Query psy4802
Match_columns 103
No_of_seqs 127 out of 945
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 18:08:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4802hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13506 formate--tetrahydrofo 100.0 1.4E-47 3E-52 329.0 7.8 99 4-102 289-389 (578)
2 PRK13507 formate--tetrahydrofo 100.0 2.6E-47 5.7E-52 327.5 8.5 99 4-102 297-397 (587)
3 PLN02759 Formate--tetrahydrofo 100.0 3.9E-46 8.3E-51 322.4 8.3 99 4-102 343-446 (637)
4 PF01268 FTHFS: Formate--tetra 100.0 1.3E-45 2.8E-50 316.0 5.5 91 4-102 275-367 (557)
5 cd00477 FTHFS Formyltetrahydro 100.0 4.1E-45 9E-50 311.2 7.7 91 4-102 259-352 (524)
6 COG2759 MIS1 Formyltetrahydrof 100.0 2.5E-44 5.5E-49 305.8 7.1 91 4-102 273-365 (554)
7 PRK13505 formate--tetrahydrofo 100.0 3.5E-44 7.7E-49 307.2 7.3 91 4-102 276-368 (557)
8 PTZ00386 formyl tetrahydrofola 100.0 4.1E-43 8.9E-48 303.1 8.1 91 4-102 338-433 (625)
9 KOG4230|consensus 100.0 5.1E-38 1.1E-42 274.8 7.3 98 5-102 638-746 (935)
10 COG0108 RibB 3,4-dihydroxy-2-b 44.0 6.4 0.00014 31.2 -0.4 21 26-56 143-163 (203)
11 PF03865 ShlB: Haemolysin secr 41.2 18 0.00038 29.9 1.7 22 69-97 12-33 (404)
12 COG2359 SpoVS Stage V sporulat 38.4 27 0.00057 24.5 2.0 38 4-41 32-70 (87)
13 PF15590 Imm15: Immunity prote 37.8 19 0.00042 24.3 1.2 18 62-85 46-63 (69)
14 TIGR01219 Pmev_kin_ERG8 phosph 33.0 16 0.00034 31.6 0.3 36 33-68 136-176 (454)
15 PRK05773 3,4-dihydroxy-2-butan 31.0 14 0.0003 29.3 -0.4 20 26-55 163-182 (219)
16 TIGR00677 fadh2_euk methylenet 27.3 21 0.00046 28.4 0.1 57 21-82 162-222 (281)
17 PRK00415 rps27e 30S ribosomal 25.9 20 0.00044 23.4 -0.2 12 35-46 7-18 (59)
18 PTZ00316 profilin; Provisional 25.8 20 0.00043 27.2 -0.3 51 10-61 43-101 (150)
19 PRK00910 ribB 3,4-dihydroxy-2- 25.5 21 0.00046 28.3 -0.2 14 42-56 162-175 (218)
20 KOG0181|consensus 25.0 35 0.00076 27.6 0.9 26 38-63 70-95 (233)
21 PRK09314 bifunctional 3,4-dihy 24.9 32 0.0007 28.9 0.7 21 26-56 143-163 (339)
22 PF01667 Ribosomal_S27e: Ribos 24.4 21 0.00046 22.8 -0.3 10 36-45 4-13 (55)
23 PRK08815 GTP cyclohydrolase; P 24.1 22 0.00048 30.1 -0.4 19 25-52 120-138 (375)
24 TIGR00506 ribB 3,4-dihydroxy-2 23.4 24 0.00051 27.5 -0.3 21 26-56 144-164 (199)
25 TIGR02869 spore_SleB spore cor 21.0 44 0.00095 25.5 0.7 79 9-90 14-94 (201)
26 PRK01792 ribB 3,4-dihydroxy-2- 20.5 29 0.00064 27.5 -0.3 13 42-55 161-173 (214)
27 PF11265 Med25_VWA: Mediator c 20.4 19 0.00041 28.7 -1.4 28 41-68 79-106 (226)
No 1
>PRK13506 formate--tetrahydrofolate ligase; Provisional
Probab=100.00 E-value=1.4e-47 Score=328.99 Aligned_cols=99 Identities=28% Similarity=0.295 Sum_probs=97.4
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccC
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYT 81 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~ 81 (103)
.||||||++||+.||+++||+|||||| |||||||||||||.+|++|||+|||||+||||||||++...+|+||+++|.
