Query 027212
Match_columns 226
No_of_seqs 150 out of 1101
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:38:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027212hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0233 Frr Ribosome recycling 100.0 4.3E-46 9.4E-51 317.8 13.3 132 93-224 4-135 (187)
2 PRK00083 frr ribosome recyclin 100.0 7.2E-45 1.6E-49 310.8 15.0 131 94-224 3-133 (185)
3 cd00520 RRF Ribosome recycling 100.0 1.2E-43 2.6E-48 301.4 13.7 128 97-224 2-129 (179)
4 TIGR00496 frr ribosome recycli 100.0 9.6E-44 2.1E-48 301.7 12.6 123 102-224 2-124 (176)
5 PF01765 RRF: Ribosome recycli 100.0 2.9E-38 6.3E-43 264.3 10.3 115 110-224 1-115 (165)
6 KOG4759 Ribosome recycling fac 100.0 1.4E-37 2.9E-42 276.6 13.7 145 80-224 68-213 (263)
7 TIGR02609 doc_partner putative 72.0 12 0.00027 27.4 5.3 50 171-222 16-72 (74)
8 PF13865 FoP_duplication: C-te 67.7 10 0.00022 28.0 4.1 33 81-113 37-69 (74)
9 TIGR00587 nfo apurinic endonuc 65.4 26 0.00056 31.2 7.1 73 144-217 26-99 (274)
10 PRK05412 putative nucleotide-b 52.5 12 0.00026 32.1 2.5 95 99-209 51-146 (161)
11 PTZ00372 endonuclease 4-like p 50.7 42 0.0009 32.7 6.1 72 144-216 156-228 (413)
12 PRK13022 secF preprotein trans 46.5 57 0.0012 29.8 6.1 64 149-212 38-104 (289)
13 PF04461 DUF520: Protein of un 35.3 14 0.0003 31.7 0.3 92 102-209 54-146 (160)
14 PF10281 Ish1: Putative stress 31.3 28 0.00062 22.2 1.2 20 191-211 18-37 (38)
15 PF13740 ACT_6: ACT domain; PD 31.1 1.3E+02 0.0028 21.5 4.8 59 155-216 2-70 (76)
16 cd06557 KPHMT-like Ketopantoat 30.0 1.1E+02 0.0023 27.8 5.0 50 165-214 115-170 (254)
17 PRK00311 panB 3-methyl-2-oxobu 29.8 1.2E+02 0.0025 27.7 5.3 48 165-214 118-173 (264)
18 PRK01060 endonuclease IV; Prov 29.5 1.8E+02 0.0038 25.3 6.3 56 160-216 43-99 (281)
19 PF07564 DUF1542: Domain of Un 29.4 1.1E+02 0.0025 21.6 4.2 31 194-224 10-40 (70)
20 cd04886 ACT_ThrD-II-like C-ter 29.4 1.6E+02 0.0035 19.2 4.9 54 158-211 3-67 (73)
21 PF02216 B: B domain; InterPr 29.0 45 0.00098 23.7 2.0 21 191-211 17-37 (54)
22 cd04905 ACT_CM-PDT C-terminal 28.4 1.3E+02 0.0028 21.4 4.5 60 155-214 3-72 (80)
23 PLN02760 4-aminobutyrate:pyruv 26.7 6.2E+02 0.013 24.9 11.3 57 165-224 443-501 (504)
24 PRK08578 preprotein translocas 26.5 2.7E+02 0.0058 25.5 7.1 65 148-213 46-110 (292)
25 cd02646 R3H_G-patch R3H domain 25.4 75 0.0016 22.0 2.6 23 190-212 18-40 (58)
26 PF00922 Phosphoprotein: Vesic 25.3 1.6E+02 0.0036 27.4 5.4 42 175-216 99-146 (283)
27 cd04887 ACT_MalLac-Enz ACT_Mal 25.3 2.1E+02 0.0045 19.5 4.9 56 155-210 1-63 (74)
28 cd02049 bacterial_SERPIN SERin 24.9 25 0.00055 32.3 0.1 60 153-212 219-279 (364)
29 PRK05783 hypothetical protein; 24.6 1.2E+02 0.0026 23.2 3.7 49 162-214 17-66 (84)
30 cd04888 ACT_PheB-BS C-terminal 24.2 2.4E+02 0.0052 19.2 5.1 56 155-210 2-65 (76)
31 PF04026 SpoVG: SpoVG; InterP 23.9 71 0.0015 24.3 2.4 74 130-216 5-84 (84)
32 PF10835 DUF2573: Protein of u 23.4 21 0.00045 27.4 -0.6 32 103-134 3-34 (82)
33 cd02043 plant_SERPIN SERine Pr 22.8 56 0.0012 30.3 2.0 58 154-211 230-290 (381)
34 cd02056 alpha-1-antitrypsin_li 22.0 20 0.00043 32.9 -1.2 60 152-212 219-279 (361)
35 COG0380 OtsA Trehalose-6-phosp 21.5 1.5E+02 0.0032 29.6 4.7 38 155-213 424-462 (486)
36 PF01361 Tautomerase: Tautomer 21.3 1.6E+02 0.0034 19.8 3.6 28 188-215 2-30 (60)
37 cd02048 neuroserpin Neuroserpi 21.3 18 0.00039 33.7 -1.6 60 153-212 229-289 (388)
38 cd00172 SERPIN SERine Proteina 21.0 15 0.00032 33.6 -2.2 60 152-211 220-280 (364)
39 cd02046 hsp47 Heat shock prote 20.9 24 0.00051 32.9 -0.9 67 145-211 215-284 (366)
40 COG1666 Uncharacterized protei 20.2 84 0.0018 27.0 2.3 48 161-210 104-151 (165)
41 TIGR00966 3a0501s07 protein-ex 20.1 4.5E+02 0.0097 23.2 7.1 65 150-214 8-75 (246)
42 TIGR00013 taut 4-oxalocrotonat 20.0 2.3E+02 0.0051 19.0 4.2 27 188-214 2-30 (63)
No 1
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-46 Score=317.81 Aligned_cols=132 Identities=50% Similarity=0.852 Sum_probs=129.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEECCccccccceEEEecCCCcEEEEeecCcccHHHHHHH
Q 027212 93 KSSIEKDVKARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEYYGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKA 172 (226)
Q Consensus 93 ~d~il~~~~~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekA 172 (226)
+..++++++++|++++++|+++|++||+||+||++||+|.|+|||.++||+|||+|+++++|+|+|+|||++.+++|++|
T Consensus 4 ~~~i~~~~e~kM~k~~e~l~~~l~~iRTGRanp~lld~i~VeyYG~~tPl~qvAsIsvpe~r~l~I~p~Dks~~~~Ieka 83 (187)
T COG0233 4 INEILKDAEEKMEKALEALKNELSKIRTGRANPSLLDRITVEYYGSPTPLNQLASISVPEARTLVIKPFDKSMVKAIEKA 83 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCChHHhcceeeeecCCCCcHHHHhhccCCCcceEEeecCccchHHHHHHH
Confidence 34678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 173 IVSSDLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 173 I~~SnLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
|..|||||||.+||+.|||+||+||+|+|++|+|.||+++|+||++||++|.
