Query 024576
Match_columns 265
No_of_seqs 59 out of 61
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:42:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024576hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01985 CRS1_YhbY: CRS1 / Yhb 99.8 1.6E-18 3.5E-23 131.9 7.2 84 21-104 1-84 (84)
2 KOG1990 Poly(A)-specific exori 99.6 1.2E-15 2.6E-20 149.4 3.0 108 16-123 378-490 (564)
3 TIGR00253 RNA_bind_YhbY putati 99.3 2.3E-11 5E-16 96.4 9.8 86 21-106 1-86 (95)
4 PRK10343 RNA-binding protein Y 99.0 3.5E-09 7.7E-14 84.6 8.7 86 21-106 3-88 (97)
5 COG1534 Predicted RNA-binding 99.0 4.1E-09 9E-14 84.8 9.1 90 21-111 2-91 (97)
6 KOG1990 Poly(A)-specific exori 98.9 5.9E-10 1.3E-14 109.8 3.4 109 6-114 156-271 (564)
7 PF03641 Lysine_decarbox: Poss 66.4 7.3 0.00016 31.7 3.4 41 18-58 61-106 (133)
8 PF03048 Herpes_UL92: UL92 fam 60.8 5.3 0.00012 36.0 1.8 23 39-61 168-190 (192)
9 PRK02714 O-succinylbenzoate sy 54.1 42 0.00091 31.0 6.4 66 23-89 123-191 (320)
10 smart00492 HELICc3 helicase su 48.5 48 0.001 27.5 5.3 56 52-111 4-67 (141)
11 TIGR00730 conserved hypothetic 47.2 22 0.00049 30.8 3.4 61 22-85 109-176 (178)
12 TIGR01444 fkbM_fam methyltrans 42.8 30 0.00064 26.8 3.1 36 60-95 107-142 (143)
13 PLN00410 U5 snRNP protein, DIM 42.0 68 0.0015 27.3 5.4 53 50-107 43-97 (142)
14 PF01188 MR_MLE: Mandelate rac 41.5 50 0.0011 23.7 3.9 35 52-86 2-37 (67)
15 KOG1014 17 beta-hydroxysteroid 39.4 99 0.0022 30.1 6.6 74 16-94 56-132 (312)
16 TIGR03264 met_CoM_red_C methyl 39.3 41 0.00088 30.8 3.8 67 18-89 88-156 (194)
17 PF01755 Glyco_transf_25: Glyc 37.7 30 0.00065 28.6 2.6 41 142-183 65-108 (200)
18 cd03322 rpsA The starvation se 37.5 69 0.0015 30.0 5.2 58 23-87 131-189 (361)
19 PF04591 DUF596: Protein of un 37.2 21 0.00045 28.0 1.4 25 39-63 5-34 (70)
20 PF08800 VirE_N: VirE N-termin 37.1 48 0.001 27.4 3.7 64 25-96 1-64 (136)
21 cd03318 MLE Muconate Lactonizi 36.5 1E+02 0.0022 28.6 6.0 62 24-87 148-214 (365)
22 KOG0469 Elongation factor 2 [T 36.3 51 0.0011 35.0 4.5 50 57-106 481-535 (842)
23 PF01695 IstB_IS21: IstB-like 35.7 44 0.00096 28.4 3.4 46 157-203 104-149 (178)
24 PF08639 SLD3: DNA replication 34.5 45 0.00097 33.3 3.6 46 40-85 100-147 (497)
25 cd03315 MLE_like Muconate lact 33.9 1.5E+02 0.0033 26.1 6.5 63 24-87 91-155 (265)
26 cd03320 OSBS o-Succinylbenzoat 33.5 1.5E+02 0.0032 26.3 6.4 63 24-87 88-153 (263)
27 PRK14017 galactonate dehydrata 33.2 1.2E+02 0.0025 28.6 6.0 63 24-87 130-203 (382)
28 cd03324 rTSbeta_L-fuconate_deh 33.0 1.3E+02 0.0028 29.3 6.4 63 24-87 202-266 (415)
29 cd03326 MR_like_1 Mandelate ra 33.0 1.4E+02 0.0031 28.6 6.6 64 23-87 165-231 (385)
30 TIGR01615 A_thal_3542 uncharac 32.9 19 0.00041 30.9 0.7 37 6-42 66-116 (131)
31 PF13304 AAA_21: AAA domain; P 32.2 25 0.00054 27.1 1.2 39 151-189 244-287 (303)
32 PF15337 Vasculin: Vascular pr 31.4 21 0.00046 29.5 0.7 39 21-60 34-72 (97)
33 PF10968 DUF2770: Protein of u 29.6 33 0.00072 24.0 1.3 15 45-59 2-16 (36)
34 cd03321 mandelate_racemase Man 28.1 1.7E+02 0.0037 27.2 6.1 64 23-87 146-212 (355)
35 cd02068 radical_SAM_B12_BD B12 27.8 2.5E+02 0.0054 21.9 6.2 69 26-99 9-77 (127)
36 PF11830 DUF3350: Domain of un 27.1 77 0.0017 24.1 3.0 24 142-165 22-45 (56)
37 PRK10076 pyruvate formate lyas 26.8 1.1E+02 0.0023 27.2 4.4 49 26-80 60-108 (213)
38 PF00690 Cation_ATPase_N: Cati 26.6 67 0.0015 23.0 2.6 38 16-55 16-54 (69)
39 COG1484 DnaC DNA replication p 25.7 60 0.0013 29.3 2.7 60 144-204 137-209 (254)
40 cd03007 PDI_a_ERp29_N PDIa fam 25.5 1.6E+02 0.0034 24.3 4.8 59 47-105 37-100 (116)
41 PF04407 DUF531: Protein of un 25.0 1.4E+02 0.0031 27.0 4.8 57 21-83 107-163 (173)
42 COG0244 RplJ Ribosomal protein 24.6 39 0.00085 29.3 1.2 31 19-49 31-61 (175)
43 COG1922 WecG Teichoic acid bio 23.2 2.1E+02 0.0046 26.8 5.8 67 28-94 100-167 (253)
44 PF02310 B12-binding: B12 bind 23.0 2.7E+02 0.0059 20.9 5.4 65 26-95 21-86 (121)
45 cd03328 MR_like_3 Mandelate ra 22.8 2.1E+02 0.0046 26.7 5.7 63 24-87 144-208 (352)
46 PRK13695 putative NTPase; Prov 22.5 1E+02 0.0022 25.2 3.2 51 151-204 86-136 (174)
47 cd02067 B12-binding B12 bindin 22.4 3.5E+02 0.0076 20.8 6.0 65 27-96 21-87 (119)
48 TIGR00046 RNA methyltransferas 22.4 72 0.0016 28.4 2.5 25 18-45 193-218 (240)
49 PF09026 CENP-B_dimeris: Centr 22.3 36 0.00077 28.5 0.5 10 250-259 60-69 (101)
50 PRK11145 pflA pyruvate formate 22.3 97 0.0021 26.8 3.2 31 65-96 102-132 (246)
51 COG1062 AdhC Zn-dependent alco 21.8 3.3E+02 0.0072 27.2 7.0 103 50-195 242-355 (366)
52 PF13411 MerR_1: MerR HTH fami 21.7 61 0.0013 22.6 1.5 56 19-80 10-65 (69)
53 PRK02901 O-succinylbenzoate sy 21.6 2.6E+02 0.0056 26.5 6.1 64 22-86 89-160 (327)
54 TIGR01228 hutU urocanate hydra 21.4 40 0.00087 35.0 0.7 74 17-90 266-377 (545)
55 TIGR01290 nifB nitrogenase cof 21.3 2.4E+02 0.0053 27.8 6.0 86 21-109 60-164 (442)
56 PF01175 Urocanase: Urocanase; 20.6 32 0.00069 35.7 -0.1 74 17-90 265-376 (546)
57 KOG3920 Uncharacterized conser 20.5 36 0.00077 31.0 0.1 20 32-51 140-159 (193)
58 PRK11713 16S ribosomal RNA met 20.2 86 0.0019 27.7 2.5 25 18-45 186-211 (234)
59 PRK15129 L-Ala-D/L-Glu epimera 20.0 2.3E+02 0.0049 26.1 5.3 62 23-87 134-196 (321)
No 1
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.76 E-value=1.6e-18 Score=131.91 Aligned_cols=84 Identities=27% Similarity=0.439 Sum_probs=75.6
Q ss_pred CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEeecCcEE
Q 024576 21 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 100 (265)
Q Consensus 21 LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd~e~I 100 (265)
||.+|++.||+.+.+|+|++.+||||++.+++++|+++|+.+|||||-|.+....|.+.++..|.+.++|.+|.+.|..+
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEe
Q 024576 101 LMWR 104 (265)
Q Consensus 101 ImwR 104 (265)
|+||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 2
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.56 E-value=1.2e-15 Score=149.41 Aligned_cols=108 Identities=24% Similarity=0.334 Sum_probs=102.8
Q ss_pred cCCCCCCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCc-chHHHHHHHhhhccCeEEEe
Q 024576 16 EAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHA-SDYKKLGAKLKELVPCVLLS 94 (265)
Q Consensus 16 ~~pEGLT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~-sD~kKiG~kLkdLvpciLls 94 (265)
..||.+|.+|..++++.|..+..++.+||+|+|.|++.|||.||+++|+|+++|+..+. +..+..|..+..++++++++
T Consensus 378 ~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~ 457 (564)
T KOG1990|consen 378 YDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVS 457 (564)
T ss_pred cchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceee
Confidence 44699999999999999999999999999999999999999999999999999998888 99999999999999999999
Q ss_pred ec----CcEEEEEecCCCCCCCCCCCCCCCccc
Q 024576 95 FD----DEQILMWRGKDWKSMYPEPPSFSNPVD 123 (265)
Q Consensus 95 fd----~e~IImwRGKdyk~~~~~~p~~ll~k~ 123 (265)
++ +++|++|||++|.++...+|.+.+++.
