Query 023433
Match_columns 282
No_of_seqs 156 out of 570
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:59:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023433.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023433hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03174 Chalcone-flavanone is 100.0 8.1E-73 1.8E-77 519.3 31.2 277 1-282 1-278 (278)
2 PLN03175 hypothetical protein; 100.0 9.5E-44 2.1E-48 337.5 24.4 203 80-282 205-414 (415)
3 PLN02311 chalcone isomerase 100.0 6.1E-43 1.3E-47 320.4 25.4 208 68-281 53-271 (271)
4 PF02431 Chalcone: Chalcone-fl 100.0 4.8E-38 1E-42 277.4 18.3 177 98-279 12-199 (199)
5 PLN02804 chalcone isomerase 100.0 2.7E-35 5.9E-40 260.1 21.8 188 88-280 7-206 (206)
6 PLN02559 chalcone--flavonone i 100.0 7.3E-34 1.6E-38 252.5 21.0 191 88-282 10-214 (230)
7 PF01052 SpoA: Surface present 70.4 7.7 0.00017 28.6 4.0 27 217-243 29-55 (77)
8 PRK06789 flagellar motor switc 69.5 8 0.00017 29.2 3.9 29 216-244 27-55 (74)
9 PLN03174 Chalcone-flavanone is 69.1 4.4 9.6E-05 38.0 3.0 36 16-51 11-46 (278)
10 TIGR02480 fliN flagellar motor 66.9 8.3 0.00018 28.8 3.6 27 217-243 29-55 (77)
11 COG1886 FliN Flagellar motor s 61.0 10 0.00022 31.7 3.5 28 217-244 92-119 (136)
12 PRK06033 hypothetical protein; 59.5 14 0.0003 28.3 3.7 27 216-242 27-53 (83)
13 PRK05698 fliN flagellar motor 55.4 17 0.00036 31.3 3.8 27 216-242 99-125 (155)
14 PRK07963 fliN flagellar motor 52.0 20 0.00043 30.2 3.7 27 216-242 80-106 (137)
15 PRK08983 fliN flagellar motor 50.7 21 0.00046 29.6 3.7 27 216-242 71-97 (127)
16 PRK08433 flagellar motor switc 50.5 23 0.0005 28.8 3.7 27 216-242 52-78 (111)
17 PRK08916 flagellar motor switc 47.6 24 0.00053 28.9 3.5 28 216-243 65-92 (116)
18 TIGR03406 FeS_long_SufT probab 45.9 45 0.00097 29.1 5.1 64 214-279 17-85 (174)
19 PRK06788 flagellar motor switc 44.2 35 0.00075 28.1 3.9 27 216-242 54-80 (119)
20 TIGR02551 SpaO_YscQ type III s 35.1 44 0.00095 31.3 3.6 29 216-244 253-281 (298)
21 PRK08035 type III secretion sy 33.1 50 0.0011 31.8 3.6 29 216-244 271-299 (323)
22 PRK06933 type III secretion sy 31.9 50 0.0011 31.5 3.5 29 216-244 257-285 (308)
23 COG1868 FliM Flagellar motor s 31.1 1.6E+02 0.0035 28.4 6.8 61 182-242 221-299 (332)
24 PF00722 Glyco_hydro_16: Glyco 29.0 95 0.0021 26.1 4.4 27 222-249 122-148 (185)
25 PF11720 Inhibitor_I78: Peptid 27.5 33 0.00071 24.5 1.1 24 216-240 28-51 (60)
26 PRK12795 fliM flagellar motor 27.2 2.5E+02 0.0053 27.6 7.4 27 216-242 322-348 (388)
27 PRK08158 type III secretion sy 26.6 67 0.0015 30.6 3.3 28 217-244 251-278 (303)
28 TIGR01397 fliM_switch flagella 25.9 83 0.0018 29.5 3.8 27 216-242 273-299 (320)
29 PRK08119 flagellar motor switc 25.8 81 0.0018 30.6 3.8 27 216-242 326-352 (382)
30 PF04014 Antitoxin-MazE: Antid 25.7 1.3E+02 0.0028 20.0 3.8 21 216-236 20-40 (47)
31 PRK06666 fliM flagellar motor 24.9 87 0.0019 29.6 3.8 27 216-242 278-304 (337)
32 PRK05933 type III secretion sy 24.8 91 0.002 30.2 3.8 29 216-244 326-355 (372)
33 PF13385 Laminin_G_3: Concanav 23.6 1.2E+02 0.0025 23.6 3.8 28 218-246 83-112 (157)
34 TIGR01439 lp_hng_hel_AbrB loop 23.5 1.4E+02 0.003 18.8 3.5 21 216-236 20-40 (43)
35 cd08023 GH16_laminarinase_like 23.4 1.4E+02 0.0031 26.3 4.7 28 221-249 161-188 (235)
36 PRK08432 flagellar motor switc 23.2 1E+02 0.0022 28.9 3.8 27 216-242 226-252 (283)
37 PF02837 Glyco_hydro_2_N: Glyc 22.5 1.3E+02 0.0029 24.7 4.1 29 219-247 83-112 (167)
38 PRK05264 transcriptional repre 21.5 87 0.0019 24.8 2.5 29 246-274 54-83 (105)
39 PF13510 Fer2_4: 2Fe-2S iron-s 21.4 1.3E+02 0.0028 22.5 3.5 26 231-256 2-27 (82)
40 cd00413 Glyco_hydrolase_16 gly 20.6 1.8E+02 0.0039 24.8 4.7 40 221-261 145-187 (210)
41 PF00986 DNA_gyraseB_C: DNA gy 20.6 1.5E+02 0.0032 21.8 3.4 27 244-273 38-64 (65)
No 1
>PLN03174 Chalcone-flavanone isomerase-related; Provisional
Probab=100.00 E-value=8.1e-73 Score=519.33 Aligned_cols=277 Identities=74% Similarity=1.078 Sum_probs=261.1
Q ss_pred CcccccccCCCCCCCCCCCCCchhHHHHHHHHHHhhhhhhhhhhhccCCCchhHhhhhhcccCCCCCccccceeeccCCC
Q 023433 1 MVSLRFPFSFSQPSNLPHTATRSFSVAVTAAAAAATASVAGIAVYHNQKHPLVQNALNCLFSNQSSSHFWASLSFADNSS 80 (282)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lsla~~~~ 80 (282)
||||||||+|+||+ |+++...+++++++++++++|+.|+|++++|+.|||+||+|| |+||++| +|++|||+|+++
T Consensus 1 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~~~a~~~~ 75 (278)
T PLN03174 1 MVSLRFPFSFSQPP--RAPSFFAAAAAVAAAAAAAAAAAAAIAASRNPPHPFLQNALN--FHNSSSP-PWASISLADPSP 75 (278)
T ss_pred CcceecccccCCCC--CCCCcchHHHHHHHHHHHHHHHHHHHHhhcCCCCchhhhhcc--cCCCCCc-ccccceeccCCC
Confidence 99999999999999 888766666666666666666679999999999999999999 8999998 999999999999
