ~~~~~~~~~~i~~l~~~~~~~~~~g~~p~~~ip~r~~~n~~~d~~~~~~~~~~~~~~r~~~~~~~a~~f~~~~~vl~~i~ 87 (367)
T PRK04342 8 KEDREKALKKLRELAEKIYEDIEKGKRPVLEIPKRTLSNIEYDEKKGLLVLGDKKSKRSFLNVKQAKKFMQTVLMAEFIK 87 (367)
T ss_pred cccHHHHHHHHHHHHHHHHHHHhcCCCCEEecccccccceEEccccCeEeeCCCceEEecCCHHHHHHHHHHHHHHHHHH
Confidence 44689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCcccceeeecCCcc--------ccCchHHHHHHHHHHHHHhcCCCCccceEecCCceEEEEEEEeeCCceEEee
Q 040782 163 QLCLRNIHVTKRDLFYTDVK--------LFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCT 234 (435)
Q Consensus 163 ~ll~~~~~~TkRdiYY~~~~--------lF~~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~G~l~~~~~g~~id~~ 234 (435)
++|.+|+++|+|||||++++ +|++|++||++|+|||+++|++|++|||+|++||+|+|++++..+++.|||+
T Consensus 88 ~~l~~~~~~T~RdiYY~~~~~~~~~~~~~F~~Q~~~d~~I~dl~~~l~~~R~~L~I~a~~KGlv~G~i~i~~~~~~id~~ 167 (367)
T PRK04342 88 ELLEENKSSTLRELYYMSKHWIPGLKENTFDDQDESDAVIEDLEVALGVLREELHIRPEEDGSVVGPLRIRDGTDEIDCS 167 (367)
T ss_pred HHHHcCCccchhhhcccCcccccccccccCCCHHHHHHHHHHHHHHHCCCHHHCCeeECCCeEEEeceEEEECCcEEEEe
Confidence 99999999999999999876 6999999999999999999999999999999999999999999988999999
Q ss_pred ccCCCccccCCCcccccccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEE
Q 040782 235 KMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLAL 314 (435)
Q Consensus 235 ~~~~~g~~Ip~~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~L 314 (435)
.++.+|+.||++++.++++.++|+|||||||+|+|++|++++|+++++|||||||||||++||+||++|++++++|||+|
T Consensus 168 ~~g~~~~~ip~~~~~i~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlItgkG~Pd~~TR~fl~~L~~~~~lpv~~l 247 (367)
T PRK04342 168 KLGEGGYSIPPNVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKGQPARATRRFIKRLNEELGLPVYVF 247 (367)
T ss_pred ccCCCceeCCCchhhheeeccCCCEEEEEechHHHHHHHHhCcccccCEEEEECCCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCchhhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccccccCChHHH
Q 040782 315 VDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWV 394 (435)
Q Consensus 315 vD~DP~Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~~~~~~~~w~ 394 (435)
||+||||++||++|||||++++|+++.+++|+++|+||+++|+.+| +|..+.+|||++|++++++||++|+++ ++.|+
T Consensus 248 ~D~DP~G~~I~~tyk~GS~~~a~~s~~l~~P~~kwlGl~~sDi~~~-~~~~~~~~Lt~~D~~~l~~lL~~~~~~-~~~w~ 325 (367)
T PRK04342 248 TDGDPWGYYIYSVVKYGSIKLAHLSERLATPDAKFIGVTPSDIVEY-ERDLPTIKLKDSDIKRAKELLNYPWFQ-TDFWQ 325 (367)
T ss_pred ECCCccHHHHHHHHHhCchhhhhhhhhccCCCCEEecCcHHHHHhh-ccccccCCCCHHHHHHHHHHhcCcccc-CHHHH
Confidence 9999999999999999999999999999999999999999999998 666788999999999999999999985 67899
Q ss_pred HHHHHHHHcCCeeeeehhhhcCcccchhchHHhhhccCCCC
Q 040782 395 EELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL 435 (435)
Q Consensus 395 ~EL~~ML~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~~i 435 (435)
+||+.|++.|+|+|||||++.|++|++++|||+||++++||
T Consensus 326 ~El~~ml~~~~KaEiEal~~~~~~~~~~~Ylp~Ki~~~~~i 366 (367)
T PRK04342 326 KEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL 366 (367)
T ss_pred HHHHHHHHhCCceeeehhhhcChhhhHHHHHHHHHhcCCCC
Confidence 99999999999999999999999999999999999999997
No 2
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=100.00 E-value=3e-94 Score=732.65 Aligned_cols=349 Identities=36% Similarity=0.627 Sum_probs=329.6
Q ss_pred hhcCChHHHHHHHHHHHHHHHHHHHcCCCce--EEeccCCCCCcccccCC---C--eEEecCCccccccCChhhHHHHHH
Q 040782 81 VTDLSLSAVQSTIETLILQIARSILAGNGFS--FQVPSRASSNQLYVPEL---D--RIVLKDKTTLRPFASLSTVRKSTI 153 (435)
Q Consensus 81 ~~~~~~~ev~~rIe~~~~~i~~~i~~g~~~~--~~ip~R~~~n~~~~~~~---~--~~~l~~~~~~r~~~~~~~~~k~a~ 153 (435)
+...+++||+++||.++++++.+|..|.++. +++|+|+++|+.|.+.. + .+.+..+.++|+|.|++++++|++
T Consensus 21 ~~~~~~~~~~~~iE~~~~~~~~~l~~~~~~~~~~~~~~r~~~n~~~~~~~~~~~~~~~~l~~~~~~r~~~~~~~a~kf~~ 100 (384)
T PLN00060 21 ADILSPEEARARIEVAVLNFLAALNSPDPAISDLPLISRNCSNVLLRRGLLQGDVSSIFLSHLFCKRSLTKAGSAKAFVR 100 (384)
T ss_pred cccCChHHHHHHHHHHHHHHHHHHhcCCCccceecccccccccccccccccccccceeeeccceeeEecCCHHHHHHHHH
Confidence 3457999999999999999999999997665 88889999999999877 5 677778888999999999999999
Q ss_pred HHHHHHHHHHHhhcCCcccceeeecC----CccccCchHHHHHHHHHHHHHhcCCCCccceEecCCceEEEEEEEee-CC
Q 040782 154 TVKILSLIHQLCLRNIHVTKRDLFYT----DVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSD-NG 228 (435)
Q Consensus 154 ~~~vl~~i~~ll~~~~~~TkRdiYY~----~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~G~l~~~~-~g 228 (435)
+++||+++|++|.+|+++|+|||||+ ++++|++|++||++|+|||+++|++|++|||+|++||+|+|++++.. ++
T Consensus 101 ~~~vl~~i~~~l~~~~~~TkRdiYY~~~~~~~~lF~~Q~~vd~~I~Di~~~l~~~R~~L~I~a~~KGlV~G~l~i~~~~~ 180 (384)
T PLN00060 101 VWKVMEMCYQILGEGKLVTQRELFYKLLCDSPEYFSCQRHVNQTVQDVVSLLRCSRYSLGIMASSRGALIGRLVLQEPNE 180 (384)
T ss_pred HHHHHHHHHHHHHcCCccchHHhhcccccCChhhcCCHHHHHHHHHHHHHHHCCCHHHCCeEecCCceEEeeeEEEecCC
Confidence 99999999999999999999999999 88999999999999999999999999999999999999999999985 56
Q ss_pred ceEEeeccCCCccccCCCccccc--ccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhc
Q 040782 229 DMIDCTKMGMGGKAIPPNIDRVG--DMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKME 306 (435)
Q Consensus 229 ~~id~~~~~~~g~~Ip~~i~~i~--~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~ 306 (435)
+.+||+.+|.+|+.||++++.++ .+.++|+|||||||||||++|++++|++++||||||||||||++||+||++|+++
T Consensus 181 ~~idcs~~g~~G~~Ip~~~~~i~~~~i~s~a~~VLVVEKeavF~rL~e~~~~~~~~cILITgKGyPD~aTR~fL~~L~~~ 260 (384)
T PLN00060 181 EPVDCSILGISGHAITGDLNLLSNLILSSDARYIIVVEKDAIFQRLAEDRFFNHIPCILITAKGYPDLATRFILHRLSQT 260 (384)
T ss_pred cEEEeeccCCCceeCCCcHHHhhhcccccCccEEEEEecHHHHHHHHHhhhhhhCCEEEEecCCCCCHHHHHHHHHHHHh
Confidence 79999998889999999887766 4679999999999999999999999999999999999999999999999999998
Q ss_pred c-CCcEEEEecCCchhhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccc
Q 040782 307 L-KLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEED 385 (435)
Q Consensus 307 ~-~lPv~~LvD~DP~Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~ 385 (435)
+ ++|||+|||+||||++||++|||||++++|+++.+++| ++|||++|+|+.. +|.++++|||++|++++++||++|
