Query 033973
Match_columns 107
No_of_seqs 200 out of 1206
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 08:21:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0544 FKBP-type peptidyl-pro 100.0 2.6E-32 5.5E-37 162.3 9.4 97 1-107 1-98 (108)
2 COG0545 FkpA FKBP-type peptidy 100.0 6.5E-31 1.4E-35 176.1 9.6 94 2-107 102-195 (205)
3 KOG0549 FKBP-type peptidyl-pro 99.9 2.1E-27 4.6E-32 156.5 8.7 95 3-107 70-166 (188)
4 PRK11570 peptidyl-prolyl cis-t 99.9 3.4E-26 7.3E-31 155.8 11.0 94 2-107 103-196 (206)
5 TIGR03516 ppisom_GldI peptidyl 99.9 1.9E-25 4.1E-30 149.0 11.0 95 2-107 70-166 (177)
6 KOG0552 FKBP-type peptidyl-pro 99.9 1.1E-25 2.4E-30 153.7 9.7 94 2-107 121-216 (226)
7 PRK10902 FKBP-type peptidyl-pr 99.9 1.9E-23 4.2E-28 147.0 11.3 94 1-107 146-239 (269)
8 PF00254 FKBP_C: FKBP-type pep 99.9 1.1E-22 2.5E-27 122.7 8.6 84 15-107 4-87 (94)
9 PRK15095 FKBP-type peptidyl-pr 99.8 3E-18 6.5E-23 112.4 9.0 73 15-93 4-76 (156)
10 KOG0543 FKBP-type peptidyl-pro 99.7 1.1E-16 2.5E-21 116.6 9.9 92 2-107 85-180 (397)
11 COG1047 SlpA FKBP-type peptidy 99.7 1.2E-16 2.6E-21 105.6 9.0 73 15-93 2-74 (174)
12 PRK10737 FKBP-type peptidyl-pr 99.7 3.5E-16 7.7E-21 105.7 8.7 72 15-93 2-73 (196)
13 KOG0543 FKBP-type peptidyl-pro 99.2 6.5E-11 1.4E-15 86.8 6.5 74 9-107 1-75 (397)
14 TIGR00115 tig trigger factor. 99.0 3.6E-09 7.8E-14 78.5 9.3 71 14-93 145-215 (408)
15 PRK01490 tig trigger factor; P 98.9 1.1E-08 2.5E-13 76.5 9.4 70 14-92 156-225 (435)
16 COG0544 Tig FKBP-type peptidyl 98.8 2.9E-08 6.2E-13 74.6 7.2 59 16-81 158-216 (441)
17 KOG0545 Aryl-hydrocarbon recep 98.6 9.5E-09 2.1E-13 71.9 1.2 81 2-84 11-93 (329)
18 KOG0549 FKBP-type peptidyl-pro 97.9 5.2E-06 1.1E-10 55.5 1.0 41 52-94 1-41 (188)
19 PHA02122 hypothetical protein 70.0 12 0.00027 20.4 3.6 19 17-39 39-57 (65)
20 PF01272 GreA_GreB: Transcript 65.0 8.8 0.00019 21.8 2.6 25 59-83 42-66 (77)
21 PF09122 DUF1930: Domain of un 50.4 25 0.00054 19.7 2.7 23 61-83 35-57 (68)
22 TIGR01462 greA transcription e 39.5 42 0.0009 21.7 3.0 26 58-83 116-141 (151)
23 PRK00226 greA transcription el 39.2 36 0.00077 22.1 2.6 25 59-83 122-146 (157)
24 PRK05753 nucleoside diphosphat 38.1 38 0.00082 21.6 2.6 26 58-83 90-115 (137)
25 COG0024 Map Methionine aminope 36.5 1.4E+02 0.0031 21.3 5.4 51 15-76 86-146 (255)
26 cd01090 Creatinase Creatine am 35.9 1.4E+02 0.003 20.4 5.3 52 14-76 75-135 (228)
27 PF00639 Rotamase: PPIC-type P 35.1 46 0.001 19.3 2.5 26 54-79 57-82 (95)
28 TIGR01461 greB transcription e 34.9 51 0.0011 21.5 2.8 25 59-83 119-143 (156)
29 cd01088 MetAP2 Methionine Amin 34.3 1.1E+02 0.0023 22.0 4.6 52 14-76 69-126 (291)
30 TIGR00501 met_pdase_II methion 33.6 1.2E+02 0.0026 21.8 4.8 52 14-76 73-130 (295)
31 COG0425 SirA Predicted redox p 33.6 66 0.0014 18.4 2.9 23 63-85 22-44 (78)
32 PRK11536 6-N-hydroxylaminopuri 32.7 44 0.00096 23.3 2.4 23 2-27 143-165 (223)
