Query 031985
Match_columns 149
No_of_seqs 154 out of 1145
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 08:03:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031985.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031985hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00123 rps6 ribosomal protei 100.0 6.6E-32 1.4E-36 194.2 11.5 92 1-96 5-97 (97)
2 PRK00453 rpsF 30S ribosomal pr 100.0 9.5E-32 2.1E-36 195.7 12.3 100 1-104 1-101 (108)
3 COG0360 RpsF Ribosomal protein 100.0 1.7E-31 3.7E-36 197.0 9.8 103 2-108 1-104 (112)
4 TIGR00166 S6 ribosomal protein 100.0 7.9E-31 1.7E-35 186.4 11.2 91 2-97 1-92 (93)
5 PF01250 Ribosomal_S6: Ribosom 100.0 1.8E-30 3.8E-35 183.4 11.0 91 2-96 1-92 (92)
6 KOG4708 Mitochondrial ribosoma 99.9 3.1E-26 6.7E-31 173.5 2.8 102 1-103 3-105 (141)
7 PRK14074 rpsF 30S ribosomal pr 99.8 1.2E-20 2.5E-25 154.3 8.4 88 14-107 160-248 (257)
8 PRK14074 rpsF 30S ribosomal pr 98.4 3.6E-07 7.8E-12 75.4 4.0 48 1-48 1-48 (257)
9 PLN02289 ribulose-bisphosphate 75.1 12 0.00025 30.0 6.1 99 2-106 65-171 (176)
10 cd03527 RuBisCO_small Ribulose 73.1 12 0.00025 27.2 5.3 87 2-106 1-95 (99)
11 cd04905 ACT_CM-PDT C-terminal 66.7 34 0.00074 22.5 6.8 52 22-84 14-68 (80)
12 cd04893 ACT_GcvR_1 ACT domains 64.2 28 0.00062 23.0 5.5 47 20-80 12-58 (77)
13 cd04902 ACT_3PGDH-xct C-termin 57.2 33 0.00072 21.5 4.7 61 21-95 11-72 (73)
14 PF00736 EF1_GNE: EF-1 guanine 57.1 58 0.0013 22.8 6.2 71 6-88 4-78 (89)
15 PLN03075 nicotianamine synthas 49.7 28 0.00061 29.8 4.3 72 3-78 195-268 (296)
16 cd04880 ACT_AAAH-PDT-like ACT 47.0 76 0.0017 20.4 6.3 51 23-84 13-66 (75)
17 PF03059 NAS: Nicotianamine sy 45.9 53 0.0011 27.8 5.3 72 3-77 192-264 (276)
18 TIGR00337 PyrG CTP synthase. C 44.8 30 0.00066 32.0 4.0 79 10-89 113-208 (525)
19 PRK02220 4-oxalocrotonate taut 43.7 40 0.00086 21.0 3.4 34 1-36 1-34 (61)
20 PLN02327 CTP synthase 43.7 37 0.0008 31.7 4.4 79 10-89 113-214 (557)
21 COG0801 FolK 7,8-dihydro-6-hyd 42.7 29 0.00064 27.2 3.1 46 3-53 54-99 (160)
22 PRK10239 2-amino-4-hydroxy-6-h 42.5 36 0.00078 26.4 3.6 47 3-53 54-100 (159)
23 PRK02289 4-oxalocrotonate taut 40.1 51 0.0011 20.8 3.5 34 1-36 1-34 (60)
24 cd03113 CTGs CTP synthetase (C 39.5 48 0.001 28.0 4.1 79 10-89 112-207 (255)
25 PRK00745 4-oxalocrotonate taut 37.7 61 0.0013 20.1 3.6 33 1-35 1-33 (62)
26 COG4689 Adc Acetoacetate decar 33.3 64 0.0014 26.5 3.7 54 58-112 26-81 (247)
27 PRK14160 heat shock protein Gr 32.6 20 0.00044 29.3 0.8 67 17-97 139-210 (211)
28 PRK14141 heat shock protein Gr 32.3 25 0.00055 28.6 1.3 67 19-98 120-191 (209)
29 cd00292 EF1B Elongation factor 31.9 1.8E+02 0.0039 20.3 6.2 68 8-87 8-76 (88)
30 PF02680 DUF211: Uncharacteriz 31.6 46 0.00099 24.1 2.4 18 25-42 62-79 (95)
31 cd04929 ACT_TPH ACT domain of 31.3 1.6E+02 0.0035 19.6 6.7 51 23-84 14-65 (74)
32 PRK11898 prephenate dehydratas 31.2 3.1E+02 0.0068 22.9 7.8 58 24-92 212-272 (283)
33 cd04904 ACT_AAAH ACT domain of 30.3 1.6E+02 0.0035 19.2 6.3 52 23-85 14-66 (74)
34 PF04914 DltD_C: DltD C-termin 29.6 1.3E+02 0.0028 22.6 4.7 42 5-46 51-101 (130)
35 PF14257 DUF4349: Domain of un 29.2 2.2E+02 0.0047 23.2 6.4 70 17-98 59-129 (262)
36 PF10741 T2SM_b: Type II secre 28.4 2.1E+02 0.0046 20.1 6.8 62 17-87 13-75 (110)
37 PF09373 PMBR: Pseudomurein-bi 28.2 70 0.0015 18.2 2.4 23 12-34 3-25 (33)
38 cd04869 ACT_GcvR_2 ACT domains 27.2 1.8E+02 0.0038 18.7 5.8 52 20-80 10-63 (81)
39 cd04879 ACT_3PGDH-like ACT_3PG 26.0 1.5E+02 0.0033 17.6 4.9 57 21-91 11-68 (71)
40 PF03147 FDX-ACB: Ferredoxin-f 25.9 85 0.0018 21.6 2.9 26 13-38 68-94 (94)
41 PF07876 Dabb: Stress responsi 25.2 2.1E+02 0.0046 18.9 7.0 57 7-70 6-62 (97)
42 COG0504 PyrG CTP synthase (UTP 25.1 1.4E+02 0.003 27.8 4.8 81 8-89 111-207 (533)
43 PRK14147 heat shock protein Gr 24.8 44 0.00095 26.3 1.4 68 18-98 98-170 (172)
44 PRK00199 ihfB integration host 24.4 1.4E+02 0.003 20.5 3.8 38 12-50 15-55 (94)
45 PF15110 TMEM141: TMEM141 prot 24.2 17 0.00036 26.3 -0.9 34 19-53 25-58 (94)
46 smart00411 BHL bacterial (prok 23.9 1.3E+02 0.0029 20.0 3.6 39 12-51 14-55 (90)
47 PF07237 DUF1428: Protein of u 23.4 1.1E+02 0.0023 22.4 3.1 40 5-45 4-43 (103)
48 cd00483 HPPK 7,8-dihydro-6-hyd 23.4 1.2E+02 0.0026 22.4 3.5 46 3-53 51-96 (128)
49 cd04416 NDPk_TX NDP kinase dom 23.1 1.7E+02 0.0036 21.5 4.2 34 6-43 3-36 (132)
50 PF00679 EFG_C: Elongation fac 22.7 2.4E+02 0.0052 19.0 4.7 41 23-80 18-58 (89)
51 PF06877 RraB: Regulator of ri 22.6 1.4E+02 0.0031 20.5 3.6 38 4-44 66-103 (104)
52 PRK00435 ef1B elongation facto 22.2 2.9E+02 0.0062 19.4 5.9 45 8-56 8-52 (88)
53 PRK14157 heat shock protein Gr 21.9 51 0.0011 27.3 1.3 69 17-98 151-224 (227)
54 PRK14163 heat shock protein Gr 21.7 64 0.0014 26.4 1.9 70 17-99 114-188 (214)
55 PF14832 Tautomerase_3: Putati 21.6 1.2E+02 0.0026 22.9 3.2 32 1-33 1-32 (136)
56 PRK14162 heat shock protein Gr 21.2 48 0.001 26.7 1.0 67 18-97 121-193 (194)
57 PF01288 HPPK: 7,8-dihydro-6-h 21.1 1.7E+02 0.0036 21.5 3.9 42 3-49 50-91 (127)
58 PRK05380 pyrG CTP synthetase; 21.0 86 0.0019 29.1 2.7 78 11-89 115-207 (533)
59 PRK14149 heat shock protein Gr 20.2 45 0.00097 26.8 0.7 67 18-98 118-189 (191)
60 PF13670 PepSY_2: Peptidase pr 20.0 1.1E+02 0.0025 20.3 2.6 45 23-73 31-76 (83)
No 1
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=99.98 E-value=6.6e-32 Score=194.20 Aligned_cols=92 Identities=26% Similarity=0.443 Sum_probs=88.7
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ 80 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~ 80 (149)
|+.||+|+|++|++++++++++++++.++|.++||.|.++++||+|+|||||+|+ .+|+|++++|.++|+++++|+
T Consensus 5 mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k~----~~G~Yv~~~f~~~~~~i~ele 80 (97)
T CHL00123 5 LNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKY----EDGIYIQMNYSGNGKLVNSLE 80 (97)
T ss_pred ccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCCC----CEEEEEEEEEEECHHHHHHHH
Confidence 7899999999999999999999999999999999999999999999999999985 499999999999999999995
Q ss_pred -hhhccCCeeEEEEEec
Q 031985 81 -YLNKEDRLLRWLLVKH 96 (149)
Q Consensus 81 -~lr~de~VLR~l~vK~ 96 (149)
.|+++++||||+++|.
T Consensus 81 r~lri~e~VlR~m~vk~ 97 (97)
T CHL00123 81 KALKLDENVLRYLTFKK 97 (97)
T ss_pred HHhCCCCCeEEEEEEeC
Confidence 8999999999999983
No 2
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=99.97 E-value=9.5e-32 Score=195.72 Aligned_cols=100 Identities=24% Similarity=0.475 Sum_probs=94.5
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ 80 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~ 80 (149)
||+||+|+|++|.++++++++++++++++|.++||+|+++++||+|+|||+|+|+ .+|+|++|+|.++|+++++|+
T Consensus 1 M~~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~I~k~----~~G~Y~~~~f~~~~~~i~el~ 76 (108)
T PRK00453 1 MRKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKL----RKGHYVLLNFEAPPAAIAELE 76 (108)
T ss_pred CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEecccccccceEcCCC----cEEEEEEEEEEeCHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999985 499999999999999999996
Q ss_pred -hhhccCCeeEEEEEeccCcccchh
Q 031985 81 -YLNKEDRLLRWLLVKHRGMKNGKE 104 (149)
Q Consensus 81 -~lr~de~VLR~l~vK~~~~~~~~~ 104 (149)
.|++|++||||+++|+++......
