Query 047111
Match_columns 106
No_of_seqs 119 out of 373
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:44:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047111.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047111hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03948 Ribosomal_L9_C: Ribos 99.9 1.5E-24 3.2E-29 147.4 10.3 85 3-105 2-86 (87)
2 CHL00160 rpl9 ribosomal protei 99.8 1.2E-20 2.6E-25 140.4 9.7 84 3-105 68-152 (153)
3 TIGR00158 L9 ribosomal protein 99.8 2.9E-20 6.3E-25 137.3 9.7 84 3-105 63-147 (148)
4 PRK00137 rplI 50S ribosomal pr 99.8 5.9E-20 1.3E-24 135.0 9.7 84 3-105 63-146 (147)
5 COG0359 RplI Ribosomal protein 99.8 2.6E-19 5.6E-24 133.6 9.1 83 4-105 64-146 (148)
6 PRK14538 putative bifunctional 99.7 3E-17 6.5E-22 146.9 10.2 84 3-104 750-833 (838)
7 KOG4607 Mitochondrial ribosoma 88.3 0.46 1E-05 38.2 2.9 56 41-104 138-193 (222)
8 PF10045 DUF2280: Uncharacteri 86.6 0.26 5.7E-06 35.6 0.6 33 45-77 21-53 (104)
9 COG2047 Uncharacterized protei 78.9 2.5 5.5E-05 34.7 3.5 58 4-63 101-159 (258)
10 PF08766 DEK_C: DEK C terminal 74.8 1.7 3.7E-05 26.7 1.1 25 41-65 18-42 (54)
11 PF13592 HTH_33: Winged helix- 56.9 6.4 0.00014 24.4 1.2 26 41-66 2-27 (60)
12 PF00571 CBS: CBS domain CBS d 53.8 23 0.00049 20.2 3.2 38 6-54 19-56 (57)
13 PF01282 Ribosomal_S24e: Ribos 49.8 11 0.00024 25.5 1.5 44 42-87 11-56 (84)
14 PF05157 T2SE_Nter: Type II se 49.3 13 0.00029 23.8 1.8 27 42-68 5-32 (109)
15 PF08960 DUF1874: Domain of un 48.6 27 0.00058 25.1 3.4 53 39-96 38-90 (105)
16 smart00089 PKD Repeats in poly 44.2 53 0.0011 20.2 3.9 28 72-103 51-78 (79)
17 cd01793 Fubi Fubi ubiquitin-li 43.3 17 0.00037 22.9 1.6 43 37-80 12-59 (74)
18 PF07523 Big_3: Bacterial Ig-l 42.8 61 0.0013 20.0 4.1 25 71-103 43-67 (67)
19 PHA01627 DNA binding protein 40.7 50 0.0011 23.9 3.8 53 40-97 40-92 (107)
20 COG5556 Uncharacterized conser 39.7 15 0.00032 26.8 1.0 30 45-74 21-50 (110)
21 PF05402 PqqD: Coenzyme PQQ sy 38.9 23 0.00049 21.6 1.6 20 42-61 28-47 (68)
22 PF13565 HTH_32: Homeodomain-l 38.4 23 0.0005 21.9 1.6 19 43-61 48-66 (77)
23 PF06481 COX_ARM: COX Aromatic 33.4 26 0.00056 21.2 1.2 20 30-49 16-35 (47)
24 COG0593 DnaA ATPase involved i 32.4 15 0.00032 31.7 0.0 59 2-62 280-338 (408)
25 PF08799 PRP4: pre-mRNA proces 30.7 17 0.00038 20.7 0.1 18 35-53 9-26 (30)
26 PRK09184 acyl carrier protein; 30.0 27 0.00058 23.7 0.9 33 43-75 44-76 (89)
27 cd06094 RP_Saci_like RP_Saci_l 29.6 78 0.0017 22.1 3.2 26 70-101 45-71 (89)
28 KOG1494 NAD-dependent malate d 29.0 28 0.00061 29.7 1.1 46 6-52 130-181 (345)
29 PF10826 DUF2551: Protein of u 28.3 44 0.00096 23.3 1.8 24 41-66 23-46 (83)
30 PRK05395 3-dehydroquinate dehy 27.6 58 0.0013 24.6 2.5 25 39-63 21-48 (146)
31 COG0236 AcpP Acyl carrier prot 27.5 14 0.0003 23.8 -0.8 26 41-66 37-62 (80)
32 TIGR00362 DnaA chromosomal rep 27.3 53 0.0012 26.8 2.4 56 2-62 304-363 (405)
33 PF04282 DUF438: Family of unk 27.1 30 0.00064 23.2 0.7 15 38-52 23-37 (71)
34 PF00788 RA: Ras association ( 25.7 58 0.0013 20.4 1.9 27 42-68 25-51 (93)
35 PTZ00191 60S ribosomal protein 25.7 2.4E+02 0.0053 21.3 5.5 41 44-88 93-133 (145)
36 PF08299 Bac_DnaA_C: Bacterial 25.6 46 0.00099 21.3 1.4 17 45-61 1-17 (70)
37 COG2062 SixA Phosphohistidine 25.5 25 0.00055 26.6 0.2 33 2-34 31-63 (163)
38 smart00116 CBS Domain in cysta 25.4 70 0.0015 16.0 1.9 16 38-53 33-48 (49)
39 cd04593 CBS_pair_EriC_assoc_ba 25.3 1.1E+02 0.0023 19.2 3.1 18 38-55 34-51 (115)
40 PRK00982 acpP acyl carrier pro 24.6 43 0.00093 20.9 1.1 26 41-66 35-60 (78)
41 PF10668 Phage_terminase: Phag 24.4 52 0.0011 21.4 1.5 13 42-54 21-33 (60)
42 PRK10475 23S rRNA pseudouridin 24.2 79 0.0017 25.6 2.8 76 8-87 102-184 (290)
43 PF04703 FaeA: FaeA-like prote 23.8 38 0.00083 21.8 0.8 14 41-54 13-26 (62)
44 cd00466 DHQase_II Dehydroquina 23.4 72 0.0016 24.0 2.3 26 39-64 19-47 (140)
45 cd04619 CBS_pair_6 The CBS dom 23.4 1.4E+02 0.003 18.9 3.4 40 5-55 12-51 (114)
46 CHL00124 acpP acyl carrier pro 23.4 48 0.001 21.0 1.2 26 41-66 37-62 (82)
47 TIGR01088 aroQ 3-dehydroquinat 22.9 74 0.0016 24.0 2.3 25 39-63 19-46 (141)
48 PF07679 I-set: Immunoglobulin 22.7 1.6E+02 0.0035 17.8 3.5 32 66-103 58-90 (90)
49 TIGR03435 Soli_TIGR03435 Solib 22.5 60 0.0013 26.1 1.8 26 43-68 197-222 (237)
50 cd04630 CBS_pair_17 The CBS do 22.5 1.4E+02 0.0031 18.7 3.3 18 38-55 35-52 (114)
51 smart00760 Bac_DnaA_C Bacteria 22.3 69 0.0015 19.6 1.7 18 45-62 1-18 (60)
52 PRK05738 rplW 50S ribosomal pr 22.1 2.1E+02 0.0046 19.4 4.3 24 43-66 30-53 (92)
53 cd00258 GM2-AP GM2 activator p 22.1 1.9E+02 0.0041 22.3 4.3 59 41-104 72-158 (162)
54 PF01498 HTH_Tnp_Tc3_2: Transp 21.9 31 0.00067 21.4 0.1 33 44-79 14-46 (72)
55 PF04358 DsrC: DsrC like prote 21.8 63 0.0014 23.0 1.6 19 46-64 24-42 (109)
56 PF13833 EF-hand_8: EF-hand do 21.7 36 0.00077 19.6 0.3 23 42-65 3-26 (54)
57 PF14338 Mrr_N: Mrr N-terminal 21.6 87 0.0019 20.6 2.2 28 41-68 17-44 (92)
58 PF11663 Toxin_YhaV: Toxin wit 21.5 33 0.00072 26.0 0.2 28 15-42 91-119 (140)
59 PF13344 Hydrolase_6: Haloacid 21.3 89 0.0019 20.9 2.2 47 6-69 20-66 (101)
60 PF00550 PP-binding: Phosphopa 21.2 13 0.00028 22.2 -1.8 26 42-67 30-55 (67)
61 smart00500 SFM Splicing Factor 21.2 40 0.00087 20.7 0.5 19 35-54 14-32 (44)
62 smart00874 B5 tRNA synthetase 21.1 26 0.00056 21.7 -0.4 26 37-63 11-37 (71)
63 cd04632 CBS_pair_19 The CBS do 20.9 1.7E+02 0.0036 18.8 3.4 17 38-54 34-50 (128)
64 KOG4607 Mitochondrial ribosoma 20.9 2.5 5.4E-05 34.1 -6.3 95 4-105 127-221 (222)
65 COG3415 Transposase and inacti 20.8 33 0.00071 25.4 -0.0 22 44-65 81-102 (138)
66 PF09183 DUF1947: Domain of un 20.3 71 0.0015 21.3 1.5 25 46-70 10-34 (65)
67 PLN03138 Protein TOC75; Provis 20.0 58 0.0012 30.6 1.4 58 43-102 164-222 (796)
No 1
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.92 E-value=1.5e-24 Score=147.38 Aligned_cols=85 Identities=28% Similarity=0.473 Sum_probs=79.4
Q ss_pred hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111 3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM 82 (106)
Q Consensus 3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I 82 (106)
+|++..+.+|++-.|.+.+-.+..- +||||||++||+++|++++|++|||++|.+++|||++|+|+|.|
T Consensus 2 ~~A~~l~~~l~~~~l~i~~k~g~~g-----------klfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~v 70 (87)
T PF03948_consen 2 AEAQALAEKLEGITLTIKRKAGENG-----------KLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVKV 70 (87)
T ss_dssp HHHHHHHHHHCSSEEEEEECBSSCS-----------SBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEEE
T ss_pred HHHHHHHHHhcCCEEEEEEEecCCc-----------ceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEEE
Confidence 5889999999999999999887443 89999999999999999999999999999999999999999999
Q ss_pred EecCCCCCCCCcEEEEEEEEEEe
Q 047111 83 RLSKTIPLPEGKVQWTFNVKVHG 105 (106)
Q Consensus 83 kLh~~Vp~p~gkV~~~lkV~V~~ 105 (106)
+||++ |+++|+|.|..