T Consensus 458 ~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~ 490 (564)
T KOG1990|consen 458 IDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRR 490 (564)
T ss_pred eccCCchhhHHHhhhhhccCCcccCchhhhccc
Confidence 97 788999999999999999999998654
No 3
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.29 E-value=2.3e-11 Score=96.43 Aligned_cols=86 Identities=22% Similarity=0.348 Sum_probs=83.5
Q ss_pred CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEeecCcEE
Q 024576 21 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 100 (265)
Q Consensus 21 LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd~e~I 100 (265)
||-.++..||..|.+|+|.+-.||||+-.++++.+.+|++.+|||||-.-+-...|.+.++..|...++|.+|..-|..+
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~ 80 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence 78899999999999999999999999999999999999999999999999888899999999999999999999999999
Q ss_pred EEEecC
Q 024576 101 LMWRGK 106 (265)
Q Consensus 101 ImwRGK 106 (265)
|+||..
T Consensus 81 vlYR~~ 86 (95)
T TIGR00253 81 VLYRPT 86 (95)
T ss_pred EEEecC
Confidence 999985
No 4
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=98.96 E-value=3.5e-09 Score=84.60 Aligned_cols=86 Identities=15% Similarity=0.256 Sum_probs=83.4
Q ss_pred CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEeecCcEE
Q 024576 21 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 100 (265)
Q Consensus 21 LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd~e~I 100 (265)
||..++..||..+-+++|++..|+||+=.+++..+.+|.+.+||+||-.-+....|-+.++..|...++|-+|..-|..+
T Consensus 3 Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~ 82 (97)
T PRK10343 3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTL 82 (97)
T ss_pred CCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEE
Confidence 89999999999999999999999999999999999999999999999999888899999999999999999999999999
Q ss_pred EEEecC
Q 024576 101 LMWRGK 106 (265)
Q Consensus 101 ImwRGK 106 (265)
|+||=.
T Consensus 83 vlYR~~ 88 (97)
T PRK10343 83 VLYRPT 88 (97)
T ss_pred EEEecC
Confidence 999965
No 5
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=98.96 E-value=4.1e-09 Score=84.82 Aligned_cols=90 Identities=24% Similarity=0.381 Sum_probs=85.6
Q ss_pred CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEeecCcEE
Q 024576 21 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI 100 (265)
Q Consensus 21 LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd~e~I 100 (265)
||-++...||.+..++.|++-.|+||+=.++++.+..+.+.+|||||-.-+-...|-+.++.+|-+.++|-||.+-|..+
T Consensus 2 Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~ 81 (97)
T COG1534 2 LTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTL 81 (97)
T ss_pred CcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEE
Confidence 78899999999999999999999999999999999999999999999999889999999999999999999999999999
Q ss_pred EEEecCCCCCC
Q 024576 101 LMWRGKDWKSM 111 (265)
Q Consensus 101 ImwRGKdyk~~ 111 (265)
|+|| .+|...
T Consensus 82 vlyr-~~~e~~ 91 (97)
T COG1534 82 VLYR-ESKEKR 91 (97)
T ss_pred EEEe-cCcccc
Confidence 9999 555543
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.91 E-value=5.9e-10 Score=109.78 Aligned_cols=109 Identities=26% Similarity=0.326 Sum_probs=102.7
Q ss_pred CCCCcccccccCCCC----CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEecc-CCCcchHHHH
Q 024576 6 AAPVYPKLIQEAPEG----LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKL 80 (265)
Q Consensus 6 ~~PvYprli~~~pEG----LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKi 80 (265)
.-|.|-++.+.+|-| ||..|.+.+|+.|..+|||+.+|+++...+++..|+.+|+.++..|+.|+ |+.....+.+
T Consensus 156 ~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~ 235 (564)
T KOG1990|consen 156 KIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERM 235 (564)
T ss_pred hhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccch
Confidence 457888899998888 99999999999999999999999999999999999999999999999999 9999999999
Q ss_pred HHHh--hhccCeEEEeecCcEEEEEecCCCCCCCCC
Q 024576 81 GAKL--KELVPCVLLSFDDEQILMWRGKDWKSMYPE 114 (265)
Q Consensus 81 G~kL--kdLvpciLlsfd~e~IImwRGKdyk~~~~~ 114 (265)
|..| +.++|++||+..+..++|||||+|..+.+.
T Consensus 236 a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~~lp~ 271 (564)
T KOG1990|consen 236 ADELQELLLTGKVLVLHNKLLDVMYRYKNFLSPLPS 271 (564)
T ss_pred HHHHHHHHhcCCeEEeeccceeeeeehhhcccccch
Confidence 9999 999999999999999999999999995543
No 7
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=66.40 E-value=7.3 Score=31.68 Aligned_cols=41 Identities=27% Similarity=0.350 Sum_probs=32.3
Q ss_pred CCCC-CHHHH---HHHHHcCcCcc-cccccccccchhhHHHHHHHH
Q 024576 18 PEGL-TKHEA---DELRRKGKSLL-PICKLAKNGVYLTLVRDVRNA 58 (265)
Q Consensus 18 pEGL-T~EE~---~emRk~Gl~l~-~~~kLgRNGVY~glV~~Vr~a 58 (265)
|-|+ |.+|. .++.+.|+.-+ |+..++.+|.|..+++.++..
T Consensus 61 PGG~GTl~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~ 106 (133)
T PF03641_consen 61 PGGIGTLDELFEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRM 106 (133)
T ss_dssp S-SHHHHHHHHHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHH
T ss_pred ecCCchHHHHHHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHH
Confidence 4443 55654 55699999999 999999999999999988543
No 8
>PF03048 Herpes_UL92: UL92 family; InterPro: IPR004289 Members of this family are functionally uncharacterised proteins from herpesviruses. The N terminus of these proteins contain 6 conserved cysteines and histidines that might form a zinc binding domain.
Probab=60.80 E-value=5.3 Score=36.04 Aligned_cols=23 Identities=17% Similarity=0.429 Sum_probs=21.0
Q ss_pred ccccccccchhhHHHHHHHHhcc
Q 024576 39 ICKLAKNGVYLTLVRDVRNAFEG 61 (265)
Q Consensus 39 ~~kLgRNGVY~glV~~Vr~afe~ 61 (265)
++|-.||..|++++++||.+|-.
T Consensus 168 lfKctrnKk~D~i~K~mR~~wm~ 190 (192)
T PF03048_consen 168 LFKCTRNKKYDSILKRMREEWMS 190 (192)
T ss_pred EEEEeccchHHHHHHHHHHHHhh
Confidence 68899999999999999999953
No 9
>PRK02714 O-succinylbenzoate synthase; Provisional
Probab=54.06 E-value=42 Score=30.98 Aligned_cols=66 Identities=9% Similarity=0.190 Sum_probs=49.6
Q ss_pred HHHHHHHHHcCcCcccccccccccch--hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhccC
Q 024576 23 KHEADELRRKGKSLLPICKLAKNGVY--LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKELVP 89 (265)
Q Consensus 23 ~EE~~emRk~Gl~l~~~~kLgRNGVY--~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdLvp 89 (265)
.+++..++..|.+.-- +|+|.+..- ...|+.||+++...--.+||+. +.+..+..+++..|+++.+
T Consensus 123 ~~~a~~~~~~G~~~~K-vKvG~~~~~~d~~~v~air~~~g~~~~l~vDaN~~w~~~~A~~~~~~l~~l~~ 191 (320)
T PRK02714 123 LQQWQTLWQQGYRTFK-WKIGVDPLEQELKIFEQLLERLPAGAKLRLDANGGLSLEEAKRWLQLCDRRLS 191 (320)
T ss_pred HHHHHHHHHcCCCEEE-EEECCCChHHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhhccC
Confidence 3577778888864322 256766544 3568999999987888999997 7899999999999998633
No 10
>smart00492 HELICc3 helicase superfamily c-terminal domain.
Probab=48.48 E-value=48 Score=27.51 Aligned_cols=56 Identities=16% Similarity=0.224 Sum_probs=43.0
Q ss_pred HHHHHHHhccCce-------EEEeccCCCcchHHHHHHHhhhccC-eEEEeecCcEEEEEecCCCCCC
Q 024576 52 VRDVRNAFEGSSL-------VKVNCKGMHASDYKKLGAKLKELVP-CVLLSFDDEQILMWRGKDWKSM 111 (265)
Q Consensus 52 V~~Vr~afe~~EL-------VKIdCkg~~~sD~kKiG~kLkdLvp-ciLlsfd~e~IImwRGKdyk~~ 111 (265)
.+.|..+|+.... -.|-+++.+.++..++-.+.+.... +||++..+ +|.|=|+...
T Consensus 4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~----~~EGiD~~g~ 67 (141)
T smart00492 4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATAR----FSEGVDFPGD 67 (141)
T ss_pred HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccc----eecceecCCC
Confidence 4667778777554 5788888887777888888887654 89998877 8999988764
No 11
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=47.19 E-value=22 Score=30.78 Aligned_cols=61 Identities=23% Similarity=0.176 Sum_probs=40.1
Q ss_pred CHHHH---HHHHHcCcCcccccccccccchhhHHHHHHH----HhccCceEEEeccCCCcchHHHHHHHhh
Q 024576 22 TKHEA---DELRRKGKSLLPICKLAKNGVYLTLVRDVRN----AFEGSSLVKVNCKGMHASDYKKLGAKLK 85 (265)
Q Consensus 22 T~EE~---~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~----afe~~ELVKIdCkg~~~sD~kKiG~kLk 85 (265)
|.||. .+++++|++-+|+..++-+|.|..+++.++. .|-..+..++.+- ..|.+.+..+|+
T Consensus 109 TL~El~e~~~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~~gfi~~~~~~~~~~---~d~~~e~~~~i~ 176 (178)
T TIGR00730 109 TLEELFEVLTWAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQEGFISESHLKLIHV---VSRPDELIEQVQ 176 (178)
T ss_pred hHHHHHHHHHHHHcCCCCCCEEEECCcchHHHHHHHHHHHHHCCCCCHHHcCcEEE---cCCHHHHHHHHH
Confidence 66665 5678999999999999999999999986553 3333333333222 234555555554
No 12
>TIGR01444 fkbM_fam methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548.