T Consensus 77 ~~l~~~~~VlR~~~vk~~~~~~~~~ 101 (108)
T PRK00453 77 RLFRINEDVLRFLTVKVEEAEEEPS 101 (108)
T ss_pred HHhCCCCCeEEEEEEEecccccccC
Confidence 899999999999999988654444
No 3
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.7e-31 Score=197.00 Aligned_cols=103 Identities=23% Similarity=0.443 Sum_probs=97.0
Q ss_pred CceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH-
Q 031985 2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ- 80 (149)
Q Consensus 2 ~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~- 80 (149)
++||+|||++|+++++++.++++++.++|+.+||+|.++++||+|+|||+|+|+. +|+|++|+|.|+|++++||+
T Consensus 1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~----~g~Y~l~~f~~~~~~i~Eler 76 (112)
T COG0360 1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLR----EGHYVLMNFEAEPAAIAELER 76 (112)
T ss_pred CceEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEehhhhhhhhcceecccc----eEEEEEEEEEcCHHHHHHHHH
Confidence 4799999999999999999999999999999999999999999999999999975 89999999999999999995
Q ss_pred hhhccCCeeEEEEEeccCcccchhhhhh
Q 031985 81 YLNKEDRLLRWLLVKHRGMKNGKEARYA 108 (149)
Q Consensus 81 ~lr~de~VLR~l~vK~~~~~~~~~~~~e 108 (149)
.|++|++|||||+||.+..+..++++..
T Consensus 77 ~~rin~~VlR~liik~~~~~~~~~~~~~ 104 (112)
T COG0360 77 LLRINEDVLRHLIIKVEKAKEELSPMLK 104 (112)
T ss_pred HhccchhhheeeEEEechhhcccchhhh
Confidence 8999999999999999998777777653
No 4
>TIGR00166 S6 ribosomal protein S6. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.
Probab=99.97 E-value=7.9e-31 Score=186.35 Aligned_cols=91 Identities=21% Similarity=0.380 Sum_probs=86.8
Q ss_pred CceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH-
Q 031985 2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ- 80 (149)
Q Consensus 2 ~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~- 80 (149)
+.||+|+|++|+++++ +++++++++++|.++||+|+++++||.|+|||||+|+ .+|+|++|+|+++|+++++|+
T Consensus 1 ~~YE~~~Il~p~~~~~-~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~k~----~~G~Y~~~~f~~~~~~i~el~~ 75 (93)
T TIGR00166 1 RHYEIIFLVRPTLSEE-VKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQ----LRAHYVLMNFSGEAQVIKEFER 75 (93)
T ss_pred CceeEEEEECCCCcHH-HHHHHHHHHHHHHhCCCEEEEEEeecceecceEcCCC----ceEEEEEEEEEeCHHHHHHHHH
Confidence 5799999999999888 9999999999999999999999999999999999985 599999999999999999996
Q ss_pred hhhccCCeeEEEEEecc
Q 031985 81 YLNKEDRLLRWLLVKHR 97 (149)
Q Consensus 81 ~lr~de~VLR~l~vK~~ 97 (149)
.|++|++||||+++|.+
T Consensus 76 ~lr~~~~VlR~~~vk~~ 92 (93)
T TIGR00166 76 TARINDNVIRSLIIKLE 92 (93)
T ss_pred HhcCCcCeEEEEEEEec
Confidence 89999999999999974
No 5
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 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 S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=99.97 E-value=1.8e-30 Score=183.37 Aligned_cols=91 Identities=31% Similarity=0.591 Sum_probs=86.2
Q ss_pred CceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH-
Q 031985 2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ- 80 (149)
Q Consensus 2 ~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~- 80 (149)
+.||+|+|++|+++++++++++++++++|.++||+|+++++||.|+|||+|+|+ .+|+|++++|+++|+++++|+
T Consensus 1 r~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~----~~G~Y~~~~f~~~~~~i~el~~ 76 (92)
T PF01250_consen 1 RKYELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQ----KEGHYFLFNFDASPSAIKELER 76 (92)
T ss_dssp EEEEEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTE----CEEEEEEEEEEESTTHHHHHHH
T ss_pred CceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCC----CEEEEEEEEEEeCHHHHHHHHH
Confidence 579999999999999999999999999999999999999999999999999985 699999999999999999996
Q ss_pred hhhccCCeeEEEEEec
Q 031985 81 YLNKEDRLLRWLLVKH 96 (149)
Q Consensus 81 ~lr~de~VLR~l~vK~ 96 (149)
.|+++++||||++||.
T Consensus 77 ~l~~~~~VlR~~~vK~ 92 (92)
T PF01250_consen 77 KLRLDEDVLRYLIVKK 92 (92)
T ss_dssp HHHTSTTEEEEEEEE-
T ss_pred HhcCCCCeEEEEEEeC
Confidence 8999999999999984
No 6
>KOG4708 consensus Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=3.1e-26 Score=173.46 Aligned_cols=102 Identities=42% Similarity=0.764 Sum_probs=94.8
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ 80 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~ 80 (149)
||+||+++|+++...++ ++.++.|.+..+...||+|++|+++|.|.|||+|+|++++|++|+||+|.|.++|++..|+.
T Consensus 3 mp~yelali~~~~~rpe-la~~l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~~v~~ei~ 81 (141)
T KOG4708|consen 3 MPLYELALITRSLSRPE-LAKLLARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSPAVQSEIK 81 (141)
T ss_pred chHHHHHHHhcccCCHH-HHHHHHHHhhHHhhcCCeEeechhcchhhhcchHHHhcCccccceEEEEeecCCHHHHHHHH
Confidence 89999999999986555 78899999999999999999999999999999999999999999999999999999999995
Q ss_pred -hhhccCCeeEEEEEeccCcccch
Q 031985 81 -YLNKEDRLLRWLLVKHRGMKNGK 103 (149)
Q Consensus 81 -~lr~de~VLR~l~vK~~~~~~~~ 103 (149)
.|+.|.+||||++||+++.+...
T Consensus 82 ~~l~~D~dviR~~IVKv~~~~~~~ 105 (141)
T KOG4708|consen 82 RILKRDPDVIRWLIVKVDDIKQEQ 105 (141)
T ss_pred HHHhcChhhHHhhheecccccccc
Confidence 79999999999999999865443
No 7
>PRK14074 rpsF 30S ribosomal protein S6; Provisional
Probab=99.83 E-value=1.2e-20 Score=154.32 Aligned_cols=88 Identities=19% Similarity=0.268 Sum_probs=78.4
Q ss_pred CCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH-hhhccCCeeEEE
Q 031985 14 VRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ-YLNKEDRLLRWL 92 (149)
Q Consensus 14 l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~-~lr~de~VLR~l 92 (149)
+.+++++++++++.++|+++| +.++++||+|+|||||+|. .+|+|++++|.|+|+++++|+ .||++++|||||
T Consensus 160 v~PDQveevvEkik~iIe~~G--iikvE~WGkRkLAYpIkK~----~eGyYvL~nFeAep~aIaELER~lRInE~VIRfL 233 (257)
T PRK14074 160 NGPNQSNKTLEMLLKNIEASG--LIKYEYWGLLDFAYPINKM----KSGHYCIMCISSTSSIMDEFVRRMKLNENIIRHL 233 (257)
T ss_pred CCHHHHHHHHHHHHHHHHhcC--eeehHhhcchhhccccCCC----CeEEEEEEEEEcCHHHHHHHHHHhcCccceeeEE
Confidence 345688999999999999995 5699999999999999985 599999999999999999995 899999999999
Q ss_pred EEeccCcccchhhhh
Q 031985 93 LVKHRGMKNGKEARY 107 (149)
Q Consensus 93 ~vK~~~~~~~~~~~~ 107 (149)
+||+++...+++++.
T Consensus 234 tVKlDe~~~~pSpim 248 (257)
T PRK14074 234 SVQVDKFFEGKSYMM 248 (257)
T ss_pred EEeeccccccCChhh
Confidence 999998776666543
No 8
>PRK14074 rpsF 30S ribosomal protein S6; Provisional
Probab=98.37 E-value=3.6e-07 Score=75.44 Aligned_cols=48 Identities=13% Similarity=0.173 Sum_probs=46.3
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeeccccccc
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQL 48 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~L 48 (149)
||+||.+||++|+++..++..+++.++.++.++||.|.+.+.||.+.-
T Consensus 1 m~lYE~~fIa~q~ls~~q~e~l~e~~~~~l~~~~~~v~~~e~wG~~~~ 48 (257)
T PRK14074 1 MNLYEFTFIAQQGLLQQEVEEMVQELAVLLKNIKADVMFQQIKGILEK 48 (257)
T ss_pred CCccceeeeecccccHHHHHHHHHHHHHHHHhcCCeeehhhhhhhhhc
Confidence 999999999999999999999999999999999999999999998753
No 9
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=75.09 E-value=12 Score=29.96 Aligned_cols=99 Identities=15% Similarity=0.166 Sum_probs=60.9
Q ss_pred CceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEE----EEe--Ccch
Q 031985 2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMT----MMS--TPNI 75 (149)
Q Consensus 2 ~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~----f~a--~p~~ 75 (149)
++||++=-| |.|+++++.. +|.=+| ++| =+-.+|-=-.--.+|+-..+-..|+.|+|+.|= |.+ +..+
T Consensus 65 kkfETfSYL-PpLtdeqI~k---QVeYli-~~G-W~pclEf~~~~~~~~r~~~~s~~yyD~rYWtMWKLPMFg~tD~~~V 138 (176)
T PLN02289 65 KKFETLSYL-PDLTDEELAK---EVDYLL-RNK-WVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQV 138 (176)
T ss_pred cceeeeecC-CCCCHHHHHH---HHHHHH-hCC-CeeeeeeccCCceeEecCCCCCCcccCceeEEeccccCCCCCHHHH
Confidence 578988888 5578877655 444444 444 444555432334556544433357889999873 544 3567
Q ss_pred HHHHHhhhc--cCCeeEEEEEeccCcccchhhh
Q 031985 76 NKELQYLNK--EDRLLRWLLVKHRGMKNGKEAR 106 (149)
Q Consensus 76 v~EL~~lr~--de~VLR~l~vK~~~~~~~~~~~ 106 (149)
+.||+..++ -+.-||.+-+---..+..++||
T Consensus 139 l~Ei~eC~kayP~~yIRiigFDn~rqvq~~sFi 171 (176)
T PLN02289 139 LKELEEAKKAYPNAFIRIIGFDNTRQVQCISFI 171 (176)
T ss_pred HHHHHHHHHHCCcceEEEEEEECCCCEEEEEEE
Confidence 899987655 5678887766544444455544
No 10
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=73.05 E-value=12 Score=27.20 Aligned_cols=87 Identities=10% Similarity=0.129 Sum_probs=51.9
Q ss_pred CceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEE----EEEe--Ccch
Q 031985 2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQM----TMMS--TPNI 75 (149)
Q Consensus 2 ~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~----~f~a--~p~~ 75 (149)
+.||++=-+ |.++++++.+ ++..+| ++|-.+ .+|.=- .+++.++|+.| -|.+ ++++
T Consensus 1 ~~~~t~syl-p~lt~~~i~~---QI~yll-~qG~~~-~lE~ad------------~~~~~~~yW~mwklP~f~~~d~~~V 62 (99)
T cd03527 1 RTFETFSYL-PPLTDEQIAK---QIDYII-SNGWAP-CLEFTE------------PEHYDNRYWTMWKLPMFGCTDPAQV 62 (99)
T ss_pred CcccccccC-CCCCHHHHHH---HHHHHH-hCCCEE-EEEccc------------CCCCCCCEEeeccCCCCCCCCHHHH
Confidence 356766655 6678877665 444444 455444 454321 13568888886 4444 3568
Q ss_pred HHHHHhhhc--cCCeeEEEEEeccCcccchhhh
Q 031985 76 NKELQYLNK--EDRLLRWLLVKHRGMKNGKEAR 106 (149)
Q Consensus 76 v~EL~~lr~--de~VLR~l~vK~~~~~~~~~~~ 106 (149)
+.||+.++. -..-||.+-+-...+...+++|
T Consensus 63 l~ei~~C~~~~p~~YVRliG~D~~~q~~~~~fI 95 (99)
T cd03527 63 LREIEACRKAYPDHYVRVVGFDNYKQSQCMSFI 95 (99)
T ss_pred HHHHHHHHHHCCCCeEEEEEEeCCccEEEEEEE
Confidence 999986544 6778887776544444444443
No 11
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=66.75 E-value=34 Score=22.53 Aligned_cols=52 Identities=15% Similarity=-0.042 Sum_probs=33.8
Q ss_pred HHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeC--cchHHHH-Hhhhc
Q 031985 22 LVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMST--PNINKEL-QYLNK 84 (149)
Q Consensus 22 lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~--p~~v~EL-~~lr~ 84 (149)
.+.++.+.+.++|..|.+++ .+|.++. ...+.|.+.+++. ...+..+ ..|+.
