Query 045235
Match_columns 117
No_of_seqs 142 out of 1016
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 11:10:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03157 spermidine hydroxycin 99.9 2.2E-27 4.8E-32 193.1 11.8 94 21-116 51-144 (447)
2 PLN02663 hydroxycinnamoyl-CoA: 99.9 5.8E-25 1.3E-29 177.9 10.8 91 24-116 53-143 (431)
3 PF02458 Transferase: Transfer 99.9 3.6E-25 7.8E-30 177.2 9.1 93 22-116 53-145 (432)
4 PLN00140 alcohol acetyltransfe 99.9 1.6E-24 3.5E-29 176.5 9.9 88 22-116 56-146 (444)
5 PLN02481 Omega-hydroxypalmitat 99.9 1.9E-24 4.2E-29 175.5 10.2 95 21-116 61-156 (436)
6 PF11631 DUF3255: Protein of u 44.3 19 0.0004 24.5 1.9 34 33-66 77-110 (123)
7 COG0771 MurD UDP-N-acetylmuram 43.1 31 0.00068 29.0 3.5 31 28-66 295-325 (448)
8 COG3580 Uncharacterized protei 41.3 19 0.00041 29.3 1.8 14 104-117 273-286 (351)
9 PRK09294 acyltransferase PapA5 32.3 82 0.0018 25.2 4.3 35 23-57 35-69 (416)
10 PF01330 RuvA_N: RuvA N termin 30.2 69 0.0015 18.9 2.7 34 41-76 5-38 (61)
11 TIGR03059 psaOeuk photosystem 29.0 76 0.0016 20.5 2.8 31 10-40 13-44 (82)
12 cd06157 NR_LBD The ligand bind 28.3 74 0.0016 21.2 3.0 35 8-43 113-147 (168)
13 PRK02801 primosomal replicatio 26.4 64 0.0014 21.2 2.3 22 40-65 6-27 (101)
14 PF09857 DUF2084: Uncharacteri 25.6 1.5E+02 0.0032 19.4 3.7 34 41-78 16-53 (85)
15 PF00380 Ribosomal_S9: Ribosom 25.6 57 0.0012 22.5 2.0 20 22-41 65-84 (121)
16 COG0736 AcpS Phosphopantethein 23.9 1.7E+02 0.0036 20.4 4.1 37 25-66 53-89 (127)
17 CHL00079 rps9 ribosomal protei 23.0 64 0.0014 22.6 1.8 19 22-40 74-92 (130)
18 PF03533 SPO11_like: SPO11 hom 22.3 76 0.0016 18.0 1.7 21 16-36 7-27 (43)
19 PLN00210 40S ribosomal protein 21.9 75 0.0016 22.6 2.0 19 22-40 74-92 (141)
20 PF05117 DUF695: Family of unk 20.8 1.2E+02 0.0026 20.6 2.8 45 16-60 53-99 (136)
21 TIGR00516 acpS holo-[acyl-carr 20.6 1.9E+02 0.0042 19.4 3.8 36 26-66 53-88 (121)
22 KOG1753 40S ribosomal protein 20.2 61 0.0013 23.1 1.3 17 24-40 80-96 (145)
23 COG3850 NarQ Signal transducti 20.1 1.8E+02 0.004 25.4 4.3 58 8-67 467-527 (574)
No 1
>PLN03157 spermidine hydroxycinnamoyl transferase; Provisional
Probab=99.95 E-value=2.2e-27 Score=193.07 Aligned_cols=94 Identities=33% Similarity=0.566 Sum_probs=82.6
Q ss_pred hhHHHHHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEEEEeccchhhhcCCCCCCchhhhhccccCCCCCCC
Q 045235 21 KDHVKVIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLEVEANFKLEQLGDAIKPPCPYLEQLIYNVPCSDGI 100 (117)
Q Consensus 21 ~~~~~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fveA~~~~~l~~~~~~~~~p~~~~~~Lvp~~~~~~~~ 100 (117)
.+++++||+|||+||++||||||||++.++|+++|+|||+||.|+||+++++|+|+++ ..|.+.+++|+|..+...+.
