Query 047153
Match_columns 100
No_of_seqs 126 out of 1169
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:12:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047153.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047153hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1068 Exosomal 3'-5' exoribo 100.0 3.9E-29 8.5E-34 172.2 7.6 99 2-100 11-128 (245)
2 TIGR02065 ECX1 archaeal exosom 99.9 9.6E-27 2.1E-31 161.0 13.3 99 2-100 6-122 (230)
3 PRK03983 exosome complex exonu 99.9 3.9E-26 8.4E-31 159.2 13.2 99 2-100 12-128 (244)
4 COG0689 Rph RNase PH [Translat 99.9 4.5E-25 9.7E-30 152.1 11.5 99 2-100 6-123 (230)
5 PRK00173 rph ribonuclease PH; 99.9 1.7E-24 3.8E-29 150.5 12.6 97 4-100 1-119 (238)
6 TIGR01966 RNasePH ribonuclease 99.9 7.8E-24 1.7E-28 147.0 12.5 96 5-100 1-118 (236)
7 KOG1069 Exosomal 3'-5' exoribo 99.9 2.4E-24 5.2E-29 144.8 7.3 88 13-100 4-100 (217)
8 TIGR03591 polynuc_phos polyrib 99.9 6.3E-23 1.4E-27 159.6 12.7 98 2-100 308-428 (684)
9 PRK11824 polynucleotide phosph 99.9 1.4E-22 3E-27 157.9 12.8 98 2-100 312-432 (693)
10 TIGR02696 pppGpp_PNP guanosine 99.9 3.8E-22 8.3E-27 154.7 11.7 98 2-100 333-453 (719)
11 PF01138 RNase_PH: 3' exoribon 99.8 2.9E-20 6.4E-25 118.3 11.4 88 13-100 1-107 (132)
12 PLN00207 polyribonucleotide nu 99.8 2.2E-20 4.8E-25 147.5 12.7 98 2-100 436-557 (891)
13 PRK04282 exosome complex RNA-b 99.8 2.9E-20 6.4E-25 131.3 12.0 99 2-100 22-144 (271)
14 COG2123 RNase PH-related exori 99.7 6.5E-17 1.4E-21 113.3 9.3 83 2-84 21-119 (272)
15 KOG1612 Exosomal 3'-5' exoribo 99.6 9.3E-15 2E-19 101.7 10.9 80 2-81 19-115 (288)
16 KOG1067 Predicted RNA-binding 99.6 2.4E-15 5.2E-20 113.9 5.8 96 2-99 356-474 (760)
17 TIGR03591 polynuc_phos polyrib 99.4 1.6E-12 3.4E-17 101.9 11.3 81 15-100 5-109 (684)
18 COG1185 Pnp Polyribonucleotide 99.4 2.8E-13 6.1E-18 104.5 5.1 91 2-92 310-423 (692)
19 PRK11824 polynucleotide phosph 99.4 5.1E-12 1.1E-16 99.1 11.0 84 15-100 14-118 (693)
20 KOG1614 Exosomal 3'-5' exoribo 99.3 1.3E-11 2.7E-16 85.9 7.8 78 2-82 20-113 (291)
21 KOG1613 Exosomal 3'-5' exoribo 99.2 7.2E-12 1.6E-16 87.0 3.8 81 2-82 34-130 (298)
22 PLN00207 polyribonucleotide nu 98.7 3.8E-08 8.1E-13 79.0 7.6 83 15-97 89-192 (891)
23 TIGR02696 pppGpp_PNP guanosine 97.6 0.00018 3.9E-09 57.2 6.8 83 15-99 17-121 (719)
24 COG1185 Pnp Polyribonucleotide 97.0 0.0024 5.3E-08 50.5 6.6 81 15-100 14-117 (692)
25 KOG1067 Predicted RNA-binding 93.6 0.069 1.5E-06 42.0 2.9 31 13-43 54-85 (760)
26 PF02962 CHMI: 5-carboxymethyl 92.0 0.71 1.5E-05 29.3 5.5 68 31-99 32-106 (124)
27 PRK15031 5-carboxymethyl-2-hyd 88.4 2.6 5.5E-05 26.9 5.8 68 30-98 32-106 (126)
28 PF08860 DUF1827: Domain of un 67.5 14 0.00031 22.2 3.9 44 32-81 28-71 (91)
29 cd03483 MutL_Trans_MLH1 MutL_T 32.9 86 0.0019 19.5 3.6 31 67-97 60-90 (127)
30 KOG4272 Predicted GTP-binding 28.9 21 0.00046 23.7 0.3 16 19-34 147-162 (164)
31 cd03485 MutL_Trans_hPMS_1_like 24.5 1.6E+02 0.0034 18.4 3.7 29 69-97 64-95 (132)
32 cd03482 MutL_Trans_MutL MutL_T 23.9 1.4E+02 0.0031 18.4 3.4 31 67-97 56-86 (123)
33 PF09457 RBD-FIP: FIP domain ; 23.6 1.2E+02 0.0026 16.0 2.5 22 67-90 22-43 (48)
34 cd00580 CHMI 5-carboxymethyl-2 22.9 1.9E+02 0.004 17.5 6.4 51 48-98 56-107 (113)
35 COG5593 Nucleic-acid-binding p 21.0 40 0.00087 27.1 0.5 25 5-38 536-560 (821)
36 PF02786 CPSase_L_D2: Carbamoy 20.4 2.9E+02 0.0063 18.8 4.8 46 55-100 41-100 (211)
37 COG3445 Acid-induced glycyl ra 20.2 1.3E+02 0.0028 18.6 2.5 27 70-96 74-101 (127)
38 COG3232 HpaF 5-carboxymethyl-2 20.0 2.5E+02 0.0055 17.9 4.8 52 31-82 33-91 (127)
No 1
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.9e-29 Score=172.24 Aligned_cols=99 Identities=31% Similarity=0.518 Sum_probs=89.0
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe----e------CCCCCceEEEEEee--CCC-------C
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----K------NENPEKVSIEVIWK--SKT-------G 62 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~----~------~~~~~~~~l~v~~~--p~~-------g 62 (100)
++.|.|||+++++|+|.++.|++.+++||||+++|||||+|. + ...++++.++|.|. +|+ .
