Query psy16608
Match_columns 202
No_of_seqs 123 out of 303
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 17:17:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16608hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09749 HVSL: Uncharacterised 100.0 3.6E-56 7.7E-61 371.6 21.3 199 1-201 20-239 (239)
2 KOG3102|consensus 100.0 1.1E-48 2.3E-53 312.2 16.8 201 1-202 59-269 (269)
3 COG1514 LigT 2'-5' RNA ligase 99.9 1.5E-23 3.3E-28 167.9 15.5 127 22-154 2-132 (180)
4 PRK15124 2'-5' RNA ligase; Pro 99.9 3E-23 6.4E-28 165.8 12.0 125 21-154 5-133 (176)
5 TIGR02258 2_5_ligase 2'-5' RNA 99.8 5.7E-20 1.2E-24 146.5 15.8 127 22-155 2-133 (179)
6 PHA02574 57B hypothetical prot 99.7 1.6E-17 3.5E-22 128.9 10.0 110 20-151 8-118 (149)
7 PRK13679 hypothetical protein; 99.7 2.4E-16 5.2E-21 124.9 15.6 154 26-197 4-159 (168)
8 PF13563 2_5_RNA_ligase2: 2'-5 99.5 2.7E-14 5.8E-19 110.0 8.4 118 34-156 3-121 (153)
9 PF10469 AKAP7_NLS: AKAP7 2'5' 99.5 2.6E-13 5.7E-18 110.9 13.8 161 23-190 3-188 (209)
10 PF02834 LigT_PEase: LigT like 99.3 3E-12 6.6E-17 90.3 6.6 77 33-109 4-87 (87)
11 PLN00108 unknown protein; Prov 98.9 4.2E-08 9.2E-13 82.3 13.0 170 21-194 36-238 (257)
12 TIGR03223 Phn_opern_protn puta 97.3 0.004 8.8E-08 51.7 11.0 92 56-153 57-177 (228)
13 PF05213 Corona_NS2A: Coronavi 97.0 0.012 2.5E-07 48.3 10.9 117 26-153 9-132 (248)
14 PF07823 CPDase: Cyclic phosph 97.0 0.0086 1.9E-07 48.6 10.0 114 35-154 14-141 (196)
15 PF02834 LigT_PEase: LigT like 97.0 0.0011 2.3E-08 46.3 4.1 68 118-191 9-77 (87)
16 KOG2814|consensus 95.4 0.13 2.7E-06 44.9 9.1 125 25-150 134-281 (345)
17 PF06299 DUF1045: Protein of u 95.2 0.36 7.9E-06 38.0 10.3 85 60-153 1-117 (160)
18 PHA02977 hypothetical protein; 94.2 0.39 8.5E-06 37.2 8.1 142 13-164 30-184 (201)
19 COG5255 Uncharacterized protei 90.8 2 4.4E-05 35.2 8.3 148 14-172 36-210 (239)
20 PF08302 tRNA_lig_CPD: Fungal 90.7 9.4 0.0002 32.3 13.4 119 22-158 72-216 (257)
21 TIGR02258 2_5_ligase 2'-5' RNA 87.3 1.8 3.9E-05 33.8 5.8 49 105-157 1-50 (179)
22 PF10469 AKAP7_NLS: AKAP7 2'5' 86.9 1.7 3.6E-05 35.2 5.6 58 105-164 1-62 (209)
23 COG1514 LigT 2'-5' RNA ligase 86.0 3.5 7.5E-05 33.0 6.8 50 105-158 1-50 (180)
24 PF07823 CPDase: Cyclic phosph 79.5 7.5 0.00016 31.4 6.5 43 107-152 4-46 (196)
25 PRK15124 2'-5' RNA ligase; Pro 78.2 9.1 0.0002 30.1 6.5 51 104-158 4-54 (176)
26 PF09749 HVSL: Uncharacterised 74.6 16 0.00035 30.3 7.3 55 21-75 140-200 (239)
27 PLN00108 unknown protein; Prov 71.5 16 0.00035 31.0 6.6 69 101-170 32-117 (257)
28 KOG3102|consensus 65.8 24 0.00051 29.3 6.2 74 21-98 170-257 (269)
29 PF06299 DUF1045: Protein of u 64.8 9.4 0.0002 30.1 3.6 48 56-105 108-155 (160)
30 cd01785 PDZ_GEF_RA Ubiquitin-l 64.6 40 0.00088 23.4 6.2 48 96-150 5-53 (85)
31 PF08302 tRNA_lig_CPD: Fungal 62.0 98 0.0021 26.2 11.4 72 73-150 28-121 (257)
32 PHA02574 57B hypothetical prot 61.3 10 0.00022 29.5 3.2 42 104-151 8-49 (149)
33 PF05213 Corona_NS2A: Coronavi 57.7 44 0.00096 27.8 6.4 70 102-174 3-72 (248)
34 cd00580 CHMI 5-carboxymethyl-2 54.9 79 0.0017 22.9 9.0 92 58-150 2-105 (113)
35 PF13563 2_5_RNA_ligase2: 2'-5 53.0 38 0.00081 25.1 5.2 85 9-103 62-151 (153)
36 cd04904 ACT_AAAH ACT domain of 46.5 38 0.00083 22.5 3.8 35 10-44 30-64 (74)
37 TIGR03223 Phn_opern_protn puta 43.5 46 0.001 27.8 4.6 53 56-110 168-220 (228)
38 PHA02977 hypothetical protein; 40.6 30 0.00065 26.9 2.8 19 143-161 68-86 (201)
39 PF05881 CNPase: 2',3'-cyclic 38.6 1.1E+02 0.0023 25.5 5.8 94 52-156 57-153 (235)
40 cd01816 Raf_RBD Ubiquitin doma 36.2 42 0.00091 23.0 2.7 35 98-140 5-39 (74)
41 TIGR00373 conserved hypothetic 35.0 30 0.00065 27.0 2.1 52 13-64 62-122 (158)
42 COG5011 Uncharacterized protei 34.7 45 0.00097 27.4 3.1 31 122-152 20-53 (228)
43 PRK13679 hypothetical protein; 34.7 2.1E+02 0.0046 22.0 9.2 87 10-106 71-158 (168)
44 PF14847 Ras_bdg_2: Ras-bindin 34.0 72 0.0016 23.2 3.8 46 98-150 5-50 (105)
45 PRK04173 glycyl-tRNA synthetas 32.8 41 0.00089 30.9 2.9 76 64-140 159-250 (456)
46 PF02962 CHMI: 5-carboxymethyl 32.7 2.1E+02 0.0046 21.4 7.4 92 58-150 2-105 (124)
47 COG4316 Uncharacterized protei 31.3 2.2E+02 0.0047 21.4 5.9 52 93-153 29-82 (138)
48 TIGR02042 sir ferredoxin-sulfi 30.5 2.1E+02 0.0045 27.2 7.3 127 6-148 352-487 (577)
49 PF14480 DNA_pol3_a_NI: DNA po 29.9 74 0.0016 21.0 3.2 40 52-91 33-72 (76)
50 cd04929 ACT_TPH ACT domain of 29.9 1.1E+02 0.0023 20.6 3.9 34 10-43 30-63 (74)
51 PF04456 DUF503: Protein of un 29.7 1E+02 0.0022 21.7 3.9 70 61-134 9-79 (90)
52 cd04931 ACT_PAH ACT domain of 29.3 94 0.002 21.8 3.7 36 10-45 44-80 (90)
53 KOG1383|consensus 28.5 1.8E+02 0.004 26.9 6.2 49 126-175 398-448 (491)
54 PF10105 DUF2344: Uncharacteri 27.2 72 0.0016 25.6 3.1 32 121-152 18-52 (187)
55 PF01797 Y1_Tnp: Transposase I 24.7 1.6E+02 0.0036 20.8 4.5 46 36-84 23-76 (121)
56 KOG2814|consensus 23.9 1.1E+02 0.0023 27.2 3.7 37 137-173 170-206 (345)
57 PF08975 2H-phosphodiest: Doma 23.7 63 0.0014 24.1 2.0 79 8-93 5-106 (118)
58 cd04930 ACT_TH ACT domain of t 22.1 1.5E+02 0.0032 21.8 3.7 34 10-43 71-104 (115)
59 PF04571 Lipin_N: lipin, N-ter 22.0 72 0.0016 23.6 2.0 19 86-104 42-60 (110)
60 cd04905 ACT_CM-PDT C-terminal 21.7 1.3E+02 0.0028 20.0 3.2 51 79-130 15-69 (80)
61 PF03958 Secretin_N: Bacterial 21.6 1.4E+02 0.003 19.7 3.3 67 63-130 2-79 (82)
62 PF13466 STAS_2: STAS domain 21.2 1.5E+02 0.0032 19.4 3.4 36 62-97 2-37 (80)
63 TIGR00254 GGDEF diguanylate cy 20.8 3.3E+02 0.0071 19.5 9.9 94 70-171 54-150 (165)
64 PF08782 c-SKI_SMAD_bind: c-SK 20.6 64 0.0014 23.2 1.5 27 18-44 62-92 (96)
65 PF03089 RAG2: Recombination a 20.4 45 0.00097 29.0 0.7 61 89-151 103-163 (337)
66 PF10209 DUF2340: Uncharacteri 20.3 1.1E+02 0.0023 23.1 2.6 69 72-141 29-102 (122)
67 PRK10664 transcriptional regul 20.1 1.3E+02 0.0029 20.9 3.1 32 71-104 24-55 (90)
68 PF15378 DUF4605: Domain of un 20.1 85 0.0018 20.6 1.8 18 123-140 2-19 (60)
69 cd04893 ACT_GcvR_1 ACT domains 20.1 2.7E+02 0.0059 18.3 7.5 71 58-137 1-71 (77)
70 TIGR00987 himA integration hos 20.0 1.5E+02 0.0033 20.7 3.3 30 71-102 25-54 (96)
No 1
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=100.00 E-value=3.6e-56 Score=371.60 Aligned_cols=199 Identities=36% Similarity=0.661 Sum_probs=178.7
Q ss_pred CCCCCCCCCcccccCccccccceEEEEecCCCHHHHHHHHHHHHHhhcccc---------------ccCCCCeEeeeeee
Q psy16608 1 MDNPNEHGGRIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEELNSVGISV---------------EVIPEPHLSLSKTL 65 (202)
Q Consensus 1 ~d~p~~h~gr~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~---------------~~~~~lHISLs~~~ 65 (202)
.|||++||||+|+|||++|||+|||||+|++ +++..+.|++++++++... +.+.+||||||+++
T Consensus 20 ~d~~~~h~gR~R~~pHv~Gnw~t~vYi~~~~-~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~s~lg~~~~lHISLSr~~ 98 (239)
T PF09749_consen 20 QDDPSLHGGRIRSFPHVEGNWPTHVYIEWPP-SEDQRELLEKLISKANSICPKLHSEFEPLLYSDLGSPDPLHISLSRTF 98 (239)
T ss_pred ccCcccccCceecccccCCccceEEEEEecC-cHHHHHHHHHHHHHHHhhhhhhhhhcccccccccCCCCCeEEEeCCCc
Confidence 4899999999999999999999999999999 7778888998888887653 46789999999999
Q ss_pred ccCcccHHHHHHHHHHhh--ccCCceEEEeCceEEEecCCCceEEEEEeecCCCcc-HHHHHHHHHHHHHhcCCCCCC-C
Q psy16608 66 VIPYHWIDTLVETLGNNL--RHLNRLTIKFNSIEIFCNEEKTRSFIALGANSCKTS-LTSIVQAVDKSAQEFKLPTYY-E 141 (202)
Q Consensus 66 ~~~~~~i~~~~~~L~~~l--~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~-L~~L~~~i~~~l~~~g~~~~~-~ 141 (202)
.++.+||++|+++|++.+ +++++|.+.|+++.+|.|+++||+|++++|..+... |..|++.|+++|++||+|++| +
T Consensus 99 ~lr~~~id~f~~~lr~~l~~~~~~~F~v~f~~~~~~~N~e~TR~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~lp~~Y~~ 178 (239)
T PF09749_consen 99 PLRTHQIDPFVDSLRQALRSSNIRPFYVSFSGLDVYTNDEKTRSFLALRVSEGSNNELKRLLDRINEVLKEFGLPPFYDE 178 (239)
T ss_pred cccHHHHHHHHHHHHHHHhhcCCceEEEEeCceEEEecCCCCeEEEEEEecccccHHHHHHHHHHHHHHHHhCCCcccCC
Confidence 999999999999999999 889999999999999999999999999999988765 999999999999999999999 9
Q ss_pred CCCceEEEEeecCCCchhHHHH-HHHHHHhhhhcc-cCCceeecccceEEEeeCCeEEEeeC
Q psy16608 142 EPNFHASIAWCLQDKTATLKPL-LTKLDNIFTQFK-LTSDESFHVVTHIHMKTGNKFYSFPL 201 (202)
Q Consensus 142 ~~~pHiSia~~~~~~~~~l~~~-~~~l~~~~~~~~-~~~~~~~~~v~~v~~k~Gn~~~~~~l 201 (202)
++.|||||||+.+++.+.+++. .+.+++.++++. ......+. |++|+|||||++|+|||
T Consensus 179 ~~~fHvSIAw~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-v~~Ik~kiGn~v~~ipL 239 (239)
T PF09749_consen 179 DPSFHVSIAWTLGDPSEELKESSLKILQEPLDELEEIENDNSFK-VNSIKCKIGNKVFSIPL 239 (239)
T ss_pred CCCCEEEEEEECCCchHHHHHHHHHHHHHHHhhhhhccceeEEE-eeEEEEEECCEEEEecC
Confidence 9999999999999999888754 355555555443 11223899 99999999999999997
No 2
>KOG3102|consensus
Probab=100.00 E-value=1.1e-48 Score=312.16 Aligned_cols=201 Identities=33% Similarity=0.588 Sum_probs=172.8
Q ss_pred CCCCCCCCCcccccCccccccceEEEEecCCCHHHHHHHHHHHHHhhcccc-------ccCCCCeEeeeeeeccCcccHH
Q psy16608 1 MDNPNEHGGRIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEELNSVGISV-------EVIPEPHLSLSKTLVIPYHWID 73 (202)
Q Consensus 1 ~d~p~~h~gr~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~-------~~~~~lHISLs~~~~~~~~~i~ 73 (202)
.|+|..||||+|+|||++|||+||||+++-.++...++..-+.+..+-..+ +..+.+||||+++..++.|||+
T Consensus 59 eDvptehGgRvR~FpHerGNwAthVYVP~~a~~~~~eEf~l~~va~l~PHl~l~~p~~~~~~~fHlSLsr~VvLr~HqI~ 138 (269)
T KOG3102|consen 59 EDVPTEHGGRVRNFPHERGNWATHVYVPVCAPPLPKEEFVLKKVASLVPHLHLVEPDVALGREFHLSLSRNVVLRVHQIN 138 (269)
T ss_pred ccCccccCceeccCccccCceeEEEEEeeccCCChHHHHHHHHHHhhcccceeeccchhccceEEEeeccceEEEeehhh
Confidence 389999999999999999999999999997632222222223333333332 4468899999999999999999
Q ss_pred HHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEeecCCC-ccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy16608 74 TLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGANSCK-TSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWC 152 (202)
Q Consensus 74 ~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~-~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~ 152 (202)
+|+.+|++++.....|-++++++.+|.|+++||+|+++++..+. ..+..+++.||++|+.++++.||++|+||+||+||
T Consensus 139 ~fi~~L~~~l~s~~rf~~t~n~~~iytN~e~TRtFi~leitt~~~~~~~~~i~~vd~Vm~~~nL~~FY~DPsfHiSL~Wc 218 (269)
T KOG3102|consen 139 SFISMLRQKLQSQKRFLITFNKWEIYTNDEHTRTFISLEITTSGLSEISKQIDAVDEVMKLHNLPEFYKDPSFHISLVWC 218 (269)
T ss_pred HHHHHHHHHHhhhhhheEeecceEEEeccccceeEEEEEechhhHHHHHHHHHHHHHHHHHcCchhhhcCCCCCceEEEE
Confidence 99999999999999999999999999999999999999997765 77888999999999999999999999999999999
Q ss_pred cCCCchhHH-HHHHHHHHhhhhccc-CCceeecccceEEEeeCCeEEEeeCC
Q psy16608 153 LQDKTATLK-PLLTKLDNIFTQFKL-TSDESFHVVTHIHMKTGNKFYSFPLT 202 (202)
Q Consensus 153 ~~~~~~~l~-~~~~~l~~~~~~~~~-~~~~~~~~v~~v~~k~Gn~~~~~~l~ 202 (202)
.||....|+ +.+.+|+++.|.+++ +-.+..+ ...|+||+|||.|+|+|.
