Query 040775
Match_columns 183
No_of_seqs 132 out of 1080
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 11:42:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040775.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040775hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13679 hypothetical protein; 100.0 4E-28 8.6E-33 179.9 18.6 161 4-178 2-168 (168)
2 COG1514 LigT 2'-5' RNA ligase 100.0 3.7E-28 7.9E-33 181.0 18.2 168 4-179 2-180 (180)
3 TIGR02258 2_5_ligase 2'-5' RNA 100.0 9.1E-27 2E-31 174.2 19.5 166 4-177 2-179 (179)
4 PRK15124 2'-5' RNA ligase; Pro 100.0 8.8E-27 1.9E-31 173.9 17.4 164 2-178 4-175 (176)
5 PF13563 2_5_RNA_ligase2: 2'-5 99.9 7.1E-25 1.5E-29 159.4 8.6 148 11-167 1-150 (153)
6 PHA02574 57B hypothetical prot 99.8 6.1E-19 1.3E-23 127.0 10.8 110 3-134 9-119 (149)
7 PF07823 CPDase: Cyclic phosph 99.8 3.7E-17 8.1E-22 123.8 14.8 170 5-177 3-196 (196)
8 PF10469 AKAP7_NLS: AKAP7 2'5' 99.7 7.6E-15 1.6E-19 112.4 17.4 172 4-177 2-209 (209)
9 PLN00108 unknown protein; Prov 99.3 2.9E-10 6.3E-15 88.4 18.1 176 1-179 34-256 (257)
10 PF02834 LigT_PEase: LigT like 99.2 4.1E-11 8.9E-16 79.1 7.5 81 9-89 1-87 (87)
11 TIGR03223 Phn_opern_protn puta 99.0 1.7E-08 3.6E-13 77.5 12.6 133 39-179 55-228 (228)
12 PF05213 Corona_NS2A: Coronavi 98.9 1.4E-08 3.1E-13 76.0 10.7 133 15-167 20-163 (248)
13 PF09749 HVSL: Uncharacterised 98.6 3.2E-06 7E-11 66.0 15.6 125 6-133 45-188 (239)
14 PHA02977 hypothetical protein; 98.5 2.2E-06 4.8E-11 60.7 10.3 92 39-133 67-171 (201)
15 PF02834 LigT_PEase: LigT like 98.2 9.6E-06 2.1E-10 53.2 7.2 72 96-172 9-86 (87)
16 PF06299 DUF1045: Protein of u 97.5 0.0029 6.3E-08 46.2 10.5 111 50-166 10-151 (160)
17 PF08302 tRNA_lig_CPD: Fungal 96.8 0.036 7.7E-07 43.9 11.7 65 69-149 161-228 (257)
18 PF07823 CPDase: Cyclic phosph 95.5 0.086 1.9E-06 40.0 7.6 72 86-163 3-83 (196)
19 COG5255 Uncharacterized protei 95.4 0.076 1.6E-06 40.2 6.7 110 13-133 52-185 (239)
20 KOG2814 Transcription coactiva 95.0 0.21 4.6E-06 40.5 8.4 93 38-133 174-282 (345)
21 TIGR02258 2_5_ligase 2'-5' RNA 94.8 0.29 6.3E-06 36.1 8.4 72 88-166 3-81 (179)
22 PRK13679 hypothetical protein; 94.5 0.27 5.9E-06 36.1 7.7 64 16-82 89-152 (168)
23 COG1514 LigT 2'-5' RNA ligase 94.0 0.44 9.5E-06 35.7 7.9 75 88-166 3-81 (180)
24 PF13563 2_5_RNA_ligase2: 2'-5 93.5 0.47 1E-05 33.7 7.1 74 6-82 75-148 (153)
25 KOG3102 Uncharacterized conser 90.7 1.8 3.8E-05 33.2 7.3 91 39-133 119-217 (269)
26 PRK15124 2'-5' RNA ligase; Pro 88.5 3.2 6.9E-05 30.7 7.4 75 87-165 6-83 (176)
27 PF11080 DUF2622: Protein of u 84.9 8.6 0.00019 25.7 7.0 78 1-78 1-88 (96)
28 PF08975 2H-phosphodiest: Doma 84.6 4.7 0.0001 28.0 5.9 37 12-48 23-60 (118)
29 PF06299 DUF1045: Protein of u 79.3 4 8.6E-05 29.9 4.2 46 38-83 105-151 (160)
30 COG5255 Uncharacterized protei 79.1 4.8 0.0001 30.7 4.7 71 12-82 149-227 (239)
31 PHA02574 57B hypothetical prot 78.0 4.2 9E-05 29.5 4.0 36 7-48 82-118 (149)
32 TIGR03223 Phn_opern_protn puta 69.6 11 0.00023 29.4 4.7 46 38-83 165-211 (228)
33 PF10469 AKAP7_NLS: AKAP7 2'5' 66.7 53 0.0011 24.7 8.4 45 124-168 40-96 (209)
34 PF07476 MAAL_C: Methylasparta 56.9 25 0.00053 27.4 4.5 65 13-82 47-116 (248)
35 PRK06646 DNA polymerase III su 52.8 12 0.00025 27.3 2.1 34 88-133 32-65 (154)
36 PF08883 DOPA_dioxygen: Dopa 4 49.0 70 0.0015 21.7 5.3 72 5-76 1-76 (104)
37 PRK05728 DNA polymerase III su 47.9 15 0.00033 26.2 2.1 34 88-133 32-65 (142)
38 PHA02977 hypothetical protein; 47.5 37 0.0008 24.5 3.9 39 17-55 134-178 (201)
39 PF12323 HTH_OrfB_IS605: Helix 47.3 50 0.0011 18.3 4.0 27 1-27 1-27 (46)
40 PF05213 Corona_NS2A: Coronavi 44.7 21 0.00046 27.5 2.4 21 124-144 41-62 (248)
41 PF04571 Lipin_N: lipin, N-ter 44.6 36 0.00078 23.3 3.3 27 68-94 42-68 (110)
42 PF04364 DNA_pol3_chi: DNA pol 38.6 20 0.00042 25.4 1.4 34 88-133 32-65 (137)
43 PF04095 NAPRTase: Nicotinate 36.3 1.6E+02 0.0035 23.0 6.4 55 7-65 114-170 (245)
44 PLN00108 unknown protein; Prov 32.8 2.5E+02 0.0055 22.3 8.6 45 124-168 89-144 (257)
45 PF09749 HVSL: Uncharacterised 32.5 2.4E+02 0.0051 21.9 8.1 94 74-167 26-137 (239)
46 COG3799 Mal Methylaspartate am 31.7 2.9E+02 0.0063 22.7 8.7 85 14-113 208-296 (410)
47 COG2927 HolC DNA polymerase II 30.2 45 0.00097 24.0 2.1 28 94-133 38-65 (144)
48 cd06406 PB1_P67 A PB1 domain i 30.0 1.6E+02 0.0034 19.0 5.2 52 86-150 11-71 (80)
49 COG1111 MPH1 ERCC4-like helica 29.2 3.3E+02 0.0071 24.1 7.4 72 39-112 160-235 (542)
50 PF07485 DUF1529: Domain of Un 26.9 2.2E+02 0.0049 19.8 6.2 55 54-110 67-121 (123)
51 PF06877 RraB: Regulator of ri 24.6 2E+02 0.0044 18.8 4.5 74 4-80 23-104 (104)
52 PF11823 DUF3343: Protein of u 24.5 1.8E+02 0.0039 17.8 4.0 49 107-155 19-67 (73)
53 PF14202 TnpW: Transposon-enco 23.7 1.1E+02 0.0025 16.4 2.5 25 4-28 11-35 (37)
54 PF06526 DUF1107: Protein of u 23.3 1.8E+02 0.0039 17.9 3.6 56 50-109 5-60 (64)
55 PF01361 Tautomerase: Tautomer 22.9 1.4E+02 0.003 17.3 3.1 21 42-62 1-21 (60)
56 cd02974 AhpF_NTD_N Alkyl hydro 22.1 2.4E+02 0.0052 18.5 8.8 80 11-104 2-92 (94)
57 COG1856 Uncharacterized homolo 21.9 1.7E+02 0.0038 23.0 4.1 98 50-151 69-179 (275)
58 PF06183 DinI: DinI-like famil 21.6 1.5E+02 0.0032 18.2 3.0 54 11-64 2-56 (65)
59 PF03869 Arc: Arc-like DNA bin 21.5 1.8E+02 0.0038 16.7 3.3 23 1-23 1-23 (50)
60 KOG2875 8-oxoguanine DNA glyco 20.2 93 0.002 25.2 2.4 43 40-82 115-160 (323)
No 1
>PRK13679 hypothetical protein; Provisional
Probab=99.96 E-value=4e-28 Score=179.94 Aligned_cols=161 Identities=17% Similarity=0.196 Sum_probs=133.4
Q ss_pred eeEEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChh---HHHHHHHHhhccCCCeeEEEceeee
Q 040775 4 GYAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPA---KLESIIKIHASKQEPLPLCLSTIGS 80 (183)
Q Consensus 4 ~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~---~l~~~l~~~~~~~~pf~l~~~~~g~ 80 (183)
.|+|++.|++++.+.+.++++.+... . ...+|||||.+.++++.+ .+.+.+++++...+||+++++++|+
T Consensus 2 ~~~iai~~p~~~~~~l~~~~~~~~~~-----~--~~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~ 74 (168)
T PRK13679 2 KYGIVLFPSKKIQDFANSYRKRYDPH-----Y--ALIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSS 74 (168)
T ss_pred eeEEEEcCCHHHHHHHHHHHHhhCcc-----c--ccCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEecccc
Confidence 69999999999999999998777422 1 136789999988877764 4577788888888999999999999
Q ss_pred eCCCCcEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcceEEEEeE
Q 040775 81 FCNDNNVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLPVTGYAMD 160 (183)
Q Consensus 81 F~~~~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 160 (183)
|++.++|+|++++++++|.+||+++.+.+.. . ...++|+|||||||..+.++..++...++....++.++|++
T Consensus 75 F~~~~~vl~l~~~~~~~L~~L~~~l~~~~~~----~---~~~~~f~PHiTlar~~~~~~~~~~~~~l~~~~~~~~~~v~~ 147 (168)
T PRK13679 75 FAPTNNVIYFKVEKTEELEELHERLHSGDFY----G---EAEYAFVPHITIGQGLSDDEHEDVLGQLKMADVDHEETIDR 147 (168)
T ss_pred CCCCCCEEEEEccCCHHHHHHHHHHHhcccc----c---ccCCCCCCeEEeeCCCCcHHHHHHHHHHhcCCcceeEEECe
Confidence 9865689999999889999999999875431 1 12356999999999888888999988887777778889999
Q ss_pred EEEEeec---CceeEEEEECC
Q 040775 161 IGLVEYS---PVRELFSFALG 178 (183)
Q Consensus 161 i~L~~~~---p~~~l~~~~l~ 178 (183)
|+|+... .|+++.+|.||
T Consensus 148 i~L~~~~~~~~w~~~~~~~~~ 168 (168)
T PRK13679 148 FHLLYQLENGSWTVYETFRLG 168 (168)
T ss_pred EEEEEECCCCeEEEEEEeeCC
Confidence 9998663 59999999986
No 2
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.7e-28 Score=181.01 Aligned_cols=168 Identities=20% Similarity=0.277 Sum_probs=137.6
Q ss_pred eeEEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChhH---HHHHHHHhhccCCCeeEEEceeee
Q 040775 4 GYAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPAK---LESIIKIHASKQEPLPLCLSTIGS 80 (183)
Q Consensus 4 ~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~~---l~~~l~~~~~~~~pf~l~~~~~g~ 80 (183)
.|+|++.+|+++.+++.++++.+.... ...+. ...++||||.|+++++++. +.+++..++... ||+|+++|+|.
