Query 043788
Match_columns 387
No_of_seqs 138 out of 425
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:20:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043788.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043788hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04187 DUF399: Protein of un 100.0 1.1E-56 2.4E-61 420.8 10.1 204 136-361 4-213 (213)
2 COG3016 PhuW Uncharacterized i 100.0 6.8E-45 1.5E-49 344.4 17.6 234 109-382 28-270 (295)
3 TIGR00261 traB pheromone shutd 95.5 0.23 4.9E-06 51.4 12.8 191 144-362 2-217 (380)
4 COG2312 Erythromycin esterase 94.7 0.088 1.9E-06 54.5 7.2 94 135-238 34-131 (405)
5 COG1916 Uncharacterized homolo 94.5 0.33 7.1E-06 49.9 10.7 186 143-361 9-226 (388)
6 PF01963 TraB: TraB family; I 89.3 0.47 1E-05 44.8 4.2 41 316-362 212-252 (259)
7 PF05139 Erythro_esteras: Eryt 88.6 0.53 1.1E-05 46.9 4.2 58 314-372 183-247 (346)
8 COG3735 Uncharacterized protei 66.6 9 0.0002 38.6 4.7 41 316-363 252-292 (299)
9 TIGR02811 formate_TAT formate 57.8 8.8 0.00019 30.2 2.4 17 59-75 7-23 (66)
10 PRK10781 rcsF outer membrane l 40.4 51 0.0011 29.6 4.7 53 141-195 56-114 (133)
11 PF10518 TAT_signal: TAT (twin 38.9 19 0.00041 23.3 1.2 19 61-79 2-20 (26)
12 PRK13587 1-(5-phosphoribosyl)- 37.6 3.6E+02 0.0079 25.8 10.4 113 135-261 87-217 (234)
13 PRK12699 flgH flagellar basal 37.5 46 0.00099 32.7 4.2 22 62-83 13-34 (246)
14 PLN02803 beta-amylase 33.7 27 0.00058 37.9 2.2 22 222-243 141-162 (548)
15 PLN00197 beta-amylase; Provisi 33.0 28 0.00061 37.9 2.2 22 222-243 161-182 (573)
16 PLN02161 beta-amylase 32.8 28 0.00062 37.6 2.1 22 222-243 151-172 (531)
17 PLN02801 beta-amylase 30.7 32 0.0007 37.1 2.1 22 222-243 71-92 (517)
18 PLN02705 beta-amylase 30.6 32 0.0007 38.0 2.1 22 222-243 302-323 (681)
19 PF14591 AF0941-like: AF0941-l 30.1 9.2 0.0002 33.9 -1.7 52 188-243 39-97 (127)
20 PLN02905 beta-amylase 29.9 34 0.00073 38.0 2.1 22 222-243 320-341 (702)
21 PF01373 Glyco_hydro_14: Glyco 28.9 32 0.00068 36.2 1.7 22 222-243 50-71 (402)
22 PF00308 Bac_DnaA: Bacterial d 28.4 1.7E+02 0.0038 27.5 6.5 60 136-198 88-147 (219)
23 PF00988 CPSase_sm_chain: Carb 26.7 56 0.0012 29.2 2.6 44 214-259 82-125 (131)
24 COG0313 Predicted methyltransf 26.3 79 0.0017 31.7 3.8 33 229-261 97-129 (275)
25 PRK11865 pyruvate ferredoxin o 26.0 2E+02 0.0044 29.0 6.7 65 316-384 73-137 (299)
26 cd02018 TPP_PFOR Thiamine pyro 25.7 1.6E+02 0.0034 28.3 5.7 58 318-382 64-131 (237)
27 PF07172 GRP: Glycine rich pro 25.4 53 0.0012 27.6 2.1 15 72-86 11-25 (95)
28 cd03376 TPP_PFOR_porB_like Thi 24.6 2.2E+02 0.0048 27.3 6.5 59 318-381 62-123 (235)
29 COG2871 NqrF Na+-transporting 23.8 2.2E+02 0.0048 29.2 6.4 63 116-186 247-309 (410)
30 PF12048 DUF3530: Protein of u 21.3 96 0.0021 31.0 3.4 34 225-258 178-214 (310)
31 PRK15098 beta-D-glucoside gluc 21.0 1.6E+02 0.0035 33.3 5.5 73 136-212 492-581 (765)
No 1
>PF04187 DUF399: Protein of unknown function, DUF399; InterPro: IPR007314 No function is known for any member of this family.; PDB: 2G5G_X.
Probab=100.00 E-value=1.1e-56 Score=420.81 Aligned_cols=204 Identities=31% Similarity=0.572 Sum_probs=145.8
Q ss_pred HHHHHHHHhcCCEEEEccccCCCCchhHHHHHHHHHHHHhhccccCCCceEEeeccCCCCchhhhhhhcCCCChHHHH--
Q 043788 136 KRKVWEKLMNARVVYLGEAEQVPVRDDRELELQIVKNLRKRCVESERTITLALEAFPSDLQDQLNQYTDKRIDGETLK-- 213 (387)
Q Consensus 136 ~~~l~~~La~adVVlLGE~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgLEMF~~d~Q~~LD~ylaG~Ide~~Ll-- 213 (387)
+++|+++|+++|||||||.|||| +||++|++||++|+++ +++++||||||++++|++||+|++|+||+++|+
T Consensus 4 ~~~l~~~l~~~~vVllGE~Hdn~--~~H~~Ql~ll~~L~~~----~~~~al~lEmf~~~~Q~~Ld~~~~g~i~e~~l~~~ 77 (213)
T PF04187_consen 4 FEQLIKQLANADVVLLGEQHDNP--DHHRLQLELLRALYAQ----RPPLALGLEMFERDQQPALDRYLAGKIDEEELLEQ 77 (213)
T ss_dssp HHHHHHHHTT-SEEEEEE-TT-H--HHHHHHHHHHHHHHHT----T--EEEEEEEEEGGGHHHHHHHHHTG--TTTHHHH
T ss_pred HHHHHHHHhCCCEEEECCCCCCH--HHHHHHHHHHHHHHhc----CCCCEEEEecCCccccHHHHHHHhCcccHHHHHHH
Confidence 89999999999999999999999 8999999999999874 669999999999999999999999999999996
Q ss_pred -HHhcCCCCCCCcccHHHHHHHHhcCCcEEecCCCHHHHHHHHHhcccCCCHHHHhhcCCCCC---Ccccchhhhhcccc
Q 043788 214 -SYASHWPPQRWQEYEPLLSYCRDNGVQLLACGTPLKVLRTVQAEGIHGLSKADRKLYAPPAG---SGFISGFTSISHRS 289 (387)
Q Consensus 214 -~w~~~W~~~~w~lYrPL~~~Ar~~gipviAlNlPre~vr~V~r~Gl~sLs~eeR~~l~pp~~---~~~~~~~~~~~~~s 289 (387)
+|.+.|+| +|++|+|||+|||++++||||+|+|++++++|+++|+++|++++|++|+++.+ ..|...+..++ ..