T Consensus 51 ~~~~~~Lk~sLs~~L~~fyplAGRl~~~~~g~~~i~c~~~Gv~fveA~~~~~l~~~~~--~~~~~~~~~l~P~~~~~~~~ 128 (447)
T PLN03157 51 GSIIEILKDSLSRALVPFYPLAGRLRWIGGGRLELECNAMGVLLIEAESEAKLDDFGD--FSPTPEFEYLIPSVDYTKPI 128 (447)
T ss_pred ccHHHHHHHHHHHHHhhccccCEEEEEcCCCcEEEEECCCCeEEEEEEeCCcHHHhhc--cCCCHHHHhhcCCCCccccc
Confidence 4678999999999999999999999998889999999999999999999999999976 24556788899976543344
Q ss_pred CCCCeEEEEEEecCCC
Q 045235 101 LGCPLLLIEVSLLFPN 116 (117)
Q Consensus 101 ~~~pll~vQvT~F~CG 116 (117)
...|+++||||+|.||
T Consensus 129 ~~~Pll~vQvT~F~cG 144 (447)
T PLN03157 129 HELPLLLVQLTKFSCG 144 (447)
T ss_pred ccCceEEEEEEEecCC
Confidence 5689999999999999
No 2
>PLN02663 hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase
Probab=99.92 E-value=5.8e-25 Score=177.90 Aligned_cols=91 Identities=38% Similarity=0.650 Sum_probs=79.1
Q ss_pred HHHHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEEEEeccchhhhcCCCCCCchhhhhccccCCCCCCCCCC
Q 045235 24 VKVIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLEVEANFKLEQLGDAIKPPCPYLEQLIYNVPCSDGILGC 103 (117)
Q Consensus 24 ~~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fveA~~~~~l~~~~~~~~~p~~~~~~Lvp~~~~~~~~~~~ 103 (117)
.++||+|||++|++||||||||+.+++|+++|+|||+||.|+||+++++++++++. .+...+++|+|..+...+..+.
T Consensus 53 ~~~Lk~sLs~~L~~~yplaGRl~~~~~g~~~i~c~~~Gv~fv~A~~~~~l~~~~~~--~~~~~~~~l~P~~~~~~~~~~~ 130 (431)
T PLN02663 53 PQVMKEALSKALVPFYPMAGRLRRDEDGRIEIDCNAEGVLFVEADTPSVIDDFGDF--APTLELRQLIPTVDYSGGISSY 130 (431)
T ss_pred HHHHHHHHHHHHhhccccceeeeECCCCCEEEEECCCCceEEEEecCCCHHHhhcc--CCCHHHHhhcCCCCCccccccC
Confidence 58999999999999999999999988899999999999999999999999999762 3555677899875443334568
Q ss_pred CeEEEEEEecCCC
Q 045235 104 PLLLIEVSLLFPN 116 (117)
Q Consensus 104 pll~vQvT~F~CG 116 (117)
|++.||||+|.||
T Consensus 131 P~l~vQvt~F~cG 143 (431)
T PLN02663 131 PLLVLQVTHFKCG 143 (431)
T ss_pred ceEEEEEEEeccC
Confidence 9999999999997
No 3
>PF02458 Transferase: Transferase family; InterPro: IPR003480 This family includes a number of transferase enzymes. These include anthranilate N-hydroxycinnamoyl/benzoyltransferase that catalyzes the first committed reaction of phytoalexin biosynthesis []. Deacetylvindoline 4-O-acetyltransferase (2.3.1.107 from EC) catalyzes the last step in vindoline biosynthesis is also a member of this family []. The motif HXXXD is probably part of the active site. The family also includes trichothecene 3-O-acetyltransferase.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups; PDB: 2BGH_B 2E1U_B 2E1T_A 2E1V_A 2XR7_A 3B30_A 2RKT_A 3B2S_A 2RKV_A 2ZBA_C ....