T Consensus 2 RlFiAl~~p~~i~~~i~~~~~~~~~~~-~~k~v-~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g~ 78 (180)
T COG1514 2 RLFIALDPPAEIAERLARIRARLKGAR-AIKWV-EPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAGS 78 (180)
T ss_pred eeEEEecCCHHHHHHHHHHHHhcCccc-ccccc-cccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEcc
Confidence 589999999999999999999999876 33333 6799999999999888765 456666766656 99999999999
Q ss_pred eCC--CCcEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcceEEEE
Q 040775 81 FCN--DNNVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLPVTGYA 158 (183)
Q Consensus 81 F~~--~~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~~~~~v 158 (183)
|++ +++|+|+++.++++|.+|++.+.+.+...|. .+ .+++|+|||||||......+.++...+...... ++.|
T Consensus 79 F~~~~~~rvi~~~v~~~~~L~~L~~~l~~~~~~~g~--~~--~~r~F~PHvTl~r~k~~~~~~~~~~~~~~~~~~-~~~v 153 (180)
T COG1514 79 FPNPRRPRVIWVGVEETEELRALAEELERALARLGL--RP--EERPFVPHVTLARVKSKDKLVEALGEFKNVEFG-EMEV 153 (180)
T ss_pred cCCCCCCcEEEEcCCCcHHHHHHHHHHHHHHHhcCC--CC--CCCCcCCCEEEEeecccchhhhhhhhhcccccc-ceEe
Confidence 996 6899999998888899999999999998873 22 246799999999954455666666666654433 6789
Q ss_pred eEEEEEeec-----C-ceeEEEEECCC
Q 040775 159 MDIGLVEYS-----P-VRELFSFALGN 179 (183)
Q Consensus 159 ~~i~L~~~~-----p-~~~l~~~~l~~ 179 (183)
++++|++|. | |+.+.+|+|.+
T Consensus 154 d~~~L~~S~l~~~gp~Y~~~~~~~L~~ 180 (180)
T COG1514 154 DRFSLYSSTLTPGGPIYETLKEFPLSG 180 (180)
T ss_pred eEEEEEEEeeCCCCCEEEEEEEEecCC
Confidence 999999985 3 99999999975
No 3
>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=99.95 E-value=9.1e-27 Score=174.21 Aligned_cols=166 Identities=19% Similarity=0.206 Sum_probs=128.5
Q ss_pred eeEEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChhHH---HHHHHHhhccCCCeeEEEceeee
Q 040775 4 GYAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPAKL---ESIIKIHASKQEPLPLCLSTIGS 80 (183)
Q Consensus 4 ~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~~l---~~~l~~~~~~~~pf~l~~~~~g~ 80 (183)
.|||++.+++++.+++.++++.+.+......+ .+..++||||.|+++.+.+++ .+.+++++ ..+|+++++|+|+
T Consensus 2 R~FiAl~~p~~~~~~l~~~~~~l~~~~~~~r~-~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--~~~f~l~l~~~~~ 78 (179)
T TIGR02258 2 RLFIAIDLPPEIREQLSRIQRKLKSPLDGIKW-VPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLEGIGV 78 (179)
T ss_pred eEEEEecCCHHHHHHHHHHHHHhhccCCCcEE-CChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--CCCeEEEEeeeee
Confidence 68999999999999999999999843222222 256788999999988877654 44566655 4679999999999
Q ss_pred eCC--CCcEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeeccCChh-hHHHHHHHHHhCCcceEEE
Q 040775 81 FCN--DNNVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKT-RMAEAFCVLRELKLPVTGY 157 (183)
Q Consensus 81 F~~--~~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~-~~~~~~~~~~~~~~~~~~~ 157 (183)
|++ +++|+|++++.+++|.+||+++.+.+...|.. +++++|+|||||||..... .+.+.+..... ..+.+++
T Consensus 79 F~~~~~~~vl~l~~~~~~~L~~L~~~l~~~~~~~g~~----~~~~~f~PHiTlar~~~~~~~~~~~~~~~~~-~~~~~~~ 153 (179)
T TIGR02258 79 FGNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFS----KEERPFTPHITLARKKSGKPGVPEFLQEFAN-EEFGSFH 153 (179)
T ss_pred CCCCCCCeEEEEeeCCCHHHHHHHHHHHHHHHHcCCC----CCCCCcCCCEEEEEecCCcHhHHHHHHHhCC-CCCCceE
Confidence 986 46899999988889999999999999988743 2446799999999944333 33333333322 3467889
Q ss_pred EeEEEEEeec-----C-ceeEEEEEC
Q 040775 158 AMDIGLVEYS-----P-VRELFSFAL 177 (183)
Q Consensus 158 v~~i~L~~~~-----p-~~~l~~~~l 177 (183)
|++|+|++|. + |+++++|||
T Consensus 154 v~~i~L~~S~~~~~g~~Y~~l~~~~l 179 (179)
T TIGR02258 154 VDEFHLYSSTLTPGGPIYEPLARFQL 179 (179)
T ss_pred eeEEEEEEeeccCCCCcceEEEEEcC
Confidence 9999999985 2 999999997
No 4
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.95 E-value=8.8e-27 Score=173.93 Aligned_cols=164 Identities=15% Similarity=0.188 Sum_probs=125.6
Q ss_pred CceeEEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChhHHHHHHHHhh-ccCCCeeEEEceeee
Q 040775 2 SQGYAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPAKLESIIKIHA-SKQEPLPLCLSTIGS 80 (183)
Q Consensus 2 ~~~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~~l~~~l~~~~-~~~~pf~l~~~~~g~ 80 (183)
+..+||++.+++++.+.+.++++.+..... ..+ .+..+.||||.|+++++++.+....+.+. ...+||+++++|+|+
T Consensus 4 ~~RlFiAl~~p~~~~~~l~~~~~~~~~~~~-~rw-v~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~~~~pF~l~l~~~g~ 81 (176)
T PRK15124 4 PKRLFFAIDLPDEIRQQIIHWRATHFPPEA-GRP-VAAANLHLTLAFLGEVSAEKQQALSQLAGRIRQPGFTLTLDDAGQ 81 (176)
T ss_pred ceEEEEEeCCCHHHHHHHHHHHHHhccccC-ccc-ccccccEEEEEecCCCCHHHHHHHHHHHHhcccCCeEEEECcccC
Confidence 358999999999999999999988865322 222 25689999999999999887654443332 147899999999999
Q ss_pred eCCCCcEEEEeec-CChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcceEEEEe
Q 040775 81 FCNDNNVLFLAPT-PSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLPVTGYAM 159 (183)
Q Consensus 81 F~~~~~vl~l~v~-~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 159 (183)
|++ ++|+|++++ +++.|.+||+++.+.+...|.. . +.++|+|||||||....... +.....+.++.|+
T Consensus 82 Fp~-prvlwlg~~~~~~~L~~L~~~l~~~l~~~G~~--~--e~r~f~PHiTLaR~~~~~~~------~~~~~~~~~~~v~ 150 (176)
T PRK15124 82 WPR-SRVVWLGMRQPPRGLLQLANMLRSQAARSGCY--Q--SPQPFHPHITLLRDASRPVA------IPPPGFNWSFPVT 150 (176)
T ss_pred cCC-CCEEEEEcCCCCHHHHHHHHHHHHHHHHcCCC--C--CCCCCCCCEeeccCCCCccc------ccCCCCCCceEcC
Confidence 984 899999996 4579999999999999998842 2 34679999999994332110 1111223457799
Q ss_pred EEEEEeec-----C-ceeEEEEECC
Q 040775 160 DIGLVEYS-----P-VRELFSFALG 178 (183)
Q Consensus 160 ~i~L~~~~-----p-~~~l~~~~l~ 178 (183)
+++||+|. | |+++++|+|.
T Consensus 151 ~~~L~~S~l~~~g~~Y~~l~~~~L~ 175 (176)
T PRK15124 151 EFTLYASSFARGRTRYTPLQRWPLT 175 (176)
T ss_pred EEEEEEEeccCCCCEEEEEEEEeCC
Confidence 99999985 2 9999999996
No 5
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.92 E-value=7.1e-25 Score=159.45 Aligned_cols=148 Identities=23% Similarity=0.239 Sum_probs=85.2
Q ss_pred eChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCCh--hHHHHHHHHhhccCCCeeEEEceeeeeCCCCcEE
Q 040775 11 FDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEP--AKLESIIKIHASKQEPLPLCLSTIGSFCNDNNVL 88 (183)
Q Consensus 11 ~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~--~~l~~~l~~~~~~~~pf~l~~~~~g~F~~~~~vl 88 (183)
||+++.++|++++ .+.+... . +..+|||||++....+. +.+.+.+..++++.+||+++|+++++|++.+++|
T Consensus 1 pp~~~~~~i~~lr---~~~~~~~-~--~~~~pHITL~~~~~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~~~F~~~~~vi 74 (153)
T PF13563_consen 1 PPDELAEEIEALR---RQKGDKR-Y--PRWPPHITLAFPFDIDDSLDELVEALARLAAGFPPFELRLDGFGSFPGKGRVI 74 (153)
T ss_dssp ------------G---T-TTEEE-----GGG-EEEEEEEEE--GGGHHHHHHHHHHHHHS--EEEEEEEEEEESSSSSSE
T ss_pred Ccccccccchhhh---cccCCCC-C--CCCCCEeEEEecCcccccHHHHHHHHHHHHccCCCeEEEEccEEEcCCCCCEE
Confidence 5677777777666 2322222 2 45779999987655544 7899999999988999999999999997535699
Q ss_pred EEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcceEEEEeEEEEEeec
Q 040775 89 FLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLPVTGYAMDIGLVEYS 167 (183)
Q Consensus 89 ~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~i~L~~~~ 167 (183)
|+.+.++.+|.+||++|.+.+...+... +..++|+||||||++.......+++..++....+.+++|++|.|++++
T Consensus 75 ~l~~~~~~~L~~L~~~l~~~~~~~~~~~---~~~~~~~PHiTia~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~L~~~~ 150 (153)
T PF13563_consen 75 FLNVEPSPELEALHRALREALRPFGFKQ---DSYRPFRPHITIARRLSPKQAAEAIEKLQSEFPPISFTVDELALVRSD 150 (153)
T ss_dssp EEEEEE-HHHHHHHHHHHHHHHHHHGGG---GGGS----EEEEEEESS-----------------EEEEE-EEEEEEEE
T ss_pred EEEcCCCHHHHHHHHHHHHHHHHcCCcc---ccCCCcceEEEEeccCCcchhHHHHHHHhCcCCCcEEEEeEEEEEEEC
Confidence 9999999999999999999998875211 111579999999998777777888888867778899999999999875
No 6
>PHA02574 57B hypothetical protein; Provisional
Probab=99.80 E-value=6.1e-19 Score=127.01 Aligned_cols=110 Identities=13% Similarity=0.057 Sum_probs=88.2
Q ss_pred ceeEEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChhHHHHHHHHhhccCCCeeEEEceeeeeC
Q 040775 3 QGYAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFC 82 (183)
Q Consensus 3 ~~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~ 82 (183)
...+|++.+|+++.+++.++++++.. ... .+..+.|+||.| +.+++. .+....+||+++++|+|+|+
T Consensus 9 ~RlF~Al~~~~~~r~~L~~lq~~l~~----~r~-V~~enLHlTL~F----~~~~v~----~l~~~~~~F~l~l~glG~F~ 75 (149)
T PHA02574 9 QGTYVAAKFSEATLDALERLQRTLRI----PNP-VPRDKLHSTIVY----SRVYVP----FIPASGSTEVASSGHLEVWE 75 (149)
T ss_pred ceEEEEEcCCHHHHHHHHHHHHhccC----Ccc-cCHHHCEEEEec----CHHHhH----HHhccCCCeEEEeccccccC
Confidence 46899999999999999999999643 112 267999999988 233333 22335799999999999998
Q ss_pred C-CCcEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeecc
Q 040775 83 N-DNNVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQE 134 (183)
Q Consensus 83 ~-~~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~ 134 (183)
+ +++|+|+++. +++|.+|++++.+.+...+ .++|+|||||+|+
T Consensus 76 ~~~~rvlWlg~~-~~~L~~L~~~l~~~l~~~~--------~r~F~PHITLaR~ 119 (149)
T PHA02574 76 TQDKNALVLVLE-SEYLQCRHKYARALGATHD--------FDDYTPHITLSYD 119 (149)
T ss_pred CCCCCEEEEEeC-CHHHHHHHHHHHHHhhcCC--------CCCcCCcEEEeec
Confidence 4 5899999997 8999999999999988742 2359999999994
No 7
>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=99.76 E-value=3.7e-17 Score=123.80 Aligned_cols=170 Identities=19% Similarity=0.173 Sum_probs=99.4
Q ss_pred eEEEEEeCh--hhHHHHHHHHHHHHHccCccccccCCCCCeeEEeec-CCCChhHHHHHHHHhhccCCCe-----eEEEc
Q 040775 5 YAIELYFDP--ALENQVLKAWNVLARRQISTQLIEIESRPHITLFSS-PTIEPAKLESIIKIHASKQEPL-----PLCLS 76 (183)
Q Consensus 5 y~i~l~~~~--~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~-~~~~~~~l~~~l~~~~~~~~pf-----~l~~~ 76 (183)
|++|+.|++ ....+++.+++.|+....+. . +...|||||... .-...+.+.+.|+..+...+++ .++|+
T Consensus 3 ~SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~-~--p~F~PHiTL~s~i~~~~~~~~~~~L~~~~~~~~~~~~~~~~v~~~ 79 (196)
T PF07823_consen 3 YSLWLVPPPGSPLYERLKTLISSLASLFPGS-P--PPFEPHITLTSGISLDSSDDVQKVLDSAAAALKPLPKNHFTVRFD 79 (196)
T ss_dssp EEEEEEE-T--TTHHHHHHHHHHHHHHST------------EEEEEEEEE--HHHHHHHHHHHHHH-B-E-----EEEEE
T ss_pred EEEEEcCCCCccHHHHHHHHHHHHHHHCCCC-C--CCcCCeEEEeCCCccCCHHHHHHHHHHHHHhccCcccceeEEEee
Confidence 999999999 99999999999999875432 1 468999999653 2225677888888888888998 99999
Q ss_pred eeeeeCCCCcEEEEeecCChhHHHHHHHHHHHHHhcCCCCC--CCCCCCCccceeeeec-cCChhhHHHHH---HHHHhC
Q 040775 77 TIGSFCNDNNVLFLAPTPSIPLLQFQSQLCEAFKREGIECG--DEFRPENWIPYCPVAQ-EVPKTRMAEAF---CVLREL 150 (183)
Q Consensus 77 ~~g~F~~~~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~--~~~~~~~f~PHiTL~~-~~~~~~~~~~~---~~~~~~ 150 (183)
++..=...-+.+|+.+.++++|..|++.+++.+........ ......+|.||++|.| +++..+...+. ..+.+.