T Consensus 11 eg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~~~ 90 (245)
T KOG1068|consen 11 EGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKKRP 90 (245)
T ss_pred cccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhccCC
Confidence 689999999999999999999999999999999999999999 1 23578899998884 332 2
Q ss_pred CCChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 63 QIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 63 ~~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
.++++++|++.+|+++|+++|++++|||++|||+|+||
T Consensus 91 ~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~Vl 128 (245)
T KOG1068|consen 91 KGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVL 128 (245)
T ss_pred CccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEE
Confidence 45789999999999999999999999999999999996
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=99.95 E-value=9.6e-27 Score=161.03 Aligned_cols=99 Identities=29% Similarity=0.461 Sum_probs=87.2
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e---------CCCCCceEEEEEee--CCCC------C
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K---------NENPEKVSIEVIWK--SKTG------Q 63 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~---------~~~~~~~~l~v~~~--p~~g------~ 63 (100)
+++|+|||+++|+|++++++|++++|||||++++|+|+|+|+ . .+.++++.|+|+|. |+++ .
T Consensus 6 ~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~~~~~ 85 (230)
T TIGR02065 6 DGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDERKRPG 85 (230)
T ss_pred CCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCccCCC
Confidence 588999999999999999999999999999999999999999 1 13467888887764 6432 3
Q ss_pred CChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 64 IGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 64 ~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
++.++.+++.+|+++|+++|++++||+++|+|+++||
T Consensus 86 ~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl 122 (230)
T TIGR02065 86 PSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVL 122 (230)
T ss_pred CCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEE
Confidence 5678899999999999999999999999999999986
No 3
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=99.94 E-value=3.9e-26 Score=159.17 Aligned_cols=99 Identities=27% Similarity=0.452 Sum_probs=86.9
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e---------CCCCCceEEEEEe--eCCCC------C
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K---------NENPEKVSIEVIW--KSKTG------Q 63 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~---------~~~~~~~~l~v~~--~p~~g------~ 63 (100)
+++|+|||+++++|++++++|++++|||||++++|+|+|+|+ . .+.++++.++|++ .|+++ .
T Consensus 12 ~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~~~~ 91 (244)
T PRK03983 12 DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKRPG 91 (244)
T ss_pred CCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCccccccCCC
Confidence 689999999999999999999999999999999999999999 2 1356778887765 46543 3
Q ss_pred CChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 64 IGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 64 ~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
++.++.+++.+|+++|+++|++++||+++|+|+++||
T Consensus 92 ~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL 128 (244)
T PRK03983 92 PDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVL 128 (244)
T ss_pred CChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEE
Confidence 4577889999999999999999999999999999986
No 4
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=4.5e-25 Score=152.07 Aligned_cols=99 Identities=25% Similarity=0.410 Sum_probs=87.2
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e---------CCCCCceEEEEEee--CCCC----C--
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K---------NENPEKVSIEVIWK--SKTG----Q-- 63 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~---------~~~~~~~~l~v~~~--p~~g----~-- 63 (100)
++.|+|||.++|+|||+++.|++++|+||+++++|+|||+|+ . ...++++.+.++|. |++. .
T Consensus 6 ~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~~~ 85 (230)
T COG0689 6 DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKRE 85 (230)
T ss_pred cCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEeccccccccccccc
Confidence 578999999999999999999999999999999999999999 2 23467799998885 6654 1
Q ss_pred CCh-hHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 64 IGK-QEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 64 ~~~-~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
+++ +++|++.+|.++|+++|++++||+++|+|.++||
T Consensus 86 ~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVl 123 (230)
T COG0689 86 ADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVL 123 (230)
T ss_pred ccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEE
Confidence 122 7899999999999999999999999999999986
No 5
>PRK00173 rph ribonuclease PH; Reviewed
Probab=99.92 E-value=1.7e-24 Score=150.49 Aligned_cols=97 Identities=26% Similarity=0.364 Sum_probs=84.2
Q ss_pred CCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e-------C-CCCCceEEEEEee--CCC-----------
Q 047153 4 DRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K-------N-ENPEKVSIEVIWK--SKT----------- 61 (100)
Q Consensus 4 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~-------~-~~~~~~~l~v~~~--p~~----------- 61 (100)
+|+|||+++|+|++++++|++++|||||++++|+|+|+|+ + . ..++++.|+|+|. |++
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~ 80 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCcccccccccC
Confidence 5999999999999999999999999999999999999999 2 1 2356788887774 543
Q ss_pred CCCChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 62 GQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 62 g~~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
|.++.++.+++.+|.++|+++|+++.||++.|+|.++||
T Consensus 81 g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL 119 (238)
T PRK00173 81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVI 119 (238)
T ss_pred CCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEE
Confidence 234567899999999999999999999999999999986
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=99.91 E-value=7.8e-24 Score=147.02 Aligned_cols=96 Identities=27% Similarity=0.390 Sum_probs=81.5
Q ss_pred CCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e--C------CCCCceEEEEEe--eCCC-----------C
