Query 027989
Match_columns 216
No_of_seqs 143 out of 566
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:34:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027989.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027989hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02597 phosphoenolpyruvate c 100.0 3.3E-63 7.1E-68 472.0 17.9 187 22-215 23-238 (555)
2 COG1866 PckA Phosphoenolpyruva 100.0 2.7E-63 5.8E-68 464.0 16.0 188 21-215 7-219 (529)
3 PTZ00311 phosphoenolpyruvate c 100.0 1.2E-61 2.6E-66 463.1 18.7 190 19-215 29-248 (561)
4 TIGR00224 pckA phosphoenolpyru 100.0 2.3E-61 4.9E-66 458.6 18.8 190 19-215 5-225 (532)
5 cd00484 PEPCK_ATP Phosphoenolp 100.0 3.7E-60 8E-65 449.9 17.7 175 34-215 2-201 (508)
6 PRK09344 phosphoenolpyruvate c 100.0 6.9E-57 1.5E-61 429.8 17.4 186 23-215 7-217 (526)
7 PF01293 PEPCK_ATP: Phosphoeno 100.0 3.5E-57 7.6E-62 427.8 13.7 176 33-215 2-202 (466)
8 cd01919 PEPCK Phosphoenolpyruv 100.0 2E-48 4.3E-53 371.7 17.8 176 34-215 2-209 (515)
9 cd00819 PEPCK_GTP Phosphoenolp 62.6 77 0.0017 32.0 10.2 136 70-214 80-228 (579)
10 PF12162 STAT1_TAZ2bind: STAT1 49.6 17 0.00036 21.5 2.0 15 71-85 8-22 (23)
11 PF08563 P53_TAD: P53 transact 35.3 10 0.00022 22.8 -0.4 15 70-84 7-21 (25)
12 PF11323 DUF3125: Protein of u 33.5 14 0.00031 25.6 0.1 27 123-149 2-30 (50)
13 PF05958 tRNA_U5-meth_tr: tRNA 33.0 48 0.001 30.7 3.5 33 72-105 176-208 (352)
14 KOG4069 Uncharacterized conser 30.9 45 0.00097 27.8 2.5 44 71-115 96-140 (154)
15 smart00115 CASc Caspase, inter 30.4 1.4E+02 0.003 26.0 5.7 95 12-111 24-136 (241)
16 PF09550 DUF2376: Conserved hy 30.4 66 0.0014 21.5 2.9 40 27-84 1-40 (43)
17 PF03440 APT: Aerolysin/Pertus 29.9 20 0.00042 27.4 0.3 15 181-197 55-69 (83)
18 cd00032 CASc Caspase, interleu 28.2 1.4E+02 0.0029 26.0 5.3 92 16-109 33-135 (243)
19 PF12091 DUF3567: Protein of u 26.7 71 0.0015 24.5 2.8 49 142-200 8-57 (85)
20 PF02499 DNA_pack_C: Probable 26.6 50 0.0011 31.4 2.4 91 81-184 75-169 (354)
21 PF13137 DUF3983: Protein of u 25.6 32 0.00069 22.1 0.6 11 117-127 22-32 (34)
22 PF11513 TA0956: Thermoplasma 23.5 1.1E+02 0.0025 24.1 3.5 30 169-200 66-95 (110)
23 cd04897 ACT_ACR_3 ACT domain-c 22.8 3E+02 0.0064 20.2 5.5 65 9-91 7-74 (75)
24 PF15603 Imm45: Immunity prote 21.6 3E+02 0.0066 20.7 5.4 38 55-93 34-76 (82)
25 PHA03372 DNA packaging termina 20.4 3.6E+02 0.0079 27.8 7.1 89 81-183 397-488 (668)
No 1
>PLN02597 phosphoenolpyruvate carboxykinase [ATP]
Probab=100.00 E-value=3.3e-63 Score=471.97 Aligned_cols=187 Identities=18% Similarity=0.238 Sum_probs=175.7
Q ss_pred hhhhhCCCCcCcceeecCChHHHHHhh----cccccc-CCceEE--------------EEecCCC-----CC----CcCC
Q 027989 22 WALAGRGVVVNDKAFQNLTTSELQQKG----ATIAES-LSGLPV--------------YVRGNLL-----GG----SSDI 73 (216)
Q Consensus 22 ~~L~~~gi~~~~~v~~Nls~~~L~e~~----eg~l~~-~Gal~v--------------iV~~~~t-----~~----n~pi 73 (216)
..|..+||+. ..+||||++++|+|++ ||.+++ +|||+| ||+++.+ |+ |+||
T Consensus 23 ~~~~~~~~~~-~~v~~nl~~~~Lye~Al~~~eG~l~~~~GaL~v~TGk~TGRSP~DKfIV~d~~t~~~iwWg~g~vN~p~ 101 (555)
T PLN02597 23 IDVSDSGLKF-THVLYNLSPAELYEQAIKYEKGSFITSTGALATLSGAKTGRSPKDKRVVRDETTEDELWWGKGSPNIEM 101 (555)
T ss_pred cccccccCCc-ceEEeCCCHHHHHHHHHHhCCCeEEecCCCEEecCCCcCCCCcccceecCCCCcccceeccCCccCccC
Confidence 4567888887 5899999999999997 998665 999999 9999977 62 7999
Q ss_pred CHHHHHHHHHHHHHHHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCC-CCCeEEEEcCCC
Q 027989 74 SKAQYAKLLKQVTAHLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHD-SCPLTVYVTTSI 152 (216)
Q Consensus 74 s~e~F~~L~~~v~~yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f-~pdfTI~~aP~f 152 (216)
++++|++|++|+++||+++++|||+|+||||||+||++||||||.||||||+|||||||+.+|+++| +|||||||+|+|
T Consensus 102 ~~~~f~~l~~~~~~~l~~~~~lfv~D~~~Gad~~~r~~vRvite~aw~alF~~nmfirP~~~el~~f~~PdftIi~ap~f 181 (555)
T PLN02597 102 DEETFLVNRERAVDYLNSLDKVFVNDQFLNWDPENRIKVRIVSARAYHSLFMHNMCIRPTPEELEDFGTPDFTIYNAGQF 181 (555)
T ss_pred CHHHHHHHHHHHHHHHccCCCEEEEeeeeccCccceeeEEEEeCHHHHHHHHHhcCCCCChHHhccCCCCCEEEEeCCCC
Confidence 9999999999999999986679999999999999999999999999999999999999999999999 999999999999
Q ss_pred CCCCCccCCcCCCCCCeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 153 SPGVVNAVGLRAQGDNGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 153 ~adp~~~~Gt~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
++|| ..|||+| ++||++||++|++|||||+ |+|||||||||+|||+||+||+|||||
T Consensus 182 ~a~~-~~~g~~S---e~~i~in~~~~~~lI~GT~--YaGE~KK~iFs~~~~ll~~rg~l~mHa 238 (555)
T PLN02597 182 PCNR-YTHYMTS---STSIDLNLKRKEMVILGTQ--YAGEMKKGLFSLMHYLMPMRGILSLHS 238 (555)
T ss_pred CCCc-cccCCCC---CcEEEEEccCCeEEEEccc--hhhhhHHHHHHHHHHHHHHCCcEeecC
Confidence 9999 4559999 6999999999999999999 899999999999999999999999997
No 2
>COG1866 PckA Phosphoenolpyruvate carboxykinase (ATP) [Energy production and conversion]
Probab=100.00 E-value=2.7e-63 Score=463.99 Aligned_cols=188 Identities=21% Similarity=0.299 Sum_probs=178.6
Q ss_pred hhhhhhCCCCcCcceeecCChHHHHHhh----ccccccCCceEE--------------EEecCCC-----CC--CcCCCH
Q 027989 21 NWALAGRGVVVNDKAFQNLTTSELQQKG----ATIAESLSGLPV--------------YVRGNLL-----GG--SSDISK 75 (216)
Q Consensus 21 n~~L~~~gi~~~~~v~~Nls~~~L~e~~----eg~l~~~Gal~v--------------iV~~~~t-----~~--n~pis~ 75 (216)
...++.+|+.+...+++||++++|+|++ ||.++++|||+| ||+|+.+ |+ ||||++
T Consensus 7 ~~~~~~~~~~~~~~v~~n~s~~~L~e~~i~~~eg~lt~~Gal~~~TG~~TGRSPkDkfiV~~~~t~~~i~W~~~Nkpi~~ 86 (529)