T Consensus 219 vGD~rt~L~g~~l~EL~~l~dg~~~~~~~l~v~-~~~i~Ck~GNK~f~~~lk 269 (269)
T KOG3102|consen 219 VGDIRTSLKGAVLVELRKLRDGGCVQNRILTVK-FCGIECKIGNKTFKICLK 269 (269)
T ss_pred eccHHHhhhhHHHHHHHHHHhccchhheeEEEe-eeeEEEecCCeeeeeecC
Confidence 999999998 788899999998873 2235666 778999999999999984
No 3
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.5e-23 Score=167.91 Aligned_cols=127 Identities=13% Similarity=0.108 Sum_probs=116.0
Q ss_pred ceEEEEecCCCHHHHHHHHHHHHHhhcccc----ccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceE
Q psy16608 22 ATLVYIPLQTNLARLYAMLKEELNSVGISV----EVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIE 97 (202)
Q Consensus 22 ~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~----~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~ 97 (202)
|.|+.|++|. ++++.|.++.+.++... +.++++||||.|+|+++.+.++.+.+.|.+..+.+ +|+|++.++|
T Consensus 2 RlFiAl~~p~---~i~~~i~~~~~~~~~~~~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g 77 (180)
T COG1514 2 RLFIALDPPA---EIAERLARIRARLKGARAIKWVEPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAG 77 (180)
T ss_pred eeEEEecCCH---HHHHHHHHHHHhcCcccccccccccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEc
Confidence 5677776655 88999999999888763 99999999999999999999999999999888777 9999999999
Q ss_pred EEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecC
Q psy16608 98 IFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQ 154 (202)
Q Consensus 98 ~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~ 154 (202)
+|+|..++||+|+ ++.+ .+.|..|.+.|+..+.+.|++++.++|.||||||+.++
T Consensus 78 ~F~~~~~~rvi~~-~v~~-~~~L~~L~~~l~~~~~~~g~~~~~r~F~PHvTl~r~k~ 132 (180)
T COG1514 78 SFPNPRRPRVIWV-GVEE-TEELRALAEELERALARLGLRPEERPFVPHVTLARVKS 132 (180)
T ss_pred ccCCCCCCcEEEE-cCCC-cHHHHHHHHHHHHHHHhcCCCCCCCCcCCCEEEEeecc
Confidence 9999999999997 8976 67899999999999999999999999999999999876
No 4
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.90 E-value=3e-23 Score=165.75 Aligned_cols=125 Identities=10% Similarity=0.004 Sum_probs=108.2
Q ss_pred cceEEEEecCCCHHHHHHHHHHHHHhhccc----cccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCce
Q psy16608 21 WATLVYIPLQTNLARLYAMLKEELNSVGIS----VEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSI 96 (202)
Q Consensus 21 w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~----~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~ 96 (202)
.|+|++|++|. ++++.|.++++.+... .+.++++||||.|+|+++.++++.+.+.+.+. ..++|.|+++++
T Consensus 5 ~RlFiAl~~p~---~~~~~l~~~~~~~~~~~~~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~--~~~pF~l~l~~~ 79 (176)
T PRK15124 5 KRLFFAIDLPD---EIRQQIIHWRATHFPPEAGRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI--RQPGFTLTLDDA 79 (176)
T ss_pred eEEEEEeCCCH---HHHHHHHHHHHHhccccCcccccccccEEEEEecCCCCHHHHHHHHHHHHhc--ccCCeEEEECcc
Confidence 57888888775 8888888888776432 28899999999999999999999888887654 468999999999
Q ss_pred EEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecC
Q psy16608 97 EIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQ 154 (202)
Q Consensus 97 ~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~ 154 (202)
|+|+ +||++|+ +++++...|..|++.++++++..|++.+.++|+||||||+...
T Consensus 80 g~Fp---~prvlwl-g~~~~~~~L~~L~~~l~~~l~~~G~~~e~r~f~PHiTLaR~~~ 133 (176)
T PRK15124 80 GQWP---RSRVVWL-GMRQPPRGLLQLANMLRSQAARSGCYQSPQPFHPHITLLRDAS 133 (176)
T ss_pred cCcC---CCCEEEE-EcCCCCHHHHHHHHHHHHHHHHcCCCCCCCCCCCCEeeccCCC
Confidence 9998 4999996 8977677899999999999999999999999999999999643
No 5
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.85 E-value=5.7e-20 Score=146.45 Aligned_cols=127 Identities=15% Similarity=0.178 Sum_probs=108.9
Q ss_pred ceEEEEecCCCHHHHHHHHHHHHHhhccc-----cccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCce
Q psy16608 22 ATLVYIPLQTNLARLYAMLKEELNSVGIS-----VEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSI 96 (202)
Q Consensus 22 ~tfi~i~~~~~~~~~~~~l~~~~~~~~~~-----~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~ 96 (202)
|+|++|.+|. ++.+.|.++++.+... .+.++++||||.|+|+++.++++.+.+.|++... .+|++.++++
T Consensus 2 R~FiAl~~p~---~~~~~l~~~~~~l~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~--~~f~l~l~~~ 76 (179)
T TIGR02258 2 RLFIAIDLPP---EIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIAE--PPFTLKLEGI 76 (179)
T ss_pred eEEEEecCCH---HHHHHHHHHHHHhhccCCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhcC--CCeEEEEeee
Confidence 5666666664 7999999999987632 2888999999999999999999999999887653 5699999999
Q ss_pred EEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCC
Q psy16608 97 EIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQD 155 (202)
Q Consensus 97 ~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~ 155 (202)
|+|++..++|++|+ ++..+ ..|..|++.+.+.+...|++.+.++|.||||||+....
T Consensus 77 ~~F~~~~~~~vl~l-~~~~~-~~L~~L~~~l~~~~~~~g~~~~~~~f~PHiTlar~~~~ 133 (179)
T TIGR02258 77 GVFGNPKRPRVLWA-GVEQS-EELTQLHADLERELAKLGFSKEERPFTPHITLARKKSG 133 (179)
T ss_pred eeCCCCCCCeEEEE-eeCCC-HHHHHHHHHHHHHHHHcCCCCCCCCcCCCEEEEEecCC
Confidence 99999889999996 78764 58999999999999999999888899999999987644
No 6
>PHA02574 57B hypothetical protein; Provisional
Probab=99.73 E-value=1.6e-17 Score=128.94 Aligned_cols=110 Identities=8% Similarity=0.087 Sum_probs=88.8
Q ss_pred ccceEEEEecCCCHHHHHHHHHHHHHhhcc-ccccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEE
Q psy16608 20 SWATLVYIPLQTNLARLYAMLKEELNSVGI-SVEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEI 98 (202)
Q Consensus 20 ~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~-~~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~ 98 (202)
..|+|++|+++. ++++.|.++++.+.. ..|.+++||+||.| ..++++.+.. ..++|.+.++++|+
T Consensus 8 ~~RlF~Al~~~~---~~r~~L~~lq~~l~~~r~V~~enLHlTL~F----~~~~v~~l~~-------~~~~F~l~l~glG~ 73 (149)
T PHA02574 8 SQGTYVAAKFSE---ATLDALERLQRTLRIPNPVPRDKLHSTIVY----SRVYVPFIPA-------SGSTEVASSGHLEV 73 (149)
T ss_pred cceEEEEEcCCH---HHHHHHHHHHHhccCCcccCHHHCEEEEec----CHHHhHHHhc-------cCCCeEEEeccccc
Confidence 457888888765 899999999988643 22999999999999 3445555522 55899999999999
Q ss_pred EecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy16608 99 FCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAW 151 (202)
Q Consensus 99 f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~ 151 (202)
|++.. +|+.|+ |++ ...|..|++.+++.+++.+ +++|+|||||||
T Consensus 74 F~~~~-~rvlWl-g~~--~~~L~~L~~~l~~~l~~~~----~r~F~PHITLaR 118 (149)
T PHA02574 74 WETQD-KNALVL-VLE--SEYLQCRHKYARALGATHD----FDDYTPHITLSY 118 (149)
T ss_pred cCCCC-CCEEEE-EeC--CHHHHHHHHHHHHHhhcCC----CCCcCCcEEEee
Confidence 97633 799997 785 6789999999999999843 558999999999
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.72 E-value=2.4e-16 Score=124.92 Aligned_cols=154 Identities=14% Similarity=0.154 Sum_probs=112.0
Q ss_pred EEecCCCHHHHHHHHHHHHHhhccccccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCc
Q psy16608 26 YIPLQTNLARLYAMLKEELNSVGISVEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKT 105 (202)
Q Consensus 26 ~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~ 105 (202)
+|.+.+ ++++++.+.++.+.+..... .-+-||||.|+|+++.++++.+.+.+++..+...+|++++++++.|++. +
T Consensus 4 ~iai~~-p~~~~~~l~~~~~~~~~~~~-~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~F~~~--~ 79 (168)
T PRK13679 4 GIVLFP-SKKIQDFANSYRKRYDPHYA-LIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAPT--N 79 (168)
T ss_pred EEEEcC-CHHHHHHHHHHHHhhCcccc-cCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEeccccCCCC--C
Confidence 445554 45899999999888875431 2223999999999999999999999999888889999999999999873 6
Q ss_pred eEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCCCchhHHHHHHHHHHhhhhcccCCceeeccc
Q psy16608 106 RSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQDKTATLKPLLTKLDNIFTQFKLTSDESFHVV 185 (202)
Q Consensus 106 RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~v 185 (202)
+++|+ ++.. .+.|..|++.+...+. ...+.++|.||||||+.... +...++... +.. . ...+.|. |
T Consensus 80 ~vl~l-~~~~-~~~L~~L~~~l~~~~~---~~~~~~~f~PHiTlar~~~~--~~~~~~~~~----l~~-~-~~~~~~~-v 145 (168)
T PRK13679 80 NVIYF-KVEK-TEELEELHERLHSGDF---YGEAEYAFVPHITIGQGLSD--DEHEDVLGQ----LKM-A-DVDHEET-I 145 (168)
T ss_pred CEEEE-EccC-CHHHHHHHHHHHhccc---ccccCCCCCCeEEeeCCCCc--HHHHHHHHH----Hhc-C-CcceeEE-E
Confidence 89886 7875 5789999999987654 34556789999999976443 222223322 221 1 3335777 8
Q ss_pred ceEEE--eeCCeEE
Q psy16608 186 THIHM--KTGNKFY 197 (202)
Q Consensus 186 ~~v~~--k~Gn~~~ 197 (202)
++|.+ +.||..+
T Consensus 146 ~~i~L~~~~~~~~w 159 (168)
T PRK13679 146 DRFHLLYQLENGSW 159 (168)
T ss_pred CeEEEEEECCCCeE
Confidence 88888 2255444
No 8
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.54 E-value=2.7e-14 Score=109.99 Aligned_cols=118 Identities=19% Similarity=0.193 Sum_probs=75.8
Q ss_pred HHHHHHHHHHHHhhccccccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEee
Q psy16608 34 ARLYAMLKEELNSVGISVEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGA 113 (202)
Q Consensus 34 ~~~~~~l~~~~~~~~~~~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v 113 (202)
+++.+.++.+..+.........+.||||.+.+...... +.+.+.|+..++..++|.++|+++++|++ +++++|+ ++
T Consensus 3 ~~~~~~i~~lr~~~~~~~~~~~~pHITL~~~~~~~~~~-~~~~~~l~~~~~~~~~f~l~l~~~~~F~~--~~~vi~l-~~ 78 (153)
T PF13563_consen 3 DELAEEIEALRRQKGDKRYPRWPPHITLAFPFDIDDSL-DELVEALARLAAGFPPFELRLDGFGSFPG--KGRVIFL-NV 78 (153)
T ss_dssp ----------GT-TTEEE--GGG-EEEEEEEEE--GGG-HHHHHHHHHHHHHS--EEEEEEEEEEESS--SSSSEEE-EE
T ss_pred ccccccchhhhcccCCCCCCCCCCEeEEEecCcccccH-HHHHHHHHHHHccCCCeEEEEccEEEcCC--CCCEEEE-Ec
Confidence 45555555544111111255566999999999999766 88899999998889999999999999999 4447775 67
Q ss_pred cCCCccHHHHHHHHHHHHHhcCCCCCC-CCCCceEEEEeecCCC
Q psy16608 114 NSCKTSLTSIVQAVDKSAQEFKLPTYY-EEPNFHASIAWCLQDK 156 (202)
Q Consensus 114 ~~~~~~L~~L~~~i~~~l~~~g~~~~~-~~~~pHiSia~~~~~~ 156 (202)
.. ...|..|++.|...+..++...+. +++.||||||+.....
T Consensus 79 ~~-~~~L~~L~~~l~~~~~~~~~~~~~~~~~~PHiTia~~~~~~ 121 (153)
T PF13563_consen 79 EP-SPELEALHRALREALRPFGFKQDSYRPFRPHITIARRLSPK 121 (153)
T ss_dssp EE--HHHHHHHHHHHHHHHHHHGGGGGGS----EEEEEEESS--
T ss_pred CC-CHHHHHHHHHHHHHHHHcCCccccCCCcceEEEEeccCCcc
Confidence 43 578999999999999999888777 8999999999875443
No 9
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=99.53 E-value=2.6e-13 Score=110.94 Aligned_cols=161 Identities=18% Similarity=0.155 Sum_probs=116.3
Q ss_pred eEEEEecCCCHHHHHHHHHHHHHhhccc--------cccCCCCeEeeeeeeccCcccHHHHHHHHHHh---hcc----CC
Q psy16608 23 TLVYIPLQTNLARLYAMLKEELNSVGIS--------VEVIPEPHLSLSKTLVIPYHWIDTLVETLGNN---LRH----LN 87 (202)
Q Consensus 23 tfi~i~~~~~~~~~~~~l~~~~~~~~~~--------~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~---l~~----~~ 87 (202)
-|++|++. .+++.+.+.++++.+... ++.+..|||||..+.-.+.++++.-.+.|++. +.. ..
T Consensus 3 hFl~ipl~--~~~i~~~~~~fq~~v~~~~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~ 80 (209)
T PF10469_consen 3 HFLCIPLN--SPEIQEKFKEFQNEVLSKDPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPP 80 (209)
T ss_pred eEEEEECC--CHHHHHHHHHHHHHHHhhcCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCC
Confidence 47777774 567888888888766532 27899999999999888887888777777665 333 38
Q ss_pred ceEEEeCceEEEec-CCCceEEEEEeecCC--CccHHHHHHHHHHHHHhcCCCC--CCCC-CCceEEEEeecCC---Cch
Q psy16608 88 RLTIKFNSIEIFCN-EEKTRSFIALGANSC--KTSLTSIVQAVDKSAQEFKLPT--YYEE-PNFHASIAWCLQD---KTA 158 (202)
Q Consensus 88 ~F~l~~~~~~~f~n-~~~~RvF~~l~v~~~--~~~L~~L~~~i~~~l~~~g~~~--~~~~-~~pHiSia~~~~~---~~~ 158 (202)
++.|++.|+++|++ .+++||+|+ +|.++ ...|..+.+.|.+.+.+.|+.. +.++ +.||+||+.+... ...
