Query gi|254780948|ref|YP_003065361.1| DNA repair protein RecO [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 240
No_of_seqs 191 out of 1615
Neff 8.4
Searched_HMMs 39220
Date Mon May 30 03:22:58 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780948.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00085 recO DNA repair prote 100.0 5.6E-45 0 294.2 18.3 222 1-233 2-233 (235)
2 TIGR00613 reco DNA repair prot 100.0 7.8E-43 0 281.1 14.1 233 3-235 1-249 (250)
3 COG1381 RecO Recombinational D 100.0 7.2E-42 0 275.2 16.4 230 2-232 5-244 (251)
4 pfam11967 RecO_N Recombination 99.7 4.8E-17 1.2E-21 123.6 5.3 75 1-76 2-79 (80)
5 pfam02565 RecO_C Recombination 99.6 2.5E-14 6.5E-19 107.0 12.9 135 83-217 2-148 (156)
6 PRK13908 putative recombinatio 97.6 0.00013 3.3E-09 47.7 5.6 145 6-157 2-147 (204)
7 COG5347 GTPase-activating prot 93.2 0.22 5.7E-06 27.9 5.2 85 136-224 8-94 (319)
8 KOG0703 consensus 85.6 1.8 4.5E-05 22.4 4.7 93 140-235 17-116 (287)
9 pfam01412 ArfGap Putative GTPa 75.7 6 0.00015 19.2 5.6 70 146-219 11-82 (117)
10 smart00105 ArfGap Putative GTP 75.0 4.9 0.00012 19.7 4.0 62 146-211 1-64 (112)
11 KOG0706 consensus 72.4 5.8 0.00015 19.3 3.9 65 137-203 12-77 (454)
12 cd05790 S1_Rrp40 S1_Rrp40: Rrp 40.9 26 0.00065 15.4 3.2 54 7-63 12-65 (86)
13 TIGR00269 TIGR00269 conserved 40.7 21 0.00053 15.9 2.2 58 110-175 38-100 (106)
14 PRK00423 tfb transcription ini 38.8 14 0.00036 16.9 1.1 16 195-210 275-290 (310)
15 pfam08271 TF_Zn_Ribbon TFIIB z 32.5 20 0.00052 16.0 1.1 32 150-183 2-33 (40)
16 PTZ00048 cytochrome c; Provisi 31.8 36 0.00091 14.5 3.8 87 149-239 24-112 (115)
17 COG3058 FdhE Uncharacterized p 29.0 40 0.001 14.2 2.8 20 149-168 226-245 (308)
18 TIGR01562 FdhE formate dehydro 28.6 28 0.00071 15.1 1.2 21 149-169 229-249 (312)
19 KOG1597 consensus 25.6 35 0.00089 14.5 1.3 103 6-115 27-136 (308)
20 COG1405 SUA7 Transcription ini 24.8 28 0.00071 15.1 0.6 14 136-149 199-212 (285)
21 pfam04216 FdhE Protein involve 24.3 37 0.00094 14.4 1.2 13 149-161 167-179 (283)
22 smart00401 ZnF_GATA zinc finge 23.9 19 0.00048 16.2 -0.4 35 149-183 4-39 (52)
23 pfam09943 DUF2175 Uncharacteri 22.9 52 0.0013 13.5 2.6 56 150-217 4-61 (101)
24 TIGR01810 betA choline dehydro 20.7 55 0.0014 13.3 1.5 151 69-224 250-446 (540)
No 1
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=100.00 E-value=5.6e-45 Score=294.24 Aligned_cols=222 Identities=35% Similarity=0.547 Sum_probs=184.4
Q ss_pred CCEEEEEEEEEECCCCCHHHHHHHCCCCCCEEEEEEECCCCCCC--CCCCCCCCEEEEEEECCCCCCCCCC-HHHHHCCC
Q ss_conf 95000169983035880244754227212869999966767553--2000344314799821577765431-01221014
Q gi|254780948|r 1 MYWQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHRM--QPILQAGNLVRVNWRSRLAQNLGEF-RFEVLESH 77 (240)
Q Consensus 1 M~~~d~giVL~~~~~~E~~~Iv~~~T~~~G~~~~i~rG~~~~k~--~~~lq~~~~~~~~~~~k~~~~l~~~-~~e~~~~~ 77 (240)
|+|+|+||||+++||||+|+||++||+++||++++|||++++|+ ++.+||++.+++.|+.+.+ ++++ ++|++.++
T Consensus 2 m~~~~~aiVL~~~~y~E~d~iv~~~T~~~Gki~~iakG~rk~ks~~~~~lqpf~~~~~~~~~~~~--l~~l~~~e~~~~~ 79 (235)
T PRK00085 2 MEWRDEGIVLHTRPYGETSLIVTVFTREHGRVRAVAKGARKPKSKLRAVLQPFTPLDLLWSAGRE--LDTLTQAETIGSY 79 (235)
T ss_pred CCCCCEEEEEECCCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEECC--CCCEEEEEECCHH
T ss_conf 86420499997210478055677897788709999833767777655434676289999997468--6738998871125
Q ss_pred CHHHCCCCHHHHHHHHHHHH-HHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCC
Q ss_conf 22210440589999999999-99621356676789999999996122343013799999999998376766122102355
Q gi|254780948|r 78 CAKLLSSSLFLYGLQSIVPL-FRFLPEREPCLELYDMLNIFLNCHKIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGV 156 (240)
Q Consensus 78 ~~~~~~~~~~l~~~~~~~~l-~~~l~e~e~~~~lf~~l~~~L~~l~~~~~~~~~~~~fEl~LL~~lGf~p~L~~C~~cg~ 156 (240)
... ..|..+++++.+++++ .+++++++|++.+|+++..+|+.++...++...++.||+++|+++||+|++++|++||.
T Consensus 80 ~~l-~~d~~~l~~a~yi~El~~~~~~e~~~~~~lf~ll~~~L~~L~~~~~~~~~~~~fel~LL~~lG~~p~l~~C~~cg~ 158 (235)
T PRK00085 80 AAI-LLDGFALAYASYLNELLDRLLPEREPHPELFELLLQTLDALAEGEDPEPLLRRFELRLLAELGYGLDLDHCAVCGA 158 (235)
T ss_pred HHH-HHCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEEHHHHCCCC
T ss_conf 566-4059999999999999999756778729999999999999857897189999999999998598871323416899
Q ss_pred CCCCEE-EEECCCCHHHHCCCCCCCCHHHHHHHHHHCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
Q ss_conf 566224-4301210011102475320000123455225-----6789989999999899999985656628999998799
Q gi|254780948|r 157 TQDLLW-VSPKSGGAVCRSVGLPYAEKMLVLPSFLWKE-----EQTIDADSLKSAFQLTDYFLNKYALQHNIIHCHLLRE 230 (240)
Q Consensus 157 ~~~l~~-~s~~~g~av~~~~~~~~~~kll~lp~fL~~~-----~~~~~~~~i~~~l~lt~~fL~k~~l~~~~~~~P~sR~ 230 (240)
.++..| |||.+|++||..++ .+.+..++.++... ....+.+...++.+++.++++.++ .+.++||.