T Consensus 14 ~L~~il~~f~~~~ini~~i~-------s~p~~~~----~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 14 ALYDVLGVFAERGINLTKIE-------SRPSKGG----LWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred HHHHHHHHHHHCCcCEEEEE-------EEEcCCC----CceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 35677778999999999997 3344322 1457777888876 4444443 55655
No 12
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=64.19 E-value=28 Score=23.04 Aligned_cols=47 Identities=9% Similarity=0.012 Sum_probs=32.6
Q ss_pred HHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH
Q 031985 20 MELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ 80 (149)
Q Consensus 20 ~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~ 80 (149)
.-++.++++.+.++||.|..+..+- +. .-.++.|.|..+.....+|+
T Consensus 12 ~GiVa~vs~~la~~g~nI~d~~q~~-------~~-------~~F~m~~~~~~~~~~~~~l~ 58 (77)
T cd04893 12 PGILNELTRAVSESGCNILDSRMAI-------LG-------TEFALTMLVEGSWDAIAKLE 58 (77)
T ss_pred ChHHHHHHHHHHHcCCCEEEceeeE-------Ec-------CEEEEEEEEEeccccHHHHH
Confidence 5678899999999999999988765 22 11245567776644455553
No 13
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=57.21 E-value=33 Score=21.48 Aligned_cols=61 Identities=13% Similarity=0.109 Sum_probs=39.5
Q ss_pred HHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHH-HhhhccCCeeEEEEEe
Q 031985 21 ELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKEL-QYLNKEDRLLRWLLVK 95 (149)
Q Consensus 21 ~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL-~~lr~de~VLR~l~vK 95 (149)
..+.++.+++.++|..|..+.. ++-.+. ...++.+.++.+ ...++ +.++..+.|++..+++
T Consensus 11 G~l~~i~~~l~~~~inI~~~~~-------~~~~~~-----~~~~~~i~v~~~--~~~~~~~~l~~~~~v~~v~~~~ 72 (73)
T cd04902 11 GVIGKVGTILGEAGINIAGMQV-------GRDEPG-----GEALMVLSVDEP--VPDEVLEELRALPGILSAKVVE 72 (73)
T ss_pred CHHHHHHHHHHHcCcChhheEe-------eccCCC-----CEEEEEEEeCCC--CCHHHHHHHHcCCCccEEEEEe
Confidence 3466788899999998877753 111111 233455555553 33466 6899999999988775
No 14
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=57.10 E-value=58 Score=22.85 Aligned_cols=71 Identities=15% Similarity=0.238 Sum_probs=44.4
Q ss_pred EEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCc--chHHHHH-hh
Q 031985 6 CMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTP--NINKELQ-YL 82 (149)
Q Consensus 6 ~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p--~~v~EL~-~l 82 (149)
+++=+.|.-.+..+.++.+++.+.|...| .. =.+.+....+||.+++. ++.+-.+- -...+|+ .+
T Consensus 4 vv~~V~P~d~e~Dl~~l~~~Ik~~i~~~g-l~-w~~~~~~epIaFGlk~L----------~v~~vv~D~~~~~d~lee~i 71 (89)
T PF00736_consen 4 VVLKVKPWDDETDLEKLEKKIKRKIPMEG-LK-WGEKSKEEPIAFGLKAL----------QVSCVVEDDEGSTDDLEEAI 71 (89)
T ss_dssp EEEEEEESSTTS-HHHHHHHHHHHS-TTT-EE-EEEEEEEEEECTTEEEE----------EEEEEECTTTCGHHHHHHHH
T ss_pred EEEEEeeCCCcccHHHHHHHHHHhchhcc-ee-eeeeeeeeeecccEEEE----------EEEEEEEcCccChHHHHHHH
Confidence 34556687777789999999988887665 32 12233356799999974 34444443 3677784 67
Q ss_pred -hccCCe
Q 031985 83 -NKEDRL 88 (149)
Q Consensus 83 -r~de~V 88 (149)
+.-+.|
T Consensus 72 ~~~~e~V 78 (89)
T PF00736_consen 72 ESFEEGV 78 (89)
T ss_dssp TTCTTTE
T ss_pred HhcCCCc
Confidence 555554
No 15
>PLN03075 nicotianamine synthase; Provisional
Probab=49.68 E-value=28 Score=29.76 Aligned_cols=72 Identities=18% Similarity=0.238 Sum_probs=52.7
Q ss_pred ceeEEEEEcCCC--CHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHH
Q 031985 3 LYDCMLLLKPHV--RKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKE 78 (149)
Q Consensus 3 ~YE~~~Ilrp~l--~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~E 78 (149)
.|.++|+. ..+ .++.-..+++++...+...|-.+... -||.|.+=|++--.. -.+|.=++..|+-.+.+++.
T Consensus 195 ~FDlVF~~-ALi~~dk~~k~~vL~~l~~~LkPGG~Lvlr~-~~G~r~~LYp~v~~~--~~~gf~~~~~~~P~~~v~Ns 268 (296)
T PLN03075 195 EYDVVFLA-ALVGMDKEEKVKVIEHLGKHMAPGALLMLRS-AHGARAFLYPVVDPC--DLRGFEVLSVFHPTDEVINS 268 (296)
T ss_pred CcCEEEEe-cccccccccHHHHHHHHHHhcCCCcEEEEec-ccchHhhcCCCCChh--hCCCeEEEEEECCCCCceee
Confidence 57788887 421 34566888999998887777666666 699999999965332 24588888888877776654
No 16
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=47.00 E-value=76 Score=20.40 Aligned_cols=51 Identities=22% Similarity=0.003 Sum_probs=34.3
Q ss_pred HHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeC--cchHHHH-Hhhhc
Q 031985 23 VARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMST--PNINKEL-QYLNK 84 (149)
Q Consensus 23 v~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~--p~~v~EL-~~lr~ 84 (149)
+.++-+.+.++|..|.+|++. |+++.. -.+.|++.+.+. ...+..+ +.|+.
T Consensus 13 L~~vL~~f~~~~vni~~I~Sr-------p~~~~~----~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 13 LAKALKVFAERGINLTKIESR-------PSRKGL----WEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred HHHHHHHHHHCCCCEEEEEee-------ecCCCC----ceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 556666889999999999875 444322 346778899884 4455554 55554
No 17
>PF03059 NAS: Nicotianamine synthase protein; InterPro: IPR004298 Nicotianamine synthase 2.5.1.43 from EC catalyzes the trimerization of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II [, ]. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron []. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency []. The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold [].; GO: 0030410 nicotianamine synthase activity, 0030418 nicotianamine biosynthetic process; PDB: 3O31_B 3FPH_A 3FPJ_A 3FPE_B 3FPF_B 3FPG_B.
Probab=45.87 E-value=53 Score=27.81 Aligned_cols=72 Identities=17% Similarity=0.204 Sum_probs=35.5
Q ss_pred ceeEEEEEcCC-CCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHH
Q 031985 3 LYDCMLLLKPH-VRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINK 77 (149)
Q Consensus 3 ~YE~~~Ilrp~-l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~ 77 (149)
.|.+++|+.-- .+.++-..+++++.+.+.. |+.|.-=--||.|.+-|+.-... -..|.=++..++-.+.+++
T Consensus 192 ~~DvV~lAalVg~~~e~K~~Il~~l~~~m~~-ga~l~~Rsa~GlR~~LYp~vd~~--~l~gf~~~~~~hP~~~ViN 264 (276)
T PF03059_consen 192 EYDVVFLAALVGMDAEPKEEILEHLAKHMAP-GARLVVRSAHGLRSFLYPVVDPE--DLRGFEVLAVVHPTDEVIN 264 (276)
T ss_dssp --SEEEE-TT-S----SHHHHHHHHHHHS-T-TSEEEEEE--GGGGGSS----TG--GGTTEEEEEEE---TT---
T ss_pred cCCEEEEhhhcccccchHHHHHHHHHhhCCC-CcEEEEecchhhHHHcCCCCChH--HCCCeEEEEEECCCCCcee
Confidence 57778887643 2345567888888887654 44444448899999999986543 2347777777766665554
No 18
>TIGR00337 PyrG CTP synthase. CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5' upstream of enolase in both beta (Nitrosomonas europaea) and gamma (E.coli) subdivisions of proteobacterium (FEMS Microbiol Lett 1998 Aug 1;165(1):153-7).
Probab=44.81 E-value=30 Score=31.97 Aligned_cols=79 Identities=19% Similarity=0.323 Sum_probs=55.6
Q ss_pred EcCCCCHHHHHHHHHHHH------hhhccCCcEEEeeecc----cccccccccccCccceeeEEEEEE-----EEEeCcc
Q 031985 10 LKPHVRKESLMELVARVG------KHVYGRNGVLTDITSF----GTVQLGYGIKKLDGRYYQGQLMQM-----TMMSTPN 74 (149)
Q Consensus 10 lrp~l~~e~~~~lv~r~~------~~I~~~GG~V~~ve~w----G~R~LAY~IkK~~~~~~~G~Y~~~-----~f~a~p~ 74 (149)
+-|.+++ ++++-+.+++ =.|.+-||.|-.++++ -.|+|.+++.+.+--+.+=.|+-. .+.+.|+
T Consensus 113 viPHvt~-ei~~~i~~~~~~~~~d~~i~EiGGTvGDiEs~pf~ea~rq~~~~~g~~~~~~ih~t~vp~l~~~~e~KtKPt 191 (525)
T TIGR00337 113 IIPHITN-EIKDRIKRVAKISGPDVVIVEIGGTVGDIESLPFLEAIRQFRNEVGRENVAFIHVTLVPYIAAAGEQKTKPT 191 (525)
T ss_pred ECCCCcH-HHHHHHHHhcccCCCCEEEEEeCCccccccccHHHHHHHHHHHhhCcCcEEEEEEeeeeeecCCCcccCCch
Confidence 3488877 5677777777 3678999999999996 579999999876543333334332 1233344
Q ss_pred --hHHHHHhhhccCCee
Q 031985 75 --INKELQYLNKEDRLL 89 (149)
Q Consensus 75 --~v~EL~~lr~de~VL 89 (149)
++++|+.+.+.+++|
T Consensus 192 Qhsv~~lr~~Gi~pd~~ 208 (525)
T TIGR00337 192 QHSVKELRSLGIQPDII 208 (525)
T ss_pred HHHHHHHHhCCCCCCEE
Confidence 578899999999976
No 19
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=43.68 E-value=40 Score=20.96 Aligned_cols=34 Identities=29% Similarity=0.294 Sum_probs=26.1
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcE
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGV 36 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~ 36 (149)
||++.+-+ .+..+.++.+++++.+...+.+.-|.