Probab=42.80 E-value=30 Score=26.81 Aligned_cols=36 Identities=17% Similarity=0.292 Sum_probs=30.6
Q ss_pred ccCceEEEeccCCCcchHHHHHHHhhhccCeEEEee
Q 024576 60 EGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSF 95 (265)
Q Consensus 60 e~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsf 95 (265)
..-.++||||.|....=.+.+...|+.-+|.|++-+
T Consensus 107 ~~i~~lKiDiEG~E~~vL~g~~~~l~~~~~~i~~E~ 142 (143)
T TIGR01444 107 DKVDLLKIDVEGAELEVLRGAKETLLRKRPGIVLEV 142 (143)
T ss_pred CCCCEEEEeCCCchHHHHhChHHHHHHhCCeEEEEe
Confidence 456899999999998888888888888899888765
No 13
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=41.95 E-value=68 Score=27.32 Aligned_cols=53 Identities=13% Similarity=0.320 Sum_probs=38.3
Q ss_pred hHHHHHHHHhcc-CceEEEeccCCCcchHHHHHHHhhhccCeEEE-eecCcEEEEEecCC
Q 024576 50 TLVRDVRNAFEG-SSLVKVNCKGMHASDYKKLGAKLKELVPCVLL-SFDDEQILMWRGKD 107 (265)
Q Consensus 50 glV~~Vr~afe~-~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLl-sfd~e~IImwRGKd 107 (265)
-+++.+-+.+.. ..++|||+.. ...++.+++=-.++.++ -|.+.++.+|||.-
T Consensus 43 p~l~~la~~~~~~~~~~kVDVDe-----~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG 97 (142)
T PLN00410 43 EVLASVAETIKNFAVIYLVDITE-----VPDFNTMYELYDPCTVMFFFRNKHIMIDLGTG 97 (142)
T ss_pred HHHHHHHHHcCCceEEEEEECCC-----CHHHHHHcCccCCCcEEEEEECCeEEEEEecc
Confidence 355566666655 7779999885 34788888766466555 88888999999954
No 14
>PF01188 MR_MLE: Mandelate racemase / muconate lactonizing enzyme, C-terminal domain; InterPro: IPR013342 Mandelate racemase 5.1.2.2 from EC (MR) and muconate lactonising enzyme 5.5.1.1 from EC (MLE) are two bacterial enzymes involved in aromatic acid catabolism. They catalyse mechanistically distinct reactions yet they are related at the level of their primary, quaternary (homooctamer) and tertiary structures [, ]. A number of other proteins also seem to be evolutionary related to these two enzymes. These include, various plasmid-encoded chloromuconate cycloisomerases 5.5.1.7 from EC, Escherichia coli protein rspA [], E. coli bifunctional DGOA protein, E. coli hypothetical proteins ycjG, yfaW and yidU and a hypothetical protein from Streptomyces ambofaciens []. This entry represents the C-terminal region of these proteins.; PDB: 3QLD_B 3CYJ_C 2QDD_B 3FVD_A 3H7V_A 2OZT_A 3NXL_A 1JDF_D 1JCT_B 1EC9_C ....
Probab=41.45 E-value=50 Score=23.66 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=30.2
Q ss_pred HHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhh
Q 024576 52 VRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKE 86 (265)
Q Consensus 52 V~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkd 86 (265)
|+.||+++...--+.+||- +.+..+..+++..|++
T Consensus 2 i~avr~~~g~~~~l~vDan~~~~~~~a~~~~~~l~~ 37 (67)
T PF01188_consen 2 IRAVREAVGPDIDLMVDANQAWTLEEAIRLARALED 37 (67)
T ss_dssp HHHHHHHHSTTSEEEEE-TTBBSHHHHHHHHHHHGG
T ss_pred HHHHHHhhCCCCeEEEECCCCCCHHHHHHHHHHcCh
Confidence 6889999877777999999 7888899999999998
No 15
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=39.43 E-value=99 Score=30.05 Aligned_cols=74 Identities=19% Similarity=0.359 Sum_probs=58.7
Q ss_pred cCCCCCCHHHHHHHHHcCcCcccccccccc-cchhhHHHHHHHHhccCc--eEEEeccCCCcchHHHHHHHhhhccCeEE
Q 024576 16 EAPEGLTKHEADELRRKGKSLLPICKLAKN-GVYLTLVRDVRNAFEGSS--LVKVNCKGMHASDYKKLGAKLKELVPCVL 92 (265)
Q Consensus 16 ~~pEGLT~EE~~emRk~Gl~l~~~~kLgRN-GVY~glV~~Vr~afe~~E--LVKIdCkg~~~sD~kKiG~kLkdLvpciL 92 (265)
-+-+|+=.+=+.+|-|+|++ +..++|+ .....+.+.+-+-.+ +| ...+||..-+ .+|++|=.+|..+-=|||
T Consensus 56 GaTDGIGKayA~eLAkrG~n---vvLIsRt~~KL~~v~kEI~~~~~-vev~~i~~Dft~~~-~~ye~i~~~l~~~~VgIL 130 (312)
T KOG1014|consen 56 GATDGIGKAYARELAKRGFN---VVLISRTQEKLEAVAKEIEEKYK-VEVRIIAIDFTKGD-EVYEKLLEKLAGLDVGIL 130 (312)
T ss_pred CCCCcchHHHHHHHHHcCCE---EEEEeCCHHHHHHHHHHHHHHhC-cEEEEEEEecCCCc-hhHHHHHHHhcCCceEEE
Confidence 34578999999999999999 7788998 577778778777777 44 4566776533 389999999999988988
Q ss_pred Ee
Q 024576 93 LS 94 (265)
Q Consensus 93 ls 94 (265)
|-
T Consensus 131 VN 132 (312)
T KOG1014|consen 131 VN 132 (312)
T ss_pred Ee
Confidence 84
No 16
>TIGR03264 met_CoM_red_C methyl-coenzyme M reductase I operon protein C. has several modified sites, so accessory proteins are expected. Several methanogens have encode two such enzymes, designated I and II; this protein occurs only operons of type I. The precise function is unknown.
Probab=39.26 E-value=41 Score=30.85 Aligned_cols=67 Identities=22% Similarity=0.452 Sum_probs=51.1
Q ss_pred CCCCCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEE-ecc-CCCcchHHHHHHHhhhccC
Q 024576 18 PEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKV-NCK-GMHASDYKKLGAKLKELVP 89 (265)
Q Consensus 18 pEGLT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKI-dCk-g~~~sD~kKiG~kLkdLvp 89 (265)
.-|||++|...+-+. =.+++.|| ++=..++..+|..|+++++=-| .|+ -++.+|..|+|.|-+..-|
T Consensus 88 ~fgl~~~E~~qI~~H---klAV~h~G--Nvk~hIi~K~r~ilr~vdIP~IiVcq~PvdfEdfak~GvkT~~vmp 156 (194)
T TIGR03264 88 TFGLTPEEIEQINRH---KLAVIHLG--NVKSHIIYKARLILKHVDIPAIIVCQAPVDFEDFAKIGVKTRAVMP 156 (194)
T ss_pred ccCCCHHHHHHHhhc---CEEEEEeC--CHHHHHHHHHHHHHhcCCCCEEEEeCCCcCHHHHHHhCcceeeccC
Confidence 357999998776554 44555554 3457788899999999998555 888 7899999999999887433
No 17
>PF01755 Glyco_transf_25: Glycosyltransferase family 25 (LPS biosynthesis protein); InterPro: IPR002654 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 25 GT25 from CAZY comprises enzymes with only one known activity; as a lipopolysaccharide biosynthesis protein. These enzymes catalyse the transfer of various sugars onto the growing lipopolysaccharide chain during its biosynthesis [].; GO: 0009103 lipopolysaccharide biosynthetic process
Probab=37.70 E-value=30 Score=28.59 Aligned_cols=41 Identities=32% Similarity=0.552 Sum_probs=27.0
Q ss_pred ccccccchhHHHHHHHHHhhc--cccccccC-CCCchhHHHhhhh
Q 024576 142 QGTIRSSPKMISLWKRAIEST--KALVLDEI-NLGPDDLLKKVEE 183 (265)
Q Consensus 142 ~~~~~~~pkm~~lw~~aiess--~al~ld~~-~l~pd~ll~~vee 183 (265)
++.+--+--=+++|+++++++ -||+|+|. -+.++ +.+.+++
T Consensus 65 ~gEiGC~lSH~~~w~~~v~~~~~~~lIlEDDv~~~~~-f~~~l~~ 108 (200)
T PF01755_consen 65 PGEIGCALSHIKAWQRIVDSGLEYALILEDDVIFDPD-FKEFLEE 108 (200)
T ss_pred cceEeehhhHHHHHHHHHHcCCCeEEEEecccccccc-HHHHHHH
Confidence 333444455689999999999 78888765 55554 4444443
No 18
>cd03322 rpsA The starvation sensing protein RpsA from E.coli and its homologs are lactonizing enzymes whose putative targets are homoserine lactone (HSL)-derivative. They are part of the mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subfamily share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and catalytic residues, a partially conserved Lys-X-Lys motif and a conserved histidine-aspartate dyad.
Probab=37.45 E-value=69 Score=29.97 Aligned_cols=58 Identities=12% Similarity=0.200 Sum_probs=43.1
Q ss_pred HHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 23 KHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 23 ~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
.+++..++.+|.+.--+ |+ ...|+.+|+++...--++||+. +.+..+..+++..|+++
T Consensus 131 ~~~a~~~~~~Gf~~~Ki-Kv------~~~v~avre~~G~~~~l~vDaN~~w~~~~A~~~~~~l~~~ 189 (361)
T cd03322 131 LEAVERHLAQGYRAIRV-QL------PKLFEAVREKFGFEFHLLHDVHHRLTPNQAARFGKDVEPY 189 (361)
T ss_pred HHHHHHHHHcCCCeEee-CH------HHHHHHHHhccCCCceEEEECCCCCCHHHHHHHHHHhhhc
Confidence 35666777888552211 11 6779999999977666899998 48889999999999874
No 19
>PF04591 DUF596: Protein of unknown function, DUF596; InterPro: IPR007670 This family contains several uncharacterised proteins.; PDB: 2O5H_B.