T Consensus 81 ~~~i~l~Gl~~f~~d~~~~~VLya-~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~~~~~~~~~ 159 (209)
T PF10469_consen 81 PLKITLKGLGYFNDDPSKARVLYA-KVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTSYRKKKKRR 159 (209)
T ss_pred CceEEeeechhhCCCCCcceEEEE-cccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEecccccccccc
Confidence 99999999999999 888999998 78764 3779999999999999999877 3333 7999999976541 111
Q ss_pred hHHHHHHHHHHhhhhcccCCce-eecccceEEE
Q psy16608 159 TLKPLLTKLDNIFTQFKLTSDE-SFHVVTHIHM 190 (202)
Q Consensus 159 ~l~~~~~~l~~~~~~~~~~~~~-~~~~v~~v~~ 190 (202)
..... ...++++++. +..+ ... |++|.+
T Consensus 160 ~~~~~--d~~~~~~~~~-~~~fG~~~-v~~i~L 188 (209)
T PF10469_consen 160 QGNKF--DASELLEKYK-DFDFGEQP-VEEIQL 188 (209)
T ss_pred ccCcc--ccHHHHHHcC-CCccceEE-ECEEEE
Confidence 00100 2234455554 4444 556 677764
No 10
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=99.34 E-value=3e-12 Score=90.32 Aligned_cols=77 Identities=16% Similarity=0.217 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHHHhhcccc-------ccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCc
Q psy16608 33 LARLYAMLKEELNSVGISV-------EVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKT 105 (202)
Q Consensus 33 ~~~~~~~l~~~~~~~~~~~-------~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~ 105 (202)
+++.++.|.++.+.+.... +.++++||||.|+|+++.++++.+.+.+.+......+|+++++++++|++..++
T Consensus 4 p~~~~~~L~~l~~~l~~~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~~~~ 83 (87)
T PF02834_consen 4 PEEIKEQLNQLQERLRQALPPLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSRLRP 83 (87)
T ss_dssp THHHHHHHHHHHHHHHHHCCSCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEEETC
T ss_pred CHHHHHHHHHHHHHHhhhccccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCCCCC
Confidence 4578888888888887322 789999999999999999999999999999888899999999999999999999
Q ss_pred eEEE
Q psy16608 106 RSFI 109 (202)
Q Consensus 106 RvF~ 109 (202)
|++|
T Consensus 84 rvi~ 87 (87)
T PF02834_consen 84 RVIW 87 (87)
T ss_dssp EEEE
T ss_pred CCcC
Confidence 9988
No 11
>PLN00108 unknown protein; Provisional
Probab=98.89 E-value=4.2e-08 Score=82.31 Aligned_cols=170 Identities=15% Similarity=0.138 Sum_probs=114.7
Q ss_pred cceEEEEecCCCHHHHHHHHHHHHHhhcc--------------------c-cccCCCCeEeeeeeeccCcccHHHHHHHH
Q psy16608 21 WATLVYIPLQTNLARLYAMLKEELNSVGI--------------------S-VEVIPEPHLSLSKTLVIPYHWIDTLVETL 79 (202)
Q Consensus 21 w~tfi~i~~~~~~~~~~~~l~~~~~~~~~--------------------~-~~~~~~lHISLs~~~~~~~~~i~~~~~~L 79 (202)
|.=||.|++.. ..++.+.+.++.+.+-. . +..|..|||||.-+.-...++++.-.+.|
T Consensus 36 ~THFlavPL~~-~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L 114 (257)
T PLN00108 36 FTHFVSLPLAI-YPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNIL 114 (257)
T ss_pred CCeEEEEEcCC-CHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHH
Confidence 77788888842 34777777776654332 1 18889999999988877677777766666
Q ss_pred HHh---hcc---CCceEEEeCceEEEecC-CCceEEEEEeecCCC--ccHHHHHHHHHHHHHhcCCCC-CC-CCCCceEE
Q psy16608 80 GNN---LRH---LNRLTIKFNSIEIFCNE-EKTRSFIALGANSCK--TSLTSIVQAVDKSAQEFKLPT-YY-EEPNFHAS 148 (202)
Q Consensus 80 ~~~---l~~---~~~F~l~~~~~~~f~n~-~~~RvF~~l~v~~~~--~~L~~L~~~i~~~l~~~g~~~-~~-~~~~pHiS 148 (202)
++. +.. -+|+.|.+.|+++|..+ .++||++| +|++.. +.|..+.+.|-+...+.|+-. ++ ++..+|+|
T Consensus 115 ~s~~~~i~~~l~~~pl~I~lkGL~~Mnddps~~~VLYA-~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d~~~~vKLH~T 193 (257)
T PLN00108 115 KSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA-PVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSRLKLHAT 193 (257)
T ss_pred HHHHHHHHHhhCCCCeEEEEEeehhcCCCcccceEEEE-eccccCchhHHHHHHHHHHHHHHHcCCcccccCcceeeEeE
Confidence 544 322 38999999999999754 55999998 897532 568888888888888899864 43 57999999
Q ss_pred EEeecCCCchhHHHHHHHHHHhhhhcccCCce-eecccceEEEeeCC
Q psy16608 149 IAWCLQDKTATLKPLLTKLDNIFTQFKLTSDE-SFHVVTHIHMKTGN 194 (202)
Q Consensus 149 ia~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~-~~~~v~~v~~k~Gn 194 (202)
|.-+.-.....-+...=+=.+++++|. +.++ .+. |++|+|-.-.
T Consensus 194 lmNt~~rk~k~~k~~sFDA~~Il~~f~-d~~FG~~~-i~~vhls~r~ 238 (257)
T PLN00108 194 LMNASYRKDKSKKMDTFDAREIHKEFE-NKDWGTYL-IREAHISQRY 238 (257)
T ss_pred EechhhhhcccCccccccHHHHHHhcc-CcccceEE-ecEEEEEeec
Confidence 994431111100000001124566665 5566 777 8888876644
No 12
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=97.30 E-value=0.004 Score=51.70 Aligned_cols=92 Identities=16% Similarity=0.192 Sum_probs=65.0
Q ss_pred CCeEeeeeeeccCccc-HHHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhc
Q psy16608 56 EPHLSLSKTLVIPYHW-IDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEF 134 (202)
Q Consensus 56 ~lHISLs~~~~~~~~~-i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~ 134 (202)
.+|+||+-++.+.... .+.+.+.++...++..||.+.-=.+.-.. -|+++........|..|...+-+.+..|
T Consensus 57 GfHaTLKaPFrLa~g~~~a~L~~al~~fA~~~~pf~i~~L~l~~Lg------~FlAL~P~~~~~~L~~LAa~~V~~~d~f 130 (228)
T TIGR03223 57 GFHATLKAPFRLAPGVTEAELLAAVAAFAATRAPFALPPLRVALLG------GFLALRPAAPCPALQALAAACVRELDPF 130 (228)
T ss_pred ccceeecCCcccCCCCCHHHHHHHHHHHHhcCCCccCCcceeeeeC------CEEEEeeCCCCHHHHHHHHHHHHhhhhc
Confidence 5999999999999874 89999999999999999987611111111 1455544455577888887776665554
Q ss_pred ----------------------------CCCCCCCCCCceEEEEeec
Q psy16608 135 ----------------------------KLPTYYEEPNFHASIAWCL 153 (202)
Q Consensus 135 ----------------------------g~~~~~~~~~pHiSia~~~ 153 (202)
|.|.=-+.|+|||||-=.+
T Consensus 131 RAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg~l 177 (228)
T TIGR03223 131 RAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTGRL 177 (228)
T ss_pred cCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecCCC
Confidence 4454456799999998444
No 13
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=97.04 E-value=0.012 Score=48.30 Aligned_cols=117 Identities=14% Similarity=0.035 Sum_probs=79.5
Q ss_pred EEecCCCH-HHHHHHHHHHHHhhccccccC---CCCeEeeeeeeccCcccHHHHHHHHHHhhccC--CceEEEeCceEEE
Q psy16608 26 YIPLQTNL-ARLYAMLKEELNSVGISVEVI---PEPHLSLSKTLVIPYHWIDTLVETLGNNLRHL--NRLTIKFNSIEIF 99 (202)
Q Consensus 26 ~i~~~~~~-~~~~~~l~~~~~~~~~~~~~~---~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~--~~F~l~~~~~~~f 99 (202)
||..|... +.+...-.+++.++-+.++.. ..-||||.-+ .+.+++|......|++.+... .-..+++++.-..
T Consensus 9 Fin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~k~QkaPHlSl~mL-~Isd~~i~~V~~~iq~ViddM~~~~~~it~tnp~ML 87 (248)
T PF05213_consen 9 FINFPLVQFEGFMLNFKDLQFQLLEEGVDCKLQKAPHLSLGML-DISDEDIPDVETAIQKVIDDMVWFEGDITFTNPHML 87 (248)
T ss_pred eeeccchhhhhHHHHHHHHHHHHHHcCCCccccccCeeEEEEE-EcChhhhhhHHHHHHHHHHHhhcccceEEecCceee
Confidence 56666622 333334444554444444222 4569999865 577788888887887777663 2347777776666
Q ss_pred ecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCC-CCCCceEEEEeec
Q psy16608 100 CNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYY-EEPNFHASIAWCL 153 (202)
Q Consensus 100 ~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~-~~~~pHiSia~~~ 153 (202)
+ |. +++.|++ +..|+..|-.++.+-|.--.. |.+.||+|||..+
T Consensus 88 g-----~~-yV~nV~G----v~slh~ki~n~~~~kgit~gQSRmwIPHiTia~~~ 132 (248)
T PF05213_consen 88 G-----RC-YVANVKG----VLSLHDKIVNVFRKKGITFGQSRMWIPHITIAQLN 132 (248)
T ss_pred c-----cE-EEEeccc----HHHHHHHHHHHHHHhCcCcCcccccccceehhhhh
Confidence 3 44 5568865 889999999999998876544 6799999999864
No 14
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=96.99 E-value=0.0086 Score=48.64 Aligned_cols=114 Identities=19% Similarity=0.183 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHhhcccc-c--cCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCce-----EEEeCceEEEecCCCce
Q psy16608 35 RLYAMLKEELNSVGISV-E--VIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRL-----TIKFNSIEIFCNEEKTR 106 (202)
Q Consensus 35 ~~~~~l~~~~~~~~~~~-~--~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F-----~l~~~~~~~f~n~~~~R 106 (202)
...+.|..++..++... + ..=.-||||.-...+. ..+.+.+.|+..+...+++ .+.|+++.. +..---+
T Consensus 14 ~~~~~L~~lI~~L~~~~~~~~p~F~PHiTL~s~i~~~--~~~~~~~~L~~~~~~~~~~~~~~~~v~~~~v~~-g~~yfq~ 90 (196)
T PF07823_consen 14 PLYERLKTLISSLASLFPGSPPPFEPHITLTSGISLD--SSDDVQKVLDSAAAALKPLPKNHFTVRFDKVAS-GDKYFQC 90 (196)
T ss_dssp TTHHHHHHHHHHHHHHST---------EEEEEEEEE----HHHHHHHHHHHHHH-B-E-----EEEEEEEEE-EEETTEE
T ss_pred cHHHHHHHHHHHHHHHCCCCCCCcCCeEEEeCCCccC--CHHHHHHHHHHHHHhccCcccceeEEEeeeEee-CCeEEEE
Confidence 35566777777776655 2 3345799999866664 4455555566565566777 899987743 2223335
Q ss_pred EEEEEeecCCCccHHHHHHHHHHHHHhcC------CCCCCCCCCceEEEEeecC
Q psy16608 107 SFIALGANSCKTSLTSIVQAVDKSAQEFK------LPTYYEEPNFHASIAWCLQ 154 (202)
Q Consensus 107 vF~~l~v~~~~~~L~~L~~~i~~~l~~~g------~~~~~~~~~pHiSia~~~~ 154 (202)
+++ .|.. ...|..|.+.+.+++.... ...-..+|.|||||.+..-
T Consensus 91 vyl--~v~~-t~~L~~l~~~~r~~~~~~~~~~~~~~~~~~~~y~PHlSLlY~d~ 141 (196)
T PF07823_consen 91 VYL--EVEK-TPELMSLAQIARELFVEGPPDEVKAAEWPREPYMPHLSLLYGDL 141 (196)
T ss_dssp EEE--EE----HHHHHHHCHHHHCT----------T----S----EEEEE----
T ss_pred EEE--EecC-ChhHHHHHHHHHHHhhhccccccccccccCCCCCCeEEEEEcCC
Confidence 554 3655 4678888888777664321 1223357999999999643
No 15
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=96.99 E-value=0.0011 Score=46.31 Aligned_cols=68 Identities=10% Similarity=0.106 Sum_probs=44.6
Q ss_pred ccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCCCchhHHHHHHHHHHhhhhccc-CCceeecccceEEEe
Q psy16608 118 TSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQDKTATLKPLLTKLDNIFTQFKL-TSDESFHVVTHIHMK 191 (202)
Q Consensus 118 ~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~~~~~l~~~~~~l~~~~~~~~~-~~~~~~~~v~~v~~k 191 (202)
+.|..+.+.+.+.+...|+... +++.|||||++. |+..+ ..+.+|.+.++.... ...+.+. |+++.+-
T Consensus 9 ~~L~~l~~~l~~~~~~~~~r~~-~~~~~HiTL~fl-g~~~~---~~~~~l~~~l~~~~~~~~~f~~~-~~~~~~f 77 (87)
T PF02834_consen 9 EQLNQLQERLRQALPPLGIRWV-RPFNPHITLAFL-GEVPP---DQLPELIEALANIASRFPPFTLT-VDGFGLF 77 (87)
T ss_dssp HHHHHHHHHHHHHCCSCTEEEG-SCGGSEEEEEEE-EEESH---HHHHHHHHHHHHHHCCCB-EEEE-EEEEEEE
T ss_pred HHHHHHHHHHhhhccccCCccc-CCCCCeEEEEeC-CCCCH---HHHHHHHHHHHhhhccCCCeEEE-EeEEEEe
Confidence 5788899999999889999888 899999999986 44332 223333333433321 1245666 7676654
No 16
>KOG2814|consensus
Probab=95.44 E-value=0.13 Score=44.86 Aligned_cols=125 Identities=10% Similarity=0.066 Sum_probs=83.1
Q ss_pred EEEecCCCHHHHHHHHHHHHH--hh----ccc------cccCCCCeEeeeeeeccCcccHHHHHHHHHHhhc------cC
Q psy16608 25 VYIPLQTNLARLYAMLKEELN--SV----GIS------VEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLR------HL 86 (202)
Q Consensus 25 i~i~~~~~~~~~~~~l~~~~~--~~----~~~------~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~------~~ 86 (202)
.|++++.+.-++++.+..+.+ -+ -.. +..|.-+|+|+.+.--+....+....+.|+..-. .-
T Consensus 134 hflal~lne~eVqe~f~~fke~~~~~esl~~~g~~~s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~ 213 (345)
T KOG2814|consen 134 HFLALPLNEHEVQEGFLAFKELKPFIESLLDGGIDKSLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGE 213 (345)
T ss_pred hhhhhhcchHHHHHHHHHHHhhhhhHHHhhccchhhccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCC
Confidence 455555534556665555541 11 111 1788899999999999999999999888877332 24
Q ss_pred CceEEEeCceEEEecC-CCceEEEEEeecCCC--ccHHHHH-HHHHHHHHhcCC-CCCCCCCCceEEEE
Q psy16608 87 NRLTIKFNSIEIFCNE-EKTRSFIALGANSCK--TSLTSIV-QAVDKSAQEFKL-PTYYEEPNFHASIA 150 (202)
Q Consensus 87 ~~F~l~~~~~~~f~n~-~~~RvF~~l~v~~~~--~~L~~L~-~~i~~~l~~~g~-~~~~~~~~pHiSia 150 (202)
+|+.+.+.++..+..+ ..+|+.+| .|.+.. ..|.... +.|-....+.|+ ....++-..|+|+.