T Consensus 1 MP~i~i~~--~~Grs~eqk~~l~~~it~~l~~~~~~ 34 (61)
T PRK02220 1 MPYVHIKL--IEGRTEEQLKALVKDVTAAVSKNTGA 34 (61)
T ss_pred CCEEEEEE--cCCCCHHHHHHHHHHHHHHHHHHhCc
Confidence 88887733 34568999999999999988766543
No 20
>PLN02327 CTP synthase
Probab=43.68 E-value=37 Score=31.68 Aligned_cols=79 Identities=22% Similarity=0.323 Sum_probs=54.8
Q ss_pred EcCCCCHHHHHHHHHHHHh------------hhccCCcEEEeeecc----cccccccccccCccceeeEEEEEE-----E
Q 031985 10 LKPHVRKESLMELVARVGK------------HVYGRNGVLTDITSF----GTVQLGYGIKKLDGRYYQGQLMQM-----T 68 (149)
Q Consensus 10 lrp~l~~e~~~~lv~r~~~------------~I~~~GG~V~~ve~w----G~R~LAY~IkK~~~~~~~G~Y~~~-----~ 68 (149)
+=|.+++ +++.-+.++++ .|.+-||+|=.|+++ -.|+|.+++.+.+--+.+=.|+-. .
T Consensus 113 viPHitd-eI~~~i~~~~~~~~~~~~~~~dv~i~EiGGTVGDiEs~pflEA~rQ~~~~~g~~n~~~iHvt~vp~l~~~gE 191 (557)
T PLN02327 113 VVPHITD-AIQEWIERVAKIPVDGKEGPADVCVIELGGTVGDIESMPFIEALRQFSFRVGPGNFCLIHVSLVPVLGVVGE 191 (557)
T ss_pred ECCCcHH-HHHHHHHHhccCCcccCCCCCCEEEEEeCceeecccccHHHHHHHHHHHHhCcCcEEEEEEeeeeeecCCCc
Confidence 3488776 56777777763 467899999999996 579999999876533333333321 1
Q ss_pred EEeCcc--hHHHHHhhhccCCee
Q 031985 69 MMSTPN--INKELQYLNKEDRLL 89 (149)
Q Consensus 69 f~a~p~--~v~EL~~lr~de~VL 89 (149)
+.+.|+ ++++|+.+.+.+++|
T Consensus 192 ~KTKPtQhsvk~Lr~~Gi~pd~l 214 (557)
T PLN02327 192 QKTKPTQHSVRGLRALGLTPHIL 214 (557)
T ss_pred cccCchHHHHHHHHhCCCCCCEE
Confidence 223343 588899999999986
No 21
>COG0801 FolK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase [Coenzyme metabolism]
Probab=42.72 E-value=29 Score=27.18 Aligned_cols=46 Identities=13% Similarity=0.253 Sum_probs=34.8
Q ss_pred ceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccc
Q 031985 3 LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIK 53 (149)
Q Consensus 3 ~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~Ik 53 (149)
+.=+++++...++..++-..+. .|+...|.++ ...||-|.|-=-|=
T Consensus 54 FlN~v~~v~T~L~p~eLL~~l~----~iE~~~gR~R-~~rwgPRtlDlDIl 99 (160)
T COG0801 54 FLNAVVEVETTLSPRELLARLQ----AIERRLGRVR-SERWGPRTLDLDIL 99 (160)
T ss_pred hheEEEEEeccCCHHHHHHHHH----HHHHHcCccc-cccCCCcceeeEEE
Confidence 3457888889898877555544 4568889998 89999999876654
No 22
>PRK10239 2-amino-4-hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase; Provisional
Probab=42.47 E-value=36 Score=26.42 Aligned_cols=47 Identities=17% Similarity=0.302 Sum_probs=35.6
Q ss_pred ceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccc
Q 031985 3 LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIK 53 (149)
Q Consensus 3 ~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~Ik 53 (149)
+|=+++.+...++..++-++++.+...+ |.++....||-|.|-=-|=
T Consensus 54 FlN~v~~i~T~l~p~~Ll~~l~~IE~~~----GR~r~~~~~gpRtiDlDIL 100 (159)
T PRK10239 54 YLNAAVALETALAPEELLNHTQRIELQQ----GRVRKAERWGPRTLDLDIM 100 (159)
T ss_pred ceEEEEEEEeCCCHHHHHHHHHHHHHHh----CCCCCCcCCCCceEEEEEE
Confidence 5678888989999988887777655444 6777767999998766554
No 23
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=40.11 E-value=51 Score=20.82 Aligned_cols=34 Identities=21% Similarity=0.134 Sum_probs=25.5
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcE
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGV 36 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~ 36 (149)
||++-+-++ |..+.++.++|++.+...+.+.=|.
T Consensus 1 MP~i~i~~~--~Grs~EqK~~L~~~it~a~~~~~~~ 34 (60)
T PRK02289 1 MPFVRIDLF--EGRSQEQKNALAREVTEVVSRIAKA 34 (60)
T ss_pred CCEEEEEEC--CCCCHHHHHHHHHHHHHHHHHHhCc
Confidence 777755444 5679999999999999988765443
No 24
>cd03113 CTGs CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent ammonia to the acceptor substrate at the synthetase domain to form an aminated product. Glutaminase domains have evolved from the same ancestor, whereas the synthetase domains are evolutionarily unrelated and have different functions. This protein family is classified based on the N-terminal synthetase domain.
Probab=39.52 E-value=48 Score=27.99 Aligned_cols=79 Identities=20% Similarity=0.350 Sum_probs=52.4
Q ss_pred EcCCCCHHHHHHHHHHHHh------hhccCCcEEEeeecc----cccccccccccCccceeeEEEEEE-----EEEeCcc
Q 031985 10 LKPHVRKESLMELVARVGK------HVYGRNGVLTDITSF----GTVQLGYGIKKLDGRYYQGQLMQM-----TMMSTPN 74 (149)
Q Consensus 10 lrp~l~~e~~~~lv~r~~~------~I~~~GG~V~~ve~w----G~R~LAY~IkK~~~~~~~G~Y~~~-----~f~a~p~ 74 (149)
+-|++++ ++++-+.+++. .|.+-||.|-.++++ -.|+|.+++.+.+-.+.+=.|+-. .+...|+
T Consensus 112 viPHit~-eIk~~i~~~~~~~~~dv~i~EiGGTvGDiEs~pf~EAirq~~~~~g~~n~~~ihvt~vp~~~~~gE~KTKPt 190 (255)
T cd03113 112 VIPHITD-EIKERIRRVAEKSGADVVIVEIGGTVGDIESLPFLEAIRQMKLELGRENVLFIHVTLVPYLKAAGELKTKPT 190 (255)
T ss_pred ECcCccH-HHHHHHHHhhccCCCCEEEEEeCCccccccccHHHHHHHHHHHHhCcCcEEEEEEeeeeeecCCCccccCch
Confidence 3488776 56777778775 778999999999996 578899999876533333333221 1223333
Q ss_pred --hHHHHHhhhccCCee
Q 031985 75 --INKELQYLNKEDRLL 89 (149)
Q Consensus 75 --~v~EL~~lr~de~VL 89 (149)
++++|+.+.+.+++|
T Consensus 191 QhSVeaLRs~GIqPDgI 207 (255)
T cd03113 191 QHSVKELRSIGIQPDIL 207 (255)
T ss_pred HHHHHHHHhCCCCCCEE
Confidence 366677777777764
No 25
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=37.69 E-value=61 Score=20.15 Aligned_cols=33 Identities=21% Similarity=0.245 Sum_probs=25.3
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCc
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNG 35 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG 35 (149)
||+..+-+.- ..+.++.+++.+.+...+.+.=|
T Consensus 1 MP~i~I~~~~--grs~eqk~~l~~~it~~l~~~~~ 33 (62)
T PRK00745 1 MPTFHIELFE--GRTVEQKRKLVEEITRVTVETLG 33 (62)
T ss_pred CCEEEEEEcC--CCCHHHHHHHHHHHHHHHHHHcC
Confidence 8888776664 35899999999999998876533
No 26
>COG4689 Adc Acetoacetate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=33.32 E-value=64 Score=26.49 Aligned_cols=54 Identities=11% Similarity=0.249 Sum_probs=42.7
Q ss_pred ceeeEEEEEEEEEeCcchHHHH--HhhhccCCeeEEEEEeccCcccchhhhhhhcch
Q 031985 58 RYYQGQLMQMTMMSTPNINKEL--QYLNKEDRLLRWLLVKHRGMKNGKEARYAETSE 112 (149)
Q Consensus 58 ~~~~G~Y~~~~f~a~p~~v~EL--~~lr~de~VLR~l~vK~~~~~~~~~~~~e~~~~ 112 (149)
||..--||.+.+...|+++..+ +-|.+++-+.||-++++.+. .+...+.|.+..
T Consensus 26 rF~nREy~iItYRTd~~~Lr~~VPePLei~EPlVkfEfirM~Ds-tGfGdYTEsGQv 81 (247)
T COG4689 26 RFRNREYFIITYRTDPDALRAVVPEPLEIDEPLVKFEFIRMPDS-TGFGDYTESGQV 81 (247)
T ss_pred eeccceEEEEEEecCHHHHHhhCCCccccCCcceeEEEEeccCC-CCccccccCCcE
Confidence 4566789999999999999998 46999999999999999874 344445554433
No 27
>PRK14160 heat shock protein GrpE; Provisional
Probab=32.64 E-value=20 Score=29.28 Aligned_cols=67 Identities=16% Similarity=0.229 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEe---Ccc-hHHHHH-hhhccCCeeEE
Q 031985 17 ESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMS---TPN-INKELQ-YLNKEDRLLRW 91 (149)
Q Consensus 17 e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a---~p~-~v~EL~-~lr~de~VLR~ 91 (149)
+.+.-+.+.+.+++.+.| |..|..-| .+ -=.-| + .++...+ ++. ++..++ -+++.++|||.