Q 047153 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K--N------ENPEKVSIEVIW--KSKT-----------G 62 (100)
Q Consensus 5 R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~--~------~~~~~~~l~v~~--~p~~-----------g 62 (100)
|+|||+++|+|++++++|++++|||||++++|+|+|+|+ . . ..++++.++|++ .|++ |
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~g 80 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCCCCccccccCC
Confidence 899999999999999999999999999999999999998 2 1 124677777665 4643 2
Q ss_pred CCChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 63 QIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 63 ~~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
.++.++.+++.+|+++|+++|+++.||++.|+|.++||
T Consensus 81 ~~~~~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL 118 (236)
T TIGR01966 81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVI 118 (236)
T ss_pred CCCccHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEE
Confidence 23346789999999999999999999999999999986
No 7
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=2.4e-24 Score=144.75 Aligned_cols=88 Identities=49% Similarity=0.771 Sum_probs=85.3
Q ss_pred CCCceEEEeCCcCCCceEEEEEeCCeEEEEe---------eCCCCCceEEEEEeeCCCCCCChhHHHHHHHHHHHHHHHh
Q 047153 13 QLRPLACYCSILHRAHGSASWSQGDTKVLAA---------KNENPEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSIC 83 (100)
Q Consensus 13 e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~---------~~~~~~~~~l~v~~~p~~g~~~~~~~e~~~~l~~~l~~~I 83 (100)
.+|++.++.|+++++||||.|++|+|+|+|+ ++|.++++.++|.|+|..|.++..++.+++.|+++|+++|
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 7899999999999999999999999999999 5789999999999999999999999999999999999999
Q ss_pred ccCCCCCcEEEEEEEEC
Q 047153 84 ILTINPNTTTSVIIQVW 100 (100)
Q Consensus 84 ~~~~~P~~~i~i~v~v~ 100 (100)
.++.||++.|+|++||+
T Consensus 84 ~l~l~Prt~iqVsiqvv 100 (217)
T KOG1069|consen 84 ILELYPRTTIQVSIQVV 100 (217)
T ss_pred eeeecCCceEEEEEEEE
Confidence 99999999999999985
No 8
>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=99.90 E-value=6.3e-23 Score=159.62 Aligned_cols=98 Identities=26% Similarity=0.430 Sum_probs=84.0
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e----C-C-C--------CCceEEEEEeeCCC-----
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K----N-E-N--------PEKVSIEVIWKSKT----- 61 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~----~-~-~--------~~~~~l~v~~~p~~----- 61 (100)
+++|+|||+++|+||++|++|++++|||||+|++|+|+|+|+ . . + . ..+..++++|.|++
T Consensus 308 ~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~ 387 (684)
T TIGR03591 308 EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVG 387 (684)
T ss_pred CCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcC
Confidence 679999999999999999999999999999999999999998 1 1 1 0 12456677788864
Q ss_pred --CCCChhHHHHHHHHHHHHHHHhcc-CCCCCcEEEEEEEEC
Q 047153 62 --GQIGKQEKEYEMILKRTLQSICIL-TINPNTTTSVIIQVW 100 (100)
Q Consensus 62 --g~~~~~~~e~~~~l~~~l~~~I~~-~~~P~~~i~i~v~v~ 100 (100)
|.+++++.+++.+++++|+++|++ ++||++ |+|.++||
T Consensus 388 ~~g~~~rrei~~~~l~~ral~~~i~~~~~~p~t-I~v~~~VL 428 (684)
T TIGR03591 388 RVGGPGRREIGHGALAERALKAVLPSEEEFPYT-IRVVSEIL 428 (684)
T ss_pred CCCCCChHHHHHHHHHHHHHHHhcCccccCCeE-EEEEEEEE
Confidence 236789999999999999999996 899997 99999986
No 9
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.89 E-value=1.4e-22 Score=157.91 Aligned_cols=98 Identities=24% Similarity=0.421 Sum_probs=83.6
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e----CC----------CCCceEEEEEeeCCC-----
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K----NE----------NPEKVSIEVIWKSKT----- 61 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~----~~----------~~~~~~l~v~~~p~~----- 61 (100)
+++|+|||+++|+||++|++|++++|||||+|++|+|+|+|+ . .+ ...+..++++|.|++
T Consensus 312 ~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~ 391 (693)
T PRK11824 312 EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETG 391 (693)
T ss_pred CCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcC
Confidence 689999999999999999999999999999999999999998 1 11 122345567778864
Q ss_pred --CCCChhHHHHHHHHHHHHHHHhcc-CCCCCcEEEEEEEEC
Q 047153 62 --GQIGKQEKEYEMILKRTLQSICIL-TINPNTTTSVIIQVW 100 (100)
Q Consensus 62 --g~~~~~~~e~~~~l~~~l~~~I~~-~~~P~~~i~i~v~v~ 100 (100)
|.+++++.+++.+++++|+++|++ ++||+ .|+|.++||
T Consensus 392 ~~~~~~rre~~~~~li~ral~~vi~~~~~~p~-~I~v~~~VL 432 (693)
T PRK11824 392 RVGSPGRREIGHGALAERALEPVLPSEEEFPY-TIRVVSEIL 432 (693)
T ss_pred CCCCCChhHHHHHHHHHHHHHHhcCcccCCCE-EEEEEEEEE
Confidence 236789999999999999999998 79998 699999986
No 10
>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=99.88 E-value=3.8e-22 Score=154.70 Aligned_cols=98 Identities=21% Similarity=0.308 Sum_probs=83.4
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e-----C---------CCCCceEEEEEeeCCCC----
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K-----N---------ENPEKVSIEVIWKSKTG---- 62 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~-----~---------~~~~~~~l~v~~~p~~g---- 62 (100)
++.|+|||+++++||++|++|+++++||||+|+.|+|+|+|+ . . +...+..++++|.|++.
T Consensus 333 ~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~er~ 412 (719)
T TIGR02696 333 EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETG 412 (719)
T ss_pred CCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcccCCC
Confidence 578999999999999999999999999999999999999999 1 0 11234567788888752
Q ss_pred ---CCChhHHHHHHHHHHHHHHHhc-cCCCCCcEEEEEEEEC
Q 047153 63 ---QIGKQEKEYEMILKRTLQSICI-LTINPNTTTSVIIQVW 100 (100)
Q Consensus 63 ---~~~~~~~e~~~~l~~~l~~~I~-~~~~P~~~i~i~v~v~ 100 (100)
.+++++.+++.+++++|+++|+ ++.||++ |.+..+||
T Consensus 413 ~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVL 453 (719)
T TIGR02696 413 RVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEAL 453 (719)
T ss_pred CCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEee
Confidence 3578999999999999999998 6999999 77777875
No 11
>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=99.85 E-value=2.9e-20 Score=118.31 Aligned_cols=88 Identities=34% Similarity=0.505 Sum_probs=74.6
Q ss_pred CCCceEEEeCCcCCCceEEEEEeCCeEEEEe------e---CCCCC-c--eEEEEEeeCCC-------CCCChhHHHHHH
Q 047153 13 QLRPLACYCSILHRAHGSASWSQGDTKVLAA------K---NENPE-K--VSIEVIWKSKT-------GQIGKQEKEYEM 73 (100)
Q Consensus 13 e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~------~---~~~~~-~--~~l~v~~~p~~-------g~~~~~~~e~~~ 73 (100)
|+|++.+++|+++++||||+|++|+|+|+|+ . .+.++ . ..++|++.|++ +.++..+.+++.