T Consensus 71 ~L~~~-------V~a~i~v~V~~ 86 (87)
T PF03948_consen 71 KLHPE-------VSAKIKVNVVA 86 (87)
T ss_dssp EEETT-------EEEEEEEEEEE
T ss_pred EeCCC-------eEEEEEEEEEe
Confidence 99999 59999999974
No 2
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=99.84 E-value=1.2e-20 Score=140.36 Aligned_cols=84 Identities=17% Similarity=0.394 Sum_probs=71.7
Q ss_pred hHHHHHHHhhhcc-ceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEE
Q 047111 3 REFEKAARRLENA-RLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVP 81 (106)
Q Consensus 3 ~~~~~~~~~l~~~-~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~ 81 (106)
.|++..+..|++- .+.+++-.. +.-+||||||++||+++|++|+|++|||++|.|++ ||++|+|+|.
T Consensus 68 ~~a~~la~~l~~~~~~~i~~k~g-----------e~gklfGSVt~~dIa~~l~~~~g~~idk~~I~l~~-Ik~~G~~~v~ 135 (153)
T CHL00160 68 EKCLKVKQLLEEIQKFSVKKKVG-----------ENNQIFGSVTEKEISQIIKNKTNIDLEKQNIELPE-IKTIGIYNIE 135 (153)
T ss_pred HHHHHHHHHhhCCceEEEEEEeC-----------CCCeEEcccCHHHHHHHHHHhhCCccccceeehhh-ccccEeEEEE
Confidence 3456666777776 366665555 44599999999999999998999999999999988 9999999999
Q ss_pred EEecCCCCCCCCcEEEEEEEEEEe
Q 047111 82 MRLSKTIPLPEGKVQWTFNVKVHG 105 (106)
Q Consensus 82 IkLh~~Vp~p~gkV~~~lkV~V~~ 105 (106)
|+||++| +++|+|.|+.
T Consensus 136 v~L~~~V-------~a~i~v~V~~ 152 (153)
T CHL00160 136 IKLTSDV-------KANINLQILP 152 (153)
T ss_pred EEecCCc-------EEEEEEEEEE
Confidence 9999995 9999999974
No 3
>TIGR00158 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.
Probab=99.83 E-value=2.9e-20 Score=137.26 Aligned_cols=84 Identities=17% Similarity=0.256 Sum_probs=70.8
Q ss_pred hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCC-CccceeEEEE
Q 047111 3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSP-LSAFGEYEVP 81 (106)
Q Consensus 3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~p-IKslGey~V~ 81 (106)
.+++..+..|++-.+.+.+-... .-+||||||++||+++|+++ |++|||++|.|++| ||++|+|+|+
T Consensus 63 ~~a~~l~~~l~~~~~~i~~k~ge-----------~gklfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~ 130 (148)
T TIGR00158 63 AAAARLKEVLELGTLTISKKVGD-----------EGKLFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVT 130 (148)
T ss_pred HHHHHHHHHhcCcEEEEEEEeCC-----------CCeEEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEE
Confidence 34556667777766666665543 34999999999999999866 99999999999996 9999999999
Q ss_pred EEecCCCCCCCCcEEEEEEEEEEe
Q 047111 82 MRLSKTIPLPEGKVQWTFNVKVHG 105 (106)
Q Consensus 82 IkLh~~Vp~p~gkV~~~lkV~V~~ 105 (106)
|+||++| +++|+|.|..
T Consensus 131 i~L~~~V-------~a~i~v~V~~ 147 (148)
T TIGR00158 131 IKLHEEV-------FAVLKVIVVP 147 (148)
T ss_pred EEEcCCc-------EEEEEEEEEE
Confidence 9999995 9999999974
No 4
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=99.82 E-value=5.9e-20 Score=135.00 Aligned_cols=84 Identities=29% Similarity=0.498 Sum_probs=74.9
Q ss_pred hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111 3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM 82 (106)
Q Consensus 3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I 82 (106)
.++++.+..|++..|.+++-.+ ++.+||||||++||+++|+++ |++|||++|.+++|||++|+|+|+|
T Consensus 63 ~~a~~l~~~l~~~~l~i~~k~g-----------~~gklfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i 130 (147)
T PRK00137 63 AEAEALAEKLEGLTVTIKAKAG-----------EDGKLFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPV 130 (147)
T ss_pred HHHHHHHHHhhCCEEEEEEEcC-----------CCCeEEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEE
Confidence 5677788889988887776655 445999999999999999877 9999999999999999999999999
Q ss_pred EecCCCCCCCCcEEEEEEEEEEe
Q 047111 83 RLSKTIPLPEGKVQWTFNVKVHG 105 (106)
Q Consensus 83 kLh~~Vp~p~gkV~~~lkV~V~~ 105 (106)
+||++| +++|+|.|..
T Consensus 131 ~L~~~v-------~a~l~v~V~~ 146 (147)
T PRK00137 131 KLHPEV-------TATIKVNVVA 146 (147)
T ss_pred EECCCc-------EEEEEEEEEE
Confidence 999995 9999999974
No 5
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=2.6e-19 Score=133.62 Aligned_cols=83 Identities=20% Similarity=0.337 Sum_probs=69.6
Q ss_pred HHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEE
Q 047111 4 EFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMR 83 (106)
Q Consensus 4 ~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~Ik 83 (106)
+++.-...|+...+.+..-...+ -+||||||++||+++++++ |++|||++|.++++||++|+|+|+|+
T Consensus 64 ~a~~lk~~Le~~~~~i~~kag~~-----------GklfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vk 131 (148)
T COG0359 64 EAEALKEKLEGKTVEIAVKAGED-----------GKLFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVK 131 (148)
T ss_pred HHHHHHHHhhCceEEEEEEcCCC-----------CceeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEE
Confidence 44455556666546665555432 5999999999999999987 99999999999999999999999999
Q ss_pred ecCCCCCCCCcEEEEEEEEEEe
Q 047111 84 LSKTIPLPEGKVQWTFNVKVHG 105 (106)
Q Consensus 84 Lh~~Vp~p~gkV~~~lkV~V~~ 105 (106)
||++| +++++|.|..
T Consensus 132 Lh~eV-------~a~v~v~V~~ 146 (148)
T COG0359 132 LHEEV-------TATVKVNVVA 146 (148)
T ss_pred ecCce-------EEEEEEEEEe
Confidence 99995 9999999974
No 6
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=99.71 E-value=3e-17 Score=146.90 Aligned_cols=84 Identities=19% Similarity=0.285 Sum_probs=74.2
Q ss_pred hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111 3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM 82 (106)
Q Consensus 3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I 82 (106)
++++..+..|+.-.|.+.+-..+.- +||||||++||+++|++++|++||||+|.|++|||++|+|+|.|
T Consensus 750 ~~a~~l~~~l~~~~~~i~~k~ge~g-----------klfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i 818 (838)
T PRK14538 750 LLMKKLKSEIDNKKITLDIQLGPKG-----------KIYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDV 818 (838)
T ss_pred HHHHHHHHHhhCcEEEEEEEeCCCC-----------eeeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEE
Confidence 3456667778877777777776444 99999999999999998999999999999999999999999999
Q ss_pred EecCCCCCCCCcEEEEEEEEEE
Q 047111 83 RLSKTIPLPEGKVQWTFNVKVH 104 (106)
Q Consensus 83 kLh~~Vp~p~gkV~~~lkV~V~ 104 (106)
+||++| +++|+|.|.