Q ss_pred CceeccCCCccCCCcccCCceeeeeEeEEEEeeceeeeEEEEEEEEeechhhHHHhhhhccCCchhHhhhhh-hHHHHhh
Q 023433 81 ATVVESKTGTSFPSVLGGSRKLLGIGLRKKSVLGLKNIDVYAFGVYADHDDVKKILSEKYGNMSVAELKENK-LNEDLME 159 (282)
Q Consensus 81 ~~~~E~~TGv~FP~~l~~~l~L~G~GvR~k~~lg~~~ikVYaagLY~~~~~~~~~L~~k~~~~s~~el~~~~-~~~~ll~ 159 (282)
+.+|||+||+.||++++.+..|+|+|+|+|.|+|+++||||++|||++++++++.|++||.+++.+|+.+++ |+++|++
T Consensus 76 ~~~vEp~tGv~FP~~l~~~~~LLGaGvR~k~i~glk~IKvYAiGlYl~~~~v~~~L~~k~kgks~~El~~s~~f~~dil~ 155 (278)
T PLN03174 76 PSVVESKTGVSFPAEIGDSRRLLGVGLRKKSILGLKNIDVYAFGVYADDDDLKKLLGEKYGKLSASELKGNKEFIDDLME 155 (278)
T ss_pred CceeccCCCCcCCCcccCCCcceeeeeeeEEEeccceEEEEEEEEEechhHhHHHhhhhhcCCChhhhhcCHHHHHHHHc
Confidence 999999999999999987777889999999999999999999999999998999899999999999999999 9999999
Q ss_pred CCcceEEEEEEEecCCChHHHHHHHHHHHHHhhhcCCCCCcHHHHHHHHHhccccCCCCCCCEEEEEEecCCEEEEEECC
Q 023433 160 ADVCMTVRLQIIYNKLSIRSVRSAFEESVGSRLQKFGGSDNKELLQKFTSQFKDEYKIPKGSVIELSKERGHVLWTTIDG 239 (282)
Q Consensus 160 ~~~~~~lrL~~~~R~v~~~~l~daf~~sl~~rl~~~~~~~~~~~L~~f~~~F~~~~kl~kGd~i~~~~~p~~~l~v~~nG 239 (282)
++.+|++||+++|++++.++++++++++++.||++.++.+.++.|++|.++|+++++++|||+|+|+|.|++++++++||
T Consensus 156 ~~~ek~iRL~iiy~~v~~~~v~~A~~esv~~rl~~~~~~e~~e~IekF~~~F~~~~~l~kGdvI~~~~~Pg~gl~vsi~G 235 (278)
T PLN03174 156 ADIKMTVRLQIVYGKLSIRSVRSAFEESVGSRLQKFGGSDNKELLQSFTSLFKDEYKIPKGSVIDLSREPGHVLRTTIDG 235 (278)
T ss_pred CCCceEEEEEEEeccccHHHHHHHHHHHHHHhhhccCCcchHHHHHHHHHHHhccccCCCCCEEEEEEcCCCeEEEEECC
Confidence 99999999999999999999999999999999999887777888999999999988889999999999999999999999
Q ss_pred EEEEEECCHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhC
Q 023433 240 KEVGSIQSKLLCRSLLDLYIGEEPFDRKAKEDIELNLSSLIQK 282 (282)
Q Consensus 240 ~~~G~I~s~~f~~Alf~IwLG~~Pvsp~lK~~llg~l~~ll~~ 282 (282)
++.|+|++++||+|+|+||||++|+||++|++|++++++||++
T Consensus 236 k~~g~Ie~~~f~~ALf~iyLGd~PVsp~lK~sll~~la~ll~~ 278 (278)
T PLN03174 236 KEVGSIQSKLLCRSILDLYIGEDPFDKNAKEDIEENLASLLQD 278 (278)
T ss_pred EEeeEECCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999975
No 2
>PLN03175 hypothetical protein; Provisional
Probab=100.00 E-value=9.5e-44 Score=337.48 Aligned_cols=203 Identities=38% Similarity=0.687 Sum_probs=192.4
Q ss_pred CCceeccCCCccCCCccc------CCceeeeeEeEEEEeeceeeeEEEEEEEEeechhhHHHhhhhccCCchhHhhhhh-
Q 023433 80 SATVVESKTGTSFPSVLG------GSRKLLGIGLRKKSVLGLKNIDVYAFGVYADHDDVKKILSEKYGNMSVAELKENK- 152 (282)
Q Consensus 80 ~~~~~E~~TGv~FP~~l~------~~l~L~G~GvR~k~~lg~~~ikVYaagLY~~~~~~~~~L~~k~~~~s~~el~~~~- 152 (282)
..++|||+||++||..++ +.+.|+|+|+|.+.|+|+++||||++|+|++++.++..|+.||.|++.+||.+++
T Consensus 205 ~~~~vEPkTgv~FP~~l~~~p~s~~sl~L~G~GvR~~eI~~~k~IKfyAiGVYle~~~v~~~L~~KwkGKsa~EL~~s~e 284 (415)
T PLN03175 205 TRDAVEPRTGIEFPMLLDENNSSLTSEVLVGTGSRTMKIIRIKSLKVYAFGFYVHPNSVCEKLGPKYASVPASELKKCPD 284 (415)
T ss_pred cccccccCCCCcCCccccCCCCCCCceeeeecccceeEEEeeceeEEEEEEEEeccchHHHHHhhhhCCCcHHHHccCHH
Confidence 466799999999999995 4589999999999999888999999999999988899999999999999999999
Q ss_pred hHHHHhhCCcceEEEEEEEecCCChHHHHHHHHHHHHHhhhcCCCCCcHHHHHHHHHhccccCCCCCCCEEEEEEecCCE
Q 023433 153 LNEDLMEADVCMTVRLQIIYNKLSIRSVRSAFEESVGSRLQKFGGSDNKELLQKFTSQFKDEYKIPKGSVIELSKERGHV 232 (282)
Q Consensus 153 ~~~~ll~~~~~~~lrL~~~~R~v~~~~l~daf~~sl~~rl~~~~~~~~~~~L~~f~~~F~~~~kl~kGd~i~~~~~p~~~ 232 (282)
||++|++++.+|++||++.++.++.++++++|+++++.||++.+..++.++|++|.++|+++++++|||.|+|+|.|+++
T Consensus 285 Ff~DIItap~~m~IRLVii~~gI~~sk~~~Afees~g~RLkkt~gdae~eAIeKF~s~F~~di~fpkGssI~Ft~sP~gg 364 (415)
T PLN03175 285 FYEDLLREDIVMTVRLVVNYNGLKINTVRDAFEKSLRNRLQKMNPNTDYNCLKTFGSFFTEDIPIPAGTKIDFRRTSDGQ 364 (415)
T ss_pred HHHHHHcCCccEEEEEEEecCCccHHHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHhhcccccCCCCEEEEEEcCCCc
Confidence 99999999999999999988899999999999999999999987777788899999999877889999999999999999
Q ss_pred EEEEECCEEEEEECCHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhC
Q 023433 233 LWTTIDGKEVGSIQSKLLCRSLLDLYIGEEPFDRKAKEDIELNLSSLIQK 282 (282)
Q Consensus 233 l~v~~nG~~~G~I~s~~f~~Alf~IwLG~~Pvsp~lK~~llg~l~~ll~~ 282 (282)
+++++||+++|+|++++||+|+|++|||++|+||++|+++..++++||++
T Consensus 365 LtisInG~~vgvIEnk~L~eALfdiyLGd~PVSPslKeslA~~La~Ll~~ 414 (415)
T PLN03175 365 LITEIGGNQIGAVRSKDLCRAFFDMYIGDVPVSEQTKEEIGQNVAGIIRR 414 (415)
T ss_pred eEEEECCeeeeEeccHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999974
No 3
>PLN02311 chalcone isomerase
Probab=100.00 E-value=6.1e-43 Score=320.40 Aligned_cols=208 Identities=22% Similarity=0.363 Sum_probs=186.3
Q ss_pred ccccceeeccCCCCceeccCCCccCCCccc-----CCceeeeeEeEEEEeeceeeeEEEEEEEEeechhhHHHhhhhccC
Q 023433 68 HFWASLSFADNSSATVVESKTGTSFPSVLG-----GSRKLLGIGLRKKSVLGLKNIDVYAFGVYADHDDVKKILSEKYGN 142 (282)
