Query 035960
Match_columns 256
No_of_seqs 86 out of 105
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 08:00:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02973 beta-fructofuranosida 100.0 5.7E-98 1E-102 719.3 12.7 251 1-255 8-294 (571)
2 PLN03005 beta-fructofuranosida 100.0 3.1E-97 7E-102 712.4 13.7 245 6-255 2-273 (550)
3 PF12899 Glyco_hydro_100: Alka 100.0 3E-86 6.6E-91 624.8 8.5 161 95-255 1-185 (436)
4 PLN02703 beta-fructofuranosida 100.0 7.1E-74 1.5E-78 555.5 9.7 191 62-255 105-326 (618)
5 TIGR01577 oligosac_amyl oligos 93.7 0.09 1.9E-06 51.8 4.6 128 95-226 253-391 (616)
6 PF06202 GDE_C: Amylo-alpha-1, 82.9 0.51 1.1E-05 44.0 0.8 85 128-226 28-122 (370)
7 TIGR01535 glucan_glucosid gluc 75.7 3.9 8.5E-05 41.9 4.5 52 113-164 271-328 (648)
8 PF00723 Glyco_hydro_15: Glyco 59.1 11 0.00024 35.5 3.7 77 96-174 3-98 (448)
9 PF07849 DUF1641: Protein of u 45.2 17 0.00037 24.9 1.9 17 208-224 20-36 (42)
10 COG3387 SGA1 Glucoamylase and 41.4 43 0.00094 34.2 4.8 42 127-168 281-322 (612)
11 TIGR01354 cyt_deam_tetra cytid 41.2 39 0.00085 27.4 3.7 30 91-120 2-31 (127)
12 PF13657 Couple_hipA: HipA N-t 41.1 15 0.00032 27.8 1.2 29 105-134 3-31 (99)
13 PF01315 Ald_Xan_dh_C: Aldehyd 40.7 19 0.00041 28.4 1.8 22 100-121 73-94 (111)
14 PF05651 Diacid_rec: Putative 40.1 25 0.00055 29.2 2.5 28 68-120 65-92 (135)
15 PF09776 Mitoc_L55: Mitochondr 34.2 19 0.00041 30.3 0.9 12 231-242 44-56 (116)
16 TIGR02861 SASP_H small acid-so 34.2 35 0.00076 25.4 2.2 26 94-120 4-32 (58)
17 KOG1552 Predicted alpha/beta h 30.7 39 0.00084 31.7 2.4 124 90-226 112-254 (258)
18 COG3408 GDB1 Glycogen debranch 29.5 24 0.00052 36.3 0.9 101 128-242 282-396 (641)
19 TIGR02389 RNA_pol_rpoA2 DNA-di 27.8 34 0.00075 33.1 1.6 31 91-122 27-60 (367)
20 cd06528 RNAP_A'' A'' subunit o 27.4 48 0.001 32.1 2.4 27 91-118 23-49 (363)
21 COG2427 Uncharacterized conser 25.3 50 0.0011 27.8 1.9 15 210-224 125-139 (148)
22 PF06543 Lac_bphage_repr: Lact 25.1 39 0.00084 25.0 1.1 31 23-53 5-35 (49)
23 PF02470 MCE: mce related prot 23.0 88 0.0019 22.7 2.6 17 103-119 19-35 (81)
24 PF00515 TPR_1: Tetratricopept 22.6 1.3E+02 0.0028 17.8 2.9 26 139-164 7-32 (34)
25 PRK14898 DNA-directed RNA poly 22.5 1E+02 0.0022 32.9 3.9 44 91-135 40-87 (858)
No 1
>PLN02973 beta-fructofuranosidase
Probab=100.00 E-value=5.7e-98 Score=719.26 Aligned_cols=251 Identities=66% Similarity=1.071 Sum_probs=238.9
Q ss_pred CCCCcccccccccCCcccccccccchhhhhccCC-CCchhhhcccccchhhhhhcccc-------CCCccCcccccCC--
Q 035960 1 MDGTKEVLGLRNVSSHCSISEMDDYDLSKLLDKP-RLNIERQRSFDERSLSELSIGLT-------RGGVDNYESTYSP-- 70 (256)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~~ll~~p-~~~ier~rs~ders~~el~~~~~-------~~~~~~~~~~~sp-- 70 (256)
+|+++|| ++|+++++++++|+|++|++||++|| ++||||||||||||++|++.... .+..+++|+++||
T Consensus 8 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (571)
T PLN02973 8 VDVNQNG-NIKNVDSLSTLDDIDDIDFAKLLEKPRPLNIDRLRSLDERSLTELTGSPQLRNADNASRAPDHADYVISPSF 86 (571)
T ss_pred ccccccc-ccccccccccccccchhhHHHHhcCCcccchhhccccchhhhhhcCcccccCCcccccccccchhhccCCCc
Confidence 4678999 99999999999999999999999999 59999999999999999974322 3568999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCChhHHHHHHHHhhcceeecCeeeEEEeecCCCCcccCCCCceeeecchHHHHHHHhcCChh
Q 035960 71 GGRSGFDTPVSSTRNSFEPHPMVAEAWEALRRSLVYFRGQPVGTIAAYDHASEEVLNYDQVFVRDFVPSALAFLMNGEPD 150 (256)
Q Consensus 71 ~~~s~~~tp~~~~~~~~~~~~~~~eAwe~L~~SlV~~~G~pVGTvAA~D~~~~~aLNYdqvFvRDFVPSalafLm~Ge~e 150 (256)
|+|||++||+ +..+|++||++++|||+|++|+|||+|||||||||+||+.+ ++||+|||+||||||||||||+|++|
T Consensus 87 ~~~~~~~~~~--~~~~~~~~~~~~~aw~~l~~s~v~~~g~pvgtvAa~d~~~~-~lNY~qVFiRDfVpsaLafLl~Ge~e 163 (571)
T PLN02973 87 GRRSGFNTPR--SQPGFESHPMVGEAWDALRRSMVYFRGQPVGTIAAVDNSEE-KLNYDQVFVRDFVPSALAFLMNGEPD 163 (571)
T ss_pred CccccCCCCc--ccccCCCCcHHHHHHHHHHhheEEECCeeeeeeeccCCccc-cccCcchhhhccHHHHHHHHHCCCHH
Confidence 9999999998 46789999999999999999999999999999999999876 89999999999999999999999999
Q ss_pred HHHHHHHHhhhcccceeeecccccCCcccccceeeEE--------e--ecCCc--------------eEEEE--EeecCC