T Consensus 80 ~v~~g~~yfq~vyl~v~~t~~L~~l~~~~r~~~~~~~~~~~~~~~~~~~~y~PHlSLlY~d~~~~e~~~~~~~~~~i~~~ 159 (196)
T PF07823_consen 80 KVASGDKYFQCVYLEVEKTPELMSLAQIARELFVEGPPDEVKAAEWPREPYMPHLSLLYGDLPPEEKAEAAEIAQRIDDA 159 (196)
T ss_dssp EEEEEEETTEEEEEEE---HHHHHHHCHHHHCT----------T----S----EEEEE-----HHHHHHHHHHHHHH-TT
T ss_pred eEeeCCeEEEEEEEEecCChhHHHHHHHHHHHhhhccccccccccccCCCCCCeEEEEEcCCCcccHHHHHHHHHHhccc
Confidence 88664433589999999999999999999998743311000 0112357999999999 65554433222 222222
Q ss_pred ------CcceEEEEeEEEEEeec----CceeEEEEEC
Q 040775 151 ------KLPVTGYAMDIGLVEYS----PVRELFSFAL 177 (183)
Q Consensus 151 ------~~~~~~~v~~i~L~~~~----p~~~l~~~~l 177 (183)
.....+.++++.||+.+ .|+++++++|
T Consensus 160 l~~~~~~~~~~~~~~~l~lv~t~g~v~~W~~l~~~~l 196 (196)
T PF07823_consen 160 LGVDSGISGLGWEGGELKLVRTDGPVEEWEVLASVDL 196 (196)
T ss_dssp ------GTT-EEEEEEEEEEE--TT-TT-EEEEEEE-
T ss_pred ccccccCCCCCEeccEEEEEEcCCCCCcEEEEEEEeC
Confidence 12346678999999987 2999999876
No 8
>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=99.67 E-value=7.6e-15 Score=112.40 Aligned_cols=172 Identities=17% Similarity=0.237 Sum_probs=119.8
Q ss_pred eeEEEEEe-ChhhHHHHHHHHHHHHHc--cCccccccCCCCCeeEEeecCCCC---hhHHHHHHHHhh----cc---CCC
Q 040775 4 GYAIELYF-DPALENQVLKAWNVLARR--QISTQLIEIESRPHITLFSSPTIE---PAKLESIIKIHA----SK---QEP 70 (183)
Q Consensus 4 ~y~i~l~~-~~~~~~~i~~~~~~l~~~--~~~~~~~~~~~~pHiTL~~~~~~~---~~~l~~~l~~~~----~~---~~p 70 (183)
+|||++.. ++++.+.++++++.+... +.+.....+...+||||..+.=.+ .+.+.++|+.+. .. .+|
T Consensus 2 thFl~ipl~~~~i~~~~~~fq~~v~~~~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~~ 81 (209)
T PF10469_consen 2 THFLCIPLNSPEIQEKFKEFQNEVLSKDPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPPP 81 (209)
T ss_pred CeEEEEECCCHHHHHHHHHHHHHHHhhcCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCCC
Confidence 68999987 577889999999999864 441222237799999997763222 333444454442 11 499
Q ss_pred eeEEEceeeeeCC---CCcEEEEeecCC---hhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec-cC---Chh--
Q 040775 71 LPLCLSTIGSFCN---DNNVLFLAPTPS---IPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ-EV---PKT-- 138 (183)
Q Consensus 71 f~l~~~~~g~F~~---~~~vl~l~v~~~---~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~-~~---~~~-- 138 (183)
+.++|.|+|+|++ .++|+|+.+.++ ..|.++.+.|.+.+...|...... ....|.|||||++ +. ...
T Consensus 82 ~~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~-~~~~~~~H~Tl~n~~~~~~~~~~~ 160 (209)
T PF10469_consen 82 LKITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDD-RRFSFKPHITLMNTSYRKKKKRRQ 160 (209)
T ss_pred ceEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccc-cCCCcceEEEEEeccccccccccc
Confidence 9999999999995 248999999863 789999999999999998543222 2224899999998 32 011
Q ss_pred ----hHHHHHHHHHhCCcceEEEEeEEEEEeec---C----ceeEEEEEC
Q 040775 139 ----RMAEAFCVLRELKLPVTGYAMDIGLVEYS---P----VRELFSFAL 177 (183)
Q Consensus 139 ----~~~~~~~~~~~~~~~~~~~v~~i~L~~~~---p----~~~l~~~~l 177 (183)
...+.+..+.+..+. ...|++|.|.+.. + |..+++++|
T Consensus 161 ~~~~d~~~~~~~~~~~~fG-~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l 209 (209)
T PF10469_consen 161 GNKFDASELLEKYKDFDFG-EQPVEEIQLCSMGSTKPSDGYYQCIASIPL 209 (209)
T ss_pred cCccccHHHHHHcCCCccc-eEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence 123444444443332 5678999998862 2 899999886
No 9
>PLN00108 unknown protein; Provisional
Probab=99.34 E-value=2.9e-10 Score=88.43 Aligned_cols=176 Identities=14% Similarity=0.088 Sum_probs=117.1
Q ss_pred CCceeEEEEEe--ChhhHHHHHHHHHHHHHc---------------cCccccccCCCCCeeEEeecC---CCChhHHHHH
Q 040775 1 MSQGYAIELYF--DPALENQVLKAWNVLARR---------------QISTQLIEIESRPHITLFSSP---TIEPAKLESI 60 (183)
Q Consensus 1 m~~~y~i~l~~--~~~~~~~i~~~~~~l~~~---------------~~~~~~~~~~~~pHiTL~~~~---~~~~~~l~~~ 60 (183)
|...|||++-+ ++++.+.+.++++.+-+. ++....--+...+||||..+. +.+.++..+.
T Consensus 34 ~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~ 113 (257)
T PLN00108 34 EVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNI 113 (257)
T ss_pred CCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHH
Confidence 45589999999 499999999999998763 222222125688999996643 2222333333
Q ss_pred HHHhh------ccCCCeeEEEceeeeeCC---CCcEEEEeecCC---hhHHHHHHHHHHHHHhcCCCCCCCCCCCCccce
Q 040775 61 IKIHA------SKQEPLPLCLSTIGSFCN---DNNVLFLAPTPS---IPLLQFQSQLCEAFKREGIECGDEFRPENWIPY 128 (183)
Q Consensus 61 l~~~~------~~~~pf~l~~~~~g~F~~---~~~vl~l~v~~~---~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PH 128 (183)
|+... -.-.|+.|.+.|+++|.. ..+|||+.|+.. ..|+.+.+.+.+.|...|..... . .++..+|
T Consensus 114 L~s~~~~i~~~l~~~pl~I~lkGL~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d-~-~~~vKLH 191 (257)
T PLN00108 114 LKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKD-A-KSRLKLH 191 (257)
T ss_pred HHHHHHHHHHhhCCCCeEEEEEeehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccc-c-CcceeeE
Confidence 33331 124899999999999975 358999998753 47999999999999999864322 1 1469999
Q ss_pred eeeeccC----Ch-----hhHHHHHHHHHhCCcceEEEEeEEEEEee---c--C-ceeEEEEECCC
Q 040775 129 CPVAQEV----PK-----TRMAEAFCVLRELKLPVTGYAMDIGLVEY---S--P-VRELFSFALGN 179 (183)
Q Consensus 129 iTL~~~~----~~-----~~~~~~~~~~~~~~~~~~~~v~~i~L~~~---~--p-~~~l~~~~l~~ 179 (183)
+||.... .. =+..++++.+.+..+ -+..|++|.|-.. + - |...++.+|.+
T Consensus 192 ~TlmNt~~rk~k~~k~~sFDA~~Il~~f~d~~F-G~~~i~~vhls~r~s~~~dGyY~~~~sl~~~~ 256 (257)
T PLN00108 192 ATLMNASYRKDKSKKMDTFDAREIHKEFENKDW-GTYLIREAHISQRYKYDPNGYFHCCASLPFPH 256 (257)
T ss_pred eEEechhhhhcccCccccccHHHHHHhccCccc-ceEEecEEEEEeecccCCCCCEEEEEEeecCC
Confidence 9999621 11 012234444444333 2567888877542 2 2 89999998865
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=99.24 E-value=4.1e-11 Score=79.08 Aligned_cols=81 Identities=20% Similarity=0.207 Sum_probs=62.0
Q ss_pred EEeChhhHHHHHHHHHHHHHcc-CccccccCCCCCeeEEeecCCCChhH---HHHHHHHhhccCCCeeEEEceeeeeCC-
Q 040775 9 LYFDPALENQVLKAWNVLARRQ-ISTQLIEIESRPHITLFSSPTIEPAK---LESIIKIHASKQEPLPLCLSTIGSFCN- 83 (183)
Q Consensus 9 l~~~~~~~~~i~~~~~~l~~~~-~~~~~~~~~~~pHiTL~~~~~~~~~~---l~~~l~~~~~~~~pf~l~~~~~g~F~~- 83 (183)
+.+++++.+++.++++.+.... ..+..+.+..+|||||.|.++.+.+. +.+.++.++....||++++++++.|+.
T Consensus 1 i~~p~~~~~~L~~l~~~l~~~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~ 80 (87)
T PF02834_consen 1 IDLPEEIKEQLNQLQERLRQALPPLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSR 80 (87)
T ss_dssp EE-THHHHHHHHHHHHHHHHHCCSCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEE
T ss_pred CCCCHHHHHHHHHHHHHHhhhccccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCC
Confidence 4578999999999999999532 22222236799999999998877654 556677777789999999999999984
Q ss_pred -CCcEEE
Q 040775 84 -DNNVLF 89 (183)
Q Consensus 84 -~~~vl~ 89 (183)
+++|+|
T Consensus 81 ~~~rvi~ 87 (87)
T PF02834_consen 81 LRPRVIW 87 (87)
T ss_dssp ETCEEEE
T ss_pred CCCCCcC
Confidence 478888
No 11
>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=98.98 E-value=1.7e-08 Score=77.52 Aligned_cols=133 Identities=16% Similarity=0.126 Sum_probs=94.4
Q ss_pred CCCCeeEEee---c-CCCChhHHHHHHHHhhccCCCeeEE------EceeeeeCCCCcEEEEeecCChhHHHHHHHHHHH
Q 040775 39 ESRPHITLFS---S-PTIEPAKLESIIKIHASKQEPLPLC------LSTIGSFCNDNNVLFLAPTPSIPLLQFQSQLCEA 108 (183)
Q Consensus 39 ~~~pHiTL~~---~-~~~~~~~l~~~l~~~~~~~~pf~l~------~~~~g~F~~~~~vl~l~v~~~~~L~~L~~~l~~~ 108 (183)
+-..|+||.. + .+.+++.+.++++.+|....||++. ++|+..|. + +.++.+|.+|+.++.+.
T Consensus 55 rYGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~~~pf~i~~L~l~~Lg~FlAL~--P------~~~~~~L~~LAa~~V~~ 126 (228)
T TIGR03223 55 RYGFHATLKAPFRLAPGVTEAELLAAVAAFAATRAPFALPPLRVALLGGFLALR--P------AAPCPALQALAAACVRE 126 (228)
T ss_pred hcccceeecCCcccCCCCCHHHHHHHHHHHHhcCCCccCCcceeeeeCCEEEEe--e------CCCCHHHHHHHHHHHHh
Confidence 4668999942 3 5677899999999999999999876 55555544 2 45778999999998887
Q ss_pred HHhcCCCCC------------------------CCCCCCCccceeeeeccCChhhHHHHHHHHHhCC---cceEEEEeEE
Q 040775 109 FKREGIECG------------------------DEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELK---LPVTGYAMDI 161 (183)
Q Consensus 109 l~~~~~~~~------------------------~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~---~~~~~~v~~i 161 (183)
+........ ..|--+.|..||||.-+++.++...+...+...+ .+-...|++|
T Consensus 127 ~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg~l~~~~~~~~~~~l~~~~~~~l~~p~~id~l 206 (228)
T TIGR03223 127 LDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTGRLDEEERAAVLARLEARFAPLLADPLAVDGL 206 (228)
T ss_pred hhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecCCCChHHHHHHHHHHHHHhhhccCCCeeeeeE
Confidence 754311000 1122245999999999888777765555555543 3335679999
Q ss_pred EEEeec----CceeEEEEECCC
Q 040775 162 GLVEYS----PVRELFSFALGN 179 (183)
Q Consensus 162 ~L~~~~----p~~~l~~~~l~~ 179 (183)
+|+.-+ |+.++..+||++
T Consensus 207 aLf~e~~~g~pF~~~~~~~l~~ 228 (228)
T TIGR03223 207 ALFVEPEPGAPFRLIARVALAG 228 (228)
T ss_pred EEEeccCCCCCcEEEEeecCCC
Confidence 998633 699999999975
No 12
>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=98.94 E-value=1.4e-08 Score=76.02 Aligned_cols=133 Identities=14% Similarity=0.163 Sum_probs=88.6
Q ss_pred hHHHHHHHHHHHHHccCccccccCCCCCeeEEeec--CCCChhHHH----HHHHHhhccCCCeeEEEceeeeeCCCCcEE
Q 040775 15 LENQVLKAWNVLARRQISTQLIEIESRPHITLFSS--PTIEPAKLE----SIIKIHASKQEPLPLCLSTIGSFCNDNNVL 88 (183)
Q Consensus 15 ~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~--~~~~~~~l~----~~l~~~~~~~~pf~l~~~~~g~F~~~~~vl 88 (183)
.-....+++-+|-+.|.+...+ ..|||||..+ .+.+...+. +.+++++ .....+++++.-..+ +..
T Consensus 20 f~~~~~~LQ~~~~~eG~d~k~Q---kaPHlSl~mL~Isd~~i~~V~~~iq~ViddM~--~~~~~it~tnp~MLg---~~y 91 (248)
T PF05213_consen 20 FMLNFKDLQFQLLEEGVDCKLQ---KAPHLSLGMLDISDEDIPDVETAIQKVIDDMV--WFEGDITFTNPHMLG---RCY 91 (248)
T ss_pred HHHHHHHHHHHHHHcCCCcccc---ccCeeEEEEEEcChhhhhhHHHHHHHHHHHhh--cccceEEecCceeec---cEE
Confidence 3466788999999999887553 7799999654 444444444 4455544 344478887776664 455
Q ss_pred EEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcceEEEE-----eEEEE
Q 040775 89 FLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLPVTGYA-----MDIGL 163 (183)
Q Consensus 89 ~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~~~~~v-----~~i~L 163 (183)
-++| ..+.+||.+|.+.+.+.|..+ ...+.|.||||||.-...+ ..++...+..++++ .++.+
T Consensus 92 V~nV---~Gv~slh~ki~n~~~~kgit~---gQSRmwIPHiTia~~~~~a------v~I~~~qFny~~~~n~~~~~rle~ 159 (248)
T PF05213_consen 92 VANV---KGVLSLHDKIVNVFRKKGITF---GQSRMWIPHITIAQLNDAA------VRIKEKQFNYKITINPSSPARLEF 159 (248)
T ss_pred EEec---ccHHHHHHHHHHHHHHhCcCc---Ccccccccceehhhhhchh------eEeccceeeeEeeccCCChhcCeE
Confidence 5555 459999999999999998654 3457799999999721111 11223345566666 66677
Q ss_pred Eeec
Q 040775 164 VEYS 167 (183)
Q Consensus 164 ~~~~ 167 (183)
++..