33 PRK08671 methionine aminopepti 31.9 1.4E+02 0.003 21.4 4.9 51 14-75 70-126 (291)
34 cd03420 SirA_RHOD_Pry_redox Si 31.9 80 0.0017 17.3 3.0 23 63-85 16-38 (69)
35 cd03422 YedF YedF is a bacteri 31.4 83 0.0018 17.3 3.0 23 63-85 16-38 (69)
36 cd01089 PA2G4-like Related to 31.3 1.7E+02 0.0037 19.9 6.0 52 14-76 81-146 (228)
37 PRK05892 nucleoside diphosphat 30.1 64 0.0014 21.1 2.7 25 59-83 121-145 (158)
38 PTZ00053 methionine aminopepti 29.6 97 0.0021 24.2 3.9 52 14-76 232-289 (470)
39 TIGR00495 crvDNA_42K 42K curve 29.2 1.7E+02 0.0038 22.0 5.2 53 14-77 99-165 (389)
40 PRK01885 greB transcription el 28.3 74 0.0016 20.8 2.8 24 60-83 122-145 (157)
41 cd01736 LSm14_N LSm14 (also kn 26.7 59 0.0013 18.7 1.8 19 88-107 41-59 (74)
42 COG2139 RPL21A Ribosomal prote 25.7 84 0.0018 19.1 2.4 23 63-85 26-48 (98)
43 TIGR02925 cis_trans_EpsD pepti 25.3 56 0.0012 22.2 1.9 28 56-85 189-216 (232)
44 PF01206 TusA: Sulfurtransfera 25.1 1E+02 0.0023 16.6 2.7 23 63-85 17-39 (70)
45 COG0048 RpsL Ribosomal protein 24.2 1.4E+02 0.0031 19.0 3.3 24 2-25 66-89 (129)
46 PF03894 XFP: D-xylulose 5-pho 23.3 84 0.0018 21.3 2.3 26 58-84 141-166 (179)
47 COG2258 Uncharacterized protei 23.2 79 0.0017 21.9 2.2 25 2-29 140-164 (210)
48 cd03423 SirA SirA (also known 23.1 1.4E+02 0.0031 16.2 3.0 22 63-84 16-37 (69)
49 TIGR00686 phnA alkylphosphonat 23.1 96 0.0021 19.2 2.4 24 7-30 42-65 (109)
50 PRK11018 hypothetical protein; 22.9 1.4E+02 0.003 16.9 2.9 22 63-84 25-46 (78)
51 TIGR00500 met_pdase_I methioni 22.1 2.3E+02 0.0051 19.3 4.5 51 14-75 82-141 (247)
52 PRK00299 sulfur transfer prote 22.1 1.5E+02 0.0032 16.9 3.0 28 57-84 16-47 (81)
53 PF03831 PhnA: PhnA protein; 21.7 43 0.00093 18.2 0.6 23 8-30 2-24 (56)
54 PRK02268 hypothetical protein; 21.6 70 0.0015 20.7 1.6 26 59-84 25-50 (141)
55 COG4922 Uncharacterized protei 21.5 1.1E+02 0.0023 19.4 2.3 17 16-32 71-87 (129)
56 COG0298 HypC Hydrogenase matur 21.5 1.8E+02 0.0039 17.1 3.1 12 15-26 38-49 (82)
57 PLN03158 methionine aminopepti 21.2 3.8E+02 0.0081 20.4 5.7 52 14-76 216-276 (396)
58 PRK04980 hypothetical protein; 21.1 1.6E+02 0.0035 18.0 3.1 74 2-81 18-98 (102)
59 TIGR03595 Obg_CgtA_exten Obg f 20.8 87 0.0019 17.5 1.8 18 61-78 43-62 (69)
60 PF04014 Antitoxin-MazE: Antid 20.4 1.3E+02 0.0029 15.0 2.3 23 59-82 11-33 (47)
No 1
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=2.6e-32 Score=162.30 Aligned_cols=97 Identities=49% Similarity=0.850 Sum_probs=92.7
Q ss_pred CCeEEEEecccCCCC-CCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEE
Q 033973 1 MGIEKQILTPGNGPK-PVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLR 79 (107)
Q Consensus 1 ~Gl~~~~~~~G~g~~-~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ 79 (107)
||+.++++++|+|.. ++.||+|++||++.+.|| +.|||+.+++ +|+.|.+|.+++|.||++++..|.+||++++.