T Consensus 214 kp~~i~lkG~~~mnddP~~~kVLYA-kv~~~~~e~~l~~~~~~~i~~~f~~~~li~k~~~~~kLH~Tvm 281 (345)
T KOG2814|consen 214 KPLFIDLKGLDKMNDDPSLTKVLYA-KVEPDDYEKFLQHRCGERILERFVASGLIKKESSSLKLHCTVM 281 (345)
T ss_pred CceeeeccchhhhcCCHhHheeeee-eccCcchHHHHHHHHHHHHHHHHHHhcchhccccccEEEEEEe
Confidence 7899999999988766 55899998 787654 2233333 333344444443 44555678999999
No 17
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=95.20 E-value=0.36 Score=38.01 Aligned_cols=85 Identities=16% Similarity=0.226 Sum_probs=59.9
Q ss_pred eeeeeeccCcc-cHHHHHHHHHHhhccCCceEEE---eCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhc-
Q psy16608 60 SLSKTLVIPYH-WIDTLVETLGNNLRHLNRLTIK---FNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEF- 134 (202)
Q Consensus 60 SLs~~~~~~~~-~i~~~~~~L~~~l~~~~~F~l~---~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~- 134 (202)
||+-++.+... .-+.+.+.++...+...||.+. +..+| -|+++-..+....|..|...+-..+..|
T Consensus 1 TLKaPF~La~g~~~~~L~~a~~~~a~~~~pf~l~~L~v~~lg---------~FlALvp~~~~~~L~~LAa~cV~~~d~fR 71 (160)
T PF06299_consen 1 TLKAPFRLAEGASEADLLAALAAFAARFAPFELPGLEVARLG---------GFLALVPAGPCPALQALAAACVRAFDPFR 71 (160)
T ss_pred CCCCCcccCCCCCHHHHHHHHHHHhccCCCccCCceeEeeEC---------CEEEEeeCCCCHHHHHHHHHHHHhhhhcc
Confidence 67777888875 6788999999888889998765 33443 4677644554567888877766555555
Q ss_pred ---------------------------CCCCCCCCCCceEEEEeec
Q psy16608 135 ---------------------------KLPTYYEEPNFHASIAWCL 153 (202)
Q Consensus 135 ---------------------------g~~~~~~~~~pHiSia~~~ 153 (202)
|.|.=-+.|+|||||--.+
T Consensus 72 APls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l 117 (160)
T PF06299_consen 72 APLSEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRL 117 (160)
T ss_pred CCCChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCC
Confidence 4444445789999998544
No 18
>PHA02977 hypothetical protein; Provisional
Probab=94.23 E-value=0.39 Score=37.24 Aligned_cols=142 Identities=11% Similarity=0.161 Sum_probs=76.9
Q ss_pred ccCccccccceEEEEecCCCHHHHHHHHHHHHHhhccccccCCCCeEeeeeeeccCcccHHHHHHHHHHhhcc--CCceE
Q psy16608 13 SFPHQRNSWATLVYIPLQTNLARLYAMLKEELNSVGISVEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRH--LNRLT 90 (202)
Q Consensus 13 ~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~--~~~F~ 90 (202)
.+|----||++--|.++++ ...+.+ ++.+.-+. +.+-.-.-||||.- -..+|-+.|.. .++.+.. .++.+
T Consensus 30 ~vpwdy~nwasinfydirl-d~~isd-~~niaiky--mtgcdi~phitlgi---an~dq~~~f~~-fk~~~~d~dl~sis 101 (201)
T PHA02977 30 EVPWDYCNWASINFYDIRL-DKDISD-LENIAIKY--MTGCDIFPHITLGI---ANKDQCDNFEN-FKELIKDIDLQSIS 101 (201)
T ss_pred eccccccccceeeeEEEEe-cCCcch-hhhhhhhh--hccCCCCcceeeec---cCccHhHHHHH-HHHHhhcccceeEE
Confidence 3566667999999999887 444433 22221111 11222345999853 34445555542 3444443 34455
Q ss_pred EEeCceEEEecCCCce-------EEEEEeecCCCccHHHHHHHHHHHH----HhcCCCCCCCCCCceEEEEeecCCCchh
Q psy16608 91 IKFNSIEIFCNEEKTR-------SFIALGANSCKTSLTSIVQAVDKSA----QEFKLPTYYEEPNFHASIAWCLQDKTAT 159 (202)
Q Consensus 91 l~~~~~~~f~n~~~~R-------vF~~l~v~~~~~~L~~L~~~i~~~l----~~~g~~~~~~~~~pHiSia~~~~~~~~~ 159 (202)
+.-...-.||....++ . .++.++. ++.|+.|...+-.++ .-||=-.-.-+-.||+|||+++.+..+.
T Consensus 102 ~~cke~icfpqs~askelga~g~a-vvmkle~-sddlkalrnvl~n~vp~pkdifg~i~~d~~w~phitigyv~~dd~dn 179 (201)
T PHA02977 102 FTCKEEICFPQSNASKELGAKGCA-VVMKLEA-SDDLKALRNVLFNAVPCPKDIFGDILSDNPWCPHITIGYVKADDEDN 179 (201)
T ss_pred EEeeeeEeccccchhhhhCcCccE-EEEEEEe-chHHHHHHHHhhcccCCcHHhhcccccCCCCCCceEEEeecccchhh
Confidence 5555666787655443 2 1233433 356777666543332 1244333344678999999998776554
Q ss_pred HHHHH
Q psy16608 160 LKPLL 164 (202)
Q Consensus 160 l~~~~ 164 (202)
-++++
T Consensus 180 k~r~i 184 (201)
T PHA02977 180 KKRFI 184 (201)
T ss_pred HHHHH
Confidence 44443
No 19
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.81 E-value=2 Score=35.20 Aligned_cols=148 Identities=14% Similarity=0.187 Sum_probs=79.4
Q ss_pred cCcccccc-ceEEEEecCCCHHHHHHHHHHHHHhhcccc-------ccCCCCeEeeee--------e----eccCcc-cH
Q psy16608 14 FPHQRNSW-ATLVYIPLQTNLARLYAMLKEELNSVGISV-------EVIPEPHLSLSK--------T----LVIPYH-WI 72 (202)
Q Consensus 14 ~pH~~G~w-~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~-------~~~~~lHISLs~--------~----~~~~~~-~i 72 (202)
|.|..||- -||++=.- +..+.+-.+.+++..+- ..+..+|+|+-- + -+++-+ -|
T Consensus 36 f~pfpGNTVVchl~~gs-----~t~~vvl~i~~r~~~mpfadklt~tP~sSlHMTvfqg~~e~~R~~~~WpqdlPLDtpi 110 (239)
T COG5255 36 FLPFPGNTVVCHLVTGS-----DTEEVVLIIRSRYLEMPFADKLTFTPVSSLHMTVFQGLIEERRELPYWPQDLPLDTPI 110 (239)
T ss_pred cccCCCCeEEEeccCCC-----chHHHHHHHHHHhhccchhhhhccCCcchhhHHHHHHHhhhcccCCCCCccCCCCCcH
Confidence 67778883 56665422 34555666677666542 778899999842 1 122222 45
Q ss_pred HHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHH-HHhcCC-CCCCCCCCceEEEE
Q psy16608 73 DTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKS-AQEFKL-PTYYEEPNFHASIA 150 (202)
Q Consensus 73 ~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~-l~~~g~-~~~~~~~~pHiSia 150 (202)
+..-+-..+.++.++-+.=.|+ .=..+.+|-.+.+.++...+ ..++.++... -..+|. -+..+.+.||||||
T Consensus 111 ~~~~~~~~erLk~F~l~~~~~~---mrvte~rp~~i~v~paddad---~~~l~~~Rd~ls~~~g~r~P~HDaY~FHITlg 184 (239)
T COG5255 111 DAITDYYAERLKIFPLLDEEFN---MRVTEMRPQGILVEPADDAD---AKILEEWRDYLSEKFGYRHPDHDAYQFHITLG 184 (239)
T ss_pred HHHHHHHHHHHhcccCCchhhc---chhhcccccceEeccCCHHH---HHHHHHHHHHHhhhhcccCCCCcceEEEEEee
Confidence 6666666677766543321222 11134456665655554432 2333444333 345664 34556799999999
Q ss_pred ----eecCCCchhHHHHHHHHHHhhh
Q psy16608 151 ----WCLQDKTATLKPLLTKLDNIFT 172 (202)
Q Consensus 151 ----~~~~~~~~~l~~~~~~l~~~~~ 172 (202)
|...+..+.+.+.++++-+++.
T Consensus 185 Yl~~wltpee~a~~q~~l~e~~e~la 210 (239)
T COG5255 185 YLRIWLTPEEEAEWQAVLDELLEILA 210 (239)
T ss_pred eEeeecChhhhHHHHHHHHHHHHHHH
Confidence 4333333334445555444443
No 20
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=90.73 E-value=9.4 Score=32.33 Aligned_cols=119 Identities=8% Similarity=0.038 Sum_probs=64.9
Q ss_pred ceEEEEecCCCHHHHHHHHHHHHHhh-----------ccccccCCCCeEeeeeeeccCccc----HHHHHHHHHHhhccC
Q psy16608 22 ATLVYIPLQTNLARLYAMLKEELNSV-----------GISVEVIPEPHLSLSKTLVIPYHW----IDTLVETLGNNLRHL 86 (202)
Q Consensus 22 ~tfi~i~~~~~~~~~~~~l~~~~~~~-----------~~~~~~~~~lHISLs~~~~~~~~~----i~~~~~~L~~~l~~~ 86 (202)
+.|+.|.++ ..++.+.|..+...- +..--....+||||........+. ++.+.+.....+...
T Consensus 72 p~Yf~i~i~--~~~i~~~l~~~f~~~~~~~~~~~~~L~~~~RvQ~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~ 149 (257)
T PF08302_consen 72 PEYFGISIP--TQDIKSLLEKLFEDSPPETARFYNQLKNSRRVQPEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKN 149 (257)
T ss_pred CeEEEEECC--HHHHHHHHHHHhccCCHHHHHHHHHHHhCCCCCCCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccc
Confidence 578888885 567777777766543 111133467999999888888744 455555544444321
Q ss_pred -----------CceEEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCC
Q psy16608 87 -----------NRLTIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQD 155 (202)
Q Consensus 87 -----------~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~ 155 (202)
..+.+++.++- .+++-=.|-+ .+......-.. .-++ ..-+..||||||-...+
T Consensus 150 ~~~~~~~~~~~~~~~v~L~rlv---wd~rimai~V-~~~~~~~~~~~----------~~~~--~c~N~~~HITVGT~~~~ 213 (257)
T PF08302_consen 150 PKQEPTQTPTLGSCDVRLERLV---WDDRIMAIVV-RIVPPEDEEDE----------VPEW--ECTNKIPHITVGTRDPG 213 (257)
T ss_pred cccccccccccceEEEEEEEEE---ECCcEEEEEE-EccCccccccc----------cCCc--ccCCCCCEEEEEcCCCC
Confidence 23556665552 4444433333 23221110000 1111 23467999999976555
Q ss_pred Cch
Q psy16608 156 KTA 158 (202)
Q Consensus 156 ~~~ 158 (202)
..+
T Consensus 214 VkP 216 (257)
T PF08302_consen 214 VKP 216 (257)
T ss_pred CCc
Confidence 444
No 21
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=87.30 E-value=1.8 Score=33.85 Aligned_cols=49 Identities=12% Similarity=0.277 Sum_probs=26.1
Q ss_pred ceEEEEEeecCCCccHHHHHHHHHHHHHh-cCCCCCCCCCCceEEEEeecCCCc
Q psy16608 105 TRSFIALGANSCKTSLTSIVQAVDKSAQE-FKLPTYYEEPNFHASIAWCLQDKT 157 (202)
Q Consensus 105 ~RvF~~l~v~~~~~~L~~L~~~i~~~l~~-~g~~~~~~~~~pHiSia~~~~~~~ 157 (202)
.|.|+|+.+.+ .+...+..+.+.+.. ...-....+..+||||+.. ++..
T Consensus 1 ~R~FiAl~~p~---~~~~~l~~~~~~l~~~~~~~r~~~~~~~HiTL~fl-g~~~ 50 (179)
T TIGR02258 1 MRLFIAIDLPP---EIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFL-GEVD 50 (179)
T ss_pred CeEEEEecCCH---HHHHHHHHHHHHhhccCCCcEECChHHCEEEEEEc-cCCC
Confidence 38999976643 344444444444331 1111222345779999964 5543
No 22
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=86.94 E-value=1.7 Score=35.22 Aligned_cols=58 Identities=10% Similarity=0.165 Sum_probs=31.6
Q ss_pred ceEEEEEeecCCCccHHHHHHHHHH-HHHhc-CC--CCCCCCCCceEEEEeecCCCchhHHHHH
Q psy16608 105 TRSFIALGANSCKTSLTSIVQAVDK-SAQEF-KL--PTYYEEPNFHASIAWCLQDKTATLKPLL 164 (202)
Q Consensus 105 ~RvF~~l~v~~~~~~L~~L~~~i~~-~l~~~-g~--~~~~~~~~pHiSia~~~~~~~~~l~~~~ 164 (202)
|--|+++++... .|..=++.+.+ ++... ++ +.+..+.+.||||+-..-...+.++++.
T Consensus 1 pthFl~ipl~~~--~i~~~~~~fq~~v~~~~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~ 62 (209)
T PF10469_consen 1 PTHFLCIPLNSP--EIQEKFKEFQNEVLSKDPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAK 62 (209)
T ss_pred CCeEEEEECCCH--HHHHHHHHHHHHHHhhcCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHH
Confidence 346899999543 33333333333 33222 34 2234578999999966555444554333
No 23
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=85.99 E-value=3.5 Score=33.03 Aligned_cols=50 Identities=18% Similarity=0.327 Sum_probs=31.9
Q ss_pred ceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCCCch
Q psy16608 105 TRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQDKTA 158 (202)
Q Consensus 105 ~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~~~~ 158 (202)
.|.|+|+.+.. .+...+..+.+-+...+.-+-+++..+||||.. +|+..+
T Consensus 1 ~RlFiAl~~p~---~i~~~i~~~~~~~~~~~~~k~v~~en~HiTL~f-lGev~e 50 (180)
T COG1514 1 MRLFIALDPPA---EIAERLARIRARLKGARAIKWVEPENLHITLKF-LGEVDE 50 (180)
T ss_pred CeeEEEecCCH---HHHHHHHHHHHhcCcccccccccccCceEEEEc-cCCcCc
Confidence 48999976643 354444444444443334456778899999998 476654
No 24
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=79.52 E-value=7.5 Score=31.38 Aligned_cols=43 Identities=9% Similarity=-0.042 Sum_probs=19.3
Q ss_pred EEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy16608 107 SFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWC 152 (202)
Q Consensus 107 vF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~ 152 (202)
..|..+-. ++..-..|...|...-..|+-. +-.|-|||||+--
T Consensus 4 SlWl~P~~-~~~~~~~L~~lI~~L~~~~~~~--~p~F~PHiTL~s~ 46 (196)
T PF07823_consen 4 SLWLVPPP-GSPLYERLKTLISSLASLFPGS--PPPFEPHITLTSG 46 (196)
T ss_dssp EEEEEE-T---TTHHHHHHHHHHHHHHST-----------EEEEEE
T ss_pred EEEEcCCC-CccHHHHHHHHHHHHHHHCCCC--CCCcCCeEEEeCC
Confidence 46776443 2344555555565555666532 4568999999963
No 25
>PRK15124 2'-5' RNA ligase; Provisional
Probab=78.20 E-value=9.1 Score=30.12 Aligned_cols=51 Identities=14% Similarity=0.155 Sum_probs=26.4
Q ss_pred CceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCCCch
Q psy16608 104 KTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQDKTA 158 (202)
Q Consensus 104 ~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~~~~ 158 (202)
..|.|+|+.+.+ .+...+..+.+.+.....-.--.+...||||+.. |+..+
T Consensus 4 ~~RlFiAl~~p~---~~~~~l~~~~~~~~~~~~~rwv~~~nlHiTL~Fl-G~v~~ 54 (176)
T PRK15124 4 PKRLFFAIDLPD---EIRQQIIHWRATHFPPEAGRPVAAANLHLTLAFL-GEVSA 54 (176)
T ss_pred ceEEEEEeCCCH---HHHHHHHHHHHHhccccCcccccccccEEEEEec-CCCCH
Confidence 369999986643 2322222222222211111222356889999984 76554
No 26
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=74.58 E-value=16 Score=30.34 Aligned_cols=55 Identities=15% Similarity=0.050 Sum_probs=32.7
Q ss_pred cceEEEEecCCCHHH-HHHHHHHHHHhhccc----cc-cCCCCeEeeeeeeccCcccHHHH
Q psy16608 21 WATLVYIPLQTNLAR-LYAMLKEELNSVGIS----VE-VIPEPHLSLSKTLVIPYHWIDTL 75 (202)
Q Consensus 21 w~tfi~i~~~~~~~~-~~~~l~~~~~~~~~~----~~-~~~~lHISLs~~~~~~~~~i~~~ 75 (202)
=|+|+.+++...... +..++..+-+.+... +- ....+|||+.....-........