Q 035960 151 IVKNFLLKTLQLQGWEKRIDRFKLGEGAMPASSKFFT--------I--LFGKQ--------------ILLLQ--ILSTGD 204 (256)
Q Consensus 151 IVkNFL~~tL~LQs~ek~iD~f~~g~GvmPASFKV~~--------L--DFGe~--------------iILLr--~k~TgD 204 (256)
||||||++||+||+|||++|+|++|+|+|||||||.+ + |||++ ||||| +|+|||
T Consensus 164 IVrnFl~~TL~lq~~ektld~~q~g~G~mPaSfkv~~~p~~~~e~l~aDfG~~aIGRV~pVDS~LWWIIllraY~k~TgD 243 (571)
T PLN02973 164 IVKNFLLKTLRLQSWEKKIDRFQLGEGVMPASFKVFHDPVRNHETLIADFGESAIGRVAPVDSGFWWIILLRAYTKSTGD 243 (571)
T ss_pred HHHHHHHHHHhhhhhHHHHHhcccCCCCcCceeeecccccCccccccccccccccccccccchhhHHHHHHHHHHHhccc
Confidence 9999999999999999999999999999999999876 3 99996 99999 999999
Q ss_pred CccccChhhhhHHHHHHHHhhccCCCCCcceeecCccccccccccccCCCC
Q 035960 205 LSLAETPECQKGMRLILALCLSEGFDTFPTLLCADGCSMIDRRMVILRDDL 255 (256)
Q Consensus 205 ~sla~~pe~QrGirLIL~LCL~~~Fd~fPTLLvpDG~~MIDRRMGV~G~~~ 255 (256)
.+|+++|||||||+|||+|||+++|||||||+|||||||||||||||||+|
T Consensus 244 ~s~~e~pevQrgi~lil~lcL~~~Fd~~ptLlVpDgs~miDrrMgv~G~pL 294 (571)
T PLN02973 244 SSLADMPECQKGIRLILSLCLSEGFDTFPTLLCADGCCMIDRRMGVYGYPI 294 (571)
T ss_pred hhhhhcHHHHHHHHHHHHHhcccccCCCceEeccCCccccccccccCCccH
Confidence 999999999999999999999999999999999999999999999999997
No 2
>PLN03005 beta-fructofuranosidase
Probab=100.00 E-value=3.1e-97 Score=712.44 Aligned_cols=245 Identities=76% Similarity=1.209 Sum_probs=234.5
Q ss_pred ccccccccCCcccccccccchhhhhccCCCCchhhhcccccchhhhhhccccCCCccCccccc-CCCCCCCCCCCCCCCC
Q 035960 6 EVLGLRNVSSHCSISEMDDYDLSKLLDKPRLNIERQRSFDERSLSELSIGLTRGGVDNYESTY-SPGGRSGFDTPVSSTR 84 (256)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~d~~~ll~~p~~~ier~rs~ders~~el~~~~~~~~~~~~~~~~-sp~~~s~~~tp~~~~~ 84 (256)
|+.++|+++++++++|+|++|++||++||++||||||||||||++|++.+. +++|+++ |||+|||++||+|...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~ 76 (550)
T PLN03005 2 EGLGLRAVGSHCSLSEMDDLDLTRALDKPRLKIERKRSFDERSMSELSTGY-----SRHDGIHDSPRGRSVLDTPLSSAR 76 (550)
T ss_pred CccccccCcccccccccchhhHHHhhcCCccchhhhcccchhhhhhcCccc-----cccccccCCCCcccCCCCCccccc
Confidence 333999999999999999999999999999999999999999999997643 8999988 9999999999997777
Q ss_pred CCCCCChhHHHHHHHHhhcceeecCeeeEEEeecCCCCcccCCCCceeeecchHHHHHHHhcCChhHHHHHHHHhhhccc
Q 035960 85 NSFEPHPMVAEAWEALRRSLVYFRGQPVGTIAAYDHASEEVLNYDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQG 164 (256)
Q Consensus 85 ~~~~~~~~~~eAwe~L~~SlV~~~G~pVGTvAA~D~~~~~aLNYdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs 164 (256)
+.|++||++++|||+|++|+|||+|+|||||||.|++.++++||+|||+||||||||||||+|++|||||||++||+||+
T Consensus 77 ~~~~~~~~~~~a~~~l~~s~v~~~g~pvGtvAA~d~~~~~~lNY~qvF~RDfvpsaLafLl~Ge~eIVrnFl~~~L~Lq~ 156 (550)
T PLN03005 77 NSFEPHPMMAEAWEALRRSMVFFRGQPVGTLAAVDNTTDEVLNYDQVFVRDFVPSALAFLMNGEPDIVKHFLLKTLQLQG 156 (550)
T ss_pred CCCCCCcHHHHHHHHHHhheEEECCccceeeeecCCccccccCCCceeecccHHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 88999999999999999999999999999999999976448999999999999999999999999999999999999999
Q ss_pred ceeeecccccCCcccccceeeEE--------e--ecCCc--------------eEEEE--EeecCCCccccChhhhhHHH
Q 035960 165 WEKRIDRFKLGEGAMPASSKFFT--------I--LFGKQ--------------ILLLQ--ILSTGDLSLAETPECQKGMR 218 (256)
Q Consensus 165 ~ek~iD~f~~g~GvmPASFKV~~--------L--DFGe~--------------iILLr--~k~TgD~sla~~pe~QrGir 218 (256)
|||+||||++|+|+|||||||.+ | |||++ ||||| +|+|||.+|+++|||||||+
T Consensus 157 ~ek~~d~~q~g~G~mPaSfkv~~~p~~~~~~l~aDfG~~aIGRv~pVDS~LWWIIllraY~k~tgD~s~~e~pevQrgi~ 236 (550)
T PLN03005 157 WEKRVDRFKLGEGVMPASFKVLHDPIRETDNIVADFGESAIGRVAPVDSGFWWIILLRAYTKSTGDLTLSETPECQKGMK 236 (550)
T ss_pred hhhhhhcccCCCCCcCceeeecccccCCCccccccccccccccccccchhhHHHHHHHHHHhhccchhhhhChHHHHHHH
Confidence 99999999999999999999876 4 99996 99999 99999999999999999999
Q ss_pred HHHHHhhccCCCCCcceeecCccccccccccccCCCC
Q 035960 219 LILALCLSEGFDTFPTLLCADGCSMIDRRMVILRDDL 255 (256)
Q Consensus 219 LIL~LCL~~~Fd~fPTLLvpDG~~MIDRRMGV~G~~~ 255 (256)
|||+|||+++|||||||+|||||||||||||||||+|
T Consensus 237 lil~lcLa~~Fd~~ptLlvpDgs~miDRrMgv~G~pL 273 (550)