T Consensus 289 IAhG~nSviAt~~aLklaDyvVTEAGFGaDlGaEKF~dIkcr~~gl~P~a~VlVaTvRALK~hGG~~~~~~g~pl~~~l~ 368 (578)
T PRK13506 289 IAHGNSSIIADRIALKLADYVVTEGGFGSDMGFEKFCNIKARQSGKAPDCAVLVATLRALKANSGLYDLRPGQALPDSIN 368 (578)
T ss_pred ccccchHHHHHHHHHhhcCeEEeeccccCCCCCceeeeeeeccCCCCCceEEEEEEeehHHhcCCCCCcccCcccchhcc
Confidence 589999999999999999999999999 999999999999999999999999999999999999989999999999999
Q ss_pred cCCHHHHHHhHhhHHHhhccC
Q psy4802 82 EVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 82 ~enl~al~kG~~NL~kHIeNi 102 (103)
+||+++|++||+||+|||+|+
T Consensus 369 ~en~~al~~G~~NL~~Hi~n~ 389 (578)
T PRK13506 369 APDQARLEAGFANLKWHINNV 389 (578)
T ss_pred ccCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999996
No 2
>PRK13507 formate--tetrahydrofolate ligase; Provisional
Probab=100.00 E-value=2.6e-47 Score=327.53 Aligned_cols=99 Identities=38% Similarity=0.590 Sum_probs=97.5
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccC
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYT 81 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~ 81 (103)
.||||||++|++.||+++||+|||||| |||||||||||||.+|++|||+|||||+||||||||++..+||+|||++|.
T Consensus 297 IAHG~nSviAt~~ALkladyvVTEAGFGaDlGaEKF~dIkcr~~gl~P~a~VlVaTvRALK~hgG~~~~~~g~~l~~~l~ 376 (587)
T PRK13507 297 IAIGQSSIIADRVGLKLADYHVTESGFGADIGFEKFWNLKCRLSGLKPDCAVIVATIRALKMHGGGPKVVPGKPLPEEYT 376 (587)
T ss_pred hhcccHHHHHHHHHHhcCCeEEeccccCCCCChhheeeeeccccCCCCCEEEEEeEhHHHHHcCCCCccccCCccchhcc
Confidence 489999999999999999999999999 999999999999999999999999999999999999999999999999999
Q ss_pred cCCHHHHHHhHhhHHHhhccC
Q psy4802 82 EVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 82 ~enl~al~kG~~NL~kHIeNi 102 (103)
+||+++|++||+||+|||+|+
T Consensus 377 ~enl~al~~G~~NL~~Hi~n~ 397 (587)
T PRK13507 377 KENVGLVEKGCANLLHHIGTV 397 (587)
T ss_pred ccCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999996
No 3
>PLN02759 Formate--tetrahydrofolate ligase
Probab=100.00 E-value=3.9e-46 Score=322.36 Aligned_cols=99 Identities=37% Similarity=0.542 Sum_probs=97.5
Q ss_pred CCCcchhHHHHHHHHHhh---cceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCC
Q psy4802 4 QAKPCRESAEIVYALLIL---EGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKP 78 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~---~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~ 78 (103)
.||||||++|++.||+++ ||+|||||| |||||||||||||.+|++||++|||||+||||||||++.++||+||++
T Consensus 343 IAhG~nSviAtk~ALkla~~~dyvVTEAGFGaDlGaEKF~dIkcR~~gl~P~a~VlVaTvRALK~hGG~~~~~pg~~l~~ 422 (637)
T PLN02759 343 IAHGNSSIVADQIALKLVGPGGFVVTEAGFGADIGTEKFMNIKCRYSGLKPQCAVIVATVRALKMHGGGPAVVAGKPLDH 422 (637)
T ss_pred ccccchHHHHHHHHHhhcCCCCeEEEecccCCCCchhheecccccccCCCCCEEEEEeehHHHHhcCCCCcccCCccchh
Confidence 589999999999999999 999999999 999999999999999999999999999999999999999999999999
Q ss_pred ccCcCCHHHHHHhHhhHHHhhccC
Q psy4802 79 EYTEVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 79 ~~~~enl~al~kG~~NL~kHIeNi 102 (103)
+|.+||+++|++||+||.|||+|+
T Consensus 423 ~l~~enl~al~~G~~NL~~Hi~n~ 446 (637)
T PLN02759 423 AYTTENVELVEAGCVNLARHIENT 446 (637)
T ss_pred hhcccCHHHHHhhhhhHHHHHHHH
Confidence 999999999999999999999996
No 4
>PF01268 FTHFS: Formate--tetrahydrofolate ligase; InterPro: IPR000559 Formate--tetrahydrofolate ligase (6.3.4.3 from EC) (formyltetrahydrofolate synthetase) (FTHFS) is one of the enzymes participating in the transfer of one-carbon units, an essential element of various biosynthetic pathways. In many of these processes the transfers of one-carbon units are mediated by the coenzyme tetrahydrofolate (THF). In eukaryotes the FTHFS activity is expressed by a multifunctional enzyme, C-1-tetrahydrofolate synthase (C1-THF synthase), which also catalyses the dehydrogenase and cyclohydrolase activities. Two forms of C1-THF synthases are known [], one is located in the mitochondrial matrix, while the second one is cytoplasmic. In both forms the FTHFS domain consists of about 600 amino acid residues and is located in the C-terminal section of C1-THF synthase. In prokaryotes FTHFS activity is expressed by a monofunctional homotetrameric enzyme of about 560 amino acid residues []. The crystal structure of N(10)-formyltetrahydrofolate synthetase from Moorella thermoacetica shows that the subunit is composed of three domains organised around three mixed beta-sheets. There are two cavities between adjacent domains. One of them was identified as the nucleotide binding site by homology modelling. The large domain contains a seven-stranded beta-sheet surrounded by helices on both sides. The second domain contains a five-stranded beta-sheet with two alpha-helices packed on one side while the other two are a wall of the active site cavity. The third domain contains a four-stranded beta-sheet forming a half-barrel. The concave side is covered by two helices while the convex side is another wall of the large cavity. Arg 97 is likely involved in formyl phosphate binding. The tetrameric molecule is relatively flat with the shape of the letter X, and the active sites are located at the end of the subunits far from the subunit interface [].; GO: 0004329 formate-tetrahydrofolate ligase activity, 0005524 ATP binding, 0009396 folic acid-containing compound biosynthetic process; PDB: 2EO2_A 3DO6_B 1FPM_A 3RBO_A 3PZX_B 3QB6_A 1FP7_A 3SIN_B 1EG7_A 3QUS_A ....