T Consensus 819 ~L~~~V-------~a~i~v~V~ 833 (838)
T PRK14538 819 FLTDQI-------KATFFLNVI 833 (838)
T ss_pred EEcCCe-------EEEEEEEEE
Confidence 999995 999999987
No 7
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=88.27 E-value=0.46 Score=38.21 Aligned_cols=56 Identities=16% Similarity=0.271 Sum_probs=47.5
Q ss_pred eecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEEecCCCCCCCCcEEEEEEEEEE
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVH 104 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~IkLh~~Vp~p~gkV~~~lkV~V~ 104 (106)
|++|+++.....+-+++-+.+||+-|..|. ++.-|+|...|++++++ ++-++..|+
T Consensus 138 ~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~-~k~e~~~~~~V~in~~~-------~vr~~~~v~ 193 (222)
T KOG4607|consen 138 PNLVKASLRKGVIVAELTIKLDKELVSGPI-TKEEGEYICEVKINPDV-------TVRVKIRVT 193 (222)
T ss_pred HHHHHHHHhcceEeccccccCcccccCCCc-ccccceEEEEEEECCcc-------eEEeeeeee
Confidence 789999988888888889999999998765 77888999999999995 777776654
No 8
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=86.64 E-value=0.26 Score=35.55 Aligned_cols=33 Identities=18% Similarity=0.298 Sum_probs=29.2
Q ss_pred CHHHHHHHHHhhcCCccccccccCCCCCcccee
Q 047111 45 TKEELVAKVASQLSISIEPEYLHLPSPLSAFGE 77 (106)
Q Consensus 45 TtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGe 77 (106)
|+.++++++++++|++|++..++.-+|=|.-|.
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~ 53 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGR 53 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHHcCchHHHHH
Confidence 789999999999999999999988888776653
No 9
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=78.93 E-value=2.5 Score=34.67 Aligned_cols=58 Identities=16% Similarity=0.307 Sum_probs=40.7
Q ss_pred HHHHHHHhhhccc-eeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCcccc
Q 047111 4 EFEKAARRLENAR-LVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEP 63 (106)
Q Consensus 4 ~~~~~~~~l~~~~-l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDK 63 (106)
+||-|-+.||-+. ++.+++..-+-+---.--++| +.+|+||++++++.|+ ++|+..-+
T Consensus 101 qyel~~~~Ld~a~e~g~~~IyTLGGy~vGkl~eep-~VlGA~ts~eLi~~lk-e~gV~fr~ 159 (258)
T COG2047 101 QYELTGKILDIAKEFGARMIYTLGGYGVGKLVEEP-RVLGAVTSKELIEELK-EHGVEFRS 159 (258)
T ss_pred hHHHHHHHHHHHHHcCCcEEEEecCcccCcccCCc-eeEEecCCHHHHHHHH-HcCeEecc
Confidence 6788888888764 366666554433333334455 8999999999999998 67887644
No 10
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=74.79 E-value=1.7 Score=26.71 Aligned_cols=25 Identities=12% Similarity=0.316 Sum_probs=17.2
Q ss_pred eecCCHHHHHHHHHhhcCCcccccc
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEY 65 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkk 65 (106)
+..||.++|-++|++.+|+++..++
T Consensus 18 l~~vT~k~vr~~Le~~~~~dL~~~K 42 (54)
T PF08766_consen 18 LDTVTKKQVREQLEERFGVDLSSRK 42 (54)
T ss_dssp GGG--HHHHHHHHHHH-SS--SHHH
T ss_pred HhHhhHHHHHHHHHHHHCCCcHHHH
Confidence 5689999999999999999987554
No 11
>PF13592 HTH_33: Winged helix-turn helix
Probab=56.92 E-value=6.4 Score=24.43 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=21.9
Q ss_pred eecCCHHHHHHHHHhhcCCccccccc
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYL 66 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI 66 (106)
+|--|.++|++.|.+++|+.+....+
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys~~~v 27 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYSPSGV 27 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEcHHHH
Confidence 35679999999999999999877654
No 12
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=53.80 E-value=23 Score=20.22 Aligned_cols=38 Identities=11% Similarity=0.160 Sum_probs=24.9
Q ss_pred HHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHH
Q 047111 6 EKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVA 54 (106)
Q Consensus 6 ~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~ 54 (106)
+.|++++.+...----++|+. -++-|.||..||..++.
T Consensus 19 ~~~~~~~~~~~~~~~~V~d~~-----------~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 19 EEALEIMRKNGISRLPVVDED-----------GKLVGIISRSDLLKALL 56 (57)
T ss_dssp HHHHHHHHHHTSSEEEEESTT-----------SBEEEEEEHHHHHHHHH
T ss_pred HHHHHHHHHcCCcEEEEEecC-----------CEEEEEEEHHHHHhhhh
Confidence 455556655553222234533 49999999999999875
No 13
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 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 [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=49.78 E-value=11 Score=25.47 Aligned_cols=44 Identities=16% Similarity=0.301 Sum_probs=31.7
Q ss_pred ecCCHHHHHHHHHhhcCCccccccccCCCCCccceeE--EEEEEecCC
Q 047111 42 SPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEY--EVPMRLSKT 87 (106)
Q Consensus 42 GSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey--~V~IkLh~~ 87 (106)
+..|.+||.+.|++++|+ |+..|.+..--..+|.. ..-.++|.+
T Consensus 11 ~Tpsr~ei~~klA~~~~~--~~~~ivv~~~~t~fG~~~s~g~a~IYd~ 56 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNV--DPDLIVVFGIKTEFGGGKSTGFAKIYDS 56 (84)
T ss_dssp SS--HHHHHHHHHHHHTS--TGCCEEEEEEEESSSSSEEEEEEEEESS
T ss_pred CCCCHHHHHHHHHHHhCC--CCCeEEEeccEecCCCceEEEEEEEeCC
Confidence 467889999999999885 89899887777777666 444455544
No 14
>PF05157 T2SE_Nter: Type II secretion system (T2SS), protein E, N-terminal domain; InterPro: IPR007831 This domain is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g. Q9X4G8 from SWISSPROT), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g. Q9RF11 from SWISSPROT) [].; GO: 0005524 ATP binding, 0006810 transport; PDB: 2D27_A 2D28_C.
Probab=49.26 E-value=13 Score=23.80 Aligned_cols=27 Identities=19% Similarity=0.453 Sum_probs=16.7
Q ss_pred ecCCHHHHHHHHHhhcCCc-cccccccC
Q 047111 42 SPVTKEELVAKVASQLSIS-IEPEYLHL 68 (106)
Q Consensus 42 GSVTtkdIaeaL~~q~gIe-IDKkkI~L 68 (106)
|-+|..++.+++++++|++ +|-..+..
T Consensus 5 g~ise~~l~~~la~~~~l~~~~~~~~~~ 32 (109)
T PF05157_consen 5 GLISEDQLLEALAEQLGLPFVDLDELPV 32 (109)
T ss_dssp T-S-HHHHHHHHHHHHT--B--GGGS-S
T ss_pred CCCCHHHHHHHHHHHhCCCeechhhcCC
Confidence 7899999999999999988 44444433
No 15
>PF08960 DUF1874: Domain of unknown function (DUF1874); InterPro: IPR015055 This entry is represented by Acidianus two-tailed virus, Orf117. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2J85_A 2X4I_C.
Probab=48.59 E-value=27 Score=25.10 Aligned_cols=53 Identities=21% Similarity=0.368 Sum_probs=22.9
Q ss_pred eeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEEecCCCCCCCCcEE
Q 047111 39 ELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQ 96 (106)
Q Consensus 39 kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~IkLh~~Vp~p~gkV~ 96 (106)
.+-.+|..++-|+.+.+.+|..|..-.+... -+-|.--+-+.|.+- +|||+|-
T Consensus 38 ~~vSaIGH~sTa~lls~llg~~ip~NR~~i~---~~~Gd~alv~~L~~R--l~EG~Vl 90 (105)
T PF08960_consen 38 GFVSAIGHDSTAQLLSELLGVNIPMNRIQIK---LDPGDKALVFQLKQR--LPEGKVL 90 (105)
T ss_dssp TEEE----HHHHHHHHHHHT--------------B-TT-EEEEEEESS-----TT---
T ss_pred ceEEeeCcHHHHHHHHHHhCCccccccEEEE---ecCCCEEEEEEeccc--CCCCcCC
Confidence 3455688888888888888766555444332 245777788888887 6999985
No 16
>smart00089 PKD Repeats in polycystic kidney disease 1 (PKD1) and other proteins. Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.