T Consensus 159 ~~~~~y~fs~~~Gg~~c~~~~---~~~~~~l~~l~~~~~~~l~~~~~~~~~~~~~~~ll~~~l~~~L-----g~~lkS~~ 230 (235)
T PRK00085 159 DPDLTYRFSPKSGGAVCRECR---ADVLLLLPLFLGGDLLALEAISSDAETKRAAKRLTRYFLQRYL-----GRPLKSRE 230 (235)
T ss_pred CCCCCEEEEECCCCEECCCCC---HHHHHHHHHHHCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHC-----CCCCCHHH
T ss_conf 888648998167978876546---7688899998144599886078999999999999999999984-----99950899
Q ss_pred HHH
Q ss_conf 999
Q gi|254780948|r 231 NFL 233 (240)
Q Consensus 231 ~f~ 233 (240)
.|.
T Consensus 231 ~l~ 233 (235)
T PRK00085 231 LLD 233 (235)
T ss_pred HHH
T ss_conf 997
No 2
>TIGR00613 reco DNA repair protein RecO; InterPro: IPR003717 The damage avoidance-tolerance pathway(s) requires functional recA, recF, recO, and recR genes, suggesting the mechanism to be daughter strand gap repair. The ruvABC genes or the recG gene is also required. The RecG pathway appears to be more active than the RuvABC pathway . RecO may contain a mononucleotide-binding fold .; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=100.00 E-value=7.8e-43 Score=281.11 Aligned_cols=233 Identities=26% Similarity=0.360 Sum_probs=199.0
Q ss_pred EEEEEEEEEECCCCCHHHHHHHCCCCCCEEEEEEECCCCCCC--CCCCCCCCEEEEEEECCC--CCCCCCCHHHHHCCCC
Q ss_conf 000169983035880244754227212869999966767553--200034431479982157--7765431012210142
Q gi|254780948|r 3 WQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHRM--QPILQAGNLVRVNWRSRL--AQNLGEFRFEVLESHC 78 (240)
Q Consensus 3 ~~d~giVL~~~~~~E~~~Iv~~~T~~~G~~~~i~rG~~~~k~--~~~lq~~~~~~~~~~~k~--~~~l~~~~~e~~~~~~ 78 (240)
|+++||||++++|+|+|+|||+||++|||++++|||||++|. ++.+|||+...+.|..+. .+..++.++|++.++.
T Consensus 1 ~~~~GivL~~~dy~E~d~iit~ft~~~Gk~~~~akGark~k~r~~~~~~pf~~~~f~~~~~~Nl~~l~~l~~~e~~~~~~ 80 (250)
T TIGR00613 1 IKIEGIVLKSRDYGETDKIITLFTEEYGKVSFVAKGARKSKSRFKAVLQPFSLGDFVLYKRKNLSGLSTLNQGELIKSFE 80 (250)
T ss_pred CCCEEEEEECCCCCCCCCEEEECCCCCCEEEEEEEEEECCCCCCHHHHHCEEEEEEEEEECCCCCCCCCCCCCHHHHHHH
T ss_conf 96324685026887255247760467871668887300155641455512033568887524422136431004788778
Q ss_pred HHHCCCCHHHHHH-HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCC
Q ss_conf 2210440589999-999999996213566767899999999961223-43013799999999998376766122102355
Q gi|254780948|r 79 AKLLSSSLFLYGL-QSIVPLFRFLPEREPCLELYDMLNIFLNCHKIP-SVIGKIFVQIELMLLKNIGFGLDLTKCVVTGV 156 (240)
Q Consensus 79 ~~~~~~~~~l~~~-~~~~~l~~~l~e~e~~~~lf~~l~~~L~~l~~~-~~~~~~~~~fEl~LL~~lGf~p~L~~C~~cg~ 156 (240)
++..|.....+|. |.++.+.++++|++|+|.+|..+..+|+.++++ .......+.||++||+.+||+|+|..|++||.
T Consensus 81 ~i~~D~~~~~ya~~y~~eL~~~~~~e~~~~~~lf~~l~~~L~~i~~~~~~~~~~~~~f~l~LL~~~G~~~~l~~C~~Cg~ 160 (250)
T TIGR00613 81 GIKSDLFLLAYASKYIAELIDRLLPEKEPNPKLFELLLKTLELIEEGSGNPELLLRLFELKLLKILGYALDLDKCAVCGS 160 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 87763889999999999999986322775778999999999873133540478999999999998454435660004775
Q ss_pred --CCCCEEEEECCCCHHHHCCC------CCCCCHHHHHHHHHHCCC-CCCCH-HHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf --56622443012100111024------753200001234552256-78998-999999989999998565662899999
Q gi|254780948|r 157 --TQDLLWVSPKSGGAVCRSVG------LPYAEKMLVLPSFLWKEE-QTIDA-DSLKSAFQLTDYFLNKYALQHNIIHCH 226 (240)
Q Consensus 157 --~~~l~~~s~~~g~av~~~~~------~~~~~kll~lp~fL~~~~-~~~~~-~~i~~~l~lt~~fL~k~~l~~~~~~~P 226 (240)
.+++.++|++++|++|..++ .+++++++.++.++.... ..... .++........+.+.+.+++++-...|
T Consensus 161 ~~~~~~~~~S~~~~g~~C~~~~~~d~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (250)
T TIGR00613 161 ELKEDLIYFSMKYGGALCKQCGEKDPHAIPLKPKLLRLLRYLLKLDLEKLLSIIELKPEIKLELRRILDEYYEEYLGDKP 240 (250)
T ss_pred CCCCCHHHHHHHCCCEECHHHHCCCCHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 34453343200026422002101452001146789999999865468887556405888999999999999876516744
Q ss_pred HHHHHHHHH
Q ss_conf 879999999
Q gi|254780948|r 227 LLRENFLGK 235 (240)
Q Consensus 227 ~sR~~f~~~ 235 (240)
.++..|++.