T Consensus 1 mGv~~~~i~~Gdg~tfpK~Gqtvt~hYtg~L~dG---~kfDSs~dr~-kPfkf~IGkgeVIkGwdegv~qmsvGekakLt 76 (108)
T KOG0544|consen 1 MGVEKQVISPGDGRTFPKKGQTVTVHYTGTLQDG---KKFDSSRDRG-KPFKFKIGKGEVIKGWDEGVAQMSVGEKAKLT 76 (108)
T ss_pred CCceeEEeeCCCCcccCCCCCEEEEEEEeEecCC---cEeecccccC-CCeeEEecCcceeechhhcchhccccccceee
Confidence 899999999999965 999999999999999888 9999999976 79999999999999999999999999999999
Q ss_pred ECCchhhccccCCCCCCCCccCCCCCCC
Q 033973 80 ITPMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 80 ip~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
|+|++| ||..|.+ .. |||||+|
T Consensus 77 i~pd~a--YG~~G~p---~~-IppNatL 98 (108)
T KOG0544|consen 77 ISPDYA--YGPRGHP---GG-IPPNATL 98 (108)
T ss_pred eccccc--cCCCCCC---Cc-cCCCcEE
Confidence 999999 9999987 66 9999986
No 2
>COG0545 FkpA FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=6.5e-31 Score=176.10 Aligned_cols=94 Identities=39% Similarity=0.685 Sum_probs=90.1
Q ss_pred CeEEEEecccCCCCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEEC
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRIT 81 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip 81 (107)
||+|++++.|+|..|+.+|.|.+||++++.|| ++|||+++++ +|+.|.++ .+|+||+++|.+|++|++|+++||
T Consensus 102 gl~y~~~~~G~G~~~~~~~~V~vhY~G~l~~G---~vFDsS~~rg-~p~~f~l~--~vI~Gw~egl~~M~vG~k~~l~IP 175 (205)
T COG0545 102 GLQYKVLKAGDGAAPKKGDTVTVHYTGTLIDG---TVFDSSYDRG-QPAEFPLG--GVIPGWDEGLQGMKVGGKRKLTIP 175 (205)
T ss_pred CcEEEEEeccCCCCCCCCCEEEEEEEEecCCC---CccccccccC-CCceeecC--CeeehHHHHHhhCCCCceEEEEeC
Confidence 79999999999999999999999999999999 9999999977 69999996 999999999999999999999999
Q ss_pred CchhhccccCCCCCCCCccCCCCCCC
Q 033973 82 PMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 82 ~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
|++| ||.+|.+ +. |||||+|
T Consensus 176 ~~la--YG~~g~~---g~-Ippns~L 195 (205)
T COG0545 176 PELA--YGERGVP---GV-IPPNSTL 195 (205)
T ss_pred chhc--cCcCCCC---CC-CCCCCeE
Confidence 9999 9999988 66 9999986
No 3
>KOG0549 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=2.1e-27 Score=156.51 Aligned_cols=95 Identities=36% Similarity=0.599 Sum_probs=84.4
Q ss_pred eEEEEecc--cCCCCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEE
Q 033973 3 IEKQILTP--GNGPKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRI 80 (107)
Q Consensus 3 l~~~~~~~--G~g~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~i 80 (107)
|+..++++ ....+.+.||++.+||++.+.|| ++||||+.++ +|+.|.+|.+++|+||+++|.+|++||++.++|
T Consensus 70 l~I~v~~~p~~C~~kak~GD~l~~HY~g~leDG---t~fdSS~~rg-~P~~f~LG~gqVIkG~Dqgl~gMCvGEkRkl~I 145 (188)
T KOG0549|consen 70 LQIGVLKKPEECPEKAKKGDTLHVHYTGSLEDG---TKFDSSYSRG-APFTFTLGTGQVIKGWDQGLLGMCVGEKRKLII 145 (188)
T ss_pred eeEEEEECCccccccccCCCEEEEEEEEEecCC---CEEeeeccCC-CCEEEEeCCCceeccHhHHhhhhCcccceEEec
Confidence 34444443 24455899999999999999888 9999999987 699999999999999999999999999999999
Q ss_pred CCchhhccccCCCCCCCCccCCCCCCC
Q 033973 81 TPMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 81 p~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
||+++ ||++|.+ +. ||++|+|
T Consensus 146 Pp~Lg--YG~~G~~---~~-IP~~A~L 166 (188)
