Query psy15057
Match_columns 151
No_of_seqs 136 out of 1013
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 19:20:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15057.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15057hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1069|consensus 100.0 3.4E-45 7.4E-50 269.2 12.0 149 3-151 4-152 (217)
2 TIGR02065 ECX1 archaeal exosom 100.0 5.2E-40 1.1E-44 252.3 19.3 150 1-151 15-173 (230)
3 KOG1068|consensus 100.0 7.6E-41 1.7E-45 253.7 10.8 150 1-151 20-179 (245)
4 PRK03983 exosome complex exonu 100.0 3.8E-39 8.2E-44 249.5 19.3 150 1-151 21-179 (244)
5 PRK00173 rph ribonuclease PH; 100.0 1.3E-37 2.9E-42 240.0 18.6 150 1-151 8-181 (238)
6 TIGR01966 RNasePH ribonuclease 100.0 2.6E-37 5.6E-42 238.2 18.8 150 1-151 7-180 (236)
7 COG0689 Rph RNase PH [Translat 100.0 3.8E-36 8.2E-41 228.5 16.0 150 1-151 15-174 (230)
8 PF01138 RNase_PH: 3' exoribon 100.0 2.1E-32 4.5E-37 193.1 15.3 121 3-123 1-132 (132)
9 PRK11824 polynucleotide phosph 100.0 1.5E-31 3.3E-36 231.9 18.8 150 1-151 321-487 (693)
10 TIGR03591 polynuc_phos polyrib 100.0 1.9E-31 4.1E-36 230.9 18.7 150 1-151 317-484 (684)
11 PRK04282 exosome complex RNA-b 100.0 2.5E-31 5.5E-36 208.6 17.1 149 1-151 31-215 (271)
12 TIGR02696 pppGpp_PNP guanosine 100.0 3.2E-30 6.8E-35 221.5 16.9 150 1-151 342-512 (719)
13 PLN00207 polyribonucleotide nu 100.0 2E-29 4.4E-34 220.4 18.6 150 1-151 445-618 (891)
14 TIGR03591 polynuc_phos polyrib 100.0 8.7E-29 1.9E-33 214.4 17.7 138 5-151 5-162 (684)
15 PRK11824 polynucleotide phosph 100.0 2.8E-28 6.1E-33 211.6 17.6 142 4-151 13-171 (693)
16 COG2123 RNase PH-related exori 100.0 5.4E-28 1.2E-32 186.1 16.9 149 1-151 30-216 (272)
17 KOG1614|consensus 99.9 5.3E-26 1.1E-30 172.3 14.4 147 1-151 29-215 (291)
18 PLN00207 polyribonucleotide nu 99.9 6.6E-24 1.4E-28 186.0 14.1 141 5-151 89-246 (891)
19 KOG1612|consensus 99.9 4.4E-21 9.5E-26 146.3 16.5 147 2-151 29-220 (288)
20 KOG1067|consensus 99.7 5.8E-18 1.3E-22 141.0 10.0 135 1-137 365-513 (760)
21 KOG1613|consensus 99.7 9.6E-18 2.1E-22 127.4 9.0 121 2-123 44-180 (298)
22 TIGR02696 pppGpp_PNP guanosine 99.7 1E-16 2.2E-21 138.6 13.4 140 5-150 17-174 (719)
23 COG1185 Pnp Polyribonucleotide 99.6 4.2E-16 9.1E-21 132.7 7.7 148 1-149 319-483 (692)
24 COG1185 Pnp Polyribonucleotide 99.6 6.9E-15 1.5E-19 125.4 13.1 139 5-150 14-169 (692)
25 KOG1067|consensus 99.4 3.8E-13 8.2E-18 112.6 5.3 140 4-150 55-211 (760)
26 PF03725 RNase_PH_C: 3' exorib 97.5 8.4E-05 1.8E-09 46.2 2.7 25 126-151 1-25 (68)
27 PRK15031 5-carboxymethyl-2-hyd 78.6 17 0.00036 25.5 7.1 63 45-107 55-118 (126)
28 PF02962 CHMI: 5-carboxymethyl 78.6 8.3 0.00018 26.9 5.5 57 45-102 54-110 (124)
29 PF07451 SpoVAD: Stage V sporu 57.1 2.9 6.2E-05 33.8 -0.5 89 32-131 17-106 (329)
30 PRK12404 stage V sporulation p 52.0 22 0.00047 29.1 3.7 89 32-132 20-110 (334)
31 TIGR02845 spore_V_AD stage V s 45.6 37 0.00079 27.7 4.1 57 32-93 16-73 (327)
32 PF03727 Hexokinase_2: Hexokin 40.8 85 0.0019 24.1 5.4 41 69-115 201-241 (243)
33 PRK08304 stage V sporulation p 36.9 49 0.0011 27.2 3.6 70 19-93 6-79 (337)
34 cd07207 Pat_ExoU_VipD_like Exo 34.4 36 0.00078 24.6 2.3 34 101-135 5-38 (194)
35 cd07198 Patatin Patatin-like p 33.8 39 0.00084 24.2 2.4 35 101-136 4-38 (172)
36 PRK05463 hypothetical protein; 32.9 19 0.0004 28.4 0.6 27 111-137 119-145 (262)
37 PF06519 TolA: TolA C-terminal 32.4 1.5E+02 0.0032 19.5 5.5 55 69-124 15-79 (96)
38 COG1240 ChlD Mg-chelatase subu 31.3 1.5E+02 0.0033 23.5 5.4 55 93-148 79-137 (261)
39 cd00580 CHMI 5-carboxymethyl-2 30.6 1.7E+02 0.0036 19.5 6.1 52 48-100 57-108 (113)
40 PF03764 EFG_IV: Elongation fa 28.3 1.8E+02 0.004 19.3 8.6 55 67-121 57-120 (120)
41 PF15645 Tox-PLDMTX: Dermonecr 28.1 59 0.0013 23.0 2.4 28 119-149 38-65 (135)
42 cd07227 Pat_Fungal_NTE1 Fungal 25.2 68 0.0015 25.3 2.6 36 100-136 15-50 (269)
43 PF14113 DUF4285: Domain of un 23.6 76 0.0016 21.6 2.3 22 107-128 5-26 (115)
44 KOG3129|consensus 21.5 65 0.0014 24.8 1.7 16 80-95 54-69 (231)
45 KOG2925|consensus 21.4 85 0.0018 22.8 2.2 19 132-150 58-76 (167)
46 COG3908 Uncharacterized protei 21.1 86 0.0019 19.6 1.9 23 16-38 17-39 (77)
47 PRK10279 hypothetical protein; 20.7 93 0.002 24.9 2.6 37 99-136 9-45 (300)
48 TIGR03279 cyano_FeS_chp putati 20.6 1.2E+02 0.0026 25.9 3.2 34 92-125 142-181 (433)
49 cd07208 Pat_hypo_Ecoli_yjju_li 20.2 1.1E+02 0.0024 23.5 2.9 36 101-136 4-39 (266)
No 1
>KOG1069|consensus
Probab=100.00 E-value=3.4e-45 Score=269.25 Aligned_cols=149 Identities=42% Similarity=0.745 Sum_probs=145.1
Q ss_pred CccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHhh
Q psy15057 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESAL 82 (151)
Q Consensus 3 e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~i 82 (151)
.+|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.+++.+++++++|.++|..|..+..||.+++.|+++|+++|
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~G~~~~~eK~~e~iI~~tl~~~I 83 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKSGVNGTVEKVLERIIRKTLSKAI 83 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEecccCcchHHHHHHHHHHHHHHHHhh
Confidence 57999999999999999999999999999999999999999999999999999999999988889999999999999999
Q ss_pred cccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 83 LTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 83 ~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
.++.||++.|+|.+||+++||+++++|+|||++||+|+||||+++++|+++++.+++.+++|||..+|+
T Consensus 84 ~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~~qek 152 (217)
T KOG1069|consen 84 ILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTAKQEK 152 (217)
T ss_pred eeeecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcHHhhh
Confidence 999999999999999999999999999999999999999999999999999999888999999999874
No 2
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=100.00 E-value=5.2e-40 Score=252.30 Aligned_cols=150 Identities=30% Similarity=0.399 Sum_probs=134.5
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKSG------LSFVQDRLKE 71 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~ 71 (151)
++|+|++++++|+++++||||++++|+|+|+|+|+||.+.+++ .+.++++.++|++. |+++ .+...+++++
T Consensus 15 ~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~~~~~~~~~~~~~s 94 (230)
T TIGR02065 15 PDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDERKRPGPSRREIEIS 94 (230)
T ss_pred cccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCccCCCCCccHHHHH
Confidence 4799999999999999999999999999999999999976543 45688888887775 5433 2345567889
Q ss_pred HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
++|+++|++++.++.||++.|+|+++||++||++++|++||+++||+|+||||+++++|++++++ ++++++|||.+||+
T Consensus 95 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~~-~~~~v~Dpt~~Ee~ 173 (230)
T TIGR02065 95 KVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGKV-DGVVVLDLNEEEDM 173 (230)
T ss_pred HHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEE-CCeEEECCCHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999998 58999999999984
No 3
>KOG1068|consensus
Probab=100.00 E-value=7.6e-41 Score=253.74 Aligned_cols=150 Identities=29% Similarity=0.457 Sum_probs=135.5
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEcC--CC-C------CCcchhhHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFRP--KS-G------LSFVQDRLK 70 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~p--~~-g------~~~~~~~~~ 70 (151)
+||+|++..++|++.+++||||+++|||||+|.|+||++++.. ...++++.++|.+.. +. | ..+.+++++
T Consensus 20 ~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~~~~~~rr~~e~ 99 (245)
T KOG1068|consen 20 PNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKKRPKGDRREKEL 99 (245)
T ss_pred hhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhccCCCccHHHHHH
Confidence 5899999999999999999999999999999999999998764 336888999888853 21 1 123467889
Q ss_pred HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057 71 ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS 150 (151)
Q Consensus 71 ~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee 150 (151)
+.+|+++|+++|.++.||+++|+|+|+|+++||+.+++|+||+.+||.|+||||+|+++|+|+++.+ +..++||++.||
T Consensus 100 s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~l~~-~~~l~Dl~~~ee 178 (245)
T KOG1068|consen 100 SLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGLAD-GTPLLDLTSLEE 178 (245)
T ss_pred HHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceeeecC-Cccccccccchh
Confidence 9999999999999999999999999999999999999999999999999999999999999999995 799999999998
Q ss_pred C
Q psy15057 151 N 151 (151)
Q Consensus 151 ~ 151 (151)
.