Probab=100.00 E-value=1.3e-45 Score=316.03 Aligned_cols=91 Identities=40% Similarity=0.518 Sum_probs=78.1
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccC
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYT 81 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~ 81 (103)
.||||||++|++.||+++||+|||||| |||||||||||||++|++|||+|||||+||||||||+. .++|.
T Consensus 275 IAhG~nSviAt~~al~l~dyvvTEAGFGaDlGaEKF~dIkcr~~gl~P~~~VlVaTvRALK~HGG~~--------~~~l~ 346 (557)
T PF01268_consen 275 IAHGCNSVIATKMALKLADYVVTEAGFGADLGAEKFFDIKCRKSGLKPDAVVLVATVRALKMHGGVA--------KDDLN 346 (557)
T ss_dssp SS--B--HHHHHHHHHHSSEEEEEBSSSTTTHHHHHHHTHHHHHT---SEEEEEEEHHHHHHHTT----------GGGTT
T ss_pred ccccCchHHHHHHHHhhcceeecccccccccChhhhcCccchhcccCcceEEEeeechHHHhhcCCC--------ccccC
Confidence 589999999999999999999999999 99999999999999999999999999999999999997 68899
Q ss_pred cCCHHHHHHhHhhHHHhhccC
Q psy4802 82 EVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 82 ~enl~al~kG~~NL~kHIeNi 102 (103)
+||+++|++||+||+|||+|+
T Consensus 347 ~eNl~al~~G~~NL~rHIeNi 367 (557)
T PF01268_consen 347 EENLEALEKGFANLERHIENI 367 (557)
T ss_dssp S--HHHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999996
No 5
>cd00477 FTHFS Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2 fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze the formylation of tetrahydrofolate, an initial step in the reduction of carbon dioxide and other one-carbon precursors to acetate. In purinolytic organisms, the enzymatic reaction is reversed, liberating formate from 10-formyltetrahydrofolate with concurrent production of ATP.
Probab=100.00 E-value=4.1e-45 Score=311.18 Aligned_cols=91 Identities=43% Similarity=0.522 Sum_probs=88.0
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccC
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYT 81 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~ 81 (103)
.||||||++||+.||+++||+|||||| |||||||||||||.+|++||++|||||+||||||||++ ++++.
T Consensus 259 IAhGcnSviAtk~al~laDyvVTEAGFGaDlGaEKF~dIkcr~~gl~P~a~VlVaTvRALK~hGG~~--------~~~l~ 330 (524)
T cd00477 259 IAHGCNSIIADKIALKLADYVVTEAGFGADLGAEKFFNIKCRYSGLKPDAVVLVATVRALKMHGGVP--------KVTLG 330 (524)
T ss_pred ccccchHHHHHHHHHhhcCeEEeeccccCCCCCceeeeeeeccCCCCCCEEEEEEehHHHHHhCCCC--------cccCC
Confidence 589999999999999999999999999 99999999999999999999999999999999999998 56777
Q ss_pred -cCCHHHHHHhHhhHHHhhccC
Q psy4802 82 -EVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 82 -~enl~al~kG~~NL~kHIeNi 102 (103)
+||+++|++||+||+|||+|+
T Consensus 331 ~~en~~al~~G~~NL~~Hi~n~ 352 (524)
T cd00477 331 LEENLEALEKGFANLRKHIENI 352 (524)
T ss_pred CccCHHHHHhHHHHHHHHHHHH
Confidence 999999999999999999996
No 6
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=100.00 E-value=2.5e-44 Score=305.76 Aligned_cols=91 Identities=42% Similarity=0.549 Sum_probs=89.3
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccC
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYT 81 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~ 81 (103)
.||||||++|++.||+++||+|||||| |||+|||||||||.+|++|||||||||+||||||||++ ++++.