T Consensus 84 I~~snLglnP~~dG~~IRv~~P~lTeErRkelvK~~k~~~EeakvaiRniRr 135 (187)
T COG0233 84 ILASNLGLNPNNDGNVIRVPLPPLTEERRKELVKVAKKYAEEAKVAVRNIRR 135 (187)
T ss_pred HHHcCCCCCcCcCCCeEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999975
No 2
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=100.00 E-value=7.2e-45 Score=310.76 Aligned_cols=131 Identities=53% Similarity=0.865 Sum_probs=128.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEECCccccccceEEEecCCCcEEEEeecCcccHHHHHHHH
Q 027212 94 SSIEKDVKARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEYYGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAI 173 (226)
Q Consensus 94 d~il~~~~~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI 173 (226)
+.++.+++++|++++++|+++|+++|+||+||++||+|+|+|||+++||++||+|+++|+++|+|+|||++++++|++||
T Consensus 3 ~~~~~~~~~~m~kai~~l~~~l~~irtGra~p~lld~I~V~~yg~~~pL~~lA~Isv~~~~~l~I~p~D~~~i~~I~kAI 82 (185)
T PRK00083 3 NEILKDAEERMEKAVEALKRELAKIRTGRANPSLLDGIKVDYYGSPTPLNQVASISVPEARTLLIQPWDKSMLKAIEKAI 82 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHcCCeEEEECCCCccHHHceeeecCCCCEEEEEeCCHhHHHHHHHHH
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 174 VSSDLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 174 ~~SnLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
++|||||||++||+.|||+||+||+|+|++++|.||+++|+||++||++|.
T Consensus 83 ~~s~lgl~P~~dg~~Iri~iP~lT~E~R~elvK~~k~~~E~aKv~iRniRr 133 (185)
T PRK00083 83 RASDLGLNPSNDGTVIRLPIPPLTEERRKELVKQVKKEAEEAKVAIRNIRR 133 (185)
T ss_pred HHCCCCCCcccCCCEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999974
No 3
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=100.00 E-value=1.2e-43 Score=301.37 Aligned_cols=128 Identities=51% Similarity=0.865 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEECCccccccceEEEecCCCcEEEEeecCcccHHHHHHHHHhC
Q 027212 97 EKDVKARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEYYGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSS 176 (226)
Q Consensus 97 l~~~~~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~S 176 (226)
+++++++|++++++|+++|+++|+||+||++||+|+|+|||+++||++||||+++|+++|+|+|||++++++|++||++|
T Consensus 2 ~~~~~~~m~k~i~~~~~~l~~irtGrasp~lld~I~V~~yg~~~pL~~lA~Vsv~~~~~l~I~p~D~~~i~~I~kAI~~s 81 (179)
T cd00520 2 LKEAKEKMEKSLEALKEELNKIRTGRANPALLDSITVEYYGAPTPLNQLASISVPEPRTIVINPFDKSAIKAIEKAILNS 81 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHhCCeEEEeCCCCccHHHceeeecCCCCEEEEeecchhhHHHHHHHHHHC
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 177 DLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 177 nLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
|||+||++||+.|+|+||+||+|+|++++|.||+.+|+||++||++|.
T Consensus 82 ~l~l~P~~dg~~iri~iP~lT~E~R~~lvK~~k~~~E~~Kv~iRniR~ 129 (179)
T cd00520 82 DLGLNPNNDGAVIRVNLPPLTEERRKELVKDAKKIAEEAKVAIRNIRR 129 (179)
T ss_pred CCCCCcCcCCCEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999874
No 4
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=100.00 E-value=9.6e-44 Score=301.73 Aligned_cols=123 Identities=50% Similarity=0.858 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEECCccccccceEEEecCCCcEEEEeecCcccHHHHHHHHHhCCCCCC
Q 027212 102 ARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEYYGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMT 181 (226)
Q Consensus 102 ~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~SnLgln 181 (226)
++|++++++|+++|++||+||+||++||+|+|+|||+++||++||||+++|+++|+|+|||++++++|++||++||||||
T Consensus 2 ~~M~k~i~~~~~~l~~irtGra~p~ild~I~V~~yg~~~pL~~lA~vsv~~~~~l~I~p~D~~~~~~I~kAI~~s~lgln 81 (176)
T TIGR00496 2 ERMDKSIQALKRELSKIRTGRANPSLLDRILVEYYGAPTPLRQLASVTVPDARTLVIQPFDKSNINAIEKAIQRSDLGLN 81 (176)
T ss_pred chHHHHHHHHHHHHHHHhcCCCCHHHhCCeEEEeCCCcccHHHceeeecCCCCEEEEecCChhhHHHHHHHHHHCCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 182 PNNDGEVIRLTLPQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 182 Pq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
|++||+.|||+||+||+|+|++++|.||+.+|+||++||++|.
T Consensus 82 P~~dg~~Iri~iP~lT~E~RkelvK~~k~~~E~aKv~iRniRr 124 (176)
T TIGR00496 82 PNNDGSVIRVNFPPLTEERRKELVKHAKKIAEQAKVAVRNVRR 124 (176)
T ss_pred cccCCCEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999985
No 5
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=100.00 E-value=2.9e-38 Score=264.28 Aligned_cols=115 Identities=49% Similarity=0.765 Sum_probs=111.5
Q ss_pred HHHHHhhhhccCCCCcCCCceeEEEECCccccccceEEEecCCCcEEEEeecCcccHHHHHHHHHhCCCCCCccCCCCeE
Q 027212 110 MVRTNFNSVRTGRSNPAMLDKIEVEYYGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMTPNNDGEVI 189 (226)
Q Consensus 110 ~lk~el~kiRtGRa~P~lLd~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~SnLglnPq~DG~~I 189 (226)
||+++|+++|+||+||++||+|+|+|||+.+||++||||+++|+++|+|+|||++++++|++||++|||||||+.||+.|
T Consensus 1 ~~~~~l~~ir~gr~~p~~ld~i~V~~~g~~~~L~~lA~V~~~~~~~l~I~~~d~~~i~~I~kAI~~s~l~l~p~~d~~~i 80 (165)
T PF01765_consen 1 HFKEELSKIRTGRANPAILDNIKVEYYGSKVPLNELAQVSVKDPRTLVITPYDPSLIKAIEKAIQKSNLNLNPQNDGNTI 80 (165)
T ss_dssp HHHHHHHTSSSSSSSGGGGTTSEEEETTEEEEGGGTEEEEEEETTEEEEEESSTTHHHHHHHHHHHTTSSSEEEEETTEE
T ss_pred ChHHHHHHHhcCCCCHHHhCCeEEEECCCCccHHHceeeecCCCCEEEEEeccccchHHHHHHHHHCCCCCCcccCCcEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 190 RLTLPQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 190 rV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
+|+||+||+|+|++++|.||+++|+||++||++|.