T Consensus 179 s 179 (245)
T KOG1068|consen 179 S 179 (245)
T ss_pred h
Confidence 4
No 4
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=3.8e-39 Score=249.45 Aligned_cols=150 Identities=30% Similarity=0.410 Sum_probs=134.1
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKSG------LSFVQDRLKE 71 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~ 71 (151)
.+|+|++++++|++++++|||++++|+|+|+|+|+||.+.+++ .+.++++.+++++. |+++ .+..++.+++
T Consensus 21 ~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~~~~~~~~~~~~s 100 (244)
T PRK03983 21 PDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKRPGPDRRSIEIS 100 (244)
T ss_pred cCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCccccccCCCCChhHHHHH
Confidence 4799999999999999999999999999999999999986543 45688888877765 5443 1234556789
Q ss_pred HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
++|+++|++++.++.||++.|+|+++||++|||+++|++||+++||+|+||||++++++++++++ ++++++|||..||+
T Consensus 101 ~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~-~~~~i~DPt~~Ee~ 179 (244)
T PRK03983 101 KVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIVLDLNKEEDN 179 (244)
T ss_pred HHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEEEE-CCEEEECCCHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999998 58999999999985
No 5
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1.3e-37 Score=240.05 Aligned_cols=150 Identities=19% Similarity=0.193 Sum_probs=131.9
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEc--CCC-----------CCCcchh
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFR--PKS-----------GLSFVQD 67 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~--p~~-----------g~~~~~~ 67 (151)
++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.....++++.++|+|. |++ |.++.++
T Consensus 8 ~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~g~~~~~~ 87 (238)
T PRK00173 8 ADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAKGKQGGRT 87 (238)
T ss_pred cccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCcccccccccCCCCCccH
Confidence 589999999999999999999999999999999999886432224467788777775 532 2233456
Q ss_pred hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhc-----------CccccceeeEEEEEEe
Q psy15057 68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINS-----------GISMRYILAAVSCIIN 136 (151)
Q Consensus 68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~a-----------gip~~~~~~avtv~~~ 136 (151)
++++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+ |+||+++|+++|++++
T Consensus 88 ~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~~vt~~~~ 167 (238)
T PRK00173 88 QEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVAAVSVGIV 167 (238)
T ss_pred HHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCcccCceeEEEEEEE
Confidence 78899999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred cCCeEEeCCCccccC
Q psy15057 137 DKNEVILDANQIQSN 151 (151)
Q Consensus 137 ~~~~~lvDpt~~Ee~ 151 (151)
++++|+|||.+||+
T Consensus 168 -~~~~lvDpt~~Ee~ 181 (238)
T PRK00173 168 -DGEPVLDLDYEEDS 181 (238)
T ss_pred -CCEEEECCCHHHHh
Confidence 58899999999984
No 6
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=100.00 E-value=2.6e-37 Score=238.18 Aligned_cols=150 Identities=18% Similarity=0.193 Sum_probs=129.3
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCCC-----------CCcchh
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKSG-----------LSFVQD 67 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~g-----------~~~~~~ 67 (151)
++|+|++++++|++++++|||+|++|+|+|+|+|+++.+.+.....++++.++|++ .|++. .+..++
T Consensus 7 ~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~g~~~~~~ 86 (236)
T TIGR01966 7 PDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKGKQSGRT 86 (236)
T ss_pred CCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCCCCccccccCCCCCccH
Confidence 57999999999999999999999999999999999877532222335667766655 45422 222356
Q ss_pred hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhc-----------CccccceeeEEEEEEe
Q psy15057 68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINS-----------GISMRYILAAVSCIIN 136 (151)
Q Consensus 68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~a-----------gip~~~~~~avtv~~~ 136 (151)
++++++|+++|+++|+++.||++.|+|+++||++|||+++|++||+++||+|+ ||||+++++++|++++
T Consensus 87 ~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~~vt~~~~ 166 (236)
T TIGR01966 87 QEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIV 166 (236)
T ss_pred HHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCccCceeEEEEEEE
Confidence 68899999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred cCCeEEeCCCccccC
Q psy15057 137 DKNEVILDANQIQSN 151 (151)
Q Consensus 137 ~~~~~lvDpt~~Ee~ 151 (151)
++.+++|||.+||+
T Consensus 167 -~~~~v~Dpt~~Ee~ 180 (236)
T TIGR01966 167 -DGEPVLDLDYEEDS 180 (236)
T ss_pred -CCEEEECCChhHHh
Confidence 48899999999984
No 7
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-36 Score=228.48 Aligned_cols=150 Identities=25% Similarity=0.343 Sum_probs=133.8
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCccccccc-CCCCeeEEEEEEc--CCCCC----Ccc---hhhHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFR--PKSGL----SFV---QDRLK 70 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~-~~~~~~~v~v~~~--p~~g~----~~~---~~~~~ 70 (151)
+||+|+++++.|++++++||+++++|+|||+|+|+||.++.++. ..++++.+.++|. |++.. +.. +.+++
T Consensus 15 ~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~~~~~~gR~~ei 94 (230)
T COG0689 15 PDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEI 94 (230)
T ss_pred cccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccccccccccccchhHH
Confidence 58999999999999999999999999999999999999887753 4466788877775 44431 111 35788
Q ss_pred HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057 71 ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS 150 (151)
Q Consensus 71 ~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee 150 (151)
+++|.++|+++++++.||++.|+|+++|+++||+.+.|++||+++||+|||+||+++++|+|+|+++ +.+++|+++.|+
T Consensus 95 srli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi~~-~~~~lDl~~~Ed 173 (230)
T COG0689 95 SRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVD-GVIVLDLDYEED 173 (230)
T ss_pred HHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEEEC-CceEecCcchhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999995 779999999987
Q ss_pred C
Q psy15057 151 N 151 (151)
Q Consensus 151 ~ 151 (151)
+
T Consensus 174 s 174 (230)
T COG0689 174 S 174 (230)
T ss_pred c
Confidence 4
No 8
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=100.00 E-value=2.1e-32 Score=193.11 Aligned_cols=121 Identities=36% Similarity=0.525 Sum_probs=106.0
Q ss_pred CccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCC-CCe--eEEEEEEcCCC-------CCCcchhhHHHH
Q psy15057 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTI-IDK--ASVEVIFRPKS-------GLSFVQDRLKES 72 (151)
Q Consensus 3 e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~-~~~--~~v~v~~~p~~-------g~~~~~~~~~~~ 72 (151)
|+|++.+++|++++++|||+|++|+|+|+|+|+||.+.+++.+. ... ..++|++.|.+ |.+...+++++.
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~l~~ 80 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSFRRGGRPDEEERELSS 80 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHHHHH
T ss_pred CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEeccccccccccccccchhHHHHHH
Confidence 79999999999999999999999999999999999987555442 223 55666667754 234456778999
Q ss_pred HHHHHHHHhhcccCCCCcEEEEEEEEEeCCC-ChhHHHHHHHHHHHHhcCcc
Q psy15057 73 VIKSTCESALLTMLHPRTSVILTIQELQDQG-SLLSCCINAACLALINSGIS 123 (151)
Q Consensus 73 ~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG-~~l~a~inaa~lAL~~agip 123 (151)
+|+++|++.+.++.||+|.|+|+++||++|| |++++++||+++||+|+|||
T Consensus 81 ~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 81 LLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999999999999999999999 99999999999999999998
No 9
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=1.5e-31 Score=231.88 Aligned_cols=150 Identities=18% Similarity=0.300 Sum_probs=124.3
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCc-cccccc----CCCCeeEEEEEEcCCCC-------CCcchh
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPV-EAKIQK----TIIDKASVEVIFRPKSG-------LSFVQD 67 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~-~~~~~~----~~~~~~~v~v~~~p~~g-------~~~~~~ 67 (151)
+||+|++++++|+++++||||+|++|+|+|+|+|+ ||. +.++.+ +...+..++++|.|++. .++.++
T Consensus 321 ~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~rre 400 (693)
T PRK11824 321 LDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRRE 400 (693)
T ss_pred cCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCChhH
Confidence 58999999999999999999999999999999995 885 322211 12234456777777532 133444
Q ss_pred hHHHHHHHHHHHHhhcc-cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057 68 RLKESVIKSTCESALLT-MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL 143 (151)
Q Consensus 68 ~~~~~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv 143 (151)
...+++++|+|++++++ +.|| |.|+|+++||++|||.++|++||+++||+||||||+++++|+++|+++++ .+++
T Consensus 401 ~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~~~~il~ 479 (693)
T PRK11824 401 IGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLT 479 (693)
T ss_pred HHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCCceEEEc
Confidence 45679999999999998 7899 58999999999999999999999999999999999999999999999644 3899
Q ss_pred CCCccccC
Q psy15057 144 DANQIQSN 151 (151)
Q Consensus 144 Dpt~~Ee~ 151 (151)
||+..||.