T Consensus 78 ~~w~~~W~~-~~~~Y~pl~~~Ar~~~ipviA~N~pr~~~~~V~~~G~~~L~~~~r~~l~~~~~~~~~~~~~~~~~~~-~~ 155 (213)
T PF04187_consen 78 LDWDRRWPN-DWALYRPLVEFARENGIPVIALNVPRELVRKVAREGLDSLSEEERAWLPPDIPLPDPAYRARLQEIF-AG 155 (213)
T ss_dssp TT--TTS----GGGTHHHHHHHHTSS--EEEEE--HHHHHHHHT---------T------SSSS-HHHHHHHHHHHH-HH
T ss_pred hccccCCCC-chHHHHHHHHHHHHCCCCEEEecCCHHHHHHHHHhcccchhhhhHhhcCCCCCCChHHHHHHHHHHH-Hh
Confidence 79999998 59999999999999999999999999999999999999999999999986443 23334443333 22
Q ss_pred cccccccCCCCCCCCcchHHHHhhhhhhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCCCCcchhhHHhh
Q 043788 290 SVDMNSLTQSVPFGPSSYLSAQARVVEDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGSRGTGLPARISK 361 (387)
Q Consensus 290 ~~~~~~~~~~~~~~~~~f~~aQAq~l~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~r~~GVP~rL~r 361 (387)
+|.+. +...++|+++| ++||++||++|++++ + ++++||+|+|+||+++| +|||.||+|
T Consensus 156 h~~~~------~~~~~~~~~aQ--~~~D~~MA~~i~~~~--~-~~~~vv~i~G~gH~~~~---~Gvp~~L~r 213 (213)
T PF04187_consen 156 HCGML------PESLERFYEAQ--QLWDATMAESIAAAL--H-PGRPVVVIAGNGHVRKG---LGVPARLAR 213 (213)
T ss_dssp HT--T------TTTHHHHHHHH--HHHHHHHHHHHHH-S------SEEEEEEEHHHH-TT---TSHHHHHHH
T ss_pred ccCCC------chhHHHHHHHH--HHHHHHHHHHHHHHH--h-ccCeEEEEeCcchhcCC---CchhHHhcC
Confidence 44432 22357899888 999999999999998 3 58899999999999977 999999975
No 2
>COG3016 PhuW Uncharacterized iron-regulated protein [Function unknown]
Probab=100.00 E-value=6.8e-45 Score=344.41 Aligned_cols=234 Identities=25% Similarity=0.423 Sum_probs=194.2
Q ss_pred ccccccceeeEEeecccCCcccccCcCHHHHHHHHhcCCEEEEccccCCCCchhHHHHHHHHHHHHhhccccCCCceEEe
Q 043788 109 TVKAEEVVVSRIYDATVIGEPLAVGKDKRKVWEKLMNARVVYLGEAEQVPVRDDRELELQIVKNLRKRCVESERTITLAL 188 (387)
Q Consensus 109 ~~~~~~~~~~rI~D~~~~G~~is~~~~~~~l~~~La~adVVlLGE~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgL 188 (387)
....+.+..++|.+..| |+.+| +++|+.+|.+||||||||.|||+ +||.+|++|+++|.+ .+++.+|+|
T Consensus 28 l~g~~d~~~~yil~t~t-g~~iS----~q~LiaeL~nadvIlvGEkHdn~--~~h~~Ql~l~kal~e----~~~q~iLam 96 (295)
T COG3016 28 LLGCSDTFYDYILATPT-GEEIS----FQALIAELLNADVILVGEKHDNE--EIHELQLKLFKALHE----RYRQVILAM 96 (295)
T ss_pred cccCCccccceeeecCc-Cceec----HHHHHHHHhcCCEEEEecccCch--hHHHHHHHHHHHHHH----hcccceehH
Confidence 34556668899999997 99998 99999999999999999999999 899999999999997 477899999
Q ss_pred eccCCCCchhhhhhhcCCCChH-HHH---HHhcCCCCCCCcccHHHHHHHHhcCCcEEecCCCHHHHHHHHHhcccC---
Q 043788 189 EAFPSDLQDQLNQYTDKRIDGE-TLK---SYASHWPPQRWQEYEPLLSYCRDNGVQLLACGTPLKVLRTVQAEGIHG--- 261 (387)
Q Consensus 189 EMF~~d~Q~~LD~ylaG~Ide~-~Ll---~w~~~W~~~~w~lYrPL~~~Ar~~gipviAlNlPre~vr~V~r~Gl~s--- 261 (387)
|||+++.|+.||+|+.|+|+++ ++. .|.+.|. |.+|+||++||...++||+|+|++|+.++.|.|+|.+-
T Consensus 97 Emf~~~~Qp~lD~~~~gk~~~k~el~eAl~w~k~w~---wkdY~plvn~a~~q~~pilaaNl~rseI~~iyr~~p~l~g~ 173 (295)
T COG3016 97 EMFQQPYQPFLDEFVEGKIDEKYELLEALRWKKTWS---WKDYEPLVNYAERQGIPILAANLPRSEIREIYRRGPELVGS 173 (295)
T ss_pred HhhCcccchhHHHHHhccccHHHHHHHHhccccccc---HhHHHHHHHHHHhcCCceeeecCCHHHHHHHHhcCCCCCCc
Confidence 9999999999999999999998 453 7998898 99999999999999999999999999999999998642
Q ss_pred --CCHHHHhhcCCCCCCcccchhhhhcccccccccccCCCCCCCCcchHHHHhhhhhhHHHHHHHHHHHHhcCCCCeEEE
Q 043788 262 --LSKADRKLYAPPAGSGFISGFTSISHRSSVDMNSLTQSVPFGPSSYLSAQARVVEDYAMSQIILKAIMDGGANGMLVV 339 (387)
Q Consensus 262 --Ls~eeR~~l~pp~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~f~~aQAq~l~D~tMAe~I~~al~~~~p~~~vVv 339 (387)
++++.+. ..|..-+.+.+ +|++ +...++|+.+| +.||.+||++|++.|..| |+++|++
T Consensus 174 vst~~ei~~-------p~y~~i~ls~~---H~gn-------p~~nk~~l~aq--vt~dq~marrma~~L~~~-p~rkvll 233 (295)
T COG3016 174 VSTPPEIVY-------PPYREILLSEL---HRGN-------PSSNKSFLDAQ--VTWDQAMARRMAKTLILH-PDRKVLL 233 (295)
T ss_pred ccCCccccc-------chHHHHHHHHH---hcCC-------cchhhhHHHHH--HHHHHHHHHHHHHHHHhC-CCcceEE
Confidence 3222221 11333333222 2332 22346799999 999999999999999876 8899999
Q ss_pred EeCCCccccCCCCcchhhHHhhhcCCCceEEEEeCCCCccccc
Q 043788 340 VTGASHVTYGSRGTGLPARISKKLQKKNQVVILLDLKGNIFEE 382 (387)
Q Consensus 340 IaG~gHv~~g~r~~GVP~rL~r~~P~~~~~vVll~p~~~~i~~ 382 (387)
|+|+||.. |++|||.+|+++.|++++++ +.|+| .|+.