T PLN03005 237 LILSLCLAEGFDTFPTLLCADGCSMIDRRMGVYGYPI 273 (550)
T ss_pred HHHHHhcccccCCCceEeccCCccccccccccCCccH
Confidence 9999999999999999999999999999999999997
No 3
>PF12899 Glyco_hydro_100: Alkaline and neutral invertase; InterPro: IPR024746 This is a family of endo-alpha-N-acetylgalactosaminidases. This is a unique enzyme that hydrolyses core 1-type O-glycan from glycoproteins. The proteins are produced in the gut-flora bacteria from Actinobacteria and Firmicutes [].; GO: 0033926 glycopeptide alpha-N-acetylgalactosaminidase activity
Probab=100.00 E-value=3e-86 Score=624.84 Aligned_cols=161 Identities=66% Similarity=1.121 Sum_probs=158.1
Q ss_pred HHHHHHhhcceeecCeeeEEEeecCCCCcccCCCCceeeecchHHHHHHHhcCChhHHHHHHHHhhhcccceeeeccccc
Q 035960 95 EAWEALRRSLVYFRGQPVGTIAAYDHASEEVLNYDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQGWEKRIDRFKL 174 (256)
Q Consensus 95 eAwe~L~~SlV~~~G~pVGTvAA~D~~~~~aLNYdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs~ek~iD~f~~ 174 (256)
||||+||+|+|||+|+|||||||+||+.+++||||||||||||||||||||+||+|||||||++||+||||||+||||++
T Consensus 1 ~a~~~l~~s~v~~~g~pvGtvAa~d~~~~~~lNY~qvF~RDfvps~l~fL~~g~~eIVrnFL~~tl~Lq~~~~~~d~~~~ 80 (436)
T PF12899_consen 1 EAWELLERSIVYYQGQPVGTVAALDPSAEEALNYDQVFVRDFVPSALAFLMKGEPEIVRNFLLETLQLQSWEKQVDCFKP 80 (436)
T ss_pred ChHHHHhhheEeeCCceeeeeeecCCcccccccccceEeecChHHHHHHHHcCCHHHHHHHHHHHHhhhhhhhhcccccc
Confidence 69999999999999999999999999996699999999999999999999999999999999999999999999999999
Q ss_pred CCcccccceeeEE------e--ecCCc--------------eEEEE--EeecCCCccccChhhhhHHHHHHHHhhccCCC
Q 035960 175 GEGAMPASSKFFT------I--LFGKQ--------------ILLLQ--ILSTGDLSLAETPECQKGMRLILALCLSEGFD 230 (256)
Q Consensus 175 g~GvmPASFKV~~------L--DFGe~--------------iILLr--~k~TgD~sla~~pe~QrGirLIL~LCL~~~Fd 230 (256)
|+|||||||||.+ | ||||+ ||||| +|+|||++|+++||||+||||||+|||+++||
T Consensus 81 g~G~mPaSFkv~~~~~~e~l~aDfGe~AIgRv~pVDs~~WWiillraY~k~tgD~s~~~~~~~Q~gi~liL~lcL~~~Fd 160 (436)
T PF12899_consen 81 GRGVMPASFKVLHENEEETLIADFGERAIGRVAPVDSGLWWIILLRAYVKATGDYSLAESPEVQRGIRLILDLCLADGFD 160 (436)
T ss_pred CCCcccceEEEecCCCCceEecCcchhhhccccCcccccHHHHHHHHHHHHhcchhhhhcHHHHHHHHHHHHHHcccccC
Confidence 9999999999987 4 99999 99999 99999999999999999999999999999999
Q ss_pred CCcceeecCccccccccccccCCCC
Q 035960 231 TFPTLLCADGCSMIDRRMVILRDDL 255 (256)
Q Consensus 231 ~fPTLLvpDG~~MIDRRMGV~G~~~ 255 (256)
|||||||||||||||||||||||||
T Consensus 161 ~~PtLlvpDg~~MiDRrMgv~G~Pl 185 (436)
T PF12899_consen 161 MFPTLLVPDGACMIDRRMGVYGHPL 185 (436)
T ss_pred CCceEEecCCceeecccccccCCcc
Confidence 9999999999999999999999997
No 4
>PLN02703 beta-fructofuranosidase
Probab=100.00 E-value=7.1e-74 Score=555.49 Aligned_cols=191 Identities=50% Similarity=0.822 Sum_probs=174.6
Q ss_pred cCcccccCCCCCCCCCCCCCCCCCCCCCChhHHHHHHHHhhcceeecCeeeEEEeecCCCCcccCCCCceeeecchHHHH
Q 035960 62 DNYESTYSPGGRSGFDTPVSSTRNSFEPHPMVAEAWEALRRSLVYFRGQPVGTIAAYDHASEEVLNYDQVFVRDFVPSAL 141 (256)
Q Consensus 62 ~~~~~~~sp~~~s~~~tp~~~~~~~~~~~~~~~eAwe~L~~SlV~~~G~pVGTvAA~D~~~~~aLNYdqvFvRDFVPSal 141 (256)
..+|.+.+|-..+ .|......+|++||++++||++|++|+|||+|+|||||||.|++.++++||+|||+||||||||
T Consensus 105 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~eA~elL~~s~v~~~g~pvGtvAA~d~~~~~~lNY~qVFiRDfVpsaL 181 (618)
T PLN02703 105 SDLDEMPLPVNGS---FSSNGNAQSVGTKSIEDEAWDLLRQSVVFYCGSPIGTIAANDPSSTSVLNYDQVFIRDFIPSGI 181 (618)
T ss_pred cccccccCcccCc---CCCCCcccccCCChHHHHHHHHHHHhhhhhcCccceeEeccCCccccccCCCceeecccHHHHH
Confidence 5566666663321 1211244579999999999999999999999999999999999874489999999999999999
Q ss_pred HHHhcCChhHHHHHHHHhhhcccceeeecccccCCcccccceeeEE-------------e--ecCCc-------------
Q 035960 142 AFLMNGEPDIVKNFLLKTLQLQGWEKRIDRFKLGEGAMPASSKFFT-------------I--LFGKQ------------- 193 (256)
Q Consensus 142 afLm~Ge~eIVkNFL~~tL~LQs~ek~iD~f~~g~GvmPASFKV~~-------------L--DFGe~------------- 193 (256)
||||+|++|||||||++||+||+|||++|+|++|+|+|||||||.+ | ||||+
T Consensus 182 afLl~Ge~eIVrnFl~~tL~lq~~ektld~~q~g~G~mPaSfkv~~~~~~~~~~~~ee~l~aDfGe~AIgRV~pVDS~LW 261 (618)
