Query psy3496
Match_columns 223
No_of_seqs 182 out of 1621
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 18:11:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3496hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1233|consensus 100.0 4.6E-30 9.9E-35 239.1 11.1 193 2-223 120-469 (613)
2 TIGR00387 glcD glycolate oxida 99.7 1.5E-16 3.4E-21 148.8 9.8 116 40-204 147-263 (413)
3 PRK11230 glycolate oxidase sub 99.6 1.6E-15 3.5E-20 145.8 10.1 117 40-205 204-321 (499)
4 PLN02805 D-lactate dehydrogena 99.6 6E-15 1.3E-19 143.8 13.6 113 40-203 281-394 (555)
5 KOG1232|consensus 99.4 1.8E-13 3.9E-18 128.0 4.0 99 14-112 197-313 (511)
6 COG0277 GlcD FAD/FMN-containin 98.8 3.5E-08 7.6E-13 91.7 11.5 81 25-105 164-250 (459)
7 PRK11183 D-lactate dehydrogena 98.8 1.7E-08 3.7E-13 98.7 7.4 71 41-112 239-313 (564)
8 PF02913 FAD-oxidase_C: FAD li 98.7 2.5E-09 5.4E-14 90.1 0.4 91 65-204 1-93 (248)
9 PRK11282 glcE glycolate oxidas 98.7 4E-08 8.8E-13 91.5 6.8 60 40-100 143-203 (352)
10 KOG1231|consensus 98.3 4E-07 8.8E-12 87.2 2.4 73 40-112 212-289 (505)
11 PLN02441 cytokinin dehydrogena 97.9 2E-05 4.3E-10 77.2 6.2 60 46-106 221-281 (525)
12 TIGR01679 bact_FAD_ox FAD-link 95.3 0.026 5.7E-07 53.5 5.1 41 50-92 160-200 (419)
13 TIGR01677 pln_FAD_oxido plant- 95.1 0.028 6.2E-07 55.6 4.8 41 50-92 196-236 (557)
14 TIGR01676 GLDHase galactonolac 95.0 0.047 1E-06 54.1 5.9 41 50-92 213-253 (541)
15 TIGR01678 FAD_lactone_ox sugar 94.6 0.078 1.7E-06 50.9 6.2 41 50-92 166-206 (438)
16 PLN02465 L-galactono-1,4-lacto 90.5 0.46 9.9E-06 47.5 5.4 40 50-91 248-287 (573)
17 PF00076 RRM_1: RNA recognitio 64.1 28 0.0006 23.0 5.5 41 50-90 20-60 (70)
18 PF14259 RRM_6: RNA recognitio 59.0 41 0.0009 22.7 5.8 38 52-89 22-59 (70)
19 PF12382 Peptidase_A2E: Retrot 57.9 7 0.00015 31.3 1.8 66 5-76 10-82 (137)
20 KOG1262|consensus 52.0 37 0.00081 33.3 5.9 41 50-90 213-253 (543)
21 KOG4730|consensus 49.1 21 0.00045 35.4 3.8 33 50-84 202-234 (518)
22 smart00360 RRM RNA recognition 40.0 84 0.0018 19.7 4.7 39 51-89 19-58 (71)
23 PRK14652 UDP-N-acetylenolpyruv 39.0 53 0.0012 30.1 4.7 42 40-92 172-213 (302)
24 PRK13905 murB UDP-N-acetylenol 38.2 38 0.00082 30.7 3.6 33 51-92 178-210 (298)
25 smart00362 RRM_2 RNA recogniti 36.1 1E+02 0.0022 19.5 4.7 39 50-89 21-59 (72)
26 smart00361 RRM_1 RNA recogniti 34.1 1.4E+02 0.0031 20.6 5.4 26 66-91 34-59 (70)
27 cd00590 RRM RRM (RNA recogniti 29.5 1.5E+02 0.0033 18.7 5.2 40 51-90 22-61 (74)
28 PF13893 RRM_5: RNA recognitio 28.1 1E+02 0.0022 20.1 3.6 36 52-91 8-43 (56)
29 PF13812 PPR_3: Pentatricopept 28.0 75 0.0016 18.1 2.6 21 76-96 14-34 (34)
30 PF13740 ACT_6: ACT domain; PD 26.5 2E+02 0.0044 20.3 5.1 34 169-202 38-71 (76)
31 TIGR00756 PPR pentatricopeptid 22.7 1.1E+02 0.0024 17.0 2.6 21 77-97 14-34 (35)
32 KOG0105|consensus 21.8 81 0.0018 28.0 2.6 35 52-88 30-64 (241)
33 KOG0146|consensus 20.0 1E+02 0.0022 28.9 3.0 56 50-105 41-101 (371)
No 1
>KOG1233|consensus
Probab=99.96 E-value=4.6e-30 Score=239.08 Aligned_cols=193 Identities=56% Similarity=1.033 Sum_probs=177.6
Q ss_pred hhhhhhcCceeChhhHHHHHHHhhhhHHHHHhchhhccCcCCceeeec--------------------------------
Q psy3496 2 LSLLEATNVSLSTQGEDRLIRAHGQTLYEVFSLRHTGLKRIPDVVVWP-------------------------------- 49 (223)
Q Consensus 2 ~~~~~~~~~~~~~~g~~r~~r~~~~~~~~l~~lR~~~~~~l~~L~~g~-------------------------------- 49 (223)
|..|..||+|.|.++.+|+.|-|+++++++.-||+.-...+||+++|+
T Consensus 120 lh~Lket~isyS~Ea~dRl~R~HGhtlhdi~~Lregkf~RiPDiVvWP~chdevVkiv~lA~khN~~iiPiGGGTSVs~a 199 (613)
T KOG1233|consen 120 LHFLKETKISYSNEARDRLMRGHGHTLHDIINLREGKFPRIPDIVVWPKCHDEVVKIVELAMKHNCAIIPIGGGTSVSNA 199 (613)
T ss_pred HHHHHhccCccchhHHHHHHhhcCchHHHHHHHhcCccCCCCceEecccchHHHHHHHHHHhhcCeEEEEeCCccccccc
Confidence 456789999999999999999999999999999999779999999997
Q ss_pred --------------------------------------------------------------------------------
Q psy3496 50 -------------------------------------------------------------------------------- 49 (223)
Q Consensus 50 -------------------------------------------------------------------------------- 49 (223)
T Consensus 200 l~cP~~E~R~iislDtsqmnriLWidreNLT~~~eaGIvGQ~LERqL~~~G~t~GHEPDS~EFSTlGGWVsTRASGMKKN 279 (613)
T KOG1233|consen 200 LDCPETEKRAIISLDTSQMNRILWIDRENLTCRAEAGIVGQSLERQLNKKGFTCGHEPDSIEFSTLGGWVSTRASGMKKN 279 (613)
T ss_pred ccCCcccceeEEEecHHhhhheeEeccccceEEEecCcchHHHHHHHhhcCcccCCCCCceeeecccceeeecccccccc
Confidence
Q ss_pred --------------------------------------------CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHH
Q psy3496 50 --------------------------------------------GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHC 85 (223)
Q Consensus 50 --------------------------------------------GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~a 85 (223)
||||||||+|+|+.|+|+.+++-.+.||++++....