T KOG0549|consen 146 PPHLG--YGERGAP---PK-IPGDAVL 166 (188)
T ss_pred Ccccc--CccCCCC---CC-CCCCeeE
Confidence 99999 9999999 87 9999976
No 4
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=99.94 E-value=3.4e-26 Score=155.82 Aligned_cols=94 Identities=31% Similarity=0.454 Sum_probs=88.1
Q ss_pred CeEEEEecccCCCCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEEC
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRIT 81 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip 81 (107)
||+|+++++|+|..|+.+|.|.+||++++.|| ++||++++++ .|+.|.++ .+++||+++|.+|++|++++++||
T Consensus 103 Gl~y~vi~~G~G~~p~~~d~V~v~Y~g~l~dG---~vfdss~~~g-~P~~f~l~--~vipG~~eaL~~M~~G~k~~~~IP 176 (206)
T PRK11570 103 GLQFRVLTQGEGAIPARTDRVRVHYTGKLIDG---TVFDSSVARG-EPAEFPVN--GVIPGWIEALTLMPVGSKWELTIP 176 (206)
T ss_pred CcEEEEEeCCCCCCCCCCCEEEEEEEEEECCC---CEEEeccCCC-CCeEEEee--chhhHHHHHHcCCCCCCEEEEEEC
Confidence 89999999999999999999999999999888 9999999855 59999994 799999999999999999999999
Q ss_pred CchhhccccCCCCCCCCccCCCCCCC
Q 033973 82 PMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 82 ~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
|++| ||+.|.+ +. ||||++|
T Consensus 177 ~~lA--YG~~g~~---~~-Ipp~s~L 196 (206)
T PRK11570 177 HELA--YGERGAG---AS-IPPFSTL 196 (206)
T ss_pred HHHc--CCCCCCC---CC-cCCCCeE
Confidence 9999 9999987 65 9999986
No 5
>TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype.
Probab=99.93 E-value=1.9e-25 Score=149.04 Aligned_cols=95 Identities=19% Similarity=0.240 Sum_probs=87.0
Q ss_pred CeEEEEecc--cCCCCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEE
Q 033973 2 GIEKQILTP--GNGPKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLR 79 (107)
Q Consensus 2 Gl~~~~~~~--G~g~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ 79 (107)
|++|.+++. |+|..|+.||.|.+||++++.|| ++|+++++. .|+.|.+|.+++++||+++|.+|++||+++|+
T Consensus 70 Gl~Y~v~~~~~g~g~~p~~gd~V~v~Y~~~~~dG---~v~~ss~~~--~P~~f~vg~~~vi~Gl~e~L~~Mk~Ge~~~~~ 144 (177)
T TIGR03516 70 GFWYYYNQKDTGEGTTPEFGDLVTFEYDIRALDG---DVIYSEEEL--GPQTYKVDQQDLFSGLRDGLKLMKEGETATFL 144 (177)
T ss_pred ccEEEEEEecCCCCCcCCCCCEEEEEEEEEeCCC---CEEEeCCCC--CCEEEEeCCcchhHHHHHHHcCCCCCCEEEEE
Confidence 788988866 66677999999999999999888 999999873 49999999999999999999999999999999
Q ss_pred ECCchhhccccCCCCCCCCccCCCCCCC
Q 033973 80 ITPMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 80 ip~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
|||++| ||.+|.+ +. |||||+|
T Consensus 145 iP~~~A--YG~~g~~---~~-Ippns~L 166 (177)
T TIGR03516 145 FPSHKA--YGYYGDQ---NK-IGPNLPI 166 (177)
T ss_pred ECHHHc--CCCCCCC---CC-cCcCCcE
Confidence 999999 9999987 66 9999986
No 6
>KOG0552 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=1.1e-25 Score=153.74 Aligned_cols=94 Identities=38% Similarity=0.634 Sum_probs=89.3
Q ss_pred CeEEEEecccCCCCCCCCCEEEEEEEEEEe-CCCceeEEecccCCCCccEE-EEeCCCCCcccHHHHhcCCCCCcEEEEE
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVHCTGYGK-NGDLSQKFWSTKDPGQQPFT-FQIGKGSVIKGWDEGVMGMQVGEVARLR 79 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~y~~~~~-~gg~~~~~~st~~~~~~p~~-~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ 79 (107)