T Consensus 261 ~p~lPv~~LvD~DP~Gi~I~~tYkyGS~~~a~es~~la~~-i~WLGl~~sDi~~--l~~~~~i~Lt~rD~~~~~~lL~~~ 337 (384)
T PLN00060 261 FPNLPILALVDWNPAGLAILCTYKFGSIGMGLEAYRYACN-VKWLGLRGDDLQL--IPPEAFVELKPRDLQIAKSLLSSK 337 (384)
T ss_pred cCCCCEEEEECCCcchHHHHHHhhcCchhhhhcccccccC-CeEecCCHHHHhc--CCHhhcCCCCHHHHHHHHHHhhCh
Confidence 6 89999999999999999999999999999999999886 9999999999985 888889999999999999999999
Q ss_pred cccCChHHHHHHHHHHHcCCeeeeehhhhcCcccchhchHHhhhccCCCC
Q 040782 386 FVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL 435 (435)
Q Consensus 386 ~~~~~~~w~~EL~~ML~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~~i 435 (435)
+++ ..|++||+.|++.|+|||||||+++|++|+++ |||+||.++|||
T Consensus 338 ~~~--~~w~~EL~~Ml~~~~KaEiEAL~~~g~~fl~~-Ylp~Ki~~~~~i 384 (384)
T PLN00060 338 FLQ--NRYREELTLMVQTGKRAEIEALYSHGYDYLGK-YVARKIVQGDYI 384 (384)
T ss_pred hHH--HHHHHHHHHHHHhCcchhhHhHHhcChHHHHH-HHHHHHhcCCcC
Confidence 996 38999999999999999999999999999996 999999999997
No 3
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=100.00 E-value=8.3e-92 Score=698.18 Aligned_cols=361 Identities=49% Similarity=0.805 Sum_probs=344.3
Q ss_pred CCcccccccchhhhhHHhhcCChHHHHHHHHHHHHHHHHHHHcCCCceEEeccCCCCCcccccCCCeEEecCCccccccC
Q 040782 64 SKPLTLSDLSLSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFA 143 (435)
Q Consensus 64 ~~~~~l~~~~~~~~~~~~~~~~~~ev~~rIe~~~~~i~~~i~~g~~~~~~ip~R~~~n~~~~~~~~~~~l~~~~~~r~~~ 143 (435)
-...++++.+.+ ..++++||..+..++.++.+.+++++.+++|..+|..+.++.+.....+..+.|.++
T Consensus 10 ~~~~~~~~~~~s-----------~~~la~I~~~v~~~~~~l~r~~~~sls~~~r~~~n~~~~~~l~~~~~~~~~~~~~~~ 78 (372)
T KOG2795|consen 10 RQSLTLNSNDLS-----------AVVLARIEDFVLSVLVQLARPEGFSLSVINRKRSNSLSSPDLDTLVSKSHNTLRFTF 78 (372)
T ss_pred CCCCcccccccc-----------hHHHHHHHHHHHHHHHHhhcccCCcccchhhhhcCCccCcchhhhhcccccccceee
Confidence 445677776666 567999999999999999999999999999999999999988877776766677777
Q ss_pred ChhhHHHHHHHHHHHHHHHHHhhcCCcccceeeecCCccccCchHHHHHHHHHHHHHhcCCCCccceEecCCceEEEEEE
Q 040782 144 SLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLI 223 (435)
Q Consensus 144 ~~~~~~k~a~~~~vl~~i~~ll~~~~~~TkRdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~G~l~ 223 (435)
+...+++|++++++|+++|+++..|+++|+|||||+|+++|++|.+||++++|||++|+|+|.+|||.|++||+|+|++.
T Consensus 79 ~~~~~~~~~~llrvL~~V~ell~~~~~~TkRdiyY~dv~lF~~Qs~Vd~~l~dI~~~l~~SR~sLnI~a~~KGLV~G~l~ 158 (372)
T KOG2795|consen 79 SSKKAKKFAILLRVLEIVHELLELGKRVTKRDIYYMDVDLFRRQSVVDRLLDDICCLLKCSRYSLNILAASKGLVAGRLR 158 (372)
T ss_pred ccccchHHHHHHHHHHHHHHHHHcCCceeeeeeeecCHHHHhhHHHHHHHHHHHHHHhcCChhcCCeeeecCceEEeeEE
Confidence 77779999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ee-eCCceEEeeccCCCccccCCCcccccccccCccEEEEEechhHHHHHHHccccCCC-CeEEEecCCcCChHHHHHHH
Q 040782 224 FS-DNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRF-PCIIVTAKGQPDVATRLFLR 301 (435)
Q Consensus 224 ~~-~~g~~id~~~~~~~g~~Ip~~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~-~~ILITgKGyPD~aTR~fL~ 301 (435)
|. ++|+.+||+..+.++.+||++++.+..+.++|+||||||||||||||+++.|++++ +||+||||||||.+||.||+
T Consensus 159 ~~~~ng~~id~~~~~~~~~~lp~d~~~i~~i~tdA~~IlIVEKeavFqrL~~d~~~~~~~~~ilITgKGyPD~~TR~fLk 238 (372)
T KOG2795|consen 159 FLEENGDVIDCTESGGGPKALPPDIDDISNITTDAKFILIVEKEAVFQRLAEDNFFNTFNRCILITGKGYPDIATRLFLK 238 (372)
T ss_pred EEEcCCcEEEeccCCCCCccCCCCHHHHhhhhccceEEEEEehHHHHHHHHHHHHHhhcCCeEEEecCCCCcHHHHHHHH
Confidence 98 49999999988889999999999999999999999999999999999999999998 79999999999999999999
Q ss_pred HHhhccCCcEEEEecCCchhhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHh
Q 040782 302 KMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDL 381 (435)
Q Consensus 302 ~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~l 381 (435)
+|++++++|||+|||+|||||+||++|||||++|+|+++++++|+++|+|++|+|+..++.|.++.+||+++|.+++++|
T Consensus 239 kL~~~~~lpv~~LvDaDP~Gi~I~~~Yk~GS~~ms~e~~~~~~p~I~wiGl~psD~~~~n~~k~~~lpL~~~D~k~i~~l 318 (372)
T KOG2795|consen 239 KLEEKLKLPVYGLVDADPYGIEILLTYKYGSKSMSYESHGLTVPTIRWIGLLPSDLEVKNIPKDQLLPLNKRDIKKIKDL 318 (372)
T ss_pred HHHHHhCCCEEEEeecCCcceEEEEEeeeCccccccccccccCCcceEEeechhhhhhcCCchheeecccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccccCChHHHHHHHHHHHcCCeeeeehhhhcCcccchhchHHhhhccCCCC
Q 040782 382 LEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL 435 (435)
Q Consensus 382 L~~~~~~~~~~w~~EL~~ML~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~~i 435 (435)
|.++.++.+|.|++||++|++.++|||||||..+|.+|+++.|+|.|+..++|+
T Consensus 319 L~~~~l~~~p~~r~el~~ml~~~~KaEieal~~~~~~~~~~~yia~k~~~~~~~ 372 (372)
T KOG2795|consen 319 LARLILQKEPVVREELERMLKNKVKAEIEALSFFGSDYLSRVYIARKLERISSL 372 (372)
T ss_pred HhhhhcccChhHHHHHHHHHhcchhhhhhhhhhcchHHHhhhhhhHHHhhcccC
Confidence 999999888999999999999999999999999999999999999999999986
No 4
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.1e-90 Score=682.16 Aligned_cols=345 Identities=39% Similarity=0.639 Sum_probs=336.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHcCCCceEEeccCCCCCcccccCCCeEEecCCccccccCChhhHHHHHHHHHHHHHHHHHh
Q 040782 86 LSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLC 165 (435)
Q Consensus 86 ~~ev~~rIe~~~~~i~~~i~~g~~~~~~ip~R~~~n~~~~~~~~~~~l~~~~~~r~~~~~~~~~k~a~~~~vl~~i~~ll 165 (435)
+.+++++|+.++..+++++.+|+.|.+.+|+|+.+|..||++.+.++||++.+.|+|.+++++++|+++++++.+|++++
T Consensus 7 ~~~a~~~l~~~~~~~~~~l~~~~~p~~~vp~r~~sn~~~d~~~~~~~lg~r~~~r~~~~v~~a~k~~q~l~~~~~i~e~l 86 (356)
T COG1697 7 RAEALSKLEHFAHKIYEQLEKGQIPIVEVPTRTKSNIIYDEESDHIVLGDRKSERSFLTVKGARKLAQTLLMLDFIKELL 86 (356)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCceecccccccccccCccccceeccccccchhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCcccceeeecC--CccccC--chHHHHHHHHHHHHHhcCCCCccceEecCCceEEEEEEEee-CCceEEeeccCCCc
Q 040782 166 LRNIHVTKRDLFYT--DVKLFQ--DQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSD-NGDMIDCTKMGMGG 240 (435)
Q Consensus 166 ~~~~~~TkRdiYY~--~~~lF~--~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~G~l~~~~-~g~~id~~~~~~~g 240 (435)