T Consensus 273 IAhGcnSiiAt~~AlkL~dy~VTEAGFgaDlGaEKF~dIK~r~~gl~PdavVlVATvRALK~hGG~~--------~~~l~ 344 (554)
T COG2759 273 IAHGCNSIIATKTALKLADYVVTEAGFGADLGAEKFFDIKCRSSGLKPDAVVLVATVRALKMHGGVP--------KEDLT 344 (554)
T ss_pred hhccchhHHHHHHHHhhcCeEEEecccccccchhhhcceeccccCCCCCeEEEeeehHHHHHcCCCC--------hHHhc
Confidence 489999999999999999999999999 99999999999999999999999999999999999999 79999
Q ss_pred cCCHHHHHHhHhhHHHhhccC
Q psy4802 82 EVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 82 ~enl~al~kG~~NL~kHIeNi 102 (103)
+||+|+|++||+||.|||+|+
T Consensus 345 ~Env~avk~G~aNL~~Hi~Ni 365 (554)
T COG2759 345 EENVDAVKKGFANLLKHIENI 365 (554)
T ss_pred chhHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999996
No 7
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=100.00 E-value=3.5e-44 Score=307.16 Aligned_cols=91 Identities=36% Similarity=0.488 Sum_probs=88.8
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccC
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYT 81 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~ 81 (103)
.||||||++||+.||+++||+|||||| |||||||||||||.+|++||++|||||+||||||||++ .++|.
T Consensus 276 IAhG~nSviAt~~al~ladyvvTEaGFGaDlGaEKF~dIkcr~~gl~P~~~VlVaTvraLK~hgg~~--------~~~l~ 347 (557)
T PRK13505 276 IAHGCNSVLATKTALKLADYVVTEAGFGADLGAEKFLDIKCRKAGLKPDAVVIVATVRALKMHGGVA--------KDDLK 347 (557)
T ss_pred hhcccHHHHHHHHHHhhCCEEEecccccCCCCCceeeeeecccCCCCCCEEEEEeehHHHHHcCCCC--------hhhcc
Confidence 489999999999999999999999999 99999999999999999999999999999999999998 68999
Q ss_pred cCCHHHHHHhHhhHHHhhccC
Q psy4802 82 EVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 82 ~enl~al~kG~~NL~kHIeNi 102 (103)
+||+|++++||.||+|||+|+
T Consensus 348 ~en~Eal~sGl~NL~RHIenv 368 (557)
T PRK13505 348 EENVEALKKGFANLERHIENI 368 (557)
T ss_pred ccCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999986
No 8
>PTZ00386 formyl tetrahydrofolate synthetase; Provisional
Probab=100.00 E-value=4.1e-43 Score=303.11 Aligned_cols=91 Identities=36% Similarity=0.376 Sum_probs=87.7
Q ss_pred CCCcchhHHHHHHHHHhh---cceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCC
Q psy4802 4 QAKPCRESAEIVYALLIL---EGHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKP 78 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~---~~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~ 78 (103)
.||||||++|++.||+++ ||+|||||| |||||||||||||.||++|||+|||||+||||||||++ +.