Probab=44.22 E-value=53 Score=20.15 Aligned_cols=28 Identities=25% Similarity=0.441 Sum_probs=22.8
Q ss_pred CccceeEEEEEEecCCCCCCCCcEEEEEEEEE
Q 047111 72 LSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKV 103 (106)
Q Consensus 72 IKslGey~V~IkLh~~Vp~p~gkV~~~lkV~V 103 (106)
..+-|.|.|.+....+. |..++++.|.|
T Consensus 51 y~~~G~y~v~l~v~n~~----g~~~~~~~i~v 78 (79)
T smart00089 51 YTKPGTYTVTLTVTNAV----GSASATVTVVV 78 (79)
T ss_pred eCCCcEEEEEEEEEcCC----CcEEEEEEEEE
Confidence 45779999999998875 67788887776
No 17
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=43.32 E-value=17 Score=22.87 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=31.2
Q ss_pred CceeeecCCHHHHHHHHHhhcCCcccccccc-----CCCCCccceeEEE
Q 047111 37 PIELCSPVTKEELVAKVASQLSISIEPEYLH-----LPSPLSAFGEYEV 80 (106)
Q Consensus 37 ~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~-----L~~pIKslGey~V 80 (106)
++.+..+-|-+++-+.++++.|+..+.-++. |.+. ++++.|.+
T Consensus 12 ~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~-~tL~~~~i 59 (74)
T cd01793 12 TLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDD-ATLGQCGV 59 (74)
T ss_pred EEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCC-CCHHHcCC
Confidence 4567788899999999998889887775553 3322 56666665
No 18
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=42.83 E-value=61 Score=20.03 Aligned_cols=25 Identities=36% Similarity=0.408 Sum_probs=19.4
Q ss_pred CCccceeEEEEEEecCCCCCCCCcEEEEEEEEE
Q 047111 71 PLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKV 103 (106)
Q Consensus 71 pIKslGey~V~IkLh~~Vp~p~gkV~~~lkV~V 103 (106)
.-...|.|.|.+.... ++.+++|.|
T Consensus 43 d~~~~G~y~Vt~~y~~--------~t~t~~VtV 67 (67)
T PF07523_consen 43 DTSKAGTYTVTYTYKG--------VTATFTVTV 67 (67)
T ss_dssp -TTS-CCEEEEEEECT--------EEEEEEEEE
T ss_pred ecCCCceEEEEEEECC--------EEEEEEEEC
Confidence 4567899999999776 489999886
No 19
>PHA01627 DNA binding protein
Probab=40.71 E-value=50 Score=23.89 Aligned_cols=53 Identities=15% Similarity=0.269 Sum_probs=35.0
Q ss_pred eeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEEecCCCCCCCCcEEE
Q 047111 40 LCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQW 97 (106)
Q Consensus 40 LFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~IkLh~~Vp~p~gkV~~ 97 (106)
.-.+|..+.=|+.+.+-+|..|..-.+.... +-|.--+-+.|.+- ||||+|-.
T Consensus 40 ~vSaIGH~sTA~lls~llg~~ip~NRi~i~~---~~GDkalv~~L~~R--l~EG~Vl~ 92 (107)
T PHA01627 40 FVSAIGHDATANLLSNLCGVNLPKNRIEIKL---DKGDKALAIMLKQR--LEEGKVLK 92 (107)
T ss_pred eEEeeccHHHHHHHHHHhCccccccceEEEe---cCCCEEEEEEeccc--CCCCeecc
Confidence 3446777777777777677655544443322 35777778888887 79999865
No 20
>COG5556 Uncharacterized conserved protein [Function unknown]
Probab=39.66 E-value=15 Score=26.76 Aligned_cols=30 Identities=13% Similarity=0.254 Sum_probs=24.4
Q ss_pred CHHHHHHHHHhhcCCccccccccCCCCCcc
Q 047111 45 TKEELVAKVASQLSISIEPEYLHLPSPLSA 74 (106)
Q Consensus 45 TtkdIaeaL~~q~gIeIDKkkI~L~~pIKs 74 (106)
|..-+++++++++||++.+.-++-.+|=|.
T Consensus 21 s~S~Va~aVkkEfGi~VsrQlveshdP~Kk 50 (110)
T COG5556 21 SPSVVAAAVKKEFGIDVSRQLVESHDPNKK 50 (110)
T ss_pred cHHHHHHHHHHHhcchHHHHHHHhcCcchh
Confidence 456789999999999999988877777543
No 21
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=38.88 E-value=23 Score=21.62 Aligned_cols=20 Identities=30% Similarity=0.453 Sum_probs=14.8
Q ss_pred ecCCHHHHHHHHHhhcCCcc
Q 047111 42 SPVTKEELVAKVASQLSISI 61 (106)
Q Consensus 42 GSVTtkdIaeaL~~q~gIeI 61 (106)
|.-|..+|+++|.++++++-
T Consensus 28 g~~t~~ei~~~l~~~y~~~~ 47 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDP 47 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--H
T ss_pred CCCCHHHHHHHHHHHcCCCH
Confidence 67899999999999976543
No 22
>PF13565 HTH_32: Homeodomain-like domain
Probab=38.43 E-value=23 Score=21.93 Aligned_cols=19 Identities=21% Similarity=0.328 Sum_probs=16.8
Q ss_pred cCCHHHHHHHHHhhcCCcc
Q 047111 43 PVTKEELVAKVASQLSISI 61 (106)
Q Consensus 43 SVTtkdIaeaL~~q~gIeI 61 (106)
--|..+|++.|++++|+.+
T Consensus 48 ~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 48 RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 5799999999999999876
No 23
>PF06481 COX_ARM: COX Aromatic Rich Motif; InterPro: IPR010514 COX2 (Cytochrome O ubiquinol OXidase 2) is a major component of the respiratory complex during vegetative growth. It transfers electrons from a quinol to the binuclear centre of the catalytic subunit 1. The function of this region is not known.; GO: 0008827 cytochrome o ubiquinol oxidase activity, 0022900 electron transport chain, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1CYX_A 1CYW_A 1FFT_G.
Probab=33.40 E-value=26 Score=21.15 Aligned_cols=20 Identities=20% Similarity=0.411 Sum_probs=11.4
Q ss_pred cccCCCCCceeeecCCHHHH
Q 047111 30 SRESKDDPIELCSPVTKEEL 49 (106)
Q Consensus 30 ~~~~~~~~~kLFGSVTtkdI 49 (106)
++.|.++|...|+||...=-
T Consensus 16 a~PS~~~pv~yfssv~p~LF 35 (47)
T PF06481_consen 16 AKPSENNPVTYFSSVEPGLF 35 (47)
T ss_dssp CSS-SS--SEEES-B-TTHH
T ss_pred HCcCcCCCceeeccCCHHHH
Confidence 35678899999999987643
No 24
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=32.44 E-value=15 Score=31.66 Aligned_cols=59 Identities=25% Similarity=0.334 Sum_probs=40.3
Q ss_pred chHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccc
Q 047111 2 SREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIE 62 (106)
Q Consensus 2 ~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeID 62 (106)
|+|.|.|+.+|+...+...+.|+..-. ++.--|...-...+|..+|.+.+++-+|+.++
T Consensus 280 vReLegaL~~l~~~a~~~~~~iTi~~v--~e~L~~~~~~~~~itie~I~~~Va~~y~v~~~ 338 (408)
T COG0593 280 VRELEGALNRLDAFALFTKRAITIDLV--KEILKDLLRAGEKITIEDIQKIVAEYYNVKVS 338 (408)
T ss_pred HHHHHHHHHHHHHHHHhcCccCcHHHH--HHHHHHhhcccccCCHHHHHHHHHHHhCCCHH
Confidence 689999999999998877775554332 22111111111139999999999998898775
No 25
>PF08799 PRP4: pre-mRNA processing factor 4 (PRP4) like; InterPro: IPR014906 This small protein is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. ; PDB: 1MZW_B 2DK4_A.