..|+++|+|||||. ++.+|+ +|++||++|+||+..+|++|++|||.|++||.|+||+.|+. ++.+|||++.|.+|
T Consensus 87 ~~~~~~TlReiYY~~~~~~~~k~~~Q~esd~lieDie~~~gl~Re~l~i~p~ekG~V~G~l~I~~~g~~~i~~sk~G~~~ 166 (356)
T COG1697 87 ELGKTSTLREIYYISKHVEVFKFDDQSESDRLIEDIEVTLGLSREDLGIRPEEKGLVYGPLRIREEGEDEIDASKLGGGG 166 (356)
T ss_pred hcCCCccHHHHhhhccCcccccccchhHHHHHHHHHHHHhccCHHHcCCCcccCceEEcceEEEecCCcEEEeeecCCCC
Confidence 99999999999999 888998 99999999999999999999999999999999999999997 88999999999999
Q ss_pred cccCCCcccccccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCch
Q 040782 241 KAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPY 320 (435)
Q Consensus 241 ~~Ip~~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~ 320 (435)
++||++++.|+++.++|+|||||||+|||+||++++||++++|||||+|||||++||+||++|++++++|||+|+|+|||
T Consensus 167 y~Ip~~~d~I~f~~~da~~VlvVEk~avf~rLv~e~~~~k~nailVt~KGqP~raTRrflkrL~eel~lpv~vftDgDPy 246 (356)
T COG1697 167 YLIPPDVDVIEFVDTDAKFVLVVEKDAVFQRLVEEGFWEKENAILVTLKGQPDRATRRFLKRLNEELDLPVYVFTDGDPY 246 (356)
T ss_pred CcCCCChhheeeccccceEEEEEechHHHHHHHHhhhhhhcCeEEEecCCCccHHHHHHHHHHHHHhCCCEEEEecCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccccccCChHHHHHHHHH
Q 040782 321 GLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLM 400 (435)
Q Consensus 321 Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~~~~~~~~w~~EL~~M 400 (435)
|++||++|+|||.++||+|+.+++|+++++||+++|+..|++| ...||+++|+++++++|++|+|..+. |++||+.|
T Consensus 247 G~~Iy~~~k~GS~k~ah~se~latp~akflGv~~~DI~~ynl~--~t~~l~~~Dik~lk~ll~~~~f~~~~-W~~el~~~ 323 (356)
T COG1697 247 GWYIYSVYKYGSIKLAHESERLATPDAKFLGVTMQDIVEYNLP--QTDKLKDRDIKRLKELLRDPRFQKEF-WKEELKLL 323 (356)
T ss_pred EEEEEEEEEecchhhhhcchhhcCCcceeeeccHHHHhhcccc--ccccchhhhHHHHHHHhccccccchh-HHHHHHHH
Confidence 9999999999999999999999999999999999999999998 45699999999999999999997666 99999999
Q ss_pred HHcCCeeeeehhhhcCcccchhchHHhhhccCC
Q 040782 401 VKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKD 433 (435)
Q Consensus 401 L~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~ 433 (435)
|+.++|||||||+++|++|+.++|||+||.+.+
T Consensus 324 l~i~kK~E~qAla~kgl~~v~~~ylpeki~e~~ 356 (356)
T COG1697 324 LKIGKKAEQQALASKGLEFVAKTYLPEKIEELK 356 (356)
T ss_pred HHHhHHHHHHHHHhcChHHhHHhhhHHHHhccC
Confidence 999999999999999999999999999998763
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=8e-45 Score=331.71 Aligned_cols=160 Identities=49% Similarity=0.883 Sum_probs=150.6
Q ss_pred cEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhcCCccccc
Q 040782 258 MFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSY 337 (435)
Q Consensus 258 ~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~GS~~~a~ 337 (435)
++||||||+|+|++|++++++...+||+||||||||.+||.||++|++++++|+|+|+|+||||++|+++|++||.+++|
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 58999999999999999999988899999999999999999999999988999999999999999999999999999999
Q ss_pred ccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccccccCChHHHHHHHHHHHcCCeeeeehhhhcCc
Q 040782 338 DSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGF 417 (435)
Q Consensus 338 ~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~~~~~~~~w~~EL~~ML~~~~KaEiEaL~~~g~ 417 (435)
++..+++|+++|+|++++|+.+ ++....+|||++|++++++|++++.+..++.|++|+++|++.|+|+|||++...|+
T Consensus 81 ~~~~~~~~~l~~~G~~~~d~~~--~~~~~~~~Ls~~d~~~l~~ll~~~~~~~~~~~~~el~~ml~~~~K~E~Eal~~~~~ 158 (160)
T cd00223 81 ESESLATPDLRWLGLRPSDIIR--LPDLPLLPLSERDLKRAKSLLRRPRFKELPEWKRELQLMLKLGKKAEIEALASCGL 158 (160)
T ss_pred ccccccCCCcEEccCCHHHHhh--ccccccCCCCHHHHHHHHHHHhccccccCHHHHHHHHHHHHhCCeeeehhHhhcCC
Confidence 9999999999999999999875 34467889999999999999999987667899999999999999999999999887
Q ss_pred cc
Q 040782 418 QY 419 (435)
Q Consensus 418 ~f 419 (435)
+|
T Consensus 159 ~~ 160 (160)
T cd00223 159 EF 160 (160)
T ss_pred CC
Confidence 65
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=99.80 E-value=2.9e-20 Score=147.02 Aligned_cols=68 Identities=37% Similarity=0.755 Sum_probs=61.8
Q ss_pred ChhhHHHHHHHHHHHHHHHHHhhcCCcccceeeecCCccccCchHHHHHHHHHHHHHhcCCCCccceE
Q 040782 144 SLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVI 211 (435)
Q Consensus 144 ~~~~~~k~a~~~~vl~~i~~ll~~~~~~TkRdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~I~ 211 (435)
|++++++|++++++|+.+|+++.+|+++|+|||||+++++|++|++||++|+|||.+|+++|++|||+
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 NVKSARKFAQLLRVLAIIHELLQNNKTSTKRDIYYRNVSLFKSQREVDRAIDDICCLLGVSREDLNIV 68 (68)
T ss_dssp -TCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHCSCS-SSHHHHHHHHHHHHHHHTS-GGGGTEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCccchHHHHHhchhhccCHHHHHHHHHHHHHHHCCCHHHcCCC
Confidence 57889999999999999999999999999999999999999999999999999999999999999996
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=99.64 E-value=4.5e-16 Score=145.25 Aligned_cols=163 Identities=19% Similarity=0.226 Sum_probs=125.0
Q ss_pred EEeeCCceEEeeccCCCccccCC-CcccccccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHH
Q 040782 223 IFSDNGDMIDCTKMGMGGKAIPP-NIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLR 301 (435)
Q Consensus 223 ~~~~~g~~id~~~~~~~g~~Ip~-~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~ 301 (435)
.++..+..++. .. .+|..++. .++.+..+..+++.||||||.++|.++.+.. +.++|+|.||+...++.|++
T Consensus 10 ~~r~~~~~~~~-~~-~~g~~~~~~~~~~l~~~~~~~~~vliVEN~~tf~~~~~~~-----~~~~Iyg~G~~~~~~~~~~~ 82 (181)
T PF09983_consen 10 RIRILDPALDL-DF-PGGLSDISVPLEELEILSLPPRRVLIVENLTTFYSLPELP-----NGLVIYGGGFAISSSRRFLK 82 (181)
T ss_pred EEEeCCccccc-cc-cCCcccccccHHHHHhccCCCCEEEEEeCHHHHHHHHhcC-----CeEEEECCCcCcHHHHHHHh
Confidence 34555556665 22 25555543 4567777888899999999999999998432 68999999999999999987
Q ss_pred HHhhccCCcEEEEecCCchhhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHh
Q 040782 302 KMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDL 381 (435)
Q Consensus 302 ~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~l 381 (435)
.+.. .|+|+|+|.||+|+.|+...+. .+|.++.+-|..+.+.+|.. ....+.+..+++++..