T Consensus 338 IAhG~nSviAt~~ALkla~~~dyvVTEAGFGaDlGaEKF~dIkcR~sgl~P~a~VlVaTvRALK~hGG~~--------~~ 409 (625)
T PTZ00386 338 IAHGNSSIVADQIALKLAGQDGFVLTEAGFGADIGCEKFFNIKCRTSGLKPDAAVLVATVRALKFHGGVE--------PV 409 (625)
T ss_pred hhcccHHHHHHHHHHHhCCCCCeEEEeccccCCCCchhhccccccccCCCcCEEEEEeehHHHHHhCCCC--------cc
Confidence 489999999999999999 899999999 99999999999999999999999999999999999998 56
Q ss_pred ccCcCCHHHHHHhHhhHHHhhccC
Q psy4802 79 EYTEVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 79 ~~~~enl~al~kG~~NL~kHIeNi 102 (103)
++.+||+++|++||+||.|||+|+
T Consensus 410 ~l~~enl~al~~G~~NL~~Hien~ 433 (625)
T PTZ00386 410 VAGKENLEAVRKGLSNLQRHIQNI 433 (625)
T ss_pred ccCccCHHHHHHHHHHHHHHHHHH
Confidence 777899999999999999999996
No 9
>KOG4230|consensus
Probab=100.00 E-value=5.1e-38 Score=274.80 Aligned_cols=98 Identities=45% Similarity=0.626 Sum_probs=95.2
Q ss_pred CCcchhHHHHHHHHHhhc---------ceecccCc--ccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCC
Q psy4802 5 AKPCRESAEIVYALLILE---------GHLWPSKY--WLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSG 73 (103)
Q Consensus 5 ~~~c~~~~~~~~~l~~~~---------~~~~~~~~--dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G 73 (103)
++|-.|+||-..||++.- |+|||||| |+|+|||||||||+|||.||+|||||||||||+|||+|.++||
T Consensus 638 sigassiiadrialklvgte~~~keagyvvteagf~~dmgmekffnikcr~sgl~p~avvlvatvralk~hgggp~v~pg 717 (935)
T KOG4230|consen 638 SIGASSIIADRIALKLVGTESRPKEAGYVVTEAGFASDMGMEKFFNIKCRYSGLVPNAVVLVATVRALKLHGGGPKVKPG 717 (935)
T ss_pred ccchHHHHHHHHHHHhcCCCCCcccCceEEEecccccccchhheeeeeeecCCCCCceEEEeehhHHHHhcCCCCCCCCC
Confidence 578899999999999964 99999999 9999999999999999999999999999999999999999999
Q ss_pred CCCCCccCcCCHHHHHHhHhhHHHhhccC
Q psy4802 74 QPLKPEYTEVSTSTEHQGCIKGRGQFSPI 102 (103)
Q Consensus 74 ~pl~~~~~~enl~al~kG~~NL~kHIeNi 102 (103)
+|||++|++||+|.+++||+||.|||+|+
T Consensus 718 ~plp~~y~~en~dlv~kg~snl~k~i~n~ 746 (935)
T KOG4230|consen 718 QPLPEEYTEENLDLVEKGCSNLVKQIENI 746 (935)
T ss_pred CCCcHHHHHhhHHHHHHHHHHHHHHHHhH
Confidence 99999999999999999999999999996
No 10
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=44.01 E-value=6.4 Score=31.20 Aligned_cols=21 Identities=29% Similarity=0.234 Sum_probs=15.7
Q ss_pred cccCcccchhhhcccccccCCCCCCeEEEEe
Q psy4802 26 WPSKYWLWMEKFFNIKCRTSGKIPDAVVLVT 56 (103)
Q Consensus 26 ~~~~~dLGaEKF~dIKcR~sGl~PdavVLVa 56 (103)
||+.-|| ||.+|++| +.|++=
T Consensus 143 TEasVdL---------arlAGl~P-a~VicE 163 (203)
T COG0108 143 TEAAVDL---------ARLAGLKP-AGVICE 163 (203)
T ss_pred HHHHHHH---------HHHcCCCC-cEEEEE
Confidence 5666677 99999999 555544
No 11
>PF03865 ShlB: Haemolysin secretion/activation protein ShlB/FhaC/HecB; InterPro: IPR005565 Haemolysin (HlyA) and related toxins are secreted across both the cytoplasmic and outer membranes of Gram-negative bacteria in a process which proceeds without a periplasmic intermediate. HlyA is directed by an uncleaved C-terminal targeting signal and the HlyD and HlyB translocator proteins [].; PDB: 2QDZ_A 3NJT_A.
Probab=41.23 E-value=18 Score=29.89 Aligned_cols=22 Identities=23% Similarity=0.221 Sum_probs=14.8
Q ss_pred CCCCCCCCCCccCcCCHHHHHHhHhhHHH
Q psy4802 69 SVVSGQPLKPEYTEVSTSTEHQGCIKGRG 97 (103)
Q Consensus 69 ~~~~G~pl~~~~~~enl~al~kG~~NL~k 97 (103)
+...|+|| |+..||+|++||.|
T Consensus 12 P~~~G~~L-------nlrdlEQgle~lnr 33 (404)
T PF03865_consen 12 PNRKGKPL-------NLRDLEQGLEQLNR 33 (404)
T ss_dssp TT-TT-B---------HHHHHHHHHHH-S
T ss_pred CCCCCCCC-------CHHHHHHHHHHhcc
Confidence 45678888 99999999999975
No 12
>COG2359 SpoVS Stage V sporulation protein SpoVS [Function unknown]
Probab=38.40 E-value=27 Score=24.49 Aligned_cols=38 Identities=32% Similarity=0.244 Sum_probs=27.5
Q ss_pred CCCcchhHHHHHHHHHhhcceecccCcccchhh-hcccc
Q psy4802 4 QAKPCRESAEIVYALLILEGHLWPSKYWLWMEK-FFNIK 41 (103)
Q Consensus 4 ~~~~c~~~~~~~~~l~~~~~~~~~~~~dLGaEK-F~dIK 41 (103)
||-|---+-..+-|+.++-+-|+|+|.||=.-- |.+|+
T Consensus 32 QAiGagAvNQaVKAiAiaRgflapsGidL~~vPaF~~i~ 70 (87)
T COG2359 32 QAIGAGAVNQAVKAIAIARGFLAPSGIDLVCVPAFTEIE 70 (87)
T ss_pred eeechHHHHHHHHHHHHHhhccCccCCcEEEeeeeEEEE
Confidence 445555555667899999999999999985543 55543
No 13
>PF15590 Imm15: Immunity protein 15
Probab=37.76 E-value=19 Score=24.32 Aligned_cols=18 Identities=39% Similarity=0.746 Sum_probs=12.8
Q ss_pred HhhCCCCCCCCCCCCCCccCcCCH
Q psy4802 62 KMHGGGPSVVSGQPLKPEYTEVST 85 (103)
Q Consensus 62 K~HGG~~~~~~G~pl~~~~~~enl 85 (103)
.||||+| |....++++..
