Query 025898
Match_columns 246
No_of_seqs 118 out of 1036
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:49:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025898hhsearch_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 2.7E-30 5.9E-35 202.8 12.5 94 56-149 3-97 (97)
2 PRK00453 rpsF 30S ribosomal pr 100.0 9.3E-30 2E-34 201.5 13.0 104 58-161 1-105 (108)
3 COG0360 RpsF Ribosomal protein 100.0 5.1E-30 1.1E-34 207.3 9.8 103 59-161 1-104 (112)
4 TIGR00166 S6 ribosomal protein 100.0 4.4E-29 9.4E-34 193.0 12.6 92 59-150 1-92 (93)
5 PF01250 Ribosomal_S6: Ribosom 100.0 8E-28 1.7E-32 184.4 11.6 91 59-149 1-92 (92)
6 PRK14074 rpsF 30S ribosomal pr 99.8 1.4E-20 2.9E-25 169.2 8.8 89 73-163 163-251 (257)
7 KOG4708 Mitochondrial ribosoma 99.7 2.1E-17 4.5E-22 138.2 2.8 97 57-153 2-102 (141)
8 PRK14074 rpsF 30S ribosomal pr 97.2 0.00036 7.7E-09 63.9 3.8 46 58-103 1-47 (257)
9 KOG1832 HIV-1 Vpr-binding prot 90.1 0.22 4.8E-06 53.5 2.9 40 92-132 1281-1320(1516)
10 PF09026 CENP-B_dimeris: Centr 88.3 0.14 3.1E-06 41.3 0.0 17 161-177 1-17 (101)
11 KOG1832 HIV-1 Vpr-binding prot 83.0 0.67 1.5E-05 50.1 1.8 9 209-217 1460-1468(1516)
12 PF04931 DNA_pol_phi: DNA poly 82.9 1.1 2.4E-05 46.7 3.3 13 134-146 597-609 (784)
13 PF11705 RNA_pol_3_Rpc31: DNA- 82.7 1.2 2.5E-05 39.9 3.0 25 188-212 194-219 (233)
14 PF06524 NOA36: NOA36 protein; 79.6 1.6 3.6E-05 41.1 2.9 12 147-158 202-213 (314)
15 cd04905 ACT_CM-PDT C-terminal 77.9 16 0.00035 26.7 7.3 54 77-137 13-68 (80)
16 cd04880 ACT_AAAH-PDT-like ACT 73.5 25 0.00053 25.2 7.2 53 77-136 11-65 (75)
17 PF11705 RNA_pol_3_Rpc31: DNA- 68.8 4.7 0.0001 36.0 3.0 7 130-136 123-129 (233)
18 PF14812 PBP1_TM: Transmembran 66.5 1.9 4.1E-05 33.7 0.0 8 164-171 23-30 (81)
19 cd04902 ACT_3PGDH-xct C-termin 65.5 26 0.00057 24.2 5.8 62 77-148 11-72 (73)
20 cd04893 ACT_GcvR_1 ACT domains 56.5 45 0.00097 24.5 5.9 47 77-133 13-59 (77)
21 cd04869 ACT_GcvR_2 ACT domains 47.2 98 0.0021 22.1 6.3 54 77-135 11-66 (81)
22 cd04904 ACT_AAAH ACT domain of 45.1 1.2E+02 0.0026 22.1 7.4 53 78-137 13-65 (74)
23 cd04931 ACT_PAH ACT domain of 43.7 1.5E+02 0.0033 22.9 7.3 55 77-138 26-85 (90)
24 COG5137 Histone chaperone invo 43.6 40 0.00087 31.4 4.6 48 112-159 108-169 (279)
25 PTZ00415 transmission-blocking 43.1 20 0.00044 41.8 3.0 11 83-93 65-75 (2849)
26 cd04929 ACT_TPH ACT domain of 41.4 1.5E+02 0.0032 22.1 7.2 52 78-136 13-64 (74)
27 KOG1999 RNA polymerase II tran 39.6 21 0.00046 39.0 2.4 12 207-218 85-96 (1024)
28 PF05764 YL1: YL1 nuclear prot 35.0 40 0.00087 30.5 3.2 6 179-184 41-46 (240)
29 PF11702 DUF3295: Protein of u 34.4 24 0.00053 35.9 1.8 12 189-200 307-318 (507)
30 PRK11898 prephenate dehydratas 33.9 2.1E+02 0.0045 26.5 7.8 54 63-126 197-251 (283)
31 KOG3540 Beta amyloid precursor 30.7 45 0.00098 34.2 3.0 26 44-69 43-68 (615)
32 PF11702 DUF3295: Protein of u 29.9 38 0.00083 34.5 2.4 21 183-203 307-327 (507)
33 PF02700 PurS: Phosphoribosylf 29.2 63 0.0014 24.8 3.0 34 108-141 33-71 (80)
34 PF03059 NAS: Nicotianamine sy 27.6 1.4E+02 0.003 28.0 5.5 71 58-129 190-264 (276)
35 PF14257 DUF4349: Domain of un 27.5 3.2E+02 0.007 24.4 7.7 75 57-141 46-120 (262)
36 PF14283 DUF4366: Domain of un 27.4 46 0.001 30.1 2.2 13 112-124 81-93 (218)
37 cd04879 ACT_3PGDH-like ACT_3PG 27.3 1.9E+02 0.004 19.0 6.3 59 77-145 11-69 (71)
38 KOG2023 Nuclear transport rece 26.6 38 0.00081 36.2 1.7 17 158-174 333-349 (885)
39 PRK13011 formyltetrahydrofolat 26.1 3E+02 0.0065 25.6 7.4 42 56-102 3-44 (286)
40 PF14851 FAM176: FAM176 family 25.2 54 0.0012 28.4 2.2 8 141-148 42-49 (153)
41 cd04930 ACT_TH ACT domain of t 24.1 3.9E+02 0.0084 21.6 7.2 53 77-136 53-105 (115)
42 KOG4032 Uncharacterized conser 21.9 50 0.0011 29.6 1.3 19 132-150 99-117 (184)
43 PF00679 EFG_C: Elongation fac 21.7 2.1E+02 0.0045 21.4 4.6 45 78-135 17-61 (89)
44 cd04875 ACT_F4HF-DF N-terminal 21.6 3E+02 0.0066 19.4 6.9 51 77-135 11-63 (74)
45 PF01842 ACT: ACT domain; Int 21.4 2.6E+02 0.0055 18.5 6.3 48 77-133 12-59 (66)
46 PLN03075 nicotianamine synthas 21.2 1.5E+02 0.0032 28.1 4.4 70 58-129 193-267 (296)
47 KOG2038 CAATT-binding transcri 21.0 92 0.002 33.9 3.2 23 31-53 696-721 (988)
48 KOG3272 Predicted coiled-coil 20.5 1.8E+02 0.0039 26.5 4.6 54 1-71 44-97 (207)
No 1
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=99.97 E-value=2.7e-30 Score=202.76 Aligned_cols=94 Identities=30% Similarity=0.525 Sum_probs=90.3
Q ss_pred ccccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHH
Q 025898 56 ERRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTM 134 (246)
Q Consensus 56 ~~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~ 134 (246)
.+|++||+|+|++|+++ +++++++++++++|+++||+|+++++||.|+|||||+|+++|||++++|.++|++|++|++.