T Consensus 480 D~~~~Ed~ 487 (693)
T PRK11824 480 DILGDEDH 487 (693)
T ss_pred CCChhhHh
Confidence 99999974
No 10
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.98 E-value=1.9e-31 Score=230.93 Aligned_cols=150 Identities=17% Similarity=0.257 Sum_probs=125.0
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCccccccc-----CCCCeeEEEEEEcCCCC-------CCcchh
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQK-----TIIDKASVEVIFRPKSG-------LSFVQD 67 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~-----~~~~~~~v~v~~~p~~g-------~~~~~~ 67 (151)
+||+|++++++|+++++||||+|++|+|+|+|+|+ ||.+..... +...+..++++|.|++. .++.++
T Consensus 317 ~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rre 396 (684)
T TIGR03591 317 LDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRRE 396 (684)
T ss_pred CCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHH
Confidence 58999999999999999999999999999999994 887542211 11224556777777532 233444
Q ss_pred hHHHHHHHHHHHHhhcc-cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC----eEE
Q psy15057 68 RLKESVIKSTCESALLT-MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN----EVI 142 (151)
Q Consensus 68 ~~~~~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~----~~l 142 (151)
...+++++++|+++|+. +.||+ .|+|+++||++|||.++|++||+++||+||||||++.++|+++|++.++ .++
T Consensus 397 i~~~~l~~ral~~~i~~~~~~p~-tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~~~~~il 475 (684)
T TIGR03591 397 IGHGALAERALKAVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVL 475 (684)
T ss_pred HHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCCcceEEE
Confidence 55679999999999986 78995 5999999999999999999999999999999999999999999999533 499
Q ss_pred eCCCccccC
Q psy15057 143 LDANQIQSN 151 (151)
Q Consensus 143 vDpt~~Ee~ 151 (151)
+||+..||.
T Consensus 476 ~D~~~~Ed~ 484 (684)
T TIGR03591 476 SDILGDEDH 484 (684)
T ss_pred eCCChHHHh
Confidence 999999974
No 11
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.98 E-value=2.5e-31 Score=208.55 Aligned_cols=149 Identities=17% Similarity=0.212 Sum_probs=122.3
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEE--EEEcCCC------CCCcchhhHHHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVE--VIFRPKS------GLSFVQDRLKES 72 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~--v~~~p~~------g~~~~~~~~~~~ 72 (151)
++|+|++++++|++++++|||++++|+|+|+|+|+++.. .+..+.+++|.++ +++.|++ |.++..+.++++
T Consensus 31 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~-~p~~~~~~~g~i~~~v~~~~~a~~~~~~~~~~~~~~~l~~ 109 (271)
T PRK04282 31 LDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIG-EPFPDTPNEGVLIVNAELLPLASPTFEPGPPDENAIELAR 109 (271)
T ss_pred CccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEe-cCCCCCCCCCEEEEEEEECCCcCccccCCCCCHHHHHHHH
Confidence 479999999999999999999999999999999996542 2233456666655 4555643 334455667889
Q ss_pred HHHHHHHHh--hcccCC---C---CcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc--------------------c
Q psy15057 73 VIKSTCESA--LLTMLH---P---RTSVILTIQELQDQGSLLSCCINAACLALINSGIS--------------------M 124 (151)
Q Consensus 73 ~l~~~l~~~--i~~~~~---p---~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip--------------------~ 124 (151)
+|+++|++. ++++.+ | .|.|+|+++||++|||+++|+++|+++||.|+++| |
T Consensus 110 ~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~ 189 (271)
T PRK04282 110 VVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLPV 189 (271)
T ss_pred HHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcEEEcCCceeccCCCcccCCC
Confidence 999998875 333322 3 58999999999999999999999999999999995 9
Q ss_pred cceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 125 RYILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 125 ~~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
+++|+++|++++ ++.+|+|||..||+
T Consensus 190 ~~~p~~vt~~~~-~~~~v~Dpt~~Ee~ 215 (271)
T PRK04282 190 NDKPVTVTFAKI-GNYLIVDPTLEEES 215 (271)
T ss_pred CCeeEEEEEEEE-CCEEEECCCHHHHh
Confidence 999999999999 58899999999984
No 12
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.97 E-value=3.2e-30 Score=221.51 Aligned_cols=150 Identities=17% Similarity=0.241 Sum_probs=124.9
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCccccccc-----CCCCeeEEEEEEcCCCC----C---Ccchh
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQK-----TIIDKASVEVIFRPKSG----L---SFVQD 67 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~-----~~~~~~~v~v~~~p~~g----~---~~~~~ 67 (151)
++|+|++.+++|+++++||||+|+.|+|+|+|++. ||.+..... +...+..++++|.|++. + ++.++
T Consensus 342 ~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~er~~~~~~~RRe 421 (719)
T TIGR02696 342 VTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETGRVGSPKRRE 421 (719)
T ss_pred ccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcccCCCCCCCCCccH
Confidence 48999999999999999999999999999999987 454322211 11234557788888642 1 23455
Q ss_pred hHHHHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecC---Ce---
Q psy15057 68 RLKESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDK---NE--- 140 (151)
Q Consensus 68 ~~~~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~---~~--- 140 (151)
.+.+.+++++|+++|+ ++.||++ |+++.+||++||+..+|++||++|||+||||||+++++|+++|++.+ +.
T Consensus 422 ighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgis~Gli~e~~~~~~~~ 500 (719)
T TIGR02696 422 IGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGETRY 500 (719)
T ss_pred HHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEEEEEEeccccCCCcce
Confidence 5678999999999998 6999998 88999999999999999999999999999999999999999999954 33
Q ss_pred -EEeCCCccccC
Q psy15057 141 -VILDANQIQSN 151 (151)
Q Consensus 141 -~lvDpt~~Ee~ 151 (151)
+++||+..|+.
T Consensus 501 ~iL~Di~g~ED~ 512 (719)
T TIGR02696 501 VALTDILGAEDA 512 (719)
T ss_pred eEEeCCCchhhh
Confidence 89999999973
No 13
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.97 E-value=2e-29 Score=220.39 Aligned_cols=150 Identities=18% Similarity=0.294 Sum_probs=125.1
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCccccccc------CCCCeeEEEEEEcCCC----CC---Ccch
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQK------TIIDKASVEVIFRPKS----GL---SFVQ 66 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~------~~~~~~~v~v~~~p~~----g~---~~~~ 66 (151)
++|+|++.+++|.++++||||+|++|+|+|+|+|+ ||.+..... +...+..++++|.|++ ++ ++.+
T Consensus 445 ~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrR 524 (891)
T PLN00207 445 PDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRR 524 (891)
T ss_pred cCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCCCCccccCCCCCCHH
Confidence 48999999999999999999999999999999996 887543221 1223456888888864 22 2334
Q ss_pred hhHHHHHHHHHHHHhhccc-CCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecC-------
Q psy15057 67 DRLKESVIKSTCESALLTM-LHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDK------- 138 (151)
Q Consensus 67 ~~~~~~~l~~~l~~~i~~~-~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~------- 138 (151)
+...+++++|+|++++..+ .|| |.|+|+++||++||+..+|++||+++||+||||||+++++|+++|++.+
T Consensus 525 Ei~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~ 603 (891)
T PLN00207 525 EIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGD 603 (891)
T ss_pred HHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCC
Confidence 4456899999999999985 899 5899999999999999999999999999999999999999999999932
Q ss_pred Ce--EEeCCCccccC
Q psy15057 139 NE--VILDANQIQSN 151 (151)
Q Consensus 139 ~~--~lvDpt~~Ee~ 151 (151)
+. +++||+..|+.
T Consensus 604 g~~~IL~Dp~g~Ed~ 618 (891)
T PLN00207 604 GSPLILSDITGSEDA 618 (891)
T ss_pred CcEEEEeCCCHHHHh
Confidence 24 56799999873
No 14
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.96 E-value=8.7e-29 Score=214.42 Aligned_cols=138 Identities=23% Similarity=0.247 Sum_probs=118.5
Q ss_pred cceEEEecCC-CCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCC--------------CCCCcchhhH
Q psy15057 5 RELKSQLNIL-SRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPK--------------SGLSFVQDRL 69 (151)
Q Consensus 5 R~i~i~~g~~-~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~--------------~g~~~~~~~~ 69 (151)
|++.+++|.+ ++|||||++++|+|+|+|+|+||.++++. .+...++|+|.+. .|+++.++.+
T Consensus 5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~---~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil 81 (684)
T TIGR03591 5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEG---QDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETL 81 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCC---CceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHH
Confidence 7999999999 57999999999999999999999875432 3567788888642 1234455666
Q ss_pred HHHHHHHHHHHhhcccCCCC---cEEEEEEEEEeCCCChh--HHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeC
Q psy15057 70 KESVIKSTCESALLTMLHPR---TSVILTIQELQDQGSLL--SCCINAACLALINSGISMRYILAAVSCIINDKNEVILD 144 (151)
Q Consensus 70 ~~~~l~~~l~~~i~~~~~p~---~~i~i~v~vl~~dG~~l--~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvD 144 (151)
++++|+|+|+++ ||+ |.++|+++||++||+.+ .|++||+++||+++||||+++++|+++|++ +|++++|
T Consensus 82 ~srlIdR~lrpl-----fp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i-dg~~ild 155 (684)
T TIGR03591 82 TSRLIDRPIRPL-----FPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYI-DGQYVLN 155 (684)
T ss_pred HHHHHhhHHHHh-----cCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEEc
Confidence 899999999985 665 89999999999999974 399999999999999999999999999999 5899999
Q ss_pred CCccccC
Q psy15057 145 ANQIQSN 151 (151)
Q Consensus 145 pt~~Ee~ 151 (151)
||..||+
T Consensus 156 Pt~~E~~ 162 (684)
T TIGR03591 156 PTVDELE 162 (684)
T ss_pred CCHHHHh
Confidence 9999874
No 15
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.96 E-value=2.8e-28 Score=211.57 Aligned_cols=142 Identities=22% Similarity=0.196 Sum_probs=119.6
Q ss_pred ccceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCC---C-----------CCCcchhh
Q psy15057 4 LRELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPK---S-----------GLSFVQDR 68 (151)
Q Consensus 4 ~R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~---~-----------g~~~~~~~ 68 (151)
-|++.+++|.++ +|||||++++|+|+|+|+|++|.++++ ..+...++|+|.+. + |+++.++.