T Consensus 234 iAGsfHt~---kglGvp~hl~dl~~g~kvv~--L~~~g-ei~~ 270 (295)
T COG3016 234 IAGSFHTY---KGLGVPYHLKDLYPGVKVVV--LYPEG-EIEK 270 (295)
T ss_pred Eeccchhh---ccCCcceeHHhhCCCcEEEE--Eeecc-cccc
Confidence 99999999 56999999999998766554 45555 4443
No 3
>TIGR00261 traB pheromone shutdown-related protein TraB. traB is a plasmid encoded gene that functions in the shutdown of the peptide sex pheromone cPD1 which is produced by the plasmid free recipient cell prior to conjugative transfer in Enterococcus faecalis. Once the recipient acquires the plasmid, production of cPD1 is shut down. The gene product may play another role in the other species in the family.
Probab=95.45 E-value=0.23 Score=51.37 Aligned_cols=191 Identities=12% Similarity=0.126 Sum_probs=101.3
Q ss_pred hcCCEEEEccccCCCCchhHHHHHHHHHHHHhhccccCCCceEEeeccCCCCchhhhhhhcCCCChHHHH----------
Q 043788 144 MNARVVYLGEAEQVPVRDDRELELQIVKNLRKRCVESERTITLALEAFPSDLQDQLNQYTDKRIDGETLK---------- 213 (387)
Q Consensus 144 a~adVVlLGE~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgLEMF~~d~Q~~LD~ylaG~Ide~~Ll---------- 213 (387)
.+.+|.++|=.|-.. .-..+|=+.+.+ .++=+|++|--+..+|..++. ...++|-.+.+
T Consensus 2 ~~~~i~lvGTAHvS~-----~S~~eV~~~I~~-----~~PD~VaVELd~~R~~~l~~~-~~~~~di~~vlk~g~~~~~l~ 70 (380)
T TIGR00261 2 HEKTIYILGTAHVSK-----KSSEEVANLIEI-----LKPDYIAVELDERRYHSLLNT-KWRNLDIDKVLKQGNAFFLII 70 (380)
T ss_pred CCcEEEEEecccCCH-----HHHHHHHHHHHH-----hCCCEEEEeCCHHHHHHHhhh-hhccCCHHHHhhcCchHHHHH
Confidence 367899999999755 122233333332 457799999988888888776 22334433321
Q ss_pred ----HH-h----cCCCCCCCcccHHHHHHHHhcCCcEEecCCCHHHHHHHHHhcccCCCHHHHhhcCC----CCCCcccc
Q 043788 214 ----SY-A----SHWPPQRWQEYEPLLSYCRDNGVQLLACGTPLKVLRTVQAEGIHGLSKADRKLYAP----PAGSGFIS 280 (387)
Q Consensus 214 ----~w-~----~~W~~~~w~lYrPL~~~Ar~~gipviAlNlPre~vr~V~r~Gl~sLs~eeR~~l~p----p~~~~~~~ 280 (387)
.| + +..+-.+=+..+-=++.|++.|+||+=+..|-.++-+=. +.+++--+|-.+.- .......+
T Consensus 71 ~~~La~~q~~l~~~~gi~PG~Em~~Ai~~A~e~g~~v~LiDRdI~iTl~R~---w~~~~~~eK~kl~~~l~~~~~~~~e~ 147 (380)
T TIGR00261 71 NLILANFQKKLGEEQGIKPGSEMKTAIEKAKKHGIPLILIDRDIETTLKRA---WISITFFEKAKIISSLFSSTDAKIED 147 (380)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCcEEEeCCCHhHHHHHH---HHhCCHHHHHHHHHHHHhccccCCHH
Confidence 11 1 112222224566679999999999999988877654211 22222222222210 00000000
Q ss_pred hhhhhcccc-cccccccC-CCCCCCCcchHHHHhhhhhhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCCCCcchhhH
Q 043788 281 GFTSISHRS-SVDMNSLT-QSVPFGPSSYLSAQARVVEDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGSRGTGLPAR 358 (387)
Q Consensus 281 ~~~~~~~~s-~~~~~~~~-~~~~~~~~~f~~aQAq~l~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~r~~GVP~r 358 (387)
.+.+...+. ...++... +..|...+.++ -=||..||++|.+... .++++|+++|+||.. ||-..
T Consensus 148 ~ie~l~~~d~L~~~~~e~~~~~P~l~~~LI-----dERD~ymA~~L~~l~~---~~~~VvaVVGAGHl~------GI~~~ 213 (380)
T TIGR00261 148 EIEKLLEQDALSKIMKELSKISPKVKKVLI-----DERDEFMANKLLEGEG---NKNIIVAVVGAGHVS------GIMRT 213 (380)
T ss_pred HHHHhhhhhHHHHHHHHHhhhCCchhhHHH-----HHHHHHHHHHHHHhhc---CCCcEEEEECcchhh------hHHHH
Confidence 110000000 00000000 01121112233 2499999999987642 345799999999999 99877
Q ss_pred Hhhh
Q 043788 359 ISKK 362 (387)
Q Consensus 359 L~r~ 362 (387)
+...
T Consensus 214 l~~~ 217 (380)
T TIGR00261 214 LKKL 217 (380)
T ss_pred HhCc
Confidence 7654
No 4
>COG2312 Erythromycin esterase homolog [General function prediction only]
Probab=94.68 E-value=0.088 Score=54.55 Aligned_cols=94 Identities=21% Similarity=0.224 Sum_probs=67.8
Q ss_pred CHHHHHHHHhcCCEEEEccc-cCCCCchhHHHHHHHHHHHHhhccccCCCceEEeeccCCCCchhhhhhhcCC-CChHHH
Q 043788 135 DKRKVWEKLMNARVVYLGEA-EQVPVRDDRELELQIVKNLRKRCVESERTITLALEAFPSDLQDQLNQYTDKR-IDGETL 212 (387)
Q Consensus 135 ~~~~l~~~La~adVVlLGE~-Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgLEMF~~d~Q~~LD~ylaG~-Ide~~L 212 (387)
+.+.+.+.|.+++||+|||. |... ++-+.-..++|.|.+.| |- -+|+||-=-.|.| .+|+|+.|. -|..+.