T Consensus 3 ~~mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k~~~G~Yv~~~f~~~~~~i~eler~ 82 (97)
T CHL00123 3 SKLNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYIQMNYSGNGKLVNSLEKA 82 (97)
T ss_pred CcccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCCCCEEEEEEEEEEECHHHHHHHHHH
Confidence 36899999999999985 47999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCeeEEEEEee
Q 025898 135 LDKDEKVIRHLVIKR 149 (246)
Q Consensus 135 Lrlde~VLR~mVVK~ 149 (246)
|+++++|||||++|.
T Consensus 83 lri~e~VlR~m~vk~ 97 (97)
T CHL00123 83 LKLDENVLRYLTFKK 97 (97)
T ss_pred hCCCCCeEEEEEEeC
Confidence 999999999999973
No 2
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=99.97 E-value=9.3e-30 Score=201.50 Aligned_cols=104 Identities=34% Similarity=0.662 Sum_probs=98.1
Q ss_pred ccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898 58 RRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD 136 (246)
Q Consensus 58 Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr 136 (246)
||+||+|+|++|..+ +++++++++++++|.++||+|+.+++||.|+|||+|+|+++|+|++|+|.++|+++++|++.|+
T Consensus 1 M~~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~ 80 (108)
T PRK00453 1 MRKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYVLLNFEAPPAAIAELERLFR 80 (108)
T ss_pred CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEecccccccceEcCCCcEEEEEEEEEEeCHHHHHHHHHHhC
Confidence 899999999999974 5799999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeEEEEEeecCCCCCCCCCCC
Q 025898 137 KDEKVIRHLVIKRDKAITEDCPPPP 161 (246)
Q Consensus 137 lde~VLR~mVVK~de~i~e~~p~~p 161 (246)
+|++|||||++|+++......+..+
T Consensus 81 ~~~~VlR~~~vk~~~~~~~~~~~~~ 105 (108)
T PRK00453 81 INEDVLRFLTVKVEEAEEEPSPMMK 105 (108)
T ss_pred CCCCeEEEEEEEecccccccChhhh
Confidence 9999999999999988776665543
No 3
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=5.1e-30 Score=207.31 Aligned_cols=103 Identities=40% Similarity=0.727 Sum_probs=98.2
Q ss_pred cceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898 59 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK 137 (246)
Q Consensus 59 r~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl 137 (246)
++||+|||++|+.+ +++++.+++++++|+++||+|.++++||.|+|||||+|+++|||++|+|+|+|+++++|+|.|++
T Consensus 1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~~g~Y~l~~f~~~~~~i~Eler~~ri 80 (112)
T COG0360 1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLMNFEAEPAAIAELERLLRI 80 (112)
T ss_pred CceEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEehhhhhhhhcceecccceEEEEEEEEEcCHHHHHHHHHHhcc
Confidence 46999999999987 57999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeEEEEEeecCCCCCCCCCCC
Q 025898 138 DEKVIRHLVIKRDKAITEDCPPPP 161 (246)
Q Consensus 138 de~VLR~mVVK~de~i~e~~p~~p 161 (246)
|++|||||++|.+...+..+|+.+
T Consensus 81 n~~VlR~liik~~~~~~~~~~~~~ 104 (112)
T COG0360 81 NEDVLRHLIIKVEKAKEELSPMLK 104 (112)
T ss_pred chhhheeeEEEechhhcccchhhh
Confidence 999999999999999888877754
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=99.96 E-value=4.4e-29 Score=192.99 Aligned_cols=92 Identities=39% Similarity=0.709 Sum_probs=88.9
Q ss_pred cceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCC
Q 025898 59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKD 138 (246)
Q Consensus 59 r~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrld 138 (246)
++||+|+|++|..++++++++++++++|.++||+|+++++||.|+|||||+|+++|+|++|+|+++|+++++|++.|+++
T Consensus 1 ~~YE~~~Il~p~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lr~~ 80 (93)
T TIGR00166 1 RHYEIIFLVRPTLSEEVKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVLMNFSGEAQVIKEFERTARIN 80 (93)
T ss_pred CceeEEEEECCCCcHHHHHHHHHHHHHHHhCCCEEEEEEeecceecceEcCCCceEEEEEEEEEeCHHHHHHHHHHhcCC
Confidence 57999999999987669999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeEEEEEeec
Q 025898 139 EKVIRHLVIKRD 150 (246)
Q Consensus 139 e~VLR~mVVK~d 150 (246)
++|||||++|++
T Consensus 81 ~~VlR~~~vk~~ 92 (93)
T TIGR00166 81 DNVIRSLIIKLE 92 (93)
T ss_pred cCeEEEEEEEec
Confidence 999999999974
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=99.95 E-value=8e-28 Score=184.35 Aligned_cols=91 Identities=34% Similarity=0.718 Sum_probs=86.6
Q ss_pred cceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898 59 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK 137 (246)
Q Consensus 59 r~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl 137 (246)
|.||+|+|++|..+ ++++++++++.++|.++||+|+.+++||.|+|||||+|+.+|+|++++|+++|+++++|++.|++
T Consensus 1 r~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~~G~Y~~~~f~~~~~~i~el~~~l~~ 80 (92)
T PF01250_consen 1 RKYELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQKEGHYFLFNFDASPSAIKELERKLRL 80 (92)
T ss_dssp EEEEEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTECEEEEEEEEEEESTTHHHHHHHHHHT
T ss_pred CceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCCCEEEEEEEEEEeCHHHHHHHHHHhcC
Confidence 68999999999975 47999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeEEEEEee
Q 025898 138 DEKVIRHLVIKR 149 (246)
Q Consensus 138 de~VLR~mVVK~ 149 (246)
+++|||||++|.