Probab=30.69 E-value=17 Score=20.73 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=8.4
Q ss_pred CCCceeeecCCHHHHHHHH
Q 047111 35 DDPIELCSPVTKEELVAKV 53 (106)
Q Consensus 35 ~~~~kLFGSVTtkdIaeaL 53 (106)
.+||.|||- |..|--+-|
T Consensus 9 gePi~lFGE-~~~~R~~RL 26 (30)
T PF08799_consen 9 GEPITLFGE-TDADRRERL 26 (30)
T ss_dssp T--SCETT---HHHHHHHH
T ss_pred CCChhhhCC-ChHHHHHHH
Confidence 589999995 344433333
No 26
>PRK09184 acyl carrier protein; Provisional
Probab=29.98 E-value=27 Score=23.67 Aligned_cols=33 Identities=3% Similarity=0.131 Sum_probs=22.7
Q ss_pred cCCHHHHHHHHHhhcCCccccccccCCCCCccc
Q 047111 43 PVTKEELVAKVASQLSISIEPEYLHLPSPLSAF 75 (106)
Q Consensus 43 SVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKsl 75 (106)
|+..=+|+-++++.+|++|+-........++++
T Consensus 44 Sld~velv~~lE~~fgi~i~~~~~~~~~~~~TV 76 (89)
T PRK09184 44 SIDILEIALVISKRYGFQLRSDNPDNQRIFASL 76 (89)
T ss_pred HHHHHHHHHHHHHHHCCcCCCcchhhhhccCCH
Confidence 677888899999999999964443333333333
No 27
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=29.59 E-value=78 Score=22.07 Aligned_cols=26 Identities=23% Similarity=0.645 Sum_probs=21.5
Q ss_pred CCCccceeEEEEEEecCC-CCCCCCcEEEEEEE
Q 047111 70 SPLSAFGEYEVPMRLSKT-IPLPEGKVQWTFNV 101 (106)
Q Consensus 70 ~pIKslGey~V~IkLh~~-Vp~p~gkV~~~lkV 101 (106)
.+|++.|++.+.+.|+-. . ..|.+.|
T Consensus 45 t~I~tyG~~~l~ldlGlrr~------~~w~Fvv 71 (89)
T cd06094 45 TPIATYGTRSLTLDLGLRRP------FAWNFVV 71 (89)
T ss_pred CeEeeeeeEEEEEEcCCCcE------EeEEEEE
Confidence 479999999999999875 3 6777766
No 28
>KOG1494 consensus NAD-dependent malate dehydrogenase [Energy production and conversion]
Probab=29.01 E-value=28 Score=29.75 Aligned_cols=46 Identities=24% Similarity=0.225 Sum_probs=28.3
Q ss_pred HHHHHhhhccce-eeEeecchhh-----cccccCCCCCceeeecCCHHHHHHH
Q 047111 6 EKAARRLENARL-VLRRFPNIEK-----LRSRESKDDPIELCSPVTKEELVAK 52 (106)
Q Consensus 6 ~~~~~~l~~~~l-~~~~~~~~~~-----~~~~~~~~~~~kLFGSVTtkdIaea 52 (106)
+.+++--.||.+ ++..=+|++- .=...-.-||.|||| ||+=|++.|
T Consensus 130 ~aia~~cP~A~i~vIsNPVNstVPIaaevlKk~G~ydpkklfG-VTtLDvVRA 181 (345)
T KOG1494|consen 130 AAIAKCCPNALILVISNPVNSTVPIAAEVLKKAGVYDPKKLFG-VTTLDVVRA 181 (345)
T ss_pred HHHHhhCccceeEeecCcccccchHHHHHHHHcCCCCccceec-eehhhhhhH
Confidence 344555566655 4444445431 112345678999999 888898875
No 29
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=28.30 E-value=44 Score=23.27 Aligned_cols=24 Identities=4% Similarity=0.182 Sum_probs=18.5
Q ss_pred eecCCHHHHHHHHHhhcCCccccccc
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYL 66 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI 66 (106)
.|+.|+.||-+.|+++ .+|..+.+
T Consensus 23 ~~~~T~~di~e~L~~~--f~vs~~~V 46 (83)
T PF10826_consen 23 GKKFTTDDIYERLKEK--FDVSYRGV 46 (83)
T ss_pred CCCeeHHHHHHHHHHH--cCchHHHH
Confidence 4789999999999988 45555543
No 30
>PRK05395 3-dehydroquinate dehydratase; Provisional
Probab=27.55 E-value=58 Score=24.65 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=19.6
Q ss_pred eeeecCCHHHHHHHHHh---hcCCcccc
Q 047111 39 ELCSPVTKEELVAKVAS---QLSISIEP 63 (106)
Q Consensus 39 kLFGSVTtkdIaeaL~~---q~gIeIDK 63 (106)
.+||+.|-+||.+.+++ ++|++++=
T Consensus 21 ~iYG~~tl~~i~~~~~~~a~~~g~~v~~ 48 (146)
T PRK05395 21 EIYGSTTLADIEALLEEEAAELGVELEF 48 (146)
T ss_pred CcCCCCCHHHHHHHHHHHHHHcCCEEEE
Confidence 68999999999998775 34666653
No 31
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.48 E-value=14 Score=23.79 Aligned_cols=26 Identities=27% Similarity=0.323 Sum_probs=22.0
Q ss_pred eecCCHHHHHHHHHhhcCCccccccc
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYL 66 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI 66 (106)
.-|+..-+++-+|.+++||+|+-..+
T Consensus 37 ~DSld~veLi~~lE~~f~i~i~~e~~ 62 (80)
T COG0236 37 LDSLDLVELVMALEEEFGIEIPDEEL 62 (80)
T ss_pred ccHHHHHHHHHHHHHHHCCcCCHHHH
Confidence 34788889999999999999988765
No 32
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=27.27 E-value=53 Score=26.82 Aligned_cols=56 Identities=21% Similarity=0.186 Sum_probs=36.2
Q ss_pred chHHHHHHHhhhccceeeEeecchhhc----ccccCCCCCceeeecCCHHHHHHHHHhhcCCccc
Q 047111 2 SREFEKAARRLENARLVLRRFPNIEKL----RSRESKDDPIELCSPVTKEELVAKVASQLSISIE 62 (106)
Q Consensus 2 ~~~~~~~~~~l~~~~l~~~~~~~~~~~----~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeID 62 (106)
+++.+.|+.+|+...+...+-|+.... +.-...+.+ .||..+|.+++++.+|+..+
T Consensus 304 ~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L~~~~~~~~~-----~it~~~I~~~Va~~~~v~~~ 363 (405)
T TIGR00362 304 VRELEGALNRLLAYASLTGKPITLELAKEALKDLLRAKKK-----EITIENIQEVVAKYYNIKVS 363 (405)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccCC-----CCCHHHHHHHHHHHcCCCHH
Confidence 467888888888666555555554322 211111111 59999999999999887654
No 33
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=27.13 E-value=30 Score=23.17 Aligned_cols=15 Identities=33% Similarity=0.355 Sum_probs=13.3
Q ss_pred ceeeecCCHHHHHHH
Q 047111 38 IELCSPVTKEELVAK 52 (106)
Q Consensus 38 ~kLFGSVTtkdIaea 52 (106)
.++|++||+.+|+.+
T Consensus 23 ~~~~~~Vs~~EI~~~ 37 (71)
T PF04282_consen 23 KKLFSDVSASEISAA 37 (71)
T ss_pred HHHHCCCCHHHHHHH
Confidence 379999999999985
No 34
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=25.69 E-value=58 Score=20.38 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=21.2
Q ss_pred ecCCHHHHHHHHHhhcCCccccccccC
Q 047111 42 SPVTKEELVAKVASQLSISIEPEYLHL 68 (106)
Q Consensus 42 GSVTtkdIaeaL~~q~gIeIDKkkI~L 68 (106)
-+-|++||.+++.+++|+.=|..+..|
T Consensus 25 ~~tTa~evi~~~l~k~~l~~~~~~y~L 51 (93)
T PF00788_consen 25 SSTTAREVIEMALEKFGLAEDPSDYCL 51 (93)
T ss_dssp TTSBHHHHHHHHHHHTTTSSSGGGEEE
T ss_pred CCCCHHHHHHHHHHHhCCCCCCCCEEE
Confidence 356899999999999998666666655
No 35
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=25.69 E-value=2.4e+02 Score=21.28 Aligned_cols=41 Identities=15% Similarity=0.164 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEEecCCC
Q 047111 44 VTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTI 88 (106)
Q Consensus 44 VTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~IkLh~~V 88 (106)
.|..||-+|+++-+|+++.+=+.... .-|.-..-|+|.+|-
T Consensus 93 AnK~qIK~AVEklf~VkV~kVNTli~----p~g~KKA~V~L~~~~ 133 (145)
T PTZ00191 93 ANKTQIKKAVEKLYDVKVVKVNTLIT----PDGLKKAYIRLSPDV 133 (145)
T ss_pred CCHHHHHHHHHHHhCCeeEEEEeEEc----CCCceEEEEEECCCC
Confidence 35689999999889998887554322 228888889998873
No 36
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=25.64 E-value=46 Score=21.30 Aligned_cols=17 Identities=29% Similarity=0.536 Sum_probs=12.3
Q ss_pred CHHHHHHHHHhhcCCcc
Q 047111 45 TKEELVAKVASQLSISI 61 (106)
Q Consensus 45 TtkdIaeaL~~q~gIeI 61 (106)
|..+|.+++.+.+|++.
T Consensus 1 t~~~Ii~~Va~~~~v~~ 17 (70)
T PF08299_consen 1 TIEDIIEAVAEYFGVSV 17 (70)
T ss_dssp -HHHHHHHHHHHTT--H
T ss_pred CHHHHHHHHHHHHCCCH
Confidence 67899999999988654
No 37
>COG2062 SixA Phosphohistidine phosphatase SixA [Signal transduction mechanisms]
Probab=25.49 E-value=25 Score=26.64 Aligned_cols=33 Identities=18% Similarity=0.122 Sum_probs=29.0
Q ss_pred chHHHHHHHhhhccceeeEeecchhhcccccCC
Q 047111 2 SREFEKAARRLENARLVLRRFPNIEKLRSRESK 34 (106)
Q Consensus 2 ~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~ 34 (106)
.+|.|.+++.|-+..+..-++.-|...|+|+|-
T Consensus 31 ~~ea~~~a~~L~~~~~~~D~VL~Spa~Ra~QTa 63 (163)
T COG2062 31 RKEAELVAAWLAGQGVEPDLVLVSPAVRARQTA 63 (163)
T ss_pred HHHHHHHHHHHHhcCCCCCEEEeChhHHHHHHH
Confidence 478999999999999988999999999988764
No 38
>smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
Probab=25.45 E-value=70 Score=16.02 Aligned_cols=16 Identities=19% Similarity=0.341 Sum_probs=13.0
Q ss_pred ceeeecCCHHHHHHHH
Q 047111 38 IELCSPVTKEELVAKV 53 (106)
Q Consensus 38 ~kLFGSVTtkdIaeaL 53 (106)
.++.|-++..++...+
T Consensus 33 ~~~~g~i~~~~l~~~~ 48 (49)
T smart00116 33 GRLVGIVTRRDIIKAL 48 (49)
T ss_pred CeEEEEEEHHHHHHhh
Confidence 3789999999987765
No 39
>cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d
Probab=25.31 E-value=1.1e+02 Score=19.23 Aligned_cols=18 Identities=11% Similarity=0.145 Sum_probs=15.1
Q ss_pred ceeeecCCHHHHHHHHHh
Q 047111 38 IELCSPVTKEELVAKVAS 55 (106)
Q Consensus 38 ~kLFGSVTtkdIaeaL~~ 55 (106)
.++.|-||.+|+..++.+
T Consensus 34 ~~~~G~v~~~dl~~~~~~ 51 (115)
T cd04593 34 GGVVGIITLPDLLRALEA 51 (115)
T ss_pred CCEEEEEEHHHHHHHHhc
Confidence 389999999999987764
No 40
>PRK00982 acpP acyl carrier protein; Provisional
Probab=24.64 E-value=43 Score=20.90 Aligned_cols=26 Identities=23% Similarity=0.309 Sum_probs=22.9
Q ss_pred eecCCHHHHHHHHHhhcCCccccccc
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYL 66 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI 66 (106)
+-|+..-+|..++++++|+.++...+
T Consensus 35 lDSl~~~~li~~le~~f~i~i~~~~~ 60 (78)
T PRK00982 35 ADSLDTVELVMALEEEFGIEIPDEDA 60 (78)
T ss_pred CCHHHHHHHHHHHHHHHCCCcCHHHH
Confidence 36888999999999999999998765
No 41
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=24.43 E-value=52 Score=21.37 Aligned_cols=13 Identities=8% Similarity=0.340 Sum_probs=11.3
Q ss_pred ecCCHHHHHHHHH
Q 047111 42 SPVTKEELVAKVA 54 (106)
Q Consensus 42 GSVTtkdIaeaL~ 54 (106)
|.++.+|||++|.
T Consensus 21 g~i~lkdIA~~Lg 33 (60)
T PF10668_consen 21 GKIKLKDIAEKLG 33 (60)
T ss_pred CCccHHHHHHHHC
Confidence 7899999998875
No 42
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=24.22 E-value=79 Score=25.63 Aligned_cols=76 Identities=13% Similarity=0.124 Sum_probs=46.5
Q ss_pred HHHhhhccceeeEeecchhhcccccCCC-------CCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEE
Q 047111 8 AARRLENARLVLRRFPNIEKLRSRESKD-------DPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEV 80 (106)
Q Consensus 8 ~~~~l~~~~l~~~~~~~~~~~~~~~~~~-------~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V 80 (106)
++.|||..+=||=.|-|.+.+-.+-+.. -=..+.|.+|..+| +.+. .|+.+|- ....+..+..+..+.+
T Consensus 102 ~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~i~K~Y~v~V~g~~~~~~l-~~l~--~Gv~l~~-~~~~~~~v~~~~~~~~ 177 (290)
T PRK10475 102 PIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFI-RGMG--AGVPILG-TVTKKCKVKKEAPFVF 177 (290)
T ss_pred ccccCCCCCcceEEEecCHHHHHHhhCcCCCCCeEEEEEECCCCCHHHH-HHHh--CCcEECC-EEecceEEEecCCcEE
Confidence 5789998877777777666665554331 11346699988776 4554 4999973 3333433444445566
Q ss_pred EEEecCC
Q 047111 81 PMRLSKT 87 (106)
Q Consensus 81 ~IkLh~~ 87 (106)
.|.|+.|
T Consensus 178 ~i~l~eG 184 (290)
T PRK10475 178 RITLVQG 184 (290)
T ss_pred EEEEECC
Confidence 6666655
No 43
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=23.76 E-value=38 Score=21.84 Aligned_cols=14 Identities=14% Similarity=0.399 Sum_probs=10.6
Q ss_pred eecCCHHHHHHHHH
Q 047111 41 CSPVTKEELVAKVA 54 (106)
Q Consensus 41 FGSVTtkdIaeaL~ 54 (106)
-+++|+.|||+++.
T Consensus 13 ~~p~~T~eiA~~~g 26 (62)
T PF04703_consen 13 NGPLKTREIADALG 26 (62)
T ss_dssp TS-EEHHHHHHHHT
T ss_pred CCCCCHHHHHHHhC
Confidence 47799999999863
No 44
>cd00466 DHQase_II Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway and the catabolic quinate pathway. There are two types of DHQases, which are distinct from each other in amino acid sequence and three-dimensional structure. Type I enzymes usually catalyze the biosynthetic reaction using a syn elimination mechanism. In contrast, type II enzymes, found in the quinate pathway of fungi and in the shikimate pathway of many bacteria, are dodecameric enzymes that employ an anti elimination reaction mechanism.
Probab=23.41 E-value=72 Score=24.00 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=20.2
Q ss_pred eeeecCCHHHHHHHHHhh---cCCccccc
Q 047111 39 ELCSPVTKEELVAKVASQ---LSISIEPE 64 (106)
Q Consensus 39 kLFGSVTtkdIaeaL~~q---~gIeIDKk 64 (106)
..||+.|-+||.+.+++. +|++++=.
T Consensus 19 ~iYG~~tl~~i~~~l~~~a~~~g~~v~~~ 47 (140)
T cd00466 19 EIYGTTTLADIEALLRELAAELGVEVEFF 47 (140)
T ss_pred CcCCcCCHHHHHHHHHHHHHHcCCEEEEE
Confidence 689999999999887754 46766543
No 45
>cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=23.37 E-value=1.4e+02 Score=18.89 Aligned_cols=40 Identities=20% Similarity=0.249 Sum_probs=25.7
Q ss_pred HHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHh
Q 047111 5 FEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVAS 55 (106)
Q Consensus 5 ~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~ 55 (106)
.+.|++++.......--.++.. -++.|-||..|+..++..
T Consensus 12 l~~a~~~~~~~~~~~~~Vvd~~-----------g~~~G~vt~~dl~~~~~~ 51 (114)
T cd04619 12 LQRAAKILGEPGIDLVVVCDPH-----------GKLAGVLTKTDVVRQMGR 51 (114)
T ss_pred HHHHHHHHHhcCCCEEEEECCC-----------CCEEEEEehHHHHHHHhh
Confidence 3557777765544333334533 378999999999887653
No 46
>CHL00124 acpP acyl carrier protein; Validated
Probab=23.36 E-value=48 Score=21.02 Aligned_cols=26 Identities=23% Similarity=0.302 Sum_probs=22.5
Q ss_pred eecCCHHHHHHHHHhhcCCccccccc
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYL 66 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI 66 (106)
+-|+..-+|+.++.+++||+|+-..+
T Consensus 37 ~DSl~~~eli~~le~~f~i~i~~~~~ 62 (82)
T CHL00124 37 ADSLDVVELVMAIEEKFDIEIPDEDA 62 (82)
T ss_pred CcHHHHHHHHHHHHHHHCCccCHHHH
Confidence 45888899999999999999997665
No 47
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II. This model specifies the type II enzyme. The type I enzyme, often found as part of a multifunctional protein, is described by TIGR01093.
Probab=22.93 E-value=74 Score=23.97 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=19.6
Q ss_pred eeeecCCHHHHHHHHHhh---cCCcccc
Q 047111 39 ELCSPVTKEELVAKVASQ---LSISIEP 63 (106)
Q Consensus 39 kLFGSVTtkdIaeaL~~q---~gIeIDK 63 (106)
.+||+.|-+||.+.+++. +|++++=
T Consensus 19 ~iYG~~tl~di~~~~~~~a~~~g~~v~~ 46 (141)
T TIGR01088 19 GVYGSQTLEEIVEIIETFAAQLNVELEF 46 (141)
T ss_pred CcCCCCCHHHHHHHHHHHHHHcCCEEEE
Confidence 689999999999877754 4676653
No 48
>PF07679 I-set: Immunoglobulin I-set domain; InterPro: IPR013098 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) []. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [, ]. Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system []. This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [].; PDB: 3MTR_A 2EDK_A 3DMK_B 1KOA_A 3NCM_A 2NCM_A 2V9Q_A 2CR3_A 3QQN_A 3QR2_A ....
Probab=22.71 E-value=1.6e+02 Score=17.78 Aligned_cols=32 Identities=19% Similarity=0.214 Sum_probs=23.2
Q ss_pred ccCCC-CCccceeEEEEEEecCCCCCCCCcEEEEEEEEE
Q 047111 66 LHLPS-PLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKV 103 (106)
Q Consensus 66 I~L~~-pIKslGey~V~IkLh~~Vp~p~gkV~~~lkV~V 103 (106)
+.+.. --..-|.|...+.-..+ ..+++++|.|
T Consensus 58 L~I~~v~~~D~G~Y~C~~~n~~g------~~~~~~~l~V 90 (90)
T PF07679_consen 58 LTIKNVTREDAGTYTCVASNSSG------EATASVNLTV 90 (90)
T ss_dssp EEESSESGGGSEEEEEEEEETTE------EEEEEEEEEE
T ss_pred EccCCCChhhCEEEEEEEEECCC------EEEEEEEEEC
Confidence 34444 35778999999997655 5888888876
No 49
>TIGR03435 Soli_TIGR03435 Solibacter paralogous family TIGR03435. This model describes a paralogous family of about 40 proteins found in Solibacter usitatus Ellin6076, one of the first three members of the Acidobacteria to be sequenced, and nowhere else. The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. Two members of the family are longer, multidomain proteins with (two different) fused peptidase domains.