Probab=99.92 E-value=3.6e-25 Score=177.23 Aligned_cols=93 Identities=38% Similarity=0.651 Sum_probs=78.5
Q ss_pred hHHHHHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEEEEeccchhhhcCCCCCCchhhhhccccCCCCCCCC
Q 045235 22 DHVKVIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLEVEANFKLEQLGDAIKPPCPYLEQLIYNVPCSDGIL 101 (117)
Q Consensus 22 ~~~~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fveA~~~~~l~~~~~~~~~p~~~~~~Lvp~~~~~~~~~ 101 (117)
.+++.||+|||++|++|||||||| .+++|+++|+|||+||.|+||+++.+++++... ..+......|+|..+...+..
T Consensus 53 ~~~~~Lk~sLs~~L~~~~~lAGrl-~~~~~~~~i~c~d~Gv~f~~a~~~~~l~~~~~~-~~~~~~~~~l~p~~~~~~~~~ 130 (432)
T PF02458_consen 53 DIVDNLKESLSKTLVHYYPLAGRL-RDPDGRLEIDCNDDGVEFVEAEADGTLDDLLDL-EPPSEFLRDLVPQLPVSSEGE 130 (432)
T ss_dssp HHHHHHHHHHHHHHTTSGGGGSEE-ESSCTTTEEEECTTTEEEEEEEESS-HHHHCSS-SCCGGGGGGGSSS-SSSEEET
T ss_pred hHHHHHHHHHHHhHhhCcccCcEE-cccccceEEEEecCCCEEEEEecccceeecccc-ccchHHHHHHhhhcccCCccc
Confidence 368999999999999999999999 666899999999999999999999999999874 334455678888766544445
Q ss_pred CCCeEEEEEEecCCC
Q 045235 102 GCPLLLIEVSLLFPN 116 (117)
Q Consensus 102 ~~pll~vQvT~F~CG 116 (117)
..|++.||||+|+||
T Consensus 131 ~~Pll~vQvt~f~~G 145 (432)
T PF02458_consen 131 DAPLLAVQVTRFKCG 145 (432)
T ss_dssp TEBSEEEEEEEETTT
T ss_pred ccceeEeeeeeeccc
Confidence 689999999999999
No 4
>PLN00140 alcohol acetyltransferase family protein; Provisional
Probab=99.91 E-value=1.6e-24 Score=176.54 Aligned_cols=88 Identities=27% Similarity=0.452 Sum_probs=74.3
Q ss_pred hHHHHHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEEEEeccchhhhcCCCCCCc-hhhhhccccCCCC--C
Q 045235 22 DHVKVIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLEVEANFKLEQLGDAIKPPC-PYLEQLIYNVPCS--D 98 (117)
Q Consensus 22 ~~~~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fveA~~~~~l~~~~~~~~~p~-~~~~~Lvp~~~~~--~ 98 (117)
+++++||+|||+||++||||||||+. +++|+|||+||.|+||+++++++|++. .+. ..+++|+|..+.. .
T Consensus 56 ~~~~~Lk~sLs~~L~~fyplAGRl~~----~~~i~cn~~Gv~fveA~~~~~l~d~l~---~~~~~~~~~l~p~~~~~~~~ 128 (444)
T PLN00140 56 QISIQLKRSLSETLSTFYPFSGRVKD----NLIIDNYEEGVPFFETRVKGSLSDFLK---HPQLELLNKFLPCQPFSYES 128 (444)
T ss_pred hHHHHHHHHHHHHHhhhhccCccccC----CceeEccCCCceEEEEEecCcHHHhcC---CCCHHHHHhhCCCCcccccC
Confidence 67899999999999999999999986 689999999999999999999999964 333 4567888865431 1
Q ss_pred CCCCCCeEEEEEEecCCC
Q 045235 99 GILGCPLLLIEVSLLFPN 116 (117)
Q Consensus 99 ~~~~~pll~vQvT~F~CG 116 (117)
+....|+++||||+|+||
T Consensus 129 ~~~~~Pll~vQvT~F~cG 146 (444)
T PLN00140 129 DPEAIPQVAIQVNTFDCG 146 (444)
T ss_pred CccCCceEEEEEEEeccC
Confidence 234579999999999998
No 5
>PLN02481 Omega-hydroxypalmitate O-feruloyl transferase
Probab=99.91 E-value=1.9e-24 Score=175.53 Aligned_cols=95 Identities=43% Similarity=0.713 Sum_probs=81.2
Q ss_pred hhHHHHHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEEEEeccchhhhcCCCCCC-chhhhhccccCCCCCC
Q 045235 21 KDHVKVIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLEVEANFKLEQLGDAIKPP-CPYLEQLIYNVPCSDG 99 (117)
Q Consensus 21 ~~~~~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fveA~~~~~l~~~~~~~~~p-~~~~~~Lvp~~~~~~~ 99 (117)