T Consensus 81 ~v~iP~~T~E~R~~l~k~~k~~~E~~k~~iR~iR~ 115 (165)
T PF01765_consen 81 RVPIPPPTEERRKELVKQAKKIAEEAKVSIRNIRR 115 (165)
T ss_dssp EEE--SSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999985
No 6
>KOG4759 consensus Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-37 Score=276.57 Aligned_cols=145 Identities=39% Similarity=0.599 Sum_probs=139.1
Q ss_pred ccccCchhhhHHhhHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEECCccccccceEEEecCCCcEEEEe
Q 027212 80 VVRCATIEEIEAEKSSIEKDVKARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEYYGSPVSLKSIAQINTPDSSSLLIQ 159 (226)
Q Consensus 80 ~v~~~~~eei~~e~d~il~~~~~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~ 159 (226)
......+++.+.|...++.+++++|+++++.|+++|+++++||++|++||+|.|++||.++||++||||+.+||++|+|+
T Consensus 68 ~~~~~~in~~~~e~~~~~~~~~sqmek~ie~lke~~~k~~~gr~~~~~~d~I~vk~~g~~~~L~~IA~vS~K~p~~ilIn 147 (263)
T KOG4759|consen 68 DHGTEKINEAELEENAVEAKANSQMEKTIEALKEDFNKIRQGRFNPGMLDKIVVKANGPKRPLNEIAQVSLKGPQTILIN 147 (263)
T ss_pred CCchhhhhhHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCChhhhhheeeecCCCcccHHHHHHHhcCCCceEEEe
Confidence 33666677777778888999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecC-cccHHHHHHHHHhCCCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 160 PYD-KSSLKSIEKAIVSSDLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 160 pyD-~s~ik~IekAI~~SnLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
||| |..|++|++||.+|+|||||++||.+|+|+||++|.|+|++|+|.+++++|++|++||.++|
T Consensus 148 ~~d~p~~ikai~kAI~~S~lnltP~~dg~~l~vsiP~~T~E~Re~laK~~~~~~ee~K~slr~ir~ 213 (263)
T KOG4759|consen 148 PFDFPVDIKAILKAIEASGLNLTPNLDGTVLRVSIPPVTKESREKLAKVLKRYFEEYKQSLRKIRT 213 (263)
T ss_pred cccCchHHHHHHHHHHhCCCCCCcCCCCcEEEecCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999 99999999999999999999999999999999999999999999999999999999999986
No 7
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=71.99 E-value=12 Score=27.39 Aligned_cols=50 Identities=16% Similarity=0.268 Sum_probs=36.0
Q ss_pred HHHHhCCCCCCcc------C-CCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027212 171 KAIVSSDLGMTPN------N-DGEVIRLTLPQLTSERRKELSKVVAKQAEEGKVVMLLL 222 (226)
Q Consensus 171 kAI~~SnLglnPq------~-DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv~IR~~ 222 (226)
++|.. .|||.+. . +|..+..+..+ +++..+++.+.+.+.+++.+..+|.|
T Consensus 16 k~i~~-~lgl~~Gd~v~v~~~~~~iii~~~~~-~~~~~~~~~~~~~~~~~~y~~~l~~L 72 (74)
T TIGR02609 16 KEVLE-SLGLKEGDTLYVDEEEGGLKLKRFDE-GKELEKKMQMAVERAMSKYDEALKEL 72 (74)
T ss_pred HHHHH-HcCcCCCCEEEEEEECCEEEEEECCC-CccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45543 4666653 1 33344444544 78999999999999999999999987
No 8
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=67.67 E-value=10 Score=28.01 Aligned_cols=33 Identities=21% Similarity=0.287 Sum_probs=27.2
Q ss_pred cccCchhhhHHhhHHHHHHHHHHHHHHHHHHHH
Q 027212 81 VRCATIEEIEAEKSSIEKDVKARMERTIDMVRT 113 (226)
Q Consensus 81 v~~~~~eei~~e~d~il~~~~~kM~kaie~lk~ 113 (226)
--..|.||.++|+|.|.....++++.-++.+-.
T Consensus 37 ~~~kT~EeLDaELD~Ym~~~~~~LD~~Ld~Y~~ 69 (74)
T PF13865_consen 37 KPPKTAEELDAELDAYMSKTKSKLDAELDSYMS 69 (74)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566799999999999998888888887776643
No 9
>TIGR00587 nfo apurinic endonuclease (APN1). All proteins in this family for which functions are known are 5' AP endonculeases that are used in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.44 E-value=26 Score=31.17 Aligned_cols=73 Identities=5% Similarity=0.005 Sum_probs=58.7
Q ss_pred ceEEEecCCCcEEEEeecCcccHHHHHHHHHhCCCCCCcc-CCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 027212 144 SIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMTPN-NDGEVIRLTLPQLTSERRKELSKVVAKQAEEGKV 217 (226)
Q Consensus 144 ~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~SnLglnPq-~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aKv 217 (226)
+-.||.+.+|+...-.++++..+..+.+++.+.++.+.+. .-+... +.+-.+.+|.|+.-++..++..+-|+.
T Consensus 26 ~~~qif~~~P~~w~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Hapy~-iNlas~~~~~r~~sv~~~~~~i~~A~~ 99 (274)
T TIGR00587 26 TAFMFFLKSPRWWRRPMLEEEVIDWFKAALETNKNLSQIVLVHAPYL-INLASPDEEKEEKSLDVLDEELKRCEL 99 (274)
T ss_pred CEEEEEecCccccCCCCCCHHHHHHHHHHHHHcCCCCcceeccCCee-eecCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3468899999988877788888999999999888886654 334444 888889999999999999998887753
No 10
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=52.55 E-value=12 Score=32.07 Aligned_cols=95 Identities=19% Similarity=0.260 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEE-CCccccccceEEEecCCCcEEEEeecCcccHHHHHHHHHhCC
Q 027212 99 DVKARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEY-YGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSD 177 (226)
Q Consensus 99 ~~~~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~-yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~Sn 177 (226)
+-+-+++.+++-|...|.+= .+++..||-=.++. .|..+. -.|.+++| -|....|.|.|+|.++.
T Consensus 51 ~~d~kl~~v~diL~~kl~KR---~i~~k~ld~~~~e~~sG~~vr----q~i~lk~G-------I~~e~AKkIvK~IKd~k 116 (161)
T PRK05412 51 ESDFQLKQVKDILRSKLIKR---GIDLKALDYGKVEKASGKTVK----QEVKLKQG-------IDQELAKKIVKLIKDSK 116 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHc---CCCHHHcCCCCccccCCCEEE----EEEehhhc-------cCHHHHHHHHHHHHhcC
Confidence 33446666777777666542 12344444322221 222211 11223333 47889999999999999
Q ss_pred CCCCccCCCCeEEEeCCCCCHHHHHHHHHHHH
Q 027212 178 LGMTPNNDGEVIRLTLPQLTSERRKELSKVVA 209 (226)
Q Consensus 178 LglnPq~DG~~IrV~IP~lT~E~RkeLvK~aK 209 (226)
|.++++..|..|||.=- ..+--++.+..+|
T Consensus 117 lKVqa~IQGd~vRVtgK--krDDLQ~viallk 146 (161)
T PRK05412 117 LKVQAQIQGDQVRVTGK--KRDDLQAVIALLR 146 (161)
T ss_pred CceeEEecCcEEEEecC--CHhHHHHHHHHHH
Confidence 99999999999998632 2344444444444
No 11
>PTZ00372 endonuclease 4-like protein; Provisional
Probab=50.69 E-value=42 Score=32.68 Aligned_cols=72 Identities=7% Similarity=0.108 Sum_probs=60.9
Q ss_pred ceEEEecCCCcEEEEeecCcccHHHHHHHHHhCCCCCCcc-CCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 027212 144 SIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMTPN-NDGEVIRLTLPQLTSERRKELSKVVAKQAEEGK 216 (226)
Q Consensus 144 ~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~SnLglnPq-~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aK 216 (226)
+.-||-+++||...-.|+++..+....+++...++++.|. .-+.++ |.+-.+.+|.|+.-++...+..+-|.
T Consensus 156 ~afqiF~~npr~w~~~~~~~~~~~~f~~~~~~~gi~~~~i~~HapYl-INLASpd~e~rekSv~~~~~eL~rA~ 228 (413)
T PTZ00372 156 QAFALFLKNQRTWNSPPLSDETIDKFKENCKKYNYDPKFILPHGSYL-INLANPDKEKREKSYDAFLDDLQRCE 228 (413)
T ss_pred CEEEEEcCCCccCCCCCCCHHHHHHHHHHHHHcCCCcceEEeecCce-ecCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999999999999999999986654 355666 88888899999998888887776653
No 12
>PRK13022 secF preprotein translocase subunit SecF; Reviewed
Probab=46.45 E-value=57 Score=29.79 Aligned_cols=64 Identities=13% Similarity=0.235 Sum_probs=43.8
Q ss_pred ecCCCcEEEEeecCcccHHHHHHHHHhCCC-CCCccC--CCCeEEEeCCCCCHHHHHHHHHHHHHHH
Q 027212 149 NTPDSSSLLIQPYDKSSLKSIEKAIVSSDL-GMTPNN--DGEVIRLTLPQLTSERRKELSKVVAKQA 212 (226)
Q Consensus 149 svkd~rtLvI~pyD~s~ik~IekAI~~SnL-glnPq~--DG~~IrV~IP~lT~E~RkeLvK~aKk~~ 212 (226)
--.+|..+.++.-.+-....+++++.+.++ +.+.|. +++.+.|..|..++|..+++.+.+++..