T Consensus 160 VKlG 163 (248)
T PF05213_consen 160 VKLG 163 (248)
T ss_pred EEcC
Confidence 7654
No 13
>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=98.63 E-value=3.2e-06 Score=66.05 Aligned_cols=125 Identities=15% Similarity=0.055 Sum_probs=87.2
Q ss_pred EEEEEeChhhHHHHHHHHHHHHHccCccccc---------cCCCCCeeEEe---ecCCCChhHHHHHHHHhh--ccCCCe
Q 040775 6 AIELYFDPALENQVLKAWNVLARRQISTQLI---------EIESRPHITLF---SSPTIEPAKLESIIKIHA--SKQEPL 71 (183)
Q Consensus 6 ~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~---------~~~~~pHiTL~---~~~~~~~~~l~~~l~~~~--~~~~pf 71 (183)
.|...++++....+.++.+++.......... ....++||+|. .+.....+.+.+.|+... ....+|
T Consensus 45 Yi~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~s~lg~~~~lHISLSr~~~lr~~~id~f~~~lr~~l~~~~~~~F 124 (239)
T PF09749_consen 45 YIEWPPSEDQRELLEKLISKANSICPKLHSEFEPLLYSDLGSPDPLHISLSRTFPLRTHQIDPFVDSLRQALRSSNIRPF 124 (239)
T ss_pred EEEecCcHHHHHHHHHHHHHHHhhhhhhhhhcccccccccCCCCCeEEEeCCCccccHHHHHHHHHHHHHHHhhcCCceE
Confidence 3677788888888888888887753321110 02478999994 333334455666777777 789999
Q ss_pred eEEEceeeeeCC--CCcE-EEEeecCC-hh-HHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 72 PLCLSTIGSFCN--DNNV-LFLAPTPS-IP-LLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 72 ~l~~~~~g~F~~--~~~v-l~l~v~~~-~~-L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
.+.|+++..|.+ +++. +-+.|..+ .. |..|.+.+.+++...| ..+.| ..+-.|||+||.
T Consensus 125 ~v~f~~~~~~~N~e~TR~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~--lp~~Y-~~~~~fHvSIAw 188 (239)
T PF09749_consen 125 YVSFSGLDVYTNDEKTRSFLALRVSEGSNNELKRLLDRINEVLKEFG--LPPFY-DEDPSFHVSIAW 188 (239)
T ss_pred EEEeCceEEEecCCCCeEEEEEEecccccHHHHHHHHHHHHHHHHhC--CCccc-CCCCCCEEEEEE
Confidence 999999999997 3443 34444433 33 9999999999999987 34445 123799999998
No 14
>PHA02977 hypothetical protein; Provisional
Probab=98.51 E-value=2.2e-06 Score=60.74 Aligned_cols=92 Identities=17% Similarity=0.195 Sum_probs=60.8
Q ss_pred CCCCeeEEeecCCCCh----hHHHHHHHHhhccCCCeeEEEceeeeeCC---------CCcEEEEeecCChhHHHHHHHH
Q 040775 39 ESRPHITLFSSPTIEP----AKLESIIKIHASKQEPLPLCLSTIGSFCN---------DNNVLFLAPTPSIPLLQFQSQL 105 (183)
Q Consensus 39 ~~~pHiTL~~~~~~~~----~~l~~~l~~~~~~~~pf~l~~~~~g~F~~---------~~~vl~l~v~~~~~L~~L~~~l 105 (183)
..+|||||.... .+. +...+.+.. ...+.+++.....-+|+. +...+-+.++.++.|..|+.-|
T Consensus 67 di~phitlgian-~dq~~~f~~fk~~~~d--~dl~sis~~cke~icfpqs~askelga~g~avvmkle~sddlkalrnvl 143 (201)
T PHA02977 67 DIFPHITLGIAN-KDQCDNFENFKELIKD--IDLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEASDDLKALRNVL 143 (201)
T ss_pred CCCcceeeeccC-ccHhHHHHHHHHHhhc--ccceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEechHHHHHHHHh
Confidence 388999996543 232 233444444 346777788888888985 2346788888899999999888
Q ss_pred HHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 106 CEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 106 ~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
.++..--...+..--...+|.||||+||
T Consensus 144 ~n~vp~pkdifg~i~~d~~w~phitigy 171 (201)
T PHA02977 144 FNAVPCPKDIFGDILSDNPWCPHITIGY 171 (201)
T ss_pred hcccCCcHHhhcccccCCCCCCceEEEe
Confidence 7655432111112223458999999999
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=98.19 E-value=9.6e-06 Score=53.18 Aligned_cols=72 Identities=26% Similarity=0.225 Sum_probs=49.6
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec--cCChhhHHHHHHHHHh---CCcceEEEEeEEEEEeec-Cc
Q 040775 96 IPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ--EVPKTRMAEAFCVLRE---LKLPVTGYAMDIGLVEYS-PV 169 (183)
Q Consensus 96 ~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~--~~~~~~~~~~~~~~~~---~~~~~~~~v~~i~L~~~~-p~ 169 (183)
++|.++++.+.+.+...|. .. . .++.|||||++ +.+++.+.++...+.. ...+++..+++++++.+. +.
T Consensus 9 ~~L~~l~~~l~~~~~~~~~--r~--~-~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~~~~ 83 (87)
T PF02834_consen 9 EQLNQLQERLRQALPPLGI--RW--V-RPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSRLRP 83 (87)
T ss_dssp HHHHHHHHHHHHHCCSCTE--EE--G-SCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEEETC
T ss_pred HHHHHHHHHHhhhccccCC--cc--c-CCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCCCCC
Confidence 5688888888876655542 11 1 46999999999 5666666666555544 357889999999999875 33
Q ss_pred eeE
Q 040775 170 REL 172 (183)
Q Consensus 170 ~~l 172 (183)
+++
T Consensus 84 rvi 86 (87)
T PF02834_consen 84 RVI 86 (87)
T ss_dssp EEE
T ss_pred CCc
Confidence 443
No 16
>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=97.46 E-value=0.0029 Score=46.23 Aligned_cols=111 Identities=16% Similarity=0.172 Sum_probs=74.9
Q ss_pred CCCChhHHHHHHHHhhccCCCeeE---EEceeeeeCCCCcEEEEeec-CChhHHHHHHHHHHHHHhcCCCC---------
Q 040775 50 PTIEPAKLESIIKIHASKQEPLPL---CLSTIGSFCNDNNVLFLAPT-PSIPLLQFQSQLCEAFKREGIEC--------- 116 (183)
Q Consensus 50 ~~~~~~~l~~~l~~~~~~~~pf~l---~~~~~g~F~~~~~vl~l~v~-~~~~L~~L~~~l~~~l~~~~~~~--------- 116 (183)
++.+++.+..+++.+|+...||++ .+..+|.|- -|.+. ++.+|..|..++.+.+.......
T Consensus 10 ~g~~~~~L~~a~~~~a~~~~pf~l~~L~v~~lg~Fl------ALvp~~~~~~L~~LAa~cV~~~d~fRAPls~aelaRR~ 83 (160)
T PF06299_consen 10 EGASEADLLAALAAFAARFAPFELPGLEVARLGGFL------ALVPAGPCPALQALAAACVRAFDPFRAPLSEAELARRR 83 (160)
T ss_pred CCCCHHHHHHHHHHHhccCCCccCCceeEeeECCEE------EEeeCCCCHHHHHHHHHHHHhhhhccCCCChHHHhhcC
Confidence 567888999999999999999964 456666553 34333 55789999988877666532110
Q ss_pred ---------------CCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcc---eEEEEeEEEEEee
Q 040775 117 ---------------GDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLP---VTGYAMDIGLVEY 166 (183)
Q Consensus 117 ---------------~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~---~~~~v~~i~L~~~ 166 (183)
...|-=+.|+.||||.-+++.++...+...+...+.+ -...|++|+|+.-
T Consensus 84 ~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l~~~~~~~~~~~l~~~f~~~l~~p~~id~laLf~e 151 (160)
T PF06299_consen 84 PAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRLDPAERARVEAALEAHFAPLLPEPLRIDSLALFGE 151 (160)
T ss_pred cccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCCCHHHHHHHHHHHHHHHHhhcCCCeeecceEEEec
Confidence 0112224699999999988777766665555554322 3457899999853
No 17
>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=96.82 E-value=0.036 Score=43.87 Aligned_cols=65 Identities=14% Similarity=0.090 Sum_probs=38.8
Q ss_pred CCeeEEEceeeeeCCCCcEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec---cCChhhHHHHHH
Q 040775 69 EPLPLCLSTIGSFCNDNNVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ---EVPKTRMAEAFC 145 (183)
Q Consensus 69 ~pf~l~~~~~g~F~~~~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~---~~~~~~~~~~~~ 145 (183)
..+++++..+- |. .+++.+.|.-...-..-.. . ......+..||||||. .+.+-+-...+.
T Consensus 161 ~~~~v~L~rlv-wd--~rimai~V~~~~~~~~~~~-----~--------~~~~c~N~~~HITVGT~~~~VkP~eSN~Ll~ 224 (257)
T PF08302_consen 161 GSCDVRLERLV-WD--DRIMAIVVRIVPPEDEEDE-----V--------PEWECTNKIPHITVGTRDPGVKPKESNDLLE 224 (257)
T ss_pred ceEEEEEEEEE-EC--CcEEEEEEEccCccccccc-----c--------CCcccCCCCCEEEEEcCCCCCCcchHHHHHH
Confidence 45788888888 66 4888888863321100000 1 1112345799999997 455666666666
Q ss_pred HHHh
Q 040775 146 VLRE 149 (183)
Q Consensus 146 ~~~~ 149 (183)
.+.+
T Consensus 225 ~~~~ 228 (257)
T PF08302_consen 225 RWLE 228 (257)
T ss_pred HHHh
Confidence 6655
No 18
>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=95.52 E-value=0.086 Score=39.95 Aligned_cols=72 Identities=13% Similarity=0.162 Sum_probs=32.3
Q ss_pred cEEEEeecCChh-HHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeecc--C-ChhhHHHHHHHHHhCCcce-----EE
Q 040775 86 NVLFLAPTPSIP-LLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQE--V-PKTRMAEAFCVLRELKLPV-----TG 156 (183)
Q Consensus 86 ~vl~l~v~~~~~-L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~--~-~~~~~~~~~~~~~~~~~~~-----~~ 156 (183)
-.||+-+.++.+ -..|...+ ..+...-+ ..+..|-|||||.-. . +.+++.+.+........++ ..
T Consensus 3 ~SlWl~P~~~~~~~~~L~~lI-~~L~~~~~-----~~~p~F~PHiTL~s~i~~~~~~~~~~~L~~~~~~~~~~~~~~~~v 76 (196)
T PF07823_consen 3 YSLWLVPPPGSPLYERLKTLI-SSLASLFP-----GSPPPFEPHITLTSGISLDSSDDVQKVLDSAAAALKPLPKNHFTV 76 (196)
T ss_dssp EEEEEEE-T--TTHHHHHHHH-HHHHHHST--------------EEEEEEEEE--HHHHHHHHHHHHHH-B-E-----EE
T ss_pred EEEEEcCCCCccHHHHHHHHH-HHHHHHCC-----CCCCCcCCeEEEeCCCccCCHHHHHHHHHHHHHhccCcccceeEE
Confidence 468998876433 34444444 33333210 112469999999983 3 3455666655544444555 66
Q ss_pred EEeEEEE
Q 040775 157 YAMDIGL 163 (183)
Q Consensus 157 ~v~~i~L 163 (183)
+++++..
T Consensus 77 ~~~~v~~ 83 (196)
T PF07823_consen 77 RFDKVAS 83 (196)
T ss_dssp EEEEEEE
T ss_pred EeeeEee
Confidence 6666654
No 19
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.44 E-value=0.076 Score=40.17 Aligned_cols=110 Identities=15% Similarity=0.179 Sum_probs=57.2
Q ss_pred hhhHHHHHHHHHHHHHccCcccccc-CCCCCeeEEeec------------CCCCh----hHHHH----HHHHhhccCCCe
Q 040775 13 PALENQVLKAWNVLARRQISTQLIE-IESRPHITLFSS------------PTIEP----AKLES----IIKIHASKQEPL 71 (183)
Q Consensus 13 ~~~~~~i~~~~~~l~~~~~~~~~~~-~~~~pHiTL~~~------------~~~~~----~~l~~----~l~~~~~~~~pf 71 (183)
.++.+.+-.+++++.+.-....... |.+..|+|++.. .+++. +.+.. .|+.+.--..+|
T Consensus 52 s~t~~vvl~i~~r~~~mpfadklt~tP~sSlHMTvfqg~~e~~R~~~~WpqdlPLDtpi~~~~~~~~erLk~F~l~~~~~ 131 (239)
T COG5255 52 SDTEEVVLIIRSRYLEMPFADKLTFTPVSSLHMTVFQGLIEERRELPYWPQDLPLDTPIDAITDYYAERLKIFPLLDEEF 131 (239)
T ss_pred CchHHHHHHHHHHhhccchhhhhccCCcchhhHHHHHHHhhhcccCCCCCccCCCCCcHHHHHHHHHHHHhcccCCchhh
Confidence 5667888888888887632222212 778899999642 12222 22222 222221111234
Q ss_pred eEEEceeeeeCCCCcEEEEeecCC---hhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 72 PLCLSTIGSFCNDNNVLFLAPTPS---IPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 72 ~l~~~~~g~F~~~~~vl~l~v~~~---~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
.+.+.+.+ |..+-+.+... ..|.++++.+.+.+... .+. .+.|+.||||||
T Consensus 132 ~mrvte~r-----p~~i~v~paddad~~~l~~~Rd~ls~~~g~r----~P~--HDaY~FHITlgY 185 (239)
T COG5255 132 NMRVTEMR-----PQGILVEPADDADAKILEEWRDYLSEKFGYR----HPD--HDAYQFHITLGY 185 (239)
T ss_pred cchhhccc-----ccceEeccCCHHHHHHHHHHHHHHhhhhccc----CCC--CcceEEEEEeee
Confidence 44443332 23333333222 24666666666654332 232 356999999998
No 20
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.95 E-value=0.21 Score=40.47 Aligned_cols=93 Identities=18% Similarity=0.186 Sum_probs=61.1
Q ss_pred CCCCCeeEEeec---CCCChhHHHHHHHHh------hccCCCeeEEEceeeeeCCC---CcEEEEeecCCh---hHHHHH
Q 040775 38 IESRPHITLFSS---PTIEPAKLESIIKIH------ASKQEPLPLCLSTIGSFCND---NNVLFLAPTPSI---PLLQFQ 102 (183)
Q Consensus 38 ~~~~pHiTL~~~---~~~~~~~l~~~l~~~------~~~~~pf~l~~~~~g~F~~~---~~vl~l~v~~~~---~L~~L~ 102 (183)
.....|+|+.++ .+.+..++.+.++.. ...-.|+.+.+.|+..+..+ .+|+|..|++.. -+....