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 7899999999999999999999999999999 1 22122 3 45566667754 345678999999
Q ss_pred HHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 74 ILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 74 ~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
+|+++|+++++++.||+.+|+|.++||
T Consensus 81 ~l~~~l~~~~~~~~~~~~~i~v~v~vl 107 (132)
T PF01138_consen 81 LLERALRSSILLEGYPRWQIHVDVQVL 107 (132)
T ss_dssp HHHHHHHHTBSTTTTSSEEEEEEEEEE
T ss_pred HHhhhccccccccccCceEEEEEEEEE
Confidence 999999999999999999999999986
No 12
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.84 E-value=2.2e-20 Score=147.46 Aligned_cols=98 Identities=29% Similarity=0.485 Sum_probs=84.4
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e---C------------CCCCceEEEEEeeCCC----
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K---N------------ENPEKVSIEVIWKSKT---- 61 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~---~------------~~~~~~~l~v~~~p~~---- 61 (100)
++.|+|||+++|+||+++++|.+++|||||+|++|+|+|+|+ . . +...+..++++|.|++
T Consensus 436 ~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~ 515 (891)
T PLN00207 436 GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEV 515 (891)
T ss_pred CCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCCCCccc
Confidence 689999999999999999999999999999999999999998 1 1 1123456788888865
Q ss_pred ---CCCChhHHHHHHHHHHHHHHHhccC-CCCCcEEEEEEEEC
Q 047153 62 ---GQIGKQEKEYEMILKRTLQSICILT-INPNTTTSVIIQVW 100 (100)
Q Consensus 62 ---g~~~~~~~e~~~~l~~~l~~~I~~~-~~P~~~i~i~v~v~ 100 (100)
+.+++++.+++.+++++|+++|..+ .||+ .|+|.++||
T Consensus 516 ~r~g~psrREi~hg~L~eRALrpvip~~~~fP~-tIrV~~~VL 557 (891)
T PLN00207 516 GRIGAPSRREIGHGMLAERALEPILPSEDDFPY-TIRVESTIT 557 (891)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCE-EEEEEEEEE
Confidence 2357889999999999999999985 9997 799999986
No 13
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.84 E-value=2.9e-20 Score=131.27 Aligned_cols=99 Identities=22% Similarity=0.339 Sum_probs=80.2
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e-------CCCCCceEEE--EEeeCCC------CCCC
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K-------NENPEKVSIE--VIWKSKT------GQIG 65 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~-------~~~~~~~~l~--v~~~p~~------g~~~ 65 (100)
+++|+|||+++|+|++++++|++++++|||++++|+|+|+|+ + .+.++++.++ |++.|++ |.++
T Consensus 22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~~~~~a~~~~~~~~~~ 101 (271)
T PRK04282 22 KGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPTFEPGPPD 101 (271)
T ss_pred cCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCCcCccccCCCCC
Confidence 689999999999999999999999999999999999999999 2 1345666665 5556653 3456
Q ss_pred hhHHHHHHHHHHHHHHHhccCC--C---CCc---EEEEEEEEC
Q 047153 66 KQEKEYEMILKRTLQSICILTI--N---PNT---TTSVIIQVW 100 (100)
Q Consensus 66 ~~~~e~~~~l~~~l~~~I~~~~--~---P~~---~i~i~v~v~ 100 (100)
..+.+++.+|+++|++....++ + |+. .|+|.++||
T Consensus 102 ~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL 144 (271)
T PRK04282 102 ENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVL 144 (271)
T ss_pred HHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEE
Confidence 7888999999999988754443 3 766 888888885
No 14
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.71 E-value=6.5e-17 Score=113.32 Aligned_cols=83 Identities=25% Similarity=0.361 Sum_probs=69.3
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e-------CCCCCceE--EEEEeeCCC------CCCC
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K-------NENPEKVS--IEVIWKSKT------GQIG 65 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~-------~~~~~~~~--l~v~~~p~~------g~~~ 65 (100)
.+.|+|||.++|+|++++++|+++.|+|||++++|+|+|+|+ + .+.|+++. +++++.|.+ |.++
T Consensus 21 ~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~El~Plas~~fE~Gppd 100 (272)
T COG2123 21 KGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASPSFEPGPPD 100 (272)
T ss_pred cCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeeeeeccccccccCCCCc
Confidence 478999999999999999999999999999999999999999 2 35566664 567888753 5566
Q ss_pred hhHHHHHHHHHHHHHHHhc
Q 047153 66 KQEKEYEMILKRTLQSICI 84 (100)
Q Consensus 66 ~~~~e~~~~l~~~l~~~I~ 84 (100)
....|+++.+.+.++.+=.
T Consensus 101 e~aielsrvvdr~lr~s~a 119 (272)
T COG2123 101 ELAIELSRVVDRGLRESKA 119 (272)
T ss_pred hhHHHHHHHHHHHHHhccC
Confidence 6778899999999887544
No 15
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.62 E-value=9.3e-15 Score=101.69 Aligned_cols=80 Identities=30% Similarity=0.397 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCC-eEEEEe-e-------CCCCCceE--EEEEeeCCCC--CCChh-
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGD-TKVLAA-K-------NENPEKVS--IEVIWKSKTG--QIGKQ- 67 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~-T~V~~~-~-------~~~~~~~~--l~v~~~p~~g--~~~~~- 67 (100)
..+|.|||.++++|||.++++++|+++|||++++|+ |.|+++ + .+.|+++. +.|++.|.+. -.++.
T Consensus 19 ~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~sasp~f~gRgg 98 (288)
T KOG1612|consen 19 PDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPSASPQFQGRGG 98 (288)
T ss_pred cccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCCcCccccCCCh
Confidence 368999999999999999999999999999999999 999999 2 34455544 5678877543 12333
Q ss_pred ---HHHHHHHHHHHHHH
Q 047153 68 ---EKEYEMILKRTLQS 81 (100)
Q Consensus 68 ---~~e~~~~l~~~l~~ 81 (100)
..|+...|+++|.+
T Consensus 99 de~~~eltsaLq~~l~~ 115 (288)
T KOG1612|consen 99 DELVEELTSALQRVLNS 115 (288)
T ss_pred hhHHHHHHHHHHHHHhC
Confidence 44555555555554
No 16
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.58 E-value=2.4e-15 Score=113.92 Aligned_cols=96 Identities=26% Similarity=0.408 Sum_probs=81.8
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe----e------------CCCCCceEEEEEeeCCC----