T Consensus 140 TR~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~lp~~Y~~~~~fHvSIAw~~~~~~~~l~~~ 200 (239)
T PF09749_consen 140 TRSFLALRVSEGSNNELKRLLDRINEVLKEFGLPPFYDEDPSFHVSIAWTLGDPSEELKES 200 (239)
T ss_pred CeEEEEEEecccccHHHHHHHHHHHHHHHHhCCCcccCCCCCCEEEEEEECCCchHHHHHH
Confidence 578888888763333 544444333333322 24 77889999998865555443333
No 27
>PLN00108 unknown protein; Provisional
Probab=71.54 E-value=16 Score=30.98 Aligned_cols=69 Identities=14% Similarity=0.227 Sum_probs=37.1
Q ss_pred cCCCceEEEEEeecCCCccHHHHHHHHH-HHHH--------------hcCCCC--CCCCCCceEEEEeecCCCchhHHHH
Q psy16608 101 NEEKTRSFIALGANSCKTSLTSIVQAVD-KSAQ--------------EFKLPT--YYEEPNFHASIAWCLQDKTATLKPL 163 (202)
Q Consensus 101 n~~~~RvF~~l~v~~~~~~L~~L~~~i~-~~l~--------------~~g~~~--~~~~~~pHiSia~~~~~~~~~l~~~ 163 (202)
+...+.-|+++++.. +.+|..=..... .+|. .+|+++ +-.|.+.|+||+...-.-.+.++++
T Consensus 32 ~~~~~THFlavPL~~-~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA 110 (257)
T PLN00108 32 HREVFTHFVSLPLAI-YPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKA 110 (257)
T ss_pred cCCCCCeEEEEEcCC-CHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHH
Confidence 445567899999952 123333333332 2333 234433 3467899999995443333455555
Q ss_pred HHHHHHh
Q psy16608 164 LTKLDNI 170 (202)
Q Consensus 164 ~~~l~~~ 170 (202)
.+.|++.
T Consensus 111 ~~~L~s~ 117 (257)
T PLN00108 111 QNILKSI 117 (257)
T ss_pred HHHHHHH
Confidence 5444443
No 28
>KOG3102|consensus
Probab=65.81 E-value=24 Score=29.31 Aligned_cols=74 Identities=19% Similarity=0.121 Sum_probs=38.8
Q ss_pred cceEEEEecCCCHHHHHHHHHHHHHhhcc---c-----c-ccCCCCeEeeeee-eccCcccHHHHHHHHHHhhcc----C
Q psy16608 21 WATLVYIPLQTNLARLYAMLKEELNSVGI---S-----V-EVIPEPHLSLSKT-LVIPYHWIDTLVETLGNNLRH----L 86 (202)
Q Consensus 21 w~tfi~i~~~~~~~~~~~~l~~~~~~~~~---~-----~-~~~~~lHISLs~~-~~~~~~~i~~~~~~L~~~l~~----~ 86 (202)
-||||.+++.. ...+.|...++.+++ . + ..| .+||||-.. |+++..---....+|++.+.+ -
T Consensus 170 TRtFi~leitt---~~~~~~~~~i~~vd~Vm~~~nL~~FY~DP-sfHiSL~WcvGD~rt~L~g~~l~EL~~l~dg~~~~~ 245 (269)
T KOG3102|consen 170 TRTFISLEITT---SGLSEISKQIDAVDEVMKLHNLPEFYKDP-SFHISLVWCVGDIRTSLKGAVLVELRKLRDGGCVQN 245 (269)
T ss_pred ceeEEEEEech---hhHHHHHHHHHHHHHHHHHcCchhhhcCC-CCCceEEEEeccHHHhhhhHHHHHHHHHHhccchhh
Confidence 57888888875 222223322222221 1 1 455 899999864 555543222455566666553 2
Q ss_pred CceEEEeCceEE
Q psy16608 87 NRLTIKFNSIEI 98 (202)
Q Consensus 87 ~~F~l~~~~~~~ 98 (202)
.-|++.+.++..
T Consensus 246 ~~l~v~~~~i~C 257 (269)
T KOG3102|consen 246 RILTVKFCGIEC 257 (269)
T ss_pred eeEEEeeeeEEE
Confidence 345565555543
No 29
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=64.78 E-value=9.4 Score=30.09 Aligned_cols=48 Identities=17% Similarity=0.206 Sum_probs=37.9
Q ss_pred CCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCc
Q psy16608 56 EPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKT 105 (202)
Q Consensus 56 ~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~ 105 (202)
.+|+||+-.. +..+++.+...++......-+=.+.++++.+|.-++.-
T Consensus 108 RFHmTLTg~l--~~~~~~~~~~~l~~~f~~~l~~p~~id~laLf~e~~~g 155 (160)
T PF06299_consen 108 RFHMTLTGRL--DPAERARVEAALEAHFAPLLPEPLRIDSLALFGEPEPG 155 (160)
T ss_pred EeeEEeCCCC--CHHHHHHHHHHHHHHHHhhcCCCeeecceEEEeccCCC
Confidence 5899997544 77788999999998887765556778999999877654
No 30
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=64.58 E-value=40 Score=23.45 Aligned_cols=48 Identities=13% Similarity=0.205 Sum_probs=36.4
Q ss_pred eEEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCC-ceEEEE
Q psy16608 96 IEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPN-FHASIA 150 (202)
Q Consensus 96 ~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~-pHiSia 150 (202)
+.+|.++...+.++. ... +.-.+.+.-+|++||++....+++ .|+|++
T Consensus 5 lkvykaDQt~kyili---~K~----Tta~evv~lal~eFgi~~~s~~~sLceVtV~ 53 (85)
T cd01785 5 LKVYKADQTCKYLLI---YKE----TTAHEVVMLALQEFGITAPSSNFSLCEVSVT 53 (85)
T ss_pred EEEEecCcceeEEEE---ecc----ccHHHHHHHHHHHhCCCCCccceEEEEEEec
Confidence 578889888888753 332 345667788999999998877776 489988
No 31
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=61.97 E-value=98 Score=26.16 Aligned_cols=72 Identities=15% Similarity=0.153 Sum_probs=39.1
Q ss_pred HHHHHHHHHhhc-cCCceEEEeCceE-----------EEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhc------
Q psy16608 73 DTLVETLGNNLR-HLNRLTIKFNSIE-----------IFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEF------ 134 (202)
Q Consensus 73 ~~~~~~L~~~l~-~~~~F~l~~~~~~-----------~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~------ 134 (202)
+.+-++++.++. -.+.|+-.+.+-+ -=....+|+.|=+ .| + ...+.+.+++++..-
T Consensus 28 e~id~A~~~Al~~Ykp~~~k~~~~~~~~~~~~~~~~~~~~kk~~p~Yf~i-~i--~---~~~i~~~l~~~f~~~~~~~~~ 101 (257)
T PF08302_consen 28 EEIDEAFQKALNEYKPDFTKIIGKGSKNNKKKNNKSSPKKKKKKPEYFGI-SI--P---TQDIKSLLEKLFEDSPPETAR 101 (257)
T ss_pred HHHHHHHHHHHhhCCCceEEECCcCCccccccccccCcccccCCCeEEEE-EC--C---HHHHHHHHHHHhccCCHHHHH
Confidence 567788888888 3556776665321 1123455677544 56 2 233444444454432
Q ss_pred --C-CCCCCC-CCCceEEEE
Q psy16608 135 --K-LPTYYE-EPNFHASIA 150 (202)
Q Consensus 135 --g-~~~~~~-~~~pHiSia 150 (202)
. +....| .+.|||||+
T Consensus 102 ~~~~L~~~~RvQ~~FHVTL~ 121 (257)
T PF08302_consen 102 FYNQLKNSRRVQPEFHVTLI 121 (257)
T ss_pred HHHHHHhCCCCCCCCeEEEE
Confidence 0 011111 478999999
No 32
>PHA02574 57B hypothetical protein; Provisional
Probab=61.27 E-value=10 Score=29.52 Aligned_cols=42 Identities=12% Similarity=0.391 Sum_probs=25.1
Q ss_pred CceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy16608 104 KTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAW 151 (202)
Q Consensus 104 ~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~ 151 (202)
..|.|+|+.+.+ .. .+.+.+..+..+..+.-++...|+||+.
T Consensus 8 ~~RlF~Al~~~~---~~---r~~L~~lq~~l~~~r~V~~enLHlTL~F 49 (149)
T PHA02574 8 SQGTYVAAKFSE---AT---LDALERLQRTLRIPNPVPRDKLHSTIVY 49 (149)
T ss_pred cceEEEEEcCCH---HH---HHHHHHHHHhccCCcccCHHHCEEEEec
Confidence 679999986643 22 2333333333333444455689999998
No 33
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=57.72 E-value=44 Score=27.76 Aligned_cols=70 Identities=10% Similarity=0.093 Sum_probs=40.5
Q ss_pred CCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEeecCCCchhHHHHHHHHHHhhhhc
Q psy16608 102 EEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQDKTATLKPLLTKLDNIFTQF 174 (202)
Q Consensus 102 ~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~~~~~~~~~l~~~~~~l~~~~~~~ 174 (202)
.++|--|+.+++..=. ....-...+.--+-+-|++-.. .-.||+|++...-. .++.+.-...||+++++.
T Consensus 3 AD~P~HFin~Pl~~f~-~f~~~~~~LQ~~~~~eG~d~k~-QkaPHlSl~mL~Is-d~~i~~V~~~iq~ViddM 72 (248)
T PF05213_consen 3 ADKPTHFINFPLVQFE-GFMLNFKDLQFQLLEEGVDCKL-QKAPHLSLGMLDIS-DEDIPDVETAIQKVIDDM 72 (248)
T ss_pred CCCCCceeeccchhhh-hHHHHHHHHHHHHHHcCCCccc-cccCeeEEEEEEcC-hhhhhhHHHHHHHHHHHh
Confidence 4678888988886511 2222222233333445666443 36899999975433 244444445777888865
No 34
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=54.89 E-value=79 Score=22.86 Aligned_cols=92 Identities=12% Similarity=0.152 Sum_probs=52.9
Q ss_pred eEeeeeeeccC-cccHHHHHHHHHHhhccCCceE-----EEeCceEEEecCCC--ceEEEEEee--cCCC--ccHHHHHH
Q psy16608 58 HLSLSKTLVIP-YHWIDTLVETLGNNLRHLNRLT-----IKFNSIEIFCNEEK--TRSFIALGA--NSCK--TSLTSIVQ 125 (202)
Q Consensus 58 HISLs~~~~~~-~~~i~~~~~~L~~~l~~~~~F~-----l~~~~~~~f~n~~~--~RvF~~l~v--~~~~--~~L~~L~~ 125 (202)
|+++...-.+. ..+++.+.+.+.+++-+...|. ..+-....|..-++ +.-|..+.+ ..|. ++-..|.+
T Consensus 2 H~~Ieys~~l~~~~~~~~l~~~v~~al~~~~~~p~~dik~r~~~~~~y~~~~~~~~~~fi~i~i~l~~GRs~eqK~~l~~ 81 (113)
T cd00580 2 HLIIEYSANLEGRADIPELLRALHDALVASGLFPLGGIKVRAIRADHYRVGDGDEDDAFIHVTLRILAGRSEEQKQELSE 81 (113)
T ss_pred eEEEEeCCCccccCCHHHHHHHHHHHHHhcCCCChhccEEeeEEcceEEECCCCCCCcEEEEEEEEcCCCCHHHHHHHHH
Confidence 88999999984 5799999999999876532222 12222233332233 344443333 2332 56777888
Q ss_pred HHHHHHHhcCCCCCCCCCCceEEEE
Q psy16608 126 AVDKSAQEFKLPTYYEEPNFHASIA 150 (202)
Q Consensus 126 ~i~~~l~~~g~~~~~~~~~pHiSia 150 (202)
.|-++|.+.-.+... .....+|+-
T Consensus 82 ~i~~~l~~~~~~~~~-~~~~~~sve 105 (113)
T cd00580 82 ALLAALRAHLAPVFA-KRYLSLSVE 105 (113)
T ss_pred HHHHHHHHhhhhhhh-ccceEEEEE
Confidence 887777665433322 233455554
No 35
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=53.01 E-value=38 Score=25.09 Aligned_cols=85 Identities=12% Similarity=0.237 Sum_probs=36.1
Q ss_pred CcccccCccccccceEEEEecCCCHHHHHHHHHHHHHhhcccc-----ccCCCCeEeeeeeeccCcccHHHHHHHHHHhh
Q psy16608 9 GRIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEELNSVGISV-----EVIPEPHLSLSKTLVIPYHWIDTLVETLGNNL 83 (202)
Q Consensus 9 gr~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~-----~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l 83 (202)
+++..|++ .|. . ||+.+.. ++.+.++-.++...+.... ..+-..||||.+...-... +.+.+.++
T Consensus 62 ~~~~~F~~-~~~-v--i~l~~~~-~~~L~~L~~~l~~~~~~~~~~~~~~~~~~PHiTia~~~~~~~~--~~~~~~~~--- 131 (153)
T PF13563_consen 62 DGFGSFPG-KGR-V--IFLNVEP-SPELEALHRALREALRPFGFKQDSYRPFRPHITIARRLSPKQA--AEAIEKLQ--- 131 (153)
T ss_dssp EEEEEESS-SSS-S--EEEEEEE--HHHHHHHHHHHHHHHHHHGGGGGGS----EEEEEEESS-----------------
T ss_pred ccEEEcCC-CCC-E--EEEEcCC-CHHHHHHHHHHHHHHHHcCCccccCCCcceEEEEeccCCcchh--HHHHHHHh---
Confidence 45667777 454 4 4455543 4455544444444433322 1455689999987665532 33333331
Q ss_pred ccCCceEEEeCceEEEecCC
Q psy16608 84 RHLNRLTIKFNSIEIFCNEE 103 (202)
Q Consensus 84 ~~~~~F~l~~~~~~~f~n~~ 103 (202)
....+....++++.++..++
T Consensus 132 ~~~~~~~~~v~~l~L~~~~~ 151 (153)
T PF13563_consen 132 SEFPPISFTVDELALVRSDG 151 (153)
T ss_dssp -----EEEEE-EEEEEEEE-
T ss_pred CcCCCcEEEEeEEEEEEECC
Confidence 23556777788887776543
No 36
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=46.48 E-value=38 Score=22.50 Aligned_cols=35 Identities=17% Similarity=0.227 Sum_probs=24.8
Q ss_pred cccccCccccccceEEEEecCCCHHHHHHHHHHHH
Q psy16608 10 RIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEEL 44 (202)
Q Consensus 10 r~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~ 44 (202)
++-+.|...+.|.-..||++....+.+++.|.++.