Q Consensus 68 ~~~~~lsla~~~~~~~~E~~TGv~FP~~l~-----~~l~L~G~GvR~k~~lg~~~ikVYaagLY~~~~~~~~~L~~k~~~ 142 (282)
|+-.+-+++-++...++||+|||+||+.+. ++|+|+|+|+|+|.|+| ++||||++|||+++..+ ++|+ +|.+
T Consensus 53 ~~~~~~~~~~~~~~~~~ep~TgV~Fp~~v~~~~~s~~L~LnGaGvR~K~I~~-~~vKVYA~GLYL~~~~~-~~L~-kwkg 129 (271)
T PLN02311 53 VIVKSAAFSVGSAEYAEETATSVKFQRSLTLPGCSSPLSLLGTGYREKVFAI-IGVKVYAAGLYVNPSIL-SGLS-AWKG 129 (271)
T ss_pred eeeeccccccCcccceecCCcCCcCCccccCCCCCCceeEeeeEEeeEEEee-eeEEEEEEEEEechhhh-hhHh-hhcC
Confidence 555566666677778999999999999984 68999999999999865 47999999999999755 4576 8999
Q ss_pred CchhHhhhhh-hHHHHhhCCcceEEEEEEEecCCChHHHHHHHHHHHHHhhhcCCCCCcHHHHHHHHHhccccCCCCCCC
Q 023433 143 MSVAELKENK-LNEDLMEADVCMTVRLQIIYNKLSIRSVRSAFEESVGSRLQKFGGSDNKELLQKFTSQFKDEYKIPKGS 221 (282)
Q Consensus 143 ~s~~el~~~~-~~~~ll~~~~~~~lrL~~~~R~v~~~~l~daf~~sl~~rl~~~~~~~~~~~L~~f~~~F~~~~kl~kGd 221 (282)
.+++||.++. |+++|++++.+|+|||+++ |++++++++++|+|++++||+.. ..++.+.|++|.++|++. ++++||
T Consensus 130 k~a~eL~~~~~ff~dIi~a~~eK~irI~~i-R~v~g~~~~~A~~eg~~~rlk~~-~~~~~~aLekF~~~F~~~-~l~kGd 206 (271)
T PLN02311 130 RSADEIQRDSSLFSSIFQAPAEKSLQIVLV-RDVDGKTFWDALDEAISPRIKAP-SPDDTSALSTFRSIFQNR-SLNKGT 206 (271)
T ss_pred CCHHHHhcchHHHHHHhcCCcceEEEEEEE-ecCCHHHHHHHHHHHHHHHHhcc-ccchHHHHHHHHHHhcCC-CCCCCC
Confidence 9999999998 9999999999999999996 99999999999999999999664 456788999999999874 789999
Q ss_pred EEEEEEecCCEEEEEEC-----CEEEEEECCHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhh
Q 023433 222 VIELSKERGHVLWTTID-----GKEVGSIQSKLLCRSLLDLYIGEEPFDRKAKEDIELNLSSLIQ 281 (282)
Q Consensus 222 ~i~~~~~p~~~l~v~~n-----G~~~G~I~s~~f~~Alf~IwLG~~Pvsp~lK~~llg~l~~ll~ 281 (282)
+|+|+|.|++++++.++ ++..|+|++++||+|+|+||||++|+||++|++++.++++||+
T Consensus 207 ~I~~~~~p~~~~~v~~s~~g~~~~~~g~Ies~~f~~ALf~i~LGd~PVs~~lK~sla~~la~ll~ 271 (271)
T PLN02311 207 VIFLTWINPSKMLVCISSEGLPSSVDATIESGNVTSALFDVFFGDSPVSPSLKASVANGLATTLK 271 (271)
T ss_pred EEEEEEeCCCceEEEEecCCcccceeEEECCHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhC
Confidence 99999999888888874 4568999999999999999999999999999999999999986
No 4
>PF02431 Chalcone: Chalcone-flavanone isomerase; InterPro: IPR003466 Chalcone isomerase (5.5.1.6 from EC) also known as chalcone-flavanone isomerase, is a plant enzyme responsible for the isomerisation of chalcone to naringenin a key step in the biosynthesis of flavonoids. The Petunia hybrida (Petunia) genome contains two genes coding for very similar enzymes, ChiA and ChiB, but only the first seems to encode a functional chalcone isomerase. Chalcone isomerase has a core 2-layer alpha/beta structure consisting of beta(3)-alpha(2)-beta-alpha(2)-beta(3) []. This entry represents a subgroup of Chalcone isomerase.; GO: 0016872 intramolecular lyase activity, 0042398 cellular modified amino acid biosynthetic process; PDB: 1JX0_B 1JEP_A 1EYP_B 1JX1_B 1EYQ_B 1FM8_A 1FM7_A 4DOL_A 4DOI_A 4DOK_B ....
Probab=100.00 E-value=4.8e-38 Score=277.37 Aligned_cols=177 Identities=36% Similarity=0.603 Sum_probs=152.9
Q ss_pred CCceeeeeEeEEEEeeceeeeEEEEEEEEeechhhHHHhhhhccCCchh-Hhhhhh-hHHHHhhCCcceEEEEEEEecCC
Q 023433 98 GSRKLLGIGLRKKSVLGLKNIDVYAFGVYADHDDVKKILSEKYGNMSVA-ELKENK-LNEDLMEADVCMTVRLQIIYNKL 175 (282)
Q Consensus 98 ~~l~L~G~GvR~k~~lg~~~ikVYaagLY~~~~~~~~~L~~k~~~~s~~-el~~~~-~~~~ll~~~~~~~lrL~~~~R~v 175 (282)
++++|+|+|+|+++|+ +||||++|+|++++++++.++ +|.+.... |+.+++ |+++|++++.++++||+++ |++
T Consensus 12 ~~l~L~G~GvR~~~~~---~ikVYavG~Yv~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ll~~~~~k~iri~~~-R~~ 86 (199)
T PF02431_consen 12 EELSLLGAGVRTVSFL---NIKVYAVGLYVDDSDAKKLLK-KWKGKSASDDLEKSEDFFDDLLDSPVEKAIRIVPV-RNV 86 (199)
T ss_dssp SEEEEEEEEEEEEEET---EEEEEEEEEEEECCHHHHHHH-HHTTT-HHHHHHT-HHHHHHHHHSSS-EEEEEEES-SSE
T ss_pred CCeEEEEEEEeeEEEE---EEEEEEEEEEEChhHhhhHHH-hhhcccCcccccccHHHHHHHhcCCccEEEEEEEE-ecC
Confidence 7899999999999996 599999999999998887654 55555444 777777 9999999999999999997 999
Q ss_pred ChHHHHHHHHHHHHHhhhcCC--CCCcHHHHHHHHHhccccCCCCCCCEEEEEEecCCEEEEEEC------CEEEEEECC
Q 023433 176 SIRSVRSAFEESVGSRLQKFG--GSDNKELLQKFTSQFKDEYKIPKGSVIELSKERGHVLWTTID------GKEVGSIQS 247 (282)
Q Consensus 176 ~~~~l~daf~~sl~~rl~~~~--~~~~~~~L~~f~~~F~~~~kl~kGd~i~~~~~p~~~l~v~~n------G~~~G~I~s 247 (282)
+++|++|+|.+++.+|+++.+ ..+.++.|++|+++|+...+++|||.|+|+|.|++++++.++ |+++|+|++
T Consensus 87 ~~~~l~d~~~~~i~~r~~~~~~~~~~~~~~l~~f~~~F~~~g~~~kG~~i~l~~~~~g~l~v~~~~~~~~~~~~~g~I~~ 166 (199)
T PF02431_consen 87 DGKHLRDAFIESIRPRLKAAGTEEEALEEALDEFKSLFKSKGSVPKGDVITLTWSPDGSLTVSYNGQGKIPGKELGTIKS 166 (199)
T ss_dssp EHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHTTB-EE-TT-EEEEEEETTTEEEEEEESSSS--SSECEEEE-