T Consensus 38 DFtGG~~~~~~~~~~~~~~~v~~~~~~~~~~~~~v~~~~~~~~~~i~~~~~~~~~~~~~~~~l~~~~ 104 (289)
T PRK13022 38 DFTGGTVIEVRFEQPADLEQVREALEKAGFEDAQVQNFGSSRDVLIRLPPASEELSEKVKKALNKAY 104 (289)
T ss_pred eeCCCeEEEEEcCCCCCHHHHHHHHHhcCCCCceEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhhc
Confidence 345666666654446678889999987654 223332 4467888888888888888888887654
No 13
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=35.26 E-value=14 Score=31.66 Aligned_cols=92 Identities=21% Similarity=0.281 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCcCCCceeEEEE-CCccccccceEEEecCCCcEEEEeecCcccHHHHHHHHHhCCCCC
Q 027212 102 ARMERTIDMVRTNFNSVRTGRSNPAMLDKIEVEY-YGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGM 180 (226)
Q Consensus 102 ~kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve~-yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~SnLgl 180 (226)
-+++.+++-|...|.+= .+++..||-=.++. .|..+. + .|.++.| -|....|.|.|+|.++.|-+
T Consensus 54 ~kl~~v~diL~~kl~KR---~i~~k~ld~~k~e~asg~~vr--q--~i~lk~G-------I~~d~AKkIvK~IKd~klKV 119 (160)
T PF04461_consen 54 FKLKQVKDILRSKLIKR---GIDLKALDFGKIESASGGTVR--Q--VIKLKQG-------IDQDTAKKIVKLIKDSKLKV 119 (160)
T ss_dssp HHHHHHHHHHHHHHHHT---T--GGGEE--SS-EEETTEEE--E--EEEE--S---------HHHHHHHHHHHHHH--SE
T ss_pred HHHHHHHHHHHHHHHHc---CCCHHHcCCCCCccccCCEEE--E--EEEeecc-------cCHHHHHHHHHHHHhcCCce
Confidence 36677777777777542 12333343222221 222211 1 1233333 47899999999999999999
Q ss_pred CccCCCCeEEEeCCCCCHHHHHHHHHHHH
Q 027212 181 TPNNDGEVIRLTLPQLTSERRKELSKVVA 209 (226)
Q Consensus 181 nPq~DG~~IrV~IP~lT~E~RkeLvK~aK 209 (226)
+++..|..|||.=. ..+--++.+..+|
T Consensus 120 qa~IQgd~vRVtgK--krDDLQ~viallk 146 (160)
T PF04461_consen 120 QAQIQGDQVRVTGK--KRDDLQEVIALLK 146 (160)
T ss_dssp EEEEETTEEEEEES---HHHHHHHHHHHH
T ss_pred eEEecCcEEEEecC--CHHHHHHHHHHHH
Confidence 99999999998743 2444455555544
No 14
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=31.28 E-value=28 Score=22.19 Aligned_cols=20 Identities=30% Similarity=0.544 Sum_probs=14.4
Q ss_pred EeCCCCCHHHHHHHHHHHHHH
Q 027212 191 LTLPQLTSERRKELSKVVAKQ 211 (226)
Q Consensus 191 V~IP~lT~E~RkeLvK~aKk~ 211 (226)
|++|+.. ..|++|++.|++.
T Consensus 18 i~~~~~~-~~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 18 IPVPKSA-KTRDELLKLAKKN 37 (38)
T ss_pred CCCCCCC-CCHHHHHHHHHHh
Confidence 3445544 7899999999864
No 15
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=31.09 E-value=1.3e+02 Score=21.47 Aligned_cols=59 Identities=15% Similarity=0.295 Sum_probs=41.0
Q ss_pred EEEEeec--C-cccHHHHHHHHHhCCCCCCcc----CCCC---eEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 027212 155 SLLIQPY--D-KSSLKSIEKAIVSSDLGMTPN----NDGE---VIRLTLPQLTSERRKELSKVVAKQAEEGK 216 (226)
Q Consensus 155 tLvI~py--D-~s~ik~IekAI~~SnLglnPq----~DG~---~IrV~IP~lT~E~RkeLvK~aKk~~E~aK 216 (226)
.++|+.+ | |..+..+-++|.+.+-|+.-. -+|. .+.|.+| .+..+++.+...+.+++-.
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~---~~~~~~l~~~L~~l~~~~~ 70 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP---EDSLERLESALEELAEELG 70 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES---HHHHHHHHHHHHHHHHHTT
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC---cccHHHHHHHHHHHHHHCC
Confidence 4677776 6 999999999999877655432 1333 5677777 6777788888877776643
No 16
>cd06557 KPHMT-like Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a precursor to coenzyme A and is required for penicillin biosynthesis.
Probab=30.00 E-value=1.1e+02 Score=27.82 Aligned_cols=50 Identities=18% Similarity=0.254 Sum_probs=33.9
Q ss_pred cHHHHHHHHHhCC------CCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 027212 165 SLKSIEKAIVSSD------LGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAEE 214 (226)
Q Consensus 165 ~ik~IekAI~~Sn------LglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~ 214 (226)
..-...+|+.+++ +|||||.+...=-..+.--|.+..+++++.++.+.|-
T Consensus 115 ~~~~~I~al~~agipV~gHiGL~pq~~~~~gg~~~~grt~~~a~~~i~ra~a~~~A 170 (254)
T cd06557 115 EVAETIRALVDAGIPVMGHIGLTPQSVNQLGGYKVQGKTEEEAERLLEDALALEEA 170 (254)
T ss_pred HHHHHHHHHHHcCCCeeccccccceeeeccCCceeccCCHHHHHHHHHHHHHHHHC
Confidence 4555666777776 7999997644321223345788889999999887653
No 17
>PRK00311 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed
Probab=29.76 E-value=1.2e+02 Score=27.74 Aligned_cols=48 Identities=19% Similarity=0.222 Sum_probs=34.1
Q ss_pred cHHHHHHHHHhCC------CCCCccCCCC--eEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 027212 165 SLKSIEKAIVSSD------LGMTPNNDGE--VIRLTLPQLTSERRKELSKVVAKQAEE 214 (226)
Q Consensus 165 ~ik~IekAI~~Sn------LglnPq~DG~--~IrV~IP~lT~E~RkeLvK~aKk~~E~ 214 (226)
..-...+|+.+++ +|||||.+.. ..++ .--|.+..+++++.++.+.|-
T Consensus 118 ~~~~~I~al~~agIpV~gHiGL~pq~~~~~gg~~i--~grt~~~a~~~i~ra~a~~eA 173 (264)
T PRK00311 118 EVAETIKRLVERGIPVMGHLGLTPQSVNVLGGYKV--QGRDEEAAEKLLEDAKALEEA 173 (264)
T ss_pred HHHHHHHHHHHCCCCEeeeecccceeecccCCeee--ecCCHHHHHHHHHHHHHHHHC
Confidence 3456667777776 7899997632 2343 356888889999999988664
No 18
>PRK01060 endonuclease IV; Provisional
Probab=29.45 E-value=1.8e+02 Score=25.34 Aligned_cols=56 Identities=9% Similarity=0.129 Sum_probs=34.3
Q ss_pred ecCcccHHHHHHHHHhCCCCCCcc-CCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q 027212 160 PYDKSSLKSIEKAIVSSDLGMTPN-NDGEVIRLTLPQLTSERRKELSKVVAKQAEEGK 216 (226)
Q Consensus 160 pyD~s~ik~IekAI~~SnLglnPq-~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~aK 216 (226)
.+++..+..+.+++...++.+.+. ..+... +.+=.+.++.|+..++..++.+|-|+
T Consensus 43 ~~~~~~~~~lk~~~~~~gl~~~~~~~h~~~~-~nl~~~d~~~r~~s~~~~~~~i~~A~ 99 (281)
T PRK01060 43 PLEELNIEAFKAACEKYGISPEDILVHAPYL-INLGNPNKEILEKSRDFLIQEIERCA 99 (281)
T ss_pred CCCHHHHHHHHHHHHHcCCCCCceEEecceE-ecCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 456667788888888777764321 122221 33334556777777777777777665
No 19
>PF07564 DUF1542: Domain of Unknown Function (DUF1542); InterPro: IPR011439 This domain is found in several cell surface proteins. Some are involved in antibiotic resistance (e.g. Q9RL69 from SWISSPROT and Q9LCJ9 from SWISSPROT) [] and/or cellular adhesion (e.g. Q931R6 from SWISSPROT) []. In some proteins it is repeated more than fifteen times.