Probab=37.17 E-value=21 Score=27.96 Aligned_cols=25 Identities=36% Similarity=0.518 Sum_probs=18.0
Q ss_pred ccccccccchhh-----HHHHHHHHhccCc
Q 024576 39 ICKLAKNGVYLT-----LVRDVRNAFEGSS 63 (265)
Q Consensus 39 ~~kLgRNGVY~g-----lV~~Vr~afe~~E 63 (265)
.+||+|||.|.. +|++.|.+|-.++
T Consensus 5 ~lKLa~~g~fl~Gt~eEqve~fr~~fP~sd 34 (70)
T PF04591_consen 5 KLKLARKGEFLEGTTEEQVEMFRKSFPASD 34 (70)
T ss_dssp SEEEEETTEEE---HHHHHHHHHHH--SSS
T ss_pred eEEeccCCEEecCCHHHHHHHHHHHCCCCh
Confidence 479999999963 7888899997643
No 20
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=37.15 E-value=48 Score=27.41 Aligned_cols=64 Identities=27% Similarity=0.309 Sum_probs=45.7
Q ss_pred HHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEeec
Q 024576 25 EADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFD 96 (265)
Q Consensus 25 E~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd 96 (265)
|+.+++++ ||.++. .|+|.+ -.+-...-.++-||=||..++..++...+=.+|. .-|.++++|-
T Consensus 1 ea~~~K~~---LP~vt~---~g~F~~-~r~~~~l~~~sglv~lDiD~l~~ee~~~~r~~l~-~~p~t~~~f~ 64 (136)
T PF08800_consen 1 EAKELKKK---LPYVTP---SGTFSG-GRNADNLKAYSGLVVLDIDHLDPEEAEELRQLLF-EDPYTLAAFV 64 (136)
T ss_pred ChhHHHhc---CCEEEE---EEEECC-CcchhhhhhCCCcEEEEeCCCCHHHHHHHHHHHh-cCCcEEEEEE
Confidence 34555544 666654 455655 4444555678999999999999888888888776 5788888885
No 21
>cd03318 MLE Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates. Some bacterial species are also capable of dehalogenating chloroaromatic compounds by the action of chloromuconate lactonizing enzymes (Cl-MLEs). MLEs are members of the enolase superfamily characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilized by coordination to the essential Mg2+ ion.
Probab=36.53 E-value=1e+02 Score=28.59 Aligned_cols=62 Identities=19% Similarity=0.239 Sum_probs=45.5
Q ss_pred HHHHHHHHcC-cC-cccccccccccc--hhhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 24 HEADELRRKG-KS-LLPICKLAKNGV--YLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 24 EE~~emRk~G-l~-l~~~~kLgRNGV--Y~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
+++.+++..| .+ +| +|.|+++. ....|+.||+++...--++|||. +.+..+..+++..|+++
T Consensus 148 ~~~~~~~~~G~f~~~K--iKvg~~~~~~d~~~v~avr~~~g~~~~l~iDaN~~~~~~~A~~~~~~l~~~ 214 (365)
T cd03318 148 AEAEEMLEAGRHRRFK--LKMGARPPADDLAHVEAIAKALGDRASVRVDVNQAWDESTAIRALPRLEAA 214 (365)
T ss_pred HHHHHHHhCCCceEEE--EEeCCCChHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHhc
Confidence 3456677888 22 11 23466542 45778999999987777899998 68999999999999875
No 22
>KOG0469 consensus Elongation factor 2 [Translation, ribosomal structure and biogenesis]
Probab=36.35 E-value=51 Score=35.03 Aligned_cols=50 Identities=30% Similarity=0.398 Sum_probs=45.0
Q ss_pred HHhccCceEEEeccCCCcchHHHHHHHhhhcc---CeEEEeec--CcEEEEEecC
Q 024576 57 NAFEGSSLVKVNCKGMHASDYKKLGAKLKELV---PCVLLSFD--DEQILMWRGK 106 (265)
Q Consensus 57 ~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLv---pciLlsfd--~e~IImwRGK 106 (265)
.-|-.+.+||+++.-.++.|.-|+-+-|+.|. ||++.-++ ||+||-=-|.
T Consensus 481 MKFSVSPVV~VAVe~Knp~DLpKLvEGLkrLakSDP~v~~~~~esGehiiAgaGe 535 (842)
T KOG0469|consen 481 MKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGE 535 (842)
T ss_pred EEeeccceEEEEEecCChhhhHHHHHHHHHHhccCCeEEEEeccCCceEEeccch
Confidence 35889999999999999999999999999885 99999996 9999988773
No 23
>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.
Probab=35.74 E-value=44 Score=28.39 Aligned_cols=46 Identities=22% Similarity=0.337 Sum_probs=32.5
Q ss_pred HHHhhccccccccCCCCchhHHHhhhhhhhhhhhhhcccCeEEeecC
Q 024576 157 RAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRE 203 (265)
Q Consensus 157 ~aiess~al~ld~~~l~pd~ll~~veef~~~sqa~ehs~pa~~~s~~ 203 (265)
+.+.....|+|||+|..+-.=-..--=|+.+.+-.++. |-++.||-
T Consensus 104 ~~l~~~dlLilDDlG~~~~~~~~~~~l~~ii~~R~~~~-~tIiTSN~ 149 (178)
T PF01695_consen 104 KRLKRVDLLILDDLGYEPLSEWEAELLFEIIDERYERK-PTIITSNL 149 (178)
T ss_dssp HHHHTSSCEEEETCTSS---HHHHHCTHHHHHHHHHT--EEEEEESS
T ss_pred CccccccEecccccceeeecccccccchhhhhHhhccc-CeEeeCCC
Confidence 45677899999999987744333444588999999986 88888874
No 24
>PF08639 SLD3: DNA replication regulator SLD3; InterPro: IPR013948 The SLD3 DNA replication regulator is required for loading and maintenance of Cdc45 on chromatin during DNA replication [].
Probab=34.46 E-value=45 Score=33.25 Aligned_cols=46 Identities=26% Similarity=0.309 Sum_probs=35.1
Q ss_pred cccccccchhhHHHHHHHHhccCceEEEeccCCCc--chHHHHHHHhh
Q 024576 40 CKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHA--SDYKKLGAKLK 85 (265)
Q Consensus 40 ~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~--sD~kKiG~kLk 85 (265)
.+||+||.|.+-.+.|+.-|....+-.=.+.+... ...+++..-||
T Consensus 100 ~klgkngly~~E~~~i~kww~~~~~~~~~~~~~~~~~~~~k~~i~~Lk 147 (497)
T PF08639_consen 100 MKLGKNGLYPEEEEFIRKWWKSNSPNDNSGEAEESDDEEIKRLISDLK 147 (497)
T ss_pred hhccccCCCCchHHHHHHhhccCCccccccccccchHHHHHHHHHHHH
Confidence 89999999999999999999999888777764322 34555554443
No 25
>cd03315 MLE_like Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions.
Probab=33.94 E-value=1.5e+02 Score=26.11 Aligned_cols=63 Identities=17% Similarity=0.257 Sum_probs=44.2
Q ss_pred HHHHHHHHcCcCcccccccccccch-hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 24 HEADELRRKGKSLLPICKLAKNGVY-LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 24 EE~~emRk~Gl~l~~~~kLgRNGVY-~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
+++..++..|.+--- +|+|++.-. ...|+.||+++-..--+++||. +.+..+..+++..|+++
T Consensus 91 ~~~~~~~~~G~~~~K-iKvg~~~~~d~~~v~~vr~~~g~~~~l~vDan~~~~~~~a~~~~~~l~~~ 155 (265)
T cd03315 91 EEARRALEAGFRTFK-LKVGRDPARDVAVVAALREAVGDDAELRVDANRGWTPKQAIRALRALEDL 155 (265)
T ss_pred HHHHHHHHCCCCEEE-EecCCCHHHHHHHHHHHHHhcCCCCEEEEeCCCCcCHHHHHHHHHHHHhc
Confidence 356667778853211 134543212 4678899999876668899998 68889999999999874
No 26
>cd03320 OSBS o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway. Menaquinone is an essential cofactor for anaerobic growth in eubacteria and some archaea. OSBS belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=33.50 E-value=1.5e+02 Score=26.35 Aligned_cols=63 Identities=16% Similarity=0.185 Sum_probs=46.4
Q ss_pred HHHHHHHHcCcCcccccccccccch--hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 24 HEADELRRKGKSLLPICKLAKNGVY--LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 24 EE~~emRk~Gl~l~~~~kLgRNGVY--~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
+++..++..|.+--- +|+|++..- ...|+.||+++...--+++|+. +.+..+..+++..|+++
T Consensus 88 ~~~~~~~~~Gf~~~K-iKvg~~~~~~d~~~v~~vr~~~g~~~~l~vDaN~~w~~~~A~~~~~~l~~~ 153 (263)
T cd03320 88 GEAKAAYGGGYRTVK-LKVGATSFEEDLARLRALREALPADAKLRLDANGGWSLEEALAFLEALAAG 153 (263)
T ss_pred HHHHHHHhCCCCEEE-EEECCCChHHHHHHHHHHHHHcCCCCeEEEeCCCCCCHHHHHHHHHhhccc
Confidence 566666777854222 356766533 4679999999987778899998 58889999999998873
No 27
>PRK14017 galactonate dehydratase; Provisional
Probab=33.19 E-value=1.2e+02 Score=28.65 Aligned_cols=63 Identities=17% Similarity=0.146 Sum_probs=44.2
Q ss_pred HHHHHHHHcCcCcccccccc-cccch---------hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 24 HEADELRRKGKSLLPICKLA-KNGVY---------LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 24 EE~~emRk~Gl~l~~~~kLg-RNGVY---------~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
+++.+++.+|.+.-=+ |.+ +.+++ ...|+.||+++...--+++||. +.+..+..+++..|+++
T Consensus 130 ~~a~~~~~~Gf~~~Ki-Kv~~~~~~~~~~~~~~~d~~~i~avr~~~g~~~~l~vDaN~~w~~~~A~~~~~~l~~~ 203 (382)
T PRK14017 130 EAARARVERGFTAVKM-NGTEELQYIDSPRKVDAAVARVAAVREAVGPEIGIGVDFHGRVHKPMAKVLAKELEPY 203 (382)
T ss_pred HHHHHHHHcCCCEEEE-cCcCCccccccHHHHHHHHHHHHHHHHHhCCCCeEEEECCCCCCHHHHHHHHHhhccc
Confidence 4667788888543222 222 33332 3568889999977667899998 58889999999999863
No 28
>cd03324 rTSbeta_L-fuconate_dehydratase Human rTS beta is encoded by the rTS gene which, through alternative RNA splicing, also encodes rTS alpha whose mRNA is complementary to thymidylate synthase mRNA. rTS beta expression is associated with the production of small molecules that appear to mediate the down-regulation of thymidylate synthase protein by a novel intercellular signaling mechanism. A member of this family, from Xanthomonas, has been characterized to be a L-fuconate dehydratase. rTS beta belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=33.02 E-value=1.3e+02 Score=29.27 Aligned_cols=63 Identities=11% Similarity=0.095 Sum_probs=46.4
Q ss_pred HHHHHHHHcCcCcccccccccccch-hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 24 HEADELRRKGKSLLPICKLAKNGVY-LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 24 EE~~emRk~Gl~l~~~~kLgRNGVY-~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
+++..++..|.+--- +|+|+.--. ...|+.||+++...--+.||+. +.+..+..++++.|+++
T Consensus 202 ~~a~~~~~~Gf~~~K-iKvg~~~~~d~~~v~avRe~vG~~~~L~vDaN~~w~~~~A~~~~~~L~~~ 266 (415)
T cd03324 202 RLCKEALAQGFTHFK-LKVGADLEDDIRRCRLAREVIGPDNKLMIDANQRWDVPEAIEWVKQLAEF 266 (415)
T ss_pred HHHHHHHHcCCCEEE-EeCCCCHHHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhcc
Confidence 466777788876322 245542111 3678889999988888999997 68999999999999875
No 29
>cd03326 MR_like_1 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown.