.+++++||+||+++|++||||||||+.+++|+++|+|||+||.|+||+++.+++|+.+. ..| ...+++|+|..+...+
T Consensus 61 ~~~~~~Lk~sLs~~L~~~~plAGRL~~~~~g~~~i~c~~~Gv~fvea~~d~~l~~l~~~-~~p~~~~~~~l~~~~~~~~~ 139 (436)
T PLN02481 61 EDPVDVIKKALSKVLVHYYPLAGRLTISSEGKLIVDCTGEGVVFVEAEANCSIEEIGDI-TKPDPETLGKLVYDVPGAKN 139 (436)
T ss_pred cCHHHHHHHHHHHHhccccCCCCeeeeCCCCcEEEEEcCCCeEEEEEEecCcHHHhccc-cCCCCHHHHHhCCCCCCccc
Confidence 46889999999999999999999999988899999999999999999999999999752 334 3467788876554333
Q ss_pred CCCCCeEEEEEEecCCC
Q 045235 100 ILGCPLLLIEVSLLFPN 116 (117)
Q Consensus 100 ~~~~pll~vQvT~F~CG 116 (117)
....|+++||||+|+||
T Consensus 140 ~~~~Pll~vQvT~F~~G 156 (436)
T PLN02481 140 ILEIPPLTAQVTRFKCG 156 (436)
T ss_pred ccccceeeeccceEecC
Confidence 44589999999999999
No 6
>PF11631 DUF3255: Protein of unknown function (DUF3255); InterPro: IPR021664 Members in this family of proteins are annotated as YxeF however no function is currently known. The family appears to be restricted to Bacillus. ; PDB: 2JOZ_A.
Probab=44.25 E-value=19 Score=24.55 Aligned_cols=34 Identities=29% Similarity=0.529 Sum_probs=23.3
Q ss_pred HhhhhhccCCeeeeeCCCCceEEEecCCCeeEEE
Q 045235 33 EALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLE 66 (117)
Q Consensus 33 ~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fve 66 (117)
+-|.+|||+-..|++.++|-+...-|++--.+..
T Consensus 77 qylg~~~plkstlkrgen~tliw~~~g~tktmtr 110 (123)
T PF11631_consen 77 QYLGPYYPLKSTLKRGENGTLIWEQNGQTKTMTR 110 (123)
T ss_dssp EEESTT-S-EEEEEE-STT-EEEEETTEEEEEEE
T ss_pred EEcCCCcchhhHhhcCCCCcEEEEecCceeEEEE
Confidence 4588999999999999988888888876544443
No 7
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=43.12 E-value=31 Score=29.00 Aligned_cols=31 Identities=32% Similarity=0.481 Sum_probs=22.7
Q ss_pred HHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEE
Q 045235 28 KEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLE 66 (117)
Q Consensus 28 k~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fve 66 (117)
.+++.++|..|.++.+|+.. .++.+||.|+-
T Consensus 295 ~e~i~~~L~~F~gl~HR~e~--------v~~~~gv~f~N 325 (448)
T COG0771 295 PEAILEALSSFTGLPHRLEF--------VGEKDGVLFIN 325 (448)
T ss_pred HHHHHHHHHhCCCCCcceEE--------EEecCCEEEec
Confidence 35689999999999998754 45555666654
No 8
>COG3580 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.34 E-value=19 Score=29.27 Aligned_cols=14 Identities=7% Similarity=-0.197 Sum_probs=11.8
Q ss_pred CeEEEEEEecCCCC
Q 045235 104 PLLLIEVSLLFPNH 117 (117)
Q Consensus 104 pll~vQvT~F~CG~ 117 (117)
-|-.||+|-|.||+
T Consensus 273 nlegV~l~SFgCG~ 286 (351)
T COG3580 273 NLEGVQLVSFGCGL 286 (351)
T ss_pred CeeeEEEeecccCc
Confidence 35669999999996
No 9
>PRK09294 acyltransferase PapA5; Provisional
Probab=32.25 E-value=82 Score=25.19 Aligned_cols=35 Identities=9% Similarity=0.121 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhhhhhccCCeeeeeCCCCceEEEe
Q 045235 23 HVKVIKEAISEALVYYYPFAGRIKEGPNRKLMVDR 57 (117)
Q Consensus 23 ~~~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~c 57 (117)
-.+.|++||.+++..|+-|..|+...++|.+.+..