T Consensus 280 ~YGNIEDLVVh~~mVtP~Giiek~Cq~PRmS~GPDihh~IlGSEGTLGVitEvtiKirPiPe~~ryGS~aFPNFEqGV~f 359 (613)
T KOG1233|consen 280 KYGNIEDLVVHLNMVTPKGIIEKQCQVPRMSSGPDIHHIILGSEGTLGVITEVTIKIRPIPEVKRYGSFAFPNFEQGVNF 359 (613)
T ss_pred ccCChhHheEEEEeecCcchhhhhhcCCcccCCCCcceEEeccCcceeEEEEEEEEEeechhhhhcCccccCcHHHHHHH
Confidence 999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCceEEEeechhhHHHhhhcCCC-CCccchhhhhhhhhhhhhhcCCCccchhhhhhhccccccCCccceeec
Q psy3496 86 LREIAKQRCQPSSIRLMDNAQFKFGQSLRPV-PGYFGLLLDGLKRMYITKIKGFSVDEMCVTTLLFEGKRVGPVGYITKI 164 (223)
Q Consensus 86 v~~i~~sgl~PsalElmD~~~l~~v~~~~~~-~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (223)
++++......|+++++||......-+.+++. .+|.+.+.+.++++|+++++||+.++
T Consensus 360 ~REvA~qRCqPAS~RLMDN~QF~fGqALKp~~~Swwas~~d~~kk~YiTswKGfd~nq---------------------- 417 (613)
T KOG1233|consen 360 FREVAIQRCQPASLRLMDNDQFVFGQALKPASDSWWASLKDSVKKMYITSWKGFDVNQ---------------------- 417 (613)
T ss_pred HHHHHHHhcCchheeeecccceecccccCcchhhHHHHHHHHHhhheeecccCcCHhh----------------------
Confidence 9999988899999999999988777776665 48888888888888766655555554
Q ss_pred cccccccceeEEEEEEcCHHHHHHHHHHHHHHHHHcCCccCCCcccccceeeeeEEecC
Q psy3496 165 KGFSVDEMCVTTLLFEGDPEDVKKNQAKIYSIALKFGGIPAGETNGMRGYMLTFVIAYI 223 (223)
Q Consensus 165 ~~~~~~~~~~~~L~~eG~~~~v~~~~~~i~~i~~~~G~~~~g~~~~~~~~~~~~~~~y~ 223 (223)
.|.++|+|||+.++|.++.+++++||++|++.++|+++|+++|.++|+|+||
T Consensus 418 -------icaATllfEGdre~V~qhE~~~y~iAekF~G~~aG~~NGqrGY~LTfvIAYi 469 (613)
T KOG1233|consen 418 -------ICAATLLFEGDREEVDQHEERLYKIAEKFHGVVAGAENGQRGYRLTFVIAYI 469 (613)
T ss_pred -------hhhhhheecccHHHHHHHHHHHHHHHHHhCCccccccccccceEEEEeHHHH
Confidence 8889999999999999999999999999999999999999999999999997
No 2
>TIGR00387 glcD glycolate oxidase, subunit GlcD. This protein, the glycolate oxidase GlcD subunit, is similar in sequence to that of several D-lactate dehydrogenases, including that of E. coli. The glycolate oxidase has been found to have some D-lactate dehydrogenase activity.
Probab=99.67 E-value=1.5e-16 Score=148.78 Aligned_cols=116 Identities=22% Similarity=0.350 Sum_probs=98.3
Q ss_pred CcCCceeeec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHcCCCceEEEeechhhHHHhhhcCCCCC
Q psy3496 40 KRIPDVVVWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPSSIRLMDNAQFKFGQSLRPVPG 118 (223)
Q Consensus 40 ~~l~~L~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~PsalElmD~~~l~~v~~~~~~~g 118 (223)
+|+.++++|+ |||||||+++|||+|.|+.+....+.|+|++++++++.++.++++.|+++|+||...++.+.+
T Consensus 147 ~dl~~l~~Gs~GtlGiit~~~lkl~p~p~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~a~el~d~~~~~~~~~------ 220 (413)
T TIGR00387 147 YDLTGLFVGSEGTLGIVTEATLKLLPKPENIVVALAFFDSIEKAMQAVYDIIAAGIIPAGMEFLDNLSIKAVED------ 220 (413)
T ss_pred CChhhhcccCCccceEEEEEEEEeecCCCccEEEEEECCCHHHHHHHHHHHHhcCCCcEEEEccCHHHHHHHHH------
Confidence 6788899998 999999999999999999999999999999999999999999999999999999999887654
Q ss_pred ccchhhhhhhhhhhhhhcCCCccchhhhhhhccccccCCccceeeccccccccceeEEEEEEcCHHHHHHHHHHHHHHHH
Q psy3496 119 YFGLLLDGLKRMYITKIKGFSVDEMCVTTLLFEGKRVGPVGYITKIKGFSVDEMCVTTLLFEGDPEDVKKNQAKIYSIAL 198 (223)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~eG~~~~v~~~~~~i~~i~~ 198 (223)
|. ..++|.+. .+.+++.|+|+.++++++.+++.++++
T Consensus 221 ------------~~--~~~~p~~~-----------------------------~~~l~v~~~g~~~~~~~~~~~~~~~~~ 257 (413)
T TIGR00387 221 ------------IS--GIGLPKDA-----------------------------GAILLVEIDGVHEAVERDEEKIEQICR 257 (413)
T ss_pred ------------hc--CCCCCCCC-----------------------------ceEEEEEecCCcHHHHHHHHHHHHHHH
Confidence 21 11333322 345566689988889999999999999
Q ss_pred HcCCcc
Q psy3496 199 KFGGIP 204 (223)
Q Consensus 199 ~~G~~~ 204 (223)
++|+..