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----K------------NENPEKVSIEVIWKSKT---- 61 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~----~------------~~~~~~~~l~v~~~p~~---- 61 (100)
+++|.|||..+++|+|+|+.+.++..||||.|+-|+|+|+|+ . ..+..+..++++|.|.+
T Consensus 356 ~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Ev 435 (760)
T KOG1067|consen 356 EGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEV 435 (760)
T ss_pred cccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcccccc
Confidence 578999999999999999999999999999999999999999 1 12334689999999964
Q ss_pred ---CCCChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEE
Q 047153 62 ---GQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQV 99 (100)
Q Consensus 62 ---g~~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v 99 (100)
|..+++|..+..+.+++|.+++. +.||.+ |.|+=+|
T Consensus 436 gkig~~nRRE~GhgaLAEkaL~~vlP-~dfPft-IRv~SeV 474 (760)
T KOG1067|consen 436 GKIGGLNRRELGHGALAEKALLPVLP-EDFPFT-IRVTSEV 474 (760)
T ss_pred ccccCCcccccCchhHhhhhhhccCc-ccCceE-EEEeeee
Confidence 34568999999999999999998 999974 5555544
No 17
>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=99.44 E-value=1.6e-12 Score=101.89 Aligned_cols=81 Identities=22% Similarity=0.359 Sum_probs=65.6
Q ss_pred CceEEEeCCc-CCCceEEEEEeCCeEEEEe-e-----CCCCCceEEEEEeeCC--------------CCCCChhHHHHHH
Q 047153 15 RPLACYCSIL-HRAHGSASWSQGDTKVLAA-K-----NENPEKVSIEVIWKSK--------------TGQIGKQEKEYEM 73 (100)
Q Consensus 15 R~i~~~~g~~-~~a~GSa~~~~G~T~V~~~-~-----~~~~~~~~l~v~~~p~--------------~g~~~~~~~e~~~ 73 (100)
|++.+++|.+ ++|||||++++|+|+|+|+ . ++..+.+.|+|+|.+. .|.|+.++.++++
T Consensus 5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil~sr 84 (684)
T TIGR03591 5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETLTSR 84 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHHHHH
Confidence 7999999999 6799999999999999999 1 1223557788888631 2446778888999
Q ss_pred HHHHHHHHHhccCCCCC---cEEEEEEEEC
Q 047153 74 ILKRTLQSICILTINPN---TTTSVIIQVW 100 (100)
Q Consensus 74 ~l~~~l~~~I~~~~~P~---~~i~i~v~v~ 100 (100)
+|.++|++. ||+ ..|+|.++||
T Consensus 85 lIdR~lrpl-----fp~~~~~~i~V~~~VL 109 (684)
T TIGR03591 85 LIDRPIRPL-----FPKGFRNEVQVVATVL 109 (684)
T ss_pred HHhhHHHHh-----cCCCCCceEEEEEEEE
Confidence 999999874 777 8899999986
No 18
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.40 E-value=2.8e-13 Score=104.52 Aligned_cols=91 Identities=25% Similarity=0.397 Sum_probs=79.9
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe------e---------CCCCCceEEEEEeeCCC-----
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA------K---------NENPEKVSIEVIWKSKT----- 61 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~------~---------~~~~~~~~l~v~~~p~~----- 61 (100)
.+.|+|||..++.||+.++.|+++.+|||+.|..|.|+.++. . .+..++..++.+|.|++
T Consensus 310 ~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g 389 (692)
T COG1185 310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETG 389 (692)
T ss_pred CCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccC
Confidence 468999999999999999999999999999999999999887 1 13356788999999986
Q ss_pred --CCCChhHHHHHHHHHHHHHHHhc-cCCCCCcE
Q 047153 62 --GQIGKQEKEYEMILKRTLQSICI-LTINPNTT 92 (100)
Q Consensus 62 --g~~~~~~~e~~~~l~~~l~~~I~-~~~~P~~~ 92 (100)
|.|++++..+..+-++++.+++. .+.||.+-
T Consensus 390 ~~g~p~RREiGHG~LA~Ral~~vlp~~e~fpyti 423 (692)
T COG1185 390 RMGSPGRREIGHGALAERALAPVLPSEEEFPYTI 423 (692)
T ss_pred CCCCCCcccccCchhhHHHHhhhCCchhcCCcee
Confidence 34679999999999999999999 57999864
No 19
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.38 E-value=5.1e-12 Score=99.13 Aligned_cols=84 Identities=21% Similarity=0.285 Sum_probs=66.2
Q ss_pred CceEEEeCCcC-CCceEEEEEeCCeEEEEe-e-----CCCCCceEEEEEeeCC--------------CCCCChhHHHHHH
Q 047153 15 RPLACYCSILH-RAHGSASWSQGDTKVLAA-K-----NENPEKVSIEVIWKSK--------------TGQIGKQEKEYEM 73 (100)
Q Consensus 15 R~i~~~~g~~~-~a~GSa~~~~G~T~V~~~-~-----~~~~~~~~l~v~~~p~--------------~g~~~~~~~e~~~ 73 (100)
|++++++|.+. +|||||++++|+|+|+|+ . ++..+.+.++|+|.+. .|.|+.++.++++
T Consensus 14 r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~eil~sr 93 (693)
T PRK11824 14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKETLTSR 93 (693)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCCeeeeEEEEEehhhhccCCCcccccCCCCCChHHHHHHH
Confidence 79999999995 799999999999999999 1 2233557788888641 2446778889999
Q ss_pred HHHHHHHHHhccCCCCCcEEEEEEEEC
Q 047153 74 ILKRTLQSICILTINPNTTTSVIIQVW 100 (100)
Q Consensus 74 ~l~~~l~~~I~~~~~P~~~i~i~v~v~ 100 (100)
+|.++|++... ..++..|+|.++||
T Consensus 94 lIdR~lrplfp--~~~~~~i~I~~~VL 118 (693)
T PRK11824 94 LIDRPIRPLFP--KGFRNEVQVVATVL 118 (693)
T ss_pred HHhhhHHHhCC--CCCCeEEEEEEEEE
Confidence 99999999532 23378999999986
No 20
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=99.30 E-value=1.3e-11 Score=85.92 Aligned_cols=78 Identities=26% Similarity=0.291 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe--------eCCCCCceE--EEEEeeCCCC------CCC
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA--------KNENPEKVS--IEVIWKSKTG------QIG 65 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~--------~~~~~~~~~--l~v~~~p~~g------~~~ 65 (100)
.|.|.|||...|+|.+++++|- -.||+.+++|+|+|+|. ..++|.++. |.++++|+++ ..+
T Consensus 20 ~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~telsPmA~~sfE~Gr~~ 96 (291)
T KOG1614|consen 20 AGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELSPMASPSFEPGRKG 96 (291)
T ss_pred hcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeeccccccccccCCCCcc
Confidence 4789999999999999999995 79999999999999999 135666664 5578898753 234
Q ss_pred hhHHHHHHHHHHHHHHH
Q 047153 66 KQEKEYEMILKRTLQSI 82 (100)
Q Consensus 66 ~~~~e~~~~l~~~l~~~ 82 (100)
..+.++.++|++++...