T ss_pred CHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhcccccccCCCEEEEEECCCCcEEEEEecCCCCCccceeEEcC
Confidence 999999999999999998875 346799999999999766578999999999999999999999 899999999
Q ss_pred HHHHHHHHHHhc-CCCCCCHHHHHHHHHHHHHh
Q 023433 248 KLLCRSLLDLYI-GEEPFDRKAKEDIELNLSSL 279 (282)
Q Consensus 248 ~~f~~Alf~IwL-G~~Pvsp~lK~~llg~l~~l 279 (282)
+.||+++|++|| |++|+||++|++++.++++|
T Consensus 167 ~~~~~al~~~yL~G~~pvs~~~k~s~~~~l~~l 199 (199)
T PF02431_consen 167 PRFARALFDIYLSGDKPVSPSLKKSVAEGLASL 199 (199)
T ss_dssp HHHHHHHHHHHH-STT-S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCCCCHHHHHHHHHHhhcC
Confidence 999999999999 99999999999999999986
No 5
>PLN02804 chalcone isomerase
Probab=100.00 E-value=2.7e-35 Score=260.07 Aligned_cols=188 Identities=22% Similarity=0.329 Sum_probs=171.2
Q ss_pred CCccCCCccc---CCceeeeeEeEEEEeeceeeeEEEEEEEEeechhhHHHhhhhccCCchhHhhhhh-hHHHHhhCCcc
Q 023433 88 TGTSFPSVLG---GSRKLLGIGLRKKSVLGLKNIDVYAFGVYADHDDVKKILSEKYGNMSVAELKENK-LNEDLMEADVC 163 (282)
Q Consensus 88 TGv~FP~~l~---~~l~L~G~GvR~k~~lg~~~ikVYaagLY~~~~~~~~~L~~k~~~~s~~el~~~~-~~~~ll~~~~~ 163 (282)
.|++||+.+. +.+.|.|+|+|.+.+.|+ +||+|++|+|+++ +++.+| .||.|++.+||.++. |+++|++++.+
T Consensus 7 ~~v~FP~~i~~ss~~l~L~G~G~R~~~I~~~-~iK~yAiGvYle~-~~~~~L-~kwkgk~a~EL~~~~~Ff~dlv~~p~e 83 (206)
T PLN02804 7 EDIPFPPQITTSSKPLSLLGHGITDIEIHFL-QIKFTAIGVYLEP-SVKGHL-QSWKGKPGSELAEDDDFFQALIQAPVE 83 (206)
T ss_pred cCcCCCceeecCCCcceEEeecccceEEEeE-EEEEEEEEEEecH-HHHHHH-HHhcCCCHHHHhcCHHHHHHHHcCChh
Confidence 6999999995 679999999999999886 8999999999998 588888 599999999999999 99999999999
Q ss_pred eEEEEEEEecCCChHHHHHHHHHHHHHhhhcCCCC--CcHHHHHHHHHhccccCCCCCCCEEEEEEec-CCEEEEE--EC
Q 023433 164 MTVRLQIIYNKLSIRSVRSAFEESVGSRLQKFGGS--DNKELLQKFTSQFKDEYKIPKGSVIELSKER-GHVLWTT--ID 238 (282)
Q Consensus 164 ~~lrL~~~~R~v~~~~l~daf~~sl~~rl~~~~~~--~~~~~L~~f~~~F~~~~kl~kGd~i~~~~~p-~~~l~v~--~n 238 (282)
|.+|++++ |++++.++++++++++++||++.+.+ +++++|++|.+.|+++ +++||+.|+|+|.| ++.+++. .+
T Consensus 84 k~~Ri~~i-~~l~g~qy~~~~ee~~~~rlk~~~~y~d~e~~aL~kf~~~Fk~~-~fp~Gs~I~ft~~~~~g~l~Isfs~d 161 (206)
T PLN02804 84 KLIRIVVI-KEIKGSQYGVQLESSVRDRLAEDDKYEEEEEEALEKVVEFFQSK-YFKKNSIITYHFPATSGIVEISFSTE 161 (206)
T ss_pred hEEEEEEE-ecCcCccHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhCCC-cCCCCCEEEEEecCCCCeEEEEEecC
Confidence 99999998 89999999999999999999999854 4689999999999876 89999999999998 6666644 46
Q ss_pred CEEE--EEECCHHHHHHHHHHhc-CCCCCCHHHHHHHHHHHHHhh
Q 023433 239 GKEV--GSIQSKLLCRSLLDLYI-GEEPFDRKAKEDIELNLSSLI 280 (282)
Q Consensus 239 G~~~--G~I~s~~f~~Alf~IwL-G~~Pvsp~lK~~llg~l~~ll 280 (282)
|.+. +.|+|+.+|+|+|+.|| |++|+||++|++++.+++.++
T Consensus 162 g~e~~~~~Ienk~l~~avl~~yi~G~~~VSp~~k~slA~~la~~~ 206 (206)
T PLN02804 162 GKEESKLTVENANVVEMIQKWYLGGENGVSPSTISSVADSIAAEL 206 (206)
T ss_pred CcccceeEEecHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhhC
Confidence 7655 56999999999999999 999999999999999999875
No 6
>PLN02559 chalcone--flavonone isomerase
Probab=100.00 E-value=7.3e-34 Score=252.50 Aligned_cols=191 Identities=27% Similarity=0.400 Sum_probs=175.8
Q ss_pred CCccCCCccc-----CCceeeeeEeEEEEeeceeeeEEEEEEEEeechhhHHHhhhhccCCchhHhhhhh-hHHHHhhCC
Q 023433 88 TGTSFPSVLG-----GSRKLLGIGLRKKSVLGLKNIDVYAFGVYADHDDVKKILSEKYGNMSVAELKENK-LNEDLMEAD 161 (282)
Q Consensus 88 TGv~FP~~l~-----~~l~L~G~GvR~k~~lg~~~ikVYaagLY~~~~~~~~~L~~k~~~~s~~el~~~~-~~~~ll~~~ 161 (282)
.|+.||+.+. +.+.|.|+|+|.+.|.| ++||+|++|+|+++..+ ..|..||.|++.+||.++. ||++|+.++
T Consensus 10 e~i~FP~~v~~p~s~~~l~L~GaG~Rg~eI~~-~~vKftAiGvYle~~av-~~L~~KWKGKsa~EL~~~~~Ff~div~~p 87 (230)
T PLN02559 10 EGVTFPPSVKPPGSSNPLFLGGAGVRGLEIQG-KFIKFTAIGVYLEGNAV-PSLAKKWKGKTAEELADSVAFFRDVVTGD 87 (230)
T ss_pred cceecCCcccCCCCCCceEEEeccccceEEee-EEEEEEEEEEEechhHH-HHHHHhhCCcCHHHHhcCHHHHHHHHcCc
Confidence 7899999985 67999999999999987 68999999999998755 6788899999999999999 999999999
Q ss_pred cceEEEEEEEecCCChHHHHHHHHHHHHHhhhcCCCC--CcHHHHHHHHHhccccCCCCCCCEEEEEEecCCEEEEEE--
Q 023433 162 VCMTVRLQIIYNKLSIRSVRSAFEESVGSRLQKFGGS--DNKELLQKFTSQFKDEYKIPKGSVIELSKERGHVLWTTI-- 237 (282)
Q Consensus 162 ~~~~lrL~~~~R~v~~~~l~daf~~sl~~rl~~~~~~--~~~~~L~~f~~~F~~~~kl~kGd~i~~~~~p~~~l~v~~-- 237 (282)
.+|.+|++++ +++++.++.+...+....+|+..+.+ ++.++|++|.++|+++ .+++|+.|+|+|.|++.+++.+
T Consensus 88 ~EK~~rV~~I-~~l~G~qy~~kv~e~~~a~~ks~g~y~daE~~aLekF~~~Fk~~-~fp~Gs~I~ft~sp~g~L~isfs~ 165 (230)
T PLN02559 88 FEKFTRVTMI-LPLTGEQYSEKVTENCVAIWKSLGIYTDAEAKAVEKFKEAFKEE-TFPPGSSILFTHSPTGSLTVAFSK 165 (230)
T ss_pred chhhEEEEEE-EeccccchHHHHhHHHHHHHHhcCCcchhHHHHHHHHHHHhcCC-CCCCCCEEEEEECCCCcEEEEEec
Confidence 9999999997 99999999999999999999998765 4689999999999986 8999999999999999998776
Q ss_pred CC----EEEEEECCHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhhC
Q 023433 238 DG----KEVGSIQSKLLCRSLLDLYIGEEPFDRKAKEDIELNLSSLIQK 282 (282)
Q Consensus 238 nG----~~~G~I~s~~f~~Alf~IwLG~~Pvsp~lK~~llg~l~~ll~~ 282 (282)
|| ...+.|+|+.+|+|+|+.|||++|+||++|++++.+++.||++
T Consensus 166 dg~ipe~~~~~Ienk~l~eAv~e~~IG~~~VSP~aK~slA~~la~ll~~ 214 (230)
T PLN02559 166 DSSVPEVGNAVIENKLLCEAVLESIIGKHGVSPAAKLSLAARLSELLKK 214 (230)
T ss_pred CCCCCccceEEEechHHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHhc
Confidence 43 4568999999999999999999999999999999999999974
No 7
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=70.35 E-value=7.7 Score=28.57 Aligned_cols=27 Identities=22% Similarity=0.330 Sum_probs=21.6
Q ss_pred CCCCCEEEEEEecCCEEEEEECCEEEE
Q 023433 217 IPKGSVIELSKERGHVLWTTIDGKEVG 243 (282)
Q Consensus 217 l~kGd~i~~~~~p~~~l~v~~nG~~~G 243 (282)
+++||.|.+....+..+.+++||+.++
T Consensus 29 L~~Gdvi~l~~~~~~~v~l~v~g~~~~ 55 (77)
T PF01052_consen 29 LKVGDVIPLDKPADEPVELRVNGQPIF 55 (77)
T ss_dssp --TT-EEEECCESSTEEEEEETTEEEE
T ss_pred CCCCCEEEeCCCCCCCEEEEECCEEEE
Confidence 469999999999889999999998753
No 8
>PRK06789 flagellar motor switch protein; Validated
Probab=69.47 E-value=8 Score=29.21 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=25.4
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEVGS 244 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~G~ 244 (282)
.+.+|+.+.++...+.-+.+++||+.+|+
T Consensus 27 ~L~~Gsvi~Ldk~~~epvdI~vNg~lia~ 55 (74)
T PRK06789 27 HITKGTLYRLENSTKNTVRLMLENEEIGT 55 (74)
T ss_pred cCCCCCEEEeCCcCCCCEEEEECCEEEeE
Confidence 34699999999999999999999998754
No 9
>PLN03174 Chalcone-flavanone isomerase-related; Provisional
Probab=69.07 E-value=4.4 Score=38.01 Aligned_cols=36 Identities=33% Similarity=0.337 Sum_probs=27.9
Q ss_pred CCCCCCchhHHHHHHHHHHhhhhhhhhhhhccCCCc
Q 023433 16 LPHTATRSFSVAVTAAAAAATASVAGIAVYHNQKHP 51 (282)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (282)
.||+..++|+++++++||++++++++-|.-..+.||
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 (278)
T PLN03174 11 SQPPRAPSFFAAAAAVAAAAAAAAAAAAAIAASRNP 46 (278)
T ss_pred CCCCCCCCcchHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 477777999999999999887777777766556644
No 10
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=66.94 E-value=8.3 Score=28.83 Aligned_cols=27 Identities=37% Similarity=0.544 Sum_probs=23.1
Q ss_pred CCCCCEEEEEEecCCEEEEEECCEEEE
Q 023433 217 IPKGSVIELSKERGHVLWTTIDGKEVG 243 (282)
Q Consensus 217 l~kGd~i~~~~~p~~~l~v~~nG~~~G 243 (282)
+++||.|.+....+..+.+++||++.+
T Consensus 29 L~~Gdvi~L~~~~~~~v~l~v~g~~~~ 55 (77)
T TIGR02480 29 LGEGSVIELDKLAGEPLDILVNGRLIA 55 (77)
T ss_pred CCCCCEEEcCCCCCCcEEEEECCEEEE
Confidence 469999999987788999999998753
No 11
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=61.05 E-value=10 Score=31.68 Aligned_cols=28 Identities=39% Similarity=0.592 Sum_probs=24.8
Q ss_pred CCCCCEEEEEEecCCEEEEEECCEEEEE
Q 023433 217 IPKGSVIELSKERGHVLWTTIDGKEVGS 244 (282)
Q Consensus 217 l~kGd~i~~~~~p~~~l~v~~nG~~~G~ 244 (282)
+.+|+.|.+....+..+.+.+||+.+|.
T Consensus 92 l~~Gsvi~Ld~~~~~~VdI~vNg~~Ig~ 119 (136)
T COG1886 92 LGKGSVIELDKLAGEPVDILVNGRLIGR 119 (136)
T ss_pred cCCCCEEEcCCcCCCceEEEECCEEEEE
Confidence 3599999999999999999999998754
No 12
>PRK06033 hypothetical protein; Validated
Probab=59.49 E-value=14 Score=28.29 Aligned_cols=27 Identities=19% Similarity=0.537 Sum_probs=22.8
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||.|.+....+..+.+++||++.
T Consensus 27 ~L~~GDVI~L~~~~~~~v~v~V~~~~~ 53 (83)
T PRK06033 27 RMGRGAVIPLDATEADEVWILANNHPI 53 (83)
T ss_pred CCCCCCEEEeCCCCCCcEEEEECCEEE
Confidence 456999999988777789999999765
No 13
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=55.41 E-value=17 Score=31.35 Aligned_cols=27 Identities=33% Similarity=0.538 Sum_probs=23.6
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+.+||+|.|....+..+.+++||+.+
T Consensus 99 ~L~~GDVI~Ldk~~~epv~V~VnG~~~ 125 (155)
T PRK05698 99 QLNQGSVIELDRLAGEPLDVLVNGTLI 125 (155)
T ss_pred CCCCCCEEEeCCCCCCCEEEEECCEEE
Confidence 456999999999888899999999875
No 14
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=52.00 E-value=20 Score=30.25 Aligned_cols=27 Identities=30% Similarity=0.439 Sum_probs=23.3
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||+|.|....+..+.+++||..+
T Consensus 80 ~L~~GDVI~Ld~~~~epv~V~Vng~~i 106 (137)
T PRK07963 80 RLTQGSVVALDGLAGEPLDILINGYLI 106 (137)
T ss_pred CCCCCCEEEeCCCCCCCEEEEECCEEE
Confidence 456999999998888899999999764
No 15
>PRK08983 fliN flagellar motor switch protein; Validated
Probab=50.69 E-value=21 Score=29.62 Aligned_cols=27 Identities=30% Similarity=0.546 Sum_probs=23.6
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||.|.+....+..+.+++||+..