T Consensus 35 D~~~L~~Al~~l~~rhp~Lr~~~~~~~~~~~~~~~ 69 (416)
T PRK09294 35 DIDALSDAFDALLRAHPVLAAHLEQDSDGGWELVA 69 (416)
T ss_pred CHHHHHHHHHHHHHhCHHhhEEEEECCCCceEEee
Confidence 46899999999999999999999665556544433
No 10
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=30.21 E-value=69 Score=18.90 Aligned_cols=34 Identities=21% Similarity=0.350 Sum_probs=21.2
Q ss_pred CCeeeeeCCCCceEEEecCCCeeEEEEEeccchhhh
Q 045235 41 FAGRIKEGPNRKLMVDRNGEGILFLEVEANFKLEQL 76 (117)
Q Consensus 41 lAGRL~~~~~g~~~I~cnd~GV~fveA~~~~~l~~~ 76 (117)
+-|++..-..+.+.|+|| ||-|-.-.+..++.++
T Consensus 5 l~G~v~~~~~~~vvi~~~--GvGy~v~v~~~~~~~l 38 (61)
T PF01330_consen 5 LKGKVVEKNPDYVVIDVN--GVGYEVFVPSNTLSEL 38 (61)
T ss_dssp EEEEEEEEESSEEEEEET--TEEEEEEE-HHHHHTS
T ss_pred EEEEEEEEcCCEEEEEEC--CEEEEEEeCCchHHhC
Confidence 457777665678899999 5555444444445554
No 11
>TIGR03059 psaOeuk photosystem I protein PsaO. Members of this family are the PsaO protein of photosystem I. This protein is found in chloroplasts but not in Cyanobacteria.
Probab=29.03 E-value=76 Score=20.46 Aligned_cols=31 Identities=19% Similarity=0.314 Sum_probs=25.0
Q ss_pred CCCC-CCCCCCchhHHHHHHHHHHHhhhhhcc
Q 045235 10 NPSS-SPPILREKDHVKVIKEAISEALVYYYP 40 (117)
Q Consensus 10 ~p~~-~~~~~~~~~~~~~Lk~SLs~aL~~yyp 40 (117)
-||. +-|.-+.+++....-+|..+-|+||+-
T Consensus 13 ~Ps~~~ip~~~g~SLtglF~~sIg~~LAhFPt 44 (82)
T TIGR03059 13 LPTVLNVPLYGGKSLTGLFASSIGENLAHFPA 44 (82)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHhcCCC
Confidence 4664 346677889999999999999999974
No 12
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=28.32 E-value=74 Score=21.20 Aligned_cols=35 Identities=26% Similarity=0.300 Sum_probs=27.1
Q ss_pred ccCCCCCCCCCCchhHHHHHHHHHHHhhhhhccCCe
Q 045235 8 LNNPSSSPPILREKDHVKVIKEAISEALVYYYPFAG 43 (117)
Q Consensus 8 ~~~p~~~~~~~~~~~~~~~Lk~SLs~aL~~yyplAG 43 (117)
+.+|..+. +......+..+++.+.++|..||...+
T Consensus 113 l~~~~~~~-s~~~~~~~~~~~~~~~~~L~~y~~~~~ 147 (168)
T cd06157 113 LFSPDRKE-SLEDRKIVEELQERLLEALQDYLRKNY 147 (168)
T ss_pred HhCCCCCC-CccCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 34566654 556778999999999999999996543
No 13
>PRK02801 primosomal replication protein N; Provisional
Probab=26.39 E-value=64 Score=21.19 Aligned_cols=22 Identities=14% Similarity=0.116 Sum_probs=13.4
Q ss_pred cCCeeeeeCCCCceEEEecCCCeeEE
Q 045235 40 PFAGRIKEGPNRKLMVDRNGEGILFL 65 (117)
Q Consensus 40 plAGRL~~~~~g~~~I~cnd~GV~fv 65 (117)
-|.|||.. .+++.++..|+.++
T Consensus 6 ~L~Grl~~----dpelr~Tp~G~~v~ 27 (101)
T PRK02801 6 VLSGTVCR----TPKRKVSPSGIPHC 27 (101)