T Consensus 174 ~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~~ 253 (345)
T KOG2814|consen 174 GPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGEKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHRC 253 (345)
T ss_pred CCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCCCceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHHH
Confidence 457789999765 333333333333331 13568999999999999974 479999998653 355544
Q ss_pred -HHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 103 -SQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 103 -~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
+++-.++...|... . ...+-.=|||+..
T Consensus 254 ~~~i~~~f~~~~li~-k--~~~~~kLH~TvmN 282 (345)
T KOG2814|consen 254 GERILERFVASGLIK-K--ESSSLKLHCTVMN 282 (345)
T ss_pred HHHHHHHHHHhcchh-c--cccccEEEEEEeh
Confidence 66667777766433 1 2245788999984
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=94.76 E-value=0.29 Score=36.10 Aligned_cols=72 Identities=22% Similarity=0.260 Sum_probs=44.4
Q ss_pred EEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccc----eeeeec--cCChhhHHHHHHHHHhC-CcceEEEEeE
Q 040775 88 LFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIP----YCPVAQ--EVPKTRMAEAFCVLREL-KLPVTGYAMD 160 (183)
Q Consensus 88 l~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~P----HiTL~~--~~~~~~~~~~~~~~~~~-~~~~~~~v~~ 160 (183)
+|+++.+++++.+.-.++.+.+.... . ...|+| ||||+. ..+.+.+.++...+... ..+|+..+++
T Consensus 3 ~FiAl~~p~~~~~~l~~~~~~l~~~~----~---~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~f~l~l~~ 75 (179)
T TIGR02258 3 LFIAIDLPPEIREQLSRIQRKLKSPL----D---GIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIAEPPFTLKLEG 75 (179)
T ss_pred EEEEecCCHHHHHHHHHHHHHhhccC----C---CcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhcCCCeEEEEee
Confidence 57788777666665555555554211 1 123554 999986 55666666665555443 3457888888
Q ss_pred EEEEee
Q 040775 161 IGLVEY 166 (183)
Q Consensus 161 i~L~~~ 166 (183)
+..+..
T Consensus 76 ~~~F~~ 81 (179)
T TIGR02258 76 IGVFGN 81 (179)
T ss_pred eeeCCC
Confidence 888754
No 22
>PRK13679 hypothetical protein; Provisional
Probab=94.55 E-value=0.27 Score=36.12 Aligned_cols=64 Identities=11% Similarity=0.058 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChhHHHHHHHHhhccCCCeeEEEceeeeeC
Q 040775 16 ENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFC 82 (183)
Q Consensus 16 ~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~ 82 (183)
...+.++.+++....... .......|||||+- ..+.+...++++.+.....++.+.++.+..|.
T Consensus 89 ~~~L~~L~~~l~~~~~~~-~~~~~f~PHiTlar--~~~~~~~~~~~~~l~~~~~~~~~~v~~i~L~~ 152 (168)
T PRK13679 89 TEELEELHERLHSGDFYG-EAEYAFVPHITIGQ--GLSDDEHEDVLGQLKMADVDHEETIDRFHLLY 152 (168)
T ss_pred CHHHHHHHHHHHhccccc-ccCCCCCCeEEeeC--CCCcHHHHHHHHHHhcCCcceeEEECeEEEEE
Confidence 457888888887643211 11134889999983 33445555555555444455566667766654
No 23
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=94.02 E-value=0.44 Score=35.66 Aligned_cols=75 Identities=15% Similarity=0.085 Sum_probs=49.5
Q ss_pred EEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec--cCChhhHHHHHHHHHhCC-c-ceEEEEeEEEE
Q 040775 88 LFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ--EVPKTRMAEAFCVLRELK-L-PVTGYAMDIGL 163 (183)
Q Consensus 88 l~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~--~~~~~~~~~~~~~~~~~~-~-~~~~~v~~i~L 163 (183)
+|+.+..++++.+.-.++.+.+...+ .. .... .-.+||||.. +++.+...++...+.+.- . +|+.++++++.
T Consensus 3 lFiAl~~p~~i~~~i~~~~~~~~~~~-~~-k~v~--~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~~f~i~l~g~g~ 78 (180)
T COG1514 3 LFIALDPPAEIAERLARIRARLKGAR-AI-KWVE--PENLHITLKFLGEVDEDKADELIEALARIAAPEPFPITLDGAGS 78 (180)
T ss_pred eEEEecCCHHHHHHHHHHHHhcCccc-cc-cccc--ccCceEEEEccCCcCchHHHHHHHHHHHhhcCCceEEEEeeEcc
Confidence 57788888888777666666665543 11 1122 3689999998 666666555555544432 2 78889999988
Q ss_pred Eee
Q 040775 164 VEY 166 (183)
Q Consensus 164 ~~~ 166 (183)
+..
T Consensus 79 F~~ 81 (180)
T COG1514 79 FPN 81 (180)
T ss_pred cCC
Confidence 764
No 24
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=93.52 E-value=0.47 Score=33.67 Aligned_cols=74 Identities=16% Similarity=0.144 Sum_probs=30.6
Q ss_pred EEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeecCCCChhHHHHHHHHhhccCCCeeEEEceeeeeC
Q 040775 6 AIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSSPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFC 82 (183)
Q Consensus 6 ~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~ 82 (183)
++.+..++++.+.-.++.+.+...+...... ....|||||+-...... ....++.+.....+.+..++++..+.
T Consensus 75 ~l~~~~~~~L~~L~~~l~~~~~~~~~~~~~~-~~~~PHiTia~~~~~~~--~~~~~~~~~~~~~~~~~~v~~l~L~~ 148 (153)
T PF13563_consen 75 FLNVEPSPELEALHRALREALRPFGFKQDSY-RPFRPHITIARRLSPKQ--AAEAIEKLQSEFPPISFTVDELALVR 148 (153)
T ss_dssp EEEEEE-HHHHHHHHHHHHHHHHHHGGGGGG-S----EEEEEEESS-------------------EEEEE-EEEEEE
T ss_pred EEEcCCCHHHHHHHHHHHHHHHHcCCccccC-CCcceEEEEeccCCcch--hHHHHHHHhCcCCCcEEEEeEEEEEE
Confidence 3444455666666666666666544332211 35899999975432211 23334444455788888888887765
No 25
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.72 E-value=1.8 Score=33.20 Aligned_cols=91 Identities=10% Similarity=0.100 Sum_probs=56.8
Q ss_pred CCCCeeEEee---cCCCChhHHHHHHHHhhccCCCeeEEEceeeeeCCCCcE-EEEeecC-C---hhHHHHHHHHHHHHH
Q 040775 39 ESRPHITLFS---SPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFCNDNNV-LFLAPTP-S---IPLLQFQSQLCEAFK 110 (183)
Q Consensus 39 ~~~pHiTL~~---~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~~~~~v-l~l~v~~-~---~~L~~L~~~l~~~l~ 110 (183)
+...||.|.- +.--........|+.....+..|-++++++..|.+.-++ -|++.+- + ..+.++-+.+.+++.
T Consensus 119 ~~~fHlSLsr~VvLr~HqI~~fi~~L~~~l~s~~rf~~t~n~~~iytN~e~TRtFi~leitt~~~~~~~~~i~~vd~Vm~ 198 (269)
T KOG3102|consen 119 GREFHLSLSRNVVLRVHQINSFISMLRQKLQSQKRFLITFNKWEIYTNDEHTRTFISLEITTSGLSEISKQIDAVDEVMK 198 (269)
T ss_pred cceEEEeeccceEEEeehhhHHHHHHHHHHhhhhhheEeecceEEEeccccceeEEEEEechhhHHHHHHHHHHHHHHHH
Confidence 5667888832 221123345556666666688899999999999973222 3444432 2 345556677777777
Q ss_pred hcCCCCCCCCCCCCccceeeeec
Q 040775 111 REGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 111 ~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
.+. ....|+. + .||++|+-
T Consensus 199 ~~n--L~~FY~D-P-sfHiSL~W 217 (269)
T KOG3102|consen 199 LHN--LPEFYKD-P-SFHISLVW 217 (269)
T ss_pred HcC--chhhhcC-C-CCCceEEE
Confidence 765 3334542 3 89999986
No 26
>PRK15124 2'-5' RNA ligase; Provisional
Probab=88.48 E-value=3.2 Score=30.69 Aligned_cols=75 Identities=13% Similarity=-0.083 Sum_probs=42.2
Q ss_pred EEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec--cCChhhHHHHHHHHHhC-CcceEEEEeEEEE
Q 040775 87 VLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ--EVPKTRMAEAFCVLREL-KLPVTGYAMDIGL 163 (183)
Q Consensus 87 vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~--~~~~~~~~~~~~~~~~~-~~~~~~~v~~i~L 163 (183)
-+|+++...+++.+.-.++.+.+..... . ..-.+ =.-||||.. .++.+.+..+...+... ..||+..+++++.
T Consensus 6 RlFiAl~~p~~~~~~l~~~~~~~~~~~~-~-rwv~~--~nlHiTL~FlG~v~~~~~~~l~~~l~~~~~~pF~l~l~~~g~ 81 (176)
T PRK15124 6 RLFFAIDLPDEIRQQIIHWRATHFPPEA-G-RPVAA--ANLHLTLAFLGEVSAEKQQALSQLAGRIRQPGFTLTLDDAGQ 81 (176)
T ss_pred EEEEEeCCCHHHHHHHHHHHHHhccccC-c-ccccc--cccEEEEEecCCCCHHHHHHHHHHHHhcccCCeEEEECcccC
Confidence 4678876665554433333333322100 0 00011 234999997 77777777666666552 4678888888876
Q ss_pred Ee
Q 040775 164 VE 165 (183)
Q Consensus 164 ~~ 165 (183)
+.
T Consensus 82 Fp 83 (176)
T PRK15124 82 WP 83 (176)
T ss_pred cC
Confidence 63
No 27
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=84.94 E-value=8.6 Score=25.67 Aligned_cols=78 Identities=19% Similarity=0.213 Sum_probs=53.8
Q ss_pred CCc----eeEEEEEeChhhHHHHHHHHHHHHHccCccccccCCCCCee----EEeecCCCChhHHHHHHHHhhc--cCCC
Q 040775 1 MSQ----GYAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHI----TLFSSPTIEPAKLESIIKIHAS--KQEP 70 (183)
Q Consensus 1 m~~----~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHi----TL~~~~~~~~~~l~~~l~~~~~--~~~p 70 (183)
||+ .|-|-+.+.++.-..+.++.++|...|...-.......||= |.......+.+.+++..+.++. --+.
T Consensus 1 ms~~~~~~YVVt~~~~e~~l~d~~~L~~~lt~~GF~~tl~D~~G~~HeLgtntfgl~S~l~~~eV~~la~~lae~algk~ 80 (96)
T PF11080_consen 1 MSSSDITRYVVTFEYQEAGLTDINELNNHLTRAGFSTTLTDEDGNPHELGTNTFGLISALSAEEVAQLARGLAESALGKT 80 (96)
T ss_pred CCCCcceEEEEEEEeccCChHHHHHHHHHHHhcCceeEEecCCCCEeecCCCeEEEEecCCHHHHHHHHHHHhhhhcCCC
Confidence 776 89999999999999999999999998776555445566662 3344456677777766666652 1233
Q ss_pred eeEEEcee
Q 040775 71 LPLCLSTI 78 (183)
Q Consensus 71 f~l~~~~~ 78 (183)
.+|.+.-+
T Consensus 81 p~V~V~t~ 88 (96)
T PF11080_consen 81 PEVEVTTW 88 (96)
T ss_pred CceEEEEH
Confidence 34544443
No 28
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=84.59 E-value=4.7 Score=28.03 Aligned_cols=37 Identities=19% Similarity=0.191 Sum_probs=25.0
Q ss_pred ChhhHHHHHHHHHHHHHccC-ccccccCCCCCeeEEee
Q 040775 12 DPALENQVLKAWNVLARRQI-STQLIEIESRPHITLFS 48 (183)
Q Consensus 12 ~~~~~~~i~~~~~~l~~~~~-~~~~~~~~~~pHiTL~~ 48 (183)
+.+....+.++++++++... ..+..-|....|+|++.