T Consensus 30 ~IeSRP~~~~~~~y~Ffvd~~~~~~~~~~~l~~L~ 64 (74)
T cd04904 30 HIESRPSRRNGSEYEFFVDCEVDRGDLDQLISSLR 64 (74)
T ss_pred EEECCCCCCCCceEEEEEEEEcChHHHHHHHHHHH
Confidence 45677888888999999999863445555555443
No 37
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=43.53 E-value=46 Score=27.76 Aligned_cols=53 Identities=13% Similarity=0.166 Sum_probs=39.8
Q ss_pred CCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEE
Q psy16608 56 EPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIA 110 (202)
Q Consensus 56 ~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~ 110 (202)
.+|+||| |.+...+.+.+.+.|+..+...-+=.+.++++.+|+-++...=|-+
T Consensus 168 rFHmTLT--g~l~~~~~~~~~~~l~~~~~~~l~~p~~id~laLf~e~~~g~pF~~ 220 (228)
T TIGR03223 168 RFHMTLT--GRLDEEERAAVLARLEARFAPLLADPLAVDGLALFVEPEPGAPFRL 220 (228)
T ss_pred EEEEEec--CCCChHHHHHHHHHHHHHhhhccCCCeeeeeEEEEeccCCCCCcEE
Confidence 5899997 5557778888888888877665444678899999998876654543
No 38
>PHA02977 hypothetical protein; Provisional
Probab=40.64 E-value=30 Score=26.95 Aligned_cols=19 Identities=11% Similarity=0.121 Sum_probs=14.3
Q ss_pred CCceEEEEeecCCCchhHH
Q psy16608 143 PNFHASIAWCLQDKTATLK 161 (202)
Q Consensus 143 ~~pHiSia~~~~~~~~~l~ 161 (202)
--||+|||-+..++-+..+
T Consensus 68 i~phitlgian~dq~~~f~ 86 (201)
T PHA02977 68 IFPHITLGIANKDQCDNFE 86 (201)
T ss_pred CCcceeeeccCccHhHHHH
Confidence 4689999988777655555
No 39
>PF05881 CNPase: 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase); InterPro: IPR008431 This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity [].; GO: 0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity, 0009214 cyclic nucleotide catabolic process, 0016020 membrane; PDB: 2YDB_A 2Y3X_B 2Y1P_A 2XMI_A 2YDD_A 2YDC_A 2ILX_A 1WOJ_A 2I3E_A.
Probab=38.56 E-value=1.1e+02 Score=25.53 Aligned_cols=94 Identities=12% Similarity=0.039 Sum_probs=47.4
Q ss_pred ccCCCCeEeeeeeeccCcccHHHHHH--HHHHhhccCCceEEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHH
Q psy16608 52 EVIPEPHLSLSKTLVIPYHWIDTLVE--TLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDK 129 (202)
Q Consensus 52 ~~~~~lHISLs~~~~~~~~~i~~~~~--~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~ 129 (202)
..|..||.|-+|..+=....-++..+ .+++. --+.|+|++..+ |. .||++=+ +|.=..++|.-.-..+++
T Consensus 57 ~~p~vLHCTtkfcdYGka~GAeeYAq~~~Vk~s--ygkaftL~isaL--fv---TprT~GA-rv~L~e~ql~LWp~D~~k 128 (235)
T PF05881_consen 57 KPPGVLHCTTKFCDYGKAAGAEEYAQQEVVKKS--YGKAFTLSISAL--FV---TPRTVGA-RVELTEEQLLLWPADVDK 128 (235)
T ss_dssp B-TSSSEEEEEE-GGGTSTTHHHHHT-HHHHHH--TT-EEEEEEEEE--EE----SSEEEE-EEE--HHHHHTS-TCSSC
T ss_pred CCCCCceEeeeeccccCcccHHHHHhhHHHHHh--ccceEEEEEEEE--Ee---ccccccc-eeeechhhhccCCcchhc
Confidence 34788999999998777666555543 22332 257899998876 43 4677544 564332334111111111
Q ss_pred HHHhcC-CCCCCCCCCceEEEEeecCCC
Q psy16608 130 SAQEFK-LPTYYEEPNFHASIAWCLQDK 156 (202)
Q Consensus 130 ~l~~~g-~~~~~~~~~pHiSia~~~~~~ 156 (202)
++. -+...+-.+.|||||...+-.
T Consensus 129 ---e~~~~~~lp~GSRAHiTLGcA~gVe 153 (235)
T PF05881_consen 129 ---ELSPSDSLPRGSRAHITLGCAAGVE 153 (235)
T ss_dssp ---SCSTTTTS-TTTTCEEEEEE-TT--
T ss_pred ---ccCCCCCCCCCcceeEeeeccCCCc
Confidence 010 011223458999999986543
No 40
>cd01816 Raf_RBD Ubiquitin domain of Raf serine/threonine kinases. The Raf serine/threonine kinases are composed of three conserved regions, CR1, CR2 and CR3. CR1 has two Ras binding domains (RBD and CRD), CR2 is a serine/threonine rich domain and CR3 is the catalytic kinase domain. The RBD of Raf is structurally similar to ubiquitin with little of no sequence similarity.The Raf signalling pathway plays an important role in the proliferation and survival of tumor cells.
Probab=36.19 E-value=42 Score=22.97 Aligned_cols=35 Identities=14% Similarity=0.124 Sum_probs=27.1
Q ss_pred EEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCC
Q psy16608 98 IFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYY 140 (202)
Q Consensus 98 ~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~ 140 (202)
.+||..+|.| +|..|. .+.++++++|+.-|+.++-
T Consensus 5 ~LPnqQrT~V----~vrpG~----tl~daL~KaLk~R~l~pe~ 39 (74)
T cd01816 5 FLPNKQRTVV----NVRPGM----TLRDALAKALKVRGLQPEC 39 (74)
T ss_pred ECCCCCeEEE----EecCCc----CHHHHHHHHHHHcCCChhH
Confidence 5788888887 677763 3788999999988887554
No 41
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=35.01 E-value=30 Score=26.99 Aligned_cols=52 Identities=13% Similarity=0.222 Sum_probs=29.2
Q ss_pred ccCccccccceEEE-EecCCCHHHHHHHHHHHHHhhcccc--------ccCCCCeEeeeee
Q psy16608 13 SFPHQRNSWATLVY-IPLQTNLARLYAMLKEELNSVGISV--------EVIPEPHLSLSKT 64 (202)
Q Consensus 13 ~~pH~~G~w~tfi~-i~~~~~~~~~~~~l~~~~~~~~~~~--------~~~~~lHISLs~~ 64 (202)
.....++.|.+|+| |......+.++..+..+++.++..+ -.+.+.|...+|.
T Consensus 62 r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~lk~~l~~e~~~~~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 62 RRKDDETGWYEYTWRINYEKALDVLKRKLEETAKKLREKLEFETNNMFFICPNMCVRFTFN 122 (158)
T ss_pred eeeecCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEECCCCCcEeeHH
Confidence 34567778999996 6554323345555555555555433 2334556555554
No 42
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.73 E-value=45 Score=27.38 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCCCCCCC-CCCc--eEEEEee
Q psy16608 122 SIVQAVDKSAQEFKLPTYYE-EPNF--HASIAWC 152 (202)
Q Consensus 122 ~L~~~i~~~l~~~g~~~~~~-~~~p--HiSia~~ 152 (202)
++.+.+|+++++.|+|-.|. -|.| -||+|-.
T Consensus 20 dlmRlidR~iRRAglpiayT~GFhP~prmsia~a 53 (228)
T COG5011 20 DLMRLIDRTIRRAGLPIAYTGGFHPHPRMSIAQA 53 (228)
T ss_pred HHHHHHHHHHHhcCCceeecCCCCCCCceeeccc
Confidence 47778999999999998886 4554 5677743
No 43
>PRK13679 hypothetical protein; Provisional
Probab=34.70 E-value=2.1e+02 Score=21.99 Aligned_cols=87 Identities=10% Similarity=0.140 Sum_probs=47.0
Q ss_pred cccccCccccccceEEEEecCCCHHHHHHHHHHHHHhhcccc-ccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCc
Q psy16608 10 RIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEELNSVGISV-EVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNR 88 (202)
Q Consensus 10 r~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~ 88 (202)
..-.||+. ..-+|+.+.. .+++.++-..+...+.... ..+=.-||||.+. .+.++...+.+.++. . ...
T Consensus 71 ~~~~F~~~----~~vl~l~~~~-~~~L~~L~~~l~~~~~~~~~~~~f~PHiTlar~--~~~~~~~~~~~~l~~--~-~~~ 140 (168)
T PRK13679 71 KVSSFAPT----NNVIYFKVEK-TEELEELHERLHSGDFYGEAEYAFVPHITIGQG--LSDDEHEDVLGQLKM--A-DVD 140 (168)
T ss_pred ccccCCCC----CCEEEEEccC-CHHHHHHHHHHHhcccccccCCCCCCeEEeeCC--CCcHHHHHHHHHHhc--C-Ccc
Confidence 34455542 2467888876 4555544333333222110 2333489999954 333556666665533 2 233
Q ss_pred eEEEeCceEEEecCCCce
Q psy16608 89 LTIKFNSIEIFCNEEKTR 106 (202)
Q Consensus 89 F~l~~~~~~~f~n~~~~R 106 (202)
|...++++.+|-..+..+
T Consensus 141 ~~~~v~~i~L~~~~~~~~ 158 (168)
T PRK13679 141 HEETIDRFHLLYQLENGS 158 (168)
T ss_pred eeEEECeEEEEEECCCCe
Confidence 566788888876644444
No 44
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=34.02 E-value=72 Score=23.24 Aligned_cols=46 Identities=11% Similarity=0.138 Sum_probs=28.4
Q ss_pred EEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy16608 98 IFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIA 150 (202)
Q Consensus 98 ~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia 150 (202)
+-.+++++|+ +.|.+ ...-.+.+.++|++||++..++++.+++.=+
T Consensus 5 ~I~~dG~tk~---VNV~~----c~~a~eI~~rvLKKfg~~~~~~~~~~~v~d~ 50 (105)
T PF14847_consen 5 FILEDGSTKT---VNVSG----CFNAQEIKRRVLKKFGLPEHPRNYCFYVLDG 50 (105)
T ss_dssp EEETTTEEEE---EE--S------HHHHHHHHHHHHHTSS--CCCEEEEEE-S
T ss_pred EECCCCcEEE---EEECC----CCCHHHHHHHHHHHcCCccccccceEEEecc
Confidence 4455666777 46655 4556778899999999999777776665544
No 45
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=32.77 E-value=41 Score=30.85 Aligned_cols=76 Identities=14% Similarity=0.113 Sum_probs=51.7
Q ss_pred eeccCcccHHHHHHHHHHhhccCC-ceEEEeCceE-EEecCCCceEEEEEeecC------------C--CccHHHHHHHH
Q psy16608 64 TLVIPYHWIDTLVETLGNNLRHLN-RLTIKFNSIE-IFCNEEKTRSFIALGANS------------C--KTSLTSIVQAV 127 (202)
Q Consensus 64 ~~~~~~~~i~~~~~~L~~~l~~~~-~F~l~~~~~~-~f~n~~~~RvF~~l~v~~------------~--~~~L~~L~~~i 127 (202)
.+.++.+.-+...-..++.+++.+ -..+.+..+| +|.|+-++|-++. +|.+ + .+.+...++.+
T Consensus 159 ~~~lRpetaqg~~~~f~~~~~syr~dLPlr~aq~g~~~RnE~s~~~gL~-RvReF~q~e~hiF~~peq~~~e~~~~l~~~ 237 (456)
T PRK04173 159 LGYLRPETAQGIFVNFKNVLRTARKKLPFGIAQIGKSFRNEITPRNFIF-RTREFEQMELEFFVKPGTDNEWFAYWIELR 237 (456)
T ss_pred ceeeccccchhHHHHHHHHHHhccccCCeeeeEEchhHhCccCCCCCce-eeceeeeeEEEEEECcChHHHHHHHHHHHH
Confidence 566777655666666777777666 4555555444 6899988876542 4422 1 14688888999
Q ss_pred HHHHHhcCCCCCC
Q psy16608 128 DKSAQEFKLPTYY 140 (202)
Q Consensus 128 ~~~l~~~g~~~~~ 140 (202)
...+..+|++.+.
T Consensus 238 ~~~l~~lG~~~~~ 250 (456)
T PRK04173 238 KNWLLDLGIDPEN 250 (456)
T ss_pred HHHHHHcCCCccc
Confidence 9999999998654
No 46
>PF02962 CHMI: 5-carboxymethyl-2-hydroxymuconate isomerase; InterPro: IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway []. Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria []. 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits []. A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene [].; PDB: 3E6Q_H 1OTG_B.
Probab=32.73 E-value=2.1e+02 Score=21.40 Aligned_cols=92 Identities=11% Similarity=0.177 Sum_probs=55.2
Q ss_pred eEeeeeeeccCcc-cHHHHHHHHHHhhccCCceE-----EEeCceEEEe-cCC-CceEEEEEe--ecCCC--ccHHHHHH
Q psy16608 58 HLSLSKTLVIPYH-WIDTLVETLGNNLRHLNRLT-----IKFNSIEIFC-NEE-KTRSFIALG--ANSCK--TSLTSIVQ 125 (202)
Q Consensus 58 HISLs~~~~~~~~-~i~~~~~~L~~~l~~~~~F~-----l~~~~~~~f~-n~~-~~RvF~~l~--v~~~~--~~L~~L~~ 125 (202)
|+++-.+-++... .++.+.+.|...+-+..-|. ...-....|. .++ ..+.|.-+. +-.|. +..+.|-+
T Consensus 2 H~viEYS~nL~~~~d~~~ll~~l~~~~~~sglF~~~~IK~Ra~~~~~y~vgdg~~~~~FvHv~l~il~GRs~e~k~~l~~ 81 (124)
T PF02962_consen 2 HLVIEYSANLEDDVDIPALLRALHDALLASGLFPEGGIKVRAIRCDHYRVGDGQPDDAFVHVTLRILAGRSEEQKKALSE 81 (124)
T ss_dssp EEEEEEECCGCCTTTHHHHHHHHHHHHHCTTSS-GGG-EEEEEEESSEEETTSSS-EEEEEEEEEEETT--HHHHHHHHH
T ss_pred eEEEEeCCCccccCCHHHHHHHHHHHHHHcCCcChhceeeeeEecccEEEccCCCCCcEEEEEeeecCCCCHHHHHHHHH
Confidence 9999999999987 99999999998876544443 3333333332 222 246665332 33333 55777888
Q ss_pred HHHHHHHhcCCCCCCCCCCceEEEE
Q psy16608 126 AVDKSAQEFKLPTYYEEPNFHASIA 150 (202)
Q Consensus 126 ~i~~~l~~~g~~~~~~~~~pHiSia 150 (202)
.|-++|++. +++-......-+|+=
T Consensus 82 ~l~~~l~~~-~~~~~~~~~~~LsvE 105 (124)
T PF02962_consen 82 ALLAVLKAH-LAPLFAQRYLQLSVE 105 (124)
T ss_dssp HHHHHHHHH-CCCHCCHSEEEEEEE
T ss_pred HHHHHHHHH-hhHhhcCCeeEEEEE
Confidence 888888775 343332223444443
No 47
>COG4316 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.25 E-value=2.2e+02 Score=21.41 Aligned_cols=52 Identities=15% Similarity=0.223 Sum_probs=31.9
Q ss_pred eCceE-EEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCC-CCCceEEEEeec
Q psy16608 93 FNSIE-IFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYE-EPNFHASIAWCL 153 (202)
Q Consensus 93 ~~~~~-~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~-~~~pHiSia~~~ 153 (202)
|.++| +|-.++.|-.|++|....+ .|-+.+..|+...-.. +.--|++|.|..