T PLN02703 182 AFLLKGEYDIVRNFILYTLQLQSWEKTMDCHSPGQGLMPCSFKVKTVPLDGDDSMTEEVLDPDFGEAAIGRVAPVDSGLW 261 (618)
T ss_pred HHHHCCCHHHHHHHHHHHHhhhhhHHHHHhccCCCCCcCceeeecccccccccccccccccCCcCccceeeeccccchhH
Confidence 9999999999999999999999999999999999999999999876 4 99998
Q ss_pred -eEEEE--EeecCCCccccChhhhhHHHHHHHHhhccCCCCCcceeecCccccccccccccCCCC
Q 035960 194 -ILLLQ--ILSTGDLSLAETPECQKGMRLILALCLSEGFDTFPTLLCADGCSMIDRRMVILRDDL 255 (256)
Q Consensus 194 -iILLr--~k~TgD~sla~~pe~QrGirLIL~LCL~~~Fd~fPTLLvpDG~~MIDRRMGV~G~~~ 255 (256)
||||| +|+|||.+|+++|+||+||||||+|||+++|||||||+|||||||||||||||||+|
T Consensus 262 WIIllraY~k~TgD~sf~e~~~~Q~gI~liL~LcLa~~Fd~fPtLlVpDgs~miDRrMgv~G~PL 326 (618)
T PLN02703 262 WIILLRAYGKCTGDLSVQERVDVQTGIKMILKLCLADGFDMFPTLLVTDGSCMIDRRMGIHGHPL 326 (618)
T ss_pred HHHHHHHHHHhhccHHHhhhhhHHHHHHHHHHHHccCcCCCCceEeccCCCchhccccCcCCccH
Confidence 99999 999999999999999999999999999999999999999999999999999999997
No 5
>TIGR01577 oligosac_amyl oligosaccharide amylase. The name of this type of amylase is based on the characterization of an glucoamylase family enzyme from Thermoactinomyces vulgaris. The T. vulgaris enzyme was expressed in E. coli and, like other glucoamylases, it releases beta-D-glucose from starch. However, unlike previously characterized glucoamylases, this T. vulgaris amylase hydrolyzes maltooligosaccharides (maltotetraose, maltose) more efficiently than starch (PubMed: 11549021), indicating this enzyme belongs to a class of glucoamylase-type enzymes with oligosaccharide-metabolizing activity.
Probab=93.65 E-value=0.09 Score=51.75 Aligned_cols=128 Identities=23% Similarity=0.217 Sum_probs=79.4
Q ss_pred HHHHHHhhcceeec---CeeeE-EEeecCCCCcccC--CCCceeeecchHHHHHHHhcCChhHHHHHHHHhhhcccceee
Q 035960 95 EAWEALRRSLVYFR---GQPVG-TIAAYDHASEEVL--NYDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQGWEKR 168 (256)
Q Consensus 95 eAwe~L~~SlV~~~---G~pVG-TvAA~D~~~~~aL--NYdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs~ek~ 168 (256)
+-|+++++|+...+ .++-| -|||...+....= .|.-||+||.+=+++||+.-|.+|.++.||.-+++.|...-.
T Consensus 253 ~~~~~~~~Sll~Lk~~~~~~~GaiiAs~s~~~~~~~~~~Y~y~W~RD~~~~a~Al~~~G~~~~a~~~l~~l~~~q~~~G~ 332 (616)
T TIGR01577 253 KIYSLYRRSLAVLRLLTDGEYGSMIAAPEFDEDFVRCGGYAYCWGRDASYIATALDRAGYHDRVDRFFRWAMQTQSRDGS 332 (616)
T ss_pred HHHHHHHHHHHHHHhccCCCCCcEEEcCCCCcccccCCCCceeccccHHHHHHHHHHCCCHHHHHHHHHHHHHhhCcCCC
Confidence 77889999966553 12223 4666554321112 399999999999999999999999999999999998864221
Q ss_pred e-cccccCCccccccee-eEEee-cCCceEEEE--EeecCCCccccChhhhhHHHHHHHHhhc
Q 035960 169 I-DRFKLGEGAMPASSK-FFTIL-FGKQILLLQ--ILSTGDLSLAETPECQKGMRLILALCLS 226 (256)
Q Consensus 169 i-D~f~~g~GvmPASFK-V~~LD-FGe~iILLr--~k~TgD~sla~~pe~QrGirLIL~LCL~ 226 (256)
. -.|.+.-+ |.++. -..+| +|+-+..++ .+.|||..|.+ ++...|+.+++.+..
T Consensus 333 ~~~~~~~dG~--~~~~~~~~Q~D~~g~~l~al~~y~~~t~d~~~~~--~~~~~v~~a~~fl~~ 391 (616)
T TIGR01577 333 WQQRYYLNGR--LAPLQWGLQIDETGSILWAMDQHYRLTNDRAFLE--EIWESVQKAAQYLIL 391 (616)
T ss_pred cceEEecCCC--CCCCCCCccccchhHHHHHHHHHHHHHCCHHHHH--HHHHHHHHHHHHHHH
Confidence 0 01111111 12211 01133 666544443 68899988753 345556666666555
No 6
>PF06202 GDE_C: Amylo-alpha-1,6-glucosidase ; InterPro: IPR010401 This family includes human glycogen branching enzyme P35573 from SWISSPROT. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue O93808 from SWISSPROT that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (3.2.1.33 from EC).; GO: 0004135 amylo-alpha-1,6-glucosidase activity, 0005978 glycogen biosynthetic process
Probab=82.92 E-value=0.51 Score=44.01 Aligned_cols=85 Identities=22% Similarity=0.208 Sum_probs=59.8
Q ss_pred CCceeeecchHHH-HHHHhcCChhHHHHHHHHhhhcccceeeecccccCCcccccceeeEEe-ecCCc------eEEEE-
Q 035960 128 YDQVFVRDFVPSA-LAFLMNGEPDIVKNFLLKTLQLQGWEKRIDRFKLGEGAMPASSKFFTI-LFGKQ------ILLLQ- 198 (256)
Q Consensus 128 YdqvFvRDFVPSa-lafLm~Ge~eIVkNFL~~tL~LQs~ek~iD~f~~g~GvmPASFKV~~L-DFGe~------iILLr- 198 (256)
|.. |=||-+=|. =.+|.-|+++..|+.|..-.+.|. .|.||-.|..-+. .||-. ++++.