T Consensus 241 ~kS~~~l~~ 249 (250)
T TIGR00613 241 LKSKKFLDQ 249 (250)
T ss_pred HHHHHHHHH
T ss_conf 237999862
No 3
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.2e-42 Score=275.23 Aligned_cols=230 Identities=27% Similarity=0.427 Sum_probs=194.5
Q ss_pred CEEEEEEEEEECCCCCHHHHHHHCCCCCCEEEEEEECCCC--CCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHHCCCCH
Q ss_conf 5000169983035880244754227212869999966767--55320003443147998215777654310122101422
Q gi|254780948|r 2 YWQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQS--HRMQPILQAGNLVRVNWRSRLAQNLGEFRFEVLESHCA 79 (240)
Q Consensus 2 ~~~d~giVL~~~~~~E~~~Iv~~~T~~~G~~~~i~rG~~~--~k~~~~lq~~~~~~~~~~~k~~~~l~~~~~e~~~~~~~ 79 (240)
.|+++||||++++|||+|+||++||++|||++++|||+|+ +|.++.+|||+.+.+.|..++.++.+..++|.+.++.+
T Consensus 5 ~~~~~giVL~~r~~~E~d~IVtvfT~~~G~~~~~akgark~~s~l~~~lqpf~~~~~~~~~~~~~l~~l~~~e~v~~~~~ 84 (251)
T COG1381 5 EIKDEGIVLRSRPYGETDKIVTVFTEEHGRVRAVAKGARKRKSKLRAVLQPFTPVDFQWYGRGRELKTLTQAEPVGSYPG 84 (251)
T ss_pred HHCCCEEEEEECCCCCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCEEEEEEECCHHH
T ss_conf 11261699980457876578999647886578773456556687400105653699999836877773665677010466
Q ss_pred HHCCCCHHHHHHHHHHHHH-HHHCCCCCCHHHHHHHHHHHH-HHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCCC
Q ss_conf 2104405899999999999-962135667678999999999-61223430137999999999983767661221023555
Q gi|254780948|r 80 KLLSSSLFLYGLQSIVPLF-RFLPEREPCLELYDMLNIFLN-CHKIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGVT 157 (240)
Q Consensus 80 ~~~~~~~~l~~~~~~~~l~-~~l~e~e~~~~lf~~l~~~L~-~l~~~~~~~~~~~~fEl~LL~~lGf~p~L~~C~~cg~~ 157 (240)
+.++...++++.++.+++ ++++|++|+|.+|+.+..+|. .+.+...+......||+++|..+||+||+++|+.||..
T Consensus 85 -i~~d~~~l~~~~y~~ell~~l~~e~~~~p~Lf~~~~~~L~~l~~~~~~~~~~l~~fel~lL~~~G~~~~l~~Ca~cg~~ 163 (251)
T COG1381 85 -IISDIFALYSASYVAELLDRLLPEEDPNPELFELYLETLEYLLSDGNDPELLLRRFELKLLGELGIGPNLTSCARCGTP 163 (251)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCC
T ss_conf -6422999999999999999985355888579999999999986178777999999999999983986162767564983
Q ss_pred CCCEEEEECCCCHHHHCC----CCCCCCHHHHHHHHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH
Q ss_conf 662244301210011102----4753200001234552256--7899899999998999999856566289999987999
Q gi|254780948|r 158 QDLLWVSPKSGGAVCRSV----GLPYAEKMLVLPSFLWKEE--QTIDADSLKSAFQLTDYFLNKYALQHNIIHCHLLREN 231 (240)
Q Consensus 158 ~~l~~~s~~~g~av~~~~----~~~~~~kll~lp~fL~~~~--~~~~~~~i~~~l~lt~~fL~k~~l~~~~~~~P~sR~~ 231 (240)
.+..++|+++|+.+|..+ +.++.+.++.++.++.+.. .....+...++.+++.++++.|+-.+.....+..|..
T Consensus 164 ~~~~~~s~~~~~~~C~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~lks~~~~~~~ 243 (251)
T COG1381 164 VDPVYFSPKSGGFLCSKCARAAPKPEKDLLLLFGRFLLDLLNRLALKAETKQAAKRITRQLLKEYLGEKPLKSRKLLRQL 243 (251)
T ss_pred CCCCEEEECCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 78741664268610132013567752267775088899864201048566999999999999998334565428899998
Q ss_pred H
Q ss_conf 9
Q gi|254780948|r 232 F 232 (240)
Q Consensus 232 f 232 (240)
+
T Consensus 244 ~ 244 (251)
T COG1381 244 F 244 (251)
T ss_pred H
T ss_conf 7
No 4
>pfam11967 RecO_N Recombination protein O N terminal. Recombination protein O (RecO) is involved in DNA repair and pfam00470 pathway recombination. This domain forms a beta barrel structure.
Probab=99.67 E-value=4.8e-17 Score=123.59 Aligned_cols=75 Identities=27% Similarity=0.518 Sum_probs=62.9
Q ss_pred CCEEEEEEEEEECCCCCHHHHHHHCCCCCCEEEEEEECCCCCC--CCCCCCCCCEEEEEEECCCCCCCCCC-HHHHHCC
Q ss_conf 9500016998303588024475422721286999996676755--32000344314799821577765431-0122101
Q gi|254780948|r 1 MYWQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHR--MQPILQAGNLVRVNWRSRLAQNLGEF-RFEVLES 76 (240)
Q Consensus 1 M~~~d~giVL~~~~~~E~~~Iv~~~T~~~G~~~~i~rG~~~~k--~~~~lq~~~~~~~~~~~k~~~~l~~~-~~e~~~~ 76 (240)
..|+++||||++++|||+|+||++||+++|+++++|||++++| .++.+||++.+++.|..+.. .+..+ ++|++++
T Consensus 2 ~~~~~~aiVL~~~~y~E~d~iv~~~T~~~G~~~~~akG~rk~ks~~~~~l~pf~~~~~~~~~~~~-~L~~l~~ae~~~~ 79 (80)
T pfam11967 2 RLWKTEGIVLHTRDYGESDKIVTLFTREHGKISGVARGARKPKSRLRAALQPFTLLELVLYAGGR-GLGTLTQAELIDS 79 (80)
T ss_pred CCEEEEEEEEEEEECCCCCEEEEEEECCCCEEEEEEECCCCCCCCCCEEECCCCEEEEEEEECCC-CCCEEEEEEEEEC
T ss_conf 83598899997556387247776871589699999984657889874391799789999994998-9887978999515
No 5
>pfam02565 RecO_C Recombination protein O C terminal. Recombination protein O (RecO) is involved in DNA repair and pfam00470 pathway recombination.