||+|+.++.|+|..+..|+.|.+||.+++. +| ++||++... +|+. |.+|.+.+|+||+.+|.+|++|.+|+|+
T Consensus 121 Gl~y~D~~vG~G~~a~~G~rV~v~Y~Gkl~~~G---kvFd~~~~~--kp~~~f~lg~g~VIkG~d~gv~GMkvGGkRrvi 195 (226)
T KOG0552|consen 121 GLRYEDLRVGSGPSAKKGKRVSVRYIGKLKGNG---KVFDSNFGG--KPFKLFRLGSGEVIKGWDVGVEGMKVGGKRRVI 195 (226)
T ss_pred CcEEEEEEecCCCCCCCCCEEEEEEEEEecCCC---eEeecccCC--CCccccccCCCCCCchHHHhhhhhccCCeeEEE
Confidence 899999999999999999999999999998 55 999999973 6888 9999999999999999999999999999
Q ss_pred ECCchhhccccCCCCCCCCccCCCCCCC
Q 033973 80 ITPMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 80 ip~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
|||++| ||.+|.+ .|||||+|
T Consensus 196 IPp~lg--Yg~~g~~-----~IppnstL 216 (226)
T KOG0552|consen 196 IPPELG--YGKKGVP-----EIPPNSTL 216 (226)
T ss_pred eCcccc--ccccCcC-----cCCCCCcE
Confidence 999999 9999998 59999997
No 7
>PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=99.90 E-value=1.9e-23 Score=147.03 Aligned_cols=94 Identities=26% Similarity=0.498 Sum_probs=86.8
Q ss_pred CCeEEEEecccCCCCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEE
Q 033973 1 MGIEKQILTPGNGPKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRI 80 (107)
Q Consensus 1 ~Gl~~~~~~~G~g~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~i 80 (107)
-||+|+++++|+|..|+.+|.|.+||++++.|| ++|++++.++ .|+.|.+ +.+++||+++|.+|++|++++|+|
T Consensus 146 sGl~y~Vi~~G~G~~p~~gD~V~V~Y~g~l~dG---~vfdss~~~g-~p~~f~l--~~vipG~~EaL~~Mk~Gek~~l~I 219 (269)
T PRK10902 146 TGLLYKVEKEGTGEAPKDSDTVVVNYKGTLIDG---KEFDNSYTRG-EPLSFRL--DGVIPGWTEGLKNIKKGGKIKLVI 219 (269)
T ss_pred CccEEEEEeCCCCCCCCCCCEEEEEEEEEeCCC---CEeeccccCC-CceEEec--CCcchHHHHHHhcCCCCcEEEEEE
Confidence 389999999999999999999999999998888 9999998755 5999988 579999999999999999999999
Q ss_pred CCchhhccccCCCCCCCCccCCCCCCC
Q 033973 81 TPMVLVDFHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 81 p~~~a~~yG~~g~~~~~~~~ipp~s~l 107 (107)
|++++ ||..|.+ +||||++|
T Consensus 220 P~~la--YG~~g~~-----gIppns~L 239 (269)
T PRK10902 220 PPELA--YGKAGVP-----GIPANSTL 239 (269)
T ss_pred Cchhh--CCCCCCC-----CCCCCCcE
Confidence 99999 9999876 59999986
No 8
>PF00254 FKBP_C: FKBP-type peptidyl-prolyl cis-trans isomerase; InterPro: IPR001179 Synonym(s): Peptidylprolyl cis-trans isomerase FKBP-type peptidylprolyl isomerases (5.2.1.8 from EC) in vertebrates, are receptors for the two immunosuppressants, FK506 and rapamycin. The drugs inhibit T cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. Peptidylprolyl isomerases accelerate protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides. These proteins are found in a variety of organisms.; GO: 0006457 protein folding; PDB: 1IX5_A 3JXV_A 3JYM_A 1T11_A 1PBK_A 1FD9_A 2VCD_A 3B7X_A 1Q6H_B 1Q6I_B ....
Probab=99.89 E-value=1.1e-22 Score=122.69 Aligned_cols=84 Identities=33% Similarity=0.616 Sum_probs=76.3
Q ss_pred CCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCCCC
Q 033973 15 KPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGGFN 94 (107)
Q Consensus 15 ~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g~~ 94 (107)
+++.||.|.+||++++.++ ++|++++..+ .|+.|.+|.+++++||+++|.+|++||++++.||+++| ||+.+..