Probab=29.42 E-value=1.1e+02 Score=21.60 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 194 PQLTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 194 P~lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
|.+|.|-+++....+....++|...|-...|
T Consensus 10 ~~~T~eEK~~A~~~v~~~~~~a~~~I~~a~t 40 (70)
T PF07564_consen 10 PNATDEEKQAAKQKVDQILNQAINAINQATT 40 (70)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 7899999999999999999999999877665
No 20
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.41 E-value=1.6e+02 Score=19.23 Aligned_cols=54 Identities=19% Similarity=0.217 Sum_probs=34.3
Q ss_pred EeecC-cccHHHHHHHHHhCCCCCC-----ccC----CCC-eEEEeCCCCCHHHHHHHHHHHHHH
Q 027212 158 IQPYD-KSSLKSIEKAIVSSDLGMT-----PNN----DGE-VIRLTLPQLTSERRKELSKVVAKQ 211 (226)
Q Consensus 158 I~pyD-~s~ik~IekAI~~SnLgln-----Pq~----DG~-~IrV~IP~lT~E~RkeLvK~aKk~ 211 (226)
|...| |..+..|...|.+.+.++. +.. +|. .+.+.+--...++.+++.+.+++.
T Consensus 3 v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~~ 67 (73)
T cd04886 3 VELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALREA 67 (73)
T ss_pred EEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHHc
Confidence 44445 9999999999998887664 221 122 344443334567777887777664
No 21
>PF02216 B: B domain; InterPro: IPR003132 This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [].; GO: 0019865 immunoglobulin binding, 0009405 pathogenesis; PDB: 1EDL_A 1EDI_A 1EDJ_A 1EDK_A 2B88_A 2B87_A 2B89_A 1FC2_C 1DEE_H 1ZXG_A ....
Probab=29.05 E-value=45 Score=23.73 Aligned_cols=21 Identities=29% Similarity=0.521 Sum_probs=17.0
Q ss_pred EeCCCCCHHHHHHHHHHHHHH
Q 027212 191 LTLPQLTSERRKELSKVVAKQ 211 (226)
Q Consensus 191 V~IP~lT~E~RkeLvK~aKk~ 211 (226)
+.+|-+|+|.|...++.+|.-
T Consensus 17 l~~~nLteeQrn~yI~~lKdd 37 (54)
T PF02216_consen 17 LHMPNLTEEQRNGYIQSLKDD 37 (54)
T ss_dssp HCSTTS-HHHHHHHHHHHHH-
T ss_pred HcCCCcCHHHHHhHHHHHhhC
Confidence 467899999999999999864
No 22
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=28.37 E-value=1.3e+02 Score=21.38 Aligned_cols=60 Identities=13% Similarity=0.223 Sum_probs=40.8
Q ss_pred EEEEeecC-cccHHHHHHHHHhCCCCCC-----ccCCCC---eEEEeCC-CCCHHHHHHHHHHHHHHHHH
Q 027212 155 SLLIQPYD-KSSLKSIEKAIVSSDLGMT-----PNNDGE---VIRLTLP-QLTSERRKELSKVVAKQAEE 214 (226)
Q Consensus 155 tLvI~pyD-~s~ik~IekAI~~SnLgln-----Pq~DG~---~IrV~IP-~lT~E~RkeLvK~aKk~~E~ 214 (226)
+|.+.+-| +..+..|-+.+.+.+.|+. |..++. .++|.+= ....+.-+++++.++..++.
T Consensus 3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~~~~ 72 (80)
T cd04905 3 SIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRLTEF 72 (80)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhCCe
Confidence 45556555 8999999999999999885 543322 4555443 24566777777887776654
No 23
>PLN02760 4-aminobutyrate:pyruvate transaminase
Probab=26.73 E-value=6.2e+02 Score=24.88 Aligned_cols=57 Identities=16% Similarity=0.141 Sum_probs=42.1
Q ss_pred cHHHHHHHHHhCCCCCCccCCCCeEEEeCCC--CCHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 027212 165 SLKSIEKAIVSSDLGMTPNNDGEVIRLTLPQ--LTSERRKELSKVVAKQAEEGKVVMLLLFT 224 (226)
Q Consensus 165 ~ik~IekAI~~SnLglnPq~DG~~IrV~IP~--lT~E~RkeLvK~aKk~~E~aKv~IR~~~~ 224 (226)
..+.+.....+.++-+.+ .|+.|++. |+ .|+|.-++++..+.+...+.+..++.+..
T Consensus 443 ~~~~i~~~~~~~Gvl~~~--~g~~lrl~-Ppl~it~eeid~~~~~l~~al~~~~~~~~~~~~ 501 (504)
T PLN02760 443 VGAYFGAECKKRGMLVRV--AGDNIMMS-PPLIITPEEVDELISIYGKALKATEERVAELKS 501 (504)
T ss_pred HHHHHHHHHHhCCcEEEe--cCCEEEEE-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 455666666666655444 35677764 55 99999999999999999988888888754
No 24
>PRK08578 preprotein translocase subunit SecF; Reviewed
Probab=26.55 E-value=2.7e+02 Score=25.50 Aligned_cols=65 Identities=15% Similarity=0.135 Sum_probs=39.5
Q ss_pred EecCCCcEEEEeecCcccHHHHHHHHHhCCCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHH
Q 027212 148 INTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAE 213 (226)
Q Consensus 148 Isvkd~rtLvI~pyD~s~ik~IekAI~~SnLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E 213 (226)
|--.++..+.++ |++-.+.++.+++.+.+++=.-..+++.+.|.+|..+.|.++++.+..++...
T Consensus 46 iDF~GGt~~~~~-~~~~~~~~vr~~l~~~~~~~~~~~~~~~~~ir~~~~~~~~~~~~~~~l~~~~~ 110 (292)
T PRK08578 46 IDFTGGTEITIQ-TNDASPDELESALSGEPGVDVRKGSGNGYIITFGSGDDTDVDKLADAVKEFFN 110 (292)
T ss_pred eeecCceEEEEe-cCCCCHHHHHHHHhhcCCCcceEecCCcEEEEecCCCchHHHHHHHHHHHHhc
Confidence 334566555554 33677888888888765532111133445677777777777777776666554
No 25
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=25.44 E-value=75 Score=22.05 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=19.7
Q ss_pred EEeCCCCCHHHHHHHHHHHHHHH
Q 027212 190 RLTLPQLTSERRKELSKVVAKQA 212 (226)
Q Consensus 190 rV~IP~lT~E~RkeLvK~aKk~~ 212 (226)
.+.+|||+.+.|+-+=+.|+.+.