Probab=32.99 E-value=1.4e+02 Score=28.60 Aligned_cols=64 Identities=11% Similarity=0.178 Sum_probs=47.2
Q ss_pred HHHHHHHHHcCcCcccccccccccch--hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 23 KHEADELRRKGKSLLPICKLAKNGVY--LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 23 ~EE~~emRk~Gl~l~~~~kLgRNGVY--~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
.+++..++..|.+---+ |+|++..= ...|+.||+++...--+.|||. +.+..+..+++..|+++
T Consensus 165 ~~~a~~~~~~Gf~~~Ki-kvg~~~~~~di~~v~avRe~~G~~~~l~vDaN~~w~~~~A~~~~~~l~~~ 231 (385)
T cd03326 165 RDEMRRYLDRGYTVVKI-KIGGAPLDEDLRRIEAALDVLGDGARLAVDANGRFDLETAIAYAKALAPY 231 (385)
T ss_pred HHHHHHHHHCCCCEEEE-eCCCCCHHHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhCc
Confidence 35667778888653222 45654433 4678889999877777899997 68899999999999875
No 30
>TIGR01615 A_thal_3542 uncharacterized plant-specific domain TIGR01615. of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=32.91 E-value=19 Score=30.90 Aligned_cols=37 Identities=27% Similarity=0.450 Sum_probs=29.4
Q ss_pred CCCCcccccccCCCC--------------CCHHHHHHHHHcCcCccccccc
Q 024576 6 AAPVYPKLIQEAPEG--------------LTKHEADELRRKGKSLLPICKL 42 (265)
Q Consensus 6 ~~PvYprli~~~pEG--------------LT~EE~~emRk~Gl~l~~~~kL 42 (265)
+++.|-++++.+|+- +.+.=..-||++|++|||-=+.
T Consensus 66 pt~~Y~~ll~~LP~vFVG~~~rL~~iV~~mc~Aak~Slk~~gmhlPPWRk~ 116 (131)
T TIGR01615 66 PTEEYKRLLESLPEVFVGTTERLRQLVRLMCDAAKKSLKKKGMPLPPWRKN 116 (131)
T ss_pred CCHHHHHHHHhCCcceECCHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCch
Confidence 456699999999986 4556667899999999997553
No 31
>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A.
Probab=32.23 E-value=25 Score=27.07 Aligned_cols=39 Identities=26% Similarity=0.364 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhc---cccccccC--CCCchhHHHhhhhhhhhhh
Q 024576 151 MISLWKRAIEST---KALVLDEI--NLGPDDLLKKVEEFEGISQ 189 (265)
Q Consensus 151 m~~lw~~aiess---~al~ld~~--~l~pd~ll~~veef~~~sq 189 (265)
++.+....+... ..+++||. +|-|...-+-++-|..+++
T Consensus 244 ~l~l~~~l~~~~~~~~illiDEpE~~LHp~~q~~l~~~l~~~~~ 287 (303)
T PF13304_consen 244 LLSLLSLLLSAKKNGSILLIDEPENHLHPSWQRKLIELLKELSK 287 (303)
T ss_dssp HHHHHHHHHTTTTT-SEEEEESSSTTSSHHHHHHHHHHHHHTGG
T ss_pred HHHHHHHHhCcCCCCeEEEecCCcCCCCHHHHHHHHHHHHhhCc
Confidence 334444444444 67999998 8999988888877765554
No 32
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=31.38 E-value=21 Score=29.54 Aligned_cols=39 Identities=23% Similarity=0.280 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhc
Q 024576 21 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFE 60 (265)
Q Consensus 21 LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe 60 (265)
||.+|.+++..+--+|. ---+||||+.++..-.+-..|.
T Consensus 34 lTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr 72 (97)
T PF15337_consen 34 LTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWR 72 (97)
T ss_pred CcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhcccccc
Confidence 99999998765555444 3347999999986655444443
No 33
>PF10968 DUF2770: Protein of unknown function (DUF2770); InterPro: IPR024494 Members in this family of proteins from Enterobacteria are annotated as YceO; however, currently no function is known.
Probab=29.56 E-value=33 Score=24.02 Aligned_cols=15 Identities=13% Similarity=0.487 Sum_probs=12.7
Q ss_pred ccchhhHHHHHHHHh
Q 024576 45 NGVYLTLVRDVRNAF 59 (265)
Q Consensus 45 NGVY~glV~~Vr~af 59 (265)
|..+.-+|+|||+||
T Consensus 2 ~rl~~~~inNiReHl 16 (36)
T PF10968_consen 2 RRLFHYLINNIREHL 16 (36)
T ss_pred hHHHHHHHHHHHHHH
Confidence 456788999999997
No 34
>cd03321 mandelate_racemase Mandelate racemase (MR) catalyzes the Mg2+-dependent 1,1-proton transfer reaction that interconverts the enantiomers of mandelic acid. MR is the first enzyme in the bacterial pathway that converts mandelic acid to benzoic acid and allows this pathway to utilize either enantiomer of mandelate. MR belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=28.12 E-value=1.7e+02 Score=27.22 Aligned_cols=64 Identities=17% Similarity=0.206 Sum_probs=46.3
Q ss_pred HHHHHHHHHcCcCcccccccccccch--hhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 23 KHEADELRRKGKSLLPICKLAKNGVY--LTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 23 ~EE~~emRk~Gl~l~~~~kLgRNGVY--~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
.+++..+++.|.+.-=+ |+|++..- ...|+.||+++...--++||+. +.+..+..++++.|+++
T Consensus 146 ~~~a~~~~~~Gf~~~Ki-Kvg~~~~~~d~~~v~air~~~g~~~~l~vDaN~~~~~~~A~~~~~~l~~~ 212 (355)
T cd03321 146 TERAVTAAEEGFHAVKT-KIGYPTADEDLAVVRSIRQAVGDGVGLMVDYNQSLTVPEAIERGQALDQE 212 (355)
T ss_pred HHHHHHHHHhhhHHHhh-hcCCCChHhHHHHHHHHHHhhCCCCEEEEeCCCCcCHHHHHHHHHHHHcC
Confidence 35777788888642211 35654432 4678899999977666789998 68889999999999875
No 35
>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Probab=27.78 E-value=2.5e+02 Score=21.92 Aligned_cols=69 Identities=17% Similarity=0.179 Sum_probs=45.5
Q ss_pred HHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEeecCcE
Q 024576 26 ADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQ 99 (265)
Q Consensus 26 ~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd~e~ 99 (265)
+..||+.|...-.+-...+ .-.++.++.. ..-.+|=+.|-.-+...++++++.+|...|.+.|-+=|.+
T Consensus 9 aa~l~~~g~~v~~~~~~~~----~~~~~~~~~~-~~pdiv~~S~~~~~~~~~~~~~~~ik~~~p~~~iv~GG~~ 77 (127)
T cd02068 9 AAVLEDAGFIVAEHDVLSA----DDIVEDIKEL-LKPDVVGISLMTSAIYEALELAKIAKEVLPNVIVVVGGPH 77 (127)
T ss_pred HHHHHHCCCeeeecCCCCH----HHHHHHHHHh-cCCCEEEEeeccccHHHHHHHHHHHHHHCCCCEEEECCcc
Confidence 4567777744333222211 3445555443 5668999999877777899999999999887666665443
No 36
>PF11830 DUF3350: Domain of unknown function (DUF3350); InterPro: IPR021785 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 50 to 64 amino acids in length.