T Consensus 81 ~~~VlR~~~vK~ 92 (92)
T PF01250_consen 81 DEDVLRYLIVKK 92 (92)
T ss_dssp STTEEEEEEEE-
T ss_pred CCCeEEEEEEeC
Confidence 999999999984
No 6
>PRK14074 rpsF 30S ribosomal protein S6; Provisional
Probab=99.83 E-value=1.4e-20 Score=169.24 Aligned_cols=89 Identities=22% Similarity=0.378 Sum_probs=83.4
Q ss_pred hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEEEeecCC
Q 025898 73 EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKA 152 (246)
Q Consensus 73 Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~mVVK~de~ 152 (246)
++++++++++.++|+++| +.++++||+|+|||||+|+++|+|++++|.++|++|++|+|.+|++++|||||++|++++
T Consensus 163 DQveevvEkik~iIe~~G--iikvE~WGkRkLAYpIkK~~eGyYvL~nFeAep~aIaELER~lRInE~VIRfLtVKlDe~ 240 (257)
T PRK14074 163 NQSNKTLEMLLKNIEASG--LIKYEYWGLLDFAYPINKMKSGHYCIMCISSTSSIMDEFVRRMKLNENIIRHLSVQVDKF 240 (257)
T ss_pred HHHHHHHHHHHHHHHhcC--eeehHhhcchhhccccCCCCeEEEEEEEEEcCHHHHHHHHHHhcCccceeeEEEEeeccc
Confidence 567788999999999995 569999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCc
Q 025898 153 ITEDCPPPPEF 163 (246)
Q Consensus 153 i~e~~p~~p~f 163 (246)
...++|+.++.
T Consensus 241 ~~~pSpimkk~ 251 (257)
T PRK14074 241 FEGKSYMMNKQ 251 (257)
T ss_pred cccCChhhhhh
Confidence 99999987653
No 7
>KOG4708 consensus Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=2.1e-17 Score=138.19 Aligned_cols=97 Identities=25% Similarity=0.396 Sum_probs=88.9
Q ss_pred cccceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCC----CCeeEEEEEEEEeCcchHHHHH
Q 025898 57 RRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQK----AKKAHYILMNFELEAKWINDFK 132 (246)
Q Consensus 57 ~Mr~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK----~~~G~Yvl~~F~a~psaI~ELe 132 (246)
.|+.||+++|+++...++.+.++.+..+.+-..||.|+.++++|.|.|+|+|+| |..|+||+|.|.++|++..++.
T Consensus 2 lmp~yelali~~~~~rpela~~l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~~v~~ei~ 81 (141)
T KOG4708|consen 2 LMPLYELALITRSLSRPELAKLLARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSPAVQSEIK 81 (141)
T ss_pred cchHHHHHHHhcccCCHHHHHHHHHHhhHHhhcCCeEeechhcchhhhcchHHHhcCccccceEEEEeecCCHHHHHHHH
Confidence 599999999999998777777777777777778899999999999999999996 5689999999999999999999
Q ss_pred HHhCCCCCeeEEEEEeecCCC
Q 025898 133 TMLDKDEKVIRHLVIKRDKAI 153 (246)
Q Consensus 133 r~Lrlde~VLR~mVVK~de~i 153 (246)
+.|+.+.+|||+++||++...
T Consensus 82 ~~l~~D~dviR~~IVKv~~~~ 102 (141)
T KOG4708|consen 82 RILKRDPDVIRWLIVKVDDIK 102 (141)
T ss_pred HHHhcChhhHHhhheeccccc
Confidence 999999999999999999853
No 8
>PRK14074 rpsF 30S ribosomal protein S6; Provisional
Probab=97.17 E-value=0.00036 Score=63.92 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=43.4
Q ss_pred ccceeEEEEecCCChh-hHHHHHHHHHHHHhhCCCEEEEEEeeeccc
Q 025898 58 RRHYEVVYLIHEKYEE-DVGSVNEKVQDFLREKKGRVWRLNDWGLRR 103 (246)
Q Consensus 58 Mr~YEim~ILrp~~eE-ei~~liekv~~iI~k~GG~I~~vedwG~Rr 103 (246)
|+.||.+||.+++++. ++..+++.+..+|.++||.|...+.||.+.
T Consensus 1 m~lYE~~fIa~q~ls~~q~e~l~e~~~~~l~~~~~~v~~~e~wG~~~ 47 (257)
T PRK14074 1 MNLYEFTFIAQQGLLQQEVEEMVQELAVLLKNIKADVMFQQIKGILE 47 (257)
T ss_pred CCccceeeeecccccHHHHHHHHHHHHHHHHhcCCeeehhhhhhhhh
Confidence 8999999999999865 799999999999999999999999999865
No 9
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=90.15 E-value=0.22 Score=53.54 Aligned_cols=40 Identities=8% Similarity=0.155 Sum_probs=22.7
Q ss_pred EEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHH
Q 025898 92 RVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFK 132 (246)
Q Consensus 92 ~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELe 132 (246)
.|++.+.|..|.+--- .....=.-..+.|+..+..+=...
T Consensus 1281 VIINSEIwD~RTF~lL-h~VP~Ldqc~VtFNstG~VmYa~~ 1320 (1516)
T KOG1832|consen 1281 VIINSEIWDMRTFKLL-HSVPSLDQCAVTFNSTGDVMYAML 1320 (1516)
T ss_pred EEeechhhhhHHHHHH-hcCccccceEEEeccCccchhhhh
Confidence 5788899999865321 011122335667777766554443
No 10
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=88.28 E-value=0.14 Score=41.33 Aligned_cols=17 Identities=24% Similarity=0.472 Sum_probs=0.0
Q ss_pred CCccccccccCCCCCcc
Q 025898 161 PEFHTLRAEMHGYDEEE 177 (246)
Q Consensus 161 p~f~s~~~~~~~~~~~~ 177 (246)
|.||-+....|.+.|.+
T Consensus 1 ~~~~~~eg~~dse~dsd 17 (101)
T PF09026_consen 1 PTLHFLEGEEDSESDSD 17 (101)
T ss_dssp -----------------
T ss_pred CceeecccCcccccccc
Confidence 34566666665444443
No 11
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=82.98 E-value=0.67 Score=50.06 Aligned_cols=9 Identities=11% Similarity=0.003 Sum_probs=3.9
Q ss_pred CCceEEEec
Q 025898 209 HGFSIVNVD 217 (246)
Q Consensus 209 ~~~~~~~~~ 217 (246)
+++..+.+|
T Consensus 1460 Gd~~d~~~D 1468 (1516)
T KOG1832|consen 1460 GDEADILID 1468 (1516)
T ss_pred cccccCCCC
Confidence 344444444
No 12
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=82.93 E-value=1.1 Score=46.69 Aligned_cols=13 Identities=15% Similarity=0.478 Sum_probs=5.8
Q ss_pred HhCCCCCeeEEEE
Q 025898 134 MLDKDEKVIRHLV 146 (246)
Q Consensus 134 ~Lrlde~VLR~mV 146 (246)
.|......||.++
T Consensus 597 lls~~s~llR~~~ 609 (784)
T PF04931_consen 597 LLSQPSALLRKVS 609 (784)
T ss_pred HHhCcchHHHHHH
Confidence 3444444555443
No 13
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=82.67 E-value=1.2 Score=39.91 Aligned_cols=25 Identities=32% Similarity=0.708 Sum_probs=14.1
Q ss_pred cCcCCCCCCCCCCCC-CCCCCCCCce
Q 025898 188 DDEYDDGEGDEMDDN-VDDDFEHGFS 212 (246)
Q Consensus 188 ~~~~~~~~~~~~~~~-~~~~~~~~~~ 212 (246)
++++++++++++.+| ..+-||.++.
T Consensus 194 dee~~dee~e~~~DYna~~YFDnGed 219 (233)
T PF11705_consen 194 DEEFEDEEDEDDDDYNAENYFDNGED 219 (233)
T ss_pred ccccchhhhccCCCcchhccCCCCCc
Confidence 444434444445556 6667776666
No 14
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=79.65 E-value=1.6 Score=41.10 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=5.1
Q ss_pred EeecCCCCCCCC
Q 025898 147 IKRDKAITEDCP 158 (246)
Q Consensus 147 VK~de~i~e~~p 158 (246)
+|.++....+||
T Consensus 202 ~ky~k~k~~PCP 213 (314)
T PF06524_consen 202 FKYEKGKPIPCP 213 (314)
T ss_pred cccccCCCCCCC
Confidence 444444334444
No 15
>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=77.90 E-value=16 Score=26.67 Aligned_cols=54 Identities=9% Similarity=0.060 Sum_probs=37.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeC--cchHHHHHHHhCC
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELE--AKWINDFKTMLDK 137 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~--psaI~ELer~Lrl 137 (246)
..+.++.+++.++|.+|..+. .+|.++....+.+++.+++. ...++.+-+.|+.
T Consensus 13 G~L~~il~~f~~~~ini~~i~-------s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 13 GALYDVLGVFAERGINLTKIE-------SRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CHHHHHHHHHHHCCcCEEEEE-------EEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 357788899999999999996 45555555667778888886 4444444444443
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=73.48 E-value=25 Score=25.21 Aligned_cols=53 Identities=11% Similarity=0.065 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeC--cchHHHHHHHhC
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELE--AKWINDFKTMLD 136 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~--psaI~ELer~Lr 136 (246)
..+.++-+.+.++|.+|..++.. |+++..-.+.+++.+.+. ...++.+-..++
T Consensus 11 G~L~~vL~~f~~~~vni~~I~Sr-------p~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~ 65 (75)
T cd04880 11 GALAKALKVFAERGINLTKIESR-------PSRKGLWEYEFFVDFEGHIDDPDVKEALEELK 65 (75)
T ss_pred CHHHHHHHHHHHCCCCEEEEEee-------ecCCCCceEEEEEEEECCCCCHHHHHHHHHHH
Confidence 34778888999999999999765 666666668889999983 555555554444
No 17
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=68.79 E-value=4.7 Score=36.00 Aligned_cols=7 Identities=14% Similarity=0.212 Sum_probs=2.7
Q ss_pred HHHHHhC
Q 025898 130 DFKTMLD 136 (246)
Q Consensus 130 ELer~Lr 136 (246)
+|...++
T Consensus 123 EL~~~~~ 129 (233)
T PF11705_consen 123 ELWPTLR 129 (233)
T ss_pred HHHhhcc
Confidence 4443333
No 18
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=66.46 E-value=1.9 Score=33.73 Aligned_cols=8 Identities=13% Similarity=0.061 Sum_probs=0.0
Q ss_pred cccccccC
Q 025898 164 HTLRAEMH 171 (246)
Q Consensus 164 ~s~~~~~~ 171 (246)
.+.+.+.+
T Consensus 23 ~~r~rrr~ 30 (81)
T PF14812_consen 23 PSRRRRRD 30 (81)
T ss_dssp --------
T ss_pred cccccccc
Confidence 34444443
No 19
>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=65.55 E-value=26 Score=24.22 Aligned_cols=62 Identities=11% Similarity=0.067 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEEEe
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIK 148 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~mVVK 148 (246)
..+.++..+|.++|..|..+.. ++-. .....++.+.++.+ ...++...++-.+.|++..+++
T Consensus 11 G~l~~i~~~l~~~~inI~~~~~-------~~~~-~~~~~~~~i~v~~~--~~~~~~~~l~~~~~v~~v~~~~ 72 (73)
T cd04902 11 GVIGKVGTILGEAGINIAGMQV-------GRDE-PGGEALMVLSVDEP--VPDEVLEELRALPGILSAKVVE 72 (73)
T ss_pred CHHHHHHHHHHHcCcChhheEe-------eccC-CCCEEEEEEEeCCC--CCHHHHHHHHcCCCccEEEEEe
Confidence 3467788999999999977752 1111 22333455555553 3458888899999999988875
No 20
>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=56.53 E-value=45 Score=24.45 Aligned_cols=47 Identities=9% Similarity=-0.050 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHH
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKT 133 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer 133 (246)
.++.++.++|.++||.|..+...- ...-.+..+.|..+......|+.
T Consensus 13 GiVa~vs~~la~~g~nI~d~~q~~----------~~~~F~m~~~~~~~~~~~~~l~~ 59 (77)
T cd04893 13 GILNELTRAVSESGCNILDSRMAI----------LGTEFALTMLVEGSWDAIAKLEA 59 (77)
T ss_pred hHHHHHHHHHHHcCCCEEEceeeE----------EcCEEEEEEEEEeccccHHHHHH
Confidence 578899999999999999988766 11122455667666444555553
No 21
>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=47.21 E-value=98 Score=22.06 Aligned_cols=54 Identities=15% Similarity=0.235 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEE-EEEEEEeCcc-hHHHHHHHh
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHY-ILMNFELEAK-WINDFKTML 135 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Y-vl~~F~a~ps-aI~ELer~L 135 (246)
.++.++..+|.++|+.|..+... .++......+.| ..+.|..++. .+.+|+..|
T Consensus 11 Giv~~it~~l~~~~~nI~~~~~~-----~~~~~~~~~~~~~~~~~v~~p~~~~~~~l~~~l 66 (81)
T cd04869 11 GIVHEVTQFLAQRNINIEDLSTE-----TYSAPMSGTPLFKAQATLALPAGTDLDALREEL 66 (81)
T ss_pred CHHHHHHHHHHHcCCCeEEeEee-----eecCCCCCcceEEEEEEEecCCCCCHHHHHHHH
Confidence 46788999999999999988763 333333333444 4677777754 466666433
No 22
>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=45.14 E-value=1.2e+02 Score=22.07 Aligned_cols=53 Identities=6% Similarity=0.103 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898 78 VNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK 137 (246)
Q Consensus 78 liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl 137 (246)
.+..+-+.+..+|-++++++.+ |++...--+++++.|++....+.++-+.|+.
T Consensus 13 ~L~~vL~~f~~~~iNlt~IeSR-------P~~~~~~~y~Ffvd~~~~~~~~~~~l~~L~~ 65 (74)
T cd04904 13 ALARALKLFEEFGVNLTHIESR-------PSRRNGSEYEFFVDCEVDRGDLDQLISSLRR 65 (74)
T ss_pred HHHHHHHHHHHCCCcEEEEECC-------CCCCCCceEEEEEEEEcChHHHHHHHHHHHH
Confidence 4677888899999999999864 5555556688899999876555555444443
No 23
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=43.67 E-value=1.5e+02 Score=22.95 Aligned_cols=55 Identities=15% Similarity=0.183 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeC-c----chHHHHHHHhCCC
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELE-A----KWINDFKTMLDKD 138 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~-p----saI~ELer~Lrld 138 (246)
..+.++-+.+..+|-.+.+++.+ |.++..-.++|++.|++. . .++.+|.+.+..+
T Consensus 26 GsL~~vL~~Fa~~~INLt~IeSR-------P~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~~~~~~ 85 (90)
T cd04931 26 GALAKVLRLFEEKDINLTHIESR-------PSRLNKDEYEFFINLDKKSAPALDPIIKSLRNDIGAT 85 (90)
T ss_pred cHHHHHHHHHHHCCCCEEEEEec-------cCCCCCceEEEEEEEEcCCCHHHHHHHHHHHHHhCCC
Confidence 34777888899999999999875 455555568889999986 2 3555666555444
No 24
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=43.61 E-value=40 Score=31.37 Aligned_cols=48 Identities=15% Similarity=0.291 Sum_probs=26.9
Q ss_pred CeeEEEEEEEEeC----------cc-h--HHHHHH-HhCCCCCeeEEEEEeecCCCCCCCCC
Q 025898 112 KKAHYILMNFELE----------AK-W--INDFKT-MLDKDEKVIRHLVIKRDKAITEDCPP 159 (246)
Q Consensus 112 ~~G~Yvl~~F~a~----------ps-a--I~ELer-~Lrlde~VLR~mVVK~de~i~e~~p~ 159 (246)
+-|||+-..|.+- |+ . +..+.| .|.-..+|-||-++--.+.--...||
T Consensus 108 RvGYyVnney~gi~~~e~~d~E~p~~kvd~~~v~r~ilaEkprvtrfnIvwDn~~d~d~apP 169 (279)
T COG5137 108 RVGYYVNNEYPGITKLEKSDVEEPSEKVDEEDVEREILAEKPRVTRFNIVWDNDEDNDEAPP 169 (279)
T ss_pred EEEEEeccCCcchhhhhhhhhcCCchhcCHHHHHHHHhccCCcceeeeeEecCCcccccCCC
Confidence 5688876666521 22 1 233444 44456789999888655543344444
No 25
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=43.11 E-value=20 Score=41.76 Aligned_cols=11 Identities=9% Similarity=0.277 Sum_probs=5.9
Q ss_pred HHHHhhCCCEE
Q 025898 83 QDFLREKKGRV 93 (246)
Q Consensus 83 ~~iI~k~GG~I 93 (246)
++-..++||.-
T Consensus 65 ~~~~~~~g~~y 75 (2849)
T PTZ00415 65 KECFDKNGGIY 75 (2849)
T ss_pred ccccccCCCEE
Confidence 34455666654
No 26
>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=41.42 E-value=1.5e+02 Score=22.08 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=39.2
Q ss_pred HHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898 78 VNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD 136 (246)
Q Consensus 78 liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr 136 (246)
.+..+-+.+..+|..+.+++.+ |.++..--+++++.++++...++.+-..|+
T Consensus 13 ~L~~iL~~f~~~~inl~~IeSR-------P~~~~~~~y~F~id~e~~~~~i~~~l~~l~ 64 (74)
T cd04929 13 GLAKALKLFQELGINVVHIESR-------KSKRRSSEFEIFVDCECDQRRLDELVQLLK 64 (74)
T ss_pred HHHHHHHHHHHCCCCEEEEEec-------cCCCCCceEEEEEEEEcCHHHHHHHHHHHH
Confidence 4777888999999999999875 455555668899999998776655555554
No 27
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=39.57 E-value=21 Score=38.95 Aligned_cols=12 Identities=25% Similarity=-0.000 Sum_probs=6.0
Q ss_pred CCCCceEEEecC
Q 025898 207 FEHGFSIVNVDD 218 (246)
Q Consensus 207 ~~~~~~~~~~~~ 218 (246)
.+++++|.+-.+
T Consensus 85 ~edEed~~~~~~ 96 (1024)
T KOG1999|consen 85 EEDEEDIELHND 96 (1024)
T ss_pred hccCcchhhccc
Confidence 355666544433
No 28
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.98 E-value=40 Score=30.52 Aligned_cols=6 Identities=17% Similarity=0.722 Sum_probs=2.3
Q ss_pred CCCCCC
Q 025898 179 DIDYDD 184 (246)
Q Consensus 179 ~~~~~~ 184 (246)
|++|..
T Consensus 41 D~ef~~ 46 (240)
T PF05764_consen 41 DEEFES 46 (240)
T ss_pred CccccC
Confidence 333333
No 29
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=34.38 E-value=24 Score=35.86 Aligned_cols=12 Identities=33% Similarity=0.296 Sum_probs=6.4
Q ss_pred CcCCCCCCCCCC
Q 025898 189 DEYDDGEGDEMD 200 (246)
Q Consensus 189 ~~~~~~~~~~~~ 200 (246)
||+||+++|+.+
T Consensus 307 dDDDDssDWEDS 318 (507)
T PF11702_consen 307 DDDDDSSDWEDS 318 (507)
T ss_pred cCCccchhhhhc
Confidence 455556666433
No 30
>PRK11898 prephenate dehydratase; Provisional
Probab=33.92 E-value=2.1e+02 Score=26.48 Aligned_cols=54 Identities=6% Similarity=0.005 Sum_probs=40.0
Q ss_pred EEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcc
Q 025898 63 VVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAK 126 (246)
Q Consensus 63 im~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~ps 126 (246)
+.+++..... . ..+-++-+.+.++|-++++++.+ |+++..-.++|++.|+++..
T Consensus 197 tslif~l~~~~p---GsL~~~L~~F~~~~INLt~IeSR-------P~~~~~~~y~F~vd~eg~~~ 251 (283)
T PRK11898 197 TSLVLTLPNNLP---GALYKALSEFAWRGINLTRIESR-------PTKTGLGTYFFFIDVEGHID 251 (283)
T ss_pred EEEEEEeCCCCc---cHHHHHHHHHHHCCCCeeeEecc-------cCCCCCccEEEEEEEEccCC
Confidence 5666665432 2 34667778888999999999986 66656667889999999766
No 31
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=30.67 E-value=45 Score=34.23 Aligned_cols=26 Identities=12% Similarity=0.075 Sum_probs=13.3
Q ss_pred HhhHHhhhhhhhccccceeEEEEecC
Q 025898 44 SLNIELESELNVERRRHYEVVYLIHE 69 (246)
Q Consensus 44 ~l~~~~~~~~~~~~Mr~YEim~ILrp 69 (246)
.|||.+.-.=..++-+.|=.+++..+
T Consensus 43 rln~h~~~qG~w~~dpe~~~tc~~~k 68 (615)
T KOG3540|consen 43 RLNMHMNEQGMWEPDPERVGTCFVLK 68 (615)
T ss_pred hhhhhhccccccCCCcchheeeehhH
Confidence 56666544433444555555555443
No 32
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=29.86 E-value=38 Score=34.49 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=11.2
Q ss_pred CCccccCcCCCCCCCCCCCCC
Q 025898 183 DDEEYDDEYDDGEGDEMDDNV 203 (246)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~ 203 (246)
||+++++||+|..++.|-..+
T Consensus 307 dDDDDssDWEDSveESG~sSv 327 (507)
T PF11702_consen 307 DDDDDSSDWEDSVEESGKSSV 327 (507)
T ss_pred cCCccchhhhhccccccCCCc
Confidence 444556677555555554333
No 33
>PF02700 PurS: Phosphoribosylformylglycinamidine (FGAM) synthase; InterPro: IPR003850 Phosphoribosylformylglycinamidine(FGAM) synthetase, 6.3.5.3 from EC, catalyses the fourth step in the de novo purine biosynthetic pathway []. 5-phosphoribosylformylglycinamide (FGAR) + glutamine + ATP = FGAM + glutamate + ADP + Pi In eukaryotes and many bacterial systems (including Escherichia coli and Salmonella typhimurium), the FGAM synthetase is encoded by the large form of PurL (lgPurL), which contains an N-terminal ATPase domain and a C-terminal glutamine-binding domain. In archaeal and other bacterial systems, however, FGAM synthetase is encoded by separate genes, making it a multisubunit (rather than multidomain) enzyme. The protein is composed of the small form of PurL (smPurL), which is homologus to the ATPase domain of lgPurL, PurQ which is homologous to the glutamine-binding domain of of lgPurL, and PurS, whose function is not known. This entry represents the PurS subunit of the multisubunit FGAM synthetase. Recent studies showed that disruption of the purS gene in Bacillus subtilis resulted in a purine auxotrophic phenotype, due to defective FGAM synthetase activity. Therefore, the PurS protein appears to be required for the function of the PurL and PurQ subunits of the FGAM synthetase, but the molecular mechanism for the functional role of PurS is currently not known. For additional information please see [, ].; GO: 0016879 ligase activity, forming carbon-nitrogen bonds; PDB: 2ZW2_B 3D54_B 1VQ3_B 1GTD_A 2YX5_A 2CUW_A 1TWJ_B 1T4A_B 2DGB_B.
Probab=29.21 E-value=63 Score=24.76 Aligned_cols=34 Identities=12% Similarity=0.312 Sum_probs=23.9
Q ss_pred cCCCCeeEEEEEEEEeC-----cchHHHHHHHhCCCCCe
Q 025898 108 IQKAKKAHYILMNFELE-----AKWINDFKTMLDKDEKV 141 (246)
Q Consensus 108 IkK~~~G~Yvl~~F~a~-----psaI~ELer~Lrlde~V 141 (246)
|+.-+.|.|+.+.+.++ .+.+.++=+.|-.|+-|
T Consensus 33 v~~Vr~GK~~~l~~~~~~~e~a~~~v~~i~~~LLaNpvi 71 (80)
T PF02700_consen 33 VKDVRVGKYIELELEADDEEEAEEQVEEICEKLLANPVI 71 (80)
T ss_dssp EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTT
T ss_pred cCcEEEEEEEEEEEeCCCHHHHHHHHHHHHHHhcCCCce
Confidence 66678899999999998 45677777777444444
No 34
>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=27.59 E-value=1.4e+02 Score=28.00 Aligned_cols=71 Identities=20% Similarity=0.269 Sum_probs=36.1
Q ss_pred ccceeEEEEecCCC--hhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCC--CeeEEEEEEEEeCcchHH
Q 025898 58 RRHYEVVYLIHEKY--EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKA--KKAHYILMNFELEAKWIN 129 (246)
Q Consensus 58 Mr~YEim~ILrp~~--eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~--~~G~Yvl~~F~a~psaI~ 129 (246)
...|.+++|..-=. .++-+.++.++.+.+.. |+.|.-=.-||.|.|-||.-.. ..|.=++..+.-.+.+++
T Consensus 190 l~~~DvV~lAalVg~~~e~K~~Il~~l~~~m~~-ga~l~~Rsa~GlR~~LYp~vd~~~l~gf~~~~~~hP~~~ViN 264 (276)
T PF03059_consen 190 LKEYDVVFLAALVGMDAEPKEEILEHLAKHMAP-GARLVVRSAHGLRSFLYPVVDPEDLRGFEVLAVVHPTDEVIN 264 (276)
T ss_dssp ----SEEEE-TT-S----SHHHHHHHHHHHS-T-TSEEEEEE--GGGGGSS----TGGGTTEEEEEEE---TT---
T ss_pred cccCCEEEEhhhcccccchHHHHHHHHHhhCCC-CcEEEEecchhhHHHcCCCCChHHCCCeEEEEEECCCCCcee
Confidence 46788888875322 24567899999999886 5555444889999999998753 337777666665554443
No 35
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=27.54 E-value=3.2e+02 Score=24.44 Aligned_cols=75 Identities=13% Similarity=0.131 Sum_probs=55.5
Q ss_pred cccceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898 57 RRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD 136 (246)
Q Consensus 57 ~Mr~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr 136 (246)
++--|...+-+.. ..+.+..+++.+++.+.||.|.....++. ..........+++..|+.....|-..|.
T Consensus 46 rkii~~~~l~lev---~d~~~a~~~i~~~~~~~gG~i~~~~~~~~-------~~~~~~~~~~ltiRVP~~~~~~~l~~l~ 115 (262)
T PF14257_consen 46 RKIIKTADLSLEV---KDVEKAVKKIENLVESYGGYIESSSSSSS-------GGSDDERSASLTIRVPADKFDSFLDELS 115 (262)
T ss_pred ceEEEEEEEEEEE---CCHHHHHHHHHHHHHHcCCEEEEEeeecc-------cCCCCcceEEEEEEECHHHHHHHHHHHh
Confidence 3444544444433 45677899999999999999999997655 4455667788999999999999988887
Q ss_pred CCCCe
Q 025898 137 KDEKV 141 (246)
Q Consensus 137 lde~V 141 (246)
--..|
T Consensus 116 ~~g~v 120 (262)
T PF14257_consen 116 ELGKV 120 (262)
T ss_pred ccCce
Confidence 44433
No 36
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=27.38 E-value=46 Score=30.15 Aligned_cols=13 Identities=8% Similarity=0.215 Sum_probs=6.6
Q ss_pred CeeEEEEEEEEeC
Q 025898 112 KKAHYILMNFELE 124 (246)
Q Consensus 112 ~~G~Yvl~~F~a~ 124 (246)
+.|+||++.++-.
T Consensus 81 k~gn~FyliIDr~ 93 (218)
T PF14283_consen 81 KSGNTFYLIIDRD 93 (218)
T ss_pred cCCCEEEEEEecC
Confidence 4455555555443
No 37
>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=27.30 E-value=1.9e+02 Score=19.03 Aligned_cols=59 Identities=17% Similarity=0.136 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEE
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHL 145 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~m 145 (246)
..+.++..+|.+.|..|..+.. ..+..+.+..+.|..+...+.++-+.|+--+.|++.-
T Consensus 11 g~l~~i~~~l~~~~~nI~~~~~----------~~~~~~~~~~~~~~v~~~~~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 11 GVIGKVGTILGEHGINIAAMQV----------GRKEKGGIAYMVLDVDSPVPEEVLEELKALPGIIRVR 69 (71)
T ss_pred CHHHHHHHHHHhcCCCeeeEEE----------eccCCCCEEEEEEEcCCCCCHHHHHHHHcCCCeEEEE
Confidence 3567788899999999988864 1111022333444443335678888888888888753
No 38
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.57 E-value=38 Score=36.19 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=11.3
Q ss_pred CCCCCccccccccCCCC
Q 025898 158 PPPPEFHTLRAEMHGYD 174 (246)
Q Consensus 158 p~~p~f~s~~~~~~~~~ 174 (246)
-.+|+||.-+..+-..+
T Consensus 333 DIkPRfhksk~~~~~~~ 349 (885)
T KOG2023|consen 333 DIKPRFHKSKEHGNGED 349 (885)
T ss_pred hccchhhhchhccCccc
Confidence 34588888777665444
No 39
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=26.12 E-value=3e+02 Score=25.60 Aligned_cols=42 Identities=17% Similarity=0.216 Sum_probs=31.1
Q ss_pred ccccceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeecc
Q 025898 56 ERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLR 102 (246)
Q Consensus 56 ~~Mr~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~R 102 (246)
++|..|-+.++- ++. . .++.++.++|.++|++|..+...+..
T Consensus 3 ~~m~~~vitv~G-~Dr-p---GIVa~VT~~La~~~vNI~dls~~~~~ 44 (286)
T PRK13011 3 RRPDTFVLTLSC-PSA-A---GIVAAVTGFLAEHGCYITELHSFDDR 44 (286)
T ss_pred CCCceEEEEEEe-CCC-C---CHHHHHHHHHHhCCCCEEEeeeeecC
Confidence 467777765554 221 2 46889999999999999999988553
No 40
>PF14851 FAM176: FAM176 family
Probab=25.18 E-value=54 Score=28.37 Aligned_cols=8 Identities=38% Similarity=0.202 Sum_probs=4.0
Q ss_pred eeEEEEEe
Q 025898 141 VIRHLVIK 148 (246)
Q Consensus 141 VLR~mVVK 148 (246)
|+|..+.+
T Consensus 42 V~risc~~ 49 (153)
T PF14851_consen 42 VIRISCRP 49 (153)
T ss_pred Hhhheeec
Confidence 45555533
No 41
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.06 E-value=3.9e+02 Score=21.61 Aligned_cols=53 Identities=11% Similarity=0.134 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD 136 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr 136 (246)
..+.++-+.+..+|-++.+++. +|+++...-++|++.|++....+..+-+.|+
T Consensus 53 GsL~~iL~~Fa~~gINLt~IES-------RP~~~~~~eY~FfIdieg~~~~~~~aL~~L~ 105 (115)
T cd04930 53 SSLSRILKVFETFEAKIHHLES-------RPSRKEGGDLEVLVRCEVHRSDLLQLISSLR 105 (115)
T ss_pred cHHHHHHHHHHHCCCCEEEEEC-------CcCCCCCceEEEEEEEEeCHHHHHHHHHHHH
Confidence 3477788889999999999986 4666666668889999988665444444443
No 42
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.89 E-value=50 Score=29.57 Aligned_cols=19 Identities=16% Similarity=0.246 Sum_probs=9.5
Q ss_pred HHHhCCCCCeeEEEEEeec
Q 025898 132 KTMLDKDEKVIRHLVIKRD 150 (246)
Q Consensus 132 er~Lrlde~VLR~mVVK~d 150 (246)
+-..+-|-.+||-|.-|+.
T Consensus 99 ~~~~~~N~~~ieells~l~ 117 (184)
T KOG4032|consen 99 HDIQNGNYAIIEELLSKLP 117 (184)
T ss_pred HHHHcccHHHHHHHHHHcc
Confidence 3444455555555554444
No 43
>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=21.74 E-value=2.1e+02 Score=21.41 Aligned_cols=45 Identities=18% Similarity=0.313 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHh
Q 025898 78 VNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135 (246)
Q Consensus 78 liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~L 135 (246)
.+.++...|.+.+|+|......|. ..+.+.+.++-..+..|...|
T Consensus 17 ~~g~v~~~l~~r~g~i~~~~~~~~-------------~~~~i~~~iP~~~~~gf~~~L 61 (89)
T PF00679_consen 17 YLGKVISDLSKRRGEILSMDPIGG-------------DRVVIEAEIPVRELFGFRSEL 61 (89)
T ss_dssp GHHHHHHHHHHTT-EEEEEEEEST-------------TEEEEEEEEEGGGHTTHHHHH
T ss_pred HHHHHHHHhcccccEEEechhhhh-------------hheeEEEEEChhhhhhHHHHh
Confidence 456777788889999999998821 156666777766665665544
No 44
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.56 E-value=3e+02 Score=19.43 Aligned_cols=51 Identities=18% Similarity=0.266 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcc--hHHHHHHHh
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAK--WINDFKTML 135 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~ps--aI~ELer~L 135 (246)
.++.++..+|.++|+.|..+...=. +.. .=.+..+.+..++. .+..|+..|
T Consensus 11 Giv~~it~~l~~~g~nI~~~~~~~~-----~~~---~~f~~~~~~~~~~~~~~~~~l~~~l 63 (74)
T cd04875 11 GIVAAVSGFLAEHGGNIVESDQFVD-----PDS---GRFFMRVEFELEGFDLSREALEAAF 63 (74)
T ss_pred CHHHHHHHHHHHcCCCEEeeeeeec-----CCC---CeEEEEEEEEeCCCCCCHHHHHHHH
Confidence 4788999999999999998866531 111 11445567777753 467776544
No 45
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=21.41 E-value=2.6e+02 Score=18.53 Aligned_cols=48 Identities=4% Similarity=0.071 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHH
Q 025898 77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKT 133 (246)
Q Consensus 77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer 133 (246)
.++.++.++|.++|.+|..+.......= +.++.+.+..+......+..
T Consensus 12 G~l~~v~~~la~~~inI~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~ 59 (66)
T PF01842_consen 12 GILADVTEILADHGINIDSISQSSDKDG---------VGIVFIVIVVDEEDLEKLLE 59 (66)
T ss_dssp THHHHHHHHHHHTTEEEEEEEEEEESST---------TEEEEEEEEEEGHGHHHHHH
T ss_pred CHHHHHHHHHHHcCCCHHHeEEEecCCC---------ceEEEEEEECCCCCHHHHHH
Confidence 4688899999999999999988766432 45555555555444444433
No 46
>PLN03075 nicotianamine synthase; Provisional
Probab=21.23 E-value=1.5e+02 Score=28.09 Aligned_cols=70 Identities=21% Similarity=0.288 Sum_probs=50.9
Q ss_pred ccceeEEEEecCCC---hhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCC--CCeeEEEEEEEEeCcchHH
Q 025898 58 RRHYEVVYLIHEKY---EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQK--AKKAHYILMNFELEAKWIN 129 (246)
Q Consensus 58 Mr~YEim~ILrp~~---eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK--~~~G~Yvl~~F~a~psaI~ 129 (246)
...|.++++. .-. .+...++++++...+...|--+.+. -||.|.|-||+-- ..+|.-++..|.-.+.+++
T Consensus 193 l~~FDlVF~~-ALi~~dk~~k~~vL~~l~~~LkPGG~Lvlr~-~~G~r~~LYp~v~~~~~~gf~~~~~~~P~~~v~N 267 (296)
T PLN03075 193 LKEYDVVFLA-ALVGMDKEEKVKVIEHLGKHMAPGALLMLRS-AHGARAFLYPVVDPCDLRGFEVLSVFHPTDEVIN 267 (296)
T ss_pred cCCcCEEEEe-cccccccccHHHHHHHHHHhcCCCcEEEEec-ccchHhhcCCCCChhhCCCeEEEEEECCCCCcee
Confidence 3579999998 432 2456789999999998755555555 7999999999753 3448777777776666554
No 47
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=20.97 E-value=92 Score=33.85 Aligned_cols=23 Identities=22% Similarity=0.237 Sum_probs=14.0
Q ss_pred CCCCCccHHHHHH---HhhHHhhhhh
Q 025898 31 PEFADDEEEKLYE---SLNIELESEL 53 (246)
Q Consensus 31 p~~~~~~~~~l~~---~l~~~~~~~~ 53 (246)
|-|..|+.--|.+ +++-.-||+-
T Consensus 696 P~f~nAd~tslWEl~~ls~HfHPSVa 721 (988)
T KOG2038|consen 696 PLFCNADHTSLWELLLLSKHFHPSVA 721 (988)
T ss_pred ccccCCccchHHHHHHHhhhcCchHH
Confidence 6677777776666 4444455554
No 48
>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]
Probab=20.52 E-value=1.8e+02 Score=26.49 Aligned_cols=54 Identities=24% Similarity=0.305 Sum_probs=44.4
Q ss_pred CCCceEEeeechhhhhhhhhccccccCCcCCCCCCccHHHHHHHhhHHhhhhhhhccccceeEEEEecCCC
Q 025898 1 MSSGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKY 71 (246)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~l~~~~~~~~~~~~Mr~YEim~ILrp~~ 71 (246)
+||+-|||.|+- |+ -+.|+++..|-+|+.|.-.--+-..-|++-|++|-.-.++
T Consensus 44 ~sS~hvyl~l~~--------------~q---tiddip~~vL~DC~QLvKaNSIQG~Kmnnv~VvYT~w~NL 97 (207)
T KOG3272|consen 44 LSSAHVYLRLRE--------------GQ---TIDDIPEFVLEDCAQLVKANSIQGNKMNNVEVVYTPWSNL 97 (207)
T ss_pred ccccceeeeecC--------------CC---CcccccHHHHHHHHHHHHhcccccccccceeEEechhHhh
Confidence 478888887652 33 4789999999999999999999999999999999876554
Done!