T Consensus 258 ~~~~~~ 263 (413)
T TIGR00387 258 KNGAVD 263 (413)
T ss_pred hCCCce
Confidence 988754
No 3
>PRK11230 glycolate oxidase subunit GlcD; Provisional
Probab=99.62 E-value=1.6e-15 Score=145.78 Aligned_cols=117 Identities=22% Similarity=0.375 Sum_probs=98.5
Q ss_pred CcCCceeeec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHcCCCceEEEeechhhHHHhhhcCCCCC
Q psy3496 40 KRIPDVVVWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPSSIRLMDNAQFKFGQSLRPVPG 118 (223)
Q Consensus 40 ~~l~~L~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~PsalElmD~~~l~~v~~~~~~~g 118 (223)
+||.++++|+ |||||||++|||+.|.|+...++++.|+|++++.+++.++.++++.|+++|+||+..++.+.+
T Consensus 204 ~dl~~l~~Gs~GtlGIIt~atlkl~p~p~~~~~~~~~f~~~~~a~~~~~~~~~~~~~p~~~el~d~~~~~~~~~------ 277 (499)
T PRK11230 204 FDLLALFTGSEGMLGVVTEVTVKLLPKPPVARVLLASFDSVEKAGLAVGDIIAAGIIPGGLEMMDNLSIRAAED------ 277 (499)
T ss_pred cchHhhhccCCCccEEEEEEEEEEEcCCcceEEEEEECCCHHHHHHHHHHHHhcCCCcEEEEeeCHHHHHHHHH------
Confidence 6777889998 999999999999999999999999999999999999999999999999999999999887654
Q ss_pred ccchhhhhhhhhhhhhhcCCCccchhhhhhhccccccCCccceeeccccccccceeEEEEEEcCHHHHHHHHHHHHHHHH
Q psy3496 119 YFGLLLDGLKRMYITKIKGFSVDEMCVTTLLFEGKRVGPVGYITKIKGFSVDEMCVTTLLFEGDPEDVKKNQAKIYSIAL 198 (223)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~eG~~~~v~~~~~~i~~i~~ 198 (223)
|+ ..++|.+. .+.+++.|+|+.++++++.+++.+++.
T Consensus 278 ------------~~--~~~~p~~~-----------------------------~~~ll~e~~g~~~~v~~~~~~l~~~~~ 314 (499)
T PRK11230 278 ------------FI--HAGYPVDA-----------------------------EAILLCELDGVESDVQEDCERVNDILL 314 (499)
T ss_pred ------------hc--CCCCCCCc-----------------------------ceEEEEEecCCchHHHHHHHHHHHHHH
Confidence 32 12333322 234566688998889999999999999
Q ss_pred HcCCccC
Q psy3496 199 KFGGIPA 205 (223)
Q Consensus 199 ~~G~~~~ 205 (223)
++|+...
T Consensus 315 ~~g~~~~ 321 (499)
T PRK11230 315 KAGATDV 321 (499)
T ss_pred hcCCceE
Confidence 9987554
No 4
>PLN02805 D-lactate dehydrogenase [cytochrome]
Probab=99.61 E-value=6e-15 Score=143.77 Aligned_cols=113 Identities=21% Similarity=0.264 Sum_probs=96.3
Q ss_pred CcCCceeeec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHcCCCceEEEeechhhHHHhhhcCCCCC
Q psy3496 40 KRIPDVVVWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPSSIRLMDNAQFKFGQSLRPVPG 118 (223)
Q Consensus 40 ~~l~~L~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~PsalElmD~~~l~~v~~~~~~~g 118 (223)
+||.++++|+ |||||||+++|||.|+|+.+.++++.|+|+++|.+++.++.++++.|+++|+||+..++.++.
T Consensus 281 ~dL~~l~~GseGtLGIIT~~tlrl~p~P~~~~~~~~~f~~~~~a~~av~~i~~~g~~psa~ElmD~~~~~~~~~------ 354 (555)
T PLN02805 281 YDLTRLVIGSEGTLGVITEVTLRLQKIPQHSVVAMCNFPTIKDAADVAIATMLSGIQVSRVELLDEVQIRAINM------ 354 (555)
T ss_pred ccHHHHhccCCCceEEEEEEEEEeecCCcceEEEEEEcCCHHHHHHHHHHHHhCCCCcEEEEEECHHHHHHHHH------
Confidence 7888999998 999999999999999999999999999999999999999999999999999999999987654
Q ss_pred ccchhhhhhhhhhhhhhcCCCccchhhhhhhccccccCCccceeeccccccccceeEEEEEEcCHHHHHHHHHHHHHHHH
Q psy3496 119 YFGLLLDGLKRMYITKIKGFSVDEMCVTTLLFEGKRVGPVGYITKIKGFSVDEMCVTTLLFEGDPEDVKKNQAKIYSIAL 198 (223)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~eG~~~~v~~~~~~i~~i~~ 198 (223)
+. ..++|. .+.+++.|+|++++++++.+.+.++++
T Consensus 355 ------------~~--~~~~p~-------------------------------~~~Ll~e~~g~~~~~~~~~~~~~~i~~ 389 (555)
T PLN02805 355 ------------AN--GKNLPE-------------------------------APTLMFEFIGTEAYAREQTLIVQKIAS 389 (555)
T ss_pred ------------hc--CCCCCc-------------------------------ceEEEEEEecCcHHHHHHHHHHHHHHH
Confidence 11 112232 234566678988889888999999999
Q ss_pred HcCCc
Q psy3496 199 KFGGI 203 (223)
Q Consensus 199 ~~G~~ 203 (223)
++|+.