T COG1866 7 AQELEALGIRDVEDVVYNLSAAQLYEEAIRRGEGVLTATGALRVDTGIYTGRSPKDKFIVRDDSTRDTIWWGTRNKPISP 86 (529)
T ss_pred hhhHHHhcccchHHHHhcCCHHHHHHHHhhcCCCccCCCCceEEecccccCCCCCCceEEecCcccccccccccCccCCH
Confidence 4567889998888999999999999994 999999999999 9999877 65 799999
Q ss_pred HHHHHHHHHHHHHHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCCCCCeEEEEcCCCCCC
Q 027989 76 AQYAKLLKQVTAHLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHDSCPLTVYVTTSISPG 155 (216)
Q Consensus 76 e~F~~L~~~v~~yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f~pdfTI~~aP~f~ad 155 (216)
|.|++|+.+|.+||++ ++|||+|++||||++||++||||||.|||+||+|||||||+.||+.+|+|||||+++|+|+||
T Consensus 87 e~f~~L~~~~~~yl~~-k~lfv~d~~~Ga~~~~~l~vrvvte~Awh~lF~~nlfIrP~~e~l~~~~~dftvin~p~f~~~ 165 (529)
T COG1866 87 ETFDRLKGDVTDYLSG-KDLFVVDGFAGADPDYRLPVRVVTEVAWHALFIRNLFIRPTGEELSTFKPDFTVINAPSFKAD 165 (529)
T ss_pred HHHHHHHHHHHHHhcc-CcEEEEEeeecCCccceeeeEeehhhHHHHHHHHhcccccchhhhccCCCCeEEEeCCcCCCC
Confidence 9999999999999999 579999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccCCcCCCCCCeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 156 VVNAVGLRAQGDNGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 156 p~~~~Gt~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
|. .||+|| |+||++||++|++|||||+ |+|||||||||||||+||++||||||.
T Consensus 166 ~~-~~g~~S---e~~i~~n~~~~~~lIggT~--YaGEMKK~~fs~mnylLP~~~i~~MHc 219 (529)
T COG1866 166 PK-RDGLRS---ETFVAFNFTERIVLIGGTW--YAGEMKKGIFSVMNYLLPLKGILSMHC 219 (529)
T ss_pred hh-hccccc---ccEEEEecccceeeeeccc--hhhhhhhhHHHHhhcccccccccccee
Confidence 84 559999 6999999999999999999 899999999999999999999999995
No 3
>PTZ00311 phosphoenolpyruvate carboxykinase; Provisional
Probab=100.00 E-value=1.2e-61 Score=463.05 Aligned_cols=190 Identities=21% Similarity=0.262 Sum_probs=178.2
Q ss_pred hhhhhhhhCCCCcCcceeecCChHHHHHhh-----ccccccCCceEE--------------EEecCCC-----CC--CcC
Q 027989 19 GLNWALAGRGVVVNDKAFQNLTTSELQQKG-----ATIAESLSGLPV--------------YVRGNLL-----GG--SSD 72 (216)
Q Consensus 19 ~ln~~L~~~gi~~~~~v~~Nls~~~L~e~~-----eg~l~~~Gal~v--------------iV~~~~t-----~~--n~p 72 (216)
.+...|+.+||.+ ..+||||++++|+|++ ||.++++|+|+| ||+++.+ || |+|
T Consensus 29 ~~~~~l~~~g~~~-~~i~~Nl~~~~L~E~al~~~~~g~~t~~GaL~v~TG~~TGRSpkDKfIV~~~~~~d~i~Wg~vN~p 107 (561)
T PTZ00311 29 QLEEELHKLGLHN-TTIHRNLTVPELYEHALKYEKNTSITSTGALCVYSGAKTGRSPKDKRIVKEDSSEDDIWWGKVNIP 107 (561)
T ss_pred hhhccHhhcCCCC-CeEEeCCCHHHHHHHHHhhcCCcEEecCCceEEecCCccCCCCCceEEeCCCCcccccccCccCcc
Confidence 3447778889987 4899999999999996 889999999999 9988766 76 899
Q ss_pred CCHHHHHHHHHHHHHHHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCcccc----CCCCCCeEEEE
Q 027989 73 ISKAQYAKLLKQVTAHLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAV----SHDSCPLTVYV 148 (216)
Q Consensus 73 is~e~F~~L~~~v~~yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el----~~f~pdfTI~~ 148 (216)
|++++|+.|+++|.+||+.++++||+|+||||||+||++||||||.||||||++||||||+.+|+ +.|+||||||+
T Consensus 108 ~~~~~f~~L~~~~~~yl~~~~~lyv~D~~vGaDp~~~l~vRvit~~a~~alF~~nmfirP~~~el~~~~~~f~PdftIi~ 187 (561)
T PTZ00311 108 LSEESFEINKKRAIDYLNTRERLFVVDGYAGWDPKYRLKVRVITTRAYHALFMRNMLIRPTNEELKKFGEDFVPDFTIYN 187 (561)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCEEEEeeeeecCcccceeEEEEecHHHHHHHHHHCCCCCChHHhhccccCCCCCEEEEE
Confidence 99999999999999999765789999999999999999999999999999999999999999999 89999999999
Q ss_pred cCCCCCCCCccCCcCCCCCCeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 149 TTSISPGVVNAVGLRAQGDNGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 149 aP~f~adp~~~~Gt~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
+|+|++||. .|||+| ++||+|||++|++|||||+ |+|||||||||+|||+||+||+|||||
T Consensus 188 ~P~f~a~~~-~~G~~s---e~~i~in~~~~~~lI~GT~--YaGEiKKgiFt~~~~ll~~rg~l~lHa 248 (561)
T PTZ00311 188 AGEFKANRL-IEGVTS---ETSVALNFKRREMVILGTQ--YAGEMKKGILTVMMYLMPKQGVLPLHS 248 (561)
T ss_pred CCCCCCCcc-cCCCCc---ccEEEEEccCCeEEEEccc--chhhhHHHHHHHHHHHHHHCCceeeee
Confidence 999999995 459999 6999999999999999999 899999999999999999999999997
No 4
>TIGR00224 pckA phosphoenolpyruvate carboxykinase (ATP). Involved in the gluconeogenesis pathway. It converts oxaloacetic acid to phosphoenolpyruvate using ATP. Enzyme is a monomer. The reaction is also catalysed by phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) using GTP instead of ATP, described in PROSITE:PDOC00421
Probab=100.00 E-value=2.3e-61 Score=458.58 Aligned_cols=190 Identities=17% Similarity=0.228 Sum_probs=178.7
Q ss_pred hhhhhhhhCCCCcCcceeecCChHHHHHhh---------ccccccCCceEE--------------EEecCCC-----CC-
Q 027989 19 GLNWALAGRGVVVNDKAFQNLTTSELQQKG---------ATIAESLSGLPV--------------YVRGNLL-----GG- 69 (216)
Q Consensus 19 ~ln~~L~~~gi~~~~~v~~Nls~~~L~e~~---------eg~l~~~Gal~v--------------iV~~~~t-----~~- 69 (216)
.+-..|+.+||.+...+||||++++|+|++ ||.++++|||+| ||+++.+ ||
T Consensus 5 ~~~~~l~~~g~~~~~~v~~Nl~~~~L~e~a~~~~~~~~~eg~~t~~Gal~v~TG~~TGRSpkDK~IV~~~~t~~~i~Wg~ 84 (532)
T TIGR00224 5 LTPQELEALGISDVHDIVYNPSYAQLYEEELKPSLTGYEKGVLTSTGAVAVDTGIFTGRSPKDKYIVEDETTKDTIWWGP 84 (532)
T ss_pred hhhhhHHhcCCCCCceEEeCCCHHHHHHHHHhhccccCCCceeccCCceEEecCCeeCCCcCceEEeCCCCcccccccCc
Confidence 445667788898877899999999999995 488999999999 9988877 76
Q ss_pred -CcCCCHHHHHHHHHHHHHHHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCCCCCeEEEE
Q 027989 70 -SSDISKAQYAKLLKQVTAHLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHDSCPLTVYV 148 (216)