T Consensus 18 ~~~fppm~~~~R~~vH~lA~~~~ 40 (58)
T cd02646 18 SLSFPPMDKHGRKTIHKLANCYN 40 (58)
T ss_pred eEecCCCCHHHHHHHHHHHHHcC
Confidence 45899999999999988888754
No 26
>PF00922 Phosphoprotein: Vesiculovirus phosphoprotein; InterPro: IPR000224 This entry contains phosphoprotein from vesiculoviruses, which are ssRNA negative-strand rhabdoviruses. It is known as the phosphoprotein or P protein [, ]. This protein may be part of the RNA dependent RNA polymerase complex []. The phosphorylation states of this protein may regulate the transcription and replication complexes [].; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2K47_A 3PMK_R 2FQM_F 3HHZ_C 3HHW_D.
Probab=25.30 E-value=1.6e+02 Score=27.41 Aligned_cols=42 Identities=26% Similarity=0.386 Sum_probs=26.5
Q ss_pred hCCCCCCcc-----CCCCeEEEeCCC-CCHHHHHHHHHHHHHHHHHHH
Q 027212 175 SSDLGMTPN-----NDGEVIRLTLPQ-LTSERRKELSKVVAKQAEEGK 216 (226)
Q Consensus 175 ~SnLglnPq-----~DG~~IrV~IP~-lT~E~RkeLvK~aKk~~E~aK 216 (226)
.+++-|.+- ..|..+.+.+|. ||.+.+.+-.+-++.++|-+|
T Consensus 99 ~~~~~Wk~p~~k~~~~~k~l~L~~P~gLT~~Q~~QW~~tI~Al~~ssk 146 (283)
T PF00922_consen 99 TSDQPWKQPELKSDGGGKSLELTAPQGLTPEQLSQWTSTIEALVQSSK 146 (283)
T ss_dssp -----S---EEEEETTEEEEEEE--TT--HHHHHHHHHHHHHHHHHCC
T ss_pred cccccccCceeecCCCCceEEEeCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 356556653 356699999998 999999999999999999876
No 27
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.25 E-value=2.1e+02 Score=19.51 Aligned_cols=56 Identities=14% Similarity=0.157 Sum_probs=37.1
Q ss_pred EEEEeecC-cccHHHHHHHHHhCCCCCCc---cC-CCC--eEEEeCCCCCHHHHHHHHHHHHH
Q 027212 155 SLLIQPYD-KSSLKSIEKAIVSSDLGMTP---NN-DGE--VIRLTLPQLTSERRKELSKVVAK 210 (226)
Q Consensus 155 tLvI~pyD-~s~ik~IekAI~~SnLglnP---q~-DG~--~IrV~IP~lT~E~RkeLvK~aKk 210 (226)
+|.|..+| +..+..|..+|.+.+.++.- .. ++. .+.+.+---..++-+.+.+.+++
T Consensus 1 ~l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L~~ 63 (74)
T cd04887 1 TLRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSEEHAETIVAAVRA 63 (74)
T ss_pred CEEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCHHHHHHHHHHHhc
Confidence 36677787 88999999999887665532 11 222 45555655667777777766554
No 28
>cd02049 bacterial_SERPIN SERine Proteinase INhibitors (serpins), prokaryotic subgroup. Little information about specific functions is available for this subgroup, most likely they are inhibitory members of the serpin superfamily. In general, serpins exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors.
Probab=24.85 E-value=25 Score=32.27 Aligned_cols=60 Identities=18% Similarity=0.195 Sum_probs=44.5
Q ss_pred CcEEEEeecCcccHHHHHHHHHhCCC-CCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHH
Q 027212 153 SSSLLIQPYDKSSLKSIEKAIVSSDL-GMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQA 212 (226)
Q Consensus 153 ~rtLvI~pyD~s~ik~IekAI~~SnL-glnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~ 212 (226)
-.+++|-|-+...+..+++.+....+ .+..+-....+.|.+|+.+-|..-+|.+..++++
T Consensus 219 ~sm~iiLP~~~~~l~~l~~~l~~~~~~~~~~~~~~~~v~v~lPkF~i~~~~~L~~~L~~mG 279 (364)
T cd02049 219 LSMYVFLPKENVSLREFVKTLTAEKWRKWIEQFRMREGSLSLPRFQLEYEIELRDALKALG 279 (364)
T ss_pred EEEEEEecCCCCCHHHHHHHhCHHHHHHHHHhCceeEEEEEeeeEEccceechHHHHHHCc
Confidence 36888889888889999988865443 1222233457899999999999888888887654
No 29
>PRK05783 hypothetical protein; Provisional
Probab=24.56 E-value=1.2e+02 Score=23.19 Aligned_cols=49 Identities=16% Similarity=0.246 Sum_probs=31.1
Q ss_pred CcccHHHHHHHHHhCCCCC-CccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 027212 162 DKSSLKSIEKAIVSSDLGM-TPNNDGEVIRLTLPQLTSERRKELSKVVAKQAEE 214 (226)
Q Consensus 162 D~s~ik~IekAI~~SnLgl-nPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~ 214 (226)
||+ =++|.+|+..-++|. .-..-|+.|.+.|..-++ ++..++++++|++
T Consensus 17 DPq-G~aI~~aL~~lg~~~V~~VRvGK~iel~l~~~~~---e~a~~~v~~mc~~ 66 (84)
T PRK05783 17 DPE-GETIQRYVIERYTGNIIEVRAGKYLVFKIEANSP---EEAKELALKIARE 66 (84)
T ss_pred Cch-HHHHHHHHHHcCCCCcceEEeeEEEEEEEcCCCH---HHHHHHHHHHHHh
Confidence 443 467888887665543 222469999999977554 4455666666665
No 30
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.23 E-value=2.4e+02 Score=19.20 Aligned_cols=56 Identities=14% Similarity=0.146 Sum_probs=38.0
Q ss_pred EEEEeecC-cccHHHHHHHHHhCCCCCCc---cC--CC-CeEEEeCCCCCHH-HHHHHHHHHHH
Q 027212 155 SLLIQPYD-KSSLKSIEKAIVSSDLGMTP---NN--DG-EVIRLTLPQLTSE-RRKELSKVVAK 210 (226)
Q Consensus 155 tLvI~pyD-~s~ik~IekAI~~SnLglnP---q~--DG-~~IrV~IP~lT~E-~RkeLvK~aKk 210 (226)
+|.|...| +..+..|...|.+.+.++.- +. +| ..+.+.++--..+ +-+++++.+++
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~ 65 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELRE 65 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhc
Confidence 36677676 88999999999887765443 11 22 2577777666666 66777776664
No 31
>PF04026 SpoVG: SpoVG; InterPro: IPR007170 This is a stage V sporulation protein G. It is essential for sporulation and specific to stage V sporulation in Bacillus megaterium and Bacillus subtilis []. In B. subtilis, expression decreases after 30-60 minutes of cold shock [].; GO: 0030435 sporulation resulting in formation of a cellular spore; PDB: 2IA9_F 2I9X_B 2I9Z_A.