T Consensus 13 ~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~~---~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~ei 89 (693)
T PRK11824 13 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKE---GQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKET 89 (693)
T ss_pred CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCC---CCCeeeeEEEEEehhhhccCCCcccccCCCCCChHHH
Confidence 379999999996 699999999999999999999997532 24567788888652 1 23445566
Q ss_pred HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh-hH-HHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057 69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL-LS-CCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN 146 (151)
Q Consensus 69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~-l~-a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt 146 (151)
+++++++|+|++++. ..++|.++|+++||++||+. .+ +++||+++||+++||||+++++|+++|++ +|++++|||
T Consensus 90 l~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i-~g~~ivdPt 166 (693)
T PRK11824 90 LTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYI-DGEFVLNPT 166 (693)
T ss_pred HHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEEcCC
Confidence 679999999999643 23479999999999999976 44 89999999999999999999999999999 589999999
Q ss_pred ccccC
Q psy15057 147 QIQSN 151 (151)
Q Consensus 147 ~~Ee~ 151 (151)
..||+
T Consensus 167 ~~E~~ 171 (693)
T PRK11824 167 VEELE 171 (693)
T ss_pred HHHHh
Confidence 99974
No 16
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=5.4e-28 Score=186.15 Aligned_cols=149 Identities=18% Similarity=0.205 Sum_probs=125.7
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeE--EEEEEcCC------CCCCcchhhHHHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPK------SGLSFVQDRLKES 72 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~------~g~~~~~~~~~~~ 72 (151)
++|+|++++++|+++.++|||+|++|+|+|+|+|+.... +|-.+.|++|. +++++.|. +|++...+-++++
T Consensus 30 ~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig-~Pf~DtP~eG~~~~n~El~Plas~~fE~Gppde~aielsr 108 (272)
T COG2123 30 FDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIG-EPFPDTPNEGVLVVNVELSPLASPSFEPGPPDELAIELSR 108 (272)
T ss_pred cccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccC-CCCCCCCCCceEEeeeeeeccccccccCCCCchhHHHHHH
Confidence 479999999999999999999999999999999998773 44567788874 57777774 4555545556889
Q ss_pred HHHHHHHH--hhcc------cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc---------------------
Q psy15057 73 VIKSTCES--ALLT------MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS--------------------- 123 (151)
Q Consensus 73 ~l~~~l~~--~i~~------~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip--------------------- 123 (151)
.++|.++. .+++ ++...|.+.++++||++|||++||+..|+++||+++++|
T Consensus 109 vvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~~~~~~v~~~~~~~~pl 188 (272)
T COG2123 109 VVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPL 188 (272)
T ss_pred HHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeecCCcceeecccCCCccc
Confidence 99998864 3333 345679999999999999999999999999999999877
Q ss_pred -ccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 124 -MRYILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 124 -~~~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
+.+.+.++|++++ ++.+++|||.+||.
T Consensus 189 ~~~~~pi~vt~a~i-g~~lvvDPsleEe~ 216 (272)
T COG2123 189 PVSNPPISVTFAKI-GNVLVVDPSLEEEL 216 (272)
T ss_pred ccCCCceEEEEEEE-CCEEEeCCCcchhh
Confidence 5788999999999 58999999999983
No 17
>KOG1614|consensus
Probab=99.94 E-value=5.3e-26 Score=172.27 Aligned_cols=147 Identities=16% Similarity=0.205 Sum_probs=123.9
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeE--EEEEEcCCCC------CCcchhhHHHH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPKSG------LSFVQDRLKES 72 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~~g------~~~~~~~~~~~ 72 (151)
++|+|++++++| .-.||+.+++|+|+|+|.|+... .+|..++|.+|. +..+++|.++ +.+..+-++.+
T Consensus 29 l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~~i-a~Py~dRP~eG~~~I~telsPmA~~sfE~Gr~~~~~v~l~R 104 (291)
T KOG1614|consen 29 LEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQI-AQPYIDRPHEGSFSIFTELSPMASPSFEPGRKGESEVELSR 104 (291)
T ss_pred hhhhhceEEEec---cccccEEEEecCeeEEEEeehhh-cCcccCCCCCCeeeeeeccccccccccCCCCccchHHHHHH
Confidence 468999999999 67899999999999999999887 456677888885 5567788644 34445667789
Q ss_pred HHHHHHH--------HhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC-----------------------
Q psy15057 73 VIKSTCE--------SALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG----------------------- 121 (151)
Q Consensus 73 ~l~~~l~--------~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag----------------------- 121 (151)
+|+++++ +++.......|.|++++++|+.|||+.||++.|+++||++.+
T Consensus 105 liek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~ev~ihp~eEr~PvP 184 (291)
T KOG1614|consen 105 LIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGEEVIIHPVEEREPVP 184 (291)
T ss_pred HHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccceeEecChhccCCcc
Confidence 9999874 445555667899999999999999999999999999999999
Q ss_pred ccccceeeEEEEEEecCC-eEEeCCCccccC
Q psy15057 122 ISMRYILAAVSCIINDKN-EVILDANQIQSN 151 (151)
Q Consensus 122 ip~~~~~~avtv~~~~~~-~~lvDpt~~Ee~ 151 (151)
+.|+++|+++|++++.+| .+++|||..||.
T Consensus 185 L~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~ 215 (291)
T KOG1614|consen 185 LSIHHMPICFTFGFFNKGEIVVIDPTEKEEA 215 (291)
T ss_pred eeeeeccceEEEEEecCceEEEeCCcHHHHh
Confidence 558999999999999755 489999999984
No 18
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.91 E-value=6.6e-24 Score=185.98 Aligned_cols=141 Identities=17% Similarity=0.160 Sum_probs=118.5
Q ss_pred cceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---CCC-----------CCcchhhH
Q psy15057 5 RELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---KSG-----------LSFVQDRL 69 (151)
Q Consensus 5 R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~~g-----------~~~~~~~~ 69 (151)
|.+.+++|.+. +|+||+.+++|+|.|+|+|..-.+++ +..+...+.|+|.. .+| +++.+|-.
T Consensus 89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~---~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~eiL 165 (891)
T PLN00207 89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPS---EPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVL 165 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCC---CCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHH
Confidence 47999999998 69999999999999999999755433 22345566777653 122 34555656
Q ss_pred HHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCC--hhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCc
Q psy15057 70 KESVIKSTCESALLTMLHPRTSVILTIQELQDQGS--LLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQ 147 (151)
Q Consensus 70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~--~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~ 147 (151)
++++|+|.|+++++.+.||.++|.+ +||++||+ ...+++|||++||+++||||+++++||++|++ +|++|+|||.
T Consensus 166 ~sRlIdR~lRPlfp~~~~~etQI~i--~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~i-dg~~VlnPt~ 242 (891)
T PLN00207 166 ICRLIDRPLRPTMPKGFYHETQILS--WVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLI-GGKFIVNPTT 242 (891)
T ss_pred HHHHHCccchhhccccCCCCcEEEE--EEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEE-CCEEEECCCH
Confidence 7999999999999999999987755 99999998 67999999999999999999999999999999 6999999999
Q ss_pred cccC
Q psy15057 148 IQSN 151 (151)
Q Consensus 148 ~Ee~ 151 (151)
.|++
T Consensus 243 ~E~~ 246 (891)
T PLN00207 243 KEME 246 (891)
T ss_pred HHHh
Confidence 9863
No 19
>KOG1612|consensus
Probab=99.88 E-value=4.4e-21 Score=146.25 Aligned_cols=147 Identities=14% Similarity=0.132 Sum_probs=113.2
Q ss_pred CCccceEEEecCCCCCCeeEEEEeCC-eEEEEEEEcCcccccccCCCCeeE--EEEEEcCCC-----CCCcch-hhHHHH
Q psy15057 2 DSLRELKSQLNILSRSDGSVIFSQGQ-TVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPKS-----GLSFVQ-DRLKES 72 (151)
Q Consensus 2 ~e~R~i~i~~g~~~~a~GSa~v~~G~-T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~~-----g~~~~~-~~~~~~ 72 (151)
+++|++.++++++++++|||+|++|+ |.|+++|+.... ++..+.|.++. +.|++.|.+ |+.+.+ -.++..
T Consensus 29 ~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg-~~~~~~p~egk~~~~VD~S~sasp~f~gRggde~~~elts 107 (288)
T KOG1612|consen 29 HQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVG-SPDDETPVEGKYLFFVDCSPSASPQFQGRGGDELVEELTS 107 (288)
T ss_pred cccceEEEEeccccCCCCcEEEEecCCceEEEEEeeecc-CccccCCCCCeEEEEEEecCCcCccccCCChhhHHHHHHH
Confidence 58999999999999999999999999 999999999885 45667777665 566666643 232211 123455
Q ss_pred HHHHHHHH---hhcc------cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccc-------------------
Q psy15057 73 VIKSTCES---ALLT------MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISM------------------- 124 (151)
Q Consensus 73 ~l~~~l~~---~i~~------~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~------------------- 124 (151)
.|+++|.+ -+++ +. -+|.|+|++.|++.|||+++|+..|+.+||.+..+|-
T Consensus 108 aLq~~l~~~~sgv~ls~L~lt~~-~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~~i~~s~~~ 186 (288)
T KOG1612|consen 108 ALQRVLNSLGSGVDLSKLQLTPG-YCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFDDDGEVEILLSDEE 186 (288)
T ss_pred HHHHHHhCcCcccchhheeccCC-eeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCccccccccCCceeeccCccc
Confidence 55666554 1111 22 3799999999999999999999999999999998883
Q ss_pred --------cceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 125 --------RYILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 125 --------~~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
..+|.=+++..+ +..++||||.+||.