T Consensus 97 ~~~v~l~Rliek~~R~S 113 (291)
T KOG1614|consen 97 ESEVELSRLIEKALRRS 113 (291)
T ss_pred chHHHHHHHHHHHHHhc
Confidence 55678888888888654
No 21
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.24 E-value=7.2e-12 Score=87.05 Aligned_cols=81 Identities=25% Similarity=0.299 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCeEEEEe-e-------CCCCCceEEEEEe--eCC------CCCCC
Q 047153 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-K-------NENPEKVSIEVIW--KSK------TGQIG 65 (100)
Q Consensus 2 ~~~R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T~V~~~-~-------~~~~~~~~l~v~~--~p~------~g~~~ 65 (100)
+++|+|||+..|+|.+.+..|.++.|||||.++.|+|.|+|+ + ...|+++.|-.+| .|- .|.++
T Consensus 34 e~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~epstdapdeg~Iv~n~~lpplcs~r~RpG~p~ 113 (298)
T KOG1613|consen 34 EGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPSTDAPDEGDIVPNYALPPLCSSRFRPGPPT 113 (298)
T ss_pred cccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeecccccCCCCCcceeecccCCcccccCCCCCCCc
Confidence 689999999999999999999999999999999999999999 2 3567888876555 342 34444
Q ss_pred hhHHHHHHHHHHHHHHH
Q 047153 66 KQEKEYEMILKRTLQSI 82 (100)
Q Consensus 66 ~~~~e~~~~l~~~l~~~ 82 (100)
..+.-+++.|..++.++
T Consensus 114 dea~viSq~LhdtIl~S 130 (298)
T KOG1613|consen 114 DEAQVISQKLHDTILHS 130 (298)
T ss_pred hHHHHHHHHHHHHHHhc
Confidence 44555555555555443
No 22
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.74 E-value=3.8e-08 Score=78.97 Aligned_cols=83 Identities=18% Similarity=0.253 Sum_probs=65.3
Q ss_pred CceEEEeCCc-CCCceEEEEEeCCeEEEEe---eC---CCCCceEEEEEee---------C-----CCCCCChhHHHHHH
Q 047153 15 RPLACYCSIL-HRAHGSASWSQGDTKVLAA---KN---ENPEKVSIEVIWK---------S-----KTGQIGKQEKEYEM 73 (100)
Q Consensus 15 R~i~~~~g~~-~~a~GSa~~~~G~T~V~~~---~~---~~~~~~~l~v~~~---------p-----~~g~~~~~~~e~~~ 73 (100)
|.+.+++|-+ .+||||+.+++|+|.|+|+ .+ +..|=.-|.|+|. | ..|.+...+.-+++
T Consensus 89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~eiL~sR 168 (891)
T PLN00207 89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVLICR 168 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHHHHH
Confidence 4688999987 4799999999999999998 22 2223345677774 1 12456677888999
Q ss_pred HHHHHHHHHhccCCCCCcEEEEEE
Q 047153 74 ILKRTLQSICILTINPNTTTSVII 97 (100)
Q Consensus 74 ~l~~~l~~~I~~~~~P~~~i~i~v 97 (100)
+|.|.|++++..+.||+++|.+.|
T Consensus 169 lIdR~lRPlfp~~~~~etQI~i~V 192 (891)
T PLN00207 169 LIDRPLRPTMPKGFYHETQILSWV 192 (891)
T ss_pred HHCccchhhccccCCCCcEEEEEE
Confidence 999999999999999999998843
No 23
>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=97.65 E-value=0.00018 Score=57.22 Aligned_cols=83 Identities=17% Similarity=0.205 Sum_probs=50.6
Q ss_pred CceEEEeCCc-CCCceEEEEEe-CCeEEEEe---eC---CCCCceEEEEEeeC---CC-----------CCCChhHHHHH
Q 047153 15 RPLACYCSIL-HRAHGSASWSQ-GDTKVLAA---KN---ENPEKVSIEVIWKS---KT-----------GQIGKQEKEYE 72 (100)
Q Consensus 15 R~i~~~~g~~-~~a~GSa~~~~-G~T~V~~~---~~---~~~~~~~l~v~~~p---~~-----------g~~~~~~~e~~ 72 (100)
+++.+++|-+ .+||||+.+++ |+|.|+|+ .+ +..|=.-|.|+|.- .+ |.|...+.-.+
T Consensus 17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~eiL~s 96 (719)
T TIGR02696 17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTC 96 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCCCCCCcceeEeeeehhhhcCccCCceeccCCCCChhhhHHH
Confidence 4699999988 47999999999 99999998 22 22233556777742 11 33444455555
Q ss_pred HHHHHHHHHHhccCCCCCcEEEEEEEE
Q 047153 73 MILKRTLQSICILTINPNTTTSVIIQV 99 (100)
Q Consensus 73 ~~l~~~l~~~I~~~~~P~~~i~i~v~v 99 (100)
++|.|.++|...-..+ -.+||.++|
T Consensus 97 RliDR~iRPLFp~~~~--~e~qi~~~v 121 (719)
T TIGR02696 97 RLIDRPLRPSFVKGLR--NEVQVVVTV 121 (719)
T ss_pred HhhCCCCccCCCCCCC--cceEEEEEE
Confidence 5555555554432222 344555544
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.03 E-value=0.0024 Score=50.46 Aligned_cols=81 Identities=21% Similarity=0.346 Sum_probs=52.3
Q ss_pred CceEEEeCCcC-CCceEEEEEeCCeEEEEe---eC--CCCCceEEEEEee---------C-----CCCCCChhHHHHHHH
Q 047153 15 RPLACYCSILH-RAHGSASWSQGDTKVLAA---KN--ENPEKVSIEVIWK---------S-----KTGQIGKQEKEYEMI 74 (100)
Q Consensus 15 R~i~~~~g~~~-~a~GSa~~~~G~T~V~~~---~~--~~~~~~~l~v~~~---------p-----~~g~~~~~~~e~~~~ 74 (100)
|++.+++|.+. +|+|++.+++|+|.|+++ .+ +..|=.-|.|+|. | ..|.|...+.-.+++
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~~~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~L~sRL 93 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKEGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEILTSRL 93 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecCCCCCCCccceeEeeeeehhccCcCCCcccccCCCCCccchhhhhh
Confidence 88999999884 799999999999999999 22 2233345667763 1 123344455555555
Q ss_pred HHHHHHHHhccCCCC---CcEEEEEEEEC
Q 047153 75 LKRTLQSICILTINP---NTTTSVIIQVW 100 (100)
Q Consensus 75 l~~~l~~~I~~~~~P---~~~i~i~v~v~ 100 (100)
|.|-+++ +|| +-.++|..+|+
T Consensus 94 IDRpiRP-----lFp~g~~~evqIv~tvl 117 (692)
T COG1185 94 IDRPIRP-----LFPKGFRNEVQIVNTVL 117 (692)
T ss_pred ccccccc-----ccchhhccceEEEEEEE
Confidence 5555544 455 34556665553
No 25