T Consensus 46 ~~hGGGp------P~L~~~sq~~~ 63 (69)
T PF15590_consen 46 HMHGGGP------PRLKVISQPDV 63 (69)
T ss_pred cccCCCC------CcccccccHHH
Confidence 5999998 45666666654
No 14
>TIGR01219 Pmev_kin_ERG8 phosphomevalonate kinase, ERG8-type, eukaryotic branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents plant and fungal forms of the ERG8 type of phosphomevalonate kinase.
Probab=33.01 E-value=16 Score=31.63 Aligned_cols=36 Identities=17% Similarity=-0.039 Sum_probs=28.3
Q ss_pred chhhhccc-----ccccCCCCCCeEEEEeehHHHHhhCCCC
Q psy4802 33 WMEKFFNI-----KCRTSGKIPDAVVLVTTVRALKMHGGGP 68 (103)
Q Consensus 33 GaEKF~dI-----KcR~sGl~PdavVLVaTvRALK~HGG~~ 68 (103)
+..+|... .-+..||-.+++|.||+++||=.|-|..
T Consensus 136 ~~~~f~~~~~~~~e~~K~GLGSSAAvtVa~v~ALl~~~~~~ 176 (454)
T TIGR01219 136 PFASITFNAAEKPEVAKTGLGSSAAMTTALVAALLHYLGVV 176 (454)
T ss_pred cccccccccccCCCccccCccHHHHHHHHHHHHHHHHhCCc
Confidence 45788887 4678899999999999999995554443
No 15
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=31.00 E-value=14 Score=29.30 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=14.1
Q ss_pred cccCcccchhhhcccccccCCCCCCeEEEE
Q psy4802 26 WPSKYWLWMEKFFNIKCRTSGKIPDAVVLV 55 (103)
Q Consensus 26 ~~~~~dLGaEKF~dIKcR~sGl~PdavVLV 55 (103)
||+..|| ||.+|+.| +.|++
T Consensus 163 TEasvdL---------a~lAGl~P-~~vic 182 (219)
T PRK05773 163 TELSIAL---------AQAAGLEP-SAVIA 182 (219)
T ss_pred hHHHHHH---------HHHcCCCc-cEEEE
Confidence 5555577 99999999 44443
No 16
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=27.26 E-value=21 Score=28.42 Aligned_cols=57 Identities=18% Similarity=0.066 Sum_probs=36.5
Q ss_pred hcceecccCcccch-hhhcccccccCCCCCCeEEEEeehHHHH---hhCCCCCCCCCCCCCCccCc
Q psy4802 21 LEGHLWPSKYWLWM-EKFFNIKCRTSGKIPDAVVLVTTVRALK---MHGGGPSVVSGQPLKPEYTE 82 (103)
Q Consensus 21 ~~~~~~~~~~dLGa-EKF~dIKcR~sGl~PdavVLVaTvRALK---~HGG~~~~~~G~pl~~~~~~ 82 (103)
+||-+|.--||.-. ++|++ +||..|+..-.+.=+.-+.++| +.-. .+|-.+|+++.+
T Consensus 162 A~f~iTQ~~Fd~~~~~~f~~-~~~~~gi~~PIi~GI~pi~s~~~~~~~~~----~~Gi~vP~~l~~ 222 (281)
T TIGR00677 162 ADFIITQLFYDVDNFLKFVN-DCRAIGIDCPIVPGIMPINNYASFLRRAK----WSKTKIPQEIMS 222 (281)
T ss_pred CCEeeccceecHHHHHHHHH-HHHHcCCCCCEEeeccccCCHHHHHHHHh----cCCCCCCHHHHH
Confidence 68999999999876 67877 6999988766544333333333 2211 346666765543
No 17
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=25.89 E-value=20 Score=23.38 Aligned_cols=12 Identities=33% Similarity=1.007 Sum_probs=9.3
Q ss_pred hhhcccccccCC
Q psy4802 35 EKFFNIKCRTSG 46 (103)
Q Consensus 35 EKF~dIKcR~sG 46 (103)
-+|+++||+-=+
T Consensus 7 S~F~~VkCp~C~ 18 (59)
T PRK00415 7 SRFLKVKCPDCG 18 (59)
T ss_pred CeEEEEECCCCC
Confidence 369999998654
No 18
>PTZ00316 profilin; Provisional
Probab=25.78 E-value=20 Score=27.15 Aligned_cols=51 Identities=20% Similarity=0.158 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhhcceecccCcccchhhhccccc------c--cCCCCCCeEEEEeehHHH
Q psy4802 10 ESAEIVYALLILEGHLWPSKYWLWMEKFFNIKC------R--TSGKIPDAVVLVTTVRAL 61 (103)