Probab=27.08 E-value=77 Score=24.07 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=19.3
Q ss_pred ccccccchhHHHHHHHHHhhcccc
Q 024576 142 QGTIRSSPKMISLWKRAIESTKAL 165 (265)
Q Consensus 142 ~~~~~~~pkm~~lw~~aiess~al 165 (265)
...-+++-..-.||+.||..-..|
T Consensus 22 ~~~krt~eelR~LWrkAI~QqIlL 45 (56)
T PF11830_consen 22 EKKKRTREELRELWRKAIHQQILL 45 (56)
T ss_pred cccccCHHHHHHHHHHHHHHHHHH
Confidence 556677888999999999876654
No 37
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=26.78 E-value=1.1e+02 Score=27.24 Aligned_cols=49 Identities=18% Similarity=0.158 Sum_probs=35.7
Q ss_pred HHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHH
Q 024576 26 ADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 80 (265)
Q Consensus 26 ~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKi 80 (265)
.+..|+.|+ ++.|--||.+.. +.++.......+|.+|+|+++...++++
T Consensus 60 ~~~~k~~gi----~~~leTnG~~~~--~~~~~l~~~~D~~l~DiK~~d~~~~~~~ 108 (213)
T PRK10076 60 LQRLRLWGV----SCAIETAGDAPA--SKLLPLAKLCDEVLFDLKIMDATQARDV 108 (213)
T ss_pred HHHHHHcCC----CEEEECCCCCCH--HHHHHHHHhcCEEEEeeccCCHHHHHHH
Confidence 344566664 567888997752 4556667789999999999988777654
No 38
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=26.64 E-value=67 Score=22.97 Aligned_cols=38 Identities=26% Similarity=0.559 Sum_probs=24.5
Q ss_pred cCCCCCCHHHHHHHHHc-CcCcccccccccccchhhHHHHH
Q 024576 16 EAPEGLTKHEADELRRK-GKSLLPICKLAKNGVYLTLVRDV 55 (265)
Q Consensus 16 ~~pEGLT~EE~~emRk~-Gl~l~~~~kLgRNGVY~glV~~V 55 (265)
..+.|||.+|+..-|++ |.+-.+ .=.+...+.-+.+.+
T Consensus 16 ~~~~GLs~~ev~~r~~~~G~N~l~--~~~~~s~~~~~~~~f 54 (69)
T PF00690_consen 16 SSSQGLSSEEVEERRKKYGPNELP--EPKKKSLWRIFLKQF 54 (69)
T ss_dssp BTSSBBTHHHHHHHHHHHSSSSTT--TTTSSSHHHHHHHHT
T ss_pred CCCCCCCHHHHHHHHHhccccccc--ccccCcHHHHHHHHH
Confidence 56899999999998854 777654 223444444444443
No 39
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=25.74 E-value=60 Score=29.33 Aligned_cols=60 Identities=22% Similarity=0.260 Sum_probs=49.2
Q ss_pred ccccchhHHHHHHHHHh-------------hccccccccCCCCchhHHHhhhhhhhhhhhhhcccCeEEeecCC
Q 024576 144 TIRSSPKMISLWKRAIE-------------STKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRED 204 (265)
Q Consensus 144 ~~~~~pkm~~lw~~aie-------------ss~al~ld~~~l~pd~ll~~veef~~~sqa~ehs~pa~~~s~~~ 204 (265)
+..+.|.+++-++.|.. ....|+|||+|--|-.=-.+.+=|..|+|-.+-..+ +++||-.
T Consensus 137 ~f~~~~el~~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~~~~~~~~~~~q~I~~r~~~~~~-~~tsN~~ 209 (254)
T COG1484 137 LFITAPDLLSKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRYESRSL-IITSNLS 209 (254)
T ss_pred EEEEHHHHHHHHHHHHhcCchHHHHHHHhhcCCEEEEecccCccCCHHHHHHHHHHHHHHHhhccc-eeecCCC
Confidence 56677888887777655 345789999999998888888999999999999999 8888743
No 40
>cd03007 PDI_a_ERp29_N PDIa family, endoplasmic reticulum protein 29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident protein expressed in high levels in secretory cells. It forms homodimers and higher oligomers in vitro and in vivo. It contains a redox inactive TRX-like domain at the N-terminus, which is homologous to the redox active TRX (a) domains of PDI, and a C-terminal helical domain similar to the C-terminal domain of P5. The expression profile of ERp29 suggests a role in secretory protein production distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase.
Probab=25.51 E-value=1.6e+02 Score=24.33 Aligned_cols=59 Identities=17% Similarity=0.239 Sum_probs=37.9
Q ss_pred chhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhh---ccCeEEEeecCc--EEEEEec
Q 024576 47 VYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKE---LVPCVLLSFDDE--QILMWRG 105 (265)
Q Consensus 47 VY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkd---LvpciLlsfd~e--~IImwRG 105 (265)
.|..|.+....|=..--|.+|||+.-+...-++++.+..- -.|-+++-.+|+ ..+-|.|
T Consensus 37 ~~~~LA~e~~~aa~~v~lakVd~~d~~~~~~~~L~~~y~I~~~gyPTl~lF~~g~~~~~~~Y~G 100 (116)
T cd03007 37 AFTRLAESSASATDDLLVAEVGIKDYGEKLNMELGERYKLDKESYPVIYLFHGGDFENPVPYSG 100 (116)
T ss_pred HHHHHHHHHHhhcCceEEEEEecccccchhhHHHHHHhCCCcCCCCEEEEEeCCCcCCCccCCC
Confidence 5667776666655556699999987666666889888754 256555544443 2344544
No 41
>PF04407 DUF531: Protein of unknown function (DUF531); InterPro: IPR007501 This is a family of hypothetical archaeal proteins.
Probab=24.96 E-value=1.4e+02 Score=26.99 Aligned_cols=57 Identities=21% Similarity=0.417 Sum_probs=50.3
Q ss_pred CCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHH
Q 024576 21 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAK 83 (265)
Q Consensus 21 LT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~k 83 (265)
+|.+|..++--+|+..-=++-|||.|.=..+.+.-+-|+. |-+||++.+-|.-||+-
T Consensus 107 i~p~e~a~~~l~~~s~~~liGLGR~GLPkei~k~a~yHLD------ITgkgiSLETCTAiG~I 163 (173)
T PF04407_consen 107 ISPEEVAEMALRGKSFLLLIGLGRHGLPKEIFKMAKYHLD------ITGKGISLETCTAIGAI 163 (173)
T ss_pred CCHHHHHHHHhcCCceEEEEecCCCCCcHHHHHhchhcee------ecCCceeeehhhHHhhH
Confidence 9999998887888888889999999999999998888875 56899999999999864
No 42
>COG0244 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=24.58 E-value=39 Score=29.35 Aligned_cols=31 Identities=32% Similarity=0.323 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHcCcCcccccccccccchh
Q 024576 19 EGLTKHEADELRRKGKSLLPICKLAKNGVYL 49 (265)
Q Consensus 19 EGLT~EE~~emRk~Gl~l~~~~kLgRNGVY~ 49 (265)
.|||..++++||+.-+.-..-++.+||-.+.
T Consensus 31 ~Gl~~~ql~~lR~~lr~~g~~lkV~KNtL~~ 61 (175)
T COG0244 31 RGLTVAQLTELRKKLREAGAKLKVVKNTLLR 61 (175)
T ss_pred CCCcHHHHHHHHHHHHhCCcEEEEEhhHHHH
Confidence 6899999999999999888899999996543
No 43
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=23.17 E-value=2.1e+02 Score=26.85 Aligned_cols=67 Identities=18% Similarity=0.213 Sum_probs=49.2
Q ss_pred HHHHcCcCccccccc-ccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHHHHHhhhccCeEEEe
Q 024576 28 ELRRKGKSLLPICKL-AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLS 94 (265)
Q Consensus 28 emRk~Gl~l~~~~kL-gRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKiG~kLkdLvpciLls 94 (265)
-|.+-|.+-.+++.| |+.||-...+.+++..|-.--+|=..-==.+.++-+.|.+++.+.-|+||+-
T Consensus 100 Ll~~a~~~~~~vfllGgkp~V~~~a~~~l~~~~p~l~ivg~h~GYf~~~e~~~i~~~I~~s~pdil~V 167 (253)
T COG1922 100 LLKRAAEEGKRVFLLGGKPGVAEQAAAKLRAKYPGLKIVGSHDGYFDPEEEEAIVERIAASGPDILLV 167 (253)
T ss_pred HHHHhCccCceEEEecCCHHHHHHHHHHHHHHCCCceEEEecCCCCChhhHHHHHHHHHhcCCCEEEE
Confidence 356666664556666 8999999999999999987655543322234444479999999999999864
No 44
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=22.99 E-value=2.7e+02 Score=20.95 Aligned_cols=65 Identities=22% Similarity=0.251 Sum_probs=46.6
Q ss_pred HHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEec-cCCCcchHHHHHHHhhhccCeEEEee
Q 024576 26 ADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNC-KGMHASDYKKLGAKLKELVPCVLLSF 95 (265)
Q Consensus 26 ~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdC-kg~~~sD~kKiG~kLkdLvpciLlsf 95 (265)
+..+|+.|.+..-+ +-|--...+++.+++. .-.+|=|.| .+-+....++++..+|...|++.+-+
T Consensus 21 a~~l~~~G~~v~~~---d~~~~~~~l~~~~~~~--~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv~ 86 (121)
T PF02310_consen 21 AAYLRKAGHEVDIL---DANVPPEELVEALRAE--RPDVVGISVSMTPNLPEAKRLARAIKERNPNIPIVV 86 (121)
T ss_dssp HHHHHHTTBEEEEE---ESSB-HHHHHHHHHHT--TCSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEEE
T ss_pred HHHHHHCCCeEEEE---CCCCCHHHHHHHHhcC--CCcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 45678888866522 2222236666666665 667899999 78888899999999999988877655
No 45
>cd03328 MR_like_3 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 3. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown.