Probab=99.60 E-value=2.5e-14 Score=106.99 Aligned_cols=135 Identities=28% Similarity=0.414 Sum_probs=95.8
Q ss_pred CCCHHHHHHHHHHHHH-HHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCE
Q ss_conf 4405899999999999-962135667678999999999612234301379999999999837676612210235556622
Q gi|254780948|r 83 SSSLFLYGLQSIVPLF-RFLPEREPCLELYDMLNIFLNCHKIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGVTQDLL 161 (240)
Q Consensus 83 ~~~~~l~~~~~~~~l~-~~l~e~e~~~~lf~~l~~~L~~l~~~~~~~~~~~~fEl~LL~~lGf~p~L~~C~~cg~~~~l~ 161 (240)
.|..++++++++++++ +++++++|+|.+|+++..+|..+++..+.....+.||+++|+.+||+|+++.|+.||......
T Consensus 2 ~d~~~l~~a~yl~El~~~~~~e~~p~~~lf~ll~~~L~~L~~~~~~~~~~~~Fel~lL~~lG~~P~l~~C~~cg~~~~~~ 81 (156)
T pfam02565 2 LDLERLAAASYINELLDRLLPEEEPNPELFDLLLQALEALDEGDDPELLLLRFELKLLAELGYAPDLDRCAVCGAPEPLA 81 (156)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 65999999999999999980468998999999999999987589769999999999999839982623003679847875
Q ss_pred EEEECCCCH-HH----HCCCCCCCCHHHHHHHHHHCC------CCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 443012100-11----102475320000123455225------678998999999989999998565
Q gi|254780948|r 162 WVSPKSGGA-VC----RSVGLPYAEKMLVLPSFLWKE------EQTIDADSLKSAFQLTDYFLNKYA 217 (240)
Q Consensus 162 ~~s~~~g~a-v~----~~~~~~~~~kll~lp~fL~~~------~~~~~~~~i~~~l~lt~~fL~k~~ 217 (240)
.+++..++. +| ...+.+.......+-..+... ....+........+++..+++-|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~hl 148 (156)
T pfam02565 82 AFSPKAGALCSGCAVSDPAALPLSPETLALLALLLLGDLDKLGEIRVSPETLRELKRLLRAYLDEHL 148 (156)
T ss_pred CEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 3232278654343567877777599999999999668999986167999999999999999999985
No 6
>PRK13908 putative recombination protein RecO; Provisional
Probab=97.62 E-value=0.00013 Score=47.66 Aligned_cols=145 Identities=15% Similarity=0.150 Sum_probs=104.5
Q ss_pred EEEEEEECCCCCHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHHCCCCHHHCCCC
Q ss_conf 16998303588024475422721286999996676755320003443147998215777654310122101422210440
Q gi|254780948|r 6 DAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHRMQPILQAGNLVRVNWRSRLAQNLGEFRFEVLESHCAKLLSSS 85 (240)
Q Consensus 6 ~giVL~~~~~~E~~~Iv~~~T~~~G~~~~i~rG~~~~k~~~~lq~~~~~~~~~~~k~~~~l~~~~~e~~~~~~~~~~~~~ 85 (240)
+|+||++.+-++-|+||+++|+++=.-..-.+|||-+ ....|..++++...- ..-++-. -++++-.++..++..
T Consensus 2 QGfIL~~~kvrdEDlIV~ILT~~~l~tlYRFYGARHS----~I~~G~KIDFe~E~~-~~~lprL-r~v~HLgf~W~~d~~ 75 (204)
T PRK13908 2 QGFILDTQKVRDEDLIVYILTPNNLKTLYRFYGARHS----VINLGYKIDFELEED-GKFLPRL-RDVLHLGFPWLRDRD 75 (204)
T ss_pred CCEEEEEEEECCCCEEEEECCHHHHHHHHHHCCCCCH----HHHCCCEEEEEEECC-CCCHHHH-CCCEECCCHHHHCCH
T ss_conf 8568742231254338998058787789875331420----231244031797146-6600440-544114736551204
Q ss_pred HHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCCC
Q ss_conf 58999999999999621356-6767899999999961223430137999999999983767661221023555
Q gi|254780948|r 86 LFLYGLQSIVPLFRFLPERE-PCLELYDMLNIFLNCHKIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGVT 157 (240)
Q Consensus 86 ~~l~~~~~~~~l~~~l~e~e-~~~~lf~~l~~~L~~l~~~~~~~~~~~~fEl~LL~~lGf~p~L~~C~~cg~~ 157 (240)
+.+....++-.+.+-|.+-+ -..-.|+++..+-..+...++- ...+.-=+++|..=|=-=....|-+|+..
T Consensus 76 k~~~WQ~firLly~HL~Dv~~lDsFYf~lL~~~a~~~~kqnpK-R~iie~Y~~LLefEGRlh~~~~Cf~Ce~~ 147 (204)
T PRK13908 76 RLLIWQRFIRLLYRHLKDVESLDSFYFDLLDDCAKKLEKQNPK-RVIIESYAKLLEFEGRLHKDFECFLCDEK 147 (204)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHCCCCCCCCEEECCCCC
T ss_conf 8799999999999986307777889999999999998652836-18999999999751445898647605876
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=93.18 E-value=0.22 Score=27.94 Aligned_cols=85 Identities=15% Similarity=0.151 Sum_probs=56.9
Q ss_pred HHHHHHHCCCCCHHHHCCCCCCCCCEEEEECCCCHHHHCCCCCCCCHHHHHHH-HHHCCC-CCCCHHHHHHHHHHHHHHH
Q ss_conf 99999837676612210235556622443012100111024753200001234-552256-7899899999998999999
Q gi|254780948|r 136 LMLLKNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKMLVLPS-FLWKEE-QTIDADSLKSAFQLTDYFL 213 (240)
Q Consensus 136 l~LL~~lGf~p~L~~C~~cg~~~~l~~~s~~~g~av~~~~~~~~~~kll~lp~-fL~~~~-~~~~~~~i~~~l~lt~~fL 213 (240)
-+++..+.-.++=.+|+.||... ..|.|..-|..+|-+|+.-+.. |.... |...-. +..+.+++.. +...|.-=
T Consensus 8 ~~~l~~l~~~~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHRs--LGvhiS~VKSitLD~wt~~~l~~-m~~gGN~~ 83 (319)
T COG5347 8 RKLLKLLKSDSSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHRS--LGVHISKVKSLTLDNWTEEELRR-MEVGGNSN 83 (319)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCC-CCEEECCCCEEEEEECCHHHHC--CCCCEEEEEEEECCCCCHHHHHH-HHHHCCHH
T ss_conf 99999986040568150379999-8448635586987412054423--55540466542014689999999-98704531
Q ss_pred HHHHHHHCCCC
Q ss_conf 85656628999
Q gi|254780948|r 214 NKYALQHNIIH 224 (240)
Q Consensus 214 ~k~~l~~~~~~ 224 (240)
-+.+++++++.