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.59 E-value=0.069 Score=41.98 Aligned_cols=31 Identities=26% Similarity=0.249 Sum_probs=27.8
Q ss_pred CCCceEEEeCCcC-CCceEEEEEeCCeEEEEe
Q 047153 13 QLRPLACYCSILH-RAHGSASWSQGDTKVLAA 43 (100)
Q Consensus 13 e~R~i~~~~g~~~-~a~GSa~~~~G~T~V~~~ 43 (100)
--|.+.+++|.+. .|+||+.+..|+|+|+++
T Consensus 54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~T 85 (760)
T KOG1067|consen 54 GNREILFETGKLARFANGSVVVQMGETAVMTT 85 (760)
T ss_pred CCeEEEEecchhhhhcCCcEEEccCCeEEEEE
Confidence 3588999999886 589999999999999998
No 26
>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=92.00 E-value=0.71 Score=29.33 Aligned_cols=68 Identities=16% Similarity=0.265 Sum_probs=44.5
Q ss_pred EEEEeCCeEEEEee-------CCCCCceEEEEEeeCCCCCCChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEE
Q 047153 31 ASWSQGDTKVLAAK-------NENPEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQV 99 (100)
Q Consensus 31 a~~~~G~T~V~~~~-------~~~~~~~~l~v~~~p~~g~~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~v 99 (100)
..|..|+.|+-+-+ ...++.++|++.++-.+|.....-++++..|-.++..-. ...+++..++++++|
T Consensus 32 glF~~~~IK~Ra~~~~~y~vgdg~~~~~FvHv~l~il~GRs~e~k~~l~~~l~~~l~~~~-~~~~~~~~~~LsvEi 106 (124)
T PF02962_consen 32 GLFPEGGIKVRAIRCDHYRVGDGQPDDAFVHVTLRILAGRSEEQKKALSEALLAVLKAHL-APLFAQRYLQLSVEI 106 (124)
T ss_dssp TSS-GGG-EEEEEEESSEEETTSSS-EEEEEEEEEEETT--HHHHHHHHHHHHHHHHHHC-CCHCCHSEEEEEEEE
T ss_pred CCcChhceeeeeEecccEEEccCCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHh-hHhhcCCeeEEEEEE
Confidence 35566777777661 345678999999988788665666677777777777653 456777778887776
No 27
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=88.44 E-value=2.6 Score=26.89 Aligned_cols=68 Identities=9% Similarity=0.114 Sum_probs=44.3
Q ss_pred EEEEEeCCeEEEEe-------eCCCCCceEEEEEeeCCCCCCChhHHHHHHHHHHHHHHHhccCCCCCcEEEEEEE
Q 047153 30 SASWSQGDTKVLAA-------KNENPEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQ 98 (100)
Q Consensus 30 Sa~~~~G~T~V~~~-------~~~~~~~~~l~v~~~p~~g~~~~~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v~ 98 (100)
|-.|..|+.|+-+- ....++.++|++.++-.+|.....-++++..|-.++..... ..|-+..+.++++
T Consensus 32 sglF~~~~IK~Ra~~~~~y~vgdg~~~~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l~~~~~-~~~~~~~~~LS~E 106 (126)
T PRK15031 32 TGIFPLGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFALIKAHFA-ALMESRYLALSFE 106 (126)
T ss_pred CCCCCccccEeeeeecCcEEEcCCCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHhh-hhhcccceEEEEE
Confidence 45677777777776 13456779999999988887666666777777777655543 3333332444443
No 28
>PF08860 DUF1827: Domain of unknown function (DUF1827); InterPro: IPR014959 This presumed domain has no known function. ; PDB: 2QZI_B.
Probab=67.54 E-value=14 Score=22.23 Aligned_cols=44 Identities=27% Similarity=0.486 Sum_probs=26.3
Q ss_pred EEEeCCeEEEEeeCCCCCceEEEEEeeCCCCCCChhHHHHHHHHHHHHHH
Q 047153 32 SWSQGDTKVLAAKNENPEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQS 81 (100)
Q Consensus 32 ~~~~G~T~V~~~~~~~~~~~~l~v~~~p~~g~~~~~~~e~~~~l~~~l~~ 81 (100)
-+++|+|.|+.+. .++. .++-+. .-.+.-++.|++-.+++.|..
T Consensus 28 VYSlGnT~Vvyt~--a~~h--~eili~--N~~R~I~~~EIefi~~~llk~ 71 (91)
T PF08860_consen 28 VYSLGNTTVVYTE--APDH--YEILIS--NKKRAIKEAEIEFIIERLLKR 71 (91)
T ss_dssp EEEETTEEEEEEE--ETTE--EEEEEE--ESSS---HHHHHHHHHHHHHH
T ss_pred EEecCCceEEEee--CCCc--eEEEEE--cCCCCCCHHHHHHHHHHHhcc
Confidence 4789999999971 1222 222222 112345788999999998887
No 29
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=32.88 E-value=86 Score=19.49 Aligned_cols=31 Identities=10% Similarity=0.010 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHHHHHHhccCCCCCcEEEEEE
Q 047153 67 QEKEYEMILKRTLQSICILTINPNTTTSVII 97 (100)
Q Consensus 67 ~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v 97 (100)
..+.+...|.+++...+...+||-..+.|.+
T Consensus 60 ~~~~l~~aI~~~Y~~~l~~~~~P~~~L~i~i 90 (127)
T cd03483 60 ECSALRRAIENVYANYLPKGAHPFVYLSLEI 90 (127)
T ss_pred cCHHHHHHHHHHHHHhCcCCCccEEEEEEEe
Confidence 4567899999999999998999987766654
No 30
>KOG4272 consensus Predicted GTP-binding protein [General function prediction only]
Probab=28.94 E-value=21 Score=23.73 Aligned_cols=16 Identities=19% Similarity=0.042 Sum_probs=13.1
Q ss_pred EEeCCcCCCceEEEEE
Q 047153 19 CYCSILHRAHGSASWS 34 (100)
Q Consensus 19 ~~~g~~~~a~GSa~~~ 34 (100)
+.+|++..||||+|+.
T Consensus 147 I~lg~vgPaDGS~yi~ 162 (164)
T KOG4272|consen 147 ISLGYVGPADGSSYII 162 (164)
T ss_pred HHhcccccCCCceEEE
Confidence 4568888999999974
No 31
>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.
Probab=24.52 E-value=1.6e+02 Score=18.35 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHh---ccCCCCCcEEEEEE
Q 047153 69 KEYEMILKRTLQSIC---ILTINPNTTTSVII 97 (100)
Q Consensus 69 ~e~~~~l~~~l~~~I---~~~~~P~~~i~i~v 97 (100)
+.+...|.+++...+ ...+||-..+.|.+
T Consensus 64 ~~l~k~i~~~y~~~~~~~~~~~~P~~~L~i~~ 95 (132)
T cd03485 64 KDIGKLLRQYYSSAYRKSSLRRYPVFFLNILC 95 (132)
T ss_pred hHHHHHHHHHHHHHhccccccCCCEEEEEEEc
Confidence 678888999999988 77888877666543
No 32
>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.