T Consensus 29 ~~rFgvvFEddgETgYFYaLDMRQ~---------gi~d~lh~yNv~~vsd~h~~~~v~I~Wd~ 82 (138)
T COG4316 29 IPRFGVVFEDDGETGYFYALDMRQD---------GILDALHIYNVEDVSDKHIPNHVLILWDD 82 (138)
T ss_pred ccceeEEEeeCCcceEEEeecchhh---------hHHHHHHhccccccccCCCCCceEEEEcc
Confidence 34333 6778889999999866532 2444445555433332 344599999964
No 48
>TIGR02042 sir ferredoxin-sulfite reductase. monomeric enzyme that also catalyzes the reduction of sulfite to sulfide.
Probab=30.53 E-value=2.1e+02 Score=27.17 Aligned_cols=127 Identities=11% Similarity=0.132 Sum_probs=64.2
Q ss_pred CCCCcccccCccccccceEEEEecC-CCHH---HHHHHHHHHHHhhccccccCCCCeEeeeeeeccCc---ccHHHHHHH
Q psy16608 6 EHGGRIRSFPHQRNSWATLVYIPLQ-TNLA---RLYAMLKEELNSVGISVEVIPEPHLSLSKTLVIPY---HWIDTLVET 78 (202)
Q Consensus 6 ~h~gr~R~~pH~~G~w~tfi~i~~~-~~~~---~~~~~l~~~~~~~~~~~~~~~~lHISLs~~~~~~~---~~i~~~~~~ 78 (202)
+|-|...+ .+|.|..-+.++.- .+++ +++..|.++.+.+.. .+++|-.....+.. +.++.+.+.
T Consensus 352 d~~G~~~q---~dG~~~v~l~vp~Grl~~~~~~~l~~~LaeIA~~yg~------~irlT~~Qnl~l~~V~~~~~~~i~~~ 422 (577)
T TIGR02042 352 DYLGWHEQ---GDGKWFLGLHIDSGRVKDDGNWQLKKALREIVEKYNL------PVRLTPNQNIILYDIQPEWKRAITTV 422 (577)
T ss_pred ccceEEEC---CCceEEEEEEecCceecCCchHHHHHHHHHHHHHhCC------CEEEcCCCCeEECCCCHHHHHHHHHH
Confidence 45565533 47888444444432 1223 445566777666532 38888887776664 566666766
Q ss_pred HHHh-hccCCceEEEeCceEEEecCCCce-EEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEE
Q psy16608 79 LGNN-LRHLNRLTIKFNSIEIFCNEEKTR-SFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHAS 148 (202)
Q Consensus 79 L~~~-l~~~~~F~l~~~~~~~f~n~~~~R-vF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiS 148 (202)
|++. +....+ .+..+...-.+|. .++.+++.+....+..|.+.+++.+..+++++ ++++.|||
T Consensus 423 L~~~Gl~~~~~-----~~~~~~~~~aC~G~~~C~lal~et~~~~~~l~~~l~~l~~~~~l~~--~~i~I~vS 487 (577)
T TIGR02042 423 LAQRGVLQPEA-----IDPLNRYAMACPALPTCGLAITESERAIPGILKRIRALLEKVGLPD--EHFVVRMT 487 (577)
T ss_pred HHhcCCCCCCC-----CCccceeeEeCCCcccccCchHHHHHHHHHHHHHHHHHHHhcCCCC--CCcEEEEE
Confidence 6644 211000 0000000001111 13333333322345568888888888888762 33555555
No 49
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=29.95 E-value=74 Score=21.01 Aligned_cols=40 Identities=15% Similarity=0.354 Sum_probs=31.9
Q ss_pred ccCCCCeEeeeeeeccCcccHHHHHHHHHHhhccCCceEE
Q psy16608 52 EVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTI 91 (202)
Q Consensus 52 ~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l 91 (202)
.....+|+.|++.-.++.+.+..|.+.|+...+......+
T Consensus 33 k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~~F~~ia~v~~ 72 (76)
T PF14480_consen 33 KKSRKWRFHLSSPHILPFEVYQKFEEKLKKQFSHIAKVEL 72 (76)
T ss_pred ccCCEEEEEEEeCCcCCHHHHHHHHHHHHHHhCCcCeEEE
Confidence 3446699999999999999999999999988666544443
No 50
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.88 E-value=1.1e+02 Score=20.62 Aligned_cols=34 Identities=18% Similarity=0.201 Sum_probs=22.5
Q ss_pred cccccCccccccceEEEEecCCCHHHHHHHHHHH
Q psy16608 10 RIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEE 43 (202)
Q Consensus 10 r~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~ 43 (202)
++-+.|-...+|....||++......+++.++++
T Consensus 30 ~IeSRP~~~~~~~y~F~id~e~~~~~i~~~l~~l 63 (74)
T cd04929 30 HIESRKSKRRSSEFEIFVDCECDQRRLDELVQLL 63 (74)
T ss_pred EEEeccCCCCCceEEEEEEEEcCHHHHHHHHHHH
Confidence 3456677778899999999987333444444433
No 51
>PF04456 DUF503: Protein of unknown function (DUF503); InterPro: IPR007546 This is a family of conserved hypothetical bacterial proteins, including TT1725 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), which has a ferredoxin-like alpha+beta-sandwich fold [].; PDB: 1J27_A.
Probab=29.69 E-value=1e+02 Score=21.71 Aligned_cols=70 Identities=16% Similarity=0.236 Sum_probs=35.6
Q ss_pred eeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEee-cCCCccHHHHHHHHHHHHHhc
Q psy16608 61 LSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGA-NSCKTSLTSIVQAVDKSAQEF 134 (202)
Q Consensus 61 Ls~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v-~~~~~~L~~L~~~i~~~l~~~ 134 (202)
|..++.-.-...-..+++|...++ +.|.+....+|.- +.-.|.-|++.+ +.+.......++.|.+.++..
T Consensus 9 l~lp~~~SLKeKR~vvksl~~klr--~rfnvSvaEv~~~--D~~q~a~lg~a~vs~~~~~~~~~l~~v~~~ie~~ 79 (90)
T PF04456_consen 9 LRLPGAHSLKEKRQVVKSLIDKLR--NRFNVSVAEVGHQ--DSWQRAVLGFAVVSNSRAHAEQILDKVERFIEEN 79 (90)
T ss_dssp EE----SSHHHHHHHHHHHHHHHH--HHSS-EEEEEE-T--T-SSEEEEEEEEEES-HHHHHHHHHHHHHHHHHS
T ss_pred EEeccccchhHhHHHHHHHHHHHH--hhCCeEEEEecCC--CcccEEEEEEEEEECCHHHHHHHHHHHHHHHHhC
Confidence 333333333455556666666654 3577777666543 444555554444 333356777777777777554
No 52
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.27 E-value=94 Score=21.81 Aligned_cols=36 Identities=25% Similarity=0.245 Sum_probs=24.4
Q ss_pred cccccCccccccceEEEEecCCC-HHHHHHHHHHHHH
Q psy16608 10 RIRSFPHQRNSWATLVYIPLQTN-LARLYAMLKEELN 45 (202)
Q Consensus 10 r~R~~pH~~G~w~tfi~i~~~~~-~~~~~~~l~~~~~ 45 (202)
++-+.|.....|....||++... ++.+++.|+++.+
T Consensus 44 ~IeSRP~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~ 80 (90)
T cd04931 44 HIESRPSRLNKDEYEFFINLDKKSAPALDPIIKSLRN 80 (90)
T ss_pred EEEeccCCCCCceEEEEEEEEcCCCHHHHHHHHHHHH
Confidence 45677877888999999999852 3445555554433
No 53
>KOG1383|consensus
Probab=28.53 E-value=1.8e+02 Score=26.93 Aligned_cols=49 Identities=6% Similarity=0.131 Sum_probs=35.5
Q ss_pred HHHHHHHhcC--CCCCCCCCCceEEEEeecCCCchhHHHHHHHHHHhhhhcc
Q psy16608 126 AVDKSAQEFK--LPTYYEEPNFHASIAWCLQDKTATLKPLLTKLDNIFTQFK 175 (202)
Q Consensus 126 ~i~~~l~~~g--~~~~~~~~~pHiSia~~~~~~~~~l~~~~~~l~~~~~~~~ 175 (202)
.+.+.|+++| ++.+..|..-|+++-+....+ ...++++.++.+.+.++.
T Consensus 398 elsd~l~~~GW~lnalq~P~a~Hi~vt~~~~~~-~~A~~~v~Di~~~~~el~ 448 (491)
T KOG1383|consen 398 ELSDLLRKKGWILNALQFPAAIHICVTRVHARE-DVADRFVADIRKVVEELK 448 (491)
T ss_pred hhhHHHHhcCcCccccCCCCceEEEEEeeeccH-HHHHHHHHHHHHHHHHHH
Confidence 5677888887 688889999999999976543 223456677777776543
No 54
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=27.22 E-value=72 Score=25.59 Aligned_cols=32 Identities=19% Similarity=0.348 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhcCCCCCCC---CCCceEEEEee
Q psy16608 121 TSIVQAVDKSAQEFKLPTYYE---EPNFHASIAWC 152 (202)
Q Consensus 121 ~~L~~~i~~~l~~~g~~~~~~---~~~pHiSia~~ 152 (202)
.++...+++++++.|+|.-|. +|+|.||+|-.
T Consensus 18 Ldl~r~~eRa~rRA~lp~a~SqGFnP~Pkisf~~a 52 (187)
T PF10105_consen 18 LDLMRVFERALRRAGLPVAYSQGFNPHPKISFAPA 52 (187)
T ss_pred HHHHHHHHHHhhhcCCCeeecCCCCCCcceeeccc
Confidence 357888999999999998886 45556677643
No 55
>PF01797 Y1_Tnp: Transposase IS200 like; InterPro: IPR002686 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This entry represents a domain found in transposases for IS200 from Escherichia coli []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2F5G_B 2F4F_B 2EC2_F 2XM3_C 2XQC_D 2XO6_A 2XMA_E 2VJV_B 2VIH_B 2VJU_A ....
Probab=24.66 E-value=1.6e+02 Score=20.81 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhcc----cc----ccCCCCeEeeeeeeccCcccHHHHHHHHHHhhc
Q psy16608 36 LYAMLKEELNSVGI----SV----EVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLR 84 (202)
Q Consensus 36 ~~~~l~~~~~~~~~----~~----~~~~~lHISLs~~~~~~~~~i~~~~~~L~~~l~ 84 (202)
.++.+.+.+..+.. .+ +-|+.+|+-++-.... .+..+++.++...+
T Consensus 23 ~~~~l~~~l~~~~~~~~~~i~~~~vm~nHvHllv~~~~~~---~is~~~~~lK~~~s 76 (121)
T PF01797_consen 23 IREALLEILREICEEYGIEIIAFVVMPNHVHLLVSIPPKQ---SISKFMQRLKGRSS 76 (121)
T ss_dssp HHHHHHHHHHHHHHHTTEEEEEEEEETTEEEEEEEE-TTS----HHHHHHHHHHHHH
T ss_pred eeeeeeeccccccccccceeeeecccCcccceeeeecccc---cchheeeccccccc
Confidence 45555555444433 22 7889999977765332 68899999987654
No 56
>KOG2814|consensus
Probab=23.94 E-value=1.1e+02 Score=27.15 Aligned_cols=37 Identities=14% Similarity=0.239 Sum_probs=23.3
Q ss_pred CCCCCCCCceEEEEeecCCCchhHHHHHHHHHHhhhh
Q psy16608 137 PTYYEEPNFHASIAWCLQDKTATLKPLLTKLDNIFTQ 173 (202)
Q Consensus 137 ~~~~~~~~pHiSia~~~~~~~~~l~~~~~~l~~~~~~ 173 (202)
..|..|-.+|+||+..+--...++.+++.-|+++..+
T Consensus 170 s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e 206 (345)
T KOG2814|consen 170 SLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQE 206 (345)
T ss_pred ccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHH
Confidence 5666778999999965544444555566555554443
No 57
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=23.66 E-value=63 Score=24.12 Aligned_cols=79 Identities=15% Similarity=0.211 Sum_probs=37.6
Q ss_pred CCcccccCccccccceEEEEecCCCHHHHHHHHHHHHHhhcccc-------ccCCCCeEeeee------------eeccC
Q psy16608 8 GGRIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEELNSVGISV-------EVIPEPHLSLSK------------TLVIP 68 (202)
Q Consensus 8 ~gr~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~~~~~~~~~-------~~~~~lHISLs~------------~~~~~ 68 (202)
.|+.+.|| || |+|+= ++. ..+..+.+.++.+.+++.- ..+..+|+|+-- +-.+.
T Consensus 5 ~G~~~~fp---GN--TvIch-l~~-~s~~~~al~~i~~~l~~~~~~~k~a~lP~sS~HMTVf~Gv~e~~R~~~~WP~~l~ 77 (118)
T PF08975_consen 5 DGNVLPFP---GN--TVICH-LPQ-DSPFYAALLAIQQRLRESPFADKLAFLPPSSYHMTVFEGVIESRREPGFWPADLP 77 (118)
T ss_dssp TS-B-------EE--EEEEE-B-T-TSHHHHHHHHHHHHHHTSGGGGGEEE--GGG-EEEEEEEEETT--STTSS-TTS-
T ss_pred CCCEecCC---CC--eEEee-cCC-CChHHHHHHHHHHHHHhCccccceEecCcchhhhhhhccccccccCCCCCCCCCC
Confidence 45555554 65 44442 343 3466677888888887642 788999999842 22333
Q ss_pred -cccHHHHHHHHHHhhcc---CCceEEEe
Q psy16608 69 -YHWIDTLVETLGNNLRH---LNRLTIKF 93 (202)
Q Consensus 69 -~~~i~~~~~~L~~~l~~---~~~F~l~~ 93 (202)
+.-++..-+.+.+.++. ..+|.+.+
T Consensus 78 ~d~~l~~~t~~~~~rL~~f~~~~~f~m~v 106 (118)
T PF08975_consen 78 LDAPLQECTRYFAERLKGFPLPGPFRMRV 106 (118)
T ss_dssp TT--HHHHHHHHHHHGGG--------EEE
T ss_pred CCCCHHHHHHHHHHHHhcCCCCCCeEEEE
Confidence 23566666666666665 34566555
No 58
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.05 E-value=1.5e+02 Score=21.84 Aligned_cols=34 Identities=12% Similarity=0.196 Sum_probs=21.1
Q ss_pred cccccCccccccceEEEEecCCCHHHHHHHHHHH
Q psy16608 10 RIRSFPHQRNSWATLVYIPLQTNLARLYAMLKEE 43 (202)
Q Consensus 10 r~R~~pH~~G~w~tfi~i~~~~~~~~~~~~l~~~ 43 (202)
++-+.|....+|...+||++.....++.+.|+.+
T Consensus 71 ~IESRP~~~~~~eY~FfIdieg~~~~~~~aL~~L 104 (115)
T cd04930 71 HLESRPSRKEGGDLEVLVRCEVHRSDLLQLISSL 104 (115)
T ss_pred EEECCcCCCCCceEEEEEEEEeCHHHHHHHHHHH
Confidence 3556777777888888888876233444444433
No 59
>PF04571 Lipin_N: lipin, N-terminal conserved region; InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=22.00 E-value=72 Score=23.56 Aligned_cols=19 Identities=16% Similarity=0.424 Sum_probs=16.6
Q ss_pred CCceEEEeCceEEEecCCC
Q psy16608 86 LNRLTIKFNSIEIFCNEEK 104 (202)
Q Consensus 86 ~~~F~l~~~~~~~f~n~~~ 104 (202)
.+||.++|++++++...++
T Consensus 42 sSPFhVRFGk~~vl~~~ek 60 (110)
T PF04571_consen 42 SSPFHVRFGKLGVLRPREK 60 (110)
T ss_pred cCccEEEEcceeeecccCc
Confidence 5899999999999987775
No 60
>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=21.74 E-value=1.3e+02 Score=19.95 Aligned_cols=51 Identities=12% Similarity=0.118 Sum_probs=29.4
Q ss_pred HHHhhccCCceEEEeCceEEEecCCCce--EEEEEeecCC--CccHHHHHHHHHHH
Q psy16608 79 LGNNLRHLNRLTIKFNSIEIFCNEEKTR--SFIALGANSC--KTSLTSIVQAVDKS 130 (202)
Q Consensus 79 L~~~l~~~~~F~l~~~~~~~f~n~~~~R--vF~~l~v~~~--~~~L~~L~~~i~~~ 130 (202)
|.+.++.+..+.+.+..+...|..+... +|.+ .++.. ...+..+++.++..