T Consensus 23 ~s~~~~al~~i~~~l~~~~~~~k~a~lP~sS~HMTVf~ 60 (118)
T PF08975_consen 23 DSPFYAALLAIQQRLRESPFADKLAFLPPSSYHMTVFE 60 (118)
T ss_dssp TSHHHHHHHHHHHHHHTSGGGGGEEE--GGG-EEEEEE
T ss_pred CChHHHHHHHHHHHHHhCccccceEecCcchhhhhhhc
Confidence 45666889999999998643 33333378889999974
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=79.27 E-value=4 Score=29.95 Aligned_cols=46 Identities=28% Similarity=0.365 Sum_probs=30.6
Q ss_pred CCCCCeeEEee-cCCCChhHHHHHHHHhhccCCCeeEEEceeeeeCC
Q 040775 38 IESRPHITLFS-SPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFCN 83 (183)
Q Consensus 38 ~~~~pHiTL~~-~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~~ 83 (183)
...++||||.. ++..+.+.+...++.......+=.+.++++..|..
T Consensus 105 deFRFHmTLTg~l~~~~~~~~~~~l~~~f~~~l~~p~~id~laLf~e 151 (160)
T PF06299_consen 105 DEFRFHMTLTGRLDPAERARVEAALEAHFAPLLPEPLRIDSLALFGE 151 (160)
T ss_pred CcCEeeEEeCCCCCHHHHHHHHHHHHHHHHhhcCCCeeecceEEEec
Confidence 57999999954 33333445666666655445555788889988874
No 30
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.15 E-value=4.8 Score=30.71 Aligned_cols=71 Identities=20% Similarity=0.079 Sum_probs=42.7
Q ss_pred ChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeec----CCCChhH----HHHHHHHhhccCCCeeEEEceeeeeC
Q 040775 12 DPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSS----PTIEPAK----LESIIKIHASKQEPLPLCLSTIGSFC 82 (183)
Q Consensus 12 ~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~----~~~~~~~----l~~~l~~~~~~~~pf~l~~~~~g~F~ 82 (183)
|++-...++++++.+.+..+-....+..-..||||.-. .+...+. +.+.++.++.+.+-+++.--.+..|.
T Consensus 149 ddad~~~l~~~Rd~ls~~~g~r~P~HDaY~FHITlgYl~~wltpee~a~~q~~l~e~~e~la~~~PvIe~~ap~yc~f~ 227 (239)
T COG5255 149 DDADAKILEEWRDYLSEKFGYRHPDHDAYQFHITLGYLRIWLTPEEEAEWQAVLDELLEILAEKAPVIEVNAPDYCVFE 227 (239)
T ss_pred CHHHHHHHHHHHHHHhhhhcccCCCCcceEEEEEeeeEeeecChhhhHHHHHHHHHHHHHHHhhCCeEEecCcchhhhh
Confidence 45566778888889988633222333567899999532 2222222 44556666666776666655555554
No 31
>PHA02574 57B hypothetical protein; Provisional
Probab=77.96 E-value=4.2 Score=29.48 Aligned_cols=36 Identities=25% Similarity=0.177 Sum_probs=18.6
Q ss_pred EEEEeC-hhhHHHHHHHHHHHHHccCccccccCCCCCeeEEee
Q 040775 7 IELYFD-PALENQVLKAWNVLARRQISTQLIEIESRPHITLFS 48 (183)
Q Consensus 7 i~l~~~-~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~ 48 (183)
+|+-+. ++..+..+++++.++..+ .+...|||||+-
T Consensus 82 lWlg~~~~~L~~L~~~l~~~l~~~~------~r~F~PHITLaR 118 (149)
T PHA02574 82 LVLVLESEYLQCRHKYARALGATHD------FDDYTPHITLSY 118 (149)
T ss_pred EEEEeCCHHHHHHHHHHHHHhhcCC------CCCcCCcEEEee
Confidence 444443 444444444444444311 145889999964
No 32
>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=69.57 E-value=11 Score=29.39 Aligned_cols=46 Identities=22% Similarity=0.185 Sum_probs=31.2
Q ss_pred CCCCCeeEEee-cCCCChhHHHHHHHHhhccCCCeeEEEceeeeeCC
Q 040775 38 IESRPHITLFS-SPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFCN 83 (183)
Q Consensus 38 ~~~~pHiTL~~-~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~~ 83 (183)
...+.||||.. +++.+.+.+.++++.......+-.+.++++..|..
T Consensus 165 deFrFHmTLTg~l~~~~~~~~~~~l~~~~~~~l~~p~~id~laLf~e 211 (228)
T TIGR03223 165 EEFRFHMTLTGRLDEEERAAVLARLEARFAPLLADPLAVDGLALFVE 211 (228)
T ss_pred cceEEEEEecCCCChHHHHHHHHHHHHHhhhccCCCeeeeeEEEEec
Confidence 45799999954 44444455666776665444555788899988874
No 33
>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=66.71 E-value=53 Score=24.74 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=28.3
Q ss_pred Cccceeeeec-cCCh-hhHHHHHHHHHhC----------CcceEEEEeEEEEEeecC
Q 040775 124 NWIPYCPVAQ-EVPK-TRMAEAFCVLREL----------KLPVTGYAMDIGLVEYSP 168 (183)
Q Consensus 124 ~f~PHiTL~~-~~~~-~~~~~~~~~~~~~----------~~~~~~~v~~i~L~~~~p 168 (183)
+-.-||||+- .+.. +++.++.+.+.+. ..|+...+.++..+..+|
T Consensus 40 ~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~~~~i~l~Gl~~f~~d~ 96 (209)
T PF10469_consen 40 PEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPPPLKITLKGLGYFNDDP 96 (209)
T ss_pred cccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCCCceEEeeechhhCCCC
Confidence 4678999997 5443 3554444433332 366777888888877655
No 34
>PF07476 MAAL_C: Methylaspartate ammonia-lyase C-terminus; InterPro: IPR022662 Methylaspartate ammonia-lyase 4.3.1.2 from EC catalyses the second step of fermentation of glutamate. It is a homodimer. This domain represents the C-terminal region of methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the PF01188 from PFAM. This domain represents the catalytic domain and contains a metal binding site []. ; PDB: 1KKO_B 1KKR_A 3ZVI_A 1KD0_B 1KCZ_B 3ZVH_A.
Probab=56.86 E-value=25 Score=27.43 Aligned_cols=65 Identities=11% Similarity=0.040 Sum_probs=40.1
Q ss_pred hhhHHHHHHHHHHHHHccCccccccCCCCCeeEEee-----cCCCChhHHHHHHHHhhccCCCeeEEEceeeeeC
Q 040775 13 PALENQVLKAWNVLARRQISTQLIEIESRPHITLFS-----SPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFC 82 (183)
Q Consensus 13 ~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~-----~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~ 82 (183)
+.+.+.++=+.+++.+.+...|. ...||-+.. |+ .+.+++.+=+..++....||.+.+.|.--.+
T Consensus 47 e~L~eYv~Wl~~Ri~~lg~~~Y~----P~lHiDVYGtiG~~f~-~d~~~~adYl~~l~~aA~P~~L~iEgP~d~g 116 (248)
T PF07476_consen 47 EKLLEYVKWLKDRIRELGDEDYR----PVLHIDVYGTIGLAFD-NDPDRMADYLAELEEAAAPFKLRIEGPMDAG 116 (248)
T ss_dssp HHHHHHHHHHHHHHHHHSSTT-------EEEEE-TTHHHHHTT-T-HHHHHHHHHHHHHHHTTS-EEEE-SB--S
T ss_pred HHHHHHHHHHHHHHHHhcCCCCC----ccEEEEccchHHHHhC-CCHHHHHHHHHHHHHhcCCCeeeeeCCcCCC
Confidence 34556677777777777665544 668998843 33 3777777777787777899999998764443
No 35
>PRK06646 DNA polymerase III subunit chi; Provisional
Probab=52.76 E-value=12 Score=27.31 Aligned_cols=34 Identities=9% Similarity=0.130 Sum_probs=21.9
Q ss_pred EEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 88 LFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 88 l~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
+++.+...+.+.+|=+.|+. +++.+|.||.+.+-
T Consensus 32 v~I~~~d~~~~~~LD~~LWt------------f~~~SFlPH~~~~~ 65 (154)
T PRK06646 32 SVILTADADQQEMLNKNLWT------------YSRKQFIPHGSKLD 65 (154)
T ss_pred EEEEcCCHHHHHHHHHHhcC------------CCCCCCCCCCCCCC
Confidence 34444344566666666653 35678999998775
No 36
>PF08883 DOPA_dioxygen: Dopa 4,5-dioxygenase family; InterPro: IPR014980 This family of proteins is related to P87064 from SWISSPROT a DOPA 4,5-dioxygenase that is involved in synthesis of betalain. DOPA-dioxygenase is the key enzyme involved in betalain biosynthesis. It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore. ; PDB: 2NYH_A 2P8I_C.
Probab=49.04 E-value=70 Score=21.66 Aligned_cols=72 Identities=13% Similarity=0.150 Sum_probs=39.4
Q ss_pred eEEEEEeChhhHHHHHHHHHHHHHccC---cccccc-CCCCCeeEEeecCCCChhHHHHHHHHhhccCCCeeEEEc
Q 040775 5 YAIELYFDPALENQVLKAWNVLARRQI---STQLIE-IESRPHITLFSSPTIEPAKLESIIKIHASKQEPLPLCLS 76 (183)
Q Consensus 5 y~i~l~~~~~~~~~i~~~~~~l~~~~~---~~~~~~-~~~~pHiTL~~~~~~~~~~l~~~l~~~~~~~~pf~l~~~ 76 (183)
|.+=+|||++..+..+++++++.+... .....+ ....||-+-.+--..+.+...+.+.=+.....+++|=+-
T Consensus 1 yHaHvYfd~~~~~~A~~Lre~i~~~f~~~~~~g~~~~~pvGPHp~~~~ev~f~~~~f~~~v~Wl~~nrg~LsVLiH 76 (104)
T PF08883_consen 1 YHAHVYFDAAEREFARALRERIREEFPDELRVGRFHEKPVGPHPMWSFEVDFPPEQFAEVVPWLMLNRGGLSVLIH 76 (104)
T ss_dssp EEEEEEE-GGGHHHHHHHHHHHHHHTTTTSEE---BSS--TT-SSEEEEEEE-HHHHHHHHHHHHHH-TT--EEEE
T ss_pred CeEEEEcCHHHHHHHHHHHHHHHHHhhcceeEeeccccCCCCccCceEEEEcCHHHHHHHHHHHHHhCCCceEEEc
Confidence 556678999999999999999997633 111111 568899887432223555555555444444566666554
No 37
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=47.94 E-value=15 Score=26.21 Aligned_cols=34 Identities=15% Similarity=0.254 Sum_probs=21.2
Q ss_pred EEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 88 LFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 88 l~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
+++.+...+...+|-+.|+. +++.+|.||...+-
T Consensus 32 v~I~~~d~~~a~~lD~~LW~------------~~~~sFlPH~~~~~ 65 (142)
T PRK05728 32 VLVQCEDEEQAEALDEALWT------------FRDESFLPHGLAGE 65 (142)
T ss_pred EEEEcCCHHHHHHHHHHhcC------------CCCCcCCCCCcCCC
Confidence 45554344555666666653 35678999997765
No 38
>PHA02977 hypothetical protein; Provisional
Probab=47.53 E-value=37 Score=24.51 Aligned_cols=39 Identities=21% Similarity=0.132 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHcc------CccccccCCCCCeeEEeecCCCChh
Q 040775 17 NQVLKAWNVLARRQ------ISTQLIEIESRPHITLFSSPTIEPA 55 (183)
Q Consensus 17 ~~i~~~~~~l~~~~------~~~~~~~~~~~pHiTL~~~~~~~~~ 55 (183)
..++.+++.|-... ...-.+.+.+.||||+......+++
T Consensus 134 ddlkalrnvl~n~vp~pkdifg~i~~d~~w~phitigyv~~dd~d 178 (201)
T PHA02977 134 DDLKALRNVLFNAVPCPKDIFGDILSDNPWCPHITIGYVKADDED 178 (201)
T ss_pred hHHHHHHHHhhcccCCcHHhhcccccCCCCCCceEEEeecccchh
Confidence 44566666665321 1112223679999999665444443
No 39
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=47.32 E-value=50 Score=18.34 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=22.2
Q ss_pred CCceeEEEEEeChhhHHHHHHHHHHHH
Q 040775 1 MSQGYAIELYFDPALENQVLKAWNVLA 27 (183)
Q Consensus 1 m~~~y~i~l~~~~~~~~~i~~~~~~l~ 27 (183)
|..+|-+-|+|+++..+.+.+.....+
T Consensus 1 M~~~~k~rl~Pt~~Q~~~L~~~~~~~R 27 (46)
T PF12323_consen 1 MLKAYKYRLYPTKEQEEKLERWFGACR 27 (46)
T ss_pred CCcceEEEEecCHHHHHHHHHHHHHHH
Confidence 777999999999999988887766544
No 40
>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=44.70 E-value=21 Score=27.54 Aligned_cols=21 Identities=5% Similarity=0.161 Sum_probs=17.1
Q ss_pred Cccceeeeec-cCChhhHHHHH
Q 040775 124 NWIPYCPVAQ-EVPKTRMAEAF 144 (183)
Q Consensus 124 ~f~PHiTL~~-~~~~~~~~~~~ 144 (183)
.-.||||++- +++++.+..+.
T Consensus 41 QkaPHlSl~mL~Isd~~i~~V~ 62 (248)
T PF05213_consen 41 QKAPHLSLGMLDISDEDIPDVE 62 (248)
T ss_pred cccCeeEEEEEEcChhhhhhHH
Confidence 3699999998 88888777665
No 41
>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=44.62 E-value=36 Score=23.30 Aligned_cols=27 Identities=11% Similarity=0.252 Sum_probs=23.2
Q ss_pred CCCeeEEEceeeeeCCCCcEEEEeecC
Q 040775 68 QEPLPLCLSTIGSFCNDNNVLFLAPTP 94 (183)
Q Consensus 68 ~~pf~l~~~~~g~F~~~~~vl~l~v~~ 94 (183)
..||.++|+.++.++...+++=+.+.+
T Consensus 42 sSPFhVRFGk~~vl~~~ek~V~I~VNG 68 (110)
T PF04571_consen 42 SSPFHVRFGKLGVLRPREKVVDIEVNG 68 (110)
T ss_pred cCccEEEEcceeeecccCcEEEEEECC
Confidence 799999999999999767888887754
No 42
>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2.7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.