T Consensus 28 F~~-~GRDt~Isl~gl~l~~~~~~~a~~~L~~~~~~~~-----------~G~ipn~~~~~~~~~Y~s~Dat~wfl~~l~~ 95 (370)
T PF06202_consen 28 FST-WGRDTFISLPGLLLSPGRFEEARNILATFAGTQR-----------HGLIPNELRDGEEPRYNSVDATLWFLIALQE 95 (370)
T ss_pred ccc-cccHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhh-----------cCcccCcccCCCCCCCCCCccHHHHHHHHHH
Confidence 445 999966441 135778999999999987666554 8999998853222 55544 66666
Q ss_pred -EeecCCCccccChhhhhHHHHHHHHhhc
Q 035960 199 -ILSTGDLSLAETPECQKGMRLILALCLS 226 (256)
Q Consensus 199 -~k~TgD~sla~~pe~QrGirLIL~LCL~ 226 (256)
.+.|||.+|. -++...|+-||+-...
T Consensus 96 Y~~~t~D~~~l--~~~~~~i~~il~~~~~ 122 (370)
T PF06202_consen 96 YYRWTGDYSFL--RELYPAIEEILEWYAD 122 (370)
T ss_pred HHHHhCCHHHH--HHHHHHHHHHHHHHHh
Confidence 9999999998 4555666777766543
No 7
>TIGR01535 glucan_glucosid glucan 1,4-alpha-glucosidase. Glucan 1,4-alpha-glucosidase catalyzes the hydrolysis of terminal 1,4-linked alpha-D-glucose residues from non-reducing ends of polysaccharides, releasing a beta-D-glucose monomer. Some forms of this enzyme can hydrolyze terminal 1,6- and 1,3-alpha-D-glucosidic bonds in polysaccharides as well.
Probab=75.66 E-value=3.9 Score=41.92 Aligned_cols=52 Identities=27% Similarity=0.238 Sum_probs=42.3
Q ss_pred EEEeecCCCCcc----cCC--CCceeeecchHHHHHHHhcCChhHHHHHHHHhhhccc
Q 035960 113 GTIAAYDHASEE----VLN--YDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQG 164 (256)
Q Consensus 113 GTvAA~D~~~~~----aLN--YdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs 164 (256)
+-|||...+-.+ .=| |.=|++||.+=++.||+.-|..+..+.|+.-+++.|.
T Consensus 271 AiIAA~Tts~pe~~g~~~n~dYryvW~RD~a~~a~AL~~~G~~~~a~~~~~~l~~~~~ 328 (648)
T TIGR01535 271 AYIASLSIPWGDGQADDNTGGYHLVWPRDLYQVANAFLAAGDVDSALRSLDYLAKVQQ 328 (648)
T ss_pred cEEEecCCCCCccCCCCCCCceEEEehhhHHHHHHHHHHCCCHHHHHHHHHHHHHHhc
Confidence 346776444211 224 9999999999999999999999999999999999987
No 8
>PF00723 Glyco_hydro_15: Glycosyl hydrolases family 15; InterPro: IPR011613 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 15 GH15 from CAZY comprises enzymes with several known activities; glucoamylase (3.2.1.3 from EC); alpha-glucosidase (3.2.1.20 from EC); glucodextranase (3.2.1.70 from EC). Glucoamylase (GA) catalyses the release of D-glucose from the non-reducing ends of starch and other oligo- or poly-saccharides. Studies of fungal GA have indicated 3 closely-clustered acidic residues that play a role in the catalytic mechanism []. This region is also conserved in a recently sequenced bacterial GA []. The 3D structure of the pseudo-tetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4A resolution []. The protein belongs to the mainly-alpha class, and contains 19 helices and 9 strands. This protein is found in higher organisms, and is represented by phosphorylase kinase subunits.; GO: 0004339 glucan 1,4-alpha-glucosidase activity, 0005976 polysaccharide metabolic process; PDB: 1GAI_A 1GAH_A 1LF6_B 1LF9_A 3EQA_A 1AYX_A 2F6D_A 2FBA_A 1DOG_A 1GLM_A ....
Probab=59.09 E-value=11 Score=35.51 Aligned_cols=77 Identities=23% Similarity=0.268 Sum_probs=48.6
Q ss_pred HHHHHhhccee----ecCeeeEEEeecCCCCcccCCCCceeeecchHHHHHHHhcCC------------hh---HHHHHH
Q 035960 96 AWEALRRSLVY----FRGQPVGTIAAYDHASEEVLNYDQVFVRDFVPSALAFLMNGE------------PD---IVKNFL 156 (256)
Q Consensus 96 Awe~L~~SlV~----~~G~pVGTvAA~D~~~~~aLNYdqvFvRDFVPSalafLm~Ge------------~e---IVkNFL 156 (256)
+++++.||+.. +++-.-|.|.|--..+. + +|.=|++||.+=++.+++.-|- .. +.+.||
T Consensus 3 ~~~~~~rs~~~l~l~~~~~~~GaiiAsps~s~-p-dY~y~W~RD~a~~~~al~~~g~~~~~~~~~~~l~~~~~~~~~~~l 80 (448)
T PF00723_consen 3 YLDAVYRSALTLKLLTQEPITGAIIASPSTSL-P-DYRYCWVRDAAYTAYALWALGYRDEARAFFYELEQSLVKLMRGYL 80 (448)
T ss_dssp HHHHHHHTBTTTHTTBTTSSTT-B-S-SSBSS-S-BTCSEEHHHHHHHHHHHHHHT-H--HHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhccCCCCCCeEEeecccCC-C-CCceeecccHHHHHHHHHHhhhhHHHHHHHhhhhHhhhhhhhhhh
Confidence 67777887764 34443676655433222 2 9999999999999999997772 22 334688
Q ss_pred HHhhhcccceeeeccccc
Q 035960 157 LKTLQLQGWEKRIDRFKL 174 (256)
Q Consensus 157 ~~tL~LQs~ek~iD~f~~ 174 (256)
....++|........+..
