Query gi|254780247|ref|YP_003064660.1| 30S ribosomal protein S8 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 129
No_of_seqs 111 out of 2009
Neff 6.5
Searched_HMMs 39220
Date Tue May 24 05:59:55 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780247.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00042 rps8 ribosomal protei 100.0 0 0 305.0 14.0 128 1-129 3-132 (132)
2 PRK00136 rpsH 30S ribosomal pr 100.0 0 0 304.1 14.4 128 1-129 3-131 (131)
3 pfam00410 Ribosomal_S8 Ribosom 100.0 0 0 300.3 14.1 128 2-129 1-129 (129)
4 COG0096 RpsH Ribosomal protein 100.0 0 0 299.9 12.6 128 1-129 4-132 (132)
5 PTZ00158 40S ribosomal protein 100.0 1.3E-43 0 265.8 12.3 125 1-129 4-130 (130)
6 PRK04034 rps8p 30S ribosomal p 100.0 2.4E-41 0 253.0 13.5 125 1-129 4-130 (130)
7 KOG1754 consensus 100.0 1.2E-31 3E-36 198.5 8.9 125 1-129 4-130 (130)
8 pfam09639 YjcQ YjcQ protein. Y 54.6 15 0.00037 18.1 3.2 44 8-51 5-48 (88)
9 pfam09271 LAG1-DNAbind LAG1, D 52.2 14 0.00035 18.3 2.7 46 36-85 85-134 (140)
10 pfam03288 Pox_D5 Poxvirus D5 p 34.7 33 0.00083 16.2 2.4 41 1-45 2-42 (88)
11 pfam09879 DUF2106 Predicted me 32.9 17 0.00043 17.8 0.7 17 97-113 106-122 (153)
12 COG1244 Predicted Fe-S oxidore 26.1 56 0.0014 14.8 3.7 38 4-42 223-261 (358)
13 TIGR01063 gyrA DNA gyrase, A s 22.0 68 0.0017 14.4 4.8 79 24-117 258-347 (864)
No 1
>CHL00042 rps8 ribosomal protein S8
Probab=100.00 E-value=0 Score=305.05 Aligned_cols=128 Identities=37% Similarity=0.661 Sum_probs=122.1
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCC--CCEECCCEEEE
Q ss_conf 9778999975254885799789951757899999977631210017998348720478872167654--30001416764
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNG--ASVIRKIDCVS 78 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~~~--~~vi~~i~~iS 78 (129)
-||||||||+||||++++|.+|.+|+||++++||++|++||||++|++.++++.+ .++|+|||.++ .|+|+++++||
T Consensus 3 ~D~iaD~ltrIrNA~~a~~~~V~ip~SKl~~~Il~iL~~eGyI~~~~~~~~~~~~-~i~V~LkY~~~~~~pvI~~i~riS 81 (132)
T CHL00042 3 NDTIADMLTSIRNANMVKKGTVRIPSTNITENIVKILLREGFIENVRKHRENNKY-FLVLTLKYRGNKKKPYITILKRIS 81 (132)
T ss_pred CCCHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCEEEEEEEEECCCCC-EEEEEEECCCCCCCEEECEEEEEC
T ss_conf 8719999999871876599889973618999999999977904127997058861-799999744798874312047971
Q ss_pred CCCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 612120328111711104971899818866003799996499958999989
Q gi|254780247|r 79 KPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 79 kP~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
|||+|+|.+.++||++.+|+|++|||||+|||||+||+++++|||+|||||
T Consensus 82 kPg~RvY~~~~~lp~~~~g~G~~IlSTskGimt~~eA~~~~vGGellc~V~ 132 (132)
T CHL00042 82 KPGLRIYSNYKRIPRILGGMGIVILSTSRGIMTDREARLKGIGGEILCYIW 132 (132)
T ss_pred CCCCEEECCHHHHHHHCCCCEEEEEECCCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf 688401767415534129973999968975537699997499848999989
No 2
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=100.00 E-value=0 Score=304.14 Aligned_cols=128 Identities=49% Similarity=0.795 Sum_probs=122.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCC-CCCCEECCCEEEEC
Q ss_conf 97789999752548857997899517578999999776312100179983487204788721676-54300014167646
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYH-NGASVIRKIDCVSK 79 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~-~~~~vi~~i~~iSk 79 (129)
+||||||||+||||++++|.+|.+|+||++.++|++|++||||++|++.++++. ..++|.|||. +++|+|+.+++|||
T Consensus 3 ~D~iaD~lt~IrNA~~a~k~~V~vp~Skl~~~il~iL~~eGyI~~~~~~~~~~~-~~i~V~LkY~~~~~p~I~~i~riSk 81 (131)
T PRK00136 3 TDPIADMLTRIRNAQMAKHETVSVPSSKLKVAIAEILKEEGYIKDYEVEEDGVK-KELEVELKYGENGEPVIEGIKRVSK 81 (131)
T ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCEEEEEEEECCCCE-EEEEEEEECCCCCCCCEEEEEEECC
T ss_conf 756999999888798769988997461899999999997892423799817985-9999999615589840411089607
Q ss_pred CCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 12120328111711104971899818866003799996499958999989
Q gi|254780247|r 80 PGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 80 P~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
||+|+|.++++||++.+|+|++|+|||+|||||+||+++++|||+|||||
T Consensus 82 Pg~RvY~~~~~l~~~~~g~G~~IlSTskGimt~~eA~~~~iGGellc~V~ 131 (131)
T PRK00136 82 PGLRVYKKKDELPKVLNGLGIAIVSTSKGVMTDREARKAGVGGEVLCYVW 131 (131)
T ss_pred CCCEEECCCCCCCCEECCCEEEEEECCCCCEEHHHHHHCCCCCEEEEEEC
T ss_conf 88547856100650518945999987996120799997399978999989
No 3
>pfam00410 Ribosomal_S8 Ribosomal protein S8.
Probab=100.00 E-value=0 Score=300.27 Aligned_cols=128 Identities=50% Similarity=0.810 Sum_probs=125.1
Q ss_pred CHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCC-CCCCEECCCEEEECC
Q ss_conf 7789999752548857997899517578999999776312100179983487204788721676-543000141676461
Q gi|254780247|r 2 SCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYH-NGASVIRKIDCVSKP 80 (129)
Q Consensus 2 D~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~-~~~~vi~~i~~iSkP 80 (129)
||||||||+||||++++|.+|.+|+||++.++|++|++||||++|++.++++++..++|.|||. +++|+|+.+++||+|
T Consensus 1 D~iaD~lt~IrNA~~~~k~~V~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~V~LKY~~~~~p~i~~i~rvSkP 80 (129)
T pfam00410 1 DPIADMLTRIRNAQMAKKETVLIPASKLKISILKILKEEGYIKGFEVIEDERNGKFIKVTLKYDKNGKPVITGIKRISKP 80 (129)
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCEEECCC
T ss_conf 97799999888898869988996274899999999998795246899874888379999986157898640656895387
Q ss_pred CCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 2120328111711104971899818866003799996499958999989
Q gi|254780247|r 81 GRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 81 ~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
|+|+|.+.++||++.+|+|++|+|||+|||||+||+++++|||+||+||
T Consensus 81 ~~R~y~~~~~i~~~~~g~G~~IlSTskGimt~~eA~~~~iGGelL~~v~ 129 (129)
T pfam00410 81 GLRVYVSYKELPKVLGGLGIAILSTSKGVMTDREARKKGVGGEVLCYVW 129 (129)
T ss_pred CCCEECCCCCCHHHCCCCCEEEECCCCCCCCHHHHHHHCCCCEEEEEEC
T ss_conf 6846735773444428961899717977435899998499977999989
No 4
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=299.95 Aligned_cols=128 Identities=53% Similarity=0.823 Sum_probs=123.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCC-CCCCEECCCEEEEC
Q ss_conf 97789999752548857997899517578999999776312100179983487204788721676-54300014167646
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYH-NGASVIRKIDCVSK 79 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~-~~~~vi~~i~~iSk 79 (129)
+||||||||+||||+++++..|.+|+||+..+||++|++||||++|+++|+++.. .++|.|||. |++|+|+++++|||
T Consensus 4 ~DpiAdmltrIrNa~~~~~~~v~~P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~-~~~v~Lky~~n~~~vI~~~~rVSk 82 (132)
T COG0096 4 TDPLADMLTRIRNAERAKKEVVSMPASKLKGAILKVLKKEGYIKDFEVIDDGRKG-KLRVQLKYRINGCGVISPIKRVSK 82 (132)
T ss_pred CCHHHHHHHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHCCCCCEEEEEECCCCE-EEEEEEECCCCCCCCCCCCEECCC
T ss_conf 2179999998675887414356224078999999999975873338997078610-799999704589725334235088
Q ss_pred CCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 12120328111711104971899818866003799996499958999989
Q gi|254780247|r 80 PGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 80 P~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
||+|+|.+.++||++.+|+|++|+|||+|||||+||+++++|||+|||||
T Consensus 83 pg~rvy~~~~~LP~v~~g~Gi~IvSTs~GVMtd~eAr~~~vGGevLcyV~ 132 (132)
T COG0096 83 PGLRVYEKKRELPAVLNGLGIAIVSTSKGVMTDKEARKKGVGGEVLCYVW 132 (132)
T ss_pred CCCEEECCHHHHHHHHCCCEEEEEECCCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf 77043058646444305853999986887647599998299967999979
No 5
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=100.00 E-value=1.3e-43 Score=265.79 Aligned_cols=125 Identities=31% Similarity=0.464 Sum_probs=116.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCC-CCCCCEECCCEEEE
Q ss_conf 977899997525488579978995-1757899999977631210017998348720478872167-65430001416764
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKY-HNGASVIRKIDCVS 78 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~i-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky-~~~~~vi~~i~~iS 78 (129)
||||||||||||||++++|.+|.+ |+||+..++|+||++||||.+|+++|+++++. +.|.|.+ .+++++|+++.++|
T Consensus 4 ~DpiaD~LtrIrNA~~~~k~~v~i~P~Sklk~~il~iLk~eGYI~~f~~~~~~~~g~-~~i~L~~~ink~~~I~~r~~v~ 82 (130)
T PTZ00158 4 MSVLADCLRSIVNAERRGRRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIVDDHRSGK-IVVELLGRLNKCGVISPRYDVT 82 (130)
T ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHCCCHHHEEECCCCCCCE-EEEEEECCCCCCCCEEEEEECC
T ss_conf 247999999857598758876999754187999999998769665689822666980-9999804578898206445658
Q ss_pred CCCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 612120328111711104971899818866003799996499958999989
Q gi|254780247|r 79 KPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 79 kP~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
+|+.+.|.+ ..+| +.++|++|+|||+|||||+||+++++|||+|||||
T Consensus 83 ~~~~~~~~~-~~lp--~~~lGi~IiSTskGvMtd~eAr~~~vGGevLayvy 130 (130)
T PTZ00158 83 LGDIEKWAN-NILP--SRQFGHVVLTTSVGIMDHEEARQRHTGGKILGFFY 130 (130)
T ss_pred CCCCCCCCC-CCCC--CCCCCEEEEECCCCCCCHHHHHHHCCCCEEEEEEC
T ss_conf 766111003-8998--54431999977987667699998299974999979
No 6
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=100.00 E-value=2.4e-41 Score=252.98 Aligned_cols=125 Identities=38% Similarity=0.510 Sum_probs=107.6
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCC-CCCCCEECCCEEEE
Q ss_conf 977899997525488579978995-1757899999977631210017998348720478872167-65430001416764
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKY-HNGASVIRKIDCVS 78 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~i-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky-~~~~~vi~~i~~iS 78 (129)
+||||||||+||||++++|++|.+ |+||++.++|++|++||||++|++.++++... +.|.|++ .++.+++++...+|
T Consensus 4 ~DpIaDmLtrIRNA~~~~k~~v~~~P~Skl~~~il~iL~~EGyI~~~~~~~~~~~~~-~~v~l~~~~n~~~~ik~r~~~~ 82 (130)
T PRK04034 4 LDPLANALSTIKNAERVGKKEVIIKPASKLIGNVLRVMQDEGYIGEFEYIDDGRGGK-FKVELLGRINKCGAIKPRFPVK 82 (130)
T ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEEEECCCCCE-EEEEEECCCCCCCCCCCCEECC
T ss_conf 377999999877098768975999767288999999998759551499986377874-8999822336678644735478
Q ss_pred CCCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 612120328111711104971899818866003799996499958999989
Q gi|254780247|r 79 KPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 79 kP~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
++..+.| ...+.+.+|+|++|+|||+|||||+||+++++|||+|||||
T Consensus 83 ~~~~~~~---~~~~lp~~glGi~IlSTSkGvmtd~eAr~~~vGGEilc~V~ 130 (130)
T PRK04034 83 YDEFEKW---EKRYLPAKNFGILIVSTSKGVMSHYEAREKGIGGVLLAYVY 130 (130)
T ss_pred CCCCCCH---HCCCCCCCCCEEEEEECCCCCCCHHHHHHHCCCCEEEEEEC
T ss_conf 8776421---01445567860899977975447699998299966999989
No 7
>KOG1754 consensus
Probab=99.97 E-value=1.2e-31 Score=198.49 Aligned_cols=125 Identities=33% Similarity=0.440 Sum_probs=115.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCC-CCCCCEECCCEEEE
Q ss_conf 977899997525488579978995-1757899999977631210017998348720478872167-65430001416764
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKY-HNGASVIRKIDCVS 78 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~i-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky-~~~~~vi~~i~~iS 78 (129)
|++|||+|++|+||+++||++|.+ |+|+.+..+|.+|++||||++|+++||++..+ +.|+|.- .|.+.+|.+...|+
T Consensus 4 ~~vLaDalksinNA~krGK~qvlirp~Skvii~FL~vmmkhGyIg~fei~ddhragk-ivv~L~gRlNkcg~IsprfdV~ 82 (130)
T KOG1754 4 MNVLADALKSINNAEKRGKRQVLIRPSSKVIIRFLTVMMKHGYIGEFEIIDDHRAGK-IVVNLTGRLNKCGVISPRFDVK 82 (130)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCE-EEEECCCCCCCCCCCCCCCCCC
T ss_conf 899999999846288647735995211789999999999748656557852774505-8973036510254235533013
Q ss_pred CCCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf 612120328111711104971899818866003799996499958999989
Q gi|254780247|r 79 KPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF 129 (129)
Q Consensus 79 kP~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~ 129 (129)
.|+.+.|.+ -.++++.+|+.+++||+|+|+|+||+.+++|||+|||+|
T Consensus 83 lkdlek~~n---~llpsrqfg~ivltts~Gimdh~ear~k~~gG~ilg~~~ 130 (130)
T KOG1754 83 LKDLEKWTN---SLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKILGFFY 130 (130)
T ss_pred CCHHHHHHH---CCCCCCEEEEEEEECCCCCCCHHHHHHHHCCCCCCEEEC
T ss_conf 553888875---368610464899855555656799868630764010039
No 8
>pfam09639 YjcQ YjcQ protein. YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is expressed in bacteria and also in viruses. It appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown. However, it is thought to be a prophage head protein in viruses.
Probab=54.59 E-value=15 Score=18.13 Aligned_cols=44 Identities=16% Similarity=0.068 Sum_probs=28.4
Q ss_pred HHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEEC
Q ss_conf 97525488579978995175789999997763121001799834
Q gi|254780247|r 8 LTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDA 51 (129)
Q Consensus 8 lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~ 51 (129)
|..|..+...+...-.=-....-..++.-|.++|||.+....++
T Consensus 5 L~~l~~~~e~~~~~~~~i~~~~f~~il~~L~d~GyI~Gv~~~~~ 48 (88)
T pfam09639 5 LKYLMFGFENGQENDPDITDDQFSDALEMLRDEGYIKGVSFTPT 48 (88)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECC
T ss_conf 99999997267778999668999999999997798331685057
No 9
>pfam09271 LAG1-DNAbind LAG1, DNA binding. Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding.
Probab=52.23 E-value=14 Score=18.28 Aligned_cols=46 Identities=20% Similarity=0.260 Sum_probs=26.4
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEEECCCCCCCC----EECCCEEEECCCCCEE
Q ss_conf 7763121001799834872047887216765430----0014167646121203
Q gi|254780247|r 36 VLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGAS----VIRKIDCVSKPGRRLY 85 (129)
Q Consensus 36 iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~~~~~----vi~~i~~iSkP~~r~y 85 (129)
...+..||.+- |.+....+.+.+-|.++.. .-++|+.||||+++.-
T Consensus 85 a~~KtL~ISd~----dKrK~f~l~~~~~~~~g~~~g~F~S~~IkVISKPSKKkq 134 (140)
T pfam09271 85 AALKTLYISDV----DKRKHFRLLVRTFLGSGQDLGTFPSLRIKVISKPSKKRQ 134 (140)
T ss_pred EEEEEEEECCC----CCCCEEEEEEEEEECCCCEEEEECCCCCEEEECCCCCHH
T ss_conf 55107887066----655336899999944985699974764127817760301
No 10
>pfam03288 Pox_D5 Poxvirus D5 protein-like. This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain.
Probab=34.65 E-value=33 Score=16.16 Aligned_cols=41 Identities=15% Similarity=0.048 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEE
Q ss_conf 977899997525488579978995175789999997763121001
Q gi|254780247|r 1 MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGE 45 (129)
Q Consensus 1 mD~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~ 45 (129)
+|+|.||+..+.... ....+|.+-+-.....-+.+.||...
T Consensus 2 nD~v~dF~~~~~~~~----~s~~vP~~~ly~~y~~~~e~~g~~~~ 42 (88)
T pfam03288 2 NDPVPDFAEELFVLF----KSDRVPSDFLYEAYKAWCEKNGYVPV 42 (88)
T ss_pred CCCHHHHHHHHHHCC----CCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 860999999997645----46407599999999999998599775
No 11
>pfam09879 DUF2106 Predicted membrane protein (DUF2106). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=32.88 E-value=17 Score=17.80 Aligned_cols=17 Identities=24% Similarity=0.403 Sum_probs=14.1
Q ss_pred CCCEEEEECCCCEECHH
Q ss_conf 97189981886600379
Q gi|254780247|r 97 GLGIMIVTTSKGVMAGH 113 (129)
Q Consensus 97 g~G~~IiSTskGimt~~ 113 (129)
-+|+.|+|||.||++--
T Consensus 106 yfGTTIvs~PGGilDEI 122 (153)
T pfam09879 106 YFGTTIVSHPGGILDEI 122 (153)
T ss_pred CCCCEEECCCCHHHHHH
T ss_conf 36735855787047889
No 12
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=26.05 E-value=56 Score=14.83 Aligned_cols=38 Identities=18% Similarity=0.282 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHHHHCCC
Q ss_conf 899997525488579978995-175789999997763121
Q gi|254780247|r 4 LGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGY 42 (129)
Q Consensus 4 iad~lt~IrNA~~~~k~~v~i-p~Skl~~~il~iL~~eGy 42 (129)
|.|++.+|+ |...+-..+++ |.+=....+++-|++.|.
T Consensus 223 I~D~i~Si~-~~~~~~d~iSinptnVqKgTlvE~lw~~g~ 261 (358)
T COG1244 223 IEDVISSIV-AAKPGTDTISINPTNVQKGTLVEKLWRRGL 261 (358)
T ss_pred HHHHHHHHH-HHCCCCCEEEECCCCCCHHHHHHHHHHCCC
T ss_conf 999999999-743678758844542213109999997378
No 13
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743 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. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are 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 . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=21.98 E-value=68 Score=14.37 Aligned_cols=79 Identities=23% Similarity=0.370 Sum_probs=55.4
Q ss_pred EEC----CHHHHHHHHHHHHCCCEEEEEEEE--C-CCCEEEEEEECCCC-CCCCEECCCEEEECCCCCEECCHHHCCCHH
Q ss_conf 517----578999999776312100179983--4-87204788721676-543000141676461212032811171110
Q gi|254780247|r 24 IPF----SRLHARVLDVLKTEGYIGEYCEID--A-GKGRIQLKVDLKYH-NGASVIRKIDCVSKPGRRLYSSFKDIPQVC 95 (129)
Q Consensus 24 ip~----Skl~~~il~iL~~eGyI~~~~~~~--~-~~~~~~i~v~Lky~-~~~~vi~~i~~iSkP~~r~y~~~~~l~~~~ 95 (129)
+|| ++|+++|++ |.+|.=|+|...+. . ++.+++|+|.+|.. ...-|+++++.. . ++.
T Consensus 258 ~PYqVNKa~LiekIAe-Lv~ek~ieGIsdiRDESSDr~GiRiVIE~KRD~~a~VvLN~LYk~-----------T---~lQ 322 (864)
T TIGR01063 258 IPYQVNKARLIEKIAE-LVREKKIEGISDIRDESSDREGIRIVIELKRDAVAEVVLNNLYKQ-----------T---QLQ 322 (864)
T ss_pred CCCCCHHHHHHHHHHH-HHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHCC-----------C---CCC
T ss_conf 8885202688899998-740000003212442566877437999974289830154212112-----------6---450
Q ss_pred CCCCEEEEECCCC---EECHHHHHH
Q ss_conf 4971899818866---003799996
Q gi|254780247|r 96 NGLGIMIVTTSKG---VMAGHQARE 117 (129)
Q Consensus 96 ~g~G~~IiSTskG---imt~~eA~~ 117 (129)
..||+-.|-=-+| +|+-+|+..
T Consensus 323 ~~Fg~NmLALv~G~Pk~lnLk~~l~ 347 (864)
T TIGR01063 323 VSFGINMLALVDGLPKVLNLKELLE 347 (864)
T ss_pred EECCEEEEEEECCCCCEECHHHHHH
T ss_conf 0148123211078975017889999
Done!