T Consensus 187 Yd~~~~~~~~~P~ivtlskI-G~~~lVD~T~eEe~ 220 (288)
T KOG1612|consen 187 YDLMVKLVENVPLIVTLSKI-GTNMLVDPTAEEES 220 (288)
T ss_pred chhhhhhcccCCEEEEEEee-cceEEccCCccHHH
Confidence 235667788888 57899999999984
No 20
>KOG1067|consensus
Probab=99.75 E-value=5.8e-18 Score=140.97 Aligned_cols=135 Identities=21% Similarity=0.303 Sum_probs=112.8
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEc-Ccccccc-c--CCCC---eeEEEEEEcCCC----CC-Ccchhh
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYG-PVEAKIQ-K--TIID---KASVEVIFRPKS----GL-SFVQDR 68 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~g-p~~~~~~-~--~~~~---~~~v~v~~~p~~----g~-~~~~~~ 68 (151)
+||+|+|.|+.+.++..|||++|+.|+|+|+|+|+- ..+...+ + ..++ +..++++|.|.+ |+ .+..+|
T Consensus 365 ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nRR 444 (760)
T KOG1067|consen 365 LDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRR 444 (760)
T ss_pred hhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCccccccccccCCccc
Confidence 589999999999999999999999999999999984 3333222 1 1222 457899998853 33 234566
Q ss_pred HH--HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEec
Q psy15057 69 LK--ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIIND 137 (151)
Q Consensus 69 ~~--~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~ 137 (151)
++ ..+-+++|.+++. +.||. .|++.-.|+++||+--.|.++.-++||+|||+|++.-++++++|++.
T Consensus 445 E~GhgaLAEkaL~~vlP-~dfPf-tIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt 513 (760)
T KOG1067|consen 445 ELGHGALAEKALLPVLP-EDFPF-TIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVT 513 (760)
T ss_pred ccCchhHhhhhhhccCc-ccCce-EEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEEEeEe
Confidence 76 5888999999998 78996 69999999999999999999999999999999999999999999985
No 21
>KOG1613|consensus
Probab=99.74 E-value=9.6e-18 Score=127.36 Aligned_cols=121 Identities=17% Similarity=0.250 Sum_probs=97.8
Q ss_pred CCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cC------CCCCCcchhhHHHHH
Q psy15057 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RP------KSGLSFVQDRLKESV 73 (151)
Q Consensus 2 ~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p------~~g~~~~~~~~~~~~ 73 (151)
.|+|.+.++.|.++.+|||+.++.|+|.|+|++++..- .|....|+++.|-.+| .| ..|+++..+..+++.
T Consensus 44 gefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~-epstdapdeg~Iv~n~~lpplcs~r~RpG~p~dea~viSq~ 122 (298)
T KOG1613|consen 44 GEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIA-EPSTDAPDEGDIVPNYALPPLCSSRFRPGPPTDEAQVISQK 122 (298)
T ss_pred hHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeec-ccccCCCCCcceeecccCCcccccCCCCCCCchHHHHHHHH
Confidence 47899999999999999999999999999999999883 4556778888775555 34 256666677777877
Q ss_pred HHHHHHH--hhcc------cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc
Q psy15057 74 IKSTCES--ALLT------MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123 (151)
Q Consensus 74 l~~~l~~--~i~~------~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip 123 (151)
|..++.+ +|++ ...-.|.++.++.+|+.||+++|+|.||.++||.+-.+|
T Consensus 123 LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP 180 (298)
T KOG1613|consen 123 LHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLP 180 (298)
T ss_pred HHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCc
Confidence 7776654 3333 233358899999999999999999999999999988777
No 22
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.72 E-value=1e-16 Score=138.56 Aligned_cols=140 Identities=16% Similarity=0.168 Sum_probs=112.1
Q ss_pred cceEEEecCCC-CCCeeEEEEe-CCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---CC-----------CCCcchhh
Q psy15057 5 RELKSQLNILS-RSDGSVIFSQ-GQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---KS-----------GLSFVQDR 68 (151)
Q Consensus 5 R~i~i~~g~~~-~a~GSa~v~~-G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~~-----------g~~~~~~~ 68 (151)
|.+.+++|.+. +|+||+.+++ |+|.|+|++..-.+++ +..+...+.|+|+. .+ |+|+.+|-
T Consensus 17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~---~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~ei 93 (719)
T TIGR02696 17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPK---DQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAI 93 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCC---CCCCCcceeEeeeehhhhcCccCCceeccCCCCChhhh
Confidence 37999999998 6999999999 9999999999655433 22345566777753 12 23455555
Q ss_pred HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCC--hhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057 69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGS--LLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN 146 (151)
Q Consensus 69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~--~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt 146 (151)
..+++++|.++|++.... +..++|.++||+.|+. .--.++|||++||.-++||+.+.++||.+|.+ +|+++++||
T Consensus 94 L~sRliDR~iRPLFp~~~--~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i-~g~~viNPt 170 (719)
T TIGR02696 94 LTCRLIDRPLRPSFVKGL--RNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALI-DGQWVAFPT 170 (719)
T ss_pred HHHHhhCCCCccCCCCCC--CcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEE-CCEEEECcC
Confidence 669999999998776543 3468888999998875 56778999999999999999999999999999 599999999
Q ss_pred cccc
Q psy15057 147 QIQS 150 (151)
Q Consensus 147 ~~Ee 150 (151)
..|-
T Consensus 171 ~~~~ 174 (719)
T TIGR02696 171 HEQL 174 (719)
T ss_pred HHHH
Confidence 8763
No 23
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.64 E-value=4.2e-16 Score=132.74 Aligned_cols=148 Identities=19% Similarity=0.291 Sum_probs=120.5
Q ss_pred CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCc-cccccc----CCCCeeEEEEEEcCCC-C---C-CcchhhH
Q psy15057 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPV-EAKIQK----TIIDKASVEVIFRPKS-G---L-SFVQDRL 69 (151)
Q Consensus 1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~-~~~~~~----~~~~~~~v~v~~~p~~-g---~-~~~~~~~ 69 (151)
.++.|++.++.|+++++|||++|..|+|+.++.++ |+. +.+.-+ +...+..++++|.|++ | + ..+.+|+
T Consensus 319 ~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RRE 398 (692)
T COG1185 319 GDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRRE 398 (692)
T ss_pred cceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccCCCCCCCccc
Confidence 37899999999999999999999999999999997 543 333222 2234567899999975 3 2 2344556
Q ss_pred H--HHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057 70 K--ESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL 143 (151)
Q Consensus 70 ~--~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv 143 (151)
+ ..+-+|++.+++. .+.||. .|++.-.|++++|+--.|.+++.+|||+|||+|++..++++..|++.++ .++-
T Consensus 399 iGHG~LA~Ral~~vlp~~e~fpy-tiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~~~~vLs 477 (692)
T COG1185 399 IGHGALAERALAPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLS 477 (692)
T ss_pred ccCchhhHHHHhhhCCchhcCCc-eeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhccceecCCceEeec
Confidence 5 6888999999998 578997 6999999999999999999999999999999999999999999999653 2666
Q ss_pred CCCccc
Q psy15057 144 DANQIQ 149 (151)
Q Consensus 144 Dpt~~E 149 (151)
|-...|
T Consensus 478 DI~G~E 483 (692)
T COG1185 478 DILGDE 483 (692)
T ss_pred cccccc
Confidence 666555
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.62 E-value=6.9e-15 Score=125.39 Aligned_cols=139 Identities=19% Similarity=0.173 Sum_probs=112.7
Q ss_pred cceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---C-----------CCCCcchhhH
Q psy15057 5 RELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---K-----------SGLSFVQDRL 69 (151)
Q Consensus 5 R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~-----------~g~~~~~~~~ 69 (151)
|.+.+++|.+. +|+|++++++|+|.|++++.+.. ++ +..+...+.|+|.- . -|+|+.++..
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~---~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~L 89 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PK---EGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEIL 89 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CC---CCCCccceeEeeeeehhccCcCCCcccccCCCCCccchh
Confidence 89999999998 79999999999999999999876 32 22344555565542 1 2345556666
Q ss_pred HHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCc
Q psy15057 70 KESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQ 147 (151)
Q Consensus 70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~ 147 (151)
.+++++|-+++++.... +..++|..+|++.|+.. .-.+++++++||.-++||+...++++.+|++ ||+++++||.
T Consensus 90 ~sRLIDRpiRPlFp~g~--~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~i-dg~~vlNPt~ 166 (692)
T COG1185 90 TSRLIDRPIRPLFPKGF--RNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYI-DGIFVLNPTL 166 (692)
T ss_pred hhhhcccccccccchhh--ccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEE-CCEEEECCCh
Confidence 79999999998665432 45689999999999864 5678999999999999999999999999999 6999999998
Q ss_pred ccc
Q psy15057 148 IQS 150 (151)
Q Consensus 148 ~Ee 150 (151)
.|.