T Consensus 83 ~~~~---~~~~ywGDiD~~G~~I~~~lr~------------~~p~~~p~~Md~~~l~~~~~--~~~~~~~~~~~~~l~~- 144 (181)
T PF09983_consen 83 WLQP---KPVYYWGDIDPGGLRILERLRR------------KFPELKPLLMDEETLERYQD--RYGKEPSEPYRRKLPR- 144 (181)
T ss_pred hcCC---CceEEeccCCHhHHHHHHHHHH------------hCCCccccccCHHHHHHHHH--hcCCCCCccccccchh-
Confidence 5543 3999999999999999999986 24888899999999888621 1222346667666777
Q ss_pred hccccccCChHHHHHHHHHHHcCCeeeeehhh
Q 040782 382 LEEDFVKKNPGWVEELNLMVKTKQKAEIQALS 413 (435)
Q Consensus 382 L~~~~~~~~~~w~~EL~~ML~~~~KaEiEaL~ 413 (435)
|+.+.. ..|+.-++.|+..+++.|||+|.
T Consensus 145 L~~~e~---~~~~~l~~~~l~~~~riEQE~I~ 173 (181)
T PF09983_consen 145 LTDEEY---ALFRELIEEMLEEGKRIEQERIP 173 (181)
T ss_pred cCHHHH---HHHHHHHHHHHhcCCeeeecccc
Confidence 654443 36888888899999999999995
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=99.39 E-value=8.3e-13 Score=120.20 Aligned_cols=133 Identities=20% Similarity=0.229 Sum_probs=98.7
Q ss_pred cccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhcCC
Q 040782 253 MQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGS 332 (435)
Q Consensus 253 i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~GS 332 (435)
+......|.||||-+||..+++. .....+.||++.|+|+.+++.||.+|. ..+.++|+.+|+||.|+.|+..++.
T Consensus 14 ~~~~~~~V~VvENp~Vf~~~~~~--~~~~~~pLVCt~G~p~~A~~~LL~~L~-~~g~~l~y~GDfDp~Gl~IA~~l~~-- 88 (152)
T PF09664_consen 14 IWPPSGRVYVVENPAVFSALADE--LGASCPPLVCTSGQPSAAARRLLDRLA-AAGARLYYSGDFDPEGLRIANRLIQ-- 88 (152)
T ss_pred ccCCCCEEEEEecHHHHHHHHHh--cCCCCCeEEEcCCcHHHHHHHHHHHHH-hCCCEEEEecCCCHHHHHHHHHHHH--
Confidence 34455669999999999999987 222467899999999999999999994 4689999999999999999999964
Q ss_pred cccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccccccCChHHHHHHHHHHHcCCeeeeehh
Q 040782 333 KNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQAL 412 (435)
Q Consensus 333 ~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~~~~~~~~w~~EL~~ML~~~~KaEiEaL 412 (435)
.| -+.| ..|.+.|..... + ..+++.+..+ +.++ .|+. .+....|.+.|++++||++
T Consensus 89 ---r~----~~~~----Wrm~~~dY~~~~-~---~~~~~~~~l~-l~~v--~p~~------~~L~~~m~~~~~a~~QE~l 144 (152)
T PF09664_consen 89 ---RY----GARP----WRMDAEDYLAAL-S---AEPLSGRRLK-LPNV--APWL------PELAEAMRERGRAVYQEAL 144 (152)
T ss_pred ---Hh----CCcc----ccCCHHHHHHhc-c---ccCCCCCcCC-cccC--Chhc------HHHHHHHHHhCceeeHHHH
Confidence 11 1223 667777764321 1 2366666554 4333 3432 4556779999999999999
Q ss_pred hh
Q 040782 413 SS 414 (435)
Q Consensus 413 ~~ 414 (435)
..
T Consensus 145 ~~ 146 (152)
T PF09664_consen 145 LD 146 (152)
T ss_pred HH
Confidence 64
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=98.69 E-value=2.5e-08 Score=103.32 Aligned_cols=126 Identities=17% Similarity=0.155 Sum_probs=89.7
Q ss_pred EEEEEechhHHHHHHHccccCCCCe-EEEecCCcCChHHHHHHHHHhhc-cCCcEEEEecCCchhhHHHHHHhcCCcccc
Q 040782 259 FILLVEKDAAYIRLAEDRFYNRFPC-IIVTAKGQPDVATRLFLRKMKME-LKLPVLALVDSDPYGLKILSVYGCGSKNMS 336 (435)
Q Consensus 259 ~VLvVEKeAvF~rL~~~~~~~~~~~-ILITgKGyPD~aTR~fL~~L~~~-~~lPv~~LvD~DP~Gi~I~~tYk~GS~~~a 336 (435)
.|.||||-+||..+++.. .. .| .|||+.|||..+.+.||.+|... ..+ .|+ +|+||.||.|+...+.-
T Consensus 252 ~V~vvENp~vf~~~~~~~-~~--~~~~lIct~G~p~~a~~~LL~~L~~~g~~l-~Yh-GDfD~~Gi~Ia~~L~~r----- 321 (385)
T TIGR02679 252 RVYVVENPNVLAIALDRL-GP--RCAPLVCTDGQPNAAQIKLLDLLAAAGARL-YYH-GDFDWPGLRIANGLIRR----- 321 (385)
T ss_pred eEEEEecHHHHHHHHHhc-CC--CCceEEECCCcchHHHHHHHHHHHhcCCeE-EEe-cCCChhHHHHHHHHHHH-----
Confidence 599999999999999853 11 23 79999999999999999999875 334 566 99999999999999851
Q ss_pred cccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccccccCChHHHHHHHHHHHcCCeeeeehhhh
Q 040782 337 YDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSS 414 (435)
Q Consensus 337 ~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~~~~~~~~w~~EL~~ML~~~~KaEiEaL~~ 414 (435)
.+ ++++.|.+.|+.+.- + ..+++....+++... .|| ++.+.. .|...++.+.+|++..