T Consensus 81 ~~~~~~~~~~~~~~~~~~ 98 (448)
T PF00723_consen 81 QPMYRQQGKVNPSGEFQS 98 (448)
T ss_dssp HHHHHHHTS-BTTB-TTT
T ss_pred hhhhhhcCccCCCccccC
Confidence 888888887554333333
No 9
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=45.17 E-value=17 Score=24.93 Aligned_cols=17 Identities=29% Similarity=0.686 Sum_probs=14.1
Q ss_pred ccChhhhhHHHHHHHHh
Q 035960 208 AETPECQKGMRLILALC 224 (256)
Q Consensus 208 a~~pe~QrGirLIL~LC 224 (256)
-..||+|+|+..++++.
T Consensus 20 l~DpdvqrgL~~ll~~l 36 (42)
T PF07849_consen 20 LRDPDVQRGLGFLLAFL 36 (42)
T ss_pred HcCHHHHHHHHHHHHHH
Confidence 35699999999999864
No 10
>COG3387 SGA1 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]
Probab=41.36 E-value=43 Score=34.23 Aligned_cols=42 Identities=26% Similarity=0.233 Sum_probs=38.8
Q ss_pred CCCceeeecchHHHHHHHhcCChhHHHHHHHHhhhcccceee
Q 035960 127 NYDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQGWEKR 168 (256)
Q Consensus 127 NYdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs~ek~ 168 (256)
.|.-|++||++=+++|++.-|-.+..+.|+.-..++|..+..
T Consensus 281 dY~y~W~RD~~~~~~AL~~~G~~~~a~~~f~~l~~~~~~~~~ 322 (612)
T COG3387 281 DYRYVWPRDASYAALALLAIGYKKEALRFFEFLPDVQTPNGK 322 (612)
T ss_pred CceEEccCcHHHHHHHHHHcCCHHHHHHHHHHHHHhhCCCCc
Confidence 388899999999999999999999999999999999988643
No 11
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=41.16 E-value=39 Score=27.39 Aligned_cols=30 Identities=17% Similarity=0.169 Sum_probs=26.8
Q ss_pred hhHHHHHHHHhhcceeecCeeeEEEeecCC
Q 035960 91 PMVAEAWEALRRSLVYFRGQPVGTIAAYDH 120 (256)
Q Consensus 91 ~~~~eAwe~L~~SlV~~~G~pVGTvAA~D~ 120 (256)
.++++|.+++++|..-|-+.|||.+...+.
T Consensus 2 ~l~~~a~~a~~~ay~PyS~~~vgAa~~~~~ 31 (127)
T TIGR01354 2 KLFKAAQEARKNAYAPYSNFKVGAALLTKD 31 (127)
T ss_pred HHHHHHHHHHHhcCCCcCCCeEEEEEEeCC
Confidence 478999999999999999999999887654
No 12
>PF13657 Couple_hipA: HipA N-terminal domain; PDB: 2WIU_C 3HZI_A 3DNT_B 3FBR_A 3DNU_A 3DNV_A.
Probab=41.12 E-value=15 Score=27.76 Aligned_cols=29 Identities=34% Similarity=0.704 Sum_probs=20.5
Q ss_pred eeecCeeeEEEeecCCCCcccCCCCceeee
Q 035960 105 VYFRGQPVGTIAAYDHASEEVLNYDQVFVR 134 (256)
Q Consensus 105 V~~~G~pVGTvAA~D~~~~~aLNYdqvFvR 134 (256)
|+++|++||+++..+...- ...|++=|++
T Consensus 3 V~~~~~~vG~L~~~~~~~~-~F~Y~~~yl~ 31 (99)
T PF13657_consen 3 VYLNGTPVGTLTRDDGGRY-SFTYDPSYLE 31 (99)
T ss_dssp -EETTEEEEEEEE-TTS-E-EEEE-HHHHH
T ss_pred ceECCEEEEEEEEeCCcEE-EEEECHHHHh
Confidence 8999999999998866533 5888887765
No 13
>PF01315 Ald_Xan_dh_C: Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; InterPro: IPR000674 Aldehyde oxidase (1.2.3.1 from EC) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (1.1.1.204 from EC) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.1.3.22 from EC) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphydryl groups.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1N63_E 1N60_B 1ZXI_E 1N5W_E 1N62_B 1N61_E 3AN1_B 2E3T_A 1WYG_A 2W3R_D ....
Probab=40.75 E-value=19 Score=28.45 Aligned_cols=22 Identities=32% Similarity=0.443 Sum_probs=16.8
Q ss_pred HhhcceeecCeeeEEEeecCCC
Q 035960 100 LRRSLVYFRGQPVGTIAAYDHA 121 (256)
Q Consensus 100 L~~SlV~~~G~pVGTvAA~D~~ 121 (256)
|-..-|.|.||||+-|+|-+..
T Consensus 73 la~~~V~y~GqpVa~VvAet~~ 94 (111)
T PF01315_consen 73 LADDKVRYVGQPVALVVAETRE 94 (111)
T ss_dssp S-SSEESSTT-EEEEEEESSHH
T ss_pred ccCCeEeECCCeEEEEEECCHH
Confidence 3556799999999999998764
No 14
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=40.14 E-value=25 Score=29.24 Aligned_cols=28 Identities=29% Similarity=0.651 Sum_probs=23.1
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCChhHHHHHHHHhhcceeecCeeeEEEeecCC
Q 035960 68 YSPGGRSGFDTPVSSTRNSFEPHPMVAEAWEALRRSLVYFRGQPVGTIAAYDH 120 (256)
Q Consensus 68 ~sp~~~s~~~tp~~~~~~~~~~~~~~~eAwe~L~~SlV~~~G~pVGTvAA~D~ 120 (256)
..+|-+.|+|.| ++|+|++||+|.=.=+
T Consensus 65 ~~~g~k~GinlP-------------------------I~~~g~~iGviGItG~ 92 (135)
T PF05651_consen 65 QYPGVKPGINLP-------------------------IIFNGEVIGVIGITGE 92 (135)
T ss_pred hccCCCcceeee-------------------------EEECCEEEEEEEEecC
Confidence 455788899999 8999999999986633
No 15
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=34.25 E-value=19 Score=30.27 Aligned_cols=12 Identities=42% Similarity=0.905 Sum_probs=10.0
Q ss_pred CCcceee-cCccc
Q 035960 231 TFPTLLC-ADGCS 242 (256)
Q Consensus 231 ~fPTLLv-pDG~~ 242 (256)
+|||+|| |||+-
T Consensus 44 ~Ypv~lV~pDGST 56 (116)
T PF09776_consen 44 LYPVLLVRPDGST 56 (116)
T ss_pred hccEEEEecCCCE
Confidence 7899888 89985
No 16
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=34.25 E-value=35 Score=25.40 Aligned_cols=26 Identities=31% Similarity=0.336 Sum_probs=18.9
Q ss_pred HHHHHHHhhcc---eeecCeeeEEEeecCC
Q 035960 94 AEAWEALRRSL---VYFRGQPVGTIAAYDH 120 (256)
Q Consensus 94 ~eAwe~L~~Sl---V~~~G~pVGTvAA~D~ 120 (256)
..|.|.+...- |+|+|+||= |-.+|.