T Consensus 390 ~~g~~ 394 (555)
T PLN02805 390 KHNGS 394 (555)
T ss_pred hCCCc
Confidence 99875
No 5
>KOG1232|consensus
Probab=99.39 E-value=1.8e-13 Score=128.04 Aligned_cols=99 Identities=28% Similarity=0.343 Sum_probs=89.0
Q ss_pred hhhHHHHHHH---------------hhhhHHHHHhchhhcc-CcCCceeeec-CceeeEeEEEEEeecCCCceeEEEEEc
Q psy3496 14 TQGEDRLIRA---------------HGQTLYEVFSLRHTGL-KRIPDVVVWP-GTFGVITKVVLKIRPLPKCRKYGSIVF 76 (223)
Q Consensus 14 ~~g~~r~~r~---------------~~~~~~~l~~lR~~~~-~~l~~L~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F 76 (223)
-+|+.|++|| ++..++.+..||++|+ +|++|||+|| |||||||++++-..|+|.....+++..
T Consensus 197 nAGGlrllRYGsLHgsvLGle~Vlp~G~vl~~~~slRKDNTgydlkhLFIGSEGtlGVvT~vSil~~~kpksvn~af~gi 276 (511)
T KOG1232|consen 197 NAGGLRLLRYGSLHGSVLGLEVVLPNGTVLDLLSSLRKDNTGYDLKHLFIGSEGTLGVVTKVSILAPPKPKSVNVAFIGI 276 (511)
T ss_pred cCCceEEEEecccccceeeeEEEcCCCchhhhhhhhcccCccccchhheecCCceeeEEeeEEEeecCCCcceeEEEEcc
Confidence 4688999998 4556699999999999 9999999999 999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHH-cCCCceEEEeechhhHHHhhh
Q psy3496 77 PNFEAGVHCLREIAK-QRCQPSSIRLMDNAQFKFGQS 112 (223)
Q Consensus 77 ~s~~~A~~av~~i~~-sgl~PsalElmD~~~l~~v~~ 112 (223)
+|++++..++.+..+ -+-..+++||||..++.++.+
T Consensus 277 ~sf~~v~k~fv~Aks~L~EILSafElmD~~s~~~~~~ 313 (511)
T KOG1232|consen 277 ESFDDVQKVFVEAKSNLTEILSAFELMDNASMELVLE 313 (511)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHH
Confidence 999999999887664 344789999999999999876
No 6
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=98.82 E-value=3.5e-08 Score=91.68 Aligned_cols=81 Identities=27% Similarity=0.414 Sum_probs=65.0
Q ss_pred hhhHHHHHhchhhcc-CcCCceeeec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHH----HcCCCceE
Q psy3496 25 GQTLYEVFSLRHTGL-KRIPDVVVWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIA----KQRCQPSS 98 (223)
Q Consensus 25 ~~~~~~l~~lR~~~~-~~l~~L~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~----~sgl~Psa 98 (223)
++..+.....+++.. ++|..+++|+ |||||||++|||+.|.|+...++++.|++.+.+........ ..+..|.+
T Consensus 164 G~i~~~~~~~~k~~~g~dl~~l~iGs~GtlGiit~~tl~l~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (459)
T COG0277 164 GEILRLGRKLRKDNAGYDLTALFVGSEGTLGIITEATLKLLPLPETKATAVAGFPSIEAAARLAVAAIALLEALGVIPAA 243 (459)
T ss_pred ceehhhcCcccCCCCCCCHHHhcccCCccceEEEEEEEEeccCCchheEEEEeCCCHHHHHHHHHHHHHhhhhcCCCcee
Confidence 444455555554433 8999999997 99999999999999999999999999999999987444333 34478999
Q ss_pred EEeechh
Q psy3496 99 IRLMDNA 105 (223)
Q Consensus 99 lElmD~~ 105 (223)
+|+||..
T Consensus 244 ~e~~~~~ 250 (459)
T COG0277 244 LEFMDRP 250 (459)
T ss_pred eeecchh
Confidence 9999998
No 7
>PRK11183 D-lactate dehydrogenase; Provisional
Probab=98.75 E-value=1.7e-08 Score=98.69 Aligned_cols=71 Identities=17% Similarity=0.099 Sum_probs=67.8
Q ss_pred cCCcee--eec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc-CCCceEEEeechhhHHHhhh
Q psy3496 41 RIPDVV--VWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ-RCQPSSIRLMDNAQFKFGQS 112 (223)
Q Consensus 41 ~l~~L~--~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s-gl~PsalElmD~~~l~~v~~ 112 (223)
|+..|+ .|| |||||| +++|++.|.|+...++.+.|+|.+++.++.+.++++ +..|.++|+||+.+++.+++
T Consensus 239 Dl~~LfeasGseGkLgV~-avrLdtfp~p~~~~vf~ig~n~~~~~~~~rr~il~~~~~lP~a~Eym~r~~~d~~~~ 313 (564)
T PRK11183 239 DPRRLFEASGCAGKLAVF-AVRLDTFPAEKNTQVFYIGTNDPAVLTEIRRHILANFKNLPVAGEYMHRDAFDIAEK 313 (564)
T ss_pred CHHHHhhccCCCceEEEE-EEEeccccCCCcceEEEEeCCCHHHHHHHHHHHHHhCCCCceeEeecCHHHHHHHHH
Confidence 778889 888 999999 999999999999999999999999999999999987 99999999999999999877
No 8
>PF02913 FAD-oxidase_C: FAD linked oxidases, C-terminal domain; InterPro: IPR004113 Some oxygen-dependent oxidoreductases are flavoproteins that contain a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. The region around the histidine that binds the FAD group is conserved in these enzymes (see IPR006093 from INTERPRO).; GO: 0003824 catalytic activity, 0050660 flavin adenine dinucleotide binding; PDB: 1WVE_B 1DII_B 1WVF_A 1DIQ_A 2UUU_B 2UUV_A 1W1M_A 1E8H_B 1E0Y_B 1DZN_B ....