T Consensus 84 a~~~~e~~~~~ 94 (319)
T COG5347 84 ANRFYEKNLLD 94 (319)
T ss_pred HHHHHCCCCCC
T ss_conf 56675148875
No 8
>KOG0703 consensus
Probab=85.61 E-value=1.8 Score=22.44 Aligned_cols=93 Identities=13% Similarity=-0.043 Sum_probs=53.5
Q ss_pred HHHCCCCCHHHHCCCCCCCCCEEEEECCCCHHHHCCCCCCCCHHHHHHHHHH-CCCCCCCHHHHHHHHHHHHHHHHH---
Q ss_conf 9837676612210235556622443012100111024753200001234552-256789989999999899999985---
Q gi|254780948|r 140 KNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKMLVLPSFLW-KEEQTIDADSLKSAFQLTDYFLNK--- 215 (240)
Q Consensus 140 ~~lGf~p~L~~C~~cg~~~~l~~~s~~~g~av~~~~~~~~~~kll~lp~fL~-~~~~~~~~~~i~~~l~lt~~fL~k--- 215 (240)
++|==.|+=..||.||.. +..|.|-+-|--+|-.|++-+.. |....--+ .-..+.+.+|-.+.+.-.|.-=-+
T Consensus 17 ~~Ll~~~~N~~CADC~a~-~P~WaSwnlGvFiC~~C~giHR~--lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~~~ 93 (287)
T KOG0703 17 RELLREPDNKVCADCGAK-GPRWASWNLGVFICLRCAGIHRS--LGVHISKVKSVTLDEWTDEQVDFMISMGNAKANSYY 93 (287)
T ss_pred HHHHCCCCCCCCCCCCCC-CCCEEEEECCEEEEEECCCCCCC--CCCHHHEEEEEECCCCCHHHHHHHHHHCCHHHHHHC
T ss_conf 999728356713014899-99747850476887641522122--110123024630145689999999997035665430
Q ss_pred --HHHHHCCCCCCH-HHHHHHHH
Q ss_conf --656628999998-79999999
Q gi|254780948|r 216 --YALQHNIIHCHL-LRENFLGK 235 (240)
Q Consensus 216 --~~l~~~~~~~P~-sR~~f~~~ 235 (240)
.+-.+...+-|. .|+.||..
T Consensus 94 ea~~p~~~~~p~~d~~~e~FIR~ 116 (287)
T KOG0703 94 EAKLPDPFRRPGPDDLVEQFIRD 116 (287)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 23588413689837999999998
No 9
>pfam01412 ArfGap Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=75.72 E-value=6 Score=19.22 Aligned_cols=70 Identities=13% Similarity=0.072 Sum_probs=43.9
Q ss_pred CCHHHHCCCCCCCCCEEEEECCCCHHHHCCCCCCCCHHHHHH-HHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 661221023555662244301210011102475320000123-4552256-7899899999998999999856566
Q gi|254780948|r 146 LDLTKCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKMLVLP-SFLWKEE-QTIDADSLKSAFQLTDYFLNKYALQ 219 (240)
Q Consensus 146 p~L~~C~~cg~~~~l~~~s~~~g~av~~~~~~~~~~kll~lp-~fL~~~~-~~~~~~~i~~~l~lt~~fL~k~~l~ 219 (240)
|.=..|+.||..+ ..|.|...|-.||..|++-+.. |... .+...-. ...+.+++ +.++..|.---+.+++
T Consensus 11 p~N~~CaDCg~~~-p~Was~n~GvfiC~~CsgvHR~--lG~his~VrSi~lD~w~~~~v-~~~~~~GN~~an~~~e 82 (117)
T pfam01412 11 PGNKVCADCGAPN-PTWASLNLGIFICIRCSGVHRS--LGVHISKVRSLTLDKWTPEQL-ERMKAGGNDRANEFWE 82 (117)
T ss_pred CCCCCCCCCCCCC-CCEEEECCCEEECHHHHHHHHH--CCCCCCEEEECCCCCCCHHHH-HHHHHHHHHHHHHHHH
T ss_conf 7909678998999-9979821898885776899974--499867677787887899999-9999980099999987
No 10
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=75.01 E-value=4.9 Score=19.75 Aligned_cols=62 Identities=19% Similarity=0.166 Sum_probs=38.0
Q ss_pred CCHHHHCCCCCCCCCEEEEECCCCHHHHCCCCCCCCHHHHHH-HHHHCCCC-CCCHHHHHHHHHHHHH
Q ss_conf 661221023555662244301210011102475320000123-45522567-8998999999989999
Q gi|254780948|r 146 LDLTKCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKMLVLP-SFLWKEEQ-TIDADSLKSAFQLTDY 211 (240)
Q Consensus 146 p~L~~C~~cg~~~~l~~~s~~~g~av~~~~~~~~~~kll~lp-~fL~~~~~-~~~~~~i~~~l~lt~~ 211 (240)
|.=..|+.||.. +..|+|...|..||..+++-+.. |... .+...-.. ..+.+++ +.++-.|.
T Consensus 1 P~N~~CaDC~~~-~p~w~s~~~GifiC~~CsgiHR~--Lg~hiSkVkSl~lD~w~~~~v-~~m~~~GN 64 (112)
T smart00105 1 PGNKKCFDCGAP-NPTWASVNLGVFLCIECSGIHRS--LGVHISKVRSLTLDTWTEEEL-RLLQKGGN 64 (112)
T ss_pred CCCCCCCCCCCC-CCCEEEECCCEEECHHHHHHHHH--CCCCCCEEEECCCCCCCHHHH-HHHHHHCH
T ss_conf 989807899899-99978824798886887899873--388756466787787899999-99999882
No 11
>KOG0706 consensus
Probab=72.36 E-value=5.8 Score=19.27 Aligned_cols=65 Identities=15% Similarity=0.239 Sum_probs=40.6
Q ss_pred HHHHHHCCCCCHHHHCCCCCCCCCEEEEECCCCHHHHCCCCCCCCHHHHHHHHHHCCCC-CCCHHHHH
Q ss_conf 99998376766122102355566224430121001110247532000012345522567-89989999
Q gi|254780948|r 137 MLLKNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKMLVLPSFLWKEEQ-TIDADSLK 203 (240)
Q Consensus 137 ~LL~~lGf~p~L~~C~~cg~~~~l~~~s~~~g~av~~~~~~~~~~kll~lp~fL~~~~~-~~~~~~i~ 203 (240)
.+++.|+-.|+=..|..||.+ +..|.|.-+|--+|-+|...+.+--.++ .|....+. ..++.++.