T ss_pred EEEEEECc----CcceEECCCCCeEE
Confidence 36799987 34555555554443
No 14
>PF09857 DUF2084: Uncharacterized protein conserved in bacteria (DUF2084); InterPro: IPR018654 This domain is found in various hypothetical bacterial proteins that have no known function.
Probab=25.62 E-value=1.5e+02 Score=19.43 Aligned_cols=34 Identities=24% Similarity=0.440 Sum_probs=25.0
Q ss_pred CCeeeee--CCCCce-EEEe-cCCCeeEEEEEeccchhhhcC
Q 045235 41 FAGRIKE--GPNRKL-MVDR-NGEGILFLEVEANFKLEQLGD 78 (117)
Q Consensus 41 lAGRL~~--~~~g~~-~I~c-nd~GV~fveA~~~~~l~~~~~ 78 (117)
-.|||.. +++|++ .|.| +-+|-.+ ++|+++-|..
T Consensus 16 qGG~I~~~rd~~gri~~v~C~TReG~~l----~dctl~vF~k 53 (85)
T PF09857_consen 16 QGGRIRHERDDSGRITAVECYTREGWLL----SDCTLAVFRK 53 (85)
T ss_pred cCCeEEEEECCCCCEEEEEEEccCCeee----CCCCHHHHHH
Confidence 4788874 467874 6899 5689776 5888887754
No 15
>PF00380 Ribosomal_S9: Ribosomal protein S9/S16; InterPro: IPR000754 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian; plant; and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V46_I 3T1H_I 3MR8_I 3F1G_I 3D5C_I 3D5A_I 2WDG_I 3MS0_I 2WDM_I 2J02_I ....
Probab=25.55 E-value=57 Score=22.49 Aligned_cols=20 Identities=35% Similarity=0.474 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHhhhhhccC
Q 045235 22 DHVKVIKEAISEALVYYYPF 41 (117)
Q Consensus 22 ~~~~~Lk~SLs~aL~~yypl 41 (117)
.-..+++.++|++|+.|+|-
T Consensus 65 gQa~Air~aiaraL~~~~~~ 84 (121)
T PF00380_consen 65 GQAGAIRLAIARALVKFNPS 84 (121)
T ss_dssp HHHHHHHHHHHHHHHHHHTT
T ss_pred eehHHHHHHHHHHHHHHhHH
Confidence 35788999999999999994
No 16
>COG0736 AcpS Phosphopantetheinyl transferase (holo-ACP synthase) [Lipid metabolism]
Probab=23.91 E-value=1.7e+02 Score=20.41 Aligned_cols=37 Identities=19% Similarity=0.130 Sum_probs=21.9
Q ss_pred HHHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEE
Q 045235 25 KVIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLE 66 (117)
Q Consensus 25 ~~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fve 66 (117)
=+.|+|.++||.. .+...+.+ ..++|.-+.-|.+.++
T Consensus 53 fAaKEA~~KAlgt--gi~~~~~~---~diei~~d~~g~P~v~ 89 (127)
T COG0736 53 FAAKEAVSKALGT--GIGKGVSF---KDIEILNDELGKPTVR 89 (127)
T ss_pred HHHHHHHHHHhcc--Ccccceee---eeEEEEEcCCCCcEEE
Confidence 3589999999987 44443444 2344444444555554
No 17
>CHL00079 rps9 ribosomal protein S9
Probab=22.95 E-value=64 Score=22.62 Aligned_cols=19 Identities=21% Similarity=0.373 Sum_probs=16.8
Q ss_pred hHHHHHHHHHHHhhhhhcc
Q 045235 22 DHVKVIKEAISEALVYYYP 40 (117)
Q Consensus 22 ~~~~~Lk~SLs~aL~~yyp 40 (117)
.-+.+++.++|++|+.|.|