Probab=23.93 E-value=71 Score=24.31 Aligned_cols=74 Identities=24% Similarity=0.421 Sum_probs=43.3
Q ss_pred eeEEEECCccccccceEEEecCCCcEEEEeecCcccHHHHHHHHHhCCCCCC---cc---CCCCeEEEeCCCCCHHHHHH
Q 027212 130 KIEVEYYGSPVSLKSIAQINTPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMT---PN---NDGEVIRLTLPQLTSERRKE 203 (226)
Q Consensus 130 ~I~Ve~yG~~~pL~~LAqIsvkd~rtLvI~pyD~s~ik~IekAI~~SnLgln---Pq---~DG~~IrV~IP~lT~E~Rke 203 (226)
.|+|.-....-.|.-+|+|+.-|. ++|+=. + |.++.-|+- |+ .+|..--|.. |+|+|.|++
T Consensus 5 dVri~~~~~~~~lka~asV~~dd~--f~I~~i-----k-----Vieg~~GlFVaMPs~k~~~g~y~Di~~-Pitke~Re~ 71 (84)
T PF04026_consen 5 DVRIRKIEPEGKLKAFASVTFDDC--FVIHDI-----K-----VIEGEKGLFVAMPSRKSKDGEYKDICH-PITKEFREQ 71 (84)
T ss_dssp EEEEEETTSSSSEEEEEEEEETTT--EEEEEE-----E-----EEEETTEEEEE--EEE-TTS-EEESEE-ESSHHHHHH
T ss_pred EEEEEEecCCCCEEEEEEEEECCE--EEEEeE-----E-----EEECCCCcEEECCCcCCCCCCEEEEEE-ECCHHHHHH
Confidence 455555444466888999999875 444300 0 111222322 21 2444444433 589999999
Q ss_pred HHHHHHHHHHHHH
Q 027212 204 LSKVVAKQAEEGK 216 (226)
Q Consensus 204 LvK~aKk~~E~aK 216 (226)
|-..+-+..+++|
T Consensus 72 i~~aVl~aY~~~~ 84 (84)
T PF04026_consen 72 IEEAVLDAYEEAK 84 (84)
T ss_dssp HHHHHHHHHHHS-
T ss_pred HHHHHHHHHHhcC
Confidence 9999988888775
No 32
>PF10835 DUF2573: Protein of unknown function (DUF2573); InterPro: IPR020393 This entry contains proteins with no known function.
Probab=23.44 E-value=21 Score=27.39 Aligned_cols=32 Identities=16% Similarity=0.397 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHhhhhccCCCCcCCCceeEEE
Q 027212 103 RMERTIDMVRTNFNSVRTGRSNPAMLDKIEVE 134 (226)
Q Consensus 103 kM~kaie~lk~el~kiRtGRa~P~lLd~I~Ve 134 (226)
+++.-++.|-+.++.+.+|..+|++-|.|++=
T Consensus 3 ~l~eq~dgLveKytELL~Ge~~~e~~EkVk~W 34 (82)
T PF10835_consen 3 KLQEQFDGLVEKYTELLLGETSPEMKEKVKQW 34 (82)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 44555677777888899999999999988764
No 33
>cd02043 plant_SERPIN SERine Proteinase INhibitors (serpins), plant specific subgroup. It has been suggested that plant serpins play a role in defense against insect predators. This subgroup corresponds to clade P of the serpin superfamily. In general, serpins exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones.
Probab=22.76 E-value=56 Score=30.31 Aligned_cols=58 Identities=26% Similarity=0.311 Sum_probs=43.7
Q ss_pred cEEEEeecCcccHHHHHHHHHhCC--C-CCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHH
Q 027212 154 SSLLIQPYDKSSLKSIEKAIVSSD--L-GMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQ 211 (226)
Q Consensus 154 rtLvI~pyD~s~ik~IekAI~~Sn--L-glnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~ 211 (226)
.+++|-|.+...+..+++.+.... + .+.+......+.|.||+.+-|..-+|...++++
T Consensus 230 sm~iiLP~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~v~l~lPKF~i~~~~dl~~~L~~m 290 (381)
T cd02043 230 SMYIYLPDKKDGLADLLEKLVSEPGFLDRHIPASEQEVGAFMIPKFKFSFGFEASEVLKKL 290 (381)
T ss_pred EEEEEccCCCCCHHHHHHhhccChhhhhhhcccceeeEEEEEcccEEEEeecchHHHHHHC
Confidence 588899999888999999986432 2 233444445689999999988888888777765
No 34
>cd02056 alpha-1-antitrypsin_like alpha-1-antitrypsin_like. This family contains a variety of different members of clade A of the serpin superfamily. They include the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and noninhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia.
Probab=21.95 E-value=20 Score=32.92 Aligned_cols=60 Identities=17% Similarity=0.337 Sum_probs=43.2
Q ss_pred CCcEEEEeecCcccHHHHHHHHHhCCC-CCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHH
Q 027212 152 DSSSLLIQPYDKSSLKSIEKAIVSSDL-GMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQA 212 (226)
Q Consensus 152 d~rtLvI~pyD~s~ik~IekAI~~SnL-glnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~ 212 (226)
+..+++|-|.+. .+..+++.+...++ .+..+-+...+.|.||+.+-|..-+|.+.+++++
T Consensus 219 ~~sm~iiLP~~~-~l~~l~~~l~~~~l~~~~~~~~~~~v~v~lPkF~i~~~~~l~~~L~~~G 279 (361)
T cd02056 219 NATAFFVLPDEG-KMKQVEAALSRDTLKKWSKLLSKRSVDLYLPKFSISGTYNLKDILPKMG 279 (361)
T ss_pred CcEEEEEecCcc-hHHHHHHhhCHHHHHHHHHhCceeEEEEEeeeEEEeeeechHHHHHhcC
Confidence 456788889765 68888888765544 2222223458999999999988888888887654
No 35
>COG0380 OtsA Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]
Probab=21.50 E-value=1.5e+02 Score=29.63 Aligned_cols=38 Identities=32% Similarity=0.550 Sum_probs=24.1
Q ss_pred EEEEeecC-cccHHHHHHHHHhCCCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHHH
Q 027212 155 SLLIQPYD-KSSLKSIEKAIVSSDLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQAE 213 (226)
Q Consensus 155 tLvI~pyD-~s~ik~IekAI~~SnLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E 213 (226)
.|+|+||| ..+-.+|.+||. |+.|.|++..+...+..+
T Consensus 424 AliVNP~d~~~va~ai~~AL~---------------------m~~eEr~~r~~~~~~~v~ 462 (486)
T COG0380 424 ALIVNPWDTKEVADAIKRALT---------------------MSLEERKERHEKLLKQVL 462 (486)
T ss_pred CEeECCCChHHHHHHHHHHhc---------------------CCHHHHHHHHHHHHHHHH
Confidence 58899999 555555666654 555666666665555444
No 36
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=21.33 E-value=1.6e+02 Score=19.84 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=20.5
Q ss_pred eEEEeCCC-CCHHHHHHHHHHHHHHHHHH
Q 027212 188 VIRLTLPQ-LTSERRKELSKVVAKQAEEG 215 (226)
Q Consensus 188 ~IrV~IP~-lT~E~RkeLvK~aKk~~E~a 215 (226)
.|.|.+++ .|.|.+++|++.+.....++
T Consensus 2 ~I~i~~~~g~~~e~K~~l~~~it~~~~~~ 30 (60)
T PF01361_consen 2 FITIKIPEGRTAEQKRELAEAITDAVVEV 30 (60)
T ss_dssp EEEEEEESTS-HHHHHHHHHHHHHHHHHH
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 35666654 48999999999998877664
No 37
>cd02048 neuroserpin Neuroserpin is a inhibitory member of the SERine Proteinase INhibitor (serpin) family that reacts preferentially with tissue-type plasminogen activator (tPA). It is located in neurons in regions of the brain where tPA is also found, suggesting that neuroserpin is the selective inhibitor of tPA in the central nervous system (CNS). This subgroup corresponds to clade I of the serpin superfamily.