T Consensus 139 ~Gv~mi~kql~~vL~k~G--Ve~I~~~G--~F--DP~~H-----E---Av~~~~~~e~~~gtVveV~qkGY~l~dRVLRp 204 (211)
T PRK14160 139 KGIEMTVKQFKTSLEKLG--VEEISTEG--EF--DPNLH-----N---AVMHVEDENYGENEIVEVFQKGYKRGDKVIRY 204 (211)
T ss_pred HHHHHHHHHHHHHHHHCC--CEEeCCCC--CC--ChHHh-----c---eeeeeCCCCCCcCeEEEEeeCCcEeCCEeeec
Confidence 356667777788888888 55666655 22 22211 2 3333322 334 444466 59999999999
Q ss_pred EEEecc
Q 031985 92 LLVKHR 97 (149)
Q Consensus 92 l~vK~~ 97 (149)
..|++.
T Consensus 205 A~V~Va 210 (211)
T PRK14160 205 SMVKVA 210 (211)
T ss_pred ceEEeC
Confidence 999864
No 28
>PRK14141 heat shock protein GrpE; Provisional
Probab=32.33 E-value=25 Score=28.63 Aligned_cols=67 Identities=10% Similarity=-0.023 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEe----CcchHHHHH-hhhccCCeeEEEE
Q 031985 19 LMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMS----TPNINKELQ-YLNKEDRLLRWLL 93 (149)
Q Consensus 19 ~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a----~p~~v~EL~-~lr~de~VLR~l~ 93 (149)
+.-+.+.+.+++.++| |..|+.-|..-=|..- ++ ++...+ ++.++..++ -+.+.++|||...
T Consensus 120 v~mi~k~l~~vLek~G--V~~I~~~Ge~FDP~~H--------EA---v~~~~~~~~~~gtVv~V~qkGY~l~dRVLRpA~ 186 (209)
T PRK14141 120 VEMTERAMLNALERHG--VKKLDPEGQKFDPNFH--------QA---MFEVPNPDVPNNTVVQVVQAGYTIGERVLRPAM 186 (209)
T ss_pred HHHHHHHHHHHHHHCC--CEEECCCCCCCChHHh--------ce---eeeecCCCCCcCEEEEEeeCCcEeCCEeecccE
Confidence 3344456677888887 5567766754333221 22 223332 233555566 5999999999999
Q ss_pred EeccC
Q 031985 94 VKHRG 98 (149)
Q Consensus 94 vK~~~ 98 (149)
|.+..
T Consensus 187 V~Vsk 191 (209)
T PRK14141 187 VGVAK 191 (209)
T ss_pred EEECC
Confidence 99876
No 29
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=31.88 E-value=1.8e+02 Score=20.33 Aligned_cols=68 Identities=19% Similarity=0.251 Sum_probs=40.8
Q ss_pred EEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH-hhhccC
Q 031985 8 LLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ-YLNKED 86 (149)
Q Consensus 8 ~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~-~lr~de 86 (149)
+=+.|.-.+..+.++.+++++++. .|..+.+ .-...+||.+++.+ +.+.+.-.--...+|+ .+..-+
T Consensus 8 l~V~P~~~e~Dl~~l~~~Ik~~~~-~gl~~~~---~~~epiaFGlk~L~--------i~~vv~D~~~~td~lee~i~~~d 75 (88)
T cd00292 8 LKVKPWDDEVDLDELEEKIRAILM-DGLLWGK---SKLEPIAFGLKALQ--------IYCVVEDDEGGTDELEEAISEED 75 (88)
T ss_pred EEEecCCCCcCHHHHHHHHHHhCc-CCcEEEE---EEEEEeeeEeeEEE--------EEEEEEeCCcCcHHHHHHHhccC
Confidence 345577667778888888887544 4555443 34567899999853 3344432333456664 555433
Q ss_pred C
Q 031985 87 R 87 (149)
Q Consensus 87 ~ 87 (149)
.
T Consensus 76 ~ 76 (88)
T cd00292 76 G 76 (88)
T ss_pred C
Confidence 3
No 30
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=31.58 E-value=46 Score=24.07 Aligned_cols=18 Identities=17% Similarity=0.331 Sum_probs=13.9
Q ss_pred HHHhhhccCCcEEEeeec
Q 031985 25 RVGKHVYGRNGVLTDITS 42 (149)
Q Consensus 25 r~~~~I~~~GG~V~~ve~ 42 (149)
.+.+.|++.||+|.+++.
T Consensus 62 ~i~~~Ie~~Gg~IHSIDe 79 (95)
T PF02680_consen 62 EIKEAIEELGGVIHSIDE 79 (95)
T ss_dssp HHHHHHHHTT-EEEEEEE
T ss_pred HHHHHHHHcCCeEEeeee
Confidence 456678889999999986
No 31
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.27 E-value=1.6e+02 Score=19.59 Aligned_cols=51 Identities=16% Similarity=0.025 Sum_probs=35.3
Q ss_pred HHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHH-Hhhhc
Q 031985 23 VARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKEL-QYLNK 84 (149)
Q Consensus 23 v~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL-~~lr~ 84 (149)
+.++-+.+..+|..+.++++.=.+ ... --++|++.++++...++.+ +.|+.
T Consensus 14 L~~iL~~f~~~~inl~~IeSRP~~-------~~~----~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 14 LAKALKLFQELGINVVHIESRKSK-------RRS----SEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred HHHHHHHHHHCCCCEEEEEeccCC-------CCC----ceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 445666888999999999975332 221 3477889999887766664 55554
No 32
>PRK11898 prephenate dehydratase; Provisional
Probab=31.17 E-value=3.1e+02 Score=22.90 Aligned_cols=58 Identities=17% Similarity=0.005 Sum_probs=37.0
Q ss_pred HHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcc--hHHH-HHhhhccCCeeEEE
Q 031985 24 ARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPN--INKE-LQYLNKEDRLLRWL 92 (149)
Q Consensus 24 ~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~--~v~E-L~~lr~de~VLR~l 92 (149)
-++-+.+.++|-.+++|++. |+++.. -.++|++.|+++.. .+.. |..|+..-.-+|++
T Consensus 212 ~~~L~~F~~~~INLt~IeSR-------P~~~~~----~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~k~L 272 (283)
T PRK11898 212 YKALSEFAWRGINLTRIESR-------PTKTGL----GTYFFFIDVEGHIDDVLVAEALKELEALGEDVKVL 272 (283)
T ss_pred HHHHHHHHHCCCCeeeEecc-------cCCCCC----ccEEEEEEEEccCCCHHHHHHHHHHHHhcCcEEEE
Confidence 34445677899999999986 444322 35788899998766 3444 46665543344543
No 33
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=30.29 E-value=1.6e+02 Score=19.20 Aligned_cols=52 Identities=17% Similarity=-0.017 Sum_probs=34.4
Q ss_pred HHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHH-Hhhhcc
Q 031985 23 VARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKEL-QYLNKE 85 (149)
Q Consensus 23 v~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL-~~lr~d 85 (149)
+.++-+.+..+|-.+++|++. |++... --++|++.|++....++.+ +.|+..
T Consensus 14 L~~vL~~f~~~~iNlt~IeSR-------P~~~~~----~~y~Ffvd~~~~~~~~~~~l~~L~~~ 66 (74)
T cd04904 14 LARALKLFEEFGVNLTHIESR-------PSRRNG----SEYEFFVDCEVDRGDLDQLISSLRRV 66 (74)
T ss_pred HHHHHHHHHHCCCcEEEEECC-------CCCCCC----ceEEEEEEEEcChHHHHHHHHHHHHh
Confidence 445555788899999999974 333221 3477889999866666554 556543
No 34
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=29.60 E-value=1.3e+02 Score=22.59 Aligned_cols=42 Identities=14% Similarity=0.217 Sum_probs=28.6
Q ss_pred eEEEEEcC---------CCCHHHHHHHHHHHHhhhccCCcEEEeeeccccc
Q 031985 5 DCMLLLKP---------HVRKESLMELVARVGKHVYGRNGVLTDITSFGTV 46 (149)
Q Consensus 5 E~~~Ilrp---------~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R 46 (149)
+.++|+-| .++.+.+....+++..++.++|..|....+-|-.
T Consensus 51 ~~lfVi~PvNg~wydytG~~~~~r~~~y~kI~~~~~~~gf~v~D~s~~~y~ 101 (130)
T PF04914_consen 51 DVLFVIQPVNGKWYDYTGLSKEMRQEYYKKIKYQLKSQGFNVADFSDDEYE 101 (130)
T ss_dssp EEEEEE----HHHHHHTT--HHHHHHHHHHHHHHHHTTT--EEE-TTGTTS
T ss_pred ceEEEecCCcHHHHHHhCCCHHHHHHHHHHHHHHHHHCCCEEEecccCCCC
Confidence 45667666 3578899999999999999999988887776643
No 35
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=29.23 E-value=2.2e+02 Score=23.15 Aligned_cols=70 Identities=9% Similarity=0.056 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHH-HhhhccCCeeEEEEEe
Q 031985 17 ESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKEL-QYLNKEDRLLRWLLVK 95 (149)
Q Consensus 17 e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL-~~lr~de~VLR~l~vK 95 (149)
..+.+..+++.+++.+.||.|.+...++. .. ...+....+.+..|+.....+ +.|.--. -+....+.
T Consensus 59 ~d~~~a~~~i~~~~~~~gG~i~~~~~~~~-------~~----~~~~~~~~ltiRVP~~~~~~~l~~l~~~g-~v~~~~~~ 126 (262)
T PF14257_consen 59 KDVEKAVKKIENLVESYGGYIESSSSSSS-------GG----SDDERSASLTIRVPADKFDSFLDELSELG-KVTSRNIS 126 (262)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEeeecc-------cC----CCCcceEEEEEEECHHHHHHHHHHHhccC-ceeeeecc
Confidence 45788899999999999999999987644 11 124555678888899999987 6777544 33444444
Q ss_pred ccC
Q 031985 96 HRG 98 (149)
Q Consensus 96 ~~~ 98 (149)
..+
T Consensus 127 ~~D 129 (262)
T PF14257_consen 127 SED 129 (262)
T ss_pred ccc
Confidence 443
No 36
>PF10741 T2SM_b: Type II secretion system (T2SS), protein M subtype b; InterPro: IPR007690 General secretion pathway (GSP) protein M is a membrane protein involved in the export of proteins in bacteria. It consists of a short cytosolic N-terminal domain, a transmembrane domain, and a C-terminal periplasmic domain. The precise function of this protein is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers [],; GO: 0006858 extracellular transport
Probab=28.37 E-value=2.1e+02 Score=20.06 Aligned_cols=62 Identities=10% Similarity=0.084 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHH-HhhhccCC
Q 031985 17 ESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKEL-QYLNKEDR 87 (149)
Q Consensus 17 e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL-~~lr~de~ 87 (149)
-..+++..++.+++...||.|.+++.+..+.-. .+.-.=+.+++.++...+..+ ..|....-
T Consensus 13 ~a~A~Lq~~l~~~v~~aG~~v~s~q~~p~~~~~---------~~~~i~v~~~~~g~~~~L~~~L~~LE~~~P 75 (110)
T PF10741_consen 13 LAAAALQQRLRALVAAAGGQVSSSQVLPPRPDG---------NFRRISVRVSLEGDIEALQAFLYALESGRP 75 (110)
T ss_pred HHHHHHHHHHHHHHHHcCCEEEEEEecCCCCCC---------cceEEEEEEEEEeCHHHHHHHHHHHhcCCC
Confidence 346889999999999999999999988744211 122333667888877666664 55554333
No 37
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=28.20 E-value=70 Score=18.19 Aligned_cols=23 Identities=17% Similarity=0.349 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHHHHHHhhhccCC
Q 031985 12 PHVRKESLMELVARVGKHVYGRN 34 (149)
Q Consensus 12 p~l~~e~~~~lv~r~~~~I~~~G 34 (149)
..++.+++..+..|+.+.+.++|
T Consensus 3 ~~i~~~~~~d~a~rv~~f~~~ng 25 (33)
T PF09373_consen 3 GTISKEEYLDMASRVNNFYESNG 25 (33)
T ss_pred ceecHHHHHHHHHHHHHHHHHcC
Confidence 45788999999999999998887
No 38
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=27.19 E-value=1.8e+02 Score=18.67 Aligned_cols=52 Identities=15% Similarity=0.074 Sum_probs=33.0
Q ss_pred HHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEE-EEEEEEeCcc-hHHHHH
Q 031985 20 MELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQL-MQMTMMSTPN-INKELQ 80 (149)
Q Consensus 20 ~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y-~~~~f~a~p~-~v~EL~ 80 (149)
..++.++++++.++|+.|.++...-. +..... .|.+ +.+.+..|+. .+.+|+
T Consensus 10 ~Giv~~it~~l~~~~~nI~~~~~~~~-----~~~~~~----~~~~~~~~~v~~p~~~~~~~l~ 63 (81)
T cd04869 10 PGIVHEVTQFLAQRNINIEDLSTETY-----SAPMSG----TPLFKAQATLALPAGTDLDALR 63 (81)
T ss_pred CCHHHHHHHHHHHcCCCeEEeEeeee-----cCCCCC----cceEEEEEEEecCCCCCHHHHH
Confidence 45678899999999999998876332 221111 2333 4577777754 466664
No 39
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=25.98 E-value=1.5e+02 Score=17.60 Aligned_cols=57 Identities=12% Similarity=0.197 Sum_probs=34.5
Q ss_pred HHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHH-HhhhccCCeeEE
Q 031985 21 ELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKEL-QYLNKEDRLLRW 91 (149)
Q Consensus 21 ~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL-~~lr~de~VLR~ 91 (149)
.++.++..++.+.|..|.++.. ... ..+.+..+.|..+...+.++ +.|+.-+.|++.
T Consensus 11 g~l~~i~~~l~~~~~nI~~~~~----------~~~----~~~~~~~~~~~v~~~~~~~l~~~l~~~~~V~~v 68 (71)
T cd04879 11 GVIGKVGTILGEHGINIAAMQV----------GRK----EKGGIAYMVLDVDSPVPEEVLEELKALPGIIRV 68 (71)
T ss_pred CHHHHHHHHHHhcCCCeeeEEE----------ecc----CCCCEEEEEEEcCCCCCHHHHHHHHcCCCeEEE
Confidence 3566777888999999988864 100 00112333444333355566 688888888874
No 40
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=25.89 E-value=85 Score=21.58 Aligned_cols=26 Identities=15% Similarity=0.151 Sum_probs=18.6
Q ss_pred CCCHHHHHHHHHHHHhhhcc-CCcEEE
Q 031985 13 HVRKESLMELVARVGKHVYG-RNGVLT 38 (149)
Q Consensus 13 ~l~~e~~~~lv~r~~~~I~~-~GG~V~ 38 (149)
+|+.+++.++.+++...+.+ .|+++|
T Consensus 68 TLt~~ev~~~~~~i~~~l~~~~~~~lR 94 (94)
T PF03147_consen 68 TLTDEEVNEIHDKIIKALEKKLGAELR 94 (94)
T ss_dssp ---HHHHHHHHHHHHHHHHHTCT-BEE
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcEeC
Confidence 58999999999999999965 566654
No 41
>PF07876 Dabb: Stress responsive A/B Barrel Domain; InterPro: IPR013097 The stress-response A/B barrel domain is found in a class of stress-response proteins in plants. It is also found in some bacterial fructose-bisphosphate aldolase such as at the C terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (Q9ZA13 from SWISSPROT) []. Q93NG5 from SWISSPROT is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The stress-response A/B barrel domain forms a very stable dimer. This dimer belongs to the superfamily of dimeric alpha+beta barrels in which the two beta-sheets form a beta-barrel. The two molecules in the dimer are related by a 2-fold axis parallel to helix H1 and beta-strands B3 and B4. C-terminal residues extending from the beta4 strand of each monomer wrap around and connect with the beta2 strand and alpha1 helix of the opposing monomer to form the dimer interface [, , ].The outer surface of the beta-sheets of the two molecules forms a beta-barrel-like structure defining a central pore. The function of the stress-response A/B barrel domain is unknown [, , ], but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar) []. Some proteins known to contain a stress response A/B barrel domain are listed below: - Arabidopsis thaliana At3g17210 - Arabidopsis thaliana At5g22580 -Populus tremula stable protein 1 (SP-1)(Populus species), a thermostable stress-responsive protein. - Pseudomonas hydrogenothermophila fructose 1,6-bisphosphate aldolase (cbbA). The structure of one of these proteins has been solved (Q9LUV2 from SWISSPROT) and the domain forms an alpha-beta barrel dimer [].; PDB: 3BB5_E 3FMB_A 3BDE_B 2QYC_A 1Q53_B 2Q3P_A 1Q4R_A 3BN7_A 3BGU_B 1RJJ_B ....
Probab=25.21 E-value=2.1e+02 Score=18.93 Aligned_cols=57 Identities=16% Similarity=0.179 Sum_probs=38.0
Q ss_pred EEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEE
Q 031985 7 MLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMM 70 (149)
Q Consensus 7 ~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~ 70 (149)
++=++|..+.+++.++++.+.++.....| |+++. +|.--.+=. . .+.|..| +.+.|.
T Consensus 6 lfklk~~~~~~~~~~~~~~l~~l~~~ip~-i~~~~-~G~~~~~~~-~--~~~~~~~--~~~~F~ 62 (97)
T PF07876_consen 6 LFKLKPDATEEEIEEVLEALRALKDKIPG-IVSFE-VGRNFSPED-L--AKGYDHA--LVSTFE 62 (97)
T ss_dssp EEEESTTTCHHHHHHHHHHHHHHHHHSTT-ECEEE-EEEESSTSS-T--STT-SEE--EEEEES
T ss_pred EEEECCCCCHHHHHHHHHHHHhcccCCCc-eEEEE-EEcccCccc-c--cCCCcEE--EEEEEC
Confidence 56678999999999999999999777777 44555 665444443 1 1235666 447774
No 42
>COG0504 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]
Probab=25.07 E-value=1.4e+02 Score=27.79 Aligned_cols=81 Identities=17% Similarity=0.301 Sum_probs=56.0
Q ss_pred EEEcCCCCHHHHHHHHHHHHh-----hhccCCcEEEeeeccc----ccccccccccCccceeeEEEEEE-----EEEeCc
Q 031985 8 LLLKPHVRKESLMELVARVGK-----HVYGRNGVLTDITSFG----TVQLGYGIKKLDGRYYQGQLMQM-----TMMSTP 73 (149)
Q Consensus 8 ~Ilrp~l~~e~~~~lv~r~~~-----~I~~~GG~V~~ve~wG----~R~LAY~IkK~~~~~~~G~Y~~~-----~f~a~p 73 (149)
+-+=|.++. +++.-+.++++ +|.+-||.|=.++++= .|+|...+.+.+.-+.+-.|+-. .+.+.|
T Consensus 111 VQvIPHiT~-eIk~~I~~~a~~~~DvvivEIGGTVGDIEslpFlEAiRQ~~~e~g~~n~~fiH~tlvpyi~~~gE~KTKP 189 (533)
T COG0504 111 VQVIPHITD-EIKDRIREAADSTADVVIVEIGGTVGDIESLPFLEAIRQLRLELGRENVLFIHVTLVPYIAAAGELKTKP 189 (533)
T ss_pred eEECCCcch-HHHHHHHHhcCCCCCEEEEEeCCceecccccHHHHHHHHHHhhhCcccEEEEEEecceeecccCccCCCC
Confidence 445588877 56777777764 4679999999999974 58888888766533333333321 233444
Q ss_pred c--hHHHHHhhhccCCee
Q 031985 74 N--INKELQYLNKEDRLL 89 (149)
Q Consensus 74 ~--~v~EL~~lr~de~VL 89 (149)
. ++++|+.+.+.+++|
T Consensus 190 TQhSVkeLR~iGI~PDii 207 (533)
T COG0504 190 TQHSVKELRSIGIQPDIL 207 (533)
T ss_pred chHHHHHHHhcCCCcceE
Confidence 4 588999999999986
No 43
>PRK14147 heat shock protein GrpE; Provisional
Probab=24.81 E-value=44 Score=26.28 Aligned_cols=68 Identities=19% Similarity=0.010 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEe---C-cchHHHHH-hhhccCCeeEEE
Q 031985 18 SLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMS---T-PNINKELQ-YLNKEDRLLRWL 92 (149)
Q Consensus 18 ~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a---~-p~~v~EL~-~lr~de~VLR~l 92 (149)
.+.-+.+++.+++.++| |..|+..|..-=|.. | ++ ++...+ + +.++..++ -+.+.++|||..
T Consensus 98 Gv~mi~k~l~~~L~~~G--v~~i~~~G~~FDP~~---H-----eA---v~~~~~~~~~~g~Vv~v~qkGY~l~~RvLRpA 164 (172)
T PRK14147 98 GLELTYKQLLKVAADNG--LTLLDPVGQPFNPEH---H-----QA---ISQGEAEGVAPGHVVQVFQKGYLLNERLLRPA 164 (172)
T ss_pred HHHHHHHHHHHHHHHCC--CEEeCCCCCCCChHH---h-----ce---eeeecCCCCCcCEEEEEeeCCcEeCCEeccCc
Confidence 45556677777888887 556666665322221 1 22 233322 2 33454566 599999999999
Q ss_pred EEeccC
Q 031985 93 LVKHRG 98 (149)
Q Consensus 93 ~vK~~~ 98 (149)
.|++..
T Consensus 165 ~V~Vak 170 (172)
T PRK14147 165 LVVVAK 170 (172)
T ss_pred eEEeCC
Confidence 998764
No 44
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=24.40 E-value=1.4e+02 Score=20.51 Aligned_cols=38 Identities=24% Similarity=0.515 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHHHHHhhhc---cCCcEEEeeeccccccccc
Q 031985 12 PHVRKESLMELVARVGKHVY---GRNGVLTDITSFGTVQLGY 50 (149)
Q Consensus 12 p~l~~e~~~~lv~r~~~~I~---~~GG~V~~ve~wG~R~LAY 50 (149)
+.++..++..+++.+.+.|. .+|+.| .+..||.=.+..
T Consensus 15 ~~~s~~~~~~vv~~~~~~i~~~L~~g~~V-~l~gfG~F~~~~ 55 (94)
T PRK00199 15 PHLSAKDVENAVKEILEEMSDALARGDRI-EIRGFGSFSLHY 55 (94)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCeE-EEcCCEEEEEEE
Confidence 45788888888888888874 456655 899999866554
No 45
>PF15110 TMEM141: TMEM141 protein family; PDB: 2LOR_A.
Probab=24.23 E-value=17 Score=26.27 Aligned_cols=34 Identities=12% Similarity=0.045 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhhccCCcEEEeeecccccccccccc
Q 031985 19 LMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIK 53 (149)
Q Consensus 19 ~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~Ik 53 (149)
-.++++.+..+|+-.|| .--.+....|+||||.+
T Consensus 25 S~Af~kG~~tFv~G~~~-~f~~Q~~iqrrlpYp~q 58 (94)
T PF15110_consen 25 SRAFMKGLFTFVLGTGA-TFFLQKAIQRRLPYPFQ 58 (94)
T ss_dssp HHHHHHHHHHHHGGGGH-HHHHHHHHHTTSSSSS-
T ss_pred HHHHHHHHHHHHHhhHH-HHHHHHHHHHhCCCCCC
Confidence 46788999999986555 44788999999999987
No 46
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.86 E-value=1.3e+02 Score=19.98 Aligned_cols=39 Identities=13% Similarity=0.190 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHHHHHHhhhc---cCCcEEEeeecccccccccc
Q 031985 12 PHVRKESLMELVARVGKHVY---GRNGVLTDITSFGTVQLGYG 51 (149)
Q Consensus 12 p~l~~e~~~~lv~r~~~~I~---~~GG~V~~ve~wG~R~LAY~ 51 (149)
..++..++..+++.+...|. .+|+.| .+..||.-.+...
T Consensus 14 ~~~~~~~v~~vl~~l~~~i~~~L~~g~~V-~i~g~G~F~~~~~ 55 (90)
T smart00411 14 AGLSKKDAKAAVDAFLEIITEALKKGEKV-ELRGFGTFEVRER 55 (90)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHhCCCeE-EEeCcEEEEEEee
Confidence 45667777777777777773 456655 6999998776654
No 47
>PF07237 DUF1428: Protein of unknown function (DUF1428); InterPro: IPR009874 This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.; PDB: 2OKQ_A.
Probab=23.40 E-value=1.1e+02 Score=22.40 Aligned_cols=40 Identities=15% Similarity=0.310 Sum_probs=31.2
Q ss_pred eEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccc
Q 031985 5 DCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGT 45 (149)
Q Consensus 5 E~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~ 45 (149)
...+|.-|.-.+++..+..++...+..++| -++-++.||.
T Consensus 4 dGfv~~VP~~nk~aY~~~A~~a~~vf~e~G-Al~~vE~wgd 43 (103)
T PF07237_consen 4 DGFVLPVPTANKDAYRAMAEKAAEVFKEHG-ALRVVECWGD 43 (103)
T ss_dssp EEEEEEEEGGGHHHHHHHHHHHHHHHHHTT--SEEEEEEEE
T ss_pred eEEEEECcHHHHHHHHHHHHHHHHHHHHhC-CEEEEEeecC
Confidence 566777788888898888888877766655 6778899998
No 48
>cd00483 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is HPPK which catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The functional enzyme is a monomer. Mammals lack many of the enzymes in the folate pathway including, HPPK.
Probab=23.39 E-value=1.2e+02 Score=22.36 Aligned_cols=46 Identities=13% Similarity=0.328 Sum_probs=33.1
Q ss_pred ceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccc
Q 031985 3 LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIK 53 (149)
Q Consensus 3 ~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~Ik 53 (149)
+|=+++.+...++..++.+.++.+.... |..+. ..||-|.|-=-|=
T Consensus 51 FlN~v~~~~T~l~p~~Ll~~l~~IE~~~----GR~r~-~~~~~RtiDlDIl 96 (128)
T cd00483 51 FLNAVVELETSLSPLELLDALQAIEQRL----GRVRK-ERWGPRTLDLDIL 96 (128)
T ss_pred HHheEEEEEECCCHHHHHHHHHHHHHHh----CCCCc-ccCCCceeeEEEE
Confidence 4567888889999988888777665554 45555 6899988755543
No 49
>cd04416 NDPk_TX NDP kinase domain of thioredoxin domain-containing proteins (TXNDC3 and TXNDC6): Txl-2 (TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of Group II N-terminal thioredoxin domains followed by one or three NDP kinase domains, respectively. Sptrx-2, which has a tissue specific distribution in human testis, has been considered as a member of the nm23 family (nm23-H8) and exhibits a high homology with sea urchin IC1 (intermediate chain-1) protein, a component of the sperm axonemal outer dynein arm complex. Txl-2 is mainly represented in close association with microtubules within tissues with cilia and flagella such as seminiferous epithelium (spermatids) and lung airway epithelium, suggesting possible role in control of microtubule stability and maintenance.
Probab=23.06 E-value=1.7e+02 Score=21.52 Aligned_cols=34 Identities=12% Similarity=0.147 Sum_probs=24.9
Q ss_pred EEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecc
Q 031985 6 CMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSF 43 (149)
Q Consensus 6 ~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~w 43 (149)
+++|++|+. +...+..+-+.|.+.|=.|...+.+
T Consensus 3 Tl~iIKPda----v~~~~g~Il~~i~~~Gf~I~~~k~~ 36 (132)
T cd04416 3 TLALIKPDA----VAEKKDEILEKIKEAGFEILAQKEM 36 (132)
T ss_pred EEEEEChHH----HHHHHHHHHHHHHHCCCEEEEeeee
Confidence 678888873 3236667777888899888887763
No 50
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=22.67 E-value=2.4e+02 Score=18.96 Aligned_cols=41 Identities=10% Similarity=0.110 Sum_probs=27.0
Q ss_pred HHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeCcchHHHHH
Q 031985 23 VARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQ 80 (149)
Q Consensus 23 v~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p~~v~EL~ 80 (149)
+.++-..|.+++|.|.++...|. ..+.+.+.+|-..+..+.
T Consensus 18 ~g~v~~~l~~r~g~i~~~~~~~~-----------------~~~~i~~~iP~~~~~gf~ 58 (89)
T PF00679_consen 18 LGKVISDLSKRRGEILSMDPIGG-----------------DRVVIEAEIPVRELFGFR 58 (89)
T ss_dssp HHHHHHHHHHTT-EEEEEEEEST-----------------TEEEEEEEEEGGGHTTHH
T ss_pred HHHHHHHhcccccEEEechhhhh-----------------hheeEEEEEChhhhhhHH
Confidence 34555678889999999988721 146677777776665553
No 51
>PF06877 RraB: Regulator of ribonuclease activity B; InterPro: IPR009671 This entry occurs in several hypothetical bacterial proteins of around 120 residues in length. The function of these proteins is unknown. The protein structure has been determined for one member of this group, the hypothetical protein VCO424 from Vibrio cholerae; it has an alpha+beta sandwich fold.; PDB: 1NXI_A.
Probab=22.63 E-value=1.4e+02 Score=20.52 Aligned_cols=38 Identities=11% Similarity=0.100 Sum_probs=27.5
Q ss_pred eeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeeccc
Q 031985 4 YDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFG 44 (149)
Q Consensus 4 YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG 44 (149)
|.+.+...-.++.+.+.++...+..+..+.||. .+-||
T Consensus 66 ~~~~~~~~~~~~~~~I~~~~~~l~~lA~~~~g~---YDGWg 103 (104)
T PF06877_consen 66 YCLDISREMVLDYEDINAITQELEDLAKEFGGE---YDGWG 103 (104)
T ss_dssp EEEEEEEEE-S-HHHHHHHHHHHHHHHHHHT-E---EEEEE
T ss_pred EEEEEEEecCCCHHHHHHHHHHHHHHHHHhCcE---ecCcc
Confidence 555555544567788999999999999999998 56676
No 52
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=22.16 E-value=2.9e+02 Score=19.41 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=31.3
Q ss_pred EEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCc
Q 031985 8 LLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLD 56 (149)
Q Consensus 8 ~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~ 56 (149)
+=+.|.-.+..+.++.+.+++++. .|..+.+ .-...+||.|++.+
T Consensus 8 ~~V~P~d~e~Dl~~L~~~ik~~~~-~g~~~~~---~~~ePIaFGLkaL~ 52 (88)
T PRK00435 8 LKVMPESPEVDLDELKEKIKEVLP-EGYKING---IEEEPIAFGLKALK 52 (88)
T ss_pred EEECCCCCCcCHHHHHHHHHHhCc-CCcEEeE---eEEEEeeccceeEE
Confidence 335577666678888888887655 4555543 45678999999853
No 53
>PRK14157 heat shock protein GrpE; Provisional
Probab=21.93 E-value=51 Score=27.32 Aligned_cols=69 Identities=13% Similarity=0.084 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeC---cc-hHHHHH-hhhccCCeeEE
Q 031985 17 ESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMST---PN-INKELQ-YLNKEDRLLRW 91 (149)
Q Consensus 17 e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~---p~-~v~EL~-~lr~de~VLR~ 91 (149)
+.+..+.+++.+++.++| |..|+..|..-=| ..| + .++....+ +. ++..++ -+++.++|||.
T Consensus 151 ~~~~~i~k~l~~vL~k~G--Ve~I~~~Ge~FDP---~~H-----E---AV~~~~~~~~~~gtVi~V~QkGY~l~dRVLRP 217 (227)
T PRK14157 151 DSFKAVAAKIDKAFEKFG--VEKFGEKGEDFDP---TKH-----D---AILHKPDPDAEKETVDTVVEAGYRIGDRVIRA 217 (227)
T ss_pred hHHHHHHHHHHHHHHHCC--CEEeCCCCCCCCh---hhh-----c---eeeeecCCCCCcCEEEEEeeCCceeCCEeccC
Confidence 346778888888998888 5677776654222 222 2 33333332 33 444466 59999999999
Q ss_pred EEEeccC
Q 031985 92 LLVKHRG 98 (149)
Q Consensus 92 l~vK~~~ 98 (149)
..|++..
T Consensus 218 A~V~Vak 224 (227)
T PRK14157 218 ARVVVAS 224 (227)
T ss_pred ceEEeCC
Confidence 9998864
No 54
>PRK14163 heat shock protein GrpE; Provisional
Probab=21.70 E-value=64 Score=26.45 Aligned_cols=70 Identities=13% Similarity=-0.024 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEeC----cchHHHHH-hhhccCCeeEE
Q 031985 17 ESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMST----PNINKELQ-YLNKEDRLLRW 91 (149)
Q Consensus 17 e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~----p~~v~EL~-~lr~de~VLR~ 91 (149)
+.+.-+.+.+.+++.+.| |..|+..|..-=| ..| + .++...++ ..++..++ -+++.++|||.