Q Consensus 70 -n~pis~e~F~~L~~~v~~yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f~pdfTI~~ 148 (216)
|+||++++|+.|+++|.+||+. +++||+|+||||||+||++||||||+||||||+|||||||+.+|++.|+||||||+
T Consensus 85 vN~p~~~~~f~~L~~~v~~~l~~-~~lyv~D~~~GaDp~~rl~vRvite~AwhalF~~nmfirP~~eel~~fePdftI~~ 163 (532)
T TIGR00224 85 VNKPLSEETWQHLKGLVTRQLSR-KRLFVVDAFCGADPKYRLSVRVVTEVAWQAHFVKNMFIRPTEEELAGFEPDFTVMN 163 (532)
T ss_pred CCcCCCHHHHHHHHHHHHHHhcC-CCEEEEeeeeccCcccceeEEEEEcHHHHHHHHHhhCCCCChHHhccCCCCEEEEe
Confidence 7999999999999999999996 68999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCC-CCCCccCCcCCCCCCeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 149 TTSIS-PGVVNAVGLRAQGDNGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 149 aP~f~-adp~~~~Gt~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
+|+|+ +|| .++|++| ++||++||++|++|||||+ |+|||||||||+|||+||+||+|||||
T Consensus 164 ~p~f~~ad~-~~~g~~S---~~~i~in~~~~~~lI~GT~--YaGEiKKgiFs~~~~ll~~rg~l~lH~ 225 (532)
T TIGR00224 164 GAKFTNPNW-KEQGLNS---ENFVAFNLTERMQLIGGTW--YGGEMKKGMFSMMNYLLPLKGILSMHC 225 (532)
T ss_pred CCCCCCCCc-ccCCCCc---CcEEEEecccCeEEEECcc--hhhhhHHHHHHHHHHHHHhCCeEeecC
Confidence 99999 998 5569999 6999999999999999999 899999999999999999999999997
No 5
>cd00484 PEPCK_ATP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the ATP-dependent groups.
Probab=100.00 E-value=3.7e-60 Score=449.86 Aligned_cols=175 Identities=19% Similarity=0.321 Sum_probs=168.2
Q ss_pred ceeecCChHHHHHhh----ccccccCCceEE--------------EEecCCC-----CC--CcCCCHHHHHHHHHHHHHH
Q 027989 34 KAFQNLTTSELQQKG----ATIAESLSGLPV--------------YVRGNLL-----GG--SSDISKAQYAKLLKQVTAH 88 (216)
Q Consensus 34 ~v~~Nls~~~L~e~~----eg~l~~~Gal~v--------------iV~~~~t-----~~--n~pis~e~F~~L~~~v~~y 88 (216)
++|||||+++|+|+| ||+++++|+|+| ||+++.+ || |+||++++|++|++++.+|
T Consensus 2 ~v~~Nls~~eL~E~A~~~~eg~~t~~GaL~v~TG~~TGRSPkDkfIV~~~~t~~~i~wg~vn~~~~~~~f~~L~~~~~~y 81 (508)
T cd00484 2 HIHHNLSPAELYEEALKRGEGVLTSTGALAVDTGKKTGRSPKDKFIVDEPSSEDDIWWGKVNQPISEETFEILRERAVDY 81 (508)
T ss_pred ccccCCCHHHHHHHHHhCCCCEEecCCCeEeccCCccCCCCCceeEeCCCCccccccccccCcCCCHHHHHHHHHHHHHH
Confidence 579999999999997 999999999999 9988866 76 8999999999999999999
Q ss_pred HcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCCCCCeEEEEcCCCCCCCCccCCcCCCCCC
Q 027989 89 LSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHDSCPLTVYVTTSISPGVVNAVGLRAQGDN 168 (216)
Q Consensus 89 L~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f~pdfTI~~aP~f~adp~~~~Gt~Se~~e 168 (216)
|++ ++|||+|+||||||+||++||||||.||||||++||||||+.+|+++|.||||||++|+|++|| ..|||+| +
T Consensus 82 l~~-~~lyv~D~~vGadp~~r~~vRvi~~~a~~alF~~nmfi~P~~eel~~f~pdftI~~~P~f~~~~-~~~G~~s---~ 156 (508)
T cd00484 82 LNT-KKLFVFDGFAGADPEYRLKVRVITERAWHALFMRNMFIRPTEEELENFGPDFTIYNAPKFKANP-ETDGMNS---E 156 (508)
T ss_pred hcC-CCEEEEeeeeecCcccceeeEEEECHHHHHHHHHhCCCCCChHHhccCCcCEEEEECCCCcCCc-cccCCCc---c
Confidence 999 5799999999999999999999999999999999999999999999999999999999999999 5559999 6
Q ss_pred eEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 169 GFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 169 ~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
+||++||++|++|||||+ |+|||||||||+|||+||+||+|||||
T Consensus 157 ~~iiin~~~~~~lI~GT~--YaGEiKKgif~~~~~ll~~~g~l~lH~ 201 (508)
T cd00484 157 TFVIINFAEREMVIGGTE--YAGEMKKGIFSVMNYLLPKKGVLSMHC 201 (508)
T ss_pred cEEEEEccCCeEEEECcc--chhhhHHHHHHHHHHHHHhCCcEeecc
Confidence 999999999999999999 899999999999999999999999997
No 6
>PRK09344 phosphoenolpyruvate carboxykinase; Provisional
Probab=100.00 E-value=6.9e-57 Score=429.76 Aligned_cols=186 Identities=21% Similarity=0.295 Sum_probs=178.0
Q ss_pred hhhhCCCCcCcceeecCChHHHHHhh----ccccccCCceEE--------------EEecCCC-----CC--CcCCCHHH
Q 027989 23 ALAGRGVVVNDKAFQNLTTSELQQKG----ATIAESLSGLPV--------------YVRGNLL-----GG--SSDISKAQ 77 (216)
Q Consensus 23 ~L~~~gi~~~~~v~~Nls~~~L~e~~----eg~l~~~Gal~v--------------iV~~~~t-----~~--n~pis~e~ 77 (216)
.|+.+||.+..++||||++++|+|++ ||.++++|+|+| ||+|+.+ |+ |+||++++
T Consensus 7 ~l~~~g~~~~~~i~~n~~~~~L~e~a~~~~~g~~t~~Gal~~~tG~~tGRSp~dk~iV~~~~~~~~i~wg~~n~~~~~~~ 86 (526)
T PRK09344 7 DLEAYGITNLSNVHYNLSYAELYEEALRRGEGVLTDTGALAVDTGKFTGRSPKDKFIVRDPSTEDTIWWGDDNKPISPEK 86 (526)
T ss_pred chhhcCCCCcceeEeCCCHHHHHHHHHHcCCCeeccCCceEEecCCccCCCcCceeeecCccccccccccccCCCCCHHH
Confidence 37889999888999999999999997 899999999999 9998877 76 89999999
Q ss_pred HHHHHHHHHHHHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCCCCCeEEEEcCCCCCCCC
Q 027989 78 YAKLLKQVTAHLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHDSCPLTVYVTTSISPGVV 157 (216)
Q Consensus 78 F~~L~~~v~~yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f~pdfTI~~aP~f~adp~ 157 (216)
|++|++++.+||+++ ++||+|+|||+||+||++||||||+|||+||++|||+||+.+|++.|+||||||++|+|+++|
T Consensus 87 f~~l~~~~~~~l~~~-~lyv~d~~vG~d~~~~~~vrvi~~~a~~~lf~~nlf~~p~~~e~~~~~Pd~~ii~~p~~~~~~- 164 (526)
T PRK09344 87 FDALKQKVLAYLSGK-DLFVVDGFAGADPEYRLPVRVITELAWHALFVRNLFIRPSEEELASFEPDFTIINAPKFKADP- 164 (526)
T ss_pred HHHHHHHHHHHhcCC-cEEEEeeeecCChhHeeeEEEEecHHHHHHHHhhcCCCCChhHhccCCCCEEEEEcCCCCCCc-
Confidence 999999999999995 899999999999999999999999999999999999999999999999999999999999997
Q ss_pred ccCCcCCCCCCeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 158 NAVGLRAQGDNGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 158 ~~~Gt~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
..||++| ++||++||++|.++||||+ |+|||||++||+|||+||.||+||||+