Probab=21.30 E-value=18 Score=33.73 Aligned_cols=60 Identities=15% Similarity=0.273 Sum_probs=45.2
Q ss_pred CcEEEEeecCcccHHHHHHHHHhCCC-CCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHHH
Q 027212 153 SSSLLIQPYDKSSLKSIEKAIVSSDL-GMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQA 212 (226)
Q Consensus 153 ~rtLvI~pyD~s~ik~IekAI~~SnL-glnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~~ 212 (226)
-.+++|-|.+...+..+++.|...++ .+..+.....+.|.+|+.+-|..-+|.+.+++++
T Consensus 229 ~sm~iiLP~~~~~l~~l~~~l~~~~l~~~~~~~~~~~v~l~lPkF~i~~~~~l~~~L~~lG 289 (388)
T cd02048 229 ISLMIILSRQEVPLATLEPLVKAPLIEEWANSVKKQKVEVYLPRFKVEQKIDLKDVLKNLG 289 (388)
T ss_pred eEEEEEccCCCCCHHHHHHHhChHHHHHHHHhCceeEEEEEccEEEEEEEechHHHHHHcC
Confidence 45778889888889999998876654 2333344568999999999888888888877654
No 38
>cd00172 SERPIN SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia.
Probab=20.96 E-value=15 Score=33.57 Aligned_cols=60 Identities=25% Similarity=0.412 Sum_probs=43.2
Q ss_pred CCcEEEEeecCcccHHHHHHHHHhCCC-CCCccCCCCeEEEeCCCCCHHHHHHHHHHHHHH
Q 027212 152 DSSSLLIQPYDKSSLKSIEKAIVSSDL-GMTPNNDGEVIRLTLPQLTSERRKELSKVVAKQ 211 (226)
Q Consensus 152 d~rtLvI~pyD~s~ik~IekAI~~SnL-glnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~ 211 (226)
+-.+++|.|.+...+..+++.|....+ .+..+.+-..+.|.||+.+-+..-+|...++++
T Consensus 220 ~~sm~iilP~~~~~l~~l~~~l~~~~l~~~~~~~~~~~v~l~lPkF~i~~~~~l~~~L~~~ 280 (364)
T cd00172 220 DLSMLIILPKEVTGLAELEEKLSAEKLDDLLSNLKEREVEVTLPKFKIESSLDLKEVLQAL 280 (364)
T ss_pred ceEEEEEecCCCCcHHHHHHhcCHHHHHHHHHhCCeEEEEEEeeEEEEeeeeCcHHHHHHc
Confidence 346788889888889999988865443 122222336799999999988877777777764
No 39
>cd02046 hsp47 Heat shock protein 47 (Hsp47), also called colligin, because of its collagen binding ability, is a chaperone specific for procollagen. It has been shown to be essential for collagen biosynthesis, but its exact function is still unclear. Hsp47 is a non-inhibitory member of the SERPIN superfamily and corresponds to clade H.
Probab=20.85 E-value=24 Score=32.87 Aligned_cols=67 Identities=22% Similarity=0.409 Sum_probs=47.7
Q ss_pred eEEEecCC--CcEEEEeecCcccHHHHHHHHHhCCCC-CCccCCCCeEEEeCCCCCHHHHHHHHHHHHHH
Q 027212 145 IAQINTPD--SSSLLIQPYDKSSLKSIEKAIVSSDLG-MTPNNDGEVIRLTLPQLTSERRKELSKVVAKQ 211 (226)
Q Consensus 145 LAqIsvkd--~rtLvI~pyD~s~ik~IekAI~~SnLg-lnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk~ 211 (226)
+.++--++ -.+++|-|.+..-+..+++.|...++. +..+-.-..+.|.||+.+-|..-+|...++++
T Consensus 215 vl~LPy~~~~~sm~iiLP~~~~~L~~l~~~L~~~~l~~~~~~~~~~~v~l~lPKF~i~~~~dL~~~L~~l 284 (366)
T cd02046 215 IVEMPLAHKLSSMIFIMPYHVEPLERLEKLLTREQLKTWISKMKKRAVAISLPKVSLEVSHDLQKHLGDL 284 (366)
T ss_pred EEEEEcCCCcEEEEEEecCCCCCHHHHHHHhCHHHHHHHHHhcceeEEEEEcceEEeeEEEcHHHHHHHc
Confidence 34444333 458888999888899999998766542 22222335799999999988888888877765
No 40
>COG1666 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.23 E-value=84 Score=27.02 Aligned_cols=48 Identities=21% Similarity=0.266 Sum_probs=36.1
Q ss_pred cCcccHHHHHHHHHhCCCCCCccCCCCeEEEeCCCCCHHHHHHHHHHHHH
Q 027212 161 YDKSSLKSIEKAIVSSDLGMTPNNDGEVIRLTLPQLTSERRKELSKVVAK 210 (226)
Q Consensus 161 yD~s~ik~IekAI~~SnLglnPq~DG~~IrV~IP~lT~E~RkeLvK~aKk 210 (226)
-|....|.|.|-|.+|.|.++.+..|..|||.=- ..+--++.+..+|+
T Consensus 104 I~~e~AKKI~KlIkDsklKVqaqIQGdqVRVtgK--~rDDLQaVialvr~ 151 (165)
T COG1666 104 IESENAKKIVKLIKDSKLKVQAQIQGDQVRVTGK--KRDDLQAVIALVRG 151 (165)
T ss_pred hhHHHHHHHHHHHHhcccceeeeeccceEEEecc--chhhHHHHHHHHHh
Confidence 3678899999999999999999999999997632 23444444554443
No 41
>TIGR00966 3a0501s07 protein-export membrane protein SecF. This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein.
Probab=20.10 E-value=4.5e+02 Score=23.17 Aligned_cols=65 Identities=9% Similarity=0.219 Sum_probs=43.8
Q ss_pred cCCCcEEEEeecCcccHHHHHHHHHhCCCCCC-cc--CCCCeEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 027212 150 TPDSSSLLIQPYDKSSLKSIEKAIVSSDLGMT-PN--NDGEVIRLTLPQLTSERRKELSKVVAKQAEE 214 (226)
Q Consensus 150 vkd~rtLvI~pyD~s~ik~IekAI~~SnLgln-Pq--~DG~~IrV~IP~lT~E~RkeLvK~aKk~~E~ 214 (226)
-.++..+.++--.+-.+..+++++.+.+.+-. .+ +++..+.+.+++...+.-.++.+.+++..++
T Consensus 8 F~GG~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~v~i~v~~~~~~~~~~v~~~v~~~~~~ 75 (246)
T TIGR00966 8 FTGGTVIETRLEQAADVAEVRDVLEKAGIEGVVIQEFGSSHTIMIRIPTLDTEQSEELREALEEALKN 75 (246)
T ss_pred cCCCcEEEEEeCCCCCHHHHHHHHHhcCCCCceEEEcCCCceEEEEecCCCcccHHHHHHHHHHHHhc
Confidence 45666666654345668888999887665422 12 3446888988887777667777777777765
No 42
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=20.00 E-value=2.3e+02 Score=19.00 Aligned_cols=27 Identities=19% Similarity=0.309 Sum_probs=20.4
Q ss_pred eEEEeCC--CCCHHHHHHHHHHHHHHHHH
Q 027212 188 VIRLTLP--QLTSERRKELSKVVAKQAEE 214 (226)
Q Consensus 188 ~IrV~IP--~lT~E~RkeLvK~aKk~~E~ 214 (226)
.|.|.+. ..|.|.+++|++.+-+...+
T Consensus 2 ~i~i~i~~~grt~eqK~~l~~~it~~l~~ 30 (63)
T TIGR00013 2 FVNIYILKEGRTDEQKRQLIEGVTEAMAE 30 (63)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHHH
Confidence 3566665 37999999999988776554
Done!