Q Consensus 10 ~~~~~~~~l~~~~~~~~~~~~dLGaEKF~dIKc------R--~sGl~PdavVLVaTvRAL 61 (103)
|+..+..+.+=. -.++..|+.+|.+|||=|+. | +.-.....++++-|-.|+
T Consensus 43 E~~~I~~~F~d~-~~l~~~Gi~l~G~KY~~lr~~~d~d~~~i~gKKg~~G~~i~kT~qai 101 (150)
T PTZ00316 43 EVAHILKCLGNF-SLVQSSGVTIYGVKFFGLQSGTEGDMKYIFFKKGAAGGCIYTSKQTA 101 (150)
T ss_pred HHHHHHHHhcCC-ccccCCCEEEcceEEEEEEeccCCCcceEEEecCCCeEEEEEcCCEE
Confidence 344444444322 35778899999999997653 2 233333456666555544
No 19
>PRK00910 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=25.47 E-value=21 Score=28.32 Aligned_cols=14 Identities=36% Similarity=0.422 Sum_probs=10.8
Q ss_pred cccCCCCCCeEEEEe
Q psy4802 42 CRTSGKIPDAVVLVT 56 (103)
Q Consensus 42 cR~sGl~PdavVLVa 56 (103)
||.+|+.| +.|++-
T Consensus 162 a~lAGl~p-~~vicE 175 (218)
T PRK00910 162 MQMAGLQP-AGVLCE 175 (218)
T ss_pred HHHcCCCc-eEEEEE
Confidence 99999999 555544
No 20
>KOG0181|consensus
Probab=24.97 E-value=35 Score=27.64 Aligned_cols=26 Identities=38% Similarity=0.427 Sum_probs=22.1
Q ss_pred cccccccCCCCCCeEEEEeehHHHHh
Q psy4802 38 FNIKCRTSGKIPDAVVLVTTVRALKM 63 (103)
Q Consensus 38 ~dIKcR~sGl~PdavVLVaTvRALK~ 63 (103)
-+|=|-+||+.||+=|+|--.|-+-.
T Consensus 70 ~~IG~vYSGmgpD~RvlV~~~rkiAe 95 (233)
T KOG0181|consen 70 PHIGCVYSGMGPDYRVLVHKSRKIAE 95 (233)
T ss_pred CCcceEEecCCCceeehhhHHHHHHH
Confidence 47889999999999999988776643
No 21
>PRK09314 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional
Probab=24.91 E-value=32 Score=28.90 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=15.0
Q ss_pred cccCcccchhhhcccccccCCCCCCeEEEEe
Q psy4802 26 WPSKYWLWMEKFFNIKCRTSGKIPDAVVLVT 56 (103)
Q Consensus 26 ~~~~~dLGaEKF~dIKcR~sGl~PdavVLVa 56 (103)
||+..|| ||.+|+.| +.|++-
T Consensus 143 TEaavdL---------a~lAGl~p-~~vicE 163 (339)
T PRK09314 143 TEGSVDL---------CKLAGLKP-VAVICE 163 (339)
T ss_pred CchhhHH---------HHHcCCCc-eEEEEE
Confidence 5666676 99999999 455543
No 22
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=24.42 E-value=21 Score=22.84 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=6.4
Q ss_pred hhcccccccC
Q psy4802 36 KFFNIKCRTS 45 (103)
Q Consensus 36 KF~dIKcR~s 45 (103)
+|||+||+-=
T Consensus 4 ~Fm~VkCp~C 13 (55)
T PF01667_consen 4 YFMDVKCPGC 13 (55)
T ss_dssp -EEEEE-TTT
T ss_pred cEEEEECCCC
Confidence 6999999753
No 23
>PRK08815 GTP cyclohydrolase; Provisional
Probab=24.13 E-value=22 Score=30.05 Aligned_cols=19 Identities=21% Similarity=0.139 Sum_probs=14.6
Q ss_pred ecccCcccchhhhcccccccCCCCCCeE
Q psy4802 25 LWPSKYWLWMEKFFNIKCRTSGKIPDAV 52 (103)
Q Consensus 25 ~~~~~~dLGaEKF~dIKcR~sGl~Pdav 52 (103)
++|++.|| ||.+|+.|.+|
T Consensus 120 f~EAavDL---------arLAGl~Paav 138 (375)
T PRK08815 120 LDAGAVEI---------ARLALLLPAMV 138 (375)
T ss_pred ccHHHHHH---------HHHcCCCceEE
Confidence 35667777 99999999543
No 24
>TIGR00506 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase. Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal.