T Consensus 322 -------~~-~~pwrmd~~dY~~a~-~---~~~~~~~~l~~l~~~--~~w---dp~L~~---~m~~~~~a~yqE~ll~ 379 (385)
T TIGR02679 322 -------YG-ARPWRFSAADYRAAV-V---GPPHTPRPLADRAAV--ASW---DPPLAP---AMARHGIAIYEEALAD 379 (385)
T ss_pred -------hC-CccccCCHHHHHHHh-c---cCCCCcccccccccc--CCC---ChHHHH---HHHHhCcchhHHHHHH
Confidence 12 667888888876532 2 124444443332221 112 233333 7999999999999953
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=96.65 E-value=0.011 Score=45.65 Aligned_cols=64 Identities=25% Similarity=0.272 Sum_probs=51.5
Q ss_pred cEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHH
Q 040782 258 MFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKIL 325 (435)
Q Consensus 258 ~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~ 325 (435)
+.|++||..+....+.+.+.. ++.++...|.+...+..++.++... ..+|+.++|.|+.|..+.
T Consensus 1 ~~viivEg~~d~~~l~~~~~~---~~~~~~~~G~~~~~~~~~~~~~~~~-~~~v~i~~D~D~~g~~~~ 64 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGY---GGAVVALGGHALNKTRELLKRLLGE-AKEVIIATDADREGEAIA 64 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCC---CEEEEEEccEEcHHHHHHHHHHhcC-CCEEEEEcCCChhHHHHH
Confidence 368999999999999887544 4678888998888777777777543 589999999999998443
No 11
>COG4924 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.86 E-value=0.36 Score=48.73 Aligned_cols=68 Identities=24% Similarity=0.261 Sum_probs=48.9
Q ss_pred ccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhc--cCCcEEEEecCCchhhHHHHHHh
Q 040782 252 DMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKME--LKLPVLALVDSDPYGLKILSVYG 329 (435)
Q Consensus 252 ~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~--~~lPv~~LvD~DP~Gi~I~~tYk 329 (435)
.+.-....|++||++-.|..|=+ --..|+|.|-||-- ....+.. .+-.+..|+|.|-||+.|+.-.+
T Consensus 236 ~l~lP~srilivENe~sfl~lP~-----~pg~i~i~GaGy~~------~~lvr~~~l~~~~l~YWGDmDt~Gf~iL~r~R 304 (386)
T COG4924 236 ELQLPQSRILIVENEDSFLALPT-----WPGVIIIWGAGYRA------VDLVRGPYLSNGRLLYWGDMDTDGFKILDRVR 304 (386)
T ss_pred hccCCceeEEEEechhhhhhcCC-----CCCeEEEecCCccH------HHhhcccccccceeeeeccccchHHHHHHHhh
Confidence 34445678999999999987632 12579999999952 1222211 24568899999999999998887
Q ss_pred c
Q 040782 330 C 330 (435)
Q Consensus 330 ~ 330 (435)
.
T Consensus 305 ~ 305 (386)
T COG4924 305 S 305 (386)
T ss_pred h
Confidence 3
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=88.05 E-value=2.8 Score=39.31 Aligned_cols=81 Identities=21% Similarity=0.252 Sum_probs=58.2
Q ss_pred cEEEEEechhHHHHHHHccccCCCCeEEEecCCcC-ChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhc--CCcc
Q 040782 258 MFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQP-DVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGC--GSKN 334 (435)
Q Consensus 258 ~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyP-D~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~--GS~~ 334 (435)
+-|+|||=-.==.+|-+- ++|-+|++.|+. +..|-..++.++.. -.|++|+|.|..|-.|-..... ....
T Consensus 3 kevIVVEGK~D~~~lk~~-----~d~~~I~T~Gs~i~~~~i~~i~~~~~~--rgVIIfTDpD~~GekIRk~i~~~vp~~k 75 (174)
T TIGR00334 3 KEIIVVEGKDDQARIKQA-----FDVDVIETNGSALKDETINLIKKAQKK--QGVIILTDPDFPGEKIRKKIEQHLPGYE 75 (174)
T ss_pred CeEEEEecchHHHHHHHh-----cCceEEEECCCccCHHHHHHHHHHhhc--CCEEEEeCCCCchHHHHHHHHHHCCCCe
Confidence 568999865544555332 357888999998 88888888888764 4689999999999999988864 3344
Q ss_pred cccccCCCCCC
Q 040782 335 MSYDSANLTTP 345 (435)
Q Consensus 335 ~a~~s~~l~~P 345 (435)
.+|-+...+.|
T Consensus 76 hafi~~~~a~~ 86 (174)
T TIGR00334 76 NCFIPKHLAKP 86 (174)
T ss_pred EEeeeHHhcCc
Confidence 45544444444
No 13
>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=82.56 E-value=4.9 Score=33.37 Aligned_cols=63 Identities=25% Similarity=0.314 Sum_probs=39.5
Q ss_pred ccEEEEEechh---HHHHHHHcc--ccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhH
Q 040782 257 AMFILLVEKDA---AYIRLAEDR--FYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLK 323 (435)
Q Consensus 257 a~~VLvVEKeA---vF~rL~~~~--~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~ 323 (435)
|+.||+||-.+ .|+.+.+.. .....++-+|-..|- .-..|.+.|. .+++|+++++|.|..+-.
T Consensus 3 a~~vIlVEG~tE~~~l~~~~~~~~~~~~~~~i~ii~~gG~---~~~~~~~ll~-~~~i~~~vi~D~D~~~~~ 70 (97)
T cd01026 3 ADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGK---NFKPFIKLLN-ALGIPVAVLTDLDAKRNE 70 (97)
T ss_pred CCeEEEEecHHHHHHHHHHHHHhCCCHHHCCEEEEEeCCc---chHHHHHHHH-HcCCCEEEEEeCCCCCCc
Confidence 57899999764 355555431 112234445555552 3444555454 478999999999998865
No 14
>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=79.08 E-value=14 Score=30.15 Aligned_cols=66 Identities=20% Similarity=0.075 Sum_probs=41.4
Q ss_pred cEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhc
Q 040782 258 MFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGC 330 (435)
Q Consensus 258 ~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~ 330 (435)
+.|+|||=..=-..|-+.++. .+.|...|..++. .+..++++. .-.|+.|+|+|..|-.|......
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~--~~~i~t~Gt~~~~-~~~~~l~~~----~~~VIiltD~D~aG~~i~~~~~~ 67 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIE--AEIIETNGSIINK-ETIELIKKA----YRGVIILTDPDRKGEKIRKKLSE 67 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCC--ccEEEECCCcCCH-HHHHHHHHh----CCEEEEEECCCHHHHHHHHHHHH
Confidence 468889876666677666542 1223333333332 344444444 33599999999999999777654
No 15
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=78.85 E-value=12 Score=28.90 Aligned_cols=65 Identities=22% Similarity=0.228 Sum_probs=41.8
Q ss_pred EEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccC-CcEEEEecCCchhhHHHHHH
Q 040782 259 FILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELK-LPVLALVDSDPYGLKILSVY 328 (435)
Q Consensus 259 ~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~-lPv~~LvD~DP~Gi~I~~tY 328 (435)
.+++||....-..+.+.++. +...+...|- ..+...+..+.+... -.|+.++|.|.-|-.+....
T Consensus 2 ~l~ivEg~~da~~~~~~~~~---~~~~~~~~G~--~~~~~~~~~l~~~~~~~~Iii~~D~D~~G~~~~~~i 67 (76)
T smart00493 2 VLIIVEGPADAIALEKAGGF---GGNVVALGGH--LLKKEIIKLLKRLAKKKEVILATDPDREGEAIAWKL 67 (76)
T ss_pred EEEEEcCHHHHHHHHHhcCC---CEEEEEEeee--ecHHHHHHHHHHHhcCCEEEEEcCCChhHHHHHHHH
Confidence 47889998888887776542 3333333342 233445555555332 36999999999998877544
No 16
>PRK04017 hypothetical protein; Provisional
Probab=75.11 E-value=8.1 Score=34.71 Aligned_cols=67 Identities=18% Similarity=0.072 Sum_probs=42.7
Q ss_pred CccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhc
Q 040782 256 DAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGC 330 (435)
Q Consensus 256 ~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~ 330 (435)
....|+|||=-.--.+|-+-++. .+.|..+|.++.+.. .++.. -.--|++|+|+|..|-.|....+.