Probab=38.62 E-value=20 Score=25.43 Aligned_cols=34 Identities=12% Similarity=0.256 Sum_probs=16.9
Q ss_pred EEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 88 LFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 88 l~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
+++-+...+.+.+|-+.|+. +++.+|.||...+-
T Consensus 32 v~V~~~d~~~a~~lD~~LW~------------~~~~sFlPH~~~~~ 65 (137)
T PF04364_consen 32 VLVLCPDEEQAEALDELLWT------------FSPDSFLPHGLAGE 65 (137)
T ss_dssp EEEE-SSHHHHHHHHHHTTT------------SSTT----EEETT-
T ss_pred EEEEeCCHHHHHHHHHHHHC------------CCCCCCCCCcccCC
Confidence 44444344556666666653 35678999999765
No 43
>PF04095 NAPRTase: Nicotinate phosphoribosyltransferase (NAPRTase) family; InterPro: IPR015977 Nicotinate phosphoribosyltransferase (2.4.2.11 from EC) is the rate-limiting enzyme that catalyses the first reaction in the NAD salvage synthesis. This family also contains a number of closely related proteins for which a catalytic activity has not been experimentally demonstrated.; GO: 0004516 nicotinate phosphoribosyltransferase activity, 0009435 NAD biosynthetic process, 0005737 cytoplasm; PDB: 3OS4_B 1VLP_C 2F7F_A 1YIR_D 1YBE_B 2H3D_A 2H3B_B 2GVL_B 2IM5_B 2G96_B ....
Probab=36.30 E-value=1.6e+02 Score=23.00 Aligned_cols=55 Identities=15% Similarity=0.174 Sum_probs=38.3
Q ss_pred EEEEeCh-hhHHHHHHHHHHHHHc-cCccccccCCCCCeeEEeecCCCChhHHHHHHHHhh
Q 040775 7 IELYFDP-ALENQVLKAWNVLARR-QISTQLIEIESRPHITLFSSPTIEPAKLESIIKIHA 65 (183)
Q Consensus 7 i~l~~~~-~~~~~i~~~~~~l~~~-~~~~~~~~~~~~pHiTL~~~~~~~~~~l~~~l~~~~ 65 (183)
+.+++|. +....++++++.+... +..++. .-+|+++.+-++++++.+.+.++...
T Consensus 114 ~gvR~DSGD~~~~~~~~r~~f~~~~~~~g~k----vl~~~~Ii~Sd~Lde~~i~~l~~~~~ 170 (245)
T PF04095_consen 114 LGVRPDSGDPAELSEKLRKIFDEAVGIKGYK----VLPSKKIIASDGLDEEKIEELLEQGA 170 (245)
T ss_dssp EEEEE-SS-HHHHHHHHHHHHHHTETTTGGE----E-TCSEEEEESS-SHHHHHHHHHHHC
T ss_pred eeeecCCCChHHHHHHHHHHHHHHhCCCCcc----ccceEEEEEeCCCCHHHHHHHHHHhh
Confidence 6677773 4556778888888887 555443 22499999889999999888887775
No 44
>PLN00108 unknown protein; Provisional
Probab=32.77 E-value=2.5e+02 Score=22.31 Aligned_cols=45 Identities=13% Similarity=0.036 Sum_probs=31.8
Q ss_pred Cccceeeeec-cCC-hhhHHHHHHHHHhC---------CcceEEEEeEEEEEeecC
Q 040775 124 NWIPYCPVAQ-EVP-KTRMAEAFCVLREL---------KLPVTGYAMDIGLVEYSP 168 (183)
Q Consensus 124 ~f~PHiTL~~-~~~-~~~~~~~~~~~~~~---------~~~~~~~v~~i~L~~~~p 168 (183)
+-+=|+||+- .+. ++++.+|...+.+. +.|++..+.++..+.-+|
T Consensus 89 p~~LHLTLgmL~L~~~eev~kA~~~L~s~~~~i~~~l~~~pl~I~lkGL~~Mnddp 144 (257)
T PLN00108 89 PKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSL 144 (257)
T ss_pred CCceEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEEeehhcCCCc
Confidence 4677999997 554 56666665554432 467888899998887665
No 45
>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=32.53 E-value=2.4e+02 Score=21.86 Aligned_cols=94 Identities=11% Similarity=0.004 Sum_probs=51.6
Q ss_pred EEceeeeeCC---C-CcEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCC----C---CCCCccceeeeec--cCChhhH
Q 040775 74 CLSTIGSFCN---D-NNVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDE----F---RPENWIPYCPVAQ--EVPKTRM 140 (183)
Q Consensus 74 ~~~~~g~F~~---~-~~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~----~---~~~~f~PHiTL~~--~~~~~~~ 140 (183)
+=+.+..|++ + +.-||+.+.++....++-+++.+.+.......... . ...+=.-||+|.| .+....+
T Consensus 26 h~gR~R~~pHv~Gnw~t~vYi~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~s~lg~~~~lHISLSr~~~lr~~~i 105 (239)
T PF09749_consen 26 HGGRIRSFPHVEGNWPTHVYIEWPPSEDQRELLEKLISKANSICPKLHSEFEPLLYSDLGSPDPLHISLSRTFPLRTHQI 105 (239)
T ss_pred ccCceecccccCCccceEEEEEecCcHHHHHHHHHHHHHHHhhhhhhhhhcccccccccCCCCCeEEEeCCCccccHHHH
Confidence 3345555654 2 46789999888765555555544444432111000 0 0012357999999 4444444
Q ss_pred HHHHHHHHh-----CCcceEEEEeEEEEEeec
Q 040775 141 AEAFCVLRE-----LKLPVTGYAMDIGLVEYS 167 (183)
Q Consensus 141 ~~~~~~~~~-----~~~~~~~~v~~i~L~~~~ 167 (183)
+..++.++. ...+|...++++.++..+
T Consensus 106 d~f~~~lr~~l~~~~~~~F~v~f~~~~~~~N~ 137 (239)
T PF09749_consen 106 DPFVDSLRQALRSSNIRPFYVSFSGLDVYTND 137 (239)
T ss_pred HHHHHHHHHHHhhcCCceEEEEeCceEEEecC
Confidence 444333322 246788888888888654
No 46
>COG3799 Mal Methylaspartate ammonia-lyase [Amino acid transport and metabolism]
Probab=31.71 E-value=2.9e+02 Score=22.68 Aligned_cols=85 Identities=14% Similarity=0.191 Sum_probs=56.3
Q ss_pred hhHHHHHHHHHHHHHccCccccccCCCCCeeEEeec-C---CCChhHHHHHHHHhhccCCCeeEEEceeeeeCCCCcEEE
Q 040775 14 ALENQVLKAWNVLARRQISTQLIEIESRPHITLFSS-P---TIEPAKLESIIKIHASKQEPLPLCLSTIGSFCNDNNVLF 89 (183)
Q Consensus 14 ~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~-~---~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~~~~~vl~ 89 (183)
...+.++=+.++....+.++|. ..+||.+... + .+++..+..-+..+....++|++.+.|.--|+.
T Consensus 208 ~l~Eyv~Wls~R~~~~g~~gYh----P~lH~DVYG~iGe~fg~dp~r~a~yi~~l~~~a~~~pL~IEgP~DaGs------ 277 (410)
T COG3799 208 KLREYVRWLSDRILSKGTSGYH----PTLHIDVYGTIGEIFGMDPLRCAQYIASLEKEAQGLPLYIEGPVDAGS------ 277 (410)
T ss_pred HHHHHHHHHHHHHHhcCCCCCC----ccEEEeehhhhHHHhCCCHHHHHHHHHHHHhhCCCCceeeeccccCCC------
Confidence 3445566666677766766644 6789988543 2 367777777788888888999999998877763
Q ss_pred EeecCChhHHHHHHHHHHHHHhcC
Q 040775 90 LAPTPSIPLLQFQSQLCEAFKREG 113 (183)
Q Consensus 90 l~v~~~~~L~~L~~~l~~~l~~~~ 113 (183)
.+.-.++..+|.+.|...|
T Consensus 278 -----~~aQI~~~a~i~~~L~~~G 296 (410)
T COG3799 278 -----KPAQIRLLAAITKELTRLG 296 (410)
T ss_pred -----CHHHHHHHHHHHHHHhhcC
Confidence 1223344455556665555
No 47
>COG2927 HolC DNA polymerase III, chi subunit [DNA replication, recombination, and repair]
Probab=30.20 E-value=45 Score=24.05 Aligned_cols=28 Identities=18% Similarity=0.291 Sum_probs=19.7
Q ss_pred CChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeec
Q 040775 94 PSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQ 133 (183)
Q Consensus 94 ~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~ 133 (183)
..+....|-+.|+. +++..|.||-+.+-
T Consensus 38 d~~q~e~LD~~LWt------------~~~~sFiPH~~~~e 65 (144)
T COG2927 38 DEAQAEALDEHLWT------------FSAESFIPHNLAGE 65 (144)
T ss_pred CHHHHHHHHHhhhc------------cchhcccCCccCCC
Confidence 33566677777764 35578999999984
No 48
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=30.00 E-value=1.6e+02 Score=19.00 Aligned_cols=52 Identities=4% Similarity=0.131 Sum_probs=37.4
Q ss_pred cEEEEeecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCccceeeeecc---------CChhhHHHHHHHHHhC
Q 040775 86 NVLFLAPTPSIPLLQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQE---------VPKTRMAEAFCVLREL 150 (183)
Q Consensus 86 ~vl~l~v~~~~~L~~L~~~l~~~l~~~~~~~~~~~~~~~f~PHiTL~~~---------~~~~~~~~~~~~~~~~ 150 (183)
.+|-+.+.++....+|++.|.+.|.-.+ =|++|-|+ ++.++++.+|...++.
T Consensus 11 ~tIaIrvp~~~~y~~L~~ki~~kLkl~~-------------e~i~LsYkde~s~~~v~l~d~dle~aws~~~~~ 71 (80)
T cd06406 11 YTVAIQVARGLSYATLLQKISSKLELPA-------------EHITLSYKSEASGEDVILSDTNMEDVWSQAKDG 71 (80)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHhCCCc-------------hhcEEEeccCCCCCccCcChHHHHHHHHhhcCC
Confidence 4788998888899999999999876421 24555552 3456788888877653
No 49
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=29.25 E-value=3.3e+02 Score=24.12 Aligned_cols=72 Identities=15% Similarity=0.247 Sum_probs=47.0
Q ss_pred CCCCeeE-EeecCCCChhHHHHHHHHhhccCCCeeEEEce---eeeeCCCCcEEEEeecCChhHHHHHHHHHHHHHhc
Q 040775 39 ESRPHIT-LFSSPTIEPAKLESIIKIHASKQEPLPLCLST---IGSFCNDNNVLFLAPTPSIPLLQFQSQLCEAFKRE 112 (183)
Q Consensus 39 ~~~pHiT-L~~~~~~~~~~l~~~l~~~~~~~~pf~l~~~~---~g~F~~~~~vl~l~v~~~~~L~~L~~~l~~~l~~~ 112 (183)
+.+|||. |...+.-+.+.+++.++++. .....++-.+ +.-+-....+-|+.|..++++.++.+.+.+++...
T Consensus 160 ~k~~~ilgLTASPGs~~ekI~eV~~nLg--Ie~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~ 235 (542)
T COG1111 160 AKNPLILGLTASPGSDLEKIQEVVENLG--IEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPR 235 (542)
T ss_pred ccCceEEEEecCCCCCHHHHHHHHHhCC--cceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHHHHHHHHHH
Confidence 3556654 44445567888888877764 5555555432 22222345789999998888888888887776653
No 50
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=26.90 E-value=2.2e+02 Score=19.82 Aligned_cols=55 Identities=4% Similarity=0.037 Sum_probs=34.6
Q ss_pred hhHHHHHHHHhhccCCCeeEEEceeeeeCCCCcEEEEeecCChhHHHHHHHHHHHHH
Q 040775 54 PAKLESIIKIHASKQEPLPLCLSTIGSFCNDNNVLFLAPTPSIPLLQFQSQLCEAFK 110 (183)
Q Consensus 54 ~~~l~~~l~~~~~~~~pf~l~~~~~g~F~~~~~vl~l~v~~~~~L~~L~~~l~~~l~ 110 (183)
++.+...++++. -..++++---=-.+..+|++.|+.......-..|.+.+++++.
T Consensus 67 ~~EV~pvi~aL~--~~GI~vtAlHNH~l~e~Prl~ymH~~~~gdp~~lA~~vr~Ald 121 (123)
T PF07485_consen 67 EDEVNPVISALR--KNGIEVTALHNHWLFEQPRLFYMHIWGVGDPAKLARKVRAALD 121 (123)
T ss_pred HHHHHHHHHHHH--HCCceEEEEecccccCCCCEEEEEEEecCCHHHHHHHHHHHHh
Confidence 344555565554 2334433222223333599999999888888888888888775
No 51
>PF06877 RraB: Regulator of ribonuclease activity B; InterPro: IPR009671 This entry occurs in several hypothetical bacterial proteins of around 120 residues in length. The function of these proteins is unknown. The protein structure has been determined for one member of this group, the hypothetical protein VCO424 from Vibrio cholerae; it has an alpha+beta sandwich fold.; PDB: 1NXI_A.