T Consensus 114 ~Gv~mi~k~l~~~L~k~G--v~~I~~~G~~FDP---~~H-----E---Av~~~~~~~~~~gtVv~v~qkGY~l~~RVLRP 180 (214)
T PRK14163 114 GGFKSVAESLETTVAKLG--LQQFGKEGEPFDP---TIH-----E---ALMHSYAPDVTETTCVAILQPGYRIGERTIRP 180 (214)
T ss_pred HHHHHHHHHHHHHHHHCC--CEEeCCCCCCCCh---hHh-----c---eeeeecCCCCCcCEEEEEeeCCcCcCCEeccC
Confidence 346667777777888777 5566666653222 111 2 33444443 33444566 59999999999
Q ss_pred EEEeccCc
Q 031985 92 LLVKHRGM 99 (149)
Q Consensus 92 l~vK~~~~ 99 (149)
..|++...
T Consensus 181 A~V~Vsk~ 188 (214)
T PRK14163 181 ARVAVAEP 188 (214)
T ss_pred ceEEECCC
Confidence 99998864
No 55
>PF14832 Tautomerase_3: Putative oxalocrotonate tautomerase enzyme; PDB: 3C6V_C 3N4D_I 3N4G_C 3N4H_A 2FLZ_C 3MF8_A 3MF7_A 2FLT_A.
Probab=21.60 E-value=1.2e+02 Score=22.94 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=21.1
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHHHHhhhccC
Q 031985 1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGR 33 (149)
Q Consensus 1 M~~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~ 33 (149)
||+|.+.--..+ ++.++-.+|.+.+.++=++.
T Consensus 1 MPlw~I~h~~~~-lt~~~K~~LA~~IT~~y~~~ 32 (136)
T PF14832_consen 1 MPLWQIYHPPGT-LTPEQKQALAEAITDIYTSI 32 (136)
T ss_dssp --EEEEEEETTS-S-HHHHHHHHHHHHHHHHHT
T ss_pred CCcEEEEeCCCC-CCHHHHHHHHHHHHHHHhCC
Confidence 999988776444 67888788877777776655
No 56
>PRK14162 heat shock protein GrpE; Provisional
Probab=21.16 E-value=48 Score=26.71 Aligned_cols=67 Identities=19% Similarity=0.095 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEe----C-cchHHHHH-hhhccCCeeEE
Q 031985 18 SLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMS----T-PNINKELQ-YLNKEDRLLRW 91 (149)
Q Consensus 18 ~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a----~-p~~v~EL~-~lr~de~VLR~ 91 (149)
.+.-+.+.+.+++.+.| |..|+..|..-=|.-- ++ ++...+ + ..++..++ -+++.++|||.
T Consensus 121 Gvemi~k~l~~vL~~~G--V~~I~~~G~~FDP~~H--------EA---v~~~~~~~~~~~gtVv~v~qkGY~l~dRVLRp 187 (194)
T PRK14162 121 GVQMTLDHLVKALKDHG--VTEIKADGEKFDPTLH--------QA---VQTVAAENDDQKDHVVQVLQKGYQYKDRTLRP 187 (194)
T ss_pred HHHHHHHHHHHHHHHCC--CEEeCCCCCCCChhHh--------hh---heeecCCCCCCcCEEEEEeeCCcEeCCEeeec
Confidence 45556777777777777 5567666653222211 22 233322 2 33454566 59999999999
Q ss_pred EEEecc
Q 031985 92 LLVKHR 97 (149)
Q Consensus 92 l~vK~~ 97 (149)
..|.+.
T Consensus 188 A~V~Va 193 (194)
T PRK14162 188 AMVVVA 193 (194)
T ss_pred ceEEeC
Confidence 999864
No 57
>PF01288 HPPK: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK); InterPro: IPR000550 All organisms require reduced folate cofactors for the synthesis of a variety of metabolites. Most microorganisms must synthesise folate de novo because they lack the active transport system of higher vertebrate cells which allows these organisms to use dietary folates. Enzymes involved in folate biosynthesis are therefore targets for a variety of antimicrobial agents such as trimethoprim or sulphonamides. 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (2.7.6.3 from EC) (HPPK) catalyses the attachment of pyrophosphate to 6-hydroxymethyl-7,8-dihydropterin to form 6-hydroxymethyl-7,8-dihydropteridine pyrophosphate. This is the first step in a three-step pathway leading to 7,8 dihydrofolate. Bacterial HPPK (gene folK or sulD) [] is a protein of 160 to 270 amino acids. In the lower eukaryote Pneumocystis carinii, HPPK is the central domain of a multifunctional folate synthesis enzyme (gene fas) [].; GO: 0003848 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity, 0009396 folic acid-containing compound biosynthetic process; PDB: 2QX0_B 1RU1_B 2F65_A 1RU2_A 1EQ0_A 3ILJ_A 3HSJ_A 3HD1_A 1TMM_B 1RB0_A ....
Probab=21.13 E-value=1.7e+02 Score=21.53 Aligned_cols=42 Identities=17% Similarity=0.439 Sum_probs=29.3
Q ss_pred ceeEEEEEcCCCCHHHHHHHHHHHHhhhccCCcEEEeeecccccccc
Q 031985 3 LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLG 49 (149)
Q Consensus 3 ~YE~~~Ilrp~l~~e~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LA 49 (149)
+|=+++.++..++.+++...++.+...+ |..++- .||-|.|-
T Consensus 50 F~N~v~~~~t~l~~~~ll~~L~~IE~~~----GR~r~~-~~~~R~lD 91 (127)
T PF01288_consen 50 FLNAVVVLETSLSPEELLDLLKQIERRL----GRDRSS-KWGPRTLD 91 (127)
T ss_dssp EEEEEEEEEESS-HHHHHHHHHHHHHHT----TSCSTS-TTSSCSEE
T ss_pred eeeeeeeecCCCCHHHHHHHHHHHHHHh----CCCCcC-CCCCceee
Confidence 5668888988898988888777665554 444444 88877654
No 58
>PRK05380 pyrG CTP synthetase; Validated
Probab=21.04 E-value=86 Score=29.14 Aligned_cols=78 Identities=21% Similarity=0.322 Sum_probs=52.4
Q ss_pred cCCCCHHHHHHHHHHHH----hhhccCCcEEEeeecc----cccccccccccCccceeeEEEEEE-----EEEeCcc--h
Q 031985 11 KPHVRKESLMELVARVG----KHVYGRNGVLTDITSF----GTVQLGYGIKKLDGRYYQGQLMQM-----TMMSTPN--I 75 (149)
Q Consensus 11 rp~l~~e~~~~lv~r~~----~~I~~~GG~V~~ve~w----G~R~LAY~IkK~~~~~~~G~Y~~~-----~f~a~p~--~ 75 (149)
=|.+++ ++++-+.+++ =.|.+-||.|-.|+++ -.|+|.+.+.+.+--+.+=.|+-. .+.+.|+ +
T Consensus 115 iPHit~-eI~~~i~~~~~~~dv~i~EiGGTvGDiEs~pf~ea~rq~~~~~g~~n~~~ih~t~vp~~~~~~E~KtKPtQhs 193 (533)
T PRK05380 115 IPHITD-EIKERILAAGTDADVVIVEIGGTVGDIESLPFLEAIRQLRLELGRENVLFIHLTLVPYIAAAGELKTKPTQHS 193 (533)
T ss_pred ccCccH-HHHHHHHhcCCCCCEEEEEeCCccccccccHHHHHHHHHHHhhCCCcEEEEEEeccceecCCCcccCCchHHH
Confidence 388776 4566666653 2467899999999996 578999999876533333333221 1233343 5
Q ss_pred HHHHHhhhccCCee
Q 031985 76 NKELQYLNKEDRLL 89 (149)
Q Consensus 76 v~EL~~lr~de~VL 89 (149)
+++|+.+.+.+++|
T Consensus 194 v~~lr~~Gi~pd~i 207 (533)
T PRK05380 194 VKELRSIGIQPDIL 207 (533)
T ss_pred HHHHHhCCCCCCEE
Confidence 88899999999986
No 59
>PRK14149 heat shock protein GrpE; Provisional
Probab=20.21 E-value=45 Score=26.84 Aligned_cols=67 Identities=16% Similarity=0.145 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhhccCCcEEEeeecccccccccccccCccceeeEEEEEEEEEe---Ccc-hHHHHH-hhhccCCeeEEE
Q 031985 18 SLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQLMQMTMMS---TPN-INKELQ-YLNKEDRLLRWL 92 (149)
Q Consensus 18 ~~~~lv~r~~~~I~~~GG~V~~ve~wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a---~p~-~v~EL~-~lr~de~VLR~l 92 (149)
.+.-+.+.+.+++.+.| |..|..-|. +-=.-| ++ ++...+ ++. ++..++ -+.+.++|||..
T Consensus 118 Gv~mi~k~l~~vL~k~G--V~~I~~~G~----FDP~~H-----EA---v~~v~~~~~~~gtVv~V~QkGY~l~dRVLRPA 183 (191)
T PRK14149 118 GLELTMEKLHEVLARHG--IEGIECLEE----FDPNFH-----NA---IMQVKSEEKENGKIVQVLQQGYKYKGRVLRPA 183 (191)
T ss_pred HHHHHHHHHHHHHHHCC--CEEeCCCCC----CChHHh-----he---eeeecCCCCCcCEEEEEeeCCcEeCCEEeecc
Confidence 45667788888888888 667777662 222222 22 333332 233 444466 599999999999
Q ss_pred EEeccC
Q 031985 93 LVKHRG 98 (149)
Q Consensus 93 ~vK~~~ 98 (149)
.|.+..
T Consensus 184 ~V~Vak 189 (191)
T PRK14149 184 MVSIAK 189 (191)
T ss_pred EEEeCC
Confidence 998764
No 60
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=20.02 E-value=1.1e+02 Score=20.34 Aligned_cols=45 Identities=4% Similarity=0.076 Sum_probs=31.5
Q ss_pred HHHHHhhhccCCcEEEeeec-ccccccccccccCccceeeEEEEEEEEEeCc
Q 031985 23 VARVGKHVYGRNGVLTDITS-FGTVQLGYGIKKLDGRYYQGQLMQMTMMSTP 73 (149)
Q Consensus 23 v~r~~~~I~~~GG~V~~ve~-wG~R~LAY~IkK~~~~~~~G~Y~~~~f~a~p 73 (149)
...+.+.+...|+.|++++- .+.. |++.-. -..|+-+-+.++...
T Consensus 31 ~~~~~~~l~~~G~~v~~ve~~~~g~---yev~~~---~~dG~~~ev~vD~~t 76 (83)
T PF13670_consen 31 IEQAVAKLEAQGYQVREVEFDDDGC---YEVEAR---DKDGKKVEVYVDPAT 76 (83)
T ss_pred HHHHHHHHHhcCCceEEEEEcCCCE---EEEEEE---ECCCCEEEEEEcCCC
Confidence 44556677778999999987 6644 888732 237777777776643
Done!