T Consensus 167 ~e~ 169 (692)
T COG1185 167 EEL 169 (692)
T ss_pred HHh
Confidence 764
No 25
>KOG1067|consensus
Probab=99.39 E-value=3.8e-13 Score=112.56 Aligned_cols=140 Identities=19% Similarity=0.177 Sum_probs=108.4
Q ss_pred ccceEEEecCCCC-CCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---CCCC---------CcchhhHH
Q psy15057 4 LRELKSQLNILSR-SDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---KSGL---------SFVQDRLK 70 (151)
Q Consensus 4 ~R~i~i~~g~~~~-a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~~g~---------~~~~~~~~ 70 (151)
-|.+.+++|.+.+ |+||+.+..|+|.|+++|..-..+.+. +...+.|.|.- ..|+ .+.++|++
T Consensus 55 nR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp~----qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdkEi 130 (760)
T KOG1067|consen 55 NREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPP----QFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKEI 130 (760)
T ss_pred CeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCcc----ccceEEEehhhhhhhhccCCCcccccccCCcchhh
Confidence 4899999999995 999999999999999999875543332 34556666653 2232 12334443
Q ss_pred --HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCC--hhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057 71 --ESVIKSTCESALLTMLHPRTSVILTIQELQDQGS--LLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN 146 (151)
Q Consensus 71 --~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~--~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt 146 (151)
.+++++.+++......| +..++-..+|..||- .-.-++|++++||.-+.|||...+.++.+|++ +|+++|+||
T Consensus 131 L~~rLidrsirplfp~g~~--~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi-~Ge~vVNPT 207 (760)
T KOG1067|consen 131 LTGRLIDRPIRPLFPKGFY--HETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLI-DGEFVVNPT 207 (760)
T ss_pred eeeeccccccccCCcccch--hHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeee-cceEEeCcc
Confidence 78888888876655443 455677888999984 34567899999999999999999999999999 699999999
Q ss_pred cccc
Q psy15057 147 QIQS 150 (151)
Q Consensus 147 ~~Ee 150 (151)
.+|.
T Consensus 208 ~kEm 211 (760)
T KOG1067|consen 208 RKEM 211 (760)
T ss_pred hhhh
Confidence 9985
No 26
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=97.51 E-value=8.4e-05 Score=46.23 Aligned_cols=25 Identities=20% Similarity=0.175 Sum_probs=20.3
Q ss_pred ceeeEEEEEEecCCeEEeCCCccccC
Q psy15057 126 YILAAVSCIINDKNEVILDANQIQSN 151 (151)
Q Consensus 126 ~~~~avtv~~~~~~~~lvDpt~~Ee~ 151 (151)
++|+++|++++ ++++++|||.+||+
T Consensus 1 ~~~~avt~~~i-~~~~v~Dpt~~Ee~ 25 (68)
T PF03725_consen 1 DPPVAVTVGII-DGELVVDPTAEEES 25 (68)
T ss_dssp SEEEEEEEEEE-TTEEEES--HHHHH
T ss_pred CCeEEEEEEEE-CCEEEECCCHHHHh
Confidence 57899999999 58899999999973
No 27
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=78.63 E-value=17 Score=25.45 Aligned_cols=63 Identities=13% Similarity=0.101 Sum_probs=41.2
Q ss_pred CCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHhhccc-CCCCcEEEEEEEEEeCCCChhH
Q psy15057 45 TIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTM-LHPRTSVILTIQELQDQGSLLS 107 (151)
Q Consensus 45 ~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~i~~~-~~p~~~i~i~v~vl~~dG~~l~ 107 (151)
..++.++|+++++-.+|++....+.++..|-.+++..+... ..+..++.+.+.-++..++..-
T Consensus 55 g~~~~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l~~~~~~~~~~~~~~LS~Ei~d~d~~~s~k~ 118 (126)
T PRK15031 55 GKHDYAFVHMTLKIGAGRSLESRQEVGEMLFALIKAHFAALMESRYLALSFEIEELHPTLNFKQ 118 (126)
T ss_pred CCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHhhhhhcccceEEEEEEEEcCCccChhh
Confidence 44567899999998899877777777777766666544332 2233556666666656665443
No 28
>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=78.58 E-value=8.3 Score=26.92 Aligned_cols=57 Identities=19% Similarity=0.150 Sum_probs=37.5
Q ss_pred CCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCC
Q psy15057 45 TIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQ 102 (151)
Q Consensus 45 ~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~d 102 (151)
..++.++|++.++-.+|++....+.++..|-.+++.-+ ...+.+..+.+.++|.+-|
T Consensus 54 g~~~~~FvHv~l~il~GRs~e~k~~l~~~l~~~l~~~~-~~~~~~~~~~LsvEi~E~~ 110 (124)
T PF02962_consen 54 GQPDDAFVHVTLRILAGRSEEQKKALSEALLAVLKAHL-APLFAQRYLQLSVEIREMD 110 (124)
T ss_dssp SSS-EEEEEEEEEEETT--HHHHHHHHHHHHHHHHHHC-CCHCCHSEEEEEEEEEEE-
T ss_pred CCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHh-hHhhcCCeeEEEEEEEEcC
Confidence 34578999999998899877777788888877777653 2334444566666666644
No 29
>PF07451 SpoVAD: Stage V sporulation protein AD (SpoVAD); InterPro: IPR010894 This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation [].; PDB: 3LMA_D 3LM6_A.
Probab=57.10 E-value=2.9 Score=33.84 Aligned_cols=89 Identities=20% Similarity=0.183 Sum_probs=42.8
Q ss_pred EEEEcCcccccccCCCCeeEEEEEEcC-CCCCCcchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHH
Q psy15057 32 ASMYGPVEAKIQKTIIDKASVEVIFRP-KSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110 (151)
Q Consensus 32 ~~V~gp~~~~~~~~~~~~~~v~v~~~p-~~g~~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~i 110 (151)
++|-||+|... |-...++..+.. ..|.. .-|+.-.++++++++.++.........|++.+- |.++.-+
T Consensus 17 asvvGpkEg~G----PL~~~FD~~~~D~~~Ge~-swEkAE~~m~~~A~~~al~Ka~l~~~dId~~~a-----GDLlnQ~- 85 (329)
T PF07451_consen 17 ASVVGPKEGEG----PLGDYFDKIYEDDYFGEK-SWEKAESKMQKEAVELALKKAGLKKEDIDYLFA-----GDLLNQI- 85 (329)
T ss_dssp EEEE-HHHHCS----TTGGGSSEE-SSTTTTSS-SHHHHHHHHHHHHHHHHHHHTT--GGG-SEEEE-----EETTCCC-
T ss_pred EEEECCccccC----CChhhCCccccccccCcc-cHHHHHHHHHHHHHHHHHHHcCCCHHHCeEEEe-----hhhhhhh-
Confidence 46678887432 333334444443 45543 234455667777777777666666666665442 4444333
Q ss_pred HHHHHHHHhcCccccceeeEE
Q psy15057 111 NAACLALINSGISMRYILAAV 131 (151)
Q Consensus 111 naa~lAL~~agip~~~~~~av 131 (151)
.++..++.+.+||+.++..||
T Consensus 86 i~s~f~ar~l~iPf~GlygAC 106 (329)
T PF07451_consen 86 ISSSFAARDLGIPFLGLYGAC 106 (329)
T ss_dssp CHHHHHHHHHT--EEEB--CC
T ss_pred HHHHHHHHhcCCCccchhhHH
Confidence 444555566666665554443
No 30
>PRK12404 stage V sporulation protein AD; Provisional
Probab=51.99 E-value=22 Score=29.11 Aligned_cols=89 Identities=16% Similarity=0.181 Sum_probs=44.2
Q ss_pred EEEEcCcccccccCCCCeeEEEEEEcC-CCCCCcchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCC-CChhHHH
Q psy15057 32 ASMYGPVEAKIQKTIIDKASVEVIFRP-KSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQ-GSLLSCC 109 (151)
Q Consensus 32 ~~V~gp~~~~~~~~~~~~~~v~v~~~p-~~g~~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~d-G~~l~a~ 109 (151)
++|-||+|.. .|-...++..+.. ..|. ..-|+....++..+++.++.........|+.. +.-+- +-...+
T Consensus 20 ~~v~G~~E~~----Gpl~~~FD~~~~d~~~g~-~swEkAE~~L~~EA~~~AL~kAGI~~~DID~i--~vGdL~nQ~ips- 91 (334)
T PRK12404 20 GVVGGPFEAK----GPLAEDFDLLHEDLWLGQ-DSYEKAERKLLEEACSRAIEKAKLRKEDIQFF--LAGDLMNQITPT- 91 (334)
T ss_pred EEEeCCcccC----CCChhhCCeeecccccCC-cchHHHHHHHHHHHHHHHHHHcCCCHHHCCEE--EEEecCCCcCcH-
Confidence 4667998743 2333445555443 3443 23355556666777776665544433334432 22211 111222
Q ss_pred HHHHHHHHHhcCccccceeeEEE
Q psy15057 110 INAACLALINSGISMRYILAAVS 132 (151)
Q Consensus 110 inaa~lAL~~agip~~~~~~avt 132 (151)
..+.-+.|||..++..||+
T Consensus 92 ----sfvar~LGIP~~gV~gACS 110 (334)
T PRK12404 92 ----SFAARTLGIPYLGLFGACS 110 (334)
T ss_pred ----HHHHHHhCCCccceeecCH
Confidence 2455666777766655544
No 31
>TIGR02845 spore_V_AD stage V sporulation protein AD. Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation.