Probab=98.72 E-value=2.5e-09 Score=90.10 Aligned_cols=91 Identities=30% Similarity=0.468 Sum_probs=70.3
Q ss_pred CCCceeEEEEEcCCHHHHHHHHHHHHHcCCCceEEEeechhhHHHhhhcCCCCCccchhhhhhhhhhhhhhcCCCccchh
Q psy3496 65 LPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPSSIRLMDNAQFKFGQSLRPVPGYFGLLLDGLKRMYITKIKGFSVDEMC 144 (223)
Q Consensus 65 ~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~PsalElmD~~~l~~v~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (223)
+|+++.++++.|+|+++|+++++++.++++.|+++|+||+.+++.+.... ....+...
T Consensus 1 lPe~~~~~~~~f~~~~~a~~~~~~i~~~g~~p~a~el~d~~~~~~~~~~~--------------------~~~~~~~~-- 58 (248)
T PF02913_consen 1 LPEARATALVFFPSFEDAADAVRAIMQSGIIPSAIELLDSAALKLALEHW--------------------GEPLPPEG-- 58 (248)
T ss_dssp --SEEEEEEEEESCHHHHHHHHCCCCHHCSSCCECCCCHHHHHHHHHHSE--------------------EETSSTTT--
T ss_pred CCcceEEEEEEcCCHHHHHHHHHHHHHcCCCceEEeeeCHHHHHHHHhhc--------------------CCCccCCc--
Confidence 59999999999999999999999999999999999999999999887611 01112222
Q ss_pred hhhhhccccccCCccceeeccccccccceeEEEEEEcCH-HHHHHHHH-HHHHHHHHcCCcc
Q psy3496 145 VTTLLFEGKRVGPVGYITKIKGFSVDEMCVTTLLFEGDP-EDVKKNQA-KIYSIALKFGGIP 204 (223)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~eG~~-~~v~~~~~-~i~~i~~~~G~~~ 204 (223)
.+.+++.|+|+. +.++++.+ .+.+++.+.++..
T Consensus 59 ---------------------------~~~llv~~~g~~~~~~~~~~~~~i~~~~~~~~~~~ 93 (248)
T PF02913_consen 59 ---------------------------GAVLLVEFEGSDEEAVEEQLEAEIEEICKKYGGED 93 (248)
T ss_dssp ---------------------------SEEEEEECCCHHHCCHHHHHHHHHHHHHCTCTCCE
T ss_pred ---------------------------ccEEEEEECCCcHHHHHHHHHHHHHHHHhhcCCce
Confidence 456677788987 45666777 8899998887765
No 9
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=98.67 E-value=4e-08 Score=91.47 Aligned_cols=60 Identities=22% Similarity=0.251 Sum_probs=50.0
Q ss_pred CcCCceeeec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHcCCCceEEE
Q psy3496 40 KRIPDVVVWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPSSIR 100 (223)
Q Consensus 40 ~~l~~L~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~PsalE 100 (223)
|||..+++|+ ||||||||+|||++|.|+...++.+.++ .+++++++.++.++++.|++.+
T Consensus 143 ~DL~~l~~Gs~GtLGVitevtlkl~P~p~~~~t~~~~~~-~~~a~~~~~~~~~~~~~~~~~~ 203 (352)
T PRK11282 143 YDVSRLMAGSLGTLGVLLEVSLKVLPRPRAELTLRLEMD-AAEALRKLNEWGGQPLPISASC 203 (352)
T ss_pred chHHHHHhhCCchhhhheEEEEEEEecCceEEEEEEecC-HHHHHHHHHHHhcCCCCCchhh
Confidence 6777788888 9999999999999999999888877765 6788888888877776666655
No 10
>KOG1231|consensus
Probab=98.26 E-value=4e-07 Score=87.16 Aligned_cols=73 Identities=25% Similarity=0.329 Sum_probs=64.6
Q ss_pred CcCCceeeec-CceeeEeEEEEEeecCC---CceeEEEE-EcCCHHHHHHHHHHHHHcCCCceEEEeechhhHHHhhh
Q psy3496 40 KRIPDVVVWP-GTFGVITKVVLKIRPLP---KCRKYGSI-VFPNFEAGVHCLREIAKQRCQPSSIRLMDNAQFKFGQS 112 (223)
Q Consensus 40 ~~l~~L~~g~-GTLGIITEatLKL~P~P---~~~~t~l~-~F~s~~~A~~av~~i~~sgl~PsalElmD~~~l~~v~~ 112 (223)
++|..++.|+ |||||||+|++||.|.| +.+...++ .||.++.++...+....++++.+.+|++|...++.++.
T Consensus 212 ~~lf~~vlGglGqfGIITrArI~le~aP~~dQe~lis~~~~fd~veg~~~~~~~gl~~n~r~s~f~l~D~~~i~~~~~ 289 (505)
T KOG1231|consen 212 SNLFFLVLGGLGQFGIITRARIKLEPAPKRDQERLISVCGSFDTVEGAAIVARNGLQSNIRVSRFELLDEVQIAAINS 289 (505)
T ss_pred ceeeeeeeccCcceeeEEEEEEEeccCCccchHHhhhhhcCCcchhhhhhhhhccccccceeeccccCcHHHHHHHHh
Confidence 6777888888 99999999999999999 77777777 89999999999888888999999999999988887654
No 11
>PLN02441 cytokinin dehydrogenase
Probab=97.89 E-value=2e-05 Score=77.18 Aligned_cols=60 Identities=20% Similarity=0.392 Sum_probs=49.7
Q ss_pred eeec-CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHcCCCceEEEeechhh
Q psy3496 46 VVWP-GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPSSIRLMDNAQ 106 (223)
Q Consensus 46 ~~g~-GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~PsalElmD~~~ 106 (223)
++|+ |+|||||++++|+.|.|+....+.+.|++++++.+.+.++.. +..+..+|+++...
T Consensus 221 v~GglG~fGIIT~atlrL~Pap~~v~~~~~~y~~~~~~~~d~~~li~-~~~~~~~d~veg~~ 281 (525)
T PLN02441 221 VLGGLGQFGIITRARIALEPAPKRVRWIRVLYSDFSTFTRDQERLIS-RPPENSFDYVEGFV 281 (525)
T ss_pred hccCCCCcEEEEEEEEEEEecCCceEEEEEEcCCHHHHHHHHHHHHh-cCCCCCcceEeEEE
Confidence 3344 999999999999999999888889999999999999998876 44566677776533
No 12
>TIGR01679 bact_FAD_ox FAD-linked oxidoreductase. This model represents a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae.
Probab=95.30 E-value=0.026 Score=53.55 Aligned_cols=41 Identities=24% Similarity=0.328 Sum_probs=33.7
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ 92 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s 92 (223)
|+|||||++|||++|.+....... ..+++++++.+.++.+.
T Consensus 160 G~lGVIt~vtl~~~p~~~~~~~~~--~~~~~~~~~~~~~~~~~ 200 (419)
T TIGR01679 160 GALGVISQVTLQTVALFRLRRRDW--RRPLAQTLERLDEFVDG 200 (419)
T ss_pred CceEEEEEEEEEeecceEeEEEEE--ecCHHHHHHHHHHHHhc
Confidence 999999999999999987666543 46888888888888764
No 13
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase. This model represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown.
Probab=95.11 E-value=0.028 Score=55.64 Aligned_cols=41 Identities=22% Similarity=0.289 Sum_probs=33.0
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ 92 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s 92 (223)
|+|||||++|||+.|.+.. .....+.+.++..+.+.++.++
T Consensus 196 G~lGVVtevTL~~~P~~~~--~~~~~~~~~~~l~~~~~~~~~~ 236 (557)
T TIGR01677 196 GVLGVISQVTLALQPMFKR--SVTYTMRDDSDFEDQFVTFGKK 236 (557)
T ss_pred CccEeeeEEEEEEEccccc--eEEEEcCCHHHHHHHHHHhhcC
Confidence 9999999999999999873 3346678888888877777643
No 14
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=95.00 E-value=0.047 Score=54.07 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=34.5
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ 92 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s 92 (223)
|+|||||++|||++|.+..+..... .++++.++-+.++.++
T Consensus 213 G~LGVItevTLr~~Pa~~l~~~~~~--~~~~e~l~~~~~~~~~ 253 (541)
T TIGR01676 213 GGLGVVAEVTLQCVERQELVEHTFI--SNMKDIKKNHKKFLAD 253 (541)
T ss_pred CceEeEEEEEEEEEeccceeEEEEe--cCHHHHHHHHHHHHhc
Confidence 9999999999999999987655444 6888999888888764
No 15
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases. This model represents a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesizing ascorbic acid or a derivative. These include L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by Prosite motif PS00862; OX2_COVAL_FAD; 1.
Probab=94.59 E-value=0.078 Score=50.87 Aligned_cols=41 Identities=15% Similarity=0.248 Sum_probs=34.4
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ 92 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s 92 (223)
|+|||||++|||++|.+..+... ...++++.++.+.++.++
T Consensus 166 G~lGIIt~vtl~l~p~~~l~~~~--~~~~~~~~~~~~~~~~~~ 206 (438)
T TIGR01678 166 GCLGIIVTVTIQVVPQFHLQETS--FVSTLKELLDNWDSHWKS 206 (438)
T ss_pred CceEeeEEEEEEEEeccceEEEE--ecCCHHHHHHHHHHHhhc
Confidence 99999999999999987766553 568999999998887654
No 16
>PLN02465 L-galactono-1,4-lactone dehydrogenase
Probab=90.55 E-value=0.46 Score=47.52 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=31.3
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHH
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAK 91 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~ 91 (223)
|+|||||++|||+.|.++-..... ..++++..+.+.++.+
T Consensus 248 G~lGVIteVTLql~P~~~L~~~~~--~~~~~~~~~~~~~~~~ 287 (573)
T PLN02465 248 GGLGVVAEVTLQCVPAHRLVEHTF--VSNRKEIKKNHKKWLS 287 (573)
T ss_pred CCCcEEEEEEEEEEecCceEEEEE--EecHHHHHHHHHHHHH
Confidence 999999999999999987544332 2467788888877765
No 17
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=64.06 E-value=28 Score=23.01 Aligned_cols=41 Identities=22% Similarity=0.337 Sum_probs=32.3
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHH
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIA 90 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~ 90 (223)
+..|.|..+.+...+.......+++.|++.++|..++..+-
T Consensus 20 ~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~ 60 (70)
T PF00076_consen 20 SQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELN 60 (70)
T ss_dssp HTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred HHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcC
Confidence 44677777777665556778899999999999999998764
No 18
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=59.02 E-value=41 Score=22.69 Aligned_cols=38 Identities=24% Similarity=0.304 Sum_probs=31.9
Q ss_pred eeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHH
Q psy3496 52 FGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREI 89 (223)
Q Consensus 52 LGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i 89 (223)
.|.|.++.+...+....+..+++.|+|.++|.+++...
T Consensus 22 ~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~ 59 (70)
T PF14259_consen 22 FGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELL 59 (70)
T ss_dssp SSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHH
T ss_pred cCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHC
Confidence 46688888888766677889999999999999998764
No 19
>PF12382 Peptidase_A2E: Retrotransposon peptidase; InterPro: IPR024648 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This entry represents a small family of fungal retroviral aspartyl peptidases.
Probab=57.91 E-value=7 Score=31.35 Aligned_cols=66 Identities=18% Similarity=0.248 Sum_probs=49.6
Q ss_pred hhhcCceeChhhHHHHHHHhhhhHHHHHhchhhccCcCCceeeec-------CceeeEeEEEEEeecCCCceeEEEEEc
Q psy3496 5 LEATNVSLSTQGEDRLIRAHGQTLYEVFSLRHTGLKRIPDVVVWP-------GTFGVITKVVLKIRPLPKCRKYGSIVF 76 (223)
Q Consensus 5 ~~~~~~~~~~~g~~r~~r~~~~~~~~l~~lR~~~~~~l~~L~~g~-------GTLGIITEatLKL~P~P~~~~t~l~~F 76 (223)
+..||||--.-....|..+...-+..+++ -.||++.+.+ ...-||||-|+|-+.+|..-+.-.+-|
T Consensus 10 ~~ktnvsrieyss~~f~~~~~~ryemvlq------a~lp~fkcsipclidtgaq~niiteetvrahklptrpw~~sviy 82 (137)
T PF12382_consen 10 PRKTNVSRIEYSSNNFTNHKRRRYEMVLQ------AKLPDFKCSIPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIY 82 (137)
T ss_pred cccccceeEEeehhhhhhhhHHHhHhhhh------hhCCCccccceeEEccCceeeeeehhhhhhccCCCCcchhheEe
Confidence 45688886666677788777777777765 6789988887 456799999999999997766544433
No 20
>KOG1262|consensus
Probab=51.96 E-value=37 Score=33.30 Aligned_cols=41 Identities=20% Similarity=0.319 Sum_probs=34.1
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHH
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIA 90 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~ 90 (223)
||||+...+|+|++|.-+....-.....+.++-++-+.++.
T Consensus 213 GTlgfLVaatiriIkvK~Yvkltyip~~~l~e~c~k~~e~~ 253 (543)
T KOG1262|consen 213 GTLGFLVAATIRIIKVKKYVKLTYIPVHGLDEYCKKITELS 253 (543)
T ss_pred CchheeeeeEEEEEeccceEEEEEEecccHHHHHHHHHhhc
Confidence 99999999999999998888877777888777776665543
No 21
>KOG4730|consensus
Probab=49.09 E-value=21 Score=35.39 Aligned_cols=33 Identities=27% Similarity=0.363 Sum_probs=23.8
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHH
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVH 84 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~ 84 (223)
|-||||.+||+++.|.= ....-..+.+..+...
T Consensus 202 G~LGVIs~VTl~~vp~F--k~s~t~~v~n~~dl~~ 234 (518)
T KOG4730|consen 202 GVLGVISQVTLSVVPAF--KRSLTYVVTNDSDLFK 234 (518)
T ss_pred cceeEEEEEEEEEEecc--eeeeEEEEechHHHHH
Confidence 99999999999999754 4444444556666443
No 22
>smart00360 RRM RNA recognition motif.
Probab=40.01 E-value=84 Score=19.75 Aligned_cols=39 Identities=23% Similarity=0.287 Sum_probs=28.0
Q ss_pred ceeeEeEEEEEeecC-CCceeEEEEEcCCHHHHHHHHHHH
Q psy3496 51 TFGVITKVVLKIRPL-PKCRKYGSIVFPNFEAGVHCLREI 89 (223)
Q Consensus 51 TLGIITEatLKL~P~-P~~~~t~l~~F~s~~~A~~av~~i 89 (223)
.+|-|.++.+.-.+. ...+..+.+.|.+.++|..++..+
T Consensus 19 ~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~ 58 (71)
T smart00360 19 KFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEAL 58 (71)
T ss_pred hhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHc
Confidence 456677777665443 344668889999999999887654
No 23
>PRK14652 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=38.96 E-value=53 Score=30.09 Aligned_cols=42 Identities=29% Similarity=0.313 Sum_probs=25.7
Q ss_pred CcCCceeeecCceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc
Q psy3496 40 KRIPDVVVWPGTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ 92 (223)
Q Consensus 40 ~~l~~L~~g~GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s 92 (223)
++.-+.+.+.| ||||+++|||.|.+.. .+.+-++.+.+.+++
T Consensus 172 f~YR~s~~~~~--~II~~a~~~L~~~~~~---------~i~~~~~~~~~~R~~ 213 (302)
T PRK14652 172 YAYRTCRLPPG--AVITRVEVRLRPGDVA---------ASEALMRADRERRRR 213 (302)
T ss_pred cccceeccCCC--eEEEEEEEEEecCCHH---------HHHHHHHHHHHHHHh
Confidence 34444444444 8999999999996532 245555555555543
No 24
>PRK13905 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=38.25 E-value=38 Score=30.72 Aligned_cols=33 Identities=12% Similarity=0.109 Sum_probs=22.1
Q ss_pred ceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHc
Q psy3496 51 TFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQ 92 (223)
Q Consensus 51 TLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~s 92 (223)
..||||+++|||.|.++ +.+++-++.+.+.+++
T Consensus 178 ~~gII~~~~l~l~~~~~---------~~i~~~~~~~~~~R~~ 210 (298)
T PRK13905 178 EGLIVLSATFQLEPGDK---------EEIKARMDELLARREA 210 (298)
T ss_pred CCEEEEEEEEEEcCCCH---------HHHHHHHHHHHHHHHh
Confidence 36999999999999742 3445555555554443
No 25
>smart00362 RRM_2 RNA recognition motif.
Probab=36.12 E-value=1e+02 Score=19.46 Aligned_cols=39 Identities=18% Similarity=0.324 Sum_probs=27.9
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHH
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREI 89 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i 89 (223)
...|-|.++.+...+ ......+.+.|.+.++|..++..+
T Consensus 21 ~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~ 59 (72)
T smart00362 21 SKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEAL 59 (72)
T ss_pred HhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHh
Confidence 345667776665544 445678889999999999987654
No 26
>smart00361 RRM_1 RNA recognition motif.
Probab=34.09 E-value=1.4e+02 Score=20.58 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=21.2
Q ss_pred CCceeEEEEEcCCHHHHHHHHHHHHH
Q psy3496 66 PKCRKYGSIVFPNFEAGVHCLREIAK 91 (223)
Q Consensus 66 P~~~~t~l~~F~s~~~A~~av~~i~~ 91 (223)
+..+..+.+.|.+.++|..|+..+..