T Consensus 4 ~~~~gd~V~i~y~~~~~~g---~~~~~~~~~~-~~~~~~~g~~~~i~g~e~al~~m~~Ge~~~~~vp~~~a--yg~~~~~ 77 (94)
T PF00254_consen 4 TPKEGDTVTIHYTGRLEDG---KVFDSSYQEG-EPFEFRLGSGQVIPGLEEALIGMKVGEKREFYVPPELA--YGEKGLE 77 (94)
T ss_dssp SBSTTSEEEEEEEEEETTS---EEEEETTTTT-SEEEEETTSSSSSHHHHHHHTTSBTTEEEEEEEEGGGT--TTTTTBC
T ss_pred cCCCCCEEEEEEEEEECCC---cEEEEeeecC-cceeeeeccCccccchhhhcccccCCCEeeeEeCChhh--cCccccC
Confidence 4899999999999999876 9999997644 69999999999999999999999999999999999999 9999885
Q ss_pred CCCCccCCCCCCC
Q 033973 95 LTQSWILRYKSCR 107 (107)
Q Consensus 95 ~~~~~~ipp~s~l 107 (107)
+..|||+++|
T Consensus 78 ---~~~ip~~~~l 87 (94)
T PF00254_consen 78 ---PPKIPPNSTL 87 (94)
T ss_dssp ---TTTBTTTSEE
T ss_pred ---CCCcCCCCeE
Confidence 4349999975
No 9
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=99.77 E-value=3e-18 Score=112.43 Aligned_cols=73 Identities=26% Similarity=0.436 Sum_probs=67.4
Q ss_pred CCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCCC
Q 033973 15 KPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGGF 93 (107)
Q Consensus 15 ~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g~ 93 (107)
.++.++.|.+||++++.|| ++||+|+..+ .|+.|.+|.+++++||+++|.+|++|+++++.|||++| ||.+..
T Consensus 4 ~i~~~~~V~v~Y~~~~~dG---~v~dst~~~~-~P~~f~~G~g~vi~gle~aL~gm~~Ge~~~v~ipp~~a--yG~~d~ 76 (156)
T PRK15095 4 SVQSNSAVLVHFTLKLDDG---STAESTRNNG-KPALFRLGDGSLSEGLEQQLLGLKVGDKKTFSLEPEAA--FGVPSP 76 (156)
T ss_pred ccCCCCEEEEEEEEEeCCC---CEEEECCCCC-CCEEEEeCCCCccHHHHHHHcCCCCCCEEEEEEChHHh--cCCCCh
Confidence 5889999999999999777 9999998744 69999999999999999999999999999999999999 998754
No 10
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=99.70 E-value=1.1e-16 Score=116.60 Aligned_cols=92 Identities=32% Similarity=0.451 Sum_probs=78.7
Q ss_pred CeEEEEecccCC--CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCC-CCCcccHHHHhcCCCCCcEEEE
Q 033973 2 GIEKQILTPGNG--PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGK-GSVIKGWDEGVMGMQVGEVARL 78 (107)
Q Consensus 2 Gl~~~~~~~G~g--~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~-~~~i~g~~~~l~~m~~Ge~~~v 78 (107)
+|.++|+++|.| ..|..|..|.+||.+++.++ +|+++.. .+.|..|+ ..++.||+.+|..|++||.+.|
T Consensus 85 ~iiKriir~G~gd~~~P~~g~~V~v~~~G~~~~~----~f~~~~~----~fe~~~Ge~~~vi~Gle~al~~M~~GE~a~v 156 (397)
T KOG0543|consen 85 GIIKRIIREGEGDYSRPNKGAVVKVHLEGELEDG----VFDQREL----RFEFGEGEDIDVIEGLEIALRMMKVGEVALV 156 (397)
T ss_pred ceEEeeeecCCCCCCCCCCCcEEEEEEEEEECCc----ceecccc----ceEEecCCccchhHHHHHHHHhcCccceEEE
Confidence 688999999999 45999999999999998544 7776543 57888887 5899999999999999999999
Q ss_pred EECCchhhccccC-CCCCCCCccCCCCCCC
Q 033973 79 RITPMVLVDFHNG-GFNLTQSWILRYKSCR 107 (107)
Q Consensus 79 ~ip~~~a~~yG~~-g~~~~~~~~ipp~s~l 107 (107)
+|+|++| ||+. +++ +. |||||+|
T Consensus 157 ~i~~~Ya--yG~~~~~~---p~-IPPnA~l 180 (397)
T KOG0543|consen 157 TIDPKYA--YGEEGGEP---PL-IPPNATL 180 (397)
T ss_pred EeCcccc--cCCCCCCC---CC-CCCCceE
Confidence 9999999 9954 444 55 9999986
No 11
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=99.70 E-value=1.2e-16 Score=105.63 Aligned_cols=73 Identities=30% Similarity=0.439 Sum_probs=67.4
Q ss_pred CCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCCC
Q 033973 15 KPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGGF 93 (107)
Q Consensus 15 ~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g~ 93 (107)
.++.||.|.+||++++.|+ ++||+|... +.|+.|.+|.+++++||++||.+|.+|++..+.|||+.| ||.+..