T Consensus 15 L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~v-d~~~~~~~~~~~~~l~~l~~~ 69 (80)
T cd04905 15 LYDVLGVFAERGINLTKIESRPSKGGLWEYVFFI-DFEGHIEDPNVAEALEELKRL 69 (80)
T ss_pred HHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEE-EEECCCCCHHHHHHHHHHHHh
Confidence 4444444555666777777888866554 3332 45443 34566666666653
No 61
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=21.65 E-value=1.4e+02 Score=19.68 Aligned_cols=67 Identities=12% Similarity=0.145 Sum_probs=36.8
Q ss_pred eeeccCcccHHHHHHHHHHhhccCC---------ce--EEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHH
Q psy16608 63 KTLVIPYHWIDTLVETLGNNLRHLN---------RL--TIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKS 130 (202)
Q Consensus 63 ~~~~~~~~~i~~~~~~L~~~l~~~~---------~F--~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~ 130 (202)
+.+.+++..-+.+...|++.+.... .. .....++.+.+.+....++.. +-......+..|++.+|.-
T Consensus 2 ~v~~L~~~~A~~v~~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~d~~tNsliv~-g~~~~~~~i~~li~~LD~p 79 (82)
T PF03958_consen 2 RVYPLKYASAEEVASVLQQLLGGGSGSSSGSGGSSGSGSSGSSSGRIVADERTNSLIVR-GTPEDLEQIRELIKQLDVP 79 (82)
T ss_dssp EEEE-SSS-HHHHHHHHHHHH----------------S-HHHTTTEEEEECTTTEEEEE-EEHHHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCcHHHHHHHHHHHhhhhcccccccccccccccCCCCCeEEEEECCCCEEEEE-eCHHHHHHHHHHHHHHCCC
Confidence 4556777777778888877764311 00 111245666667776666554 4444346677777777753
No 62
>PF13466 STAS_2: STAS domain
Probab=21.22 E-value=1.5e+02 Score=19.42 Aligned_cols=36 Identities=11% Similarity=0.055 Sum_probs=22.2
Q ss_pred eeeeccCcccHHHHHHHHHHhhccCCceEEEeCceE
Q psy16608 62 SKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIE 97 (202)
Q Consensus 62 s~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~ 97 (202)
+-.|+++....+++.+.+.+.+..-.+..|.++++.
T Consensus 2 ~l~G~l~~~~~~~l~~~l~~~~~~~~~v~lDls~v~ 37 (80)
T PF13466_consen 2 RLSGELDIATAPELRQALQALLASGRPVVLDLSGVE 37 (80)
T ss_pred EEEEEEeHHHHHHHHHHHHHHHcCCCeEEEECCCCC
Confidence 445667777777777777766644445555555553
No 63
>TIGR00254 GGDEF diguanylate cyclase (GGDEF) domain. The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein.
Probab=20.77 E-value=3.3e+02 Score=19.52 Aligned_cols=94 Identities=12% Similarity=0.058 Sum_probs=46.3
Q ss_pred ccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEeecC-CCccHHHHHHHHHHHHHhcCCCCCC-CCCCceE
Q psy16608 70 HWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGANS-CKTSLTSIVQAVDKSAQEFKLPTYY-EEPNFHA 147 (202)
Q Consensus 70 ~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~-~~~~L~~L~~~i~~~l~~~g~~~~~-~~~~pHi 147 (202)
+..+.++..+.+.++..- ..-.+...-+..+. .++ +.. +......+.+.+.+.+....+.... .....++
T Consensus 54 ~~~~~ll~~~a~~l~~~~------~~~~~i~r~~~~~f-~il-~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~ 125 (165)
T TIGR00254 54 DVGDEVLREVARILQSSV------RGSDVVGRYGGEEF-VVI-LPGTPLEDALSKAERLRDAINSKPIEVAGSETLTVTV 125 (165)
T ss_pred hhHHHHHHHHHHHHHHhc------CcCCEEEEecCCeE-EEE-eCCCChHHHHHHHHHHHHHHHhCeeccCCCceEEEEE
Confidence 456777777776665421 11112223333333 333 322 2245677777777777655444332 3455777
Q ss_pred EEEeecCCCc-hhHHHHHHHHHHhh
Q psy16608 148 SIAWCLQDKT-ATLKPLLTKLDNIF 171 (202)
Q Consensus 148 Sia~~~~~~~-~~l~~~~~~l~~~~ 171 (202)
++|++..+.. ......+......+
T Consensus 126 ~~g~~~~~~~~~~~~~l~~~a~~al 150 (165)
T TIGR00254 126 SIGVACYPGHGLTLEELLKRADEAL 150 (165)
T ss_pred EEEEEEcCCCCCCHHHHHHHHHHHH
Confidence 7887654332 23334444433333
No 64
>PF08782 c-SKI_SMAD_bind: c-SKI Smad4 binding domain; InterPro: IPR014890 c-SKI is an oncoprotein that inhibits TGF-beta signalling through interaction with Smad proteins []. This protein binds to Smad4 [].; GO: 0005634 nucleus; PDB: 1MR1_C.
Probab=20.62 E-value=64 Score=23.24 Aligned_cols=27 Identities=15% Similarity=0.306 Sum_probs=13.8
Q ss_pred ccccceEEEEecC----CCHHHHHHHHHHHH
Q psy16608 18 RNSWATLVYIPLQ----TNLARLYAMLKEEL 44 (202)
Q Consensus 18 ~G~w~tfi~i~~~----~~~~~~~~~l~~~~ 44 (202)
--|||.|+-|.-. ...+++...|+++-
T Consensus 62 s~nWr~yL~l~~d~~~~~~~~~l~~~le~~k 92 (96)
T PF08782_consen 62 SANWRRYLHLSQDYRDKEEQERLKQALEDVK 92 (96)
T ss_dssp GGGHHHC-EE-TT---TTCHHHHHHHHHHHH
T ss_pred HhHhhHHheecccccCcchHHHHHHHHHHHH
Confidence 3479999988842 11334555555443
No 65
>PF03089 RAG2: Recombination activating protein 2; InterPro: IPR004321 The variable portion of the genes encoding immunoglobulins and T cell receptors are assembled from component V, D, and J DNA segments by a site-specific recombination reaction termed V(D)J recombination. V(D)J recombination is targeted to specific sites on the chromosome by recombination signal sequences (RSSs) that flank antigen receptor gene segments. The RSS consists of a conserved heptamer (consensus, 5'-CACAGTG-3') and nonamer (consensus, 5'-ACAAAAACC-3') separated by a spacer of either 12 or 23 bp. Efficient recombination occurs between a 12-RSS and a 23-RSS, a restriction known as the 12/23 rule. V(D)J recombination can be divided into two phases, DNA cleavage and DNA joining. DNA cleavage requires two lymphocyte-specific factors, the products of the recombination activating genes, RAG1 and RAG2, which together recognise the RSSs and create double strand breaks at the RSS-coding segment junctions []. RAG-mediated DNA cleavage occurs in a synaptic complex termed the paired complex, which is constituted from two distinct RSS-RAG complexes, a 12-SC and a 23-SC (where SC stands for signal complex). The DNA cleavage reaction involves two distinct enzymatic steps, initial nicking that creates a 3'-OH between a coding segment and its RSS, followed by hairpin formation in which the newly created 3'-OH attacks a phosphodiester bond on the opposite DNA strand. This generates a blunt, 5' phosphorylated signal end containing all of the RSS elements, and a covalently sealed hairpin coding end. The second phase of V(D)J recombination, in which broken DNA fragments are processed and joined, is less well characterised. Signal ends are typically joined precisely to form a signal joint, whereas joining of the coding ends requires the hairpin structure to be opened and typically involves nucleotide addition and deletion before formation of the coding joint. The factors involved in these processes include ubiquitously expressed proteins involved in the repair of DNA double strand breaks by nonhomologous end joining, terminal deoxynucleotidyl transferase, and Artemis protein. In addition to their critical roles in RSS recognition and DNA cleavage, the RAG proteins may perform two distinct types of functions in the postcleavage phase of V(D)J. A structural function has been inferred from the finding that, after DNA cleavage in vitro, the DNA ends remain associated with the RAG proteins in a "four end" complex known as the cleaved signal complex. After release of the coding ends in vitro, and after coding joint formation in vivo, the RAG proteins remain in a stable signal end complex (SEC) containing the two signal ends. These postcleavage complexes may serve as essential scaffolds for the second phase of the reaction, with the RAG proteins acting to organise the DNA processing and joining events. The second type of RAG protein-mediated postcleavage activity is the catalysis of phosphodiester bond hydrolysis and strand transfer reactions. The RAG proteins are capable of opening hairpin coding ends in vitro. The RAG proteins also show 3' flap endonuclease activity that may contribute to coding end processing/joining and can utilise the 3' OH group on the signal ends to attack hairpin coding ends (forming hybrid or open/shut joints) or virtually any DNA duplex (forming a transposition product).; GO: 0003677 DNA binding, 0006310 DNA recombination, 0005634 nucleus
Probab=20.41 E-value=45 Score=29.03 Aligned_cols=61 Identities=15% Similarity=0.212 Sum_probs=37.3
Q ss_pred eEEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy16608 89 LTIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAW 151 (202)
Q Consensus 89 F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~~~~pHiSia~ 151 (202)
-.+-|++=.+.|..++|.--|- .|.... ...-|++.==.|...+-+|...+-.+||++||+
T Consensus 103 a~VlFGGRSY~P~~qRTTenWN-sVvDC~-P~VfLiDleFGC~tah~lpEl~dG~SFHvslar 163 (337)
T PF03089_consen 103 ACVLFGGRSYMPPGQRTTENWN-SVVDCP-PQVFLIDLEFGCCTAHTLPELQDGQSFHVSLAR 163 (337)
T ss_pred EEEEECCcccCCccccchhhcc-eeccCC-CeEEEEeccccccccccchhhcCCeEEEEEEec
Confidence 4445565556666666655554 233322 111123222357788889999999999999996
No 66
>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown.
Probab=20.28 E-value=1.1e+02 Score=23.10 Aligned_cols=69 Identities=14% Similarity=0.345 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhhcc---CCceE-EEeCceEEEecCCCceEE-EEEeecCCCccHHHHHHHHHHHHHhcCCCCCCC
Q psy16608 72 IDTLVETLGNNLRH---LNRLT-IKFNSIEIFCNEEKTRSF-IALGANSCKTSLTSIVQAVDKSAQEFKLPTYYE 141 (202)
Q Consensus 72 i~~~~~~L~~~l~~---~~~F~-l~~~~~~~f~n~~~~RvF-~~l~v~~~~~~L~~L~~~i~~~l~~~g~~~~~~ 141 (202)
...|.+.+++.+++ .+||. +.++.+.+|...-.+.+- ++++.+.+.+-+.. ...=+..|.+.|...+.+
T Consensus 29 v~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~-~~~~~~tL~~~gv~nETE 102 (122)
T PF10209_consen 29 VKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILD-VSDDDKTLKELGVENETE 102 (122)
T ss_pred HHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeee-cCCCCCcHHHcCCCccce
Confidence 34455555555443 56774 677788888777665532 23344332111110 011244566777766554
No 67
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=20.11 E-value=1.3e+02 Score=20.90 Aligned_cols=32 Identities=13% Similarity=0.362 Sum_probs=22.7
Q ss_pred cHHHHHHHHHHhhccCCceEEEeCceEEEecCCC
Q psy16608 71 WIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEK 104 (202)
Q Consensus 71 ~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~ 104 (202)
-+|.|.+.+.++|..-. .+.|.++|.|-...+
T Consensus 24 ~v~~~~~~i~~~L~~~~--~v~l~gfG~F~v~~r 55 (90)
T PRK10664 24 ALDAIIASVTESLKEGD--DVALVGFGTFAVKER 55 (90)
T ss_pred HHHHHHHHHHHHHhCCC--EEEECCcEEEEEEEe
Confidence 56777777777776655 477888888876654
No 68
>PF15378 DUF4605: Domain of unknown function (DUF4605)
Probab=20.09 E-value=85 Score=20.59 Aligned_cols=18 Identities=11% Similarity=0.423 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhcCCCCCC
Q psy16608 123 IVQAVDKSAQEFKLPTYY 140 (202)
Q Consensus 123 L~~~i~~~l~~~g~~~~~ 140 (202)
+.+.+++.|..+|+|..|
T Consensus 2 ~f~~iN~~L~~~Gf~~~~ 19 (60)
T PF15378_consen 2 LFGEINQRLLGLGFPRMY 19 (60)
T ss_pred chHHHHHHHHHCCCCCee
Confidence 457899999999999877
No 69
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=20.08 E-value=2.7e+02 Score=18.35 Aligned_cols=71 Identities=11% Similarity=0.051 Sum_probs=38.4
Q ss_pred eEeeeeeeccCcccHHHHHHHHHHhhccCCceEEEeCceEEEecCCCceEEEEEeecCCCccHHHHHHHHHHHHHhcCCC
Q psy16608 58 HLSLSKTLVIPYHWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGANSCKTSLTSIVQAVDKSAQEFKLP 137 (202)
Q Consensus 58 HISLs~~~~~~~~~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~~~~RvF~~l~v~~~~~~L~~L~~~i~~~l~~~g~~ 137 (202)
|+-|+..|.=+ ..++..+.+.+.....--+..+. |. ...+.|..+-++.+......|.+.+++..+++|+.
T Consensus 1 ~~iltv~g~Dr----~GiVa~vs~~la~~g~nI~d~~q---~~--~~~~F~m~~~~~~~~~~~~~l~~~l~~~~~~~~l~ 71 (77)
T cd04893 1 HLVISALGTDR----PGILNELTRAVSESGCNILDSRM---AI--LGTEFALTMLVEGSWDAIAKLEAALPGLARRLDLT 71 (77)
T ss_pred CEEEEEEeCCC----ChHHHHHHHHHHHcCCCEEEcee---eE--EcCEEEEEEEEEeccccHHHHHHHHHHHHHHcCCE
Confidence 45566666666 55566666665544332222221 22 23344554444433335777888888877777763
No 70
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=20.01 E-value=1.5e+02 Score=20.71 Aligned_cols=30 Identities=13% Similarity=0.237 Sum_probs=19.4
Q ss_pred cHHHHHHHHHHhhccCCceEEEeCceEEEecC
Q psy16608 71 WIDTLVETLGNNLRHLNRLTIKFNSIEIFCNE 102 (202)
Q Consensus 71 ~i~~~~~~L~~~l~~~~~F~l~~~~~~~f~n~ 102 (202)
-++.|.+.|.+.|.. --.++|.++|.|.-.
T Consensus 25 vv~~~~~~i~~~L~~--g~~V~l~gfG~F~~~ 54 (96)
T TIGR00987 25 LVELFFEEIRRALEN--GEQVKLSGFGNFDLR 54 (96)
T ss_pred HHHHHHHHHHHHHHc--CCeEEecCCEEEEEE
Confidence 455666666666644 346888999988443
Done!