Probab=23.43 E-value=24 Score=27.53 Aligned_cols=21 Identities=24% Similarity=0.174 Sum_probs=15.0
Q ss_pred cccCcccchhhhcccccccCCCCCCeEEEEe
Q psy4802 26 WPSKYWLWMEKFFNIKCRTSGKIPDAVVLVT 56 (103)
Q Consensus 26 ~~~~~dLGaEKF~dIKcR~sGl~PdavVLVa 56 (103)
||+..|| ||.+|+.| +.|++-
T Consensus 144 TEaavdL---------~~lAGl~p-~~vicE 164 (199)
T TIGR00506 144 TEASVDL---------AELAGLKP-AGVICE 164 (199)
T ss_pred HHHHHHH---------HHHcCCCc-eEEEEE
Confidence 5666677 99999999 444443
No 25
>TIGR02869 spore_SleB spore cortex-lytic enzyme. Members of this protein family are the spore cortex-lytic enzyme SleB from Bacillus subtilis and other Gram-positive, endospore-forming bacterial species. This protein is stored in an inactive form in the spore and activated during germination.
Probab=20.96 E-value=44 Score=25.47 Aligned_cols=79 Identities=14% Similarity=-0.058 Sum_probs=45.2
Q ss_pred hhHHHHHHHHHhhcceecc--cCcccchhhhcccccccCCCCCCeEEEEeehHHHHhhCCCCCCCCCCCCCCccCcCCHH
Q psy4802 9 RESAEIVYALLILEGHLWP--SKYWLWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTEVSTS 86 (103)
Q Consensus 9 ~~~~~~~~~l~~~~~~~~~--~~~dLGaEKF~dIKcR~sGl~PdavVLVaTvRALK~HGG~~~~~~G~pl~~~~~~enl~ 86 (103)
..+..+...|..+.|..-+ .-||-..++-.--==+.-||.||.+|=-.|.++|.+-...+++.. .+..++.++++
T Consensus 14 ~~V~~LQ~~L~~lG~~~g~idG~fg~~T~~AV~~FQ~~~GL~~dG~vg~~T~~~L~~~~~~~~~~~---~~~~~s~~di~ 90 (201)
T TIGR02869 14 SDVIEIQRRLKAWGYYNGKVDGVFGWLTYWAVRKFQSKNGLTVDGIVGPKTKAALGIATTQQSSAN---SSFGYSNQDID 90 (201)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCccCHHHHHHHHHHHHHhCCCCCCCcCHHHHHHhCCccccCccCC---CCCCCCHHHHH
Confidence 3455666666666553211 112222221100002456899999999999999966655554321 13566777888
Q ss_pred HHHH
Q psy4802 87 TEHQ 90 (103)
Q Consensus 87 al~k 90 (103)
.|.+
T Consensus 91 ~Lar 94 (201)
T TIGR02869 91 LLAR 94 (201)
T ss_pred HHHH
Confidence 7765
No 26
>PRK01792 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=20.48 E-value=29 Score=27.45 Aligned_cols=13 Identities=31% Similarity=0.314 Sum_probs=9.9
Q ss_pred cccCCCCCCeEEEE
Q psy4802 42 CRTSGKIPDAVVLV 55 (103)
Q Consensus 42 cR~sGl~PdavVLV 55 (103)
||.+|+.| +.|++
T Consensus 161 a~lAGl~p-~~vic 173 (214)
T PRK01792 161 ARLAGYKE-AGVIC 173 (214)
T ss_pred HHHcCCCc-eEEEE
Confidence 99999999 44443
No 27
>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].
Probab=20.35 E-value=19 Score=28.73 Aligned_cols=28 Identities=21% Similarity=0.367 Sum_probs=23.7
Q ss_pred ccccCCCCCCeEEEEeehHHHHhhCCCC
Q psy4802 41 KCRTSGKIPDAVVLVTTVRALKMHGGGP 68 (103)
Q Consensus 41 KcR~sGl~PdavVLVaTvRALK~HGG~~ 68 (103)
-|..+|.++|.-.++-++-++++.||+.
T Consensus 79 ~v~~~g~T~~~~~fl~~L~~I~f~GGG~ 106 (226)
T PF11265_consen 79 IVQRSGPTSSPQKFLQWLDAIQFSGGGF 106 (226)
T ss_pred ceeccCCcCCHHHHHHHHHccCcCCCCc
Confidence 4556788888888899999999999988
Done!