T Consensus 74 gQa~Air~aIaraLv~~~~ 92 (130)
T CHL00079 74 GQAEAIRLGLARALCKINP 92 (130)
T ss_pred HHHHHHHHHHHHHHHHHCH
Confidence 4578999999999999987
No 18
>PF03533 SPO11_like: SPO11 homologue; InterPro: IPR004084 Spo11 is a meiosis-specific protein in yeast that covalently binds to DNA double-strand breaks (DSBs) during the early stages of meiosis []. These DSBs initiate homologous recombination, which is required for chromosomal segregation and generation of genetic diversity during meiosis. Mouse and human homologues of Spo11 have been cloned and characterised. The proteins are 82% identical and share ~25% identity with other family members. Mouse Spo11 has been localised to chromosome 2H4, and human SPO11 to chromosome 20q13.2-q13.3, a region amplified in some breast and ovarian tumours []. Similarity between SPO11 and archaebacterial TOP6A proteins points to evolutionary specialisation of a DNA-cleavage function for meiotic recombination []. Note that the yeast SPO11 protein shares far less similarity to other SPO11 proteins than the human and mouse homologues do to each other.; GO: 0003677 DNA binding, 0007131 reciprocal meiotic recombination
Probab=22.33 E-value=76 Score=18.03 Aligned_cols=21 Identities=14% Similarity=0.066 Sum_probs=17.9
Q ss_pred CCCCchhHHHHHHHHHHHhhh
Q 045235 16 PILREKDHVKVIKEAISEALV 36 (117)
Q Consensus 16 ~~~~~~~~~~~Lk~SLs~aL~ 36 (117)
|...|.+++++=|.||..+|.
T Consensus 7 PeASFf~vLdrHRasLlaal~ 27 (43)
T PF03533_consen 7 PEASFFEVLDRHRASLLAALR 27 (43)
T ss_pred cchHHHHHHHHHHHHHHHHHH
Confidence 556788899999999999886
No 19
>PLN00210 40S ribosomal protein S16; Provisional
Probab=21.92 E-value=75 Score=22.57 Aligned_cols=19 Identities=37% Similarity=0.730 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHhhhhhcc
Q 045235 22 DHVKVIKEAISEALVYYYP 40 (117)
Q Consensus 22 ~~~~~Lk~SLs~aL~~yyp 40 (117)
.-+.+++.++|++|+.|+|
T Consensus 74 gQa~Air~aiaraL~~~~~ 92 (141)
T PLN00210 74 SQIYAIRQSIAKALVAYYQ 92 (141)
T ss_pred HHHHHHHHHHHHHHHHhcc
Confidence 4578999999999999986
No 20
>PF05117 DUF695: Family of unknown function (DUF695) ; InterPro: IPR016097 This entry is found at the N terminus of a number of proteobacterial proteins of unknown function.
Probab=20.76 E-value=1.2e+02 Score=20.57 Aligned_cols=45 Identities=27% Similarity=0.302 Sum_probs=31.3
Q ss_pred CCCCchhHHHHHHHHHHHhhhhh--ccCCeeeeeCCCCceEEEecCC
Q 045235 16 PILREKDHVKVIKEAISEALVYY--YPFAGRIKEGPNRKLMVDRNGE 60 (117)
Q Consensus 16 ~~~~~~~~~~~Lk~SLs~aL~~y--yplAGRL~~~~~g~~~I~cnd~ 60 (117)
|.......+..+.+.|...|... .-++||+..+....+..-|.+.