Probab=23.95 E-value=1.4e+02 Score=18.37 Aligned_cols=31 Identities=6% Similarity=0.068 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHHHHHhccCCCCCcEEEEEE
Q 047153 67 QEKEYEMILKRTLQSICILTINPNTTTSVII 97 (100)
Q Consensus 67 ~~~e~~~~l~~~l~~~I~~~~~P~~~i~i~v 97 (100)
....+...+.+++...+....||-..+.+.+
T Consensus 56 ~~~~l~~ai~~~y~~~~~~~~~P~~vL~l~i 86 (123)
T cd03482 56 RDKLISHAVRQAYSDVLHGGRHPAYVLYLEL 86 (123)
T ss_pred CChHHHHHHHHHHHHhccCCCCcEEEEEEEc
Confidence 4567889999999999988899877766654
No 33
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=23.59 E-value=1.2e+02 Score=15.95 Aligned_cols=22 Identities=18% Similarity=0.298 Sum_probs=16.4
Q ss_pred hHHHHHHHHHHHHHHHhccCCCCC
Q 047153 67 QEKEYEMILKRTLQSICILTINPN 90 (100)
Q Consensus 67 ~~~e~~~~l~~~l~~~I~~~~~P~ 90 (100)
.-++++.+|...|..++ +..|.
T Consensus 22 ~v~eLe~YiD~LL~rVm--E~~P~ 43 (48)
T PF09457_consen 22 RVRELEDYIDNLLVRVM--EQTPS 43 (48)
T ss_dssp HHHHHHHHHHHHHHHHH--CC-GG
T ss_pred HHHHHHHHHHHHHHHHH--HhCcc
Confidence 45678999999998887 56664
No 34
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=22.91 E-value=1.9e+02 Score=17.48 Aligned_cols=51 Identities=20% Similarity=0.170 Sum_probs=29.5
Q ss_pred CCceEEEEEeeCCCCCCChhHHHHHHHHHHHHHHHhccC-CCCCcEEEEEEE
Q 047153 48 PEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILT-INPNTTTSVIIQ 98 (100)
Q Consensus 48 ~~~~~l~v~~~p~~g~~~~~~~e~~~~l~~~l~~~I~~~-~~P~~~i~i~v~ 98 (100)
++...+++.+.-.+|.....-+.+...|...+....... .-+...+.|.+.
T Consensus 56 ~~~~fi~i~i~l~~GRs~eqK~~l~~~i~~~l~~~~~~~~~~~~~~~svei~ 107 (113)
T cd00580 56 EDDAFIHVTLRILAGRSEEQKQELSEALLAALRAHLAPVFAKRYLSLSVEIR 107 (113)
T ss_pred CCCcEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHhhhhhhhccceEEEEEEE
Confidence 357888888876667555555566666666666655421 112245555443
No 35
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=20.99 E-value=40 Score=27.13 Aligned_cols=25 Identities=24% Similarity=0.419 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCceEEEeCCcCCCceEEEEEeCCe
Q 047153 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDT 38 (100)
Q Consensus 5 R~DGR~~~e~R~i~~~~g~~~~a~GSa~~~~G~T 38 (100)
-.|||+.+.. .++|+||+.+++.+-
T Consensus 536 eydgrkrdpk---------~anae~s~lwei~~f 560 (821)
T COG5593 536 EYDGRKRDPK---------FANAEKSSLWEINNF 560 (821)
T ss_pred hccCcccCcc---------cccccccchhhhhhh
Confidence 3688887653 568999999999763
No 36
>PF02786 CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain; InterPro: IPR005479 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the ATP-binding domain found in the large subunit of carbamoyl phosphate synthase, as well as in related proteins.; GO: 0003824 catalytic activity, 0005524 ATP binding, 0008152 metabolic process; PDB: 3U9S_A 3U9T_A 2C00_B 2VQD_A 1W96_B 1W93_A 1M6V_C 1CS0_C 1C30_E 1C3O_G ....
Probab=20.42 E-value=2.9e+02 Score=18.80 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=27.4
Q ss_pred EEeeCCCCCCC------hhHHHHHHHHHHHHHHHh--------ccCCCCCcEEEEEEEEC
Q 047153 55 VIWKSKTGQIG------KQEKEYEMILKRTLQSIC--------ILTINPNTTTSVIIQVW 100 (100)
Q Consensus 55 v~~~p~~g~~~------~~~~e~~~~l~~~l~~~I--------~~~~~P~~~i~i~v~v~ 100 (100)
|-++|..|..+ ....++...++++...+- .+++|=..--.|.||||
T Consensus 41 VliKas~ggGG~gm~iv~~~~eL~~~~~~~~~~s~~~fg~~~v~iek~i~~~reiEvqvi 100 (211)
T PF02786_consen 41 VLIKASAGGGGRGMRIVHNEEELEEAFERAQRESPAAFGDGPVLIEKFIEGAREIEVQVI 100 (211)
T ss_dssp EEEEETTSSTTTSEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSEEEEEEEEE
T ss_pred eEEeecccccccccccccchhhhhhhhhhccccCccccccceEEEeeehhhhhhhhhhhh
Confidence 34566554332 356688888888777663 55666666556666664
No 37
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=20.18 E-value=1.3e+02 Score=18.60 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHhc-cCCCCCcEEEEE
Q 047153 70 EYEMILKRTLQSICI-LTINPNTTTSVI 96 (100)
Q Consensus 70 e~~~~l~~~l~~~I~-~~~~P~~~i~i~ 96 (100)
....+=+.+|+.++. .++||...|.|.
T Consensus 74 nvnvl~retledav~~pekypqltirvs 101 (127)
T COG3445 74 NVNVLRRETLEDAVKHPEKYPQLTIRVS 101 (127)
T ss_pred eeeeeehhhHHHHhhCcccCCceEEEEe
Confidence 334444567777776 479999988875
No 38
>COG3232 HpaF 5-carboxymethyl-2-hydroxymuconate isomerase [Amino acid transport and metabolism]
Probab=20.00 E-value=2.5e+02 Score=17.93 Aligned_cols=52 Identities=15% Similarity=0.170 Sum_probs=34.1
Q ss_pred EEEEeCCeEEEEe-------eCCCCCceEEEEEeeCCCCCCChhHHHHHHHHHHHHHHH
Q 047153 31 ASWSQGDTKVLAA-------KNENPEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSI 82 (100)
Q Consensus 31 a~~~~G~T~V~~~-------~~~~~~~~~l~v~~~p~~g~~~~~~~e~~~~l~~~l~~~ 82 (100)
..|.+|.-+.=+. .+..++.++|+..++-.+|.....-+++...|-.++..-
T Consensus 33 G~FplggIRsRa~rld~y~maD~~~~~aFvH~tl~IgaGRs~e~rq~vge~Lf~~l~~~ 91 (127)
T COG3232 33 GLFPLGGIRSRALRLDAYRMADGAEDDAFVHMTLKIGAGRSEEQRQEVGEALFAVLTAH 91 (127)
T ss_pred CCCcccceeehhhhhhHHHhcccCCCcceEEEEEEecCCCCHHHHHHHHHHHHHHHHHH
Confidence 3777787776665 245678899999998777765555555555555444443
Done!