Probab=22.55 E-value=60 Score=26.09 Aligned_cols=26 Identities=19% Similarity=0.328 Sum_probs=20.8
Q ss_pred cCCHHHHHHHHHhhcCCccccccccC
Q 047111 43 PVTKEELVAKVASQLSISIEPEYLHL 68 (106)
Q Consensus 43 SVTtkdIaeaL~~q~gIeIDKkkI~L 68 (106)
+.+...|..||++|+|+.+..++..+
T Consensus 197 ~~~~~sL~~ALq~QLGLKLe~~K~pv 222 (237)
T TIGR03435 197 DPSGPSLFTALQEQLGLKLEPRKAPV 222 (237)
T ss_pred CCccchHHHHHHHhhCceEcccccCc
Confidence 34555799999999999999988544
No 50
>cd04630 CBS_pair_17 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=22.55 E-value=1.4e+02 Score=18.67 Aligned_cols=18 Identities=22% Similarity=0.309 Sum_probs=15.2
Q ss_pred ceeeecCCHHHHHHHHHh
Q 047111 38 IELCSPVTKEELVAKVAS 55 (106)
Q Consensus 38 ~kLFGSVTtkdIaeaL~~ 55 (106)
-++.|.||..|+..++.+
T Consensus 35 ~~~~G~v~~~dl~~~~~~ 52 (114)
T cd04630 35 SDAYGIVTMRDILKKVVA 52 (114)
T ss_pred CcEEEEEehHHHHHHHHh
Confidence 489999999999987654
No 51
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=22.29 E-value=69 Score=19.58 Aligned_cols=18 Identities=33% Similarity=0.445 Sum_probs=14.2
Q ss_pred CHHHHHHHHHhhcCCccc
Q 047111 45 TKEELVAKVASQLSISIE 62 (106)
Q Consensus 45 TtkdIaeaL~~q~gIeID 62 (106)
|..+|.+++.+.+||+.+
T Consensus 1 ~~~~I~~~Va~~~~i~~~ 18 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPE 18 (60)
T ss_pred CHHHHHHHHHHHhCCCHH
Confidence 467899999999886654
No 52
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=22.10 E-value=2.1e+02 Score=19.42 Aligned_cols=24 Identities=25% Similarity=0.297 Sum_probs=20.1
Q ss_pred cCCHHHHHHHHHhhcCCccccccc
Q 047111 43 PVTKEELVAKVASQLSISIEPEYL 66 (106)
Q Consensus 43 SVTtkdIaeaL~~q~gIeIDKkkI 66 (106)
..|..||-+++++-+|+.+.+=+.
T Consensus 30 ~a~K~eIK~aie~lf~VkV~~VnT 53 (92)
T PRK05738 30 DATKPEIKAAVEKLFGVKVESVNT 53 (92)
T ss_pred CCCHHHHHHHHHHHcCCceeEEEE
Confidence 467899999999999999887554
No 53
>cd00258 GM2-AP GM2 activator protein (GM2-AP) is a non-enzymatic lysosomal protein that acts as cofactor in the sequential degradation of gangliosides. GM2A is an essential cofactor for beta-hexosaminidase A (Hex A) in the enzymatic hydrolysis of GM2 ganglioside to GM3. Mutation of the gene results in the AB variant of Tay-Sachs disease. GM2-AP and similar proteins belong to the ML domain family.
Probab=22.07 E-value=1.9e+02 Score=22.31 Aligned_cols=59 Identities=17% Similarity=0.187 Sum_probs=37.4
Q ss_pred eecCCHHHHHHHHHh------------------------hcCCccccccccCCC---C-CccceeEEEEEEecCCCCCCC
Q 047111 41 CSPVTKEELVAKVAS------------------------QLSISIEPEYLHLPS---P-LSAFGEYEVPMRLSKTIPLPE 92 (106)
Q Consensus 41 FGSVTtkdIaeaL~~------------------------q~gIeIDKkkI~L~~---p-IKslGey~V~IkLh~~Vp~p~ 92 (106)
|||=|-.|+.+.+.. +....+....+.+++ | .-.-|.|.++..|.+ +
T Consensus 72 ~GSCty~d~C~~l~~~~~~~~~Cp~~l~~~g~pC~CP~~~G~y~lp~s~f~lP~~~LPs~l~~G~Y~i~~~l~~-----~ 146 (162)
T cd00258 72 IGSCTYDNACDLLDTLIPPGQQCPEPLRTYGLPCHCPFKEGVYSLPDSTFTLPNVDLPSWLTNGNYRITGILMA-----D 146 (162)
T ss_pred cCcccccchhhchhcccCCCCCCCchhhccCCccCCCCCCcceEccceeeecccccCCCccCCCcEEEEEEECC-----C
Confidence 799999999998742 112233334444433 2 335688888888843 4
Q ss_pred CcEEEEEEEEEE
Q 047111 93 GKVQWTFNVKVH 104 (106)
Q Consensus 93 gkV~~~lkV~V~ 104 (106)
|+--+-++|...
T Consensus 147 g~~l~C~~~~~s 158 (162)
T cd00258 147 GKELGCGKFTFS 158 (162)
T ss_pred CCEEEEEEEEEE
Confidence 788887777653
No 54
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=21.92 E-value=31 Score=21.37 Aligned_cols=33 Identities=15% Similarity=0.264 Sum_probs=16.5
Q ss_pred CCHHHHHHHHHhhcCCccccccccCCCCCccceeEE
Q 047111 44 VTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYE 79 (106)
Q Consensus 44 VTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~ 79 (106)
+|..||+.+|.++ |+.|.+.-|.- -+++.|.+.
T Consensus 14 ~s~~~i~~~l~~~-~~~vS~~TI~r--~L~~~g~~~ 46 (72)
T PF01498_consen 14 ISAREIAQELQEA-GISVSKSTIRR--RLREAGLKK 46 (72)
T ss_dssp --HHHHHHHT----T--S-HHHHHH--HHHHT-EEE
T ss_pred CCHHHHHHHHHHc-cCCcCHHHHHH--HHHHcCccc
Confidence 8999999999977 99988876632 245555443
No 55
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=21.85 E-value=63 Score=22.96 Aligned_cols=19 Identities=26% Similarity=0.403 Sum_probs=12.9
Q ss_pred HHHHHHHHHhhcCCccccc
Q 047111 46 KEELVAKVASQLSISIEPE 64 (106)
Q Consensus 46 tkdIaeaL~~q~gIeIDKk 64 (106)
+.+||.+|+++-||+++-.
T Consensus 24 ~eevA~~lA~~egI~Ltd~ 42 (109)
T PF04358_consen 24 NEEVAEALAKEEGIELTDE 42 (109)
T ss_dssp -HHHHHHHHHCTT-S--HH
T ss_pred CHHHHHHHHHHcCCCCCHH
Confidence 6799999999999887643
No 56
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=21.70 E-value=36 Score=19.64 Aligned_cols=23 Identities=26% Similarity=0.445 Sum_probs=16.1
Q ss_pred ecCCHHHHHHHHHhhcCCc-ccccc
Q 047111 42 SPVTKEELVAKVASQLSIS-IEPEY 65 (106)
Q Consensus 42 GSVTtkdIaeaL~~q~gIe-IDKkk 65 (106)
|.||..++..++. ..|+. +....
T Consensus 3 G~i~~~~~~~~l~-~~g~~~~s~~e 26 (54)
T PF13833_consen 3 GKITREEFRRALS-KLGIKDLSEEE 26 (54)
T ss_dssp SEEEHHHHHHHHH-HTTSSSSCHHH
T ss_pred CEECHHHHHHHHH-HhCCCCCCHHH
Confidence 6788888888884 55776 55443
No 57
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=21.60 E-value=87 Score=20.58 Aligned_cols=28 Identities=21% Similarity=0.327 Sum_probs=21.0
Q ss_pred eecCCHHHHHHHHHhhcCCccccccccC
Q 047111 41 CSPVTKEELVAKVASQLSISIEPEYLHL 68 (106)
Q Consensus 41 FGSVTtkdIaeaL~~q~gIeIDKkkI~L 68 (106)
=|+.|.+||.+++.+.+++.=+-++..+
T Consensus 17 g~~~~~~ei~~~v~~~~~ls~e~~~~~~ 44 (92)
T PF14338_consen 17 GGSASRKEIYERVAERFGLSDEERNERL 44 (92)
T ss_pred CCCcCHHHHHHHHHHHhCCCHHHHHHHc
Confidence 3789999999999988886655444333
No 58
>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF. The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].
Probab=21.49 E-value=33 Score=25.95 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=22.1
Q ss_pred cceeeEeec-chhhcccccCCCCCceeee
Q 047111 15 ARLVLRRFP-NIEKLRSRESKDDPIELCS 42 (106)
Q Consensus 15 ~~l~~~~~~-~~~~~~~~~~~~~~~kLFG 42 (106)
+...+.-.+ +++++|+-.+|.||-++|+
T Consensus 91 skiIv~aWvNDe~tlR~ygsk~DaY~VF~ 119 (140)
T PF11663_consen 91 SKIIVYAWVNDEQTLRAYGSKTDAYAVFR 119 (140)
T ss_pred cCEEEEEEeCCCcchhhhccCCcHHHHHH
Confidence 344555556 6889999999999999996
No 59
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=21.29 E-value=89 Score=20.94 Aligned_cols=47 Identities=19% Similarity=0.220 Sum_probs=28.9
Q ss_pred HHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCC
Q 047111 6 EKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLP 69 (106)
Q Consensus 6 ~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~ 69 (106)
..|+++|-....-+.-+=|. ++-|.+++++.|+ .+|++++...|..+
T Consensus 20 ~e~l~~L~~~g~~~~~lTNn----------------s~~s~~~~~~~L~-~~Gi~~~~~~i~ts 66 (101)
T PF13344_consen 20 VEALDALRERGKPVVFLTNN----------------SSRSREEYAKKLK-KLGIPVDEDEIITS 66 (101)
T ss_dssp HHHHHHHHHTTSEEEEEES-----------------SSS-HHHHHHHHH-HTTTT--GGGEEEH
T ss_pred HHHHHHHHHcCCCEEEEeCC----------------CCCCHHHHHHHHH-hcCcCCCcCEEECh
Confidence 45666666665444433342 3567899999996 68999999887543
No 60
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=21.25 E-value=13 Score=22.17 Aligned_cols=26 Identities=27% Similarity=0.456 Sum_probs=21.4
Q ss_pred ecCCHHHHHHHHHhhcCCcccccccc
Q 047111 42 SPVTKEELVAKVASQLSISIEPEYLH 67 (106)
Q Consensus 42 GSVTtkdIaeaL~~q~gIeIDKkkI~ 67 (106)
-|+..-+++.++++++|+.++-..+.
T Consensus 30 DSl~~~~l~~~l~~~~g~~i~~~~~~ 55 (67)
T PF00550_consen 30 DSLDAIELVSELEEEFGIKIPPSDLF 55 (67)
T ss_dssp SHHHHHHHHHHHHHHHTSSTTHHHHC
T ss_pred chHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 47788889999999999998877664
No 61
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=21.20 E-value=40 Score=20.66 Aligned_cols=19 Identities=21% Similarity=0.399 Sum_probs=13.5
Q ss_pred CCCceeeecCCHHHHHHHHH
Q 047111 35 DDPIELCSPVTKEELVAKVA 54 (106)
Q Consensus 35 ~~~~kLFGSVTtkdIaeaL~ 54 (106)
.+||.|||- +..+--+-|+
T Consensus 14 gePi~lFGE-~~~~Rr~RL~ 32 (44)
T smart00500 14 GEPITLFGE-DDQERRQRLR 32 (44)
T ss_pred CCCeeecCC-ChHHHHHHHH
Confidence 589999996 5555555555
No 62
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=21.06 E-value=26 Score=21.67 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=20.2
Q ss_pred Cceeee-cCCHHHHHHHHHhhcCCcccc
Q 047111 37 PIELCS-PVTKEELVAKVASQLSISIEP 63 (106)
Q Consensus 37 ~~kLFG-SVTtkdIaeaL~~q~gIeIDK 63 (106)
.+++-| ++|..+|++.|. .+|++++.
T Consensus 11 i~~llG~~i~~~ei~~~L~-~lg~~~~~ 37 (71)
T smart00874 11 INRLLGLDLSAEEIEEILK-RLGFEVEV 37 (71)
T ss_pred HHHHHCCCCCHHHHHHHHH-HCCCeEEe
Confidence 346667 889999999988 67988854
No 63
>cd04632 CBS_pair_19 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=20.94 E-value=1.7e+02 Score=18.80 Aligned_cols=17 Identities=29% Similarity=0.311 Sum_probs=14.3
Q ss_pred ceeeecCCHHHHHHHHH
Q 047111 38 IELCSPVTKEELVAKVA 54 (106)
Q Consensus 38 ~kLFGSVTtkdIaeaL~ 54 (106)
.++.|-||..|+.+++.
T Consensus 34 ~~~~G~it~~dl~~~~~ 50 (128)
T cd04632 34 GKLTGIVTRHDIVDFVV 50 (128)
T ss_pred CcEEEEEEHHHHHHHHh
Confidence 38999999999987764
No 64
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=20.92 E-value=2.5 Score=34.09 Aligned_cols=95 Identities=26% Similarity=0.342 Sum_probs=70.8
Q ss_pred HHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEE
Q 047111 4 EFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMR 83 (106)
Q Consensus 4 ~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~Ik 83 (106)
+++.+.++.=|..||.+.+.+...++.+..++|--.+=|.+|..++ .-+.-+.|++..+..-.+--..++|++.-+
T Consensus 127 ~~~k~~kw~l~~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~~k~e~----~~~~~V~in~~~~vr~~~~v~~~e~d~s~r 202 (222)
T KOG4607|consen 127 VMNKGGKWKLNPNLVKASLRKGVIVAELTIKLDKELVSGPITKEEG----EYICEVKINPDVTVRVKIRVTHNEYDVSKR 202 (222)
T ss_pred eeccCCceeecHHHHHHHHhcceEeccccccCcccccCCCcccccc----eEEEEEEECCcceEEeeeeeeccccChhhc
Confidence 3455566777888888888885566666666666667889998877 335568899988877666778899999999
Q ss_pred ecCCCCCCCCcEEEEEEEEEEe
Q 047111 84 LSKTIPLPEGKVQWTFNVKVHG 105 (106)
Q Consensus 84 Lh~~Vp~p~gkV~~~lkV~V~~ 105 (106)
+..-+| | .+.|-++|+++.
T Consensus 203 ~~~~l~-~--q~e~ll~~~~~~ 221 (222)
T KOG4607|consen 203 FPYTLP-P--QVEWLLKVKSRG 221 (222)
T ss_pred cCCcCc-c--hhHHHhccccCC
Confidence 988876 5 777777777653
No 65
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.76 E-value=33 Score=25.44 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHhhcCCcccccc
Q 047111 44 VTKEELVAKVASQLSISIEPEY 65 (106)
Q Consensus 44 VTtkdIaeaL~~q~gIeIDKkk 65 (106)
.|++.++..|+.++|+.++.+.
T Consensus 81 wTl~~~~~~l~~e~gv~y~~~~ 102 (138)
T COG3415 81 WTLKELVEELGLEFGVWYHASA 102 (138)
T ss_pred chHHHHHHHHhhhcCeEEeHHH
Confidence 9999999999989999999764
No 66
>PF09183 DUF1947: Domain of unknown function (DUF1947); InterPro: IPR015266 Members of this entry are a set of hypothetical archaeal proteins. Their exact function has not, as yet, been defined. ; PDB: 1Q7H_A.
Probab=20.32 E-value=71 Score=21.30 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=14.3
Q ss_pred HHHHHHHHHhhcCCccccccccCCC
Q 047111 46 KEELVAKVASQLSISIEPEYLHLPS 70 (106)
Q Consensus 46 tkdIaeaL~~q~gIeIDKkkI~L~~ 70 (106)
.++|.+.+++.+||+|...+|+...
T Consensus 10 ~k~~~~k~~~~ygIdi~~~~vEI~~ 34 (65)
T PF09183_consen 10 IKEIKEKIKEKYGIDISGEKVEIGK 34 (65)
T ss_dssp HHHHHHHHHT-TT---TT---EEEE
T ss_pred HHHHHHHHHHHhCcCCCccceeeee
Confidence 4678889987799999998887654
No 67
>PLN03138 Protein TOC75; Provisional
Probab=20.04 E-value=58 Score=30.65 Aligned_cols=58 Identities=17% Similarity=0.208 Sum_probs=44.4
Q ss_pred cCCHHHHHHHHHhhcCCccccccccCCC-CCccceeEEEEEEecCCCCCCCCcEEEEEEEE
Q 047111 43 PVTKEELVAKVASQLSISIEPEYLHLPS-PLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVK 102 (106)
Q Consensus 43 SVTtkdIaeaL~~q~gIeIDKkkI~L~~-pIKslGey~V~IkLh~~Vp~p~gkV~~~lkV~ 102 (106)
..+-.+|.+++.-+-|-..++.++.-.. .|.+.|.|. .|+..- .|+|.|.|..++.|.
T Consensus 164 ~~~e~~l~~~i~~kpG~v~trsqLq~dv~~I~~tG~F~-~V~~~v-~~~~dg~v~V~~~i~ 222 (796)
T PLN03138 164 VGTEDSFFEMVTLRPGGVYTKAQLQKELETLASCGMFE-KVDLEG-KTKPDGTLGLTISFT 222 (796)
T ss_pred cchHHHHHHHHhcCCCCccCHHHHHHHHHHHHhcCCce-EEEEEE-EeCCCCeEEEEEEEE
Confidence 5566777777776668888998885544 688999999 888744 578999888877776
Done!