T Consensus 12 ~vfkkLRs~~~NKvCFDCgAk-nPtWaSVTYGIFLCiDCSAvHRnLGVHi-SFVRSTnLDsWs~~qLR 77 (454)
T KOG0706 12 TVFKKLRSQSENKVCFDCGAK-NPTWASVTYGIFLCIDCSAVHRNLGVHI-SFVRSTNLDSWSWEQLR 77 (454)
T ss_pred HHHHHHHCCCCCCEECCCCCC-CCCCEEECCEEEEEEECCHHHHCCCCCE-EEEEECCCCCCCHHHHH
T ss_conf 999998547778642136999-9983665110799876205552345423-78750354648899876
No 12
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=40.93 E-value=26 Score=15.35 Aligned_cols=54 Identities=17% Similarity=0.203 Sum_probs=38.3
Q ss_pred EEEEEECCCCCHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCC
Q ss_conf 699830358802447542272128699999667675532000344314799821577
Q gi|254780948|r 7 AIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHRMQPILQAGNLVRVNWRSRLA 63 (240)
Q Consensus 7 giVL~~~~~~E~~~Iv~~~T~~~G~~~~i~rG~~~~k~~~~lq~~~~~~~~~~~k~~ 63 (240)
|+|.++ .+|. ..|++-...-...+.++.-+.+||+|+.+++|..+++....-..
T Consensus 12 GiV~~~--~~d~-y~vdi~~~~~a~L~~laFegATKknrP~L~~GdlVYaRV~~a~~ 65 (86)
T cd05790 12 GIVVAK--AGDF-FKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANR 65 (86)
T ss_pred EEEEEE--CCCE-EEEECCCCCCEEECCCEECCCCCCCCCCCCCCCEEEEEEEECCC
T ss_conf 999443--2766-89976798664850010178765568878878899999987489
No 13
>TIGR00269 TIGR00269 conserved hypothetical protein TIGR00269; InterPro: IPR000541 The following uncharacterised proteins have been shown to share regions of similarities, yeast chromosome VII hypothetical protein YGL211w; Dictyostelium discoideum (Slime mold) protein veg136; and Methanococcus jannaschii hypothetical proteins MJ1157 and MJ1478..
Probab=40.72 E-value=21 Score=15.89 Aligned_cols=58 Identities=24% Similarity=0.374 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHCCCCCCHH--HHHHHHH---HHHHHHCCCCCHHHHCCCCCCCCCEEEEECCCCHHHHCC
Q ss_conf 89999999996122343013--7999999---999983767661221023555662244301210011102
Q gi|254780948|r 110 LYDMLNIFLNCHKIPSVIGK--IFVQIEL---MLLKNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCRSV 175 (240)
Q Consensus 110 lf~~l~~~L~~l~~~~~~~~--~~~~fEl---~LL~~lGf~p~L~~C~~cg~~~~l~~~s~~~g~av~~~~ 175 (240)
.=....++|..+++..+-.. +..-||- -+++.+--.-++..|..||. |.|-|.+|+.+
T Consensus 38 ~R~~~~dfL~~le~~~pG~kfsvl~sf~ki~~~~~~~L~~~~~~~~C~~CGe--------P~SPG~~CkaC 100 (106)
T TIGR00269 38 VRARIRDFLKDLEEKKPGVKFSVLRSFEKIKIILLKELSEKEELRRCERCGE--------PASPGKICKAC 100 (106)
T ss_pred HHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHCCCCCCCCCCCCCCC--------CCCCCCHHHHH
T ss_conf 3588999999863038970231000046677776321143355650001478--------88875443666
No 14
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=38.75 E-value=14 Score=16.89 Aligned_cols=16 Identities=6% Similarity=0.090 Sum_probs=7.0
Q ss_pred CCCCHHHHHHHHHHHH
Q ss_conf 7899899999998999
Q gi|254780948|r 195 QTIDADSLKSAFQLTD 210 (240)
Q Consensus 195 ~~~~~~~i~~~l~lt~ 210 (240)
...+..++.+...++.
T Consensus 275 ~~~t~~~Ia~v~~vse 290 (310)
T PRK00423 275 ERRTQREVAEVAGVTE 290 (310)
T ss_pred CCCCHHHHHHHHCCCH
T ss_conf 8989999998969889
No 15
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=32.53 E-value=20 Score=15.97 Aligned_cols=32 Identities=28% Similarity=0.542 Sum_probs=25.1
Q ss_pred HHCCCCCCCCCEEEEECCCCHHHHCCCCCCCCHH
Q ss_conf 2102355566224430121001110247532000
Q gi|254780948|r 150 KCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKM 183 (240)
Q Consensus 150 ~C~~cg~~~~l~~~s~~~g~av~~~~~~~~~~kl 183 (240)
+|-.||+.. ..+.+.+|..||..+|.-.++..