T Consensus 53 P~~ee~~~L~~iEd~i~~~l~~~~~~i~vG~~t~~g~r~~~fY~~d~ 99 (136)
T PF05117_consen 53 PSEEEYEELNDIEDAIIEALEADGNAIYVGRITGNGRREFYFYCKDP 99 (136)
T ss_pred CCHHHHHHHHHHHHHHHHHhhcCCcceEEEEEEECCEEEEEEEECCh
Confidence 44444567888999999999877 5889988875333455555543
No 21
>TIGR00516 acpS holo-[acyl-carrier-protein] synthase. Formerly dpj. This enzyme adds the prosthetic group, phosphopantethiene, to the acyl carrier protein (ACP) apo-enzyme to generate the holo-enzyme. Related phosphopantethiene--protein transferases also exist. There is an orthologous domain in eukaryotic proteins.
Probab=20.63 E-value=1.9e+02 Score=19.42 Aligned_cols=36 Identities=17% Similarity=0.268 Sum_probs=23.9
Q ss_pred HHHHHHHHhhhhhccCCeeeeeCCCCceEEEecCCCeeEEE
Q 045235 26 VIKEAISEALVYYYPFAGRIKEGPNRKLMVDRNGEGILFLE 66 (117)
Q Consensus 26 ~Lk~SLs~aL~~yyplAGRL~~~~~g~~~I~cnd~GV~fve 66 (117)
..|+|++++|.. -+...+.+ ..++|..+..|.+.+.
T Consensus 53 AaKEA~~KAlg~--g~~~~~~~---~diei~~~~~G~P~v~ 88 (121)
T TIGR00516 53 AAKEAFSKAFGT--GIGRQLSF---QDIEIRKDQNGKPLIT 88 (121)
T ss_pred HHHHHHHHHhcc--ccCCCccc---eEEEEEECCCcCeEEE
Confidence 489999999974 22223444 3567777777877776
No 22
>KOG1753 consensus 40S ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=20.20 E-value=61 Score=23.06 Aligned_cols=17 Identities=47% Similarity=0.808 Sum_probs=15.0
Q ss_pred HHHHHHHHHHhhhhhcc
Q 045235 24 VKVIKEAISEALVYYYP 40 (117)
Q Consensus 24 ~~~Lk~SLs~aL~~yyp 40 (117)
+=+++.|.+++|+.||-
T Consensus 80 iyairqa~~kalvayyq 96 (145)
T KOG1753|consen 80 IYAIRQAIAKALVAYYQ 96 (145)
T ss_pred HHHHHHHhhHHHHHHHH
Confidence 44699999999999997
No 23
>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]
Probab=20.09 E-value=1.8e+02 Score=25.37 Aligned_cols=58 Identities=19% Similarity=0.291 Sum_probs=39.6
Q ss_pred ccCCCCCCCCCCchhHHHHHHHHHHHhhhhhccCCeeeeeC---CCCceEEEecCCCeeEEEE
Q 045235 8 LNNPSSSPPILREKDHVKVIKEAISEALVYYYPFAGRIKEG---PNRKLMVDRNGEGILFLEV 67 (117)
Q Consensus 8 ~~~p~~~~~~~~~~~~~~~Lk~SLs~aL~~yyplAGRL~~~---~~g~~~I~cnd~GV~fveA 67 (117)
+.-|+...|..-.-.++..+++||+.+..| --|-|+.+. ..|+.++...|+|+-|=++
T Consensus 467 ~qlp~~~lpa~qqvHlLqIvREAlsNa~KH--a~As~i~V~~~~~~g~~~~~VeDnG~Gi~~~ 527 (574)
T COG3850 467 YQLPPRALPAHQQVHLLQIVREALSNAIKH--AQASEIKVTVSQNDGQVTLTVEDNGVGIDEA 527 (574)
T ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHh--cccCeEEEEEEecCCeEEEEEeeCCcCCCCc
Confidence 344555544444456889999999999986 456677654 2478888887777766444
Done!