T Consensus 4 ~RAkeI~~S~~~i~V~Y~G~pV~-Ie~vde 32 (58)
T TIGR02861 4 QRAKEIAASPEMINVTYKGVPVY-IEHVDE 32 (58)
T ss_pred HHHHHHHcCccceEEEECCEEEE-EEEEcC
Confidence 56777777766 999999993 445553
No 17
>KOG1552 consensus Predicted alpha/beta hydrolase [General function prediction only]
Probab=30.69 E-value=39 Score=31.73 Aligned_cols=124 Identities=21% Similarity=0.243 Sum_probs=64.2
Q ss_pred ChhHHHHHHHHhhcc-----eeecCeeeEEEeecCCCCcccCCCCceeeecchHHHHHHHhcCChhHHHHHHHHhhhccc
Q 035960 90 HPMVAEAWEALRRSL-----VYFRGQPVGTIAAYDHASEEVLNYDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQG 164 (256)
Q Consensus 90 ~~~~~eAwe~L~~Sl-----V~~~G~pVGTvAA~D~~~~~aLNYdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs 164 (256)
-.=++.|||.|+..- |..-||.+||+.++|-.+..++ =.=|-...| -|++-.+... +.+-|-.-.-..+.
T Consensus 112 y~Di~avye~Lr~~~g~~~~Iil~G~SiGt~~tv~Lasr~~~-~alVL~SPf-~S~~rv~~~~---~~~~~~~d~f~~i~ 186 (258)
T KOG1552|consen 112 YADIKAVYEWLRNRYGSPERIILYGQSIGTVPTVDLASRYPL-AAVVLHSPF-TSGMRVAFPD---TKTTYCFDAFPNIE 186 (258)
T ss_pred hhhHHHHHHHHHhhcCCCceEEEEEecCCchhhhhHhhcCCc-ceEEEeccc-hhhhhhhccC---cceEEeeccccccC
Confidence 345679999998755 6777999999998876653220 011223333 2344333332 00000000000133
Q ss_pred ceeeecccccCCcccccceeeEE----eec--CCc-------e-EEEEEeecCCCccccChhhhhHHHHHHHHhhc
Q 035960 165 WEKRIDRFKLGEGAMPASSKFFT----ILF--GKQ-------I-LLLQILSTGDLSLAETPECQKGMRLILALCLS 226 (256)
Q Consensus 165 ~ek~iD~f~~g~GvmPASFKV~~----LDF--Ge~-------i-ILLr~k~TgD~sla~~pe~QrGirLIL~LCL~ 226 (256)
+-+.|+| |-.|-.-. +|| |.+ . ==+|+|--|+.++...|+.-.=++-+....+.
T Consensus 187 kI~~i~~--------PVLiiHgtdDevv~~sHg~~Lye~~k~~~epl~v~g~gH~~~~~~~~yi~~l~~f~~~~~~ 254 (258)
T KOG1552|consen 187 KISKITC--------PVLIIHGTDDEVVDFSHGKALYERCKEKVEPLWVKGAGHNDIELYPEYIEHLRRFISSVLP 254 (258)
T ss_pred cceeccC--------CEEEEecccCceecccccHHHHHhccccCCCcEEecCCCcccccCHHHHHHHHHHHHHhcc
Confidence 3444444 44431000 133 222 0 11456788888888888888777777665543
No 18
>COG3408 GDB1 Glycogen debranching enzyme [Carbohydrate transport and metabolism]
Probab=29.50 E-value=24 Score=36.32 Aligned_cols=101 Identities=26% Similarity=0.331 Sum_probs=69.6
Q ss_pred CCceeeecchHHHHHHHhcCChhHHHHHHHHhhhcccceeeecccccCCcccccceeeEEeecCCc----------eEEE
Q 035960 128 YDQVFVRDFVPSALAFLMNGEPDIVKNFLLKTLQLQGWEKRIDRFKLGEGAMPASSKFFTILFGKQ----------ILLL 197 (256)
Q Consensus 128 YdqvFvRDFVPSalafLm~Ge~eIVkNFL~~tL~LQs~ek~iD~f~~g~GvmPASFKV~~LDFGe~----------iILL 197 (256)
|+ +|=||-+=|++.+|+=|++|+.|.=|..-++. .-.|.+|-.| -..+|+..- ++++
T Consensus 282 F~-~fGRD~lIS~lgll~~g~~elArg~L~~~a~~-----------~~~GkIPhe~-~~~~~~~~~Y~tvD~t~~~i~~~ 348 (641)
T COG3408 282 FS-PFGRDTLISALGLLLVGRFELARGTLNTLARY-----------SEPGKIPHEI-LLSIPGEPYYNTVDATPLFIYLL 348 (641)
T ss_pred cc-ccchHHHHHHHHHHhcCCHHHHHHHHHHHHhh-----------ccCCCCcchh-hhcCCCcceeccCCCcHHHHHHH
Confidence 55 99999999999999999999999998888876 2468888887 111133222 5555
Q ss_pred E--EeecCCCccccC--hhhhhHHHHHHHHhhccCCCCCcceeecCccc
Q 035960 198 Q--ILSTGDLSLAET--PECQKGMRLILALCLSEGFDTFPTLLCADGCS 242 (256)
Q Consensus 198 r--~k~TgD~sla~~--pe~QrGirLIL~LCL~~~Fd~fPTLLvpDG~~ 242 (256)
. .+.|||..+.+. |.++..++-|+..-=.. |++.=..+-.+|.+
T Consensus 349 ~~y~~~t~d~~~i~e~~~~v~~a~d~~~~~~~~~-~~~~~~~l~~~~~~ 396 (641)
T COG3408 349 GAYLKYTGDTEFIRELWPSVGAALDWILKGFDFG-FDTYGDGLLEGGSN 396 (641)
T ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHhcCCcc-ceecCcccccCCCC
Confidence 5 899999999764 45555555554432111 66666666665543
No 19
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=27.78 E-value=34 Score=33.13 Aligned_cols=31 Identities=29% Similarity=0.404 Sum_probs=25.8
Q ss_pred hhHHHHHHHHhhcceeecCeeeEEEeec---CCCC
Q 035960 91 PMVAEAWEALRRSLVYFRGQPVGTIAAY---DHAS 122 (256)
Q Consensus 91 ~~~~eAwe~L~~SlV~~~G~pVGTvAA~---D~~~ 122 (256)
.++++.|+.+.+|+|.- |.+||+|||. +|+.
T Consensus 27 ~~l~~i~~ky~~alv~P-GeaVG~IAAQSIGEP~T 60 (367)
T TIGR02389 27 EIIKRVEEEYLRSLIDP-GEAVGIVAAQSIGEPGT 60 (367)
T ss_pred HHHHHHHHHHHHhcCCC-ccccchhhhhhcCCccc
Confidence 46788899999999874 8899999998 6653
No 20
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=27.38 E-value=48 Score=32.05 Aligned_cols=27 Identities=33% Similarity=0.501 Sum_probs=23.2
Q ss_pred hhHHHHHHHHhhcceeecCeeeEEEeec
Q 035960 91 PMVAEAWEALRRSLVYFRGQPVGTIAAY 118 (256)
Q Consensus 91 ~~~~eAwe~L~~SlV~~~G~pVGTvAA~ 118 (256)
.++++-++.+.+|+|. -|.+||+|||.
T Consensus 23 ~~~~~~~~~~~~~~~~-~Ge~vG~iaAQ 49 (363)
T cd06528 23 EIIKEVLREYLRSLIE-PGEAVGIVAAQ 49 (363)
T ss_pred HHHHHHHHHHHHHhhc-cCccccceeee
Confidence 5678888899999986 58899999997
No 21
>COG2427 Uncharacterized conserved protein [Function unknown]
Probab=25.27 E-value=50 Score=27.78 Aligned_cols=15 Identities=27% Similarity=0.784 Sum_probs=13.1
Q ss_pred ChhhhhHHHHHHHHh
Q 035960 210 TPECQKGMRLILALC 224 (256)
Q Consensus 210 ~pe~QrGirLIL~LC 224 (256)
.||+|||++.++++.
T Consensus 125 DPdvq~~Lg~lls~l 139 (148)
T COG2427 125 DPDVQRGLGFLLSIL 139 (148)
T ss_pred CHHHHHHHHHHHHHH
Confidence 499999999999864
No 22
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=25.11 E-value=39 Score=24.96 Aligned_cols=31 Identities=32% Similarity=0.628 Sum_probs=27.1
Q ss_pred ccchhhhhccCCCCchhhhcccccchhhhhh
Q 035960 23 DDYDLSKLLDKPRLNIERQRSFDERSLSELS 53 (256)
Q Consensus 23 ~~~d~~~ll~~p~~~ier~rs~ders~~el~ 53 (256)
+-+|+++|.++|+++-.+--|||-|-++|--
T Consensus 5 epiDLa~lvDd~kvdWd~wvSf~GrPltdev 35 (49)
T PF06543_consen 5 EPIDLADLVDDPKVDWDKWVSFDGRPLTDEV 35 (49)
T ss_pred CcccHHHHcCCcccchHHheeeCCeeCCHHH
Confidence 5689999999999999999999999987653
No 23
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=23.04 E-value=88 Score=22.66 Aligned_cols=17 Identities=35% Similarity=0.643 Sum_probs=15.1
Q ss_pred cceeecCeeeEEEeecC
Q 035960 103 SLVYFRGQPVGTIAAYD 119 (256)
Q Consensus 103 SlV~~~G~pVGTvAA~D 119 (256)
+-|+|+|-.||+|..++
T Consensus 19 s~V~~~Gv~VG~V~~i~ 35 (81)
T PF02470_consen 19 SPVRYRGVEVGKVTSIE 35 (81)
T ss_pred CEEEECCEEEEEEEEEE
Confidence 44999999999999994
No 24
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=22.60 E-value=1.3e+02 Score=17.82 Aligned_cols=26 Identities=15% Similarity=0.281 Sum_probs=22.0
Q ss_pred HHHHHHhcCChhHHHHHHHHhhhccc
Q 035960 139 SALAFLMNGEPDIVKNFLLKTLQLQG 164 (256)
Q Consensus 139 SalafLm~Ge~eIVkNFL~~tL~LQs 164 (256)
-|.+++..|+++-.-..+.++|++.+
T Consensus 7 ~g~~~~~~~~~~~A~~~~~~al~~~p 32 (34)
T PF00515_consen 7 LGNAYFQLGDYEEALEYYQRALELDP 32 (34)
T ss_dssp HHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHhCCchHHHHHHHHHHHHCc
Confidence 47789999999999999999998865
No 25
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=22.52 E-value=1e+02 Score=32.94 Aligned_cols=44 Identities=27% Similarity=0.437 Sum_probs=32.8
Q ss_pred hhHHHHHHHHhhcceeecCeeeEEEeec---CCCCcccCCCCc-eeeec
Q 035960 91 PMVAEAWEALRRSLVYFRGQPVGTIAAY---DHASEEVLNYDQ-VFVRD 135 (256)
Q Consensus 91 ~~~~eAwe~L~~SlV~~~G~pVGTvAA~---D~~~~~aLNYdq-vFvRD 135 (256)
.++.+-++.+.+++|. -|.+||+|||. +|.....+.||+ |.++|
T Consensus 40 ~Il~~I~~~y~~a~ve-pge~vG~~aaqsi~~~~~~~~~~~De~i~v~~ 87 (858)
T PRK14898 40 EIIDEVVSAYLNALVE-PYEAVGIVAAQSIGEPGTQMSLPYDEKIIVKE 87 (858)
T ss_pred HHHHHHHHHHhhCCCC-CCceeeeeeehhcCCCCccccCCCCceEEEec
Confidence 4667777888888887 57799999998 776544688875 44443
Done!