T Consensus 2 ~Cp~Cg~~~--~~~D~~~Ge~vC~~CG~Vlee~~ 33 (40)
T pfam08271 2 KCPNCGSTE--IVFDYERGEYVCTECGLVLEDNI 33 (40)
T ss_pred CCCCCCCCC--EEEECCCCCEECCCCCEEEECCC
T ss_conf 388799970--67727789787057971900023
No 16
>PTZ00048 cytochrome c; Provisional
Probab=31.80 E-value=36 Score=14.46 Aligned_cols=87 Identities=11% Similarity=0.072 Sum_probs=47.3
Q ss_pred HHHCCCCCCC--CCEEEEECCCCHHHHCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 2210235556--62244301210011102475320000123455225678998999999989999998565662899999
Q gi|254780948|r 149 TKCVVTGVTQ--DLLWVSPKSGGAVCRSVGLPYAEKMLVLPSFLWKEEQTIDADSLKSAFQLTDYFLNKYALQHNIIHCH 226 (240)
Q Consensus 149 ~~C~~cg~~~--~l~~~s~~~g~av~~~~~~~~~~kll~lp~fL~~~~~~~~~~~i~~~l~lt~~fL~k~~l~~~~~~~P 226 (240)
.+|+.|...+ ....+-|.-.+.|.+.+|.+ + +....-|.......+.+.+..-|.=-.-|+.-.--.--.++.|
T Consensus 24 ~~C~~CHs~~~~~~~~~GP~L~gv~gR~ags~--~--f~YS~Alk~~~~~W~~~~L~~fL~~P~~~~pGTkM~f~Gl~~~ 99 (115)
T PTZ00048 24 SKCAQCHTINKGGAVKQGPNLYGFYGRKSGSS--D--YAYSDANKNSGIVWSDKHLFVYLVNPKLYIPGTKMIFAGLKKE 99 (115)
T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC--C--CCCCHHHHHCCCEECHHHHHHHHHCHHHHCCCCCCCCCCCCCH
T ss_conf 87587088788999887998878678757679--9--8748878627885389999999968400078987347798999
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 8799999999973
Q gi|254780948|r 227 LLRENFLGKLLEL 239 (240)
Q Consensus 227 ~sR~~f~~~i~~~ 239 (240)
.-|..+|.+|+++
T Consensus 100 ~dR~dlIaYLk~~ 112 (115)
T PTZ00048 100 QDRADLIAYLKEA 112 (115)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999987
No 17
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=28.96 E-value=40 Score=14.16 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=15.0
Q ss_pred HHHCCCCCCCCCEEEEECCC
Q ss_conf 22102355566224430121
Q gi|254780948|r 149 TKCVVTGVTQDLLWVSPKSG 168 (240)
Q Consensus 149 ~~C~~cg~~~~l~~~s~~~g 168 (240)
.+|+.||+++++.|-|-.++
T Consensus 226 ~KC~nC~~t~~l~y~sl~s~ 245 (308)
T COG3058 226 VKCSNCEQSKKLHYWSLESS 245 (308)
T ss_pred HHHCCCCCCCCCCCEECCCH
T ss_conf 87336666677650000310
No 18
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex . The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. .
Probab=28.58 E-value=28 Score=15.11 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=18.6
Q ss_pred HHHCCCCCCCCCEEEEECCCC
Q ss_conf 221023555662244301210
Q gi|254780948|r 149 TKCVVTGVTQDLLWVSPKSGG 169 (240)
Q Consensus 149 ~~C~~cg~~~~l~~~s~~~g~ 169 (240)
-+|..||++..+.|.|..+|+
T Consensus 229 vKCs~Ce~sk~l~Y~sle~~~ 249 (312)
T TIGR01562 229 VKCSACEESKKLAYLSLEDDD 249 (312)
T ss_pred EEECCCCCCCCEEEEEECCCC
T ss_conf 665277876760256632787
No 19
>KOG1597 consensus
Probab=25.60 E-value=35 Score=14.54 Aligned_cols=103 Identities=15% Similarity=0.224 Sum_probs=42.2
Q ss_pred EEEEEEECCCCCHHHHHHHCCCCC-CEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHHCCCCHHHC--
Q ss_conf 169983035880244754227212-86999996676755320003443147998215777654310122101422210--
Q gi|254780948|r 6 DAIILGVRSYGEKNIILEVMTRQY-GRHLGFVRNGQSHRMQPILQAGNLVRVNWRSRLAQNLGEFRFEVLESHCAKLL-- 82 (240)
Q Consensus 6 ~giVL~~~~~~E~~~Iv~~~T~~~-G~~~~i~rG~~~~k~~~~lq~~~~~~~~~~~k~~~~l~~~~~e~~~~~~~~~~-- 82 (240)
=|.|+..+...+.|-.=++ +.+. |.-.--| |+ -..+.+.-|....+ .+++.+.-..+...+-+......+
T Consensus 27 CGlVl~~r~Id~~sEwrtf-snd~~~~DPsrv-G~---~sNPlL~~g~L~T~--I~~g~g~~s~~~s~l~~~Q~~~sm~~ 99 (308)
T KOG1597 27 CGLVLEDRIIDEGSEWRTF-SNDDSDADPSRV-GA---SSNPLLDGGDLSTF--ISKGTGTSSSFASSLGKAQNRNSMSN 99 (308)
T ss_pred CCEEECCCCCCCCCCCCCC-CCCCCCCCCCCC-CC---CCCCCCCCCCCCEE--EECCCCCCHHHHHHHHHHHCCCCCCC
T ss_conf 7726214242565221001-467778896546-88---88987889985405--40588877788998888742312478
Q ss_pred CCCHHHHHHHHHHHHHHH--HCC--CCCCHHHHHHHH
Q ss_conf 440589999999999996--213--566767899999
Q gi|254780948|r 83 SSSLFLYGLQSIVPLFRF--LPE--REPCLELYDMLN 115 (240)
Q Consensus 83 ~~~~~l~~~~~~~~l~~~--l~e--~e~~~~lf~~l~ 115 (240)
.+.....++-.+..+... ||- .+.-.++|..++
T Consensus 100 ~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~ 136 (308)
T KOG1597 100 SDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVE 136 (308)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 5389999999999999873773677888999999988
No 20
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=24.78 E-value=28 Score=15.14 Aligned_cols=14 Identities=7% Similarity=0.235 Sum_probs=5.9
Q ss_pred HHHHHHHCCCCCHH
Q ss_conf 99999837676612
Q gi|254780948|r 136 LMLLKNIGFGLDLT 149 (240)
Q Consensus 136 l~LL~~lGf~p~L~ 149 (240)
-++-+.||..++..
T Consensus 199 ~rf~s~L~l~~~v~ 212 (285)
T COG1405 199 PRFASKLGLSDEVR 212 (285)
T ss_pred HHHHHHCCCCHHHH
T ss_conf 99999859988999
No 21
>pfam04216 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase.