Probab=45.57 E-value=37 Score=27.75 Aligned_cols=57 Identities=14% Similarity=0.130 Sum_probs=25.9
Q ss_pred EEEEcCcccccccCCCCeeEEEEEEcC-CCCCCcchhhHHHHHHHHHHHHhhcccCCCCcEEE
Q psy15057 32 ASMYGPVEAKIQKTIIDKASVEVIFRP-KSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVI 93 (151)
Q Consensus 32 ~~V~gp~~~~~~~~~~~~~~v~v~~~p-~~g~~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~ 93 (151)
++|-||+|... |-...++..+.. ..|..+ .|+....+..++.+.++.........|+
T Consensus 16 ~~~~g~~e~~g----pl~~~fd~~~~d~~~g~ks-~EkAe~eLa~eAa~~ALekAGL~~~DID 73 (327)
T TIGR02845 16 GTAVGPKEGEG----PLGDYFDKIYDDLYCGEDS-WEKAERKLMEDAVNLALKKANLKKDDVD 73 (327)
T ss_pred EEEecCccccC----CChhhCCEEEeccccCCcC-cchhHHHHHHHHHHHHHHHcCCCHHHCC
Confidence 56779987532 333334444432 344422 2333344555555555543333333333
No 32
>PF03727 Hexokinase_2: Hexokinase; InterPro: IPR022673 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways []. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains []. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. Hexokinase (2.7.1.1 from EC), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and PF00349 from PFAM. Some members of the family have two copies of each of these domains. This entry represents the more C-terminal domain.; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 4DHY_A 3ID8_A 4DCH_A 3FGU_A 3QIC_A 3A0I_X 3VEY_A 3IDH_A 3VEV_A 3VF6_A ....
Probab=40.84 E-value=85 Score=24.10 Aligned_cols=41 Identities=17% Similarity=0.141 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHH
Q psy15057 69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACL 115 (151)
Q Consensus 69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~l 115 (151)
.+...+++.+..++..+ .. +|.+ ++.+||+..-|++.|+.+
T Consensus 201 ~f~~~l~~~l~~L~~~~---~~--~v~~-~~~~dgsg~GAAi~AA~a 241 (243)
T PF03727_consen 201 NFRERLQEALDELLPEE---GC--KVEF-VLSEDGSGVGAAIAAAVA 241 (243)
T ss_dssp THHHHHHHHHHHHSTT----CE--EEEE-EE-SSTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcccc---cc--eEEE-EEecCchHHHHHHHHHHh
Confidence 45667777777655433 22 3333 577999999999988865
No 33
>PRK08304 stage V sporulation protein AD; Validated
Probab=36.94 E-value=49 Score=27.15 Aligned_cols=70 Identities=11% Similarity=0.153 Sum_probs=31.6
Q ss_pred eeEEEEeCC-eEE--EEEEEcCcccccccCCCCeeEEEEEEcC-CCCCCcchhhHHHHHHHHHHHHhhcccCCCCcEEE
Q psy15057 19 GSVIFSQGQ-TVV--VASMYGPVEAKIQKTIIDKASVEVIFRP-KSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVI 93 (151)
Q Consensus 19 GSa~v~~G~-T~V--~~~V~gp~~~~~~~~~~~~~~v~v~~~p-~~g~~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~ 93 (151)
|.-.|.+.+ -.| .++|-||+|.. .|-...++..+.. ..|..+ -|+....+..++.+.++.........|+
T Consensus 6 g~qt~~f~~~p~i~~~~~~~g~~E~~----gpl~~~fd~~~~d~~~Ge~s-wEkAeseLa~eAa~~ALekAGI~~~DID 79 (337)
T PRK08304 6 GKQTWVFENPPYIISTGTIVGPKEGE----GPLGKYFDKILDDDYCGEKS-WEKAERKMMEDAIQQALQKANLKKSDID 79 (337)
T ss_pred CcEEEEecCCCEEEEEEEEecCcccC----CCChhhCCeEecccccCCcC-ccccHHHHHHHHHHHHHHHcCCCHHHCC
Confidence 455566655 222 34567998743 2333344444433 233221 2333344555555555544333333333
No 34
>cd07207 Pat_ExoU_VipD_like ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa enzyme, is a potent virulence factor of Pseudomonas aeruginosa. One of the pathogenic mechanisms of P. aeruginosa is to induce cytotoxicity by the injection of effector proteins (e.g. ExoU) using the type III secretion (T3S) system. ExoU is homologus to patatin and also has the conserved catalytic residues of mammalian calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2. In vitro, ExoU cytotoxity is blocked by the inhibitor of cytosolic and Ca2-independent phospholipase A2 (cPLA2 and iPLA2) enzymes, suggesting that phospholipase A2 inhibitors may represent a novel mode of treatment for acute P. aeruginosa infections. ExoU requires eukaryotic superoxide dismutase as a cofactor and cleaves phosphatidylcholine and phosphatidylethanolamine in vitro. VipD, a 69-kDa cytosolic protein, belongs to the members of Legionella pneumophila family and is homologus to ExoU from Pseudomona
Probab=34.39 E-value=36 Score=24.65 Aligned_cols=34 Identities=24% Similarity=0.114 Sum_probs=25.5
Q ss_pred CCCChhHHHHHHHHHHHHhcCccccceeeEEEEEE
Q psy15057 101 DQGSLLSCCINAACLALINSGISMRYILAAVSCII 135 (151)
Q Consensus 101 ~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~ 135 (151)
+.|+...+.-..+.-||.+.|++. ++++++|.|-
T Consensus 5 ~GGG~rG~~~~Gvl~~L~e~~~~~-d~i~GtSaGa 38 (194)
T cd07207 5 EGGGAKGIAYIGALKALEEAGILK-KRVAGTSAGA 38 (194)
T ss_pred cCchHHHHHHHHHHHHHHHcCCCc-ceEEEECHHH
Confidence 456677777778888888888876 7778877763
No 35
>cd07198 Patatin Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes PNPLA (1-9), TGL (3-5), ExoU-like, and SDP1-like subfamilies. There are some additional hypothetical proteins included in this family.
Probab=33.77 E-value=39 Score=24.22 Aligned_cols=35 Identities=23% Similarity=0.082 Sum_probs=28.0
Q ss_pred CCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEe
Q psy15057 101 DQGSLLSCCINAACLALINSGISMRYILAAVSCIIN 136 (151)
Q Consensus 101 ~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~ 136 (151)
+.|+.+.+.-..+.-||.+.|+. .+.++++|.|-+
T Consensus 4 ~GGG~rG~~~~Gvl~aL~e~gi~-~d~v~GtSaGAi 38 (172)
T cd07198 4 SGGGALGIYHVGVAKALRERGPL-IDIIAGTSAGAI 38 (172)
T ss_pred CCcHHHHHHHHHHHHHHHHcCCC-CCEEEEECHHHH
Confidence 45677888888999999999998 777788887743
No 36
>PRK05463 hypothetical protein; Provisional
Probab=32.91 E-value=19 Score=28.43 Aligned_cols=27 Identities=22% Similarity=0.198 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCccccceeeEEEEEEec
Q psy15057 111 NAACLALINSGISMRYILAAVSCIIND 137 (151)
Q Consensus 111 naa~lAL~~agip~~~~~~avtv~~~~ 137 (151)
-+-=-||+.+|||++++--+..+.+++
T Consensus 119 FSFE~AL~~aGip~Rhi~~g~nVpMYr 145 (262)
T PRK05463 119 FSFEHALLEAGIPVRHIEEGRNVPMYR 145 (262)
T ss_pred CcHHHHHHHCCCCcccccCCCccCcEe
Confidence 344468999999999998888888875
No 37
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=32.36 E-value=1.5e+02 Score=19.53 Aligned_cols=55 Identities=15% Similarity=0.030 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHH-hhcccCCCCcEEEEEEEEEeCCCCh--------hHHHHHHHHHHHHh-cCccc
Q psy15057 69 LKESVIKSTCES-ALLTMLHPRTSVILTIQELQDQGSL--------LSCCINAACLALIN-SGISM 124 (151)
Q Consensus 69 ~~~~~l~~~l~~-~i~~~~~p~~~i~i~v~vl~~dG~~--------l~a~inaa~lAL~~-agip~ 124 (151)
.+...++..+++ +...+.|......+.+. |..||.+ -.+.+.|+..|+.. +.+|+
T Consensus 15 ~Y~~~I~~~Iq~~l~~~~~y~GK~C~v~i~-l~~dG~v~~v~~~~GD~~lC~aa~~Ai~k~~~~P~ 79 (96)
T PF06519_consen 15 RYAAQIKQAIQRNLYDDESYKGKECRVRIR-LAPDGLVLSVTVESGDPALCRAAKSAIAKAAKFPP 79 (96)
T ss_dssp HHHHHHHHHHHTTTTTGGGGTT--EEEEEE-EETTSEEEEEEEEEE-HHHHHHHHHH-HCCS----
T ss_pred HHHHHHHHHHHHhcCCccccCCCEEEEEEE-ECCCCcEEEeeecCCCHHHHHHHHHHHHHhcCCCC
Confidence 456677777766 44446677666666665 5556532 34666777777555 45764
No 38
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=31.33 E-value=1.5e+02 Score=23.45 Aligned_cols=55 Identities=20% Similarity=0.246 Sum_probs=41.5
Q ss_pred EEEEEEEeCCCCh----hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcc
Q psy15057 93 ILTIQELQDQGSL----LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQI 148 (151)
Q Consensus 93 ~i~v~vl~~dG~~----l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~ 148 (151)
...|.|++..||+ ..++.-.+.+.|+.--..+++-++=++|-=. +-+++++||+.
T Consensus 79 ~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G~-~A~lll~pT~s 137 (261)
T COG1240 79 NLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRGE-KAELLLPPTSS 137 (261)
T ss_pred CcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecCC-cceEEeCCccc
Confidence 4668899999986 3567788888999988999998765444332 35799999975
No 39
>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=30.64 E-value=1.7e+02 Score=19.53 Aligned_cols=52 Identities=17% Similarity=0.196 Sum_probs=30.8
Q ss_pred CeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEe
Q psy15057 48 DKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQ 100 (151)
Q Consensus 48 ~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~ 100 (151)
+...|.+.++-..|++..+.+.+.+.|...|...+....- .-.+.+.|.+.+
T Consensus 57 ~~~fi~i~i~l~~GRs~eqK~~l~~~i~~~l~~~~~~~~~-~~~~~~svei~e 108 (113)
T cd00580 57 DDAFIHVTLRILAGRSEEQKQELSEALLAALRAHLAPVFA-KRYLSLSVEIRE 108 (113)
T ss_pred CCcEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHhhhhhhh-ccceEEEEEEEe
Confidence 5678888888778876566666766666666655533211 112445555544
No 40
>PF03764 EFG_IV: Elongation factor G, domain IV; InterPro: IPR005517 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3J0E_H 1FNM_A 3IZP_E 2OM7_L 1KTV_A 2J7K_A 2BM1_A 2BM0_A 2BV3_A 1ZM3_E ....
Probab=28.30 E-value=1.8e+02 Score=19.26 Aligned_cols=55 Identities=24% Similarity=0.212 Sum_probs=36.1
Q ss_pred hhHHHHHHHHHHHHhhcc---cCCCCcEEEEEEEEEeCC------CChhHHHHHHHHHHHHhcC
Q psy15057 67 DRLKESVIKSTCESALLT---MLHPRTSVILTIQELQDQ------GSLLSCCINAACLALINSG 121 (151)
Q Consensus 67 ~~~~~~~l~~~l~~~i~~---~~~p~~~i~i~v~vl~~d------G~~l~a~inaa~lAL~~ag 121 (151)
.+++...|.+.++..+.. -.||-..+.|.++=.+.. +.+..|+-+|..-||..|+
T Consensus 57 ~~~~~~ai~~G~~~a~~~Gpl~g~pv~~v~v~l~~~~~~~~~s~~~a~~~aa~~a~~~al~~A~ 120 (120)
T PF03764_consen 57 PKEFQDAIEEGFQSALSSGPLCGYPVTDVKVTLTDGEYHEVDSSPGAFRAAARRAFREALKKAG 120 (120)
T ss_dssp GGGGHHHHHHHHHHHHCSSTTTSSEB-SEEEEEEEEEC-TTTBSHHHHHHHHHHHHHHHHHHS-
T ss_pred cHHHHHHHhhhhhheecccccCCCceEEEEEEEEEeeecCCcCCHHHHHHHHHHHHHHHHHhcC
Confidence 345667777777776643 458887787777666632 2367788888888887765
No 41
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=28.11 E-value=59 Score=23.03 Aligned_cols=28 Identities=14% Similarity=0.199 Sum_probs=19.4
Q ss_pred hcCccccceeeEEEEEEecCCeEEeCCCccc
Q psy15057 119 NSGISMRYILAAVSCIINDKNEVILDANQIQ 149 (151)
Q Consensus 119 ~agip~~~~~~avtv~~~~~~~~lvDpt~~E 149 (151)
..-.|++|.++ ++...+-++++|||..+
T Consensus 38 ~~~~p~NH~vv---~~k~~g~eyV~D~Ta~Q 65 (135)
T PF15645_consen 38 NDDSPTNHFVV---VAKKNGKEYVFDPTAHQ 65 (135)
T ss_pred CccCCcceEEE---EEEECCEEEEEeCcHHH
Confidence 45578888743 45565567999999753
No 42
>cd07227 Pat_Fungal_NTE1 Fungal patatin-like phospholipase domain containing protein 6. These are fungal Neuropathy Target Esterase (NTE), commonly referred to as NTE1. Patatin-like phospholipase. NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. This family includes NTE1 from fungi.
Probab=25.20 E-value=68 Score=25.28 Aligned_cols=36 Identities=17% Similarity=-0.013 Sum_probs=29.7
Q ss_pred eCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEe
Q psy15057 100 QDQGSLLSCCINAACLALINSGISMRYILAAVSCIIN 136 (151)
Q Consensus 100 ~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~ 136 (151)
=..|+...++-..+.-||...||| -+.++++|.|-+
T Consensus 15 L~GGGaRG~ahiGVL~aLeE~gi~-~d~v~GtSaGAi 50 (269)
T cd07227 15 LGGGGARGISHIGILQALEEAGIP-IDAIGGTSIGSF 50 (269)
T ss_pred ECCcHHHHHHHHHHHHHHHHcCCC-ccEEEEECHHHH
Confidence 356778999999999999999999 577788888744
No 43
>PF14113 DUF4285: Domain of unknown function (DUF4285)
Probab=23.55 E-value=76 Score=21.59 Aligned_cols=22 Identities=27% Similarity=0.375 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHhcCcccccee
Q psy15057 107 SCCINAACLALINSGISMRYIL 128 (151)
Q Consensus 107 ~a~inaa~lAL~~agip~~~~~ 128 (151)
.+|..=++.||..+|+||+...
T Consensus 5 N~CAiRmS~aL~~~G~~i~~~~ 26 (115)
T PF14113_consen 5 NTCAIRMSYALNYSGIPIKSFS 26 (115)
T ss_pred chhHHHHHHHHHhCCCccCccc
Confidence 4567778999999999998876
No 44
>KOG3129|consensus
Probab=21.45 E-value=65 Score=24.79 Aligned_cols=16 Identities=13% Similarity=0.098 Sum_probs=12.5
Q ss_pred HhhcccCCCCcEEEEE
Q psy15057 80 SALLTMLHPRTSVILT 95 (151)
Q Consensus 80 ~~i~~~~~p~~~i~i~ 95 (151)
++++-+.|||+.|+|.
T Consensus 54 pLvd~eGfPRsDIDV~ 69 (231)
T KOG3129|consen 54 PLVDAEGFPRSDIDVY 69 (231)
T ss_pred cccCCCCCccccccHH
Confidence 4667789999988764
No 45
>KOG2925|consensus
Probab=21.44 E-value=85 Score=22.81 Aligned_cols=19 Identities=21% Similarity=0.186 Sum_probs=14.4
Q ss_pred EEEEecCCeEEeCCCcccc
Q psy15057 132 SCIINDKNEVILDANQIQS 150 (151)
Q Consensus 132 tv~~~~~~~~lvDpt~~Ee 150 (151)
++.+-+++.+||||+.+|+
T Consensus 58 siWiRRg~FvvVdpiee~~ 76 (167)
T KOG2925|consen 58 SIWIRRGSFVVVDPIEEEK 76 (167)
T ss_pred ceEEeeCCEEEEccccccc
Confidence 3456667889999998865
No 46
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.13 E-value=86 Score=19.61 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=17.3
Q ss_pred CCCeeEEEEeCCeEEEEEEEcCc
Q psy15057 16 RSDGSVIFSQGQTVVVASMYGPV 38 (151)
Q Consensus 16 ~a~GSa~v~~G~T~V~~~V~gp~ 38 (151)
--||--.+-.-...|+|.|+|..
T Consensus 17 yldgdf~vv~~GsfV~CAVtgk~ 39 (77)
T COG3908 17 YLDGDFQVVSPGSFVLCAVTGKP 39 (77)
T ss_pred EecCceEEEcCCcEEEEEecCCc
Confidence 34677777777889999999843
No 47
>PRK10279 hypothetical protein; Provisional
Probab=20.75 E-value=93 Score=24.91 Aligned_cols=37 Identities=22% Similarity=0.073 Sum_probs=29.5
Q ss_pred EeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEe
Q psy15057 99 LQDQGSLLSCCINAACLALINSGISMRYILAAVSCIIN 136 (151)
Q Consensus 99 l~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~ 136 (151)
.=..|+...++-..+.-||...||+. +.++++|+|-+
T Consensus 9 vL~GGGarG~ahiGVL~aL~E~gi~~-d~i~GtS~GAl 45 (300)
T PRK10279 9 ALGSGAARGWSHIGVINALKKVGIEI-DIVAGCSIGSL 45 (300)
T ss_pred EEcCcHHHHHHHHHHHHHHHHcCCCc-CEEEEEcHHHH
Confidence 33567778888999999999999985 77788888743
No 48
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=20.60 E-value=1.2e+02 Score=25.87 Aligned_cols=34 Identities=3% Similarity=0.015 Sum_probs=17.6
Q ss_pred EEEEEEEEeCC------CChhHHHHHHHHHHHHhcCcccc
Q psy15057 92 VILTIQELQDQ------GSLLSCCINAACLALINSGISMR 125 (151)
Q Consensus 92 i~i~v~vl~~d------G~~l~a~inaa~lAL~~agip~~ 125 (151)
++|+||-.+.+ |+-.+.-+.-..-.|..+||+|+
T Consensus 142 l~iSVhat~p~lR~~ll~n~~a~~il~~l~~l~~~~I~~h 181 (433)
T TIGR03279 142 LYVSVHATEPSLRARLLKNPRAGLILEQLKWFQERRLQLH 181 (433)
T ss_pred EEEEEecCCHHHHHHHhCCCCHHHHHHHHHHHHHcCCeEE
Confidence 45555555543 33344444555555566666554
No 49
>cd07208 Pat_hypo_Ecoli_yjju_like Hypothetical patatin similar to yjju protein of Escherichia coli. Patatin-like phospholipase similar to yjju protein of Escherichia coli. This family predominantly consists of bacterial patatin glycoproteins, and some representatives from eukaryotes and archaea. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates.
Probab=20.24 E-value=1.1e+02 Score=23.51 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=26.4
Q ss_pred CCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEe
Q psy15057 101 DQGSLLSCCINAACLALINSGISMRYILAAVSCIIN 136 (151)
Q Consensus 101 ~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~ 136 (151)
++|+...+.-.++.-||.+.|+..-+.++++|.|-+
T Consensus 4 ~GGG~rG~~~~Gvl~al~e~~~~~fd~i~GtSaGAi 39 (266)
T cd07208 4 EGGGMRGAYTAGVLDAFLEAGIRPFDLVIGVSAGAL 39 (266)
T ss_pred ccchhhHHHHHHHHHHHHHcCCCCCCEEEEECHHHH
Confidence 456677777778888888888875666778777743
Done!