T Consensus 21 ~~g~vIVVEGk~D~~~L~~lGv~--~~iI~t~g~~~~~~~-----e~ia~-~~r~VIILTD~D~~GekIr~~l~~ 87 (132)
T PRK04017 21 EAGAPIIVEGKRDVESLRKLGVE--GEIIKVSRTPLAEIA-----ELIAS-RGKEVIILTDFDRKGEELAKKLSE 87 (132)
T ss_pred CCCCEEEEeCccHHHHHHHcCCC--ccEEEECCeecchHH-----HHHHh-cCCeEEEEECCCcchHHHHHHHHH
Confidence 34478999876666677665543 234444444443333 22222 233699999999999999887764
No 17
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=73.72 E-value=7.6 Score=42.94 Aligned_cols=102 Identities=18% Similarity=0.201 Sum_probs=62.8
Q ss_pred EeeCCceEEeeccCCCccccCCCcccccc----ccc---CccEEEEEechh---HHHHHHHccccC--CCCeEEEecCCc
Q 040782 224 FSDNGDMIDCTKMGMGGKAIPPNIDRVGD----MQS---DAMFILLVEKDA---AYIRLAEDRFYN--RFPCIIVTAKGQ 291 (435)
Q Consensus 224 ~~~~g~~id~~~~~~~g~~Ip~~i~~i~~----i~~---~a~~VLvVEKeA---vF~rL~~~~~~~--~~~~ILITgKGy 291 (435)
+.+....+.+...+......+.+...+.+ -.+ -|+.||.||=+| +.+.|+.....+ +....||-..|
T Consensus 356 lvr~~~~v~~~~~~~~~~~~~~~~r~i~r~l~~trs~~lFAr~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~g- 434 (581)
T COG3593 356 LVRVSSRVAAFQLGPNNFSKEEDKRRIKRHLDATRSSLLFARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAG- 434 (581)
T ss_pred EEEcccceeeeccCccccccccchhhhhhhcccccchhhhhceeEEEeccchhhhHHHHHHHhccccccCcEEEEeecc-
Confidence 34445555555444444444422222221 112 268899999887 356666654443 23344554333
Q ss_pred CChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHh
Q 040782 292 PDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYG 329 (435)
Q Consensus 292 PD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk 329 (435)
.....|++ +.+..++++++++|+||.|...-.+-+
T Consensus 435 --s~~k~f~k-f~~~~gI~~~vitD~D~~g~~~~~~~~ 469 (581)
T COG3593 435 --SGLKPFIK-FAEAMGIRVHVITDGDEAGKKYEATVR 469 (581)
T ss_pred --cCcHHHHH-HhhccCceEEEEecCCcccchhhhhhh
Confidence 56678888 777788999999999999998777665
No 18
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=54.07 E-value=77 Score=25.12 Aligned_cols=66 Identities=18% Similarity=0.155 Sum_probs=37.5
Q ss_pred EEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhcc-CCcEEEEecCCchhhHHHHHHhc
Q 040782 259 FILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMEL-KLPVLALVDSDPYGLKILSVYGC 330 (435)
Q Consensus 259 ~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~-~lPv~~LvD~DP~Gi~I~~tYk~ 330 (435)
.|++||-+.-=..|.+.++. +++.+.|... .+..-+....-.. .-.|+.++|.|.-|.........
T Consensus 2 ~viIvEG~~D~~~l~~~g~~---~~v~~~g~~~---~~~~~~~~~~~~~~~~~Vii~~D~D~~G~~~a~~i~~ 68 (81)
T PF13662_consen 2 EVIIVEGEFDAIALEQAGYK---NVVAVLGGNL---SPLDQILREKLEKKVKEVIIAFDNDKAGEKAAQKIAK 68 (81)
T ss_dssp -EEEESSHHHHHHHHHTT-T---TEEEESSSS------HHHHHHHHHH---SEEEEEEESSHHHHHHHHHHHH
T ss_pred EEEEECCHHHHHHHHHhCCC---eEEEECCCCC---ChHHHhChHhhhccCceEEEEeCcCHHHHHHHHHHHH
Confidence 47888877666666666443 3455555322 3333333222111 36799999999999877666553
No 19
>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=53.56 E-value=44 Score=27.65 Aligned_cols=68 Identities=18% Similarity=0.168 Sum_probs=44.1
Q ss_pred EEEEechhHHHHHHHccccCCCCeEEEecCCcC-C---------hHHHHHHHHHhhcc--CCcEEEEecCCchhhHHHHH
Q 040782 260 ILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQP-D---------VATRLFLRKMKMEL--KLPVLALVDSDPYGLKILSV 327 (435)
Q Consensus 260 VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyP-D---------~aTR~fL~~L~~~~--~lPv~~LvD~DP~Gi~I~~t 327 (435)
++||||.+.-..+.+... .....++.+.|-- + ......++.|.+.+ --.|+.++|+|.-|-.|...
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 689999999888877533 2346666666643 1 22234445444431 24689999999999998876
Q ss_pred Hh
Q 040782 328 YG 329 (435)
Q Consensus 328 Yk 329 (435)
..
T Consensus 80 i~ 81 (100)
T PF01751_consen 80 II 81 (100)
T ss_dssp HH
T ss_pred HH
Confidence 64
No 20
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=52.04 E-value=83 Score=28.12 Aligned_cols=67 Identities=19% Similarity=0.144 Sum_probs=41.6
Q ss_pred cEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHh
Q 040782 258 MFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYG 329 (435)
Q Consensus 258 ~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk 329 (435)
+.|+|||=-.==.+|-+-... +.|.+.|.|-=...|-..++..+. .-.|+.|+|.|-.|=.|-....
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 678999965444444332222 334444444222666666666443 2469999999999999877765
No 21
>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=49.53 E-value=1.5e+02 Score=28.12 Aligned_cols=105 Identities=10% Similarity=0.085 Sum_probs=51.5
Q ss_pred CCCeEEEecCC--cCChHHHHHHHHHhhcc-CCcEEEEecC--CchhhHHHHHH--hcCCcccccccCCCC--CCCc---
Q 040782 280 RFPCIIVTAKG--QPDVATRLFLRKMKMEL-KLPVLALVDS--DPYGLKILSVY--GCGSKNMSYDSANLT--TPDI--- 347 (435)
Q Consensus 280 ~~~~ILITgKG--yPD~aTR~fL~~L~~~~-~lPv~~LvD~--DP~Gi~I~~tY--k~GS~~~a~~s~~l~--~P~l--- 347 (435)
+..+|+++..+ -.-.....+...|.... +.||++.+++ .-.|+.+++.- .+-+....+.+..+. .+.+
T Consensus 42 ~i~~Vvl~~~s~gg~~~~~~~l~~~l~~~~~~KpViA~v~g~a~s~gy~lA~~aD~i~a~~~a~~g~iG~~~~~~~~~~l 121 (214)
T cd07022 42 DVRAIVLDIDSPGGEVAGVFELADAIRAARAGKPIVAFVNGLAASAAYWIASAADRIVVTPTAGVGSIGVVASHVDQSKA 121 (214)
T ss_pred CCcEEEEEEeCCCCcHHHHHHHHHHHHHHhcCCCEEEEECCchhhHHHHHHhcCCEEEEcCCCeEEeeeEEEecCCHHHH
Confidence 34677765422 12222333444443211 6899999994 66677766533 222111111111111 1111
Q ss_pred -eecccCcccccc--cCCCcccccCCCHHHHHHHHHhhcc
Q 040782 348 -KWLGIRPSDLDK--YKIPEQCRLPMTEQDIKTGKDLLEE 384 (435)
Q Consensus 348 -~wLGv~~sDl~~--y~~~~~~~lpLt~rD~k~~~~lL~~ 384 (435)
.=+||.+..+.. |+.......++|+.+++.++++|..
T Consensus 122 l~k~Gi~~~~~~~g~~K~~~~~~~~~s~~~re~~~~~l~~ 161 (214)
T cd07022 122 LEKAGLKVTLIFAGAHKVDGNPDEPLSDEARARLQAEVDA 161 (214)
T ss_pred HHhCCCeEEEEEcCCCccCCCCCCCCCHHHHHHHHHHHHH
Confidence 224555554432 2211122348999999999999875
No 22
>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=45.21 E-value=1.2e+02 Score=24.32 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=15.5
Q ss_pred EEEecCCcCChHHHHHHHHHhhc-cCCcEEEEe
Q 040782 284 IIVTAKGQPDVATRLFLRKMKME-LKLPVLALV 315 (435)
Q Consensus 284 ILITgKGyPD~aTR~fL~~L~~~-~~lPv~~Lv 315 (435)
++|..-..|+..--.+++.|... .++|++.++
T Consensus 46 ~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t 78 (112)
T PF00072_consen 46 LIIIDLELPDGDGLELLEQIRQINPSIPIIVVT 78 (112)
T ss_dssp EEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEE
T ss_pred EEEEEeeeccccccccccccccccccccEEEec
Confidence 44444555555555555555443 245555555
No 23
>PRK04031 DNA primase; Provisional
Probab=36.57 E-value=98 Score=32.92 Aligned_cols=65 Identities=26% Similarity=0.266 Sum_probs=44.8
Q ss_pred CccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhc
Q 040782 256 DAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGC 330 (435)
Q Consensus 256 ~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~ 330 (435)
..++|+|||=-+=--.|.+.++. +.|-.-|-..|+. +.+|.. .-.|..|+|+|..|-.|+.....
T Consensus 168 k~~~iIVVEG~~DVi~L~~aGi~---nvVAt~GT~l~~~-----i~~l~k--~~~Vil~~DgD~aGe~I~k~l~~ 232 (408)
T PRK04031 168 DSDAIIVVEGRADVLNLLRYGIK---NAIAVEGTNVPET-----IIELSK--KKTVTAFLDGDRGGELILKELLQ 232 (408)
T ss_pred cCCeEEEEeCHHHHHHHHhcccc---eEEEeCCcccHHH-----HHHHhc--CCCEEEEECCCHHHHHHHHHHHh
Confidence 34789999988777778777765 3444444443333 444443 34689999999999999887764
No 24
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=36.07 E-value=2.6e+02 Score=25.09 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=34.0
Q ss_pred eEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhcCC
Q 040782 283 CIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGS 332 (435)
Q Consensus 283 ~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~GS 332 (435)
-++|..-.+|+...-.+++.+.....+|+..+.+.+- .-.+...+..|.
T Consensus 46 dlvi~d~~~~~~~g~~~~~~l~~~~~~~ii~ls~~~~-~~~~~~a~~~Ga 94 (223)
T PRK11517 46 ALIILDIMLPGMDGWQILQTLRTAKQTPVICLTARDS-VDDRVRGLDSGA 94 (223)
T ss_pred CEEEEECCCCCCCHHHHHHHHHcCCCCCEEEEECCCC-HHHHHHHHhcCC
Confidence 3556667789988888999888766799998886433 233445555553
No 25
>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=34.67 E-value=1.3e+02 Score=23.55 Aligned_cols=57 Identities=19% Similarity=0.240 Sum_probs=33.0
Q ss_pred EEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhH
Q 040782 259 FILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLK 323 (435)
Q Consensus 259 ~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~ 323 (435)
.|+++|=.--.-.+.+.++ .+++-..|..+.+ ..-.+|... .-.|+.++|.|+.|..
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 4677775544455555542 2455555555542 223333332 2458999999999974
No 26
>PRK08252 enoyl-CoA hydratase; Provisional
Probab=31.97 E-value=1.5e+02 Score=28.91 Aligned_cols=45 Identities=16% Similarity=0.264 Sum_probs=29.8
Q ss_pred ccCCcEEEEecCCchhhH----HHHHHhcCCcccccccCCCCCCCceecccCccc
Q 040782 306 ELKLPVLALVDSDPYGLK----ILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSD 356 (435)
Q Consensus 306 ~~~lPv~~LvD~DP~Gi~----I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sD 356 (435)
.++.|+++.+.+...|.- ..|-|+..+. +..+..|.++ +|+.|..
T Consensus 89 ~~~kPvIaav~G~a~GgG~~lalacD~~ia~~-----~a~f~~pe~~-~Gl~p~~ 137 (254)
T PRK08252 89 PPRKPLIAAVEGYALAGGFELALACDLIVAAR-----DAKFGLPEVK-RGLVAAG 137 (254)
T ss_pred cCCCCEEEEECCEEehHHHHHHHhCCEEEEeC-----CCEEeCchhh-cCCCCCc
Confidence 468999999999987643 3344455443 3346678777 6887753
No 27
>PRK13856 two-component response regulator VirG; Provisional
Probab=31.05 E-value=2.4e+02 Score=26.24 Aligned_cols=50 Identities=8% Similarity=0.089 Sum_probs=35.7
Q ss_pred CeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHHHHHhcC
Q 040782 282 PCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCG 331 (435)
Q Consensus 282 ~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~G 331 (435)
+-++|..-..|+...-.+++.+....++|++.+++..+....+...+..|
T Consensus 46 ~dlvi~d~~l~~~~g~~l~~~i~~~~~~pii~lt~~~~~~~~~~~~l~~G 95 (241)
T PRK13856 46 VDVVVVDLNLGREDGLEIVRSLATKSDVPIIIISGDRLEEADKVVALELG 95 (241)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhcCCCcEEEEECCCCcHHHHHHHHhcC
Confidence 34677788889988888999998767899999987543334444445544
No 28
>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=27.55 E-value=2.9e+02 Score=21.28 Aligned_cols=59 Identities=19% Similarity=0.174 Sum_probs=33.4
Q ss_pred EEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCchhhHHH
Q 040782 259 FILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKIL 325 (435)
Q Consensus 259 ~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~Gi~I~ 325 (435)
.|+++|=.----.+.+.++ .+++...|.+... .-+..+... .-.|+.+.|.|.-|....
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 4677775554455656554 2445444555443 222222221 357999999999996543
No 29
>PRK00933 ribosomal biogenesis protein; Validated
Probab=25.93 E-value=71 Score=29.75 Aligned_cols=28 Identities=21% Similarity=0.356 Sum_probs=24.5
Q ss_pred EEEecCCcCChHHHHHHHHHhhccCCcE
Q 040782 284 IIVTAKGQPDVATRLFLRKMKMELKLPV 311 (435)
Q Consensus 284 ILITgKGyPD~aTR~fL~~L~~~~~lPv 311 (435)
++||+.-.|+..|+.|.+.|+..++++.
T Consensus 1 mIITTSrkPs~~t~~fAkeLa~~ln~~y 28 (165)
T PRK00933 1 MIITTSRKPSQRTRSLVKDLARFLNCKY 28 (165)
T ss_pred CEEECCCCCCHHHHHHHHHHHHHhCCEE
Confidence 4899999999999999999998776654
No 30
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=25.37 E-value=40 Score=33.50 Aligned_cols=17 Identities=59% Similarity=1.023 Sum_probs=14.1
Q ss_pred ccCCcEEEEec--CCchhh
Q 040782 306 ELKLPVLALVD--SDPYGL 322 (435)
Q Consensus 306 ~~~lPv~~LvD--~DP~Gi 322 (435)
.+++||++++| +||.++
T Consensus 177 klgIPVvAlvDTn~dpd~V 195 (252)
T COG0052 177 KLGIPVVALVDTNCDPDGV 195 (252)
T ss_pred HcCCCEEEEecCCCCCccC
Confidence 47999999998 677776
No 31
>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=24.69 E-value=93 Score=25.90 Aligned_cols=35 Identities=23% Similarity=0.488 Sum_probs=21.2
Q ss_pred CCeEEEecCCcCChHHHHHHHHHhhccCCcEEEEecCCch
Q 040782 281 FPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPY 320 (435)
Q Consensus 281 ~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~LvD~DP~ 320 (435)
..||++||...|+..+..+.+... +|++ .++.|-|
T Consensus 62 i~~iIltg~~~~~~~v~~la~~~~----i~vi-~t~~dtf 96 (105)
T PF07085_consen 62 IACIILTGGLEPSEEVLELAKELG----IPVI-STPYDTF 96 (105)
T ss_dssp ECEEEEETT----HHHHHHHHHHT-----EEE-E-SS-HH
T ss_pred CCEEEEeCCCCCCHHHHHHHHHCC----CEEE-EECCCHH
Confidence 589999999999999988887764 7754 4555544
No 32
>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=22.34 E-value=1.4e+02 Score=25.62 Aligned_cols=57 Identities=14% Similarity=0.412 Sum_probs=36.3
Q ss_pred EEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhc-cCCcEEEEecCC
Q 040782 260 ILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKME-LKLPVLALVDSD 318 (435)
Q Consensus 260 VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~-~~lPv~~LvD~D 318 (435)
|+.+.+-.--..++++ .....||+|+--+-..-....++..+... .++|||.++|-+
T Consensus 20 vv~~~~~dd~~~~i~~--~~~i~avvi~~d~~~~~~~~~ll~~i~~~~~~iPVFl~~~~~ 77 (115)
T PF03709_consen 20 VVDADSTDDALAIIES--FTDIAAVVISWDGEEEDEAQELLDKIRERNFGIPVFLLAERD 77 (115)
T ss_dssp EEEESSHHHHHHHHHC--TTTEEEEEEECHHHHHHHHHHHHHHHHHHSTT-EEEEEESCC
T ss_pred EEEeCChHHHHHHHHh--CCCeeEEEEEcccccchhHHHHHHHHHHhCCCCCEEEEecCC
Confidence 4444444444455544 12346888885433335678899999874 799999999977
No 33
>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=22.26 E-value=71 Score=30.46 Aligned_cols=19 Identities=37% Similarity=0.531 Sum_probs=15.9
Q ss_pred ecCCcC-ChHHHHHHHH-Hhh
Q 040782 287 TAKGQP-DVATRLFLRK-MKM 305 (435)
Q Consensus 287 TgKGyP-D~aTR~fL~~-L~~ 305 (435)
.|+||| |..|+.|++. +..
T Consensus 166 ~GsGY~sd~~t~~~l~~~~~~ 186 (206)
T TIGR00729 166 FGSGYPSDPRTREWLEEYFKS 186 (206)
T ss_pred CCCcCCCCHHHHHHHHHHHHh
Confidence 689999 6999999997 443
No 34
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=21.21 E-value=1.8e+02 Score=24.03 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=30.3
Q ss_pred chhhhhHHhhcCChHHHHHHHHHHHHHHHHHHHcCCC
Q 040782 73 SLSATCREVTDLSLSAVQSTIETLILQIARSILAGNG 109 (435)
Q Consensus 73 ~~~~~~~~~~~~~~~ev~~rIe~~~~~i~~~i~~g~~ 109 (435)
++-+.+.+...++..++..-++.++..+.++|.+|+.
T Consensus 6 eli~~ia~~~~~s~~~v~~vv~~~~~~i~~~L~~g~~ 42 (96)
T TIGR00987 6 EMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQ 42 (96)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcCCe
Confidence 3444555667789999999999999999999999865
No 35
>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=20.94 E-value=6.9e+02 Score=23.31 Aligned_cols=78 Identities=21% Similarity=0.220 Sum_probs=39.4
Q ss_pred cCCcEEEEecCCc--hhhHHHHHH--hcCCcccccccCCCC--CCC----ceecccCcccccc--cCCCcccccCCCHHH
Q 040782 307 LKLPVLALVDSDP--YGLKILSVY--GCGSKNMSYDSANLT--TPD----IKWLGIRPSDLDK--YKIPEQCRLPMTEQD 374 (435)
Q Consensus 307 ~~lPv~~LvD~DP--~Gi~I~~tY--k~GS~~~a~~s~~l~--~P~----l~wLGv~~sDl~~--y~~~~~~~lpLt~rD 374 (435)
.+.|+++++++-. .|+.|.+.- .+-+....+.+..+. .+. +.=+|+.+..+.. |....+.+-++|+.+
T Consensus 65 ~~kpvia~v~g~~~s~g~~lA~aaD~i~a~~~s~~g~iG~~~~~~~~~~~l~k~Gi~~~~~~~g~~K~~~~~~~~~s~~~ 144 (208)
T cd07023 65 AKKPVVASMGDVAASGGYYIAAAADKIVANPTTITGSIGVIGQGPNLEELLDKLGIERDTIKSGPGKDKGSPDRPLTEEE 144 (208)
T ss_pred cCCcEEEEECCcchhHHHHHHhhCCEEEECCCCeEEeCcEEEecCCHHHHHHhcCCceEEEecCCCccCCCCCCCCCHHH
Confidence 3789999999654 356665543 221111111110010 011 1224555544432 221112245799999
Q ss_pred HHHHHHhhcc
Q 040782 375 IKTGKDLLEE 384 (435)
Q Consensus 375 ~k~~~~lL~~ 384 (435)
+..++++|..
T Consensus 145 ~e~~~~~l~~ 154 (208)
T cd07023 145 RAILQALVDD 154 (208)
T ss_pred HHHHHHHHHH
Confidence 9999998874
No 36
>PRK07511 enoyl-CoA hydratase; Provisional
Probab=20.81 E-value=3.7e+02 Score=26.08 Aligned_cols=43 Identities=21% Similarity=0.378 Sum_probs=28.2
Q ss_pred cCCcEEEEecCCchhhHHH----HHHhcCCcccccccCCCCCCCceecccCcc
Q 040782 307 LKLPVLALVDSDPYGLKIL----SVYGCGSKNMSYDSANLTTPDIKWLGIRPS 355 (435)
Q Consensus 307 ~~lPv~~LvD~DP~Gi~I~----~tYk~GS~~~a~~s~~l~~P~l~wLGv~~s 355 (435)
++.|+++.+++...|.-.. |-|+..+.. ..+..|.++ +|+.|.
T Consensus 97 ~~kpvIAav~G~a~GgG~~lala~D~~ia~~~-----a~f~~pe~~-~Gl~p~ 143 (260)
T PRK07511 97 FPKPVIAAVEGAAAGAGFSLALACDLLVAARD-----AKFVMAYVK-VGLTPD 143 (260)
T ss_pred CCCCEEEEECCeeehHHHHHHHhCCEEEeeCC-----CEEeccccc-cCcCCC
Confidence 5899999999998765433 334444433 335677777 577764
No 37
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=20.49 E-value=1.8e+02 Score=24.05 Aligned_cols=41 Identities=20% Similarity=0.249 Sum_probs=32.9
Q ss_pred ccccchhhhhHHhhcCChHHHHHHHHHHHHHHHHHHHcCCC
Q 040782 69 LSDLSLSATCREVTDLSLSAVQSTIETLILQIARSILAGNG 109 (435)
Q Consensus 69 l~~~~~~~~~~~~~~~~~~ev~~rIe~~~~~i~~~i~~g~~ 109 (435)
++-.++-+.+.+....+..++..-++.++..+.++|.+|+.
T Consensus 3 mtk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~g~~ 43 (99)
T PRK00285 3 LTKADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQ 43 (99)
T ss_pred cCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcCCe
Confidence 34445555666667889999999999999999999999865
Done!