T Consensus 34 ~~~rG~~fV~f~~~~dA~~A~~~l~g 59 (70)
T smart00361 34 NHKRGNVYITFERSEDAARAIVDLNG 59 (70)
T ss_pred CCCcEEEEEEECCHHHHHHHHHHhCC
Confidence 34567899999999999999987653
No 27
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=29.45 E-value=1.5e+02 Score=18.73 Aligned_cols=40 Identities=18% Similarity=0.285 Sum_probs=29.8
Q ss_pred ceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHH
Q psy3496 51 TFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIA 90 (223)
Q Consensus 51 TLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~ 90 (223)
..|-|.++.+.-.+.......+.+.|.+.++|..++..+.
T Consensus 22 ~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~ 61 (74)
T cd00590 22 KFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALN 61 (74)
T ss_pred hcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC
Confidence 3466777777655554456788999999999999987643
No 28
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=28.15 E-value=1e+02 Score=20.07 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=25.8
Q ss_pred eeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHH
Q psy3496 52 FGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAK 91 (223)
Q Consensus 52 LGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~ 91 (223)
.|-|.++.+ .+.. ...+.+.|.|.++|..++..+..
T Consensus 8 fG~V~~i~~--~~~~--~~~a~V~f~~~~~A~~a~~~l~~ 43 (56)
T PF13893_consen 8 FGEVKKIKI--FKKK--RGFAFVEFASVEDAQKAIEQLNG 43 (56)
T ss_dssp TS-EEEEEE--ETTS--TTEEEEEESSHHHHHHHHHHHTT
T ss_pred cccEEEEEE--EeCC--CCEEEEEECCHHHHHHHHHHhCC
Confidence 466766655 3322 57788999999999999987753
No 29
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=28.04 E-value=75 Score=18.07 Aligned_cols=21 Identities=19% Similarity=0.335 Sum_probs=17.7
Q ss_pred cCCHHHHHHHHHHHHHcCCCc
Q psy3496 76 FPNFEAGVHCLREIAKQRCQP 96 (223)
Q Consensus 76 F~s~~~A~~av~~i~~sgl~P 96 (223)
..+++.|.+.+..+.+.|+.|
T Consensus 14 ~g~~~~a~~~~~~M~~~gv~P 34 (34)
T PF13812_consen 14 AGDPDAALQLFDEMKEQGVKP 34 (34)
T ss_pred CCCHHHHHHHHHHHHHhCCCC
Confidence 468889999999998888876
No 30
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=26.52 E-value=2e+02 Score=20.32 Aligned_cols=34 Identities=9% Similarity=0.144 Sum_probs=24.4
Q ss_pred cccceeEEEEEEcCHHHHHHHHHHHHHHHHHcCC
Q psy3496 169 VDEMCVTTLLFEGDPEDVKKNQAKIYSIALKFGG 202 (223)
Q Consensus 169 ~~~~~~~~L~~eG~~~~v~~~~~~i~~i~~~~G~ 202 (223)
.+.....++.++++++..++-.+.+.+++++.|-
T Consensus 38 ~~~~f~~~~~v~~~~~~~~~l~~~L~~l~~~~~l 71 (76)
T PF13740_consen 38 LGGRFTLIMLVSIPEDSLERLESALEELAEELGL 71 (76)
T ss_dssp ETTEEEEEEEEEESHHHHHHHHHHHHHHHHHTT-
T ss_pred EcCeEEEEEEEEeCcccHHHHHHHHHHHHHHCCc
Confidence 3334456777899988777778888888887763
No 31
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=22.73 E-value=1.1e+02 Score=17.01 Aligned_cols=21 Identities=14% Similarity=0.376 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHHHHcCCCce
Q psy3496 77 PNFEAGVHCLREIAKQRCQPS 97 (223)
Q Consensus 77 ~s~~~A~~av~~i~~sgl~Ps 97 (223)
.++++|.+.+.++.+.|+.|.
T Consensus 14 ~~~~~a~~~~~~M~~~g~~p~ 34 (35)
T TIGR00756 14 GRVEEALELFKEMLERGIEPD 34 (35)
T ss_pred CCHHHHHHHHHHHHHcCCCCC
Confidence 578899999999998888875
No 32
>KOG0105|consensus
Probab=21.82 E-value=81 Score=28.04 Aligned_cols=35 Identities=23% Similarity=0.390 Sum_probs=28.7
Q ss_pred eeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHH
Q psy3496 52 FGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLRE 88 (223)
Q Consensus 52 LGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~ 88 (223)
.|-|+++.||..|-|+- ++++-|++..+|-+|+..
T Consensus 30 yg~i~~ieLK~r~g~pp--fafVeFEd~RDAeDAiyg 64 (241)
T KOG0105|consen 30 YGRIREIELKNRPGPPP--FAFVEFEDPRDAEDAIYG 64 (241)
T ss_pred hcceEEEEeccCCCCCC--eeEEEecCccchhhhhhc
Confidence 57899999999998754 566788999999888763
No 33
>KOG0146|consensus
Probab=20.01 E-value=1e+02 Score=28.88 Aligned_cols=56 Identities=13% Similarity=0.270 Sum_probs=43.5
Q ss_pred CceeeEeEEEEEeecCCCceeEEEEEcCCHHHHHHHHHHHHHcCCCce-----EEEeechh
Q psy3496 50 GTFGVITKVVLKIRPLPKCRKYGSIVFPNFEAGVHCLREIAKQRCQPS-----SIRLMDNA 105 (223)
Q Consensus 50 GTLGIITEatLKL~P~P~~~~t~l~~F~s~~~A~~av~~i~~sgl~Ps-----alElmD~~ 105 (223)
-++|.|+|+|+-=-|.-..+-.+++-|.+-.+|-.+++.+-.+.-.|- .+-|-|.+
T Consensus 41 ~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTd 101 (371)
T KOG0146|consen 41 QPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTD 101 (371)
T ss_pred cccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccch
Confidence 689999999997667767788999999999999999998876654443 34455543
Done!