Probab=22.81 E-value=2.1e+02 Score=26.72 Aligned_cols=63 Identities=11% Similarity=0.090 Sum_probs=44.3
Q ss_pred HHHHHHHHcCcCcccccccccc-cchhhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 24 HEADELRRKGKSLLPICKLAKN-GVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 24 EE~~emRk~Gl~l~~~~kLgRN-GVY~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
+++..++..|.+--- +|+|.+ .-=...|+.||+++...--+.||+. +.+..+..++++.|+++
T Consensus 144 ~~a~~~~~~Gf~~~K-ikvg~~~~~d~~~v~~vRe~~G~~~~l~vDaN~~~~~~~A~~~~~~l~~~ 208 (352)
T cd03328 144 EQLSGWVAQGIPRVK-MKIGRDPRRDPDRVAAARRAIGPDAELFVDANGAYSRKQALALARAFADE 208 (352)
T ss_pred HHHHHHHHCCCCEEE-eecCCCHHHHHHHHHHHHHHcCCCCeEEEECCCCCCHHHHHHHHHHHHHh
Confidence 456777788854211 234432 1123578899999987777889998 58889999999999874
No 46
>PRK13695 putative NTPase; Provisional
Probab=22.49 E-value=1e+02 Score=25.21 Aligned_cols=51 Identities=20% Similarity=0.351 Sum_probs=36.1
Q ss_pred HHHHHHHHHhhccccccccCCCCchhHHHhhhhhhhhhhhhhcccCeEEeecCC
Q 024576 151 MISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRED 204 (265)
Q Consensus 151 m~~lw~~aiess~al~ld~~~l~pd~ll~~veef~~~sqa~ehs~pa~~~s~~~ 204 (265)
+..+=+++++....++|||+ +|.+.+. -.-++.+.++.+.--|-+++++..
T Consensus 86 ~~~l~~~~l~~~~~lllDE~--~~~e~~~-~~~~~~l~~~~~~~~~~i~v~h~~ 136 (174)
T PRK13695 86 GIPALERALEEADVIIIDEI--GKMELKS-PKFVKAVEEVLDSEKPVIATLHRR 136 (174)
T ss_pred HHHHHHhccCCCCEEEEECC--Ccchhhh-HHHHHHHHHHHhCCCeEEEEECch
Confidence 44555667788999999997 5655555 334677888887667777777754
No 47
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=22.43 E-value=3.5e+02 Score=20.76 Aligned_cols=65 Identities=15% Similarity=0.119 Sum_probs=45.9
Q ss_pred HHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhccC-eEEEeec
Q 024576 27 DELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKELVP-CVLLSFD 96 (265)
Q Consensus 27 ~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdLvp-ciLlsfd 96 (265)
..||+.|.+. .-||-+==...+++.+++. ...+|=|.|. +-+..+.+++.+.||...| .+.|-+=
T Consensus 21 ~~l~~~G~~V---~~lg~~~~~~~l~~~~~~~--~pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vG 87 (119)
T cd02067 21 RALRDAGFEV---IDLGVDVPPEEIVEAAKEE--DADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVG 87 (119)
T ss_pred HHHHHCCCEE---EECCCCCCHHHHHHHHHHc--CCCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEE
Confidence 4678888776 4455443345666766654 4568999888 8888999999999999866 5554443
No 48
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=22.42 E-value=72 Score=28.39 Aligned_cols=25 Identities=32% Similarity=0.497 Sum_probs=20.0
Q ss_pred CCC-CCHHHHHHHHHcCcCcccccccccc
Q 024576 18 PEG-LTKHEADELRRKGKSLLPICKLAKN 45 (265)
Q Consensus 18 pEG-LT~EE~~emRk~Gl~l~~~~kLgRN 45 (265)
||| +|++|...+++.|. .-+.||.|
T Consensus 193 PEGGfs~~Ei~~~~~~gf---~~vsLG~r 218 (240)
T TIGR00046 193 PEGGFSEKEIQLLKEKGF---TPVLLGPR 218 (240)
T ss_pred CCCCCCHHHHHHHHHCCC---EEEccCCc
Confidence 887 99999999999994 33556665
No 49
>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=22.34 E-value=36 Score=28.45 Aligned_cols=10 Identities=40% Similarity=0.697 Sum_probs=4.6
Q ss_pred CCCccHHHHH
Q 024576 250 LGSLPVDHIA 259 (265)
Q Consensus 250 lgslpvd~~~ 259 (265)
|+|+|||.=+
T Consensus 60 ltSf~id~~v 69 (101)
T PF09026_consen 60 LTSFPIDDKV 69 (101)
T ss_dssp HCTS---HHH
T ss_pred hhccchhHhh
Confidence 6788887643
No 50
>PRK11145 pflA pyruvate formate lyase-activating enzyme 1; Provisional
Probab=22.25 E-value=97 Score=26.85 Aligned_cols=31 Identities=13% Similarity=0.213 Sum_probs=16.6
Q ss_pred EEEeccCCCcchHHHHHHHhhhccCeEEEeec
Q 024576 65 VKVNCKGMHASDYKKLGAKLKELVPCVLLSFD 96 (265)
Q Consensus 65 VKIdCkg~~~sD~kKiG~kLkdLvpciLlsfd 96 (265)
|.|...|.-... .+..+++...+-.|.|+++
T Consensus 102 i~l~TNG~~~~~-~~~~~~ll~~~d~v~islk 132 (246)
T PRK11145 102 TCLDTNGFVRRY-DPVIDELLDVTDLVMLDLK 132 (246)
T ss_pred EEEECCCCCCcc-hHHHHHHHHhCCEEEECCC
Confidence 566666754322 2333333334567888887
No 51
>COG1062 AdhC Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]
Probab=21.75 E-value=3.3e+02 Score=27.24 Aligned_cols=103 Identities=17% Similarity=0.293 Sum_probs=67.4
Q ss_pred hHHHHHHHHhc-cCceEEEeccCCCcchHHHHHHHhhhc-cCeEEEeec--CcEE-----EEEecCCCCCCCCC--CCCC
Q 024576 50 TLVRDVRNAFE-GSSLVKVNCKGMHASDYKKLGAKLKEL-VPCVLLSFD--DEQI-----LMWRGKDWKSMYPE--PPSF 118 (265)
Q Consensus 50 glV~~Vr~afe-~~ELVKIdCkg~~~sD~kKiG~kLkdL-vpciLlsfd--~e~I-----ImwRGKdyk~~~~~--~p~~ 118 (265)
.+|+.+++.+. .-..+ |+|-|... .-+.+-....- =-+|++.+- +..| -+..||.|+.++-- +|+.
T Consensus 242 ~vv~~i~~~T~gG~d~~-~e~~G~~~--~~~~al~~~~~~G~~v~iGv~~~~~~i~~~~~~lv~gr~~~Gs~~G~~~p~~ 318 (366)
T COG1062 242 DVVEAIVELTDGGADYA-FECVGNVE--VMRQALEATHRGGTSVIIGVAGAGQEISTRPFQLVTGRVWKGSAFGGARPRS 318 (366)
T ss_pred hHHHHHHHhcCCCCCEE-EEccCCHH--HHHHHHHHHhcCCeEEEEecCCCCceeecChHHeeccceEEEEeecCCcccc
Confidence 78999999999 45555 99998443 22333333333 223444442 3333 34566777776644 3444
Q ss_pred CCccccccccCCCCCCCCCCCCCccccccchhHHHHHHHHHhhccccccccCCCCchhHHHhhhhhhhhhhhhhccc
Q 024576 119 SNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSY 195 (265)
Q Consensus 119 ll~k~~~~~~~~~~s~~s~~~~~~~~~~~~pkm~~lw~~aiess~al~ld~~~l~pd~ll~~veef~~~sqa~ehs~ 195 (265)
.+ |++..||+. =.|..|.|++..-.++.|.||.++..
T Consensus 319 di----------------------------P~lv~~y~~------------Gkl~~d~lvt~~~~Le~INeaf~~m~ 355 (366)
T COG1062 319 DI----------------------------PRLVDLYMA------------GKLPLDRLVTHTIPLEDINEAFDLMH 355 (366)
T ss_pred ch----------------------------hHHHHHHHc------------CCCchhHHhhccccHHHHHHHHHHHh
Confidence 44 899999974 24888999999999999999998754
No 52
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.70 E-value=61 Score=22.56 Aligned_cols=56 Identities=30% Similarity=0.316 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEeccCCCcchHHHH
Q 024576 19 EGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 80 (265)
Q Consensus 19 EGLT~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCkg~~~sD~kKi 80 (265)
-|+|..-.....+.|+ ++|-- ..||...-..++|.....-..|.+ .|++..+++++
T Consensus 10 ~gvs~~tlr~y~~~gl-l~~~~--~~~g~r~y~~~dv~~l~~i~~l~~---~G~sl~~I~~~ 65 (69)
T PF13411_consen 10 LGVSPSTLRYYEREGL-LPPPR--DENGYRYYSEEDVERLREIKELRK---QGMSLEEIKKL 65 (69)
T ss_dssp TTTTHHHHHHHHHTTS-STTBE--STTSSEEE-HHHHHHHHHHHHHHH---TTTHHHHHHHH
T ss_pred HCcCHHHHHHHHHhcC-ccccc--ccCceeeccHHHHHHHHHHHHHHH---CcCCHHHHHHH
Confidence 3788888899999999 55555 667766656666666655555544 56666666554
No 53
>PRK02901 O-succinylbenzoate synthase; Provisional
Probab=21.55 E-value=2.6e+02 Score=26.46 Aligned_cols=64 Identities=20% Similarity=0.274 Sum_probs=46.4
Q ss_pred CHHHHHHHHHc--CcCcccccccccccc----hhhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHh-hh
Q 024576 22 TKHEADELRRK--GKSLLPICKLAKNGV----YLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKL-KE 86 (265)
Q Consensus 22 T~EE~~emRk~--Gl~l~~~~kLgRNGV----Y~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kL-kd 86 (265)
|.+++..+.++ |.+--- +|+|..|. =...|+.||+++...--++||+. +.+..+..++++.| ++
T Consensus 89 ~~e~~~~~~~~~~G~~~~K-vKVg~~~~~~~~Di~rv~avRe~lGpd~~LrvDAN~~ws~~~Ai~~~~~L~e~ 160 (327)
T PRK02901 89 DAAQVPEVLARFPGCRTAK-VKVAEPGQTLADDVARVNAVRDALGPDGRVRVDANGGWSVDEAVAAARALDAD 160 (327)
T ss_pred CHHHHHHHHHHhCCCCEEE-EEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHhhhc
Confidence 66777766664 654211 35665542 25678999999988889999998 58888999998888 44
No 54
>TIGR01228 hutU urocanate hydratase. This model represents the second of four enzymes involved in the degradation of histidine to glutamate.
Probab=21.42 E-value=40 Score=34.96 Aligned_cols=74 Identities=30% Similarity=0.416 Sum_probs=47.9
Q ss_pred CCCCCCHHHHHHHHHcC-------------cCcccccccccccch----hhHHHH------HHHHhccCceE--------
Q 024576 17 APEGLTKHEADELRRKG-------------KSLLPICKLAKNGVY----LTLVRD------VRNAFEGSSLV-------- 65 (265)
Q Consensus 17 ~pEGLT~EE~~emRk~G-------------l~l~~~~kLgRNGVY----~glV~~------Vr~afe~~ELV-------- 65 (265)
+|.|+|.||+.+||+.- +++.++.+|.++|.| .|-+.. +.++|..--.|
T Consensus 266 ~P~g~t~ee~~~lr~~dp~~~~~~~~~Sm~rhv~Am~~~~~~Ga~~fDYGN~~r~~a~~aG~~~aF~~PgfV~~~irplF 345 (545)
T TIGR01228 266 IPEGYTVEDADKLRQEEPEAYVKAAKQSMAKHVRAMLAFQKQGSVTFDYGNNIRQVAKEEGVEDAFDFPGFVPAYIRPLF 345 (545)
T ss_pred CCCCCCHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHCCCeeeeccHHHHHHHHHcCccccCCCCCchhhhcchhh
Confidence 67899999999999764 456778888888874 232221 12355554444
Q ss_pred -------EEeccCCCcchHHHHHHHhhhccCe
Q 024576 66 -------KVNCKGMHASDYKKLGAKLKELVPC 90 (265)
Q Consensus 66 -------KIdCkg~~~sD~kKiG~kLkdLvpc 90 (265)
|-.|--=++.|+.++=+.+..+.|-
T Consensus 346 ~~G~GPFRWvaLSGdpeDi~~TD~~~~e~~~~ 377 (545)
T TIGR01228 346 CRGKGPFRWVALSGDPADIYRTDAAVKELFPE 377 (545)
T ss_pred hCcCCCceeEecCCCHHHHHHHHHHHHHHCCC
Confidence 3334433567888887777776653
No 55
>TIGR01290 nifB nitrogenase cofactor biosynthesis protein NifB. This model describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model.
Probab=21.33 E-value=2.4e+02 Score=27.77 Aligned_cols=86 Identities=15% Similarity=0.220 Sum_probs=0.0
Q ss_pred CCHHHHHHH-HHcCcCccccccccccc------chhhHHHHHHHHhcc--CceEEEeccCCCcchHHHHHHHhhhc-cCe
Q 024576 21 LTKHEADEL-RRKGKSLLPICKLAKNG------VYLTLVRDVRNAFEG--SSLVKVNCKGMHASDYKKLGAKLKEL-VPC 90 (265)
Q Consensus 21 LT~EE~~em-Rk~Gl~l~~~~kLgRNG------VY~glV~~Vr~afe~--~ELVKIdCkg~~~sD~kKiG~kLkdL-vpc 90 (265)
||.+|+... ++.-..++.+-.++--| -+..+.+.++..-+. .--+-|...|+-. .+...+|.++ +-.
T Consensus 60 Ltpee~~~~i~~v~~~~~~~~~V~iaG~GEPLl~~e~~~~~l~~~~~~~~~i~i~lsTNG~~l---~e~i~~L~~~gvd~ 136 (442)
T TIGR01290 60 LTPEQALRKARQVAAEIPQLSVVGIAGPGDPLANIGKTFQTLELVARQLPDVKLCLSTNGLML---PEHVDRLVDLGVGH 136 (442)
T ss_pred CCHHHHHHHHHHHHHhcCCCCEEEEecCCCcccCccccHHHHHHHHHhcCCCeEEEECCCCCC---HHHHHHHHHCCCCe
Q ss_pred EEEeec------CcEE---EEEecCCCC
Q 024576 91 VLLSFD------DEQI---LMWRGKDWK 109 (265)
Q Consensus 91 iLlsfd------~e~I---ImwRGKdyk 109 (265)
|.||++ ...| |-|||+.|.
T Consensus 137 V~islka~d~e~~~~Iy~~v~~~g~~~t 164 (442)
T TIGR01290 137 VTITINAIDPAVGEKIYPWVWYEGERYT 164 (442)
T ss_pred EEEeccCCCHHHHhhcchhhcccccccc
No 56
>PF01175 Urocanase: Urocanase; InterPro: IPR023637 Urocanase [] (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyzes the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate. urocanate + H2O = 4,5-dihydro-4-oxo-5-imidazolepropanoate Urocanase is found in some bacteria (gene hutU), in the liver of many vertebrates and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD+ and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD+. This enzyme is a symmetric homodimer with tightly bound NAD+ cofactors. Each subunit consists of a typical NAD-binding domain inserted into a larger core domain that forms the dimer interface []. This entry represents the Urocanase subunit structural domain.; GO: 0016153 urocanate hydratase activity; PDB: 2V7G_A 1UWK_A 1UWL_B 1W1U_B 2FKN_C 1X87_B.
Probab=20.57 E-value=32 Score=35.68 Aligned_cols=74 Identities=30% Similarity=0.413 Sum_probs=44.2
Q ss_pred CCCCCCHHHHHHHHHcC-------------cCcccccccccccchh----hHH-------------------H-HHHHHh
Q 024576 17 APEGLTKHEADELRRKG-------------KSLLPICKLAKNGVYL----TLV-------------------R-DVRNAF 59 (265)
Q Consensus 17 ~pEGLT~EE~~emRk~G-------------l~l~~~~kLgRNGVY~----glV-------------------~-~Vr~af 59 (265)
+|.|||.||+.+||+.- +++.++.+|.++|.|. |-+ + -||..|
T Consensus 265 ~P~g~t~eea~~l~~~dp~~~~~~v~~Sl~rhv~Am~~~~~~G~~~fDYGN~~r~~a~~aG~~~aF~~P~fV~~~irplF 344 (546)
T PF01175_consen 265 YPAGLTFEEANELRAEDPEEFKERVQESLARHVEAMLELQDRGAYFFDYGNNFRLEAFDAGVDEAFDYPSFVPAYIRPLF 344 (546)
T ss_dssp --TT--HHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHTT-EE-B-SSSHHHHHHHTT-TTGGGS-BHHHHTTHHHH
T ss_pred CCCCCCHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEecCchHHHHHHHcCcceeecccccHHHHhhHHh
Confidence 57899999999999754 5677888898888752 211 1 123333
Q ss_pred -ccCceEEEeccCCCcchHHHHHHHhhhccCe
Q 024576 60 -EGSSLVKVNCKGMHASDYKKLGAKLKELVPC 90 (265)
Q Consensus 60 -e~~ELVKIdCkg~~~sD~kKiG~kLkdLvpc 90 (265)
++.==.|-.|--=+++|+.|+=+.+.++.|-
T Consensus 345 ~~G~GPFRWv~lSGdpeDi~~TD~~~~e~~~~ 376 (546)
T PF01175_consen 345 CEGFGPFRWVCLSGDPEDIYKTDEAALELFPD 376 (546)
T ss_dssp TTT-EEEEEEETT--HHHHHHHHHHHHHHSTT
T ss_pred hcCCCCceeeecCCCHHHHHHHHHHHHHhChh
Confidence 1222346667644788999888888777664
No 57
>KOG3920 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=20.46 E-value=36 Score=31.01 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=16.6
Q ss_pred cCcCcccccccccccchhhH
Q 024576 32 KGKSLLPICKLAKNGVYLTL 51 (265)
Q Consensus 32 ~Gl~l~~~~kLgRNGVY~gl 51 (265)
.--++||.+.|||||+|.-.
T Consensus 140 ~~AniPa~fllg~~Gy~ir~ 159 (193)
T KOG3920|consen 140 DRANIPAVFLLGVTGYYIRV 159 (193)
T ss_pred cccCCceEEEeccceEEEeh
Confidence 34589999999999999753
No 58
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=20.20 E-value=86 Score=27.73 Aligned_cols=25 Identities=32% Similarity=0.521 Sum_probs=20.0
Q ss_pred CCC-CCHHHHHHHHHcCcCcccccccccc
Q 024576 18 PEG-LTKHEADELRRKGKSLLPICKLAKN 45 (265)
Q Consensus 18 pEG-LT~EE~~emRk~Gl~l~~~~kLgRN 45 (265)
||| +|++|...|++.|.. .+.||.|
T Consensus 186 PEGGfs~~Ei~~l~~~g~~---~vsLG~~ 211 (234)
T PRK11713 186 PEGGFSPEEIELLREAGFT---PVSLGPR 211 (234)
T ss_pred CCCCCCHHHHHHHHHCCCE---EeccCCC
Confidence 887 999999999999953 3556655
No 59
>PRK15129 L-Ala-D/L-Glu epimerase; Provisional
Probab=20.03 E-value=2.3e+02 Score=26.12 Aligned_cols=62 Identities=21% Similarity=0.261 Sum_probs=41.8
Q ss_pred HHHHHHHHHcCcCcccccccccccchhhHHHHHHHHhccCceEEEecc-CCCcchHHHHHHHhhhc
Q 024576 23 KHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKLKEL 87 (265)
Q Consensus 23 ~EE~~emRk~Gl~l~~~~kLgRNGVY~glV~~Vr~afe~~ELVKIdCk-g~~~sD~kKiG~kLkdL 87 (265)
.+++..++..|.+--- +|++.. .=...|+.||+++ ..--.+||+. +.+..+..+++..|+++
T Consensus 134 ~~~~~~~~~~G~~~~K-lKv~~~-~d~~~v~avr~~~-~~~~l~vDaN~~w~~~~A~~~~~~l~~~ 196 (321)
T PRK15129 134 ANSASALWQAGAKLLK-VKLDNH-LISERMVAIRSAV-PDATLIVDANESWRAEGLAARCQLLADL 196 (321)
T ss_pred HHHHHHHHHcCCCEEE-EeCCCc-hHHHHHHHHHHhC-CCCeEEEECCCCCCHHHHHHHHHHHHhc
Confidence 3455667778843210 123322 2236788999999 4556899997 78888988888888774
Done!