T Consensus 34 ~~~~l~~~l~~~RiV~LGE~sHGt~--e~~~~k~rm~r~Lvee~---Gf-~~iA~EA~~~d~~-av~~Yv~~~~~d~~~~ 106 (405)
T COG2312 34 ALEALATLLTDARIVLLGEPSHGTG--EFFAFKARMFRALVEEL---GF-RAIAFEADFPDAQ-AVNRYVRGGGDDLREA 106 (405)
T ss_pred hHHHHHhhccCCeEEEecCCCCCcc--HHHHHHHHHHHHHHHHh---Cc-ceEEeccCcHHHH-HHHHHHhccCCChHHH
Confidence 37899999999999999995 5432 45566678999999854 33 4899998555554 679999866 344443
Q ss_pred HH--HhcCCCCCCCcccHHHHHHHHhcC
Q 043788 213 KS--YASHWPPQRWQEYEPLLSYCRDNG 238 (387)
Q Consensus 213 l~--w~~~W~~~~w~lYrPL~~~Ar~~g 238 (387)
.. ...-|.+ +.-++||++-|+.+
T Consensus 107 ~~~~~~~~Wr~---~~v~~lv~wlr~~n 131 (405)
T COG2312 107 MDGFIFWVWRR---AEVRDLVEWLREFN 131 (405)
T ss_pred HhccchhhhhH---HHHHHHHHHHHHHh
Confidence 32 2224774 58999999988764
No 5
>COG1916 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]
Probab=94.51 E-value=0.33 Score=49.88 Aligned_cols=186 Identities=17% Similarity=0.167 Sum_probs=101.9
Q ss_pred HhcCCEEEEccccCCCCchhHHHHHHHHHHHHhhccccCCCceEEeeccCCCCchhhhhhhcCCCChHHHH---------
Q 043788 143 LMNARVVYLGEAEQVPVRDDRELELQIVKNLRKRCVESERTITLALEAFPSDLQDQLNQYTDKRIDGETLK--------- 213 (387)
Q Consensus 143 La~adVVlLGE~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgLEMF~~d~Q~~LD~ylaG~Ide~~Ll--------- 213 (387)
....+|+++|-.|-... .- .++=+.+.. ..+=+|+.|.-+...|..|+.-.. ++|-.+.+
T Consensus 9 ~~~~~v~iiGTAHVS~~--Sv---eeVrr~I~~-----~~PDaVAVELd~~R~~sLl~~~~~-~ldl~~vlk~Gk~~~~l 77 (388)
T COG1916 9 FEEKEVYILGTAHVSKD--SV---EEVRRIILE-----EKPDAVAVELDEARLLSLLGGSRE-ELDLAQVLKEGKAFFLL 77 (388)
T ss_pred cccceEEEEeeeecCHh--HH---HHHHHHHHh-----cCCCeEEEEecHHHHHHHhcCCcc-cCCHHHHHHcCchHHHH
Confidence 34458999999997652 11 222233332 346799999999888888875432 44443321
Q ss_pred -----HH-hcC----CCCCCCcccHHHHHHHHhcCCcEEecCCCHHHHHHHHHhcccCCCHHHHhhcC--------CCCC
Q 043788 214 -----SY-ASH----WPPQRWQEYEPLLSYCRDNGVQLLACGTPLKVLRTVQAEGIHGLSKADRKLYA--------PPAG 275 (387)
Q Consensus 214 -----~w-~~~----W~~~~w~lYrPL~~~Ar~~gipviAlNlPre~vr~V~r~Gl~sLs~eeR~~l~--------pp~~ 275 (387)
.+ ++. -+-.+=++-.--++.|++.|+||+=..-+=+++-+= =+..++.-|+-++. -+..
T Consensus 78 ~~~lLa~~Qrklg~~~Gv~PGsEmk~AIe~A~e~ga~V~lIDRdI~vTl~R---~~~~~~~~EKlK~~~~L~~~~~~~g~ 154 (388)
T COG1916 78 AGLLLAYFQRKLGKELGVKPGSEMKAAIEAARELGAPVALIDRDIGVTLRR---AWAKMPFWEKLKLISSLISGLLFPGQ 154 (388)
T ss_pred HHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCCEEEecccHHHHHHH---HHHhCCHHHHHHHHHHHHHhcccCCC
Confidence 11 111 111122578888999999999999988776654322 12234443433331 1100
Q ss_pred Ccc-cchhhhhcccccccccccC-CC-CCCCCcchH--HHHhhhhhhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCC
Q 043788 276 SGF-ISGFTSISHRSSVDMNSLT-QS-VPFGPSSYL--SAQARVVEDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGS 350 (387)
Q Consensus 276 ~~~-~~~~~~~~~~s~~~~~~~~-~~-~~~~~~~f~--~aQAq~l~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~ 350 (387)
.+. ...+. ..|+.... +. ..+. +..+ .+- =||+.||.+|.+..... -.+|.|.|+||..
T Consensus 155 ~e~ei~~l~------~~D~~~al~~efr~~~-P~~~~vLID---ERd~ymA~nll~~~~~~---~~vvAVVGAGH~~--- 218 (388)
T COG1916 155 SEIEIDELK------QEDVLSALMQEFRRFS-PTVYKVLID---ERDRYMARNLLEIVSIL---NDVVAVVGAGHVR--- 218 (388)
T ss_pred chHHHHHHh------hhhHHHHHHHHHHHhC-hhHHHHHHH---HHHHHHHHHHHHHHccc---CcEEEEEccccHH---
Confidence 000 00000 00111000 00 0000 1222 111 29999999999987543 2399999999999
Q ss_pred CCcchhhHHhh
Q 043788 351 RGTGLPARISK 361 (387)
Q Consensus 351 r~~GVP~rL~r 361 (387)
||-.+|..
T Consensus 219 ---GI~~~L~~ 226 (388)
T COG1916 219 ---GIERYLKN 226 (388)
T ss_pred ---HHHHHHhc
Confidence 99999955
No 6
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=89.26 E-value=0.47 Score=44.78 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCCCCcchhhHHhhh
Q 043788 316 EDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGSRGTGLPARISKK 362 (387)
Q Consensus 316 ~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~r~~GVP~rL~r~ 362 (387)
||..|+..|.+.+.. ++++++++|+||..- .-||...|+++
T Consensus 212 RN~~~~~~i~~~l~~---~~~~fvvVGa~HL~G---~~gvl~lLr~~ 252 (259)
T PF01963_consen 212 RNRRWAEKIEELLKE---GGTVFVVVGAGHLPG---EDGVLDLLRKK 252 (259)
T ss_pred HhHHHHHHHHHHHhc---CCCEEEEEcchhccc---hhhHHHHHHhC
Confidence 999999999998863 246999999999994 48999999764
No 7
>PF05139 Erythro_esteras: Erythromycin esterase; InterPro: IPR007815 This family includes erythromycin esterase enzymes [, ] that confer resistance to the erythromycin antibiotic.; GO: 0046677 response to antibiotic; PDB: 2QGM_A 3B55_A 2RAD_B.
Probab=88.56 E-value=0.53 Score=46.94 Aligned_cols=58 Identities=10% Similarity=0.107 Sum_probs=41.5
Q ss_pred hhhhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCCCCc-------chhhHHhhhcCCCceEEEE
Q 043788 314 VVEDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGSRGT-------GLPARISKKLQKKNQVVIL 372 (387)
Q Consensus 314 ~l~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~r~~-------GVP~rL~r~~P~~~~~vVl 372 (387)
.+||..||+++.-.+...+|+.++||.+.++|+......+ .+=.+|+++.++ +..+|-
T Consensus 183 ~~RD~~MAenl~wl~~~~~~~~KiivwaHN~Hi~k~~~~~~~~~~~~~~G~~L~~~~g~-~y~~Ig 247 (346)
T PF05139_consen 183 NYRDRYMAENLEWLLEHEGPDEKIIVWAHNGHIAKAPSTWMGDLGEKSMGQYLKERYGD-DYYSIG 247 (346)
T ss_dssp HHHHHHHHHHHHHHHHHH---SSEEEEEEHHHHSSS-STTTT---SS-HHHHHHHHHGG-GEEEEE
T ss_pred hhhHHHHHHHHHHHHHhhcccccEEEEccchhhcccccccccccCcccHHHHHHHHhCC-cEEEEE
Confidence 4699999999977766555778999999999999763322 256788888884 466663
No 8
>COG3735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.64 E-value=9 Score=38.59 Aligned_cols=41 Identities=22% Similarity=0.179 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCCCCcchhhHHhhhc
Q 043788 316 EDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGSRGTGLPARISKKL 363 (387)
Q Consensus 316 ~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~r~~GVP~rL~r~~ 363 (387)
|+..||+.-... - ++|..+|.+|++|.- ..-|++.-|++..