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg---~v~Dtt~e~-~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~A--fGe~~~ 74 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDG---EVVDTTDEN-YGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDA--FGEYDP 74 (174)
T ss_pred cccCCCEEEEEEEEEecCC---cEEEccccc-CCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHh--cCCCCh
Confidence 4789999999999999886 999999872 359999999999999999999999999999999999999 998754
No 12
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=99.67 E-value=3.5e-16 Score=105.67 Aligned_cols=72 Identities=17% Similarity=0.221 Sum_probs=66.7
Q ss_pred CCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCCC
Q 033973 15 KPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGGF 93 (107)
Q Consensus 15 ~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g~ 93 (107)
+++.++.|+++|++++.+| ++|++|+. ..|+.|.+|.++++|+|+++|.+|++|++++|.|||+.| ||.+..
T Consensus 2 kI~~~~vV~l~Y~l~~~dG---~v~dst~~--~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeA--yGe~d~ 73 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDG---VLVDESPV--SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDA--YGQYDE 73 (196)
T ss_pred ccCCCCEEEEEEEEEeCCC---CEEEecCC--CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHh--cCCCCh
Confidence 4788999999999999777 99999986 369999999999999999999999999999999999999 998754
No 13
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=99.18 E-value=6.5e-11 Score=86.78 Aligned_cols=74 Identities=45% Similarity=0.761 Sum_probs=65.9
Q ss_pred cccCCCC-CCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhc
Q 033973 9 TPGNGPK-PVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVD 87 (107)
Q Consensus 9 ~~G~g~~-~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~ 87 (107)
++|+|.. |..||.|.+||++++.|| +.||||.+ + .|+.|.+|.+.++.+|+.++..|+.
T Consensus 1 ~eg~g~~~p~~g~~v~~hytg~l~dg---t~fdss~d-~-~~~~~~lg~g~vi~~~~~gv~tm~~--------------- 60 (397)
T KOG0543|consen 1 KEGTGTETPMTGDKVEVHYTGTLLDG---TKFDSSRD-G-DPFKFDLGKGSVIKGWDLGVATMKK--------------- 60 (397)
T ss_pred CCCCCccCCCCCceeEEEEeEEecCC---eecccccC-C-CceeeecCCCccccccccccccccc---------------
Confidence 4788876 999999999999999999 99999998 4 6999999999999999999999987
Q ss_pred cccCCCCCCCCccCCCCCCC
Q 033973 88 FHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 88 yG~~g~~~~~~~~ipp~s~l 107 (107)
|+.+.+ |. ||++++|
T Consensus 61 -g~~~~p---p~-ip~~a~l 75 (397)
T KOG0543|consen 61 -GEAGSP---PK-IPSNATL 75 (397)
T ss_pred -cccCCC---CC-CCCCcce
Confidence 466777 76 8888875
No 14
>TIGR00115 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.
Probab=98.99 E-value=3.6e-09 Score=78.53 Aligned_cols=71 Identities=27% Similarity=0.565 Sum_probs=62.7
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCCC
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGGF 93 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g~ 93 (107)
.+++.||.|.++|+++. +| +.++++.. .++.|.+|.+.+++||+++|.||++|+++.+.++.... |+....