T Consensus 165 ~~~g~~s---~~~i~~~~~~~~~~I~Gt~--Y~GE~KK~~lt~~~~~l~~rg~l~lH~ 217 (526)
T PRK09344 165 ERDGTNS---ETFIAINFTERIVLIGGTD--YAGEMKKSIFSVMNYLLPLKGVLPMHC 217 (526)
T ss_pred cccCCCC---CceEEEecccCeEEEEcch--hHHHHHHHHHHHHHHHHHHCCcEeeeC
Confidence 6669999 6999999999999999999 899999999999999999999999997
No 7
>PF01293 PEPCK_ATP: Phosphoenolpyruvate carboxykinase The Prosite pattern is specific to the ATP binding region; InterPro: IPR001272 Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the first committed (rate-limiting) step in hepatic gluconeogenesis, namely the reversible decarboxylation of oxaloacetate to phosphoenolpyruvate (PEP) and carbon dioxide, using either ATP or GTP as a source of phosphate. The ATP-utilising (4.1.1.49 from EC) and GTP-utilising (4.1.1.32 from EC) enzymes form two divergent subfamilies, which have little sequence similarity but which retain conserved active site residues. ATP-utilising PEPCKs are monomers or oligomers of identical subunits found in certain bacteria, yeast, trypanosomatids, and plants, while GTP-utilising PEPCKs are mainly monomers found in animals and some bacteria []. Both require divalent cations for activity, such as magnesium or manganese. One cation interacts with the enzyme at metal binding site 1 to elicit activation, while the second cation interacts at metal binding site 2 to serve as a metal-nucleotide substrate. In bacteria, fungi and plants, PEPCK is involved in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle. PEPCK helps to regulate blood glucose levels. The rate of gluconeogenesis can be controlled through transcriptional regulation of the PEPCK gene by cAMP (the mediator of glucagon and catecholamines), glucocorticoids and insulin. In general, PEPCK expression is induced by glucagon, catecholamines and glucocorticoids during periods of fasting and in response to stress, but is inhibited by (glucose-induced) insulin upon feeding []. With type II diabetes, this regulation system can fail, resulting in increased gluconeogenesis that in turn raises glucose levels []. PEPCK consists of an N-terminal and a catalytic C-terminal domain, with the active site and metal ions located in a cleft between them. Both domains have an alpha/beta topology that is partly similar to one another [, ]. Substrate binding causes PEPCK to undergo a conformational change, which accelerates catalysis by forcing bulk solvent molecules out of the active site []. PCK uses an alpha/beta/alpha motif for nucleotide binding, this motif differing from other kinase domains. GTP-utilising PEPCK has a PEP-binding domain and two kinase motifs to bind GTP and magnesium. This entry represents ATP-utilising phosphoenolpyruvate carboxykinase enzymes.; GO: 0004612 phosphoenolpyruvate carboxykinase (ATP) activity, 0005524 ATP binding, 0006094 gluconeogenesis; PDB: 2PY7_X 2OLR_A 1AYL_A 1K3D_A 1OEN_A 1AQ2_A 1OS1_A 2OLQ_A 1K3C_A 2PXZ_X ....
Probab=100.00 E-value=3.5e-57 Score=427.82 Aligned_cols=176 Identities=24% Similarity=0.350 Sum_probs=153.1
Q ss_pred cceeecCChHHHHHhh----ccccccCCceEE--------------EEecCCC-----CC--CcCCCHHHHHHHHHHHHH
Q 027989 33 DKAFQNLTTSELQQKG----ATIAESLSGLPV--------------YVRGNLL-----GG--SSDISKAQYAKLLKQVTA 87 (216)
Q Consensus 33 ~~v~~Nls~~~L~e~~----eg~l~~~Gal~v--------------iV~~~~t-----~~--n~pis~e~F~~L~~~v~~ 87 (216)
.++|||||+++|+|+| ||.++++|||+| ||+++.+ |+ |+||++++|++|+++|.+
T Consensus 2 ~~v~~Nls~~~L~e~a~~~~eg~lt~~Gal~v~tG~~TGRSp~dkfIV~~~~~~~~v~Wg~~n~~i~~e~f~~L~~~v~~ 81 (466)
T PF01293_consen 2 ANVYRNLSPPELYEEAIKRGEGVLTKTGALVVNTGKFTGRSPKDKFIVDEPGTEDKVWWGSVNQPISEEQFEKLLERVVD 81 (466)
T ss_dssp SEEEES--HHHHHHHHCHTTTEEE-TTSSEEE--TT-SSB-GGGEEEE-STTTTTTS-BTTSBEEE-HHHHHHHHHHHHH
T ss_pred CeeEeCCCHHHHHHHHHhcCCCEEccCCCEEEeCCCccCCCCCceEEecCCccccccccccCCcccCHHHHHHHHHHHHH
Confidence 4789999999999997 999999999999 9998877 76 799999999999999999
Q ss_pred HHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCCCCCeEEEEcCCCCCCCCccCCcCCCCC
Q 027989 88 HLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHDSCPLTVYVTTSISPGVVNAVGLRAQGD 167 (216)
Q Consensus 88 yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f~pdfTI~~aP~f~adp~~~~Gt~Se~~ 167 (216)
||+++ +|||+|+||||||+||++||||||.||||||++|||+||+.+|+.+|+|||||+++|+|++||+.+ |++|
T Consensus 82 yL~~k-~lyv~D~~vG~d~~~~~~vRvit~~a~~aLF~~nL~~~p~~~e~~~f~pd~tI~~~p~f~~~p~~~-g~~s--- 156 (466)
T PF01293_consen 82 YLSTK-ELYVQDGYVGADPDYRIKVRVITERAWHALFARNLFIRPPPEELQNFEPDFTIINAPDFKADPEID-GTNS--- 156 (466)
T ss_dssp HHTTS-EEEEEEEEESSSTTT-EEEEEEESSHHHHHHHHHHSB-GSHHHHHT-S-SEEEEEETTS--TTCHC-T-SS---
T ss_pred Hhccc-ceEEEEEEEecCHHHceeEEEEeCcHHHHHHHHHhhcCCChhHhcccCCCEEEEeCCccccCCCcC-CCCC---
Confidence 99995 999999999999999999999999999999999999999999999999999999999999999666 9999
Q ss_pred CeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 168 NGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 168 e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
++||++|+++|++||+||+ |+|||||++||+|||+||.+|+||||+
T Consensus 157 ~~~i~~d~~~~~~vI~Gt~--Y~GEiKK~ift~~n~ll~~~g~l~mH~ 202 (466)
T PF01293_consen 157 DTFIIFDFERNVAVILGTR--YAGEIKKGIFTVMNYLLPRNGVLPMHC 202 (466)
T ss_dssp S-EEEEETTTTEEEEES-----THHHHHHHHHHHHHHHHHTT-EEEEE
T ss_pred CcEEEEccccCeEEEECCc--ccccchHHHHHHHHHhhHhcCeEEEEe
Confidence 6999999999999999999 899999999999999999999999997
No 8
>cd01919 PEPCK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).
Probab=100.00 E-value=2e-48 Score=371.70 Aligned_cols=176 Identities=16% Similarity=0.137 Sum_probs=165.5
Q ss_pred ceeecCChHHHHHhh-----ccccccCCceEE--------------EEecCCC----C-------CCcCCCHHHHHHHHH
Q 027989 34 KAFQNLTTSELQQKG-----ATIAESLSGLPV--------------YVRGNLL----G-------GSSDISKAQYAKLLK 83 (216)
Q Consensus 34 ~v~~Nls~~~L~e~~-----eg~l~~~Gal~v--------------iV~~~~t----~-------~n~pis~e~F~~L~~ 83 (216)
.+|||+++++|+|++ ||+++++|+|+| ||+++.+ | -|+++++++|++|++
T Consensus 2 ~v~~n~~~~~L~e~~~~~~g~~~~~~~g~l~~~tg~~tgRsp~dkfIv~~~~~~~~~~w~~~w~~~N~~~~~~~~~~~~~ 81 (515)
T cd01919 2 HIHINDENGRLLQQMLEEYGILRLTKNGALAVTDPRDTGRSPSDKVIVTQDQRRTVPIPKTGLSQLNRWLSEEDFEKAFN 81 (515)
T ss_pred ceEECCCHHHHHHHHHHhcCCEEECCCceEEECCCCccccCCCceEEeCCCccccCccccccccccCCCCCHHHHHHHHH
Confidence 589999999999994 678999999999 8987766 2 389999999999999
Q ss_pred HHHHHH-cCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCccccCCC-CCCeEEEEcCCCCCCCCccCC
Q 027989 84 QVTAHL-SSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPSRAVSHD-SCPLTVYVTTSISPGVVNAVG 161 (216)
Q Consensus 84 ~v~~yL-~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~~el~~f-~pdfTI~~aP~f~adp~~~~G 161 (216)
++.+|+ ++ +++||+|+++|+||.||+++|+|||+|||+||+|||||||+.+|++.| +|+|||||+|+|++||...+|
T Consensus 82 ~~~~~~m~g-r~myV~d~~~G~~~~~~~~~r~it~~ay~~lf~~~m~~~p~~~~l~~~~~p~~~ii~~~g~~~~~~~w~g 160 (515)
T cd01919 82 ARFPGLMKG-RTLFVVDFFMGPGSPLRLIVRELTDSPYVAAFMRIMTIMPTDEELAAFGDPDVKCLNSVGCPLPLQKWPG 160 (515)
T ss_pred HHHHHHhcC-CCEEEEeceECCCCcccccEEEEEChHHHHHHHHHhccCCChHHHhhCCCCCEEEEeCCCCcCCccCCCC
Confidence 999999 77 689999999999999999999999999999999999999998999999 699999999999999966469
Q ss_pred cCCCCCCeEEEEecccCeEEEecCCCCccchhhhHHHHhhhhccccCCcccccC
Q 027989 162 LRAQGDNGFIAADIERSSLILCGKGFSDANGVKEALAALSGPVIIARGGLLLCA 215 (216)
Q Consensus 162 t~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsvmNylLP~~gvlpm~~ 215 (216)
++| ++||++|+++|+|+|+||+ |+|||||++|++|||++|++|+||||+
T Consensus 161 ~~s---~~~I~~~~~~~~i~i~Gt~--Y~Ge~KK~~l~~~~~l~~~~g~L~~H~ 209 (515)
T cd01919 161 LPS---LTLVAHNPDRREQIIFGTG--YGGEMKKGFLRMMSRLAPEEGWLAMHM 209 (515)
T ss_pred CCC---CcEEEEEcccCEEEEecCc--cccchHHHHHHHHHHHHHhcCceeeec
Confidence 999 6999999999999999999 899999999999999999999999997
No 9
>cd00819 PEPCK_GTP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the GTP-dependent group.
Probab=62.56 E-value=77 Score=32.05 Aligned_cols=136 Identities=13% Similarity=0.122 Sum_probs=86.2
Q ss_pred CcCCCHHHH-HHHHHHHHHHHcCCCceEeEeeeecC--CcCCcceEEEEcchhhhHHhhhhcCCCCC--ccccC--CCCC
Q 027989 70 SSDISKAQY-AKLLKQVTAHLSSIANVFVQDGAVGS--SSECDAKVRVISDSPSAVLKLSSILWKTP--SRAVS--HDSC 142 (216)
Q Consensus 70 n~pis~e~F-~~L~~~v~~yL~~~~~lyV~D~~aGa--d~~~rl~VRvIte~AwhaLF~~nmfirp~--~~el~--~f~p 142 (216)
|+-++++.+ ..|.+.+..=+++ +.+||.=-.-|- +|-..+.|- ||++||-.+=+|-|...=. -+.+. .|.
T Consensus 80 nnw~~p~e~~~~l~~lf~G~M~G-RTMYVipfsmGP~gSp~s~~gVq-iTDS~YVv~sm~imtR~g~~vl~~lg~~~Fv- 156 (579)
T cd00819 80 NNWMDPEEMKAELKELFKGCMRG-RTMYVIPFSMGPLGSPISKIGVE-LTDSPYVVHSMRIMTRMGKAVLDALGEGEFV- 156 (579)
T ss_pred cccCCHHHHHHHHHhhCCcccCC-CeEEEEeeecCCCCCCcccceEE-EeCCHHHHHhHHHHHhcCHHHHHhcCcCCee-
Confidence 678999887 4455555666678 689999766665 455566665 6999998887766653221 12222 232
Q ss_pred CeEEEEcCCCCCCCCccC--CcCCCCCCeEEEEecccCeEEEecCCCCccchh---hhHH-HHhhhhccccCCccccc
Q 027989 143 PLTVYVTTSISPGVVNAV--GLRAQGDNGFIAADIERSSLILCGKGFSDANGV---KEAL-AALSGPVIIARGGLLLC 214 (216)
Q Consensus 143 dfTI~~aP~f~adp~~~~--Gt~Se~~e~fiiinf~~r~ilIgGT~Y~YaGEi---KKsi-FsvmNylLP~~gvlpm~ 214 (216)
.-+|+-+..-.+-+.+ =++-+ ...|+.+-+.+.|..-||+ |+|.- ||.. .-+-.++-=++|-|..|
T Consensus 157 --~~vHSvG~pl~~~~~~~wpcn~~--~~~I~h~pe~~~I~S~gSg--YGGNaLlgKKcfaLRiAs~~ar~eGWLAEH 228 (579)
T cd00819 157 --PCLHSVGAPLSAGQKDVWPCNPE--KKYIVHFPEEREIWSFGSG--YGGNALLGKKCFALRIASVMARDEGWLAEH 228 (579)
T ss_pred --eeeccCCCcCCCCCCCCCCCCCC--ccEEEEEcCCCeEEEecCC--cCCCcccchhHHHHHHHHHHhHhcCcHHHh
Confidence 3445444322221111 01222 3799999999999999999 79999 9987 55555554456666544
No 10
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=49.63 E-value=17 Score=21.48 Aligned_cols=15 Identities=27% Similarity=0.392 Sum_probs=10.0
Q ss_pred cCCCHHHHHHHHHHH
Q 027989 71 SDISKAQYAKLLKQV 85 (216)
Q Consensus 71 ~pis~e~F~~L~~~v 85 (216)
-|+||+.|+.|.+-|
T Consensus 8 mPMSPddy~~l~~~V 22 (23)
T PF12162_consen 8 MPMSPDDYDELERMV 22 (23)
T ss_dssp --S-HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHhh
Confidence 699999999987644
No 11
>PF08563 P53_TAD: P53 transactivation motif; InterPro: IPR013872 The binding of this protein by regulatory proteins regulates p53 transcription activation. This entry is comprised of a single amphipathic alpha helix and contains a highly conserved motif [, ]. ; GO: 0005515 protein binding; PDB: 1YCQ_B 2Z5T_R 3DAB_B 3DAC_B 2Z5S_Q 2K8F_B 2L14_B 1YCR_B.
Probab=35.33 E-value=10 Score=22.82 Aligned_cols=15 Identities=13% Similarity=0.293 Sum_probs=9.7
Q ss_pred CcCCCHHHHHHHHHH
Q 027989 70 SSDISKAQYAKLLKQ 84 (216)
Q Consensus 70 n~pis~e~F~~L~~~ 84 (216)
+.|+|.|+|..|++-
T Consensus 7 ~~PLSQeTF~~LW~~ 21 (25)
T PF08563_consen 7 ELPLSQETFSDLWNL 21 (25)
T ss_dssp ----STCCHHHHHHT
T ss_pred CCCccHHHHHHHHHh
Confidence 579999999999864
No 12
>PF11323 DUF3125: Protein of unknown function (DUF3125); InterPro: IPR021472 This family of proteins with unknown function appears to be restricted to Staphylococcus.
Probab=33.52 E-value=14 Score=25.58 Aligned_cols=27 Identities=0% Similarity=-0.034 Sum_probs=20.5
Q ss_pred HhhhhcCCCCCcc--ccCCCCCCeEEEEc
Q 027989 123 LKLSSILWKTPSR--AVSHDSCPLTVYVT 149 (216)
Q Consensus 123 LF~~nmfirp~~~--el~~f~pdfTI~~a 149 (216)
.|.+|||.+|++. -..+++-.|.++-+
T Consensus 2 ifsQnLfr~~~p~~~~~~~~e~~fS~Lga 30 (50)
T PF11323_consen 2 IFSQNLFRCPTPTCIVCRNWESNFSMLGA 30 (50)
T ss_pred ccccccccCCCCceeeeeeecccchhhcc
Confidence 4788999999877 66677777777754
No 13
>PF05958 tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferase; InterPro: IPR010280 This family consists of (uracil-5-)-methyltransferases 2.1.1.35 from EC from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity []. This protein family also contains the 23SrRNA methyltransferases, first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA [].; GO: 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 2VS1_A 2JJQ_A 2BH2_A 1UWV_A 3BT7_B.
Probab=32.97 E-value=48 Score=30.66 Aligned_cols=33 Identities=24% Similarity=0.171 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHHHcCCCceEeEeeeecCC
Q 027989 72 DISKAQYAKLLKQVTAHLSSIANVFVQDGAVGSS 105 (216)
Q Consensus 72 pis~e~F~~L~~~v~~yL~~~~~lyV~D~~aGad 105 (216)
-+.+++.++|++.+.++|..+++ -|.|+|||.-
T Consensus 176 QvN~~~~~~l~~~~~~~l~~~~~-~vlDlycG~G 208 (352)
T PF05958_consen 176 QVNPEQNEKLYEQALEWLDLSKG-DVLDLYCGVG 208 (352)
T ss_dssp -SBHHHHHHHHHHHHHHCTT-TT-EEEEES-TTT
T ss_pred cCcHHHHHHHHHHHHHHhhcCCC-cEEEEeecCC
Confidence 45667889999999999987655 4789999975
No 14
>KOG4069 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.87 E-value=45 Score=27.79 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=36.1
Q ss_pred cCCCHHHHHHHHHHHHHHHcCC-CceEeEeeeecCCcCCcceEEEE
Q 027989 71 SDISKAQYAKLLKQVTAHLSSI-ANVFVQDGAVGSSSECDAKVRVI 115 (216)
Q Consensus 71 ~pis~e~F~~L~~~v~~yL~~~-~~lyV~D~~aGad~~~rl~VRvI 115 (216)
-.+++.+|++-++++..||+.+ +++|-.-|+-=-||-+| .+|||
T Consensus 96 y~ctethYek~L~klskfl~~qNe~IY~~~Gl~l~dP~eR-GLRVi 140 (154)
T KOG4069|consen 96 YACTETHYEKKLDKLSKFLNRQNEEIYHHVGLHLRDPMER-GLRVI 140 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhccccceeecCchhh-ceEEE
Confidence 3678889999999999999765 57999888888888776 46665
No 15
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=30.45 E-value=1.4e+02 Score=26.03 Aligned_cols=95 Identities=13% Similarity=0.105 Sum_probs=56.7
Q ss_pred CCCC---ccchhhhhhhhCCCCcCcceeecCChHHHHHhh--ccc---cccCCceEEEEecCCC-----CC-CcCCCHHH
Q 027989 12 PGRA---FSYGLNWALAGRGVVVNDKAFQNLTTSELQQKG--ATI---AESLSGLPVYVRGNLL-----GG-SSDISKAQ 77 (216)
Q Consensus 12 ~~~g---~~y~ln~~L~~~gi~~~~~v~~Nls~~~L~e~~--eg~---l~~~Gal~viV~~~~t-----~~-n~pis~e~ 77 (216)
.|.| |.-+|...|+++|... .++.|++..++.+.- .+. .+..-.++|++=.... +. .++++-+.
T Consensus 24 ~r~g~~~D~~~l~~~f~~lgF~V--~~~~dlt~~em~~~l~~~~~~~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~ 101 (241)
T smart00115 24 RRNGTDVDAENLTELFQSLGYEV--HVKNNLTAEEMLEELKEFAERPEHSDSDSFVCVLLSHGEEGGIYGTDHSPLPLDE 101 (241)
T ss_pred CCCCcHHHHHHHHHHHHHCCCEE--EEecCCCHHHHHHHHHHHHhccccCCCCEEEEEEcCCCCCCeEEEecCCEEEHHH
Confidence 4555 5567888899999975 679999999888873 222 1122234443211111 11 24555543
Q ss_pred HHHHHHHHH----HHHcCCCceEeEeeeecCCcCCcce
Q 027989 78 YAKLLKQVT----AHLSSIANVFVQDGAVGSSSECDAK 111 (216)
Q Consensus 78 F~~L~~~v~----~yL~~~~~lyV~D~~aGad~~~rl~ 111 (216)
|++.+. .-|.++.+||+.|+.=|..-.....
T Consensus 102 ---i~~~f~~~~c~~L~~kPKlffiqACRg~~~~~g~~ 136 (241)
T smart00115 102 ---IFSLFNGDNCPSLAGKPKLFFIQACRGDELDGGVP 136 (241)
T ss_pred ---HHHhccccCChhhcCCCcEEEEeCCCCCCCCCCee
Confidence 444332 3577778999999988875544443
No 16
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=30.39 E-value=66 Score=21.50 Aligned_cols=40 Identities=23% Similarity=0.395 Sum_probs=25.4
Q ss_pred CCCCcCcceeecCChHHHHHhhccccccCCceEEEEecCCCCCCcCCCHHHHHHHHHH
Q 027989 27 RGVVVNDKAFQNLTTSELQQKGATIAESLSGLPVYVRGNLLGGSSDISKAQYAKLLKQ 84 (216)
Q Consensus 27 ~gi~~~~~v~~Nls~~~L~e~~eg~l~~~Gal~viV~~~~t~~n~pis~e~F~~L~~~ 84 (216)
+|+.+ ..||.+++.|| ..-.|... +..|++.+..++|.++
T Consensus 1 Lgl~P--~~FW~lTP~El-~a~~g~~~---------------~~~pl~R~~L~~Lm~~ 40 (43)
T PF09550_consen 1 LGLSP--EEFWRLTPAEL-RAMLGADA---------------GAAPLDRAELDALMRR 40 (43)
T ss_pred CCCCH--HHHHhcCHHHH-HHhcCccc---------------CCCCCCHHHHHHHHHH
Confidence 35555 56999999999 43233211 1367777777777654
No 17
>PF03440 APT: Aerolysin/Pertussis toxin (APT) domain; InterPro: IPR005138 This is the N-terminal domain of aerolysin and pertussis toxin which contains a type-C lectin like fold. Aerolysin causes the pathogenicity of Aeromonas hydrophila, a bacterium associated with diarrhoeal diseases and deep wound infections. Like many other microbial toxins, the protein changes in a multistep process from a completely water-soluble form to produce a transmembrane channel that breaks the permeability barrier of cells []. Pertussis toxin is a major virulence factor of Bordetella pertussis, which causes whooping cough. The protein is a hexamer containing a catalytic subunit (S1) that is tightly associated with a pentameric cell-binding component (B-oligomer). ATP, detergents and phospholipids assist in activating the holotoxin by destabilising the interaction between S1 and the B-oligomer []. Pertussis toxin is an exotoxin and is an essential component of acellular vaccines [, ]. The catalytic A-subunit (S1) shares structural homology with other ADP-ribosylating bacterial toxins, although differences in the carboxy-terminal portion explain its unique activation mechanism []. The diverse biological activities of the toxin depend on its ability to recognise carbohydrate-containing receptors on a wide variety of eukaryotic cells.; GO: 0005488 binding, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1PTO_I 1BCP_C 1PRT_C 3G4N_B 3C0N_B 3C0O_B 1PRE_A 1Z52_B 3C0M_A 3G4O_A ....
Probab=29.94 E-value=20 Score=27.41 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=9.8
Q ss_pred EEecCCCCccchhhhHH
Q 027989 181 ILCGKGFSDANGVKEAL 197 (216)
Q Consensus 181 lIgGT~Y~YaGEiKKsi 197 (216)
+|-|.+ |.||||-+-
T Consensus 55 vimG~g--Y~G~IK~~~ 69 (83)
T PF03440_consen 55 VIMGSG--YNGEIKQGR 69 (83)
T ss_dssp EEE-GG--GTSEEEE--
T ss_pred EEECCc--cCcEeccCC
Confidence 466888 799999764
No 18
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=28.21 E-value=1.4e+02 Score=25.96 Aligned_cols=92 Identities=13% Similarity=0.126 Sum_probs=54.4
Q ss_pred ccchhhhhhhhCCCCcCcceeecCChHHHHHhh----ccccccCCceEEEEecCCC-----CCC-cCCCHHHHHHHHH-H
Q 027989 16 FSYGLNWALAGRGVVVNDKAFQNLTTSELQQKG----ATIAESLSGLPVYVRGNLL-----GGS-SDISKAQYAKLLK-Q 84 (216)
Q Consensus 16 ~~y~ln~~L~~~gi~~~~~v~~Nls~~~L~e~~----eg~l~~~Gal~viV~~~~t-----~~n-~pis~e~F~~L~~-~ 84 (216)
|.-++...|+++|.+. .++.|++..++.+.- +-.......++|++=.... +.+ ++++-+..-.++. +
T Consensus 33 D~~~l~~~f~~lgF~V--~~~~nlt~~~~~~~l~~f~~~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~ 110 (243)
T cd00032 33 DAENLTKLFESLGYEV--EVKNNLTAEEILEELKEFASPDHSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFNGD 110 (243)
T ss_pred HHHHHHHHHHHCCCEE--EEeCCCCHHHHHHHHHHHHhccCCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhccC
Confidence 4456888899999975 579999999988872 2123333444443311111 212 5666544322221 1
Q ss_pred HHHHHcCCCceEeEeeeecCCcCCc
Q 027989 85 VTAHLSSIANVFVQDGAVGSSSECD 109 (216)
Q Consensus 85 v~~yL~~~~~lyV~D~~aGad~~~r 109 (216)
-..-|.++.+||+.|+.=|......
T Consensus 111 ~~~sl~~kPKl~~iqACRg~~~~~~ 135 (243)
T cd00032 111 NCPSLAGKPKLFFIQACRGDELDLG 135 (243)
T ss_pred CCccccCCCcEEEEECCCCCcCCCc
Confidence 1234556678999998887766544
No 19
>PF12091 DUF3567: Protein of unknown function (DUF3567); InterPro: IPR021951 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.
Probab=26.65 E-value=71 Score=24.48 Aligned_cols=49 Identities=22% Similarity=0.261 Sum_probs=33.8
Q ss_pred CCeEEEEcCCCCCCCCccCCcCCCCCCeEEEEe-cccCeEEEecCCCCccchhhhHHHHh
Q 027989 142 CPLTVYVTTSISPGVVNAVGLRAQGDNGFIAAD-IERSSLILCGKGFSDANGVKEALAAL 200 (216)
Q Consensus 142 pdfTI~~aP~f~adp~~~~Gt~Se~~e~fiiin-f~~r~ilIgGT~Y~YaGEiKKsiFsv 200 (216)
+.|.|+.- .+++ ....+.. ..|=|+| ..+|.|-|.|.+ |.--++.|-.+
T Consensus 8 d~y~VV~~---~~~~-~~~~l~~---gGyEIVDK~~~rEifi~G~~---Ae~Fr~~V~~l 57 (85)
T PF12091_consen 8 DNYCVVEF---PPDA-GHPALAR---GGYEIVDKNARREIFIDGSW---AEMFREDVQAL 57 (85)
T ss_pred CceEEEEe---cCCC-Cccchhc---CCcEEeecCCCceEEeCcHH---HHHHHHHHHHH
Confidence 45666653 4443 2224544 5788888 679999999999 88888887554
No 20
>PF02499 DNA_pack_C: Probable DNA packing protein, C-terminus; InterPro: IPR003498 This family includes proteins that are probably involved in DNA packing in Herpesviridae. This domain is found at the C terminus of the protein.; GO: 0006323 DNA packaging; PDB: 3N4Q_C 3N4P_D 2KN8_A.
Probab=26.57 E-value=50 Score=31.37 Aligned_cols=91 Identities=19% Similarity=0.215 Sum_probs=32.5
Q ss_pred HHHHHHHHHcCCCceEeEeeeecC-CcCCcceEEEEcchhhhHHhhhhcCCCCC---ccccCCCCCCeEEEEcCCCCCCC
Q 027989 81 LLKQVTAHLSSIANVFVQDGAVGS-SSECDAKVRVISDSPSAVLKLSSILWKTP---SRAVSHDSCPLTVYVTTSISPGV 156 (216)
Q Consensus 81 L~~~v~~yL~~~~~lyV~D~~aGa-d~~~rl~VRvIte~AwhaLF~~nmfirp~---~~el~~f~pdfTI~~aP~f~adp 156 (216)
+++-+--+|.+ -|-+..-.|. +....-.-+++|+.|-..+. +-||+ ....+...+...||.=|-|.++-
T Consensus 75 vk~TanLFl~g---sF~~ElmGg~~~~~~~~~~~v~t~~a~~~F~----l~R~sT~~~~~~~~l~~~LyVYvDPAfT~Nt 147 (354)
T PF02499_consen 75 VKKTANLFLEG---SFMTELMGGGDSNSRLSDNPVFTESALEQFD----LYRPSTVNQQFIQHLSSTLYVYVDPAFTNNT 147 (354)
T ss_dssp -------------------------------------HHHHHHHH----HEEE-GGC-S-TTTB-SEEEEEEE----SSS
T ss_pred HHHHHHHhccC---chhhhhccCccccccCcCCCccchhhHhhee----eccCCCcchhhhhccCCeEEEEECCCCcCCC
Confidence 34444445544 4777777774 45556788999999988763 34664 23344457889999999999886
Q ss_pred CccCCcCCCCCCeEEEEecccCeEEEec
Q 027989 157 VNAVGLRAQGDNGFIAADIERSSLILCG 184 (216)
Q Consensus 157 ~~~~Gt~Se~~e~fiiinf~~r~ilIgG 184 (216)
... || +..+|.....+.||.|=
T Consensus 148 ~AS-GT-----GIa~v~~~~~~~II~Gl 169 (354)
T PF02499_consen 148 RAS-GT-----GIAAVGRYRPKYIILGL 169 (354)
T ss_dssp -----E-----EEEEEEEETTEEEEEEE
T ss_pred ccc-ce-----eEEEEEEcCCCEEEEec
Confidence 333 76 46778888666666553
No 21
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=25.64 E-value=32 Score=22.07 Aligned_cols=11 Identities=9% Similarity=0.051 Sum_probs=9.0
Q ss_pred chhhhHHhhhh
Q 027989 117 DSPSAVLKLSS 127 (216)
Q Consensus 117 e~AwhaLF~~n 127 (216)
+.||.|+|++.
T Consensus 22 ~kAWRNiFvqa 32 (34)
T PF13137_consen 22 DKAWRNIFVQA 32 (34)
T ss_pred HHHHHHHHHHc
Confidence 67999999864
No 22
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=23.47 E-value=1.1e+02 Score=24.05 Aligned_cols=30 Identities=10% Similarity=0.309 Sum_probs=23.4
Q ss_pred eEEEEecccCeEEEecCCCCccchhhhHHHHh
Q 027989 169 GFIAADIERSSLILCGKGFSDANGVKEALAAL 200 (216)
Q Consensus 169 ~fiiinf~~r~ilIgGT~Y~YaGEiKKsiFsv 200 (216)
+||+||=.+|++-|.=|- -...||++|=.+
T Consensus 66 GFvviN~dKK~mSvsFsd--ideNmK~~i~ei 95 (110)
T PF11513_consen 66 GFVVINKDKKMMSVSFSD--IDENMKNSIEEI 95 (110)
T ss_dssp EEEEEETTTTEEEEEE-S----CCHHHHHHHH
T ss_pred EEEEEecCCeEEEEEecc--hhHHHHHHHHHH
Confidence 699999999999998886 468899988654
No 23
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.84 E-value=3e+02 Score=20.20 Aligned_cols=65 Identities=14% Similarity=0.221 Sum_probs=44.6
Q ss_pred hcCCCCCccchhhhhhhhCCCCcCcceeecCChHHHHHhhccccccCCceEE---EEecCCCCCCcCCCHHHHHHHHHHH
Q 027989 9 LCFPGRAFSYGLNWALAGRGVVVNDKAFQNLTTSELQQKGATIAESLSGLPV---YVRGNLLGGSSDISKAQYAKLLKQV 85 (216)
Q Consensus 9 ~~~~~~g~~y~ln~~L~~~gi~~~~~v~~Nls~~~L~e~~eg~l~~~Gal~v---iV~~~~t~~n~pis~e~F~~L~~~v 85 (216)
.+++|+|+=|++-..|..+|+.-. . .+++..|.-++ +|++. .|.+..+++.-++|.+..
T Consensus 7 ~~~DRpGLL~~i~~~l~~~~l~I~-~---------------A~I~T~gera~D~FyV~d~--~g~kl~~~~~~~~l~~~L 68 (75)
T cd04897 7 QCRDRPKLLFDVVCTLTDMDYVVF-H---------------ATIDTDGDDAHQEYYIRHK--DGRTLSTEGERQRVIKCL 68 (75)
T ss_pred EeCCcCcHHHHHHHHHHhCCeEEE-E---------------EEEeecCceEEEEEEEEcC--CCCccCCHHHHHHHHHHH
Confidence 468999999999999999987642 1 33444444333 66555 344556788888888887
Q ss_pred HHHHcC
Q 027989 86 TAHLSS 91 (216)
Q Consensus 86 ~~yL~~ 91 (216)
.+-|+.
T Consensus 69 ~~al~~ 74 (75)
T cd04897 69 EAAIER 74 (75)
T ss_pred HHHHhc
Confidence 766643
No 24
>PF15603 Imm45: Immunity protein 45
Probab=21.58 E-value=3e+02 Score=20.70 Aligned_cols=38 Identities=16% Similarity=0.231 Sum_probs=28.1
Q ss_pred CCceEEEEecCCC-CC----CcCCCHHHHHHHHHHHHHHHcCCC
Q 027989 55 LSGLPVYVRGNLL-GG----SSDISKAQYAKLLKQVTAHLSSIA 93 (216)
Q Consensus 55 ~Gal~viV~~~~t-~~----n~pis~e~F~~L~~~v~~yL~~~~ 93 (216)
.|+++|+ ++..+ |. |.||+++.=+++-+.+.++++++.
T Consensus 34 ~~~Fvvy-~~si~~We~P~e~~~it~~e~q~II~aI~~~~~~~~ 76 (82)
T PF15603_consen 34 DGDFVVY-KDSIKNWEPPHENEPITIAERQKIIEAIEKYFSERG 76 (82)
T ss_pred CcCEEEE-ccccccccCCCCCcccCHHHHHHHHHHHHHHHhcCc
Confidence 3455554 33444 53 579999999999999999999853
No 25
>PHA03372 DNA packaging terminase subunit 1; Provisional
Probab=20.36 E-value=3.6e+02 Score=27.85 Aligned_cols=89 Identities=12% Similarity=0.196 Sum_probs=61.1
Q ss_pred HHHHHHHHHcCCCceEeEeeeecCCcCCcceEEEEcchhhhHHhhhhcCCCCCc---cccCCCCCCeEEEEcCCCCCCCC
Q 027989 81 LLKQVTAHLSSIANVFVQDGAVGSSSECDAKVRVISDSPSAVLKLSSILWKTPS---RAVSHDSCPLTVYVTTSISPGVV 157 (216)
Q Consensus 81 L~~~v~~yL~~~~~lyV~D~~aGad~~~rl~VRvIte~AwhaLF~~nmfirp~~---~el~~f~pdfTI~~aP~f~adp~ 157 (216)
+++-+--+|.+ -|-+..-.|.+...+-. ++|||.|-.... +-||+. ...+...+...||.=|-|.+|-.
T Consensus 397 vk~tanlFl~G---sF~~ELmGg~~~~~~~~-~vite~a~~~F~----l~R~sT~~~~~~~~l~~~LyvYiDPAfT~N~~ 468 (668)
T PHA03372 397 VRKTANMFLEG---AFMDEIMGGTNKIVENT-VLITDQGREEFD----IFRYSTINKNLIPFLGKTLYVYLDPAFTSNRR 468 (668)
T ss_pred HHHHHHHhCCC---chhheecCCCcCccCCC-cccchhhhhhee----eeccCCCCcccccccCCeEEEEECCccccCCc
Confidence 44444445555 58888888876655533 799999987753 356642 22334578999999999999964
Q ss_pred ccCCcCCCCCCeEEEEecccCeEEEe
Q 027989 158 NAVGLRAQGDNGFIAADIERSSLILC 183 (216)
Q Consensus 158 ~~~Gt~Se~~e~fiiinf~~r~ilIg 183 (216)
.. || +..++--...+.||.|
T Consensus 469 AS-GT-----Gia~vg~~~~~~ii~G 488 (668)
T PHA03372 469 AS-GT-----GIAAVGTYRDQYIIYG 488 (668)
T ss_pred cc-cc-----eEEEEEEecCCEEEEe
Confidence 44 87 4677778888766655
Done!