T Consensus 252 RN~~wad~~~~~---l-~~G~~fvaVGAlHL~---G~e~L~e~Lrk~g 292 (299)
T COG3735 252 RNRAWADKKTPL---L-QGGRYFVAVGALHLP---GPEGLVELLRKDG 292 (299)
T ss_pred HHHHHHHhhccc---c-CCCCEEEEecccccc---CcccHHHHHHHcC
Confidence 899999982222 2 345699999999998 3479999997643
No 9
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=57.79 E-value=8.8 Score=30.24 Aligned_cols=17 Identities=24% Similarity=0.255 Sum_probs=12.1
Q ss_pred ccccccchhhhhHHHhh
Q 043788 59 AEFSRRHVFLSPLIAVG 75 (387)
Q Consensus 59 ~~~~~~~~~~~~~~~~~ 75 (387)
...|||+||-..+++++
T Consensus 7 ~~~sRR~Flk~lg~~aa 23 (66)
T TIGR02811 7 ADPSRRDLLKGLGVGAA 23 (66)
T ss_pred CCccHHHHHHHHHHHHH
Confidence 34589999998666443
No 10
>PRK10781 rcsF outer membrane lipoprotein; Reviewed
Probab=40.42 E-value=51 Score=29.58 Aligned_cols=53 Identities=13% Similarity=0.013 Sum_probs=27.8
Q ss_pred HHHhcCCEEEEccccCCCCchhHHH------HHHHHHHHHhhccccCCCceEEeeccCCCC
Q 043788 141 EKLMNARVVYLGEAEQVPVRDDREL------ELQIVKNLRKRCVESERTITLALEAFPSDL 195 (387)
Q Consensus 141 ~~La~adVVlLGE~Hdnp~~~hH~l------Ql~llraL~~r~~e~g~~~aLgLEMF~~d~ 195 (387)
++|.+.+.-+|||.-... +.-.. ....-+.|..+-..-|-+.+|.+|-+....
T Consensus 56 eel~~~~~~~LG~V~Ges--Cq~~~~~~p~s~~~Ar~~~r~kAa~~gaN~Vvl~~C~~~~~ 114 (133)
T PRK10781 56 EELVGKPFRDLGEVSGES--CQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEITSG 114 (133)
T ss_pred HHHcCCCCceeeeEEccc--cccCCCCCCCCHHHHHHHHHHHHHHcCCCEEEEEEeeccCC
Confidence 346677888888866543 11111 112223332222225677888888776543
No 11
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=38.89 E-value=19 Score=23.28 Aligned_cols=19 Identities=32% Similarity=0.375 Sum_probs=11.7
Q ss_pred ccccchhhhhHHHhhHHHh
Q 043788 61 FSRRHVFLSPLIAVGASIL 79 (387)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~~ 79 (387)
-|||+||-+-.-+++++.+
T Consensus 2 ~sRR~fLk~~~a~~a~~~~ 20 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAAAAL 20 (26)
T ss_pred CcHHHHHHHHHHHHHHHHh
Confidence 3799998874444444433
No 12
>PRK13587 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=37.62 E-value=3.6e+02 Score=25.78 Aligned_cols=113 Identities=12% Similarity=0.227 Sum_probs=68.1
Q ss_pred CHHHHHHHHh-cCCEEEEcc-ccCCCCchhHHHHHHHHHHHHhhccccCCCceEEeeccCCCCchhhhhhhc-CCCChHH
Q 043788 135 DKRKVWEKLM-NARVVYLGE-AEQVPVRDDRELELQIVKNLRKRCVESERTITLALEAFPSDLQDQLNQYTD-KRIDGET 211 (387)
Q Consensus 135 ~~~~l~~~La-~adVVlLGE-~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgLEMF~~d~Q~~LD~yla-G~Ide~~ 211 (387)
+.+++-+-+. .++-|+||= ...|| ++++.+.++. +.++++++.... .+...+.|.. ..++..+
T Consensus 87 s~e~v~~~l~~Ga~kvvigt~a~~~~---------~~l~~~~~~f---g~~ivvslD~~~--g~v~~~gw~~~~~~~~~~ 152 (234)
T PRK13587 87 TKSQIMDYFAAGINYCIVGTKGIQDT---------DWLKEMAHTF---PGRIYLSVDAYG--EDIKVNGWEEDTELNLFS 152 (234)
T ss_pred CHHHHHHHHHCCCCEEEECchHhcCH---------HHHHHHHHHc---CCCEEEEEEeeC--CEEEecCCcccCCCCHHH
Confidence 3666555554 477788884 34444 6888888764 456999999853 3555666654 2355566
Q ss_pred HHHHhcCCCCCC--Cc-----------ccHHHHHHHHhcCCcEEecC--CCHHHHHHHHHhcccC
Q 043788 212 LKSYASHWPPQR--WQ-----------EYEPLLSYCRDNGVQLLACG--TPLKVLRTVQAEGIHG 261 (387)
Q Consensus 212 Ll~w~~~W~~~~--w~-----------lYrPL~~~Ar~~gipviAlN--lPre~vr~V~r~Gl~s 261 (387)
+.+....|+... +. ++.=+-+.++..++||++.+ -..+.+.++.+-|.++
T Consensus 153 ~~~~~~~~g~~~ii~tdi~~dGt~~G~~~~li~~l~~~~~ipvi~~GGi~s~edi~~l~~~G~~~ 217 (234)
T PRK13587 153 FVRQLSDIPLGGIIYTDIAKDGKMSGPNFELTGQLVKATTIPVIASGGIRHQQDIQRLASLNVHA 217 (234)
T ss_pred HHHHHHHcCCCEEEEecccCcCCCCccCHHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHcCCCE
Confidence 665555566310 01 12223334445689999887 5666777777767654
No 13
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=37.45 E-value=46 Score=32.74 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=15.7
Q ss_pred cccchhhhhHHHhhHHHhhhcc
Q 043788 62 SRRHVFLSPLIAVGASILLQSA 83 (387)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~ 83 (387)
.||.-||.|.+++++.+|.+++
T Consensus 13 ~~~~~~~~~~~~~~~~~L~gCa 34 (246)
T PRK12699 13 RRRGRLLGPVLIVMLALVGGCS 34 (246)
T ss_pred hhcccchHHHHHHHHHHhhccc
Confidence 3677778899888887665543
No 14
>PLN02803 beta-amylase
Probab=33.74 E-value=27 Score=37.94 Aligned_cols=22 Identities=23% Similarity=0.643 Sum_probs=20.2
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.||+.+|+.|++|.+
T Consensus 141 YdWsgY~~l~~mvr~~GLKlq~ 162 (548)
T PLN02803 141 YNWEGYAELVQMVQKHGLKLQV 162 (548)
T ss_pred CCcHHHHHHHHHHHHcCCeEEE
Confidence 5799999999999999999865
No 15
>PLN00197 beta-amylase; Provisional
Probab=32.98 E-value=28 Score=37.95 Aligned_cols=22 Identities=27% Similarity=0.664 Sum_probs=20.2
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.||+.+|+.|++|.+
T Consensus 161 YdWsgY~~L~~mvr~~GLKlq~ 182 (573)
T PLN00197 161 YNWGGYNELLEMAKRHGLKVQA 182 (573)
T ss_pred CCcHHHHHHHHHHHHcCCeEEE
Confidence 5899999999999999999864
No 16
>PLN02161 beta-amylase
Probab=32.85 E-value=28 Score=37.61 Aligned_cols=22 Identities=27% Similarity=0.631 Sum_probs=20.0
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.||+.+|+.|++|.+
T Consensus 151 YdWsgY~~l~~mvr~~GLKlq~ 172 (531)
T PLN02161 151 FKWSLYEELFRLISEAGLKLHV 172 (531)
T ss_pred CCcHHHHHHHHHHHHcCCeEEE
Confidence 5799999999999999999864
No 17
>PLN02801 beta-amylase
Probab=30.72 E-value=32 Score=37.13 Aligned_cols=22 Identities=23% Similarity=0.600 Sum_probs=19.9
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.|++.+|+.|++|.+
T Consensus 71 YdWsgY~~l~~mvr~~GLKlq~ 92 (517)
T PLN02801 71 YDWSAYRSLFELVQSFGLKIQA 92 (517)
T ss_pred cCcHHHHHHHHHHHHcCCeEEE
Confidence 5799999999999999999943
No 18
>PLN02705 beta-amylase
Probab=30.61 E-value=32 Score=38.04 Aligned_cols=22 Identities=23% Similarity=0.481 Sum_probs=20.2
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.||+.+|+.|++|.+
T Consensus 302 YdWsgY~~L~~mvr~~GLKlqv 323 (681)
T PLN02705 302 YVWSGYRELFNIIREFKLKLQV 323 (681)
T ss_pred CCcHHHHHHHHHHHHcCCeEEE
Confidence 5899999999999999999864
No 19
>PF14591 AF0941-like: AF0941-like; PDB: 1YOZ_B.
Probab=30.12 E-value=9.2 Score=33.93 Aligned_cols=52 Identities=33% Similarity=0.401 Sum_probs=35.4
Q ss_pred eeccCCCCchhhhhhhcCCCChHHHH-------HHhcCCCCCCCcccHHHHHHHHhcCCcEEe
Q 043788 188 LEAFPSDLQDQLNQYTDKRIDGETLK-------SYASHWPPQRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 188 LEMF~~d~Q~~LD~ylaG~Ide~~Ll-------~w~~~W~~~~w~lYrPL~~~Ar~~gipviA 243 (387)
.|||-.|.|.+|+.|.+|.|++++-+ .+...-. ..|.-+.+++.+.+..+-.
T Consensus 39 ~emFr~D~e~Il~~~~~Gdi~eEEA~~ll~eL~~~asqL~----~~~~~~~e~l~~le~k~~k 97 (127)
T PF14591_consen 39 EEMFRSDLEDILEDYKSGDIDEEEALQLLDELKSYASQLQ----EHYFRVRELLEDLERKIQK 97 (127)
T ss_dssp HHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHTHH----HHHHHHHHHHHCTT-----
T ss_pred HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999987632 4552222 4688888888777766543
No 20
>PLN02905 beta-amylase
Probab=29.92 E-value=34 Score=38.00 Aligned_cols=22 Identities=23% Similarity=0.545 Sum_probs=20.2
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.||+.+|+.|++|.+
T Consensus 320 YdWsgY~~L~~mvr~~GLKlqv 341 (702)
T PLN02905 320 YNWNGYKRLFQMVRELKLKLQV 341 (702)
T ss_pred CCcHHHHHHHHHHHHcCCeEEE
Confidence 5899999999999999999864
No 21
>PF01373 Glyco_hydro_14: Glycosyl hydrolase family 14; InterPro: IPR001554 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 14 GH14 from CAZY comprises enzymes with only one known activity; beta-amylase (3.2.1.2 from EC). A Glu residue has been proposed as a catalytic residue, but it is not known if it is the nucleophile or the proton donor. Beta-amylase [, ] is an enzyme that hydrolyses 1,4-alpha-glucosidic linkages in starch-type polysaccharide substrates so as to remove successive maltose units from the non-reducing ends of the chains. Beta-amylase is present in certain bacteria as well as in plants. Three highly conserved sequence regions are found in all known beta-amylases. The first of these regions is located in the N-terminal section of the enzymes and contains an aspartate which is known [] to be involved in the catalytic mechanism. The second, located in a more central location, is centred around a glutamate which is also involved [] in the catalytic mechanism. The 3D structure of a complex of soybean beta-amylase with an inhibitor (alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray diffraction []. The enzyme folds into large and small domains: the large domain has a (beta alpha)8 super-secondary structural core, while the smaller is formed from two long loops extending from the beta-3 and beta-4 strands of the (beta alpha)8 fold []. The interface of the two domains, together with shorter loops from the (beta alpha)8 core, form a deep cleft, in which the inhibitor binds []. Two maltose molecules also bind in the cleft, one sharing a binding site with alpha-cyclodextrin, and the other sitting more deeply in the cleft [].; GO: 0016161 beta-amylase activity, 0000272 polysaccharide catabolic process; PDB: 1FA2_A 2DQX_A 1WDP_A 1UKP_C 1BYC_A 1BYA_A 1Q6C_A 1V3I_A 1BTC_A 1BYB_A ....
Probab=28.86 E-value=32 Score=36.18 Aligned_cols=22 Identities=32% Similarity=0.709 Sum_probs=17.4
Q ss_pred CCCcccHHHHHHHHhcCCcEEe
Q 043788 222 QRWQEYEPLLSYCRDNGVQLLA 243 (387)
Q Consensus 222 ~~w~lYrPL~~~Ar~~gipviA 243 (387)
|+|+.|+.|++.+|+.|++|.+
T Consensus 50 ydWs~Y~~l~~~vr~~GLk~~~ 71 (402)
T PF01373_consen 50 YDWSGYRELFEMVRDAGLKLQV 71 (402)
T ss_dssp ---HHHHHHHHHHHHTT-EEEE
T ss_pred cCcHHHHHHHHHHHHcCCeEEE
Confidence 5799999999999999999887
No 22
>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.
Probab=28.42 E-value=1.7e+02 Score=27.47 Aligned_cols=60 Identities=13% Similarity=0.255 Sum_probs=45.1
Q ss_pred HHHHHHHHhcCCEEEEccccCCCCchhHHHHHHHHHHHHhhccccCCCceEEeeccCCCCchh
Q 043788 136 KRKVWEKLMNARVVYLGEAEQVPVRDDRELELQIVKNLRKRCVESERTITLALEAFPSDLQDQ 198 (387)
Q Consensus 136 ~~~l~~~La~adVVlLGE~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgLEMF~~d~Q~~ 198 (387)
.+++.+.+..+|++++=..|.-. +...+|.+++.-+-... ++|.++.|+-+.-|.+....
T Consensus 88 ~~~~~~~~~~~DlL~iDDi~~l~--~~~~~q~~lf~l~n~~~-~~~k~li~ts~~~P~~l~~~ 147 (219)
T PF00308_consen 88 IEEFKDRLRSADLLIIDDIQFLA--GKQRTQEELFHLFNRLI-ESGKQLILTSDRPPSELSGL 147 (219)
T ss_dssp HHHHHHHHCTSSEEEEETGGGGT--THHHHHHHHHHHHHHHH-HTTSEEEEEESS-TTTTTTS
T ss_pred chhhhhhhhcCCEEEEecchhhc--CchHHHHHHHHHHHHHH-hhCCeEEEEeCCCCcccccc
Confidence 56788999999999999999865 56678887776664432 36889999999987765433
No 23
>PF00988 CPSase_sm_chain: Carbamoyl-phosphate synthase small chain, CPSase domain; InterPro: IPR002474 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the small subunit of carbamoyl phosphate synthase. The small subunit has a 3-layer beta/beta/alpha structure, and is thought to be mobile in most proteins that carry it. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity.; GO: 0006807 nitrogen compound metabolic process; PDB: 1CE8_B 1KEE_B 1CS0_D 1T36_D 1M6V_H 1A9X_F 1JDB_I 1BXR_F 1C3O_B 1C30_F ....
Probab=26.75 E-value=56 Score=29.20 Aligned_cols=44 Identities=11% Similarity=0.247 Sum_probs=29.5
Q ss_pred HHhcCCCCCCCcccHHHHHHHHhcCCcEEecCCCHHHHHHHHHhcc
Q 043788 214 SYASHWPPQRWQEYEPLLSYCRDNGVQLLACGTPLKVLRTVQAEGI 259 (387)
Q Consensus 214 ~w~~~W~~~~w~lYrPL~~~Ar~~gipviAlNlPre~vr~V~r~Gl 259 (387)
++..... +|.....|-+|.++++||.|..==-|.+++++.+.|.
T Consensus 82 e~~~~~s--~~~~~~sL~~~L~~~~ipgi~gvDTRaLt~~lR~~G~ 125 (131)
T PF00988_consen 82 ELSDIPS--HWRSEMSLDEWLKEHGIPGISGVDTRALTRKLREKGS 125 (131)
T ss_dssp B--SS-----TT-SB-HHHHHHHTT-EEEESS-HHHHHHHHHHH--
T ss_pred cccCCCc--cccccCCHHHHHHHCCCeeeeCCcHHHHHHHHHhcCC
Confidence 4444444 4888999999999999999988888999999999884
No 24
>COG0313 Predicted methyltransferases [General function prediction only]
Probab=26.34 E-value=79 Score=31.68 Aligned_cols=33 Identities=18% Similarity=0.454 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCcEEecCCCHHHHHHHHHhcccC
Q 043788 229 PLLSYCRDNGVQLLACGTPLKVLRTVQAEGIHG 261 (387)
Q Consensus 229 PL~~~Ar~~gipviAlNlPre~vr~V~r~Gl~s 261 (387)
-|+..|+++||+|+.++=|..++..++..|+.+
T Consensus 97 ~LV~~a~~~gi~V~~lPG~sA~~tAL~~SGl~~ 129 (275)
T COG0313 97 ELVRAAREAGIRVVPLPGPSALITALSASGLPS 129 (275)
T ss_pred HHHHHHHHcCCcEEecCCccHHHHHHHHcCCCC
Confidence 399999999999999999999999999999754
No 25
>PRK11865 pyruvate ferredoxin oxidoreductase subunit beta; Provisional
Probab=25.96 E-value=2e+02 Score=29.01 Aligned_cols=65 Identities=15% Similarity=0.129 Sum_probs=45.0
Q ss_pred hhHHHHHHHHHHHHhcCCCCeEEEEeCCCccccCCCCcchhhHHhhhcCCCceEEEEeCCCCccccccc
Q 043788 316 EDYAMSQIILKAIMDGGANGMLVVVTGASHVTYGSRGTGLPARISKKLQKKNQVVILLDLKGNIFEERE 384 (387)
Q Consensus 316 ~D~tMAe~I~~al~~~~p~~~vVvIaG~gHv~~g~r~~GVP~rL~r~~P~~~~~vVll~p~~~~i~~~~ 384 (387)
+-..||.-|..++...+++..||++.|-| .-|+ .|+..-..-..-+.++++|++|-+.-.-|+.|
T Consensus 73 ~~~a~a~Gi~~a~~~~~~~~~Vv~~~GDG-~~~d---IG~~~L~~a~~r~~ni~~ivlDNe~Y~nTGgQ 137 (299)
T PRK11865 73 NAAAVASGIERAVKALGKKVNVVAIGGDG-GTAD---IGFQSLSGAMERGHNILYLMYDNEAYMNTGIQ 137 (299)
T ss_pred chHHHHHHHHHHHHHhcCCCeEEEEeCCc-hHhh---ccHHHHHHHHHcCCCeEEEEECCccccCCCCC
Confidence 44577777776664323456799999999 4444 78876666666678899999988776655544
No 26
>cd02018 TPP_PFOR Thiamine pyrophosphate (TPP family), Pyruvate ferredoxin/flavodoxin oxidoreductase (PFOR) subfamily, TPP-binding module; PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. PFORs can be homodimeric, heterodimeric, or heterotetrameric, depending on the organism. These enzymes are dependent on TPP and a divalent metal cation as cofactors.