T Consensus 145 ~~~~~gD~V~v~~~~~~-dg---~~~~~~~~---~~~~~~lg~~~~~~~~ee~L~G~k~Gd~~~~~v~~p~~--~~~~~~ 215 (408)
T TIGR00115 145 RAAEKGDRVTIDFEGFI-DG---EAFEGGKA---ENFSLELGSGQFIPGFEEQLVGMKAGEEKEIKVTFPED--YHAEEL 215 (408)
T ss_pred cccCCCCEEEEEEEEEE-CC---EECcCCCC---CCeEEEECCCCcchhHHHHhCCCCCCCeeEEEecCccc--cCcccC
Confidence 35899999999999986 77 88988754 58999999999999999999999999999999998777 876554
No 15
>PRK01490 tig trigger factor; Provisional
Probab=98.91 E-value=1.1e-08 Score=76.47 Aligned_cols=70 Identities=27% Similarity=0.525 Sum_probs=61.2
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCC
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGG 92 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g 92 (107)
.+++.||.|.++|.++. +| +.|+++.. .++.|.+|.+.+++||+++|.||++|+++.+.++.... |+...
T Consensus 156 ~~~~~gD~V~vd~~~~~-~g---~~~~~~~~---~~~~~~lg~~~~~~~fee~L~G~k~Ge~~~~~~~~p~~--~~~~~ 225 (435)
T PRK01490 156 RPAENGDRVTIDFVGSI-DG---EEFEGGKA---EDFSLELGSGRFIPGFEEQLVGMKAGEEKTIDVTFPED--YHAED 225 (435)
T ss_pred ccCCCCCEEEEEEEEEE-CC---EECcCCCC---CceEEEEcCCCcchhHHHHhCCCCCCCeeEEEecCccc--ccccc
Confidence 35899999999999997 77 88887654 58999999999999999999999999999999987777 76543
No 16
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=98.76 E-value=2.9e-08 Score=74.61 Aligned_cols=59 Identities=29% Similarity=0.658 Sum_probs=52.5
Q ss_pred CCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEEEC
Q 033973 16 PVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLRIT 81 (107)
Q Consensus 16 ~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip 81 (107)
++.||.|+|+|.++. || ..|.+... ..+.+.+|++++||||+++|.||+.|++..|.+.
T Consensus 158 a~~gD~v~IDf~g~i-Dg---~~fegg~a---e~~~l~lGs~~fipgFe~~LvG~k~Ge~k~i~vt 216 (441)
T COG0544 158 AENGDRVTIDFEGSV-DG---EEFEGGKA---ENFSLELGSGRFIPGFEDQLVGMKAGEEKDIKVT 216 (441)
T ss_pred cccCCEEEEEEEEEE-cC---eeccCccc---cCeEEEEcCCCchhhHHhhhccCcCCCeeEEEEE
Confidence 899999999999976 88 88887654 5799999999999999999999999999886554
No 17
>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=9.5e-09 Score=71.94 Aligned_cols=81 Identities=25% Similarity=0.386 Sum_probs=70.2
Q ss_pred CeEEEEecccCCCC--CCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCCCcccHHHHhcCCCCCcEEEEE
Q 033973 2 GIEKQILTPGNGPK--PVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGSVIKGWDEGVMGMQVGEVARLR 79 (107)
Q Consensus 2 Gl~~~~~~~G~g~~--~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ 79 (107)
||+++++..|+|.- ..+|..|.+||.....++ +++++|+|...+ +|+.+++|+..-++-||..|..|+++|.+.|+
T Consensus 11 gv~Kril~~G~g~l~e~~dGTrv~FHfrtl~~~e-~~tviDDsRk~g-kPmeiiiGkkFkL~VwE~il~tM~v~EvaqF~ 88 (329)
T KOG0545|consen 11 GVKKRILHGGTGELPEFIDGTRVIFHFRTLKCDE-ERTVIDDSRKVG-KPMEIIIGKKFKLEVWEIILTTMRVHEVAQFW 88 (329)
T ss_pred hhhHhhccCCCccCccccCCceEEEEEEecccCc-ccccccchhhcC-CCeEEeeccccccHHHHHHHHHHhhhhHHHhh
Confidence 78899999999975 778999999999876543 237999999876 69999999999999999999999999999988
Q ss_pred ECCch
Q 033973 80 ITPMV 84 (107)
Q Consensus 80 ip~~~ 84 (107)
+.-..
T Consensus 89 ~d~~~ 93 (329)
T KOG0545|consen 89 CDTIH 93 (329)
T ss_pred hhhhh
Confidence 86443
No 18
>KOG0549 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=5.2e-06 Score=55.48 Aligned_cols=41 Identities=39% Similarity=0.669 Sum_probs=36.6
Q ss_pred EEeCCCCCcccHHHHhcCCCCCcEEEEEECCchhhccccCCCC
Q 033973 52 FQIGKGSVIKGWDEGVMGMQVGEVARLRITPMVLