Query 021931
Match_columns 305
No_of_seqs 120 out of 1166
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:44:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021931hhsearch_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 1.1E-29 2.4E-34 204.6 12.5 94 115-208 3-97 (97)
2 PRK00453 rpsF 30S ribosomal pr 100.0 3.8E-29 8.1E-34 203.0 13.0 103 117-219 1-104 (108)
3 COG0360 RpsF Ribosomal protein 100.0 1.3E-29 2.9E-34 210.6 9.6 103 118-220 1-104 (112)
4 TIGR00166 S6 ribosomal protein 100.0 1.5E-28 3.3E-33 194.8 12.6 92 118-209 1-92 (93)
5 PF01250 Ribosomal_S6: Ribosom 99.9 2.3E-27 5E-32 186.3 11.3 91 118-208 1-92 (92)
6 PRK14074 rpsF 30S ribosomal pr 99.8 1.5E-20 3.2E-25 173.9 8.0 111 98-222 140-251 (257)
7 KOG4708 Mitochondrial ribosoma 99.6 4.7E-17 1E-21 140.1 3.1 96 116-211 2-101 (141)
8 PRK14074 rpsF 30S ribosomal pr 97.2 0.00035 7.6E-09 66.0 3.8 46 117-162 1-47 (257)
9 PF10446 DUF2457: Protein of u 93.6 0.056 1.2E-06 55.1 3.1 20 259-278 98-117 (458)
10 KOG1832 HIV-1 Vpr-binding prot 93.2 0.061 1.3E-06 59.2 2.9 57 134-191 1256-1320(1516)
11 PF09026 CENP-B_dimeris: Centr 89.2 0.11 2.4E-06 43.4 0.0 21 221-241 2-22 (101)
12 PF06524 NOA36: NOA36 protein; 84.9 0.76 1.6E-05 44.7 2.9 14 204-217 200-213 (314)
13 PF04931 DNA_pol_phi: DNA poly 83.2 1.3 2.7E-05 47.6 4.0 10 193-202 597-606 (784)
14 PF04931 DNA_pol_phi: DNA poly 75.7 2.1 4.5E-05 45.9 2.8 14 182-195 620-633 (784)
15 PF06524 NOA36: NOA36 protein; 75.1 2.7 5.9E-05 41.0 3.1 6 71-76 102-107 (314)
16 cd04905 ACT_CM-PDT C-terminal 70.3 31 0.00067 26.0 7.4 54 136-196 13-68 (80)
17 KOG1832 HIV-1 Vpr-binding prot 69.7 4.2 9E-05 45.7 3.3 11 230-240 1404-1414(1516)
18 cd04880 ACT_AAAH-PDT-like ACT 67.3 40 0.00086 24.9 7.3 53 136-195 11-65 (75)
19 cd04902 ACT_3PGDH-xct C-termin 60.4 35 0.00076 24.3 5.8 62 136-207 11-72 (73)
20 KOG3130 Uncharacterized conser 51.8 11 0.00024 38.9 2.5 11 261-271 301-311 (514)
21 PF04147 Nop14: Nop14-like fam 50.2 12 0.00026 41.0 2.6 10 55-64 118-127 (840)
22 cd04893 ACT_GcvR_1 ACT domains 49.3 76 0.0017 24.0 6.3 47 136-192 13-59 (77)
23 PF05285 SDA1: SDA1; InterPro 45.1 14 0.0003 36.0 2.0 27 134-160 20-46 (324)
24 PF02724 CDC45: CDC45-like pro 42.4 19 0.00042 38.1 2.7 16 188-203 64-79 (622)
25 KOG2038 CAATT-binding transcri 42.0 23 0.0005 39.3 3.2 54 89-142 695-753 (988)
26 cd04931 ACT_PAH ACT domain of 39.3 1.9E+02 0.0041 23.3 7.4 55 136-197 26-85 (90)
27 PF11705 RNA_pol_3_Rpc31: DNA- 38.4 25 0.00054 32.4 2.5 7 68-74 33-39 (233)
28 cd04869 ACT_GcvR_2 ACT domains 37.9 1.6E+02 0.0034 21.7 6.3 54 136-194 11-66 (81)
29 cd04904 ACT_AAAH ACT domain of 37.4 1.8E+02 0.0039 21.9 7.3 53 137-196 13-65 (74)
30 KOG0943 Predicted ubiquitin-pr 36.9 22 0.00048 41.7 2.1 7 88-94 1572-1578(3015)
31 PTZ00415 transmission-blocking 35.3 22 0.00047 42.8 1.8 12 266-277 205-216 (2849)
32 PTZ00415 transmission-blocking 34.5 29 0.00062 41.9 2.6 7 145-151 68-74 (2849)
33 cd04879 ACT_3PGDH-like ACT_3PG 33.7 1.5E+02 0.0033 20.1 5.8 58 136-203 11-68 (71)
34 cd04929 ACT_TPH ACT domain of 30.1 2.6E+02 0.0056 21.5 6.7 52 137-195 13-64 (74)
35 KOG2023 Nuclear transport rece 27.6 35 0.00076 37.5 1.7 16 218-233 334-349 (885)
36 KOG4032 Uncharacterized conser 27.5 73 0.0016 29.5 3.5 14 182-195 104-117 (184)
37 PF11702 DUF3295: Protein of u 26.0 44 0.00095 35.2 2.1 12 245-256 307-318 (507)
38 KOG0943 Predicted ubiquitin-pr 25.7 51 0.0011 39.0 2.6 6 189-194 1682-1687(3015)
39 KOG0526 Nucleosome-binding fac 24.7 59 0.0013 34.8 2.7 26 70-95 182-207 (615)
40 PF11705 RNA_pol_3_Rpc31: DNA- 22.9 87 0.0019 28.9 3.2 9 188-196 122-130 (233)
41 PF09569 RE_ScaI: ScaI restric 22.2 1.1E+02 0.0024 28.5 3.6 76 121-216 92-170 (191)
42 PF14257 DUF4349: Domain of un 22.0 5.7E+02 0.012 23.6 8.4 62 132-200 59-120 (262)
43 PLN03075 nicotianamine synthas 21.8 1.4E+02 0.003 29.2 4.5 71 117-189 193-268 (296)
44 PRK11898 prephenate dehydratas 21.3 3.6E+02 0.0079 25.7 7.1 55 122-185 197-251 (283)
45 PF01842 ACT: ACT domain; Int 21.3 2.8E+02 0.0061 19.0 6.2 50 136-194 12-61 (66)
46 PTZ00482 membrane-attack compl 21.0 74 0.0016 35.5 2.7 26 220-245 77-102 (844)
47 PF12253 CAF1A: Chromatin asse 20.0 84 0.0018 25.2 2.2 14 230-243 42-55 (77)
No 1
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=99.96 E-value=1.1e-29 Score=204.60 Aligned_cols=94 Identities=30% Similarity=0.525 Sum_probs=90.4
Q ss_pred ccCcCcceEEEecCCCh-HhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHH
Q 021931 115 ERRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTM 193 (305)
Q Consensus 115 ~~MR~YEimlILrP~le-EEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~ 193 (305)
.+||+||+|+|++|+++ +++++++++++++|.++||+|+++++||+|+|||+|+|+++|+|++++|.++|++|++|++.
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 57999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCeeEEEEEee
Q 021931 194 LDKDEKVIRHLVIKR 208 (305)
Q Consensus 194 LrLDE~VLR~LIVK~ 208 (305)
|+++++|||||++|.
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=99.96 E-value=3.8e-29 Score=203.04 Aligned_cols=103 Identities=35% Similarity=0.682 Sum_probs=97.7
Q ss_pred CcCcceEEEecCCC-hHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhC
Q 021931 117 RRHYEVVYLIHEKY-EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD 195 (305)
Q Consensus 117 MR~YEimlILrP~l-eEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~Lr 195 (305)
|++||+|+|++|.+ +++++++++++.++|.+.||+|+++++||.|+|||+|+|+.+|+|++|+|.++|+++++|++.|+
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 89999999999997 46899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeEEEEEeecCCCCCCCCCC
Q 021931 196 KDEKVIRHLVIKRDKAITEDCPPP 219 (305)
Q Consensus 196 LDE~VLR~LIVK~ek~i~e~~p~~ 219 (305)
+|++|||||++|+++...+..+..
T Consensus 81 ~~~~VlR~~~vk~~~~~~~~~~~~ 104 (108)
T PRK00453 81 INEDVLRFLTVKVEEAEEEPSPMM 104 (108)
T ss_pred CCCCeEEEEEEEecccccccChhh
Confidence 999999999999998877666544
No 3
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.3e-29 Score=210.64 Aligned_cols=103 Identities=40% Similarity=0.727 Sum_probs=98.4
Q ss_pred cCcceEEEecCCCh-HhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCC
Q 021931 118 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK 196 (305)
Q Consensus 118 R~YEimlILrP~le-EEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrL 196 (305)
++||+|||++|+++ ++++++++++.++|+++||+|.++++||+|+|||+|+|+++|||++|+|+|+|+++++|+|.|++
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 46999999999986 57999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeEEEEEeecCCCCCCCCCCC
Q 021931 197 DEKVIRHLVIKRDKAITEDCPPPP 220 (305)
Q Consensus 197 DE~VLR~LIVK~ek~i~e~~p~~~ 220 (305)
+++||||||||.+......+++.+
T Consensus 81 n~~VlR~liik~~~~~~~~~~~~~ 104 (112)
T COG0360 81 NEDVLRHLIIKVEKAKEELSPMLK 104 (112)
T ss_pred chhhheeeEEEechhhcccchhhh
Confidence 999999999999999888887753
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=1.5e-28 Score=194.82 Aligned_cols=92 Identities=39% Similarity=0.709 Sum_probs=89.0
Q ss_pred cCcceEEEecCCChHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCCC
Q 021931 118 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKD 197 (305)
Q Consensus 118 R~YEimlILrP~leEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrLD 197 (305)
++||+|+|++|+.+++++++++++.++|.++||+|+++++||.|+|||+|+|+++|+|++|+|+++|++|++|++.|++|
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 021931 198 EKVIRHLVIKRD 209 (305)
Q Consensus 198 E~VLR~LIVK~e 209 (305)
++|||||++|++
T Consensus 81 ~~VlR~~~vk~~ 92 (93)
T TIGR00166 81 DNVIRSLIIKLE 92 (93)
T ss_pred cCeEEEEEEEec
Confidence 999999999975
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=2.3e-27 Score=186.27 Aligned_cols=91 Identities=34% Similarity=0.718 Sum_probs=86.6
Q ss_pred cCcceEEEecCCCh-HhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCC
Q 021931 118 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK 196 (305)
Q Consensus 118 R~YEimlILrP~le-EEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrL 196 (305)
|.||+|+|++|+.+ ++++++++++.++|.++||+|+++++||.|+|||+|+|+.+|+|++|+|+++|+++++|++.|++
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 57999999999975 58999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeEEEEEee
Q 021931 197 DEKVIRHLVIKR 208 (305)
Q Consensus 197 DE~VLR~LIVK~ 208 (305)
|++|||||++|.
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=99.82 E-value=1.5e-20 Score=173.91 Aligned_cols=111 Identities=22% Similarity=0.337 Sum_probs=94.2
Q ss_pred HHHHHHHhHHhhhhh-ccccCcCcceEEEecCCChHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEE
Q 021931 98 EKLYESLNIELESEL-NVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 176 (305)
Q Consensus 98 ~~l~~~l~~~~~s~~-~~~~MR~YEimlILrP~leEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yv 176 (305)
+.+-+||---+|..+ +.. |++| ++++++++++.++|+++| +.++++||+|+|||||+|+++|+|+
T Consensus 140 ~~~~~~~~~~~~~~~~~~~---------Iv~P---DQveevvEkik~iIe~~G--iikvE~WGkRkLAYpIkK~~eGyYv 205 (257)
T PRK14074 140 ENISEHLIKIFQDILKDFR---------INGP---NQSNKTLEMLLKNIEASG--LIKYEYWGLLDFAYPINKMKSGHYC 205 (257)
T ss_pred HHHHHHHHHHHHHHHHhcC---------CCCH---HHHHHHHHHHHHHHHhcC--eeehHhhcchhhccccCCCCeEEEE
Confidence 344456655555554 322 3344 577788999999999995 6799999999999999999999999
Q ss_pred EEEEEeCcchHHHHHHHhCCCCCeeEEEEEeecCCCCCCCCCCCCc
Q 021931 177 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEF 222 (305)
Q Consensus 177 lm~Fea~psaIkELer~LrLDE~VLR~LIVK~ek~i~e~~p~~~ef 222 (305)
+|+|.++|++|++|+|.||++++|||||+||++++..+++|+.++.
T Consensus 206 L~nFeAep~aIaELER~lRInE~VIRfLtVKlDe~~~~pSpimkk~ 251 (257)
T PRK14074 206 IMCISSTSSIMDEFVRRMKLNENIIRHLSVQVDKFFEGKSYMMNKQ 251 (257)
T ss_pred EEEEEcCHHHHHHHHHHhcCccceeeEEEEeeccccccCChhhhhh
Confidence 9999999999999999999999999999999999999999988654
No 7
>KOG4708 consensus Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=4.7e-17 Score=140.14 Aligned_cols=96 Identities=25% Similarity=0.408 Sum_probs=89.6
Q ss_pred cCcCcceEEEecCCChHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCC----CCeEEEEEEEEEeCcchHHHHH
Q 021931 116 RRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQK----AKKAHYILMNFELEAKWINDFK 191 (305)
Q Consensus 116 ~MR~YEimlILrP~leEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK----~keG~Yvlm~Fea~psaIkELe 191 (305)
.|+.||+++|+++....+...++.+..+.+...||.|+.++++|.|.|+|+|+| |..|+||+|.|.++|++..+|.
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 699999999999998777778888888888888999999999999999999996 6789999999999999999999
Q ss_pred HHhCCCCCeeEEEEEeecCC
Q 021931 192 TMLDKDEKVIRHLVIKRDKA 211 (305)
Q Consensus 192 r~LrLDE~VLR~LIVK~ek~ 211 (305)
+.|+.|.+|||+++||++..
T Consensus 82 ~~l~~D~dviR~~IVKv~~~ 101 (141)
T KOG4708|consen 82 RILKRDPDVIRWLIVKVDDI 101 (141)
T ss_pred HHHhcChhhHHhhheecccc
Confidence 99999999999999999984
No 8
>PRK14074 rpsF 30S ribosomal protein S6; Provisional
Probab=97.17 E-value=0.00035 Score=65.95 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=43.3
Q ss_pred CcCcceEEEecCCChH-hHHHHHHHHHHHHHhCCCEEEEEEeeeccc
Q 021931 117 RRHYEVVYLIHEKYEE-DVGSVNEKVQDFLREKKGRVWRLNDWGLRR 162 (305)
Q Consensus 117 MR~YEimlILrP~leE-EVkalvekv~~iL~e~GG~I~kvEdWG~Rr 162 (305)
|+.||.+||.+++++. ++..+++.+..+|.++||.|...+.||.+.
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 899999999999999999999999999864
No 9
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=93.56 E-value=0.056 Score=55.09 Aligned_cols=20 Identities=35% Similarity=0.559 Sum_probs=11.9
Q ss_pred CCCCCCCCCCceEEEeCCCC
Q 021931 259 DDNVDDDFEHGFSIVNVDDN 278 (305)
Q Consensus 259 ~~~~~~~~~~~~~~~~~~~~ 278 (305)
.++|.-|.|.||---|+.++
T Consensus 98 ddG~~TDnE~GFAdSDDEdD 117 (458)
T PF10446_consen 98 DDGNETDNEAGFADSDDEDD 117 (458)
T ss_pred ccCccCcccccccccccccc
Confidence 34666678888765443333
No 10
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=93.21 E-value=0.061 Score=59.22 Aligned_cols=57 Identities=9% Similarity=0.174 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCC--------EEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHH
Q 021931 134 VGSVNEKVQDFLREKKG--------RVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFK 191 (305)
Q Consensus 134 Vkalvekv~~iL~e~GG--------~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELe 191 (305)
+++.+-++-.+-...|| .|++.+-|.+|.|--- ..--.=.-..+.|+..+..+-.+.
T Consensus 1256 ~~~aIh~FD~ft~~~~G~FHP~g~eVIINSEIwD~RTF~lL-h~VP~Ldqc~VtFNstG~VmYa~~ 1320 (1516)
T KOG1832|consen 1256 IPEAIHRFDQFTDYGGGGFHPSGNEVIINSEIWDMRTFKLL-HSVPSLDQCAVTFNSTGDVMYAML 1320 (1516)
T ss_pred cHHHHhhhhhheecccccccCCCceEEeechhhhhHHHHHH-hcCccccceEEEeccCccchhhhh
Confidence 34555555554333333 5889999999876421 111122234566776666555444
No 11
>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=89.24 E-value=0.11 Score=43.38 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=0.0
Q ss_pred CccchhhccCCCCCccCCCCC
Q 021931 221 EFHTLRAEMHGYDEEEDDIDY 241 (305)
Q Consensus 221 ef~s~~~~~d~~~~~~~~~~~ 241 (305)
-||-+.+..|.+.|.++++++
T Consensus 2 ~~~~~eg~~dse~dsdEdeee 22 (101)
T PF09026_consen 2 TLHFLEGEEDSESDSDEDEEE 22 (101)
T ss_dssp ---------------------
T ss_pred ceeecccCcccccccccchhh
Confidence 455566666655554444333
No 12
>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=84.87 E-value=0.76 Score=44.69 Aligned_cols=14 Identities=29% Similarity=0.408 Sum_probs=6.6
Q ss_pred EEEeecCCCCCCCC
Q 021931 204 LVIKRDKAITEDCP 217 (305)
Q Consensus 204 LIVK~ek~i~e~~p 217 (305)
-.+|.++...-+||
T Consensus 200 Kg~ky~k~k~~PCP 213 (314)
T PF06524_consen 200 KGFKYEKGKPIPCP 213 (314)
T ss_pred cccccccCCCCCCC
Confidence 33555554444444
No 13
>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=83.19 E-value=1.3 Score=47.56 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=4.0
Q ss_pred HhCCCCCeeE
Q 021931 193 MLDKDEKVIR 202 (305)
Q Consensus 193 ~LrLDE~VLR 202 (305)
.|......||
T Consensus 597 lls~~s~llR 606 (784)
T PF04931_consen 597 LLSQPSALLR 606 (784)
T ss_pred HHhCcchHHH
Confidence 3333344444
No 14
>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=75.75 E-value=2.1 Score=45.95 Aligned_cols=14 Identities=21% Similarity=0.233 Sum_probs=6.7
Q ss_pred eCcchHHHHHHHhC
Q 021931 182 LEAKWINDFKTMLD 195 (305)
Q Consensus 182 a~psaIkELer~Lr 195 (305)
..+..+..|-..|.
T Consensus 620 ~t~~~l~~ll~vl~ 633 (784)
T PF04931_consen 620 LTESGLQLLLDVLD 633 (784)
T ss_pred cCHHHHHHHHHHhc
Confidence 34445555544444
No 15
>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=75.12 E-value=2.7 Score=40.96 Aligned_cols=6 Identities=50% Similarity=0.506 Sum_probs=2.4
Q ss_pred cchhhh
Q 021931 71 FPEAVL 76 (305)
Q Consensus 71 ~~~~~~ 76 (305)
|=||.+
T Consensus 102 fCEawv 107 (314)
T PF06524_consen 102 FCEAWV 107 (314)
T ss_pred cchhhe
Confidence 334433
No 16
>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=70.27 E-value=31 Score=25.98 Aligned_cols=54 Identities=9% Similarity=0.060 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeC--cchHHHHHHHhCC
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELE--AKWINDFKTMLDK 196 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~--psaIkELer~LrL 196 (305)
..+.++.+++.++|..|.+++ .+|.++....++|.+.+++. ...+..+-..|+.
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 357788899999999999997 34444455567777788875 4444444444443
No 17
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=69.73 E-value=4.2 Score=45.69 Aligned_cols=11 Identities=27% Similarity=0.438 Sum_probs=4.3
Q ss_pred CCCCCccCCCC
Q 021931 230 HGYDEEEDDID 240 (305)
Q Consensus 230 d~~~~~~~~~~ 240 (305)
+++.|||+|++
T Consensus 1404 ~dd~DeeeD~e 1414 (1516)
T KOG1832|consen 1404 DDDSDEEEDDE 1414 (1516)
T ss_pred ccccCccccch
Confidence 33334443333
No 18
>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=67.30 E-value=40 Score=24.92 Aligned_cols=53 Identities=11% Similarity=0.080 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEe--CcchHHHHHHHhC
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFEL--EAKWINDFKTMLD 195 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea--~psaIkELer~Lr 195 (305)
..+.++.+.+.++|..|..++.. |+++....+.|++.+.+ ....+..+-..|+
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 35678889999999999999875 56666666778899988 3555555555544
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=60.43 E-value=35 Score=24.31 Aligned_cols=62 Identities=11% Similarity=0.064 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEEEe
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIK 207 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrLDE~VLR~LIVK 207 (305)
..+.++..+|.++|..|..+.. ++- +.....++.+.++. ....++.+.|+-.+.|++..+++
T Consensus 11 G~l~~i~~~l~~~~inI~~~~~-------~~~-~~~~~~~~~i~v~~--~~~~~~~~~l~~~~~v~~v~~~~ 72 (73)
T cd04902 11 GVIGKVGTILGEAGINIAGMQV-------GRD-EPGGEALMVLSVDE--PVPDEVLEELRALPGILSAKVVE 72 (73)
T ss_pred CHHHHHHHHHHHcCcChhheEe-------ecc-CCCCEEEEEEEeCC--CCCHHHHHHHHcCCCccEEEEEe
Confidence 3566788999999999977742 111 12233344555555 33458888999999999988875
No 20
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.76 E-value=11 Score=38.89 Aligned_cols=11 Identities=18% Similarity=0.069 Sum_probs=4.9
Q ss_pred CCCCCCCCceE
Q 021931 261 NVDDDFEHGFS 271 (305)
Q Consensus 261 ~~~~~~~~~~~ 271 (305)
.+++-..+.|.
T Consensus 301 ~v~dN~~p~i~ 311 (514)
T KOG3130|consen 301 GVGDNSIPTIY 311 (514)
T ss_pred ccCCCcCcccc
Confidence 44444444433
No 21
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=50.22 E-value=12 Score=40.98 Aligned_cols=10 Identities=20% Similarity=-0.090 Sum_probs=6.0
Q ss_pred ccccCCccCC
Q 021931 55 EDSHSFFSKA 64 (305)
Q Consensus 55 ~~~~~~~~~~ 64 (305)
.-||.=.+..
T Consensus 118 ~LTH~G~sL~ 127 (840)
T PF04147_consen 118 TLTHGGQSLS 127 (840)
T ss_pred hhccCCCCcc
Confidence 4677655554
No 22
>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=49.26 E-value=76 Score=24.03 Aligned_cols=47 Identities=9% Similarity=-0.050 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHH
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKT 192 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer 192 (305)
.++..+.++|.++||.|..+.-.. ...-.+..+.|..+......|+.
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 578899999999999999988776 11222455667766444555553
No 23
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=45.13 E-value=14 Score=36.00 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHhCCCEEEEEEeeec
Q 021931 134 VGSVNEKVQDFLREKKGRVWRLNDWGL 160 (305)
Q Consensus 134 Vkalvekv~~iL~e~GG~I~kvEdWG~ 160 (305)
|..+...+-.++....-.+..-.++|+
T Consensus 20 V~~Aarsli~l~Rev~P~lL~kkdRGr 46 (324)
T PF05285_consen 20 VMMAARSLINLFREVNPELLHKKDRGR 46 (324)
T ss_pred HHHHHHHHHHHHHHHCHHhcCchhcCC
Confidence 444445555555555556666667775
No 24
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=42.36 E-value=19 Score=38.10 Aligned_cols=16 Identities=31% Similarity=0.393 Sum_probs=8.6
Q ss_pred HHHHHHhCCCCCeeEE
Q 021931 188 NDFKTMLDKDEKVIRH 203 (305)
Q Consensus 188 kELer~LrLDE~VLR~ 203 (305)
-.|...|.+++++.=|
T Consensus 64 ~dl~~~l~~~~~~~iy 79 (622)
T PF02724_consen 64 VDLEEFLELDEDVTIY 79 (622)
T ss_pred hhHHHHhCCCCceEEE
Confidence 3455566666555433
No 25
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=41.98 E-value=23 Score=39.33 Aligned_cols=54 Identities=11% Similarity=0.051 Sum_probs=30.4
Q ss_pred CCCCCcchHHHHHH---HHhHHhhhhhcc-ccCcCcceEEEecCCChH-hHHHHHHHHH
Q 021931 89 LPEFADDEEEKLYE---SLNIELESELNV-ERRRHYEVVYLIHEKYEE-DVGSVNEKVQ 142 (305)
Q Consensus 89 ~p~~~~~~~~~l~~---~l~~~~~s~~~~-~~MR~YEimlILrP~leE-EVkalvekv~ 142 (305)
=|-|..|+.--|.+ +++-.-||+--. +..-.=|.+.+-.|.+.+ ..-+.+.++.
T Consensus 695 ~P~f~nAd~tslWEl~~ls~HfHPSVa~~Akall~G~~i~y~g~~L~dfTL~~FLDrF~ 753 (988)
T KOG2038|consen 695 NPLFCNADHTSLWELLLLSKHFHPSVATFAKALLEGEEIQYGGPPLNDFTLMAFLDRFA 753 (988)
T ss_pred CccccCCccchHHHHHHHhhhcCchHHHHHHHHhcCceeecCCCchhHHHHHHHHHHHH
Confidence 48899999998888 444455665422 222223334444555555 4455555553
No 26
>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=39.27 E-value=1.9e+02 Score=23.26 Aligned_cols=55 Identities=15% Similarity=0.177 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeC-c----chHHHHHHHhCCC
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELE-A----KWINDFKTMLDKD 197 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~-p----saIkELer~LrLD 197 (305)
..+.++...+..+|-.+.+++.+= +++..-.++|++.|++. . .++.+|.+.++.+
T Consensus 26 GsL~~vL~~Fa~~~INLt~IeSRP-------~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~~~~~~ 85 (90)
T cd04931 26 GALAKVLRLFEEKDINLTHIESRP-------SRLNKDEYEFFINLDKKSAPALDPIIKSLRNDIGAT 85 (90)
T ss_pred cHHHHHHHHHHHCCCCEEEEEecc-------CCCCCceEEEEEEEEcCCCHHHHHHHHHHHHHhCCC
Confidence 346688889999999999999754 44445567889999985 2 2555666555543
No 27
>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=38.45 E-value=25 Score=32.37 Aligned_cols=7 Identities=29% Similarity=0.557 Sum_probs=3.7
Q ss_pred cCCcchh
Q 021931 68 NLFFPEA 74 (305)
Q Consensus 68 ~~~~~~~ 74 (305)
+=+||..
T Consensus 33 ~~lfP~~ 39 (233)
T PF11705_consen 33 PPLFPPL 39 (233)
T ss_pred CCCCCCC
Confidence 3456654
No 28
>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=37.90 E-value=1.6e+02 Score=21.69 Aligned_cols=54 Identities=15% Similarity=0.224 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEE-EEEEEEeCcc-hHHHHHHHh
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHY-ILMNFELEAK-WINDFKTML 194 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Y-vlm~Fea~ps-aIkELer~L 194 (305)
.++.++..+|.++|+.|..+...- +.......+.| +.+.|..++. .+.+|+..|
T Consensus 11 Giv~~it~~l~~~~~nI~~~~~~~-----~~~~~~~~~~~~~~~~v~~p~~~~~~~l~~~l 66 (81)
T cd04869 11 GIVHEVTQFLAQRNINIEDLSTET-----YSAPMSGTPLFKAQATLALPAGTDLDALREEL 66 (81)
T ss_pred CHHHHHHHHHHHcCCCeEEeEeee-----ecCCCCCcceEEEEEEEecCCCCCHHHHHHHH
Confidence 467889999999999999887633 33333333444 3567777654 466666443
No 29
>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=37.36 E-value=1.8e+02 Score=21.88 Aligned_cols=53 Identities=6% Similarity=0.103 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCC
Q 021931 137 VNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK 196 (305)
Q Consensus 137 lvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrL 196 (305)
.+..+.+.+..+|-.+++++.+ |++...--++|++.|++....+..+-..|+.
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 4667888899999999999975 4455555688899999866555555555543
No 30
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=36.88 E-value=22 Score=41.68 Aligned_cols=7 Identities=57% Similarity=0.482 Sum_probs=3.7
Q ss_pred CCCCCCc
Q 021931 88 ALPEFAD 94 (305)
Q Consensus 88 ~~p~~~~ 94 (305)
.||-|+-
T Consensus 1572 aL~~fAV 1578 (3015)
T KOG0943|consen 1572 ALLPFAV 1578 (3015)
T ss_pred HhhhHHH
Confidence 4565653
No 31
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=35.30 E-value=22 Score=42.80 Aligned_cols=12 Identities=8% Similarity=0.196 Sum_probs=5.7
Q ss_pred CCCceEEEeCCC
Q 021931 266 FEHGFSIVNVDD 277 (305)
Q Consensus 266 ~~~~~~~~~~~~ 277 (305)
--+-|.++....
T Consensus 205 ~~d~f~~~e~g~ 216 (2849)
T PTZ00415 205 KTDCFKFIEAGA 216 (2849)
T ss_pred ccceeeeccCCC
Confidence 334555554433
No 32
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=34.46 E-value=29 Score=41.86 Aligned_cols=7 Identities=14% Similarity=0.325 Sum_probs=3.1
Q ss_pred HHhCCCE
Q 021931 145 LREKKGR 151 (305)
Q Consensus 145 L~e~GG~ 151 (305)
...+||.
T Consensus 68 ~~~~g~~ 74 (2849)
T PTZ00415 68 FDKNGGI 74 (2849)
T ss_pred cccCCCE
Confidence 3444543
No 33
>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=33.74 E-value=1.5e+02 Score=20.11 Aligned_cols=58 Identities=17% Similarity=0.151 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCCCCCeeEE
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRH 203 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrLDE~VLR~ 203 (305)
..+..+..+|.+.|..|..+.. .....+.+..+.|......+.++-+.|+--+.|++.
T Consensus 11 g~l~~i~~~l~~~~~nI~~~~~----------~~~~~~~~~~~~~~v~~~~~~~l~~~l~~~~~V~~v 68 (71)
T cd04879 11 GVIGKVGTILGEHGINIAAMQV----------GRKEKGGIAYMVLDVDSPVPEEVLEELKALPGIIRV 68 (71)
T ss_pred CHHHHHHHHHHhcCCCeeeEEE----------eccCCCCEEEEEEEcCCCCCHHHHHHHHcCCCeEEE
Confidence 3566788899999999988864 111112234444444334677888888888888874
No 34
>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=30.14 E-value=2.6e+02 Score=21.54 Aligned_cols=52 Identities=12% Similarity=0.192 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhC
Q 021931 137 VNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD 195 (305)
Q Consensus 137 lvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~Lr 195 (305)
.+.++.+++..+|..+.+++.+= .++..--++|++.+++....+..+-..|+
T Consensus 13 ~L~~iL~~f~~~~inl~~IeSRP-------~~~~~~~y~F~id~e~~~~~i~~~l~~l~ 64 (74)
T cd04929 13 GLAKALKLFQELGINVVHIESRK-------SKRRSSEFEIFVDCECDQRRLDELVQLLK 64 (74)
T ss_pred HHHHHHHHHHHCCCCEEEEEecc-------CCCCCceEEEEEEEEcCHHHHHHHHHHHH
Confidence 46688889999999999999764 44455568889999988776666555554
No 35
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.57 E-value=35 Score=37.55 Aligned_cols=16 Identities=31% Similarity=0.526 Sum_probs=11.0
Q ss_pred CCCCccchhhccCCCC
Q 021931 218 PPPEFHTLRAEMHGYD 233 (305)
Q Consensus 218 ~~~ef~s~~~~~d~~~ 233 (305)
.+|+||..|...-.++
T Consensus 334 IkPRfhksk~~~~~~~ 349 (885)
T KOG2023|consen 334 IKPRFHKSKEHGNGED 349 (885)
T ss_pred ccchhhhchhccCccc
Confidence 3488988877765444
No 36
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.45 E-value=73 Score=29.54 Aligned_cols=14 Identities=14% Similarity=0.074 Sum_probs=6.6
Q ss_pred eCcchHHHHHHHhC
Q 021931 182 LEAKWINDFKTMLD 195 (305)
Q Consensus 182 a~psaIkELer~Lr 195 (305)
.+-+.|.+|-..|.
T Consensus 104 ~N~~~ieells~l~ 117 (184)
T KOG4032|consen 104 GNYAIIEELLSKLP 117 (184)
T ss_pred ccHHHHHHHHHHcc
Confidence 34445555554443
No 37
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=26.03 E-value=44 Score=35.20 Aligned_cols=12 Identities=33% Similarity=0.432 Sum_probs=7.0
Q ss_pred ccCCccCCCCCC
Q 021931 245 EYDDEYDDGEGD 256 (305)
Q Consensus 245 ~~~~~~~~~~~~ 256 (305)
+||||+.|||+.
T Consensus 307 dDDDDssDWEDS 318 (507)
T PF11702_consen 307 DDDDDSSDWEDS 318 (507)
T ss_pred cCCccchhhhhc
Confidence 455666666553
No 38
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=25.65 E-value=51 Score=38.96 Aligned_cols=6 Identities=17% Similarity=0.429 Sum_probs=2.3
Q ss_pred HHHHHh
Q 021931 189 DFKTML 194 (305)
Q Consensus 189 ELer~L 194 (305)
++...+
T Consensus 1682 e~qesl 1687 (3015)
T KOG0943|consen 1682 EIQESL 1687 (3015)
T ss_pred hhhhcc
Confidence 344333
No 39
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=24.69 E-value=59 Score=34.80 Aligned_cols=26 Identities=31% Similarity=0.325 Sum_probs=19.6
Q ss_pred CcchhhhhhhhhhccccCCCCCCCcc
Q 021931 70 FFPEAVLLKEKKVQEDGRALPEFADD 95 (305)
Q Consensus 70 ~~~~~~~~~~~~~~~~g~~~p~~~~~ 95 (305)
.|-++|+-|-.-.+..|...--|.++
T Consensus 182 ~F~~~v~~kAdv~~~~gdaI~~f~~i 207 (615)
T KOG0526|consen 182 AFYENVLAKADVSSAVGDAIVSFEEI 207 (615)
T ss_pred HHHHHHHHhcCcccccCCceEEeeee
Confidence 37788888888888888876666543
No 40
>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=22.91 E-value=87 Score=28.87 Aligned_cols=9 Identities=22% Similarity=0.313 Sum_probs=4.0
Q ss_pred HHHHHHhCC
Q 021931 188 NDFKTMLDK 196 (305)
Q Consensus 188 kELer~LrL 196 (305)
.+|...++.
T Consensus 122 ~EL~~~~~~ 130 (233)
T PF11705_consen 122 KELWPTLRK 130 (233)
T ss_pred HHHHhhccc
Confidence 344444443
No 41
>PF09569 RE_ScaI: ScaI restriction endonuclease; InterPro: IPR019069 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the restriction endonuclease ScaI, which recognises and cleaves the double-stranded sequence AGT^ACT.
Probab=22.23 E-value=1.1e+02 Score=28.52 Aligned_cols=76 Identities=18% Similarity=0.254 Sum_probs=48.5
Q ss_pred ceEEEecCCChHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccC---CCCeEEEEEEEEEeCcchHHHHHHHhCCC
Q 021931 121 EVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQ---KAKKAHYILMNFELEAKWINDFKTMLDKD 197 (305)
Q Consensus 121 EimlILrP~leEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IK---K~keG~Yvlm~Fea~psaIkELer~LrLD 197 (305)
.+++|.++..+=|++..- . .-.-+|.|..||+=+ |.+.|+|+-++|+--... .++--
T Consensus 92 Div~i~~~~ysiEiKTSS---------~-----~~~i~gNRSy~q~~~~~kKsK~GYYlaINfekf~~~------~~~p~ 151 (191)
T PF09569_consen 92 DIVNIPNPFYSIEIKTSS---------S-----PKQIYGNRSYGQNSDNSKKSKDGYYLAINFEKFSET------DLRPK 151 (191)
T ss_pred ceeeccCCceeEEEeccC---------C-----ccceecccccccCCCCCccccCceEEEEEeeccCcc------CCCcc
Confidence 467777776554332211 1 223467788887643 788999999999975554 23333
Q ss_pred CCeeEEEEEeecCCCCCCC
Q 021931 198 EKVIRHLVIKRDKAITEDC 216 (305)
Q Consensus 198 E~VLR~LIVK~ek~i~e~~ 216 (305)
-..|||--+-..+=+.+.+
T Consensus 152 I~~IRFGwld~tDWi~Q~a 170 (191)
T PF09569_consen 152 IRLIRFGWLDHTDWIGQKA 170 (191)
T ss_pred eEEEEEecccchhhhcccc
Confidence 4578998887777555443
No 42
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=22.04 E-value=5.7e+02 Score=23.59 Aligned_cols=62 Identities=15% Similarity=0.175 Sum_probs=50.0
Q ss_pred HhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHhCCCCCe
Q 021931 132 EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKV 200 (305)
Q Consensus 132 EEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~LrLDE~V 200 (305)
+.+.+..+.+..++.+.||.|.....++. ..........+.+..++.....+-..|.--..|
T Consensus 59 ~d~~~a~~~i~~~~~~~gG~i~~~~~~~~-------~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v 120 (262)
T PF14257_consen 59 KDVEKAVKKIENLVESYGGYIESSSSSSS-------GGSDDERSASLTIRVPADKFDSFLDELSELGKV 120 (262)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEeeecc-------cCCCCcceEEEEEEECHHHHHHHHHHHhccCce
Confidence 45778899999999999999999997654 445566777889999999999999888855433
No 43
>PLN03075 nicotianamine synthase; Provisional
Probab=21.78 E-value=1.4e+02 Score=29.23 Aligned_cols=71 Identities=21% Similarity=0.271 Sum_probs=51.2
Q ss_pred CcCcceEEEecCCC---hHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccC--CCCeEEEEEEEEEeCcchHHH
Q 021931 117 RRHYEVVYLIHEKY---EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQ--KAKKAHYILMNFELEAKWIND 189 (305)
Q Consensus 117 MR~YEimlILrP~l---eEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IK--K~keG~Yvlm~Fea~psaIkE 189 (305)
...|.++|+. .-. .+.-..+++.+...+...|--+.+. .||.|.|-|++- ..-+|.-++..|.-.+..++.
T Consensus 193 l~~FDlVF~~-ALi~~dk~~k~~vL~~l~~~LkPGG~Lvlr~-~~G~r~~LYp~v~~~~~~gf~~~~~~~P~~~v~Ns 268 (296)
T PLN03075 193 LKEYDVVFLA-ALVGMDKEEKVKVIEHLGKHMAPGALLMLRS-AHGARAFLYPVVDPCDLRGFEVLSVFHPTDEVINS 268 (296)
T ss_pred cCCcCEEEEe-cccccccccHHHHHHHHHHhcCCCcEEEEec-ccchHhhcCCCCChhhCCCeEEEEEECCCCCceee
Confidence 3579999998 432 2456789999999988755555555 799999999965 344488888887776665543
No 44
>PRK11898 prephenate dehydratase; Provisional
Probab=21.31 E-value=3.6e+02 Score=25.74 Aligned_cols=55 Identities=5% Similarity=-0.019 Sum_probs=39.4
Q ss_pred eEEEecCCChHhHHHHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcc
Q 021931 122 VVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAK 185 (305)
Q Consensus 122 imlILrP~leEEVkalvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~ps 185 (305)
+.+++...... ...+-++.+++...|-.+++++.+ |+++..-.++|++.|++...
T Consensus 197 tslif~l~~~~--pGsL~~~L~~F~~~~INLt~IeSR-------P~~~~~~~y~F~vd~eg~~~ 251 (283)
T PRK11898 197 TSLVLTLPNNL--PGALYKALSEFAWRGINLTRIESR-------PTKTGLGTYFFFIDVEGHID 251 (283)
T ss_pred EEEEEEeCCCC--ccHHHHHHHHHHHCCCCeeeEecc-------cCCCCCccEEEEEEEEccCC
Confidence 56666643321 134667778889999999999987 55555567888999998666
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=21.27 E-value=2.8e+02 Score=18.96 Aligned_cols=50 Identities=6% Similarity=0.082 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhCCCEEEEEEeeeccccccccCCCCeEEEEEEEEEeCcchHHHHHHHh
Q 021931 136 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 194 (305)
Q Consensus 136 alvekv~~iL~e~GG~I~kvEdWG~RrLAY~IKK~keG~Yvlm~Fea~psaIkELer~L 194 (305)
-++.++.++|.++|..|..+.......= +.++.+.+..+......+...|
T Consensus 12 G~l~~v~~~la~~~inI~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~l 61 (66)
T PF01842_consen 12 GILADVTEILADHGINIDSISQSSDKDG---------VGIVFIVIVVDEEDLEKLLEEL 61 (66)
T ss_dssp THHHHHHHHHHHTTEEEEEEEEEEESST---------TEEEEEEEEEEGHGHHHHHHHH
T ss_pred CHHHHHHHHHHHcCCCHHHeEEEecCCC---------ceEEEEEEECCCCCHHHHHHHH
Confidence 4778999999999999999988775432 5556666666555555554443
No 46
>PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional
Probab=20.95 E-value=74 Score=35.50 Aligned_cols=26 Identities=31% Similarity=0.538 Sum_probs=15.4
Q ss_pred CCccchhhccCCCCCccCCCCCCCcc
Q 021931 220 PEFHTLRAEMHGYDEEEDDIDYDDEE 245 (305)
Q Consensus 220 ~ef~s~~~~~d~~~~~~~~~~~~~~~ 245 (305)
.-|..-+++.++++|.|.|..|+||+
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (844)
T PTZ00482 77 ASFLNQRKSLDDDDDDEFDFLYEDDE 102 (844)
T ss_pred cchhhhhcccccCcchhhhhhccccc
Confidence 34555566667777666665555543
No 47
>PF12253 CAF1A: Chromatin assembly factor 1 subunit A; InterPro: IPR022043 The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A []. The A domain is uniquely required for the progression of S phase in mouse cells [], independent of its ability to promote histone deposition [] but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints [].
Probab=20.05 E-value=84 Score=25.15 Aligned_cols=14 Identities=7% Similarity=0.020 Sum_probs=5.7
Q ss_pred CCCCCccCCCCCCC
Q 021931 230 HGYDEEEDDIDYDD 243 (305)
Q Consensus 230 d~~~~~~~~~~~~~ 243 (305)
+|++++|=++++++
T Consensus 42 dyDSd~EWeE~e~G 55 (77)
T PF12253_consen 42 DYDSDDEWEEEEEG 55 (77)
T ss_pred ecCCccccccCCCC
Confidence 34444444333333
Done!