Probab=25.65 E-value=1.6e+02 Score=28.29 Aligned_cols=58 Identities=17% Similarity=0.243 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHh--c-----CCCCeEEEEeCCC---ccccCCCCcchhhHHhhhcCCCceEEEEeCCCCccccc
Q 043788 318 YAMSQIILKAIMD--G-----GANGMLVVVTGAS---HVTYGSRGTGLPARISKKLQKKNQVVILLDLKGNIFEE 382 (387)
Q Consensus 318 ~tMAe~I~~al~~--~-----~p~~~vVvIaG~g---Hv~~g~r~~GVP~rL~r~~P~~~~~vVll~p~~~~i~~ 382 (387)
-+|+..+-.++-. . .++++||.|+|-| |.-.+ ++..-+. -++++++|++|-..-..++
T Consensus 64 g~mG~GlpaAiGA~~a~~~~~~p~~~Vv~i~GDG~~~~~g~~----~l~ta~~---~~l~i~ivVlNN~~yg~~~ 131 (237)
T cd02018 64 NAVASGLKRGLKARFPKDRELDKKKDVVVIGGDGATYDIGFG----ALSHSLF---RGEDITVIVLDNEVYSNTG 131 (237)
T ss_pred HHHHHHHHHHHHhhcccccccCCCCcEEEEeCchHHHhccHH----HHHHHHH---cCCCeEEEEECCccccCCC
Confidence 5788777666532 1 3678999999999 44432 4444443 3477888888877554443
No 27
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=25.41 E-value=53 Score=27.64 Aligned_cols=15 Identities=27% Similarity=0.439 Sum_probs=7.2
Q ss_pred HHhhHHHhhhccccc
Q 043788 72 IAVGASILLQSATAS 86 (387)
Q Consensus 72 ~~~~~~~~~~~~~~~ 86 (387)
|..++.||.+|..++
T Consensus 11 l~LA~lLlisSevaa 25 (95)
T PF07172_consen 11 LLLAALLLISSEVAA 25 (95)
T ss_pred HHHHHHHHHHhhhhh
Confidence 334445566654333
No 28
>cd03376 TPP_PFOR_porB_like Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The 36-kDa porB subunit contains the binding sites for the cofactors, TPP and a divalent metal cation, which are required for activity.
Probab=24.60 E-value=2.2e+02 Score=27.27 Aligned_cols=59 Identities=17% Similarity=0.145 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHh--cCCCCeEEEEeCCCcc-ccCCCCcchhhHHhhhcCCCceEEEEeCCCCcccc
Q 043788 318 YAMSQIILKAIMD--GGANGMLVVVTGASHV-TYGSRGTGLPARISKKLQKKNQVVILLDLKGNIFE 381 (387)
Q Consensus 318 ~tMAe~I~~al~~--~~p~~~vVvIaG~gHv-~~g~r~~GVP~rL~r~~P~~~~~vVll~p~~~~i~ 381 (387)
.+|+..+-.++.. ..|+++||.|+|-|=. . .|+.+-..-..-+.++++|++|-..-..+
T Consensus 62 gsmG~GlpaAiGa~~a~p~r~VV~i~GDG~~~~-----m~~~eL~ta~~~~~pv~~vVlNN~~yg~t 123 (235)
T cd03376 62 AAVASGIEAALKALGRGKDITVVAFAGDGGTAD-----IGFQALSGAAERGHDILYICYDNEAYMNT 123 (235)
T ss_pred HHHHHHHHHHHHHhccCCCCeEEEEEcCchHHh-----hHHHHHHHHHHcCCCeEEEEECCcccccC
Confidence 4999988777632 2267899999999984 4 56555443333357788888887765543
No 29
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=23.76 E-value=2.2e+02 Score=29.24 Aligned_cols=63 Identities=19% Similarity=0.345 Sum_probs=45.6
Q ss_pred eeeEEeecccCCcccccCcCHHHHHHHHhcCCEEEEccccCCCCchhHHHHHHHHHHHHhhccccCCCceE
Q 043788 116 VVSRIYDATVIGEPLAVGKDKRKVWEKLMNARVVYLGEAEQVPVRDDRELELQIVKNLRKRCVESERTITL 186 (387)
Q Consensus 116 ~~~rI~D~~~~G~~is~~~~~~~l~~~La~adVVlLGE~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aL 186 (387)
..+-||..+. |..+++.+.+.+...+=.++.+||+|---...--..| =++.|+.|+ +.+++.+
T Consensus 247 mSSyi~sLKp-GDKvtisGPfGEfFaKdtdaemvFigGGAGmapmRSH--IfDqL~rlh-----SkRkis~ 309 (410)
T COG2871 247 MSSYIWSLKP-GDKVTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSH--IFDQLKRLH-----SKRKISF 309 (410)
T ss_pred eeeeEEeecC-CCeEEEeccchhhhhccCCCceEEEecCcCcCchHHH--HHHHHHhhc-----ccceeee
Confidence 5678999986 9999999999999999999999999875554322233 245566665 3455554
No 30
>PF12048 DUF3530: Protein of unknown function (DUF3530); InterPro: IPR022529 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.
Probab=21.27 E-value=96 Score=31.01 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=24.4
Q ss_pred cccHHHHHHHHhcCCc---EEecCCCHHHHHHHHHhc
Q 043788 225 QEYEPLLSYCRDNGVQ---LLACGTPLKVLRTVQAEG 258 (387)
Q Consensus 225 ~lYrPL~~~Ar~~gip---viAlNlPre~vr~V~r~G 258 (387)
.-..-++.|++.+|.. |||-+.--.++-+...+.
T Consensus 178 ari~Aa~~~~~~~~~~~ivlIg~G~gA~~~~~~la~~ 214 (310)
T PF12048_consen 178 ARIEAAIAFAQQQGGKNIVLIGHGTGAGWAARYLAEK 214 (310)
T ss_pred HHHHHHHHHHHhcCCceEEEEEeChhHHHHHHHHhcC
Confidence 4567788899998776 677777777766655553
No 31
>PRK15098 beta-D-glucoside glucohydrolase; Provisional
Probab=20.99 E-value=1.6e+02 Score=33.29 Aligned_cols=73 Identities=15% Similarity=0.157 Sum_probs=43.9
Q ss_pred HHHHHHHHhcCCEEEE--cc-------ccCCCCchhHHHHHHHHHHHHhhccccCCCceEEe------ec--cCCCCchh
Q 043788 136 KRKVWEKLMNARVVYL--GE-------AEQVPVRDDRELELQIVKNLRKRCVESERTITLAL------EA--FPSDLQDQ 198 (387)
Q Consensus 136 ~~~l~~~La~adVVlL--GE-------~Hdnp~~~hH~lQl~llraL~~r~~e~g~~~aLgL------EM--F~~d~Q~~ 198 (387)
.++.++.+.++|+|+| |+ ..|-....--.-|.++|+++.+. ++++++.+ .| +......+
T Consensus 492 ~~~a~~~A~~aD~vIv~vg~~~~~~~E~~Dr~~l~Lp~~Q~~Li~~v~~~----~~~vVvVl~~g~P~~l~~~~~~v~Ai 567 (765)
T PRK15098 492 IDEAVQAAKQADVVVAVVGEAQGMAHEASSRTDITIPQSQRDLIAALKAT----GKPLVLVLMNGRPLALVKEDQQADAI 567 (765)
T ss_pred HHHHHHHHhcCCEEEEEEcCCCCccccCCCcccccCCHHHHHHHHHHHHh----CcCEEEEEeCCceeeccchhhcCCeE
Confidence 4566777888887665 43 33322112234699999999873 44555443 23 33345677
Q ss_pred hhhhhcCCCChHHH
Q 043788 199 LNQYTDKRIDGETL 212 (387)
Q Consensus 199 LD~ylaG~Ide~~L 212 (387)
|..|..|......+
T Consensus 568 L~a~~pG~e~G~Ai 581 (765)
T PRK15098 568 LETWFAGTEGGNAI 581 (765)
T ss_pred EeecCCchhhhHHH
Confidence 77788887665543
Done!