T Consensus 71 ~L~~GDVI~Ld~~~ddpv~v~Vng~~~ 97 (127)
T PRK08983 71 QLNQGSVVELDRVAGEPLDVMVNGTLI 97 (127)
T ss_pred CCCCCCEEEeCCCCCCCEEEEECCEEE
Confidence 457999999999888899999999764
No 16
>PRK08433 flagellar motor switch protein; Validated
Probab=50.54 E-value=23 Score=28.79 Aligned_cols=27 Identities=41% Similarity=0.597 Sum_probs=23.0
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||.|.+....+..+.+++||.+.
T Consensus 52 ~Lq~GDVI~Ld~~~~e~v~v~V~g~~~ 78 (111)
T PRK08433 52 KFEKGSVIDLEKPAGESVELYINGRII 78 (111)
T ss_pred CCCCCCEEEeCCCCCCCEEEEECCEEE
Confidence 356999999998888889999999764
No 17
>PRK08916 flagellar motor switch protein; Reviewed
Probab=47.55 E-value=24 Score=28.86 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=23.5
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEVG 243 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~G 243 (282)
.+++||.|.+....+..+.+++||+..+
T Consensus 65 ~L~~GDVI~Ld~~~~e~V~I~Vng~~~~ 92 (116)
T PRK08916 65 KLGPGSVLELDRKVGEAIDIYVNNRLVA 92 (116)
T ss_pred cCCCCCEEEcCCCCCCCEEEEECCEEEE
Confidence 3469999999988888999999998753
No 18
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=45.94 E-value=45 Score=29.11 Aligned_cols=64 Identities=16% Similarity=0.299 Sum_probs=43.7
Q ss_pred cCCCCCCCEEEEEEecCCEEEEEECCEEEEEECCHHHHHHH-----HHHhcCCCCCCHHHHHHHHHHHHHh
Q 023433 214 EYKIPKGSVIELSKERGHVLWTTIDGKEVGSIQSKLLCRSL-----LDLYIGEEPFDRKAKEDIELNLSSL 279 (282)
Q Consensus 214 ~~kl~kGd~i~~~~~p~~~l~v~~nG~~~G~I~s~~f~~Al-----f~IwLG~~Pvsp~lK~~llg~l~~l 279 (282)
.+.+++|+.+.++-.=|+..++.++|+ +.+|++++ +.|+ ...=+.+.+..+..++++...|..+
T Consensus 17 ~~~~~~~~~~~~~q~lgg~~t~~~~g~-~~r~~~~~-~da~g~~~~~~~~~~~~~~~~~~ee~V~eaL~tV 85 (174)
T TIGR03406 17 PITLPAGTEVTITQALGGNFTVVVEGN-MARIDGKD-ADALGKEPPPPLDLPENADGEDNEDQVWEQLRTV 85 (174)
T ss_pred eEEcCCCCEEEEEEccCCeEEEEEcCe-EEEecCcC-hhhhcCCCCCcCCCCcCccccccHHHHHHHHcCC
Confidence 346789999999988889999999986 66676655 2332 0111445566777777777766554
No 19
>PRK06788 flagellar motor switch protein; Validated
Probab=44.18 E-value=35 Score=28.10 Aligned_cols=27 Identities=26% Similarity=0.437 Sum_probs=22.9
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+..||.|.+...-+.-+.+++||+..
T Consensus 54 ~L~vGDVI~Ldk~~~dpv~v~Vng~~~ 80 (119)
T PRK06788 54 QLKVGDVLEVEKNLGHKVDVYLSNMKV 80 (119)
T ss_pred CCCCCCEEEeCCcCCCCEEEEECCEEE
Confidence 456999999998888899999999764
No 20
>TIGR02551 SpaO_YscQ type III secretion system apparatus protein YscQ/HrcQ. Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion, while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid, and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae.
Probab=35.08 E-value=44 Score=31.25 Aligned_cols=29 Identities=24% Similarity=0.376 Sum_probs=24.4
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEVGS 244 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~G~ 244 (282)
.+++||+|.+....++.+++++||+.+++
T Consensus 253 ~L~~G~vl~L~~~~~~~v~l~~~g~~~~~ 281 (298)
T TIGR02551 253 ALQPGSVLELNVPVDGPVRLRANGRLLGR 281 (298)
T ss_pred CCCCCCEEEcCCCCCCcEEEEECCEEEEE
Confidence 45699999998888889999999987643
No 21
>PRK08035 type III secretion system protein SsaQ; Validated
Probab=33.14 E-value=50 Score=31.76 Aligned_cols=29 Identities=14% Similarity=0.261 Sum_probs=24.7
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEVGS 244 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~G~ 244 (282)
.+++|+++.+....++.+.+++||+.+|+
T Consensus 271 ~L~~GsVl~L~~~~~~~VdI~vNG~~ia~ 299 (323)
T PRK08035 271 QLAVGDVLPVGGCFYPEVTIRLNGRIIGQ 299 (323)
T ss_pred cCCCCCEEEcCCCCCCceEEEECCEEEEE
Confidence 45699999999877788999999998764
No 22
>PRK06933 type III secretion system protein; Validated
Probab=31.85 E-value=50 Score=31.46 Aligned_cols=29 Identities=21% Similarity=0.381 Sum_probs=24.4
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEVGS 244 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~G~ 244 (282)
.+++||.|.+....++.+.+++||+.+++
T Consensus 257 ~L~~GdVi~L~~~~~~~V~I~vng~~i~~ 285 (308)
T PRK06933 257 SLQPGSLIDLTTPVDGEVRLLANGRLLGH 285 (308)
T ss_pred cCCCCCEEEcCCCCCCCEEEEECCEEEEE
Confidence 45699999998888889999999987643
No 23
>COG1868 FliM Flagellar motor switch protein [Cell motility and secretion]
Probab=31.13 E-value=1.6e+02 Score=28.36 Aligned_cols=61 Identities=21% Similarity=0.322 Sum_probs=39.0
Q ss_pred HHHHHHHHHhhhcCCCCCcHHHHHHHHHhcccc------------------CCCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 182 SAFEESVGSRLQKFGGSDNKELLQKFTSQFKDE------------------YKIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 182 daf~~sl~~rl~~~~~~~~~~~L~~f~~~F~~~------------------~kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
+-+.+.+..+++........+|.+++.+..... ..+..||+|.+...-+..++++++|+++
T Consensus 221 e~i~~kl~~~~~~~~~~~~~~w~~~L~~~v~~v~V~l~A~l~~~~ltl~~il~L~vGDVI~l~~~~~d~v~v~v~g~~~ 299 (332)
T COG1868 221 EPIREKLSSRMQENTREKDPEWRKELRQQVQRVEVELEARLGEISLTLREILRLEVGDVIPLEKPADDRVTVSVGGKPK 299 (332)
T ss_pred HHHHHHHhhhhhhcccccChHHHHHHHHHHhcCceEEEEEeecceeeHHHHhCCCCCcEEECCCCCCceEEEEECCEEE
Confidence 333334444444444444566766665543221 1678999999998767899999999875
No 24
>PF00722 Glyco_hydro_16: Glycosyl hydrolases family 16; InterPro: IPR000757 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 16 GH16 from CAZY comprises enzymes with a number of known activities; lichenase (3.2.1.73 from EC); xyloglucan xyloglucosyltransferase (2.4.1.207 from EC); agarase (3.2.1.81 from EC); kappa-carrageenase (3.2.1.83 from EC); endo-beta-1,3-glucanase (3.2.1.39 from EC); endo-beta-1,3-1,4-glucanase (3.2.1.6 from EC); endo-beta-galactosidase (3.2.1.103 from EC).; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DGT_A 2CL2_A 2WLQ_A 2WNE_A 2W39_A 2W52_A 3ILN_A 4DFS_A 1UMZ_A 1UN1_B ....