Probab=24.26 E-value=37 Score=14.37 Aligned_cols=13 Identities=23% Similarity=0.238 Sum_probs=6.9
Q ss_pred HHHCCCCCCCCCE
Q ss_conf 2210235556622
Q gi|254780948|r 149 TKCVVTGVTQDLL 161 (240)
Q Consensus 149 ~~C~~cg~~~~l~ 161 (240)
..|=+||+.--.+
T Consensus 167 ~~CPvCGs~P~~s 179 (283)
T pfam04216 167 GLCPVCGSAPVAS 179 (283)
T ss_pred CCCCCCCCCCHHH
T ss_conf 9699999810001
No 22
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=23.89 E-value=19 Score=16.18 Aligned_cols=35 Identities=31% Similarity=0.645 Sum_probs=27.7
Q ss_pred HHHCCCCCCCCCEEEEECCCC-HHHHCCCCCCCCHH
Q ss_conf 221023555662244301210-01110247532000
Q gi|254780948|r 149 TKCVVTGVTQDLLWVSPKSGG-AVCRSVGLPYAEKM 183 (240)
Q Consensus 149 ~~C~~cg~~~~l~~~s~~~g~-av~~~~~~~~~~kl 183 (240)
..|..||.++...|-.-.+|. .+|..+|.-|...-
T Consensus 4 ~~C~nC~tt~Tp~WR~~~~g~~~LCNaCGl~~kk~g 39 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf 899798898995235489898721289999999919
No 23
>pfam09943 DUF2175 Uncharacterized protein conserved in archaea (DUF2175). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=22.92 E-value=52 Score=13.47 Aligned_cols=56 Identities=18% Similarity=0.169 Sum_probs=25.1
Q ss_pred HHCCCCCC--CCCEEEEECCCCHHHHCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 21023555--662244301210011102475320000123455225678998999999989999998565
Q gi|254780948|r 150 KCVVTGVT--QDLLWVSPKSGGAVCRSVGLPYAEKMLVLPSFLWKEEQTIDADSLKSAFQLTDYFLNKYA 217 (240)
Q Consensus 150 ~C~~cg~~--~~l~~~s~~~g~av~~~~~~~~~~kll~lp~fL~~~~~~~~~~~i~~~l~lt~~fL~k~~ 217 (240)
+|++||.. ++..+-..+- |.|.-+|-..-. ......+..+...+|....+++...+
T Consensus 4 kC~iCg~~I~~gelFTF~k~-G~VH~~C~~~~~-----------~~k~~~d~~e~l~~L~~l~d~l~~~i 61 (101)
T pfam09943 4 KCYICGKPIIEGELFTFTSK-GPVHYECLVEDA-----------SKKIKGDKPEDLVALLRLEDYLHEGI 61 (101)
T ss_pred EEEECCCEEEECCEEEEECC-CCEEHHHHHHHH-----------HHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 68843987465536888159-866199999988-----------62215563889999999999999999
No 24
>TIGR01810 betA choline dehydrogenase; InterPro: IPR011533 Choline dehydrogenase catalyzes the conversion of exogenously supplied choline into the intermediate glycine betaine aldehyde, as part of a two-step oxidative reaction leading to the formation of osmoprotectant betaine. This enzymatic system can be found in both Gram-positive and Gram-negative bacteria. As in Escherichia coli , Staphylococcus xylosus , and Sinorhizobium meliloti , this enzyme is found associated in a transcriptionally co-induced gene cluster with betaine aldehyde dehydrogenase, the second catalytic enzyme in this reaction. Other Gram-positive organisms have been shown to employ a different enzymatic system, utilising a soluble choline oxidase or type III alcohol dehydrogenase instead of choline dehydrogenase . This enzyme is a member of the GMC oxidoreductase family, sharing a common evolutionary origin and enzymatic reaction with alcohol dehydrogenase . Out grouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified. ; GO: 0008812 choline dehydrogenase activity, 0019285 glycine betaine biosynthetic process from choline.
Probab=20.72 E-value=55 Score=13.31 Aligned_cols=151 Identities=18% Similarity=0.095 Sum_probs=75.3
Q ss_pred CHHHHHCCCCHHHCCCCHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHH----HHHCCCCCCHHHHHH-HH------H
Q ss_conf 10122101422210440589999999999996-213566767899999999----961223430137999-99------9
Q gi|254780948|r 69 FRFEVLESHCAKLLSSSLFLYGLQSIVPLFRF-LPEREPCLELYDMLNIFL----NCHKIPSVIGKIFVQ-IE------L 136 (240)
Q Consensus 69 ~~~e~~~~~~~~~~~~~~~l~~~~~~~~l~~~-l~e~e~~~~lf~~l~~~L----~~l~~~~~~~~~~~~-fE------l 136 (240)
.+-|++-+..++--=..+.++++--.+.|-.+ .+....-|.+=+.+++-| .....+-....-.+. |. -
T Consensus 250 ankEVilsagainSPqlL~lSGiG~aehL~e~gI~~~~~lPGVGeNl~DHlE~Y~Q~~ck~PVSlyp~L~w~~~p~iGaq 329 (540)
T TIGR01810 250 ANKEVILSAGAINSPQLLQLSGIGDAEHLKELGIELKVELPGVGENLQDHLEVYLQYACKKPVSLYPALNWLKQPVIGAQ 329 (540)
T ss_pred CCCEEEEECCHHHHHHHHHHCCCCCHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCEECCCHHHHHCCCCCCHH
T ss_conf 24457883341213589976289717999855896065278787633435642322422887435602565438722101
Q ss_pred HHH--HHHCCCCCHHHHCCCCCCCCCEEEEEC-------------------------------CCCHHHHCCCCCCCCHH
Q ss_conf 999--983767661221023555662244301-------------------------------21001110247532000
Q gi|254780948|r 137 MLL--KNIGFGLDLTKCVVTGVTQDLLWVSPK-------------------------------SGGAVCRSVGLPYAEKM 183 (240)
Q Consensus 137 ~LL--~~lGf~p~L~~C~~cg~~~~l~~~s~~-------------------------------~g~av~~~~~~~~~~kl 183 (240)
.|+ +=+|-.=.++.|+.--+.++..|=... |=|-|.-+...|..
T Consensus 330 Wlfg~~G~gaSNhFE~ggF~RS~~~v~~Pni~yHFLPvAi~YdG~~A~k~HGfQvHVG~~~S~SRGhv~ikS~DP~~--- 406 (540)
T TIGR01810 330 WLFGKKGVGASNHFEAGGFVRSADDVKYPNIQYHFLPVAIRYDGKKAAKEHGFQVHVGSMLSKSRGHVKIKSKDPKE--- 406 (540)
T ss_pred HHCCCCCCEEEECCCCCCEEECCCCCCCCCCEEECCCEEEECCCHHHHHCCCCEEEECCCCCCCCCCEEEECCCCCC---
T ss_conf 11047652044020243110146678888520101436872274356660797588777777865304763048767---
Q ss_pred HHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 0123455225-6789989999999899999985656628999
Q gi|254780948|r 184 LVLPSFLWKE-EQTIDADSLKSAFQLTDYFLNKYALQHNIIH 224 (240)
Q Consensus 184 l~lp~fL~~~-~~~~~~~~i~~~l~lt~~fL~k~~l~~~~~~ 224 (240)
-|.|+-+- +...|+++..++.+||+.+|.+..|++.++.
T Consensus 407 --~P~i~FNYmSheeDw~efr~air~tReI~~QkAlD~yrG~ 446 (540)
T TIGR01810 407 --KPAILFNYMSHEEDWREFREAIRVTREILKQKALDLYRGR 446 (540)
T ss_pred --CCEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf --8707870478875789999998888987278656767778
Done!