Probab=24.62 E-value=2e+02 Score=18.78 Aligned_cols=74 Identities=14% Similarity=0.067 Sum_probs=31.8
Q ss_pred eeEEEEEeChhhHHHHHHHHHHHHHccCccccccC----CCCC-eeEEeecCCCChhHHH---HHHHHhhccCCCeeEEE
Q 040775 4 GYAIELYFDPALENQVLKAWNVLARRQISTQLIEI----ESRP-HITLFSSPTIEPAKLE---SIIKIHASKQEPLPLCL 75 (183)
Q Consensus 4 ~y~i~l~~~~~~~~~i~~~~~~l~~~~~~~~~~~~----~~~p-HiTL~~~~~~~~~~l~---~~l~~~~~~~~pf~l~~ 75 (183)
.+.|..++--+..+.+.++...+.+.|........ ...+ -+++..-...+.+.|. ..|..++ .+|....
T Consensus 23 ~r~ieh~~~f~~~~~~~~f~~~~~~~g~~v~~~~~~~~d~~~~~~~~~~~~~~~~~~~I~~~~~~l~~lA---~~~~g~Y 99 (104)
T PF06877_consen 23 PRPIEHWFYFEDEEDAEKFAEELEKLGYEVESAEEDEEDGDGPYCLDISREMVLDYEDINAITQELEDLA---KEFGGEY 99 (104)
T ss_dssp -EEEEEEEEES-HHHHHHHHHHHHHHS---B----B-SS-SSBEEEEEEEEE-S-HHHHHHHHHHHHHHH---HHHT-EE
T ss_pred CeEEEEEEEeCCHHHHHHHHHHHHHCCCEEEEeecccCCCCceEEEEEEEecCCCHHHHHHHHHHHHHHH---HHhCcEe
Confidence 44455444445566667777777776543222101 1111 2333222334444444 4455554 5566667
Q ss_pred ceeee
Q 040775 76 STIGS 80 (183)
Q Consensus 76 ~~~g~ 80 (183)
+|+|+
T Consensus 100 DGWg~ 104 (104)
T PF06877_consen 100 DGWGT 104 (104)
T ss_dssp EEEEE
T ss_pred cCccC
Confidence 77764
No 52
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=24.52 E-value=1.8e+02 Score=17.84 Aligned_cols=49 Identities=16% Similarity=0.174 Sum_probs=32.9
Q ss_pred HHHHhcCCCCCCCCCCCCccceeeeeccCChhhHHHHHHHHHhCCcceE
Q 040775 107 EAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLRELKLPVT 155 (183)
Q Consensus 107 ~~l~~~~~~~~~~~~~~~f~PHiTL~~~~~~~~~~~~~~~~~~~~~~~~ 155 (183)
+.+...|....--..|+.....|.++-+.+.++...+...+++....+.
T Consensus 19 k~lk~~gi~~~liP~P~~i~~~CG~al~~~~~d~~~i~~~l~~~~i~~~ 67 (73)
T PF11823_consen 19 KLLKKNGIPVRLIPTPREISAGCGLALRFEPEDLEKIKEILEENGIEYE 67 (73)
T ss_pred HHHHHCCCcEEEeCCChhccCCCCEEEEEChhhHHHHHHHHHHCCCCee
Confidence 3444444322222345678999999998888888888888888765543
No 53
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=23.68 E-value=1.1e+02 Score=16.40 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=20.2
Q ss_pred eeEEEEEeChhhHHHHHHHHHHHHH
Q 040775 4 GYAIELYFDPALENQVLKAWNVLAR 28 (183)
Q Consensus 4 ~y~i~l~~~~~~~~~i~~~~~~l~~ 28 (183)
.|-|.+.|++...+-+++-..+|-.
T Consensus 11 ty~V~~~F~~~s~et~~DKi~rli~ 35 (37)
T PF14202_consen 11 TYVVEVHFSETSKETMQDKIKRLIR 35 (37)
T ss_pred EEEEEEEECCCccccHHHHHHHHHh
Confidence 6889999999988888877776643
No 54
>PF06526 DUF1107: Protein of unknown function (DUF1107); InterPro: IPR009491 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2JRO_A.
Probab=23.32 E-value=1.8e+02 Score=17.88 Aligned_cols=56 Identities=18% Similarity=0.257 Sum_probs=30.3
Q ss_pred CCCChhHHHHHHHHhhccCCCeeEEEceeeeeCCCCcEEEEeecCChhHHHHHHHHHHHH
Q 040775 50 PTIEPAKLESIIKIHASKQEPLPLCLSTIGSFCNDNNVLFLAPTPSIPLLQFQSQLCEAF 109 (183)
Q Consensus 50 ~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~~~~~vl~l~v~~~~~L~~L~~~l~~~l 109 (183)
..+.+.++..-++. +-.-.+.+.|+|.|+-+.+-+-+.-..+..-...-.++.+..
T Consensus 5 k~Y~P~~IAk~Vk~----lF~Gr~~I~g~G~feFd~Gkillp~~~~~~~~~~~~EiN~~I 60 (64)
T PF06526_consen 5 KRYRPRQIAKYVKT----LFRGRIYIKGIGAFEFDNGKILLPKKADKRHLSVMSEINQEI 60 (64)
T ss_dssp SS--HHHHHHHHHH----H-SEEEEETTTEEEEEETTEE---SS--HHHHHHHHHHHHHH
T ss_pred cccCHHHHHHHHHH----HccceEEEEecccEEEcCCEEeCCccccHHHHHHHHHHHHHH
Confidence 34455555544444 455689999999999656666665445555555555555544
No 55
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=22.87 E-value=1.4e+02 Score=17.32 Aligned_cols=21 Identities=14% Similarity=0.184 Sum_probs=11.2
Q ss_pred CeeEEeecCCCChhHHHHHHH
Q 040775 42 PHITLFSSPTIEPAKLESIIK 62 (183)
Q Consensus 42 pHiTL~~~~~~~~~~l~~~l~ 62 (183)
|||++......+.++-.+.++
T Consensus 1 P~I~i~~~~g~~~e~K~~l~~ 21 (60)
T PF01361_consen 1 PFITIKIPEGRTAEQKRELAE 21 (60)
T ss_dssp -EEEEEEESTS-HHHHHHHHH
T ss_pred CEEEEEECCCCCHHHHHHHHH
Confidence 788987665556655443333
No 56
>cd02974 AhpF_NTD_N Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The N-terminal TRX-fold subdomain of AhpF NTD is redox inactive, but is proposed to contain an important residue that aids in the catalytic function of the redox-active CXXC motif contained in the C-terminal TRX-
Probab=22.08 E-value=2.4e+02 Score=18.47 Aligned_cols=80 Identities=16% Similarity=0.130 Sum_probs=43.9
Q ss_pred eChhhHHHHHHHHHHHHHccCccccccCCCCCeeEEeec-C-CCChhHHHHHHHHhhccCCCeeEEEceee-------ee
Q 040775 11 FDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSS-P-TIEPAKLESIIKIHASKQEPLPLCLSTIG-------SF 81 (183)
Q Consensus 11 ~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~pHiTL~~~-~-~~~~~~l~~~l~~~~~~~~pf~l~~~~~g-------~F 81 (183)
+|+++.++++.+-++|.+ .++|..+ + +...+.+.+.++++++-...+++...... ..
T Consensus 2 l~~~~~~qL~~~f~~l~~--------------pV~l~~f~~~~~~~~e~~~ll~e~a~lSdkI~~~~~~~~~~~P~~~i~ 67 (94)
T cd02974 2 LDANLKQQLKAYLERLEN--------------PVELVASLDDSEKSAELLELLEEIASLSDKITLEEDNDDERKPSFSIN 67 (94)
T ss_pred CCHHHHHHHHHHHHhCCC--------------CEEEEEEeCCCcchHHHHHHHHHHHHhCCceEEEEecCCCCCCEEEEe
Confidence 567777777777654431 2444222 2 22234567778888765666666654322 11
Q ss_pred CC--CCcEEEEeecCChhHHHHHHH
Q 040775 82 CN--DNNVLFLAPTPSIPLLQFQSQ 104 (183)
Q Consensus 82 ~~--~~~vl~l~v~~~~~L~~L~~~ 104 (183)
.+ +.++-|.++-.+.++..|-..
T Consensus 68 ~~~~~~gIrF~GiP~GhEf~Slila 92 (94)
T cd02974 68 RPGEDTGIRFAGIPMGHEFTSLVLA 92 (94)
T ss_pred cCCCcccEEEEecCCchhHHHHHHH
Confidence 11 246777777555666655443
No 57
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=21.94 E-value=1.7e+02 Score=22.99 Aligned_cols=98 Identities=8% Similarity=-0.018 Sum_probs=45.5
Q ss_pred CCCChhHHHHHHHHhhccCCCeeEEE-cee-e-----eeCC-CCcEEEEeecCC-hhHHHHHHH---HHHHHHhcCCCCC
Q 040775 50 PTIEPAKLESIIKIHASKQEPLPLCL-STI-G-----SFCN-DNNVLFLAPTPS-IPLLQFQSQ---LCEAFKREGIECG 117 (183)
Q Consensus 50 ~~~~~~~l~~~l~~~~~~~~pf~l~~-~~~-g-----~F~~-~~~vl~l~v~~~-~~L~~L~~~---l~~~l~~~~~~~~ 117 (183)
+.++..+..+.++++..+. .+.+.+ .|+ . .|.. .-.++-++...+ +.+.+.+.. +.+.++......
T Consensus 69 g~VPl~kf~d~lK~lke~~-~l~inaHvGfvdE~~~eklk~~~vdvvsLDfvgDn~vIk~vy~l~ksv~dyl~~l~~L~- 146 (275)
T COG1856 69 GKVPLWKFKDELKALKERT-GLLINAHVGFVDESDLEKLKEELVDVVSLDFVGDNDVIKRVYKLPKSVEDYLRSLLLLK- 146 (275)
T ss_pred CCccHHHHHHHHHHHHHhh-CeEEEEEeeeccHHHHHHHHHhcCcEEEEeecCChHHHHHHHcCCccHHHHHHHHHHHH-
Confidence 3456677777777775332 222222 111 1 1211 246777777654 334443333 333333221000
Q ss_pred CCCCCCCccceeeeeccCC-hhhHHHHHHHHHhCC
Q 040775 118 DEFRPENWIPYCPVAQEVP-KTRMAEAFCVLRELK 151 (183)
Q Consensus 118 ~~~~~~~f~PHiTL~~~~~-~~~~~~~~~~~~~~~ 151 (183)
..+ -+-+||||+|.+-. -..-.++++.+.+..
T Consensus 147 e~~--irvvpHitiGL~~gki~~e~kaIdiL~~~~ 179 (275)
T COG1856 147 ENG--IRVVPHITIGLDFGKIHGEFKAIDILVNYE 179 (275)
T ss_pred HcC--ceeceeEEEEeccCcccchHHHHHHHhcCC
Confidence 001 23799999997211 112234566666543
No 58
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=21.64 E-value=1.5e+02 Score=18.17 Aligned_cols=54 Identities=15% Similarity=0.067 Sum_probs=25.2
Q ss_pred eChhhHHHHHHHHHHHHHccCcccccc-CCCCCeeEEeecCCCChhHHHHHHHHh
Q 040775 11 FDPALENQVLKAWNVLARRQISTQLIE-IESRPHITLFSSPTIEPAKLESIIKIH 64 (183)
Q Consensus 11 ~~~~~~~~i~~~~~~l~~~~~~~~~~~-~~~~pHiTL~~~~~~~~~~l~~~l~~~ 64 (183)
|.....+.-.++..++...+-...... +.....+++....+.+-+.+.+.|+++
T Consensus 2 p~ga~~AL~~EL~kRl~~~yPd~~v~Vr~~s~~~l~v~g~~~~~k~~i~~iLqe~ 56 (65)
T PF06183_consen 2 PAGALEALESELTKRLHRQYPDAEVRVRPGSANGLSVSGGKKDDKERIEEILQEM 56 (65)
T ss_dssp -TTHHHHHHHHHHHHHHHH-SS-EEEEEEESS-EEEEES--HHHHHHHHHHHHHH
T ss_pred CccHHHHHHHHHHHHHHHHCCCceEeeeecccCccccCCcCchHHHHHHHHHHHH
Confidence 445555666666667766543221111 345566666544322244566666654
No 59
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=21.49 E-value=1.8e+02 Score=16.68 Aligned_cols=23 Identities=9% Similarity=0.088 Sum_probs=16.9
Q ss_pred CCceeEEEEEeChhhHHHHHHHH
Q 040775 1 MSQGYAIELYFDPALENQVLKAW 23 (183)
Q Consensus 1 m~~~y~i~l~~~~~~~~~i~~~~ 23 (183)
|+...-+.+.+|+++..+|++..
T Consensus 1 ~r~~~~f~lRlP~~l~~~lk~~A 23 (50)
T PF03869_consen 1 SRKDPQFNLRLPEELKEKLKERA 23 (50)
T ss_dssp TCCSEEEEEECEHHHHHHHHHHH
T ss_pred CCCCCceeeECCHHHHHHHHHHH
Confidence 56667788888888877776654
No 60
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=20.16 E-value=93 Score=25.16 Aligned_cols=43 Identities=16% Similarity=0.211 Sum_probs=32.0
Q ss_pred CCCeeEEee--c-CCCChhHHHHHHHHhhccCCCeeEEEceeeeeC
Q 040775 40 SRPHITLFS--S-PTIEPAKLESIIKIHASKQEPLPLCLSTIGSFC 82 (183)
Q Consensus 40 ~~pHiTL~~--~-~~~~~~~l~~~l~~~~~~~~pf~l~~~~~g~F~ 82 (183)
.-|==||+. | .+-+...|-.-++.+|..+.++=++++|+.+-.
T Consensus 115 QdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~ 160 (323)
T KOG2875|consen 115 QDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHG 160 (323)
T ss_pred cCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCccccc
Confidence 345556643 3 456778888888889999999999999987743
Done!