Probab=28.98 E-value=95 Score=26.08 Aligned_cols=27 Identities=19% Similarity=0.139 Sum_probs=23.0
Q ss_pred EEEEEEecCCEEEEEECCEEEEEECCHH
Q 023433 222 VIELSKERGHVLWTTIDGKEVGSIQSKL 249 (282)
Q Consensus 222 ~i~~~~~p~~~l~v~~nG~~~G~I~s~~ 249 (282)
++.+.|.|+ .+.+++||+.+.++....
T Consensus 122 ~y~~~W~~~-~i~fyiDg~~~~~~~~~~ 148 (185)
T PF00722_consen 122 TYGFEWTPD-RIRFYIDGKLVRTVTNSD 148 (185)
T ss_dssp EEEEEEETT-EEEEEETTEEEEEEESSG
T ss_pred EEEEEEecC-eEEEEECCEEEEEEeccc
Confidence 577899887 799999999999987664
No 25
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=27.51 E-value=33 Score=24.46 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=20.6
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGK 240 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~ 240 (282)
-+.+|+.++++|.|+ .|.|.+|..
T Consensus 28 vi~Pg~~vTmDyr~d-RLnv~~D~~ 51 (60)
T PF11720_consen 28 VIRPGDAVTMDYRPD-RLNVEVDDD 51 (60)
T ss_pred EeCCCCcCcccCCCC-cEEEEECCC
Confidence 457999999999988 699999864
No 26
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=27.17 E-value=2.5e+02 Score=27.64 Aligned_cols=27 Identities=7% Similarity=0.118 Sum_probs=23.7
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.++.||+|.|...++..+.++++|++.
T Consensus 322 ~LkvGDVI~Ld~~~~~~v~v~v~g~p~ 348 (388)
T PRK12795 322 NLKVGDTLMLDARPDALVTLRCGDVPL 348 (388)
T ss_pred CCCCCCEEEeCCCCCCCEEEEECCEEE
Confidence 778999999998888889999998764
No 27
>PRK08158 type III secretion system protein SpaO; Validated
Probab=26.57 E-value=67 Score=30.62 Aligned_cols=28 Identities=11% Similarity=0.191 Sum_probs=24.5
Q ss_pred CCCCCEEEEEEecCCEEEEEECCEEEEE
Q 023433 217 IPKGSVIELSKERGHVLWTTIDGKEVGS 244 (282)
Q Consensus 217 l~kGd~i~~~~~p~~~l~v~~nG~~~G~ 244 (282)
+.+|+.+.+....++.+.+++||+.+|+
T Consensus 251 L~~GsVl~L~~~~~~~V~I~vNg~lva~ 278 (303)
T PRK08158 251 LCQQQLLSLPTNAELNVEIRANGALLGN 278 (303)
T ss_pred cCCCCEEECCCCCCCceEEEECCEEEEE
Confidence 4599999999888999999999998765
No 28
>TIGR01397 fliM_switch flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself.
Probab=25.93 E-value=83 Score=29.48 Aligned_cols=27 Identities=19% Similarity=0.321 Sum_probs=24.3
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||.|.+....+..+.+++||+++
T Consensus 273 ~L~~GDVI~L~~~~~~~v~v~v~g~~~ 299 (320)
T TIGR01397 273 NLQVGDVIPLNTDMPEEVSLRVGGRPK 299 (320)
T ss_pred CCCCCCEEEeCCCCCCcEEEEECCEEE
Confidence 778999999998888889999999875
No 29
>PRK08119 flagellar motor switch protein; Validated
Probab=25.84 E-value=81 Score=30.60 Aligned_cols=27 Identities=33% Similarity=0.514 Sum_probs=23.7
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||.|.|...-+..+.+++||+..
T Consensus 326 ~L~~Gdvi~Ld~~~~~~v~v~v~g~~~ 352 (382)
T PRK08119 326 ELGTGSIIELDKLAGEPVDILVNGKLI 352 (382)
T ss_pred cCCCCCEEEeCCCCCCcEEEEECCEEE
Confidence 667999999998778899999999864
No 30
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=25.70 E-value=1.3e+02 Score=19.96 Aligned_cols=21 Identities=14% Similarity=0.204 Sum_probs=16.2
Q ss_pred CCCCCCEEEEEEecCCEEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTT 236 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~ 236 (282)
.+.+||.+.+....++.+.+.
T Consensus 20 ~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 20 GLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp TSSTTTEEEEEEETTSEEEEE
T ss_pred CCCCCCEEEEEEeCCCEEEEE
Confidence 356999999999988656554
No 31
>PRK06666 fliM flagellar motor switch protein FliM; Validated
Probab=24.95 E-value=87 Score=29.63 Aligned_cols=27 Identities=33% Similarity=0.445 Sum_probs=24.2
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+++||.|.+....+..+.+++||+++
T Consensus 278 ~L~vGDVI~L~~~~~~~v~v~v~~~~~ 304 (337)
T PRK06666 278 NLKVGDVIPLEKPADDPLIVYVDGKPK 304 (337)
T ss_pred CCCCCCEEEeCCCCCCcEEEEECCEEE
Confidence 678999999999888899999999875
No 32
>PRK05933 type III secretion system protein; Validated
Probab=24.78 E-value=91 Score=30.24 Aligned_cols=29 Identities=21% Similarity=0.365 Sum_probs=24.8
Q ss_pred CCCCCCEEEEEEec-CCEEEEEECCEEEEE
Q 023433 216 KIPKGSVIELSKER-GHVLWTTIDGKEVGS 244 (282)
Q Consensus 216 kl~kGd~i~~~~~p-~~~l~v~~nG~~~G~ 244 (282)
++.+|+.|.++... +..+.+++||+.+|+
T Consensus 326 ~L~~GSVIeLDk~a~GEpVDI~VNGrLIAR 355 (372)
T PRK05933 326 KLGPGSILQFDGVHPTLGVDIILNGAKVGR 355 (372)
T ss_pred ccCCCCEEEeCCcCCCCCEEEEECCEEEee
Confidence 56799999998775 789999999998765
No 33
>PF13385 Laminin_G_3: Concanavalin A-like lectin/glucanases superfamily; PDB: 4DQA_A 1N1Y_A 1MZ6_A 1MZ5_A 1N1S_A 2A75_A 1WCS_A 1N1T_A 1N1V_A 2FHR_A ....
Probab=23.59 E-value=1.2e+02 Score=23.58 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=20.6
Q ss_pred CCCC--EEEEEEecCCEEEEEECCEEEEEEC
Q 023433 218 PKGS--VIELSKERGHVLWTTIDGKEVGSIQ 246 (282)
Q Consensus 218 ~kGd--~i~~~~~p~~~l~v~~nG~~~G~I~ 246 (282)
+.+. .+.+++. ++.+.+|+||+..++..
T Consensus 83 ~~~~W~~l~~~~~-~~~~~lyvnG~~~~~~~ 112 (157)
T PF13385_consen 83 PDNKWHHLALTYD-GSTVTLYVNGELVGSST 112 (157)
T ss_dssp -TT-EEEEEEEEE-TTEEEEEETTEEETTCT
T ss_pred CCCCEEEEEEEEE-CCeEEEEECCEEEEeEe
Confidence 3444 7888888 66799999999876543
No 34
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=23.52 E-value=1.4e+02 Score=18.84 Aligned_cols=21 Identities=10% Similarity=0.181 Sum_probs=15.9
Q ss_pred CCCCCCEEEEEEecCCEEEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTT 236 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~ 236 (282)
.+.+||.+.+...+++.+.++
T Consensus 20 ~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 20 GLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred CcCCCCEEEEEEeCCCEEEEE
Confidence 346999999997777767654
No 35
>cd08023 GH16_laminarinase_like Laminarinase, member of the glycosyl hydrolase family 16. Laminarinase, also known as glucan endo-1,3-beta-D-glucosidase, is a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans.
Probab=23.44 E-value=1.4e+02 Score=26.29 Aligned_cols=28 Identities=11% Similarity=-0.035 Sum_probs=23.9
Q ss_pred CEEEEEEecCCEEEEEECCEEEEEECCHH
Q 023433 221 SVIELSKERGHVLWTTIDGKEVGSIQSKL 249 (282)
Q Consensus 221 d~i~~~~~p~~~l~v~~nG~~~G~I~s~~ 249 (282)
-++.+.|+|+ .+++++||+++.++....
T Consensus 161 HtY~~~W~p~-~i~~yvDG~~v~~~~~~~ 188 (235)
T cd08023 161 HTYAVEWTPD-KITFYVDGKLYFTYTNPN 188 (235)
T ss_pred EEEEEEEECC-EEEEEECCEEEEEEcccc
Confidence 4688999986 699999999999987665
No 36
>PRK08432 flagellar motor switch protein FliY; Validated
Probab=23.25 E-value=1e+02 Score=28.92 Aligned_cols=27 Identities=30% Similarity=0.382 Sum_probs=23.9
Q ss_pred CCCCCCEEEEEEecCCEEEEEECCEEE
Q 023433 216 KIPKGSVIELSKERGHVLWTTIDGKEV 242 (282)
Q Consensus 216 kl~kGd~i~~~~~p~~~l~v~~nG~~~ 242 (282)
.+.+||.|.+...-+.-+.+++||+..
T Consensus 226 ~L~~GdVI~Ld~~~~~pv~v~v~~~~~ 252 (283)
T PRK08432 226 SMDIGSVVELNQLANDPLEILVDDKVI 252 (283)
T ss_pred CCCCCCEEEeCCCCCCcEEEEECCEEE
Confidence 567999999999888999999999764
No 37
>PF02837 Glyco_hydro_2_N: Glycosyl hydrolases family 2, sugar binding domain; InterPro: IPR006104 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This domain has a jelly-roll fold [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3FN9_C 2VZU_A 2X09_A 2VZO_A 2X05_A 2VZV_B ....
Probab=22.52 E-value=1.3e+02 Score=24.68 Aligned_cols=29 Identities=31% Similarity=0.291 Sum_probs=23.2
Q ss_pred CCCEEEEEEec-CCEEEEEECCEEEEEECC
Q 023433 219 KGSVIELSKER-GHVLWTTIDGKEVGSIQS 247 (282)
Q Consensus 219 kGd~i~~~~~p-~~~l~v~~nG~~~G~I~s 247 (282)
+|..+.|.... +....|++||+.+|..++
T Consensus 83 ~~~~~~L~f~gv~~~a~v~vNG~~vg~~~~ 112 (167)
T PF02837_consen 83 KGKRVFLRFEGVDYAAEVYVNGKLVGSHEG 112 (167)
T ss_dssp TTSEEEEEESEEESEEEEEETTEEEEEEES
T ss_pred cCceEEEEeccceEeeEEEeCCeEEeeeCC
Confidence 57888888764 468899999999998654
No 38
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=21.53 E-value=87 Score=24.76 Aligned_cols=29 Identities=28% Similarity=0.529 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHhcC-CCCCCHHHHHHHHH
Q 023433 246 QSKLLCRSLLDLYIG-EEPFDRKAKEDIEL 274 (282)
Q Consensus 246 ~s~~f~~Alf~IwLG-~~Pvsp~lK~~llg 274 (282)
.|+.+|.||+-.|-| +=|-+.+++++--.
T Consensus 54 NSELLCEAFLHA~TGQPLP~D~Dl~Kd~~d 83 (105)
T PRK05264 54 NSELLCEAFLHAFTGQPLPDDEDLRKERSD 83 (105)
T ss_pred cHHHHHHHHHHHHcCCCCCChhhhhhcCcc
Confidence 588999999999999 67888888775433
No 39
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=21.45 E-value=1.3e+02 Score=22.53 Aligned_cols=26 Identities=31% Similarity=0.386 Sum_probs=21.9
Q ss_pred CEEEEEECCEEEEEECCHHHHHHHHH
Q 023433 231 HVLWTTIDGKEVGSIQSKLLCRSLLD 256 (282)
Q Consensus 231 ~~l~v~~nG~~~G~I~s~~f~~Alf~ 256 (282)
..++|++||+++-.-++..+..|+..
T Consensus 2 ~~v~i~idG~~v~~~~G~til~al~~ 27 (82)
T PF13510_consen 2 KMVTITIDGKPVEVPPGETILEALLA 27 (82)
T ss_dssp EEEEEEETTEEEEEEET-BHHHHHHH
T ss_pred CEEEEEECCEEEEEcCCCHHHHHHHH
Confidence 46889999999998899999999875
No 40
>cd00413 Glyco_hydrolase_16 glycosyl hydrolase family 16. The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues.
Probab=20.62 E-value=1.8e+02 Score=24.84 Aligned_cols=40 Identities=18% Similarity=0.257 Sum_probs=28.8
Q ss_pred CEEEEEEecCCEEEEEECCEEEEEECCHH---HHHHHHHHhcCC
Q 023433 221 SVIELSKERGHVLWTTIDGKEVGSIQSKL---LCRSLLDLYIGE 261 (282)
Q Consensus 221 d~i~~~~~p~~~l~v~~nG~~~G~I~s~~---f~~Alf~IwLG~ 261 (282)
-++.+.|.|+ .+++++||+++.++.... =...+|.+|.+.
T Consensus 145 H~Y~~~W~~~-~i~~yvDG~~~~~~~~~~p~~p~~i~ln~~~~~ 187 (210)
T cd00413 145 HTYRVDWTPG-EITFYVDGVLVATITNQVPDDPMNIILNLWSDG 187 (210)
T ss_pred EEEEEEEeCC-EEEEEECCEEEEEECCCCCCCCcEEEEEEEECC
Confidence 4688999984 899999999999987651 123445566553
No 41
>PF00986 DNA_gyraseB_C: DNA gyrase B subunit, carboxyl terminus The Prosite motif does not match this Pfam entry.; InterPro: IPR002288 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 []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. 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 topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents the C-terminal region (C-terminal part of domain 2) of subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), which are primarily of bacterial origin. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. This region is involved in subunit interaction, which accounts for the difference between subunit B and single polypeptide topoisomerase II. 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, 0005694 chromosome; PDB: 3LTN_D 3RAF_C 3FOF_C 3RAE_C 3KSA_D 3RAD_C 3FOE_D 3KSB_D 3K9F_D 2XCT_D ....
Probab=20.57 E-value=1.5e+02 Score=21.83 Aligned_cols=27 Identities=11% Similarity=0.368 Sum_probs=21.8
Q ss_pred EECCHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 023433 244 SIQSKLLCRSLLDLYIGEEPFDRKAKEDIE 273 (282)
Q Consensus 244 ~I~s~~f~~Alf~IwLG~~Pvsp~lK~~ll 273 (282)
+|++..-+..+|+.|+|+ +.+.|+.++
T Consensus 38 ~i~d~~~~~~~~~~LMG~---~v~~Rr~fI 64 (65)
T PF00986_consen 38 TIEDAEEADELFEMLMGK---NVEPRREFI 64 (65)
T ss_dssp EHCCHHHHHHHHHHHHSS---THHHHHHHH
T ss_pred EECCHHHHHHHHHHHcCC---CcHHHHHHh
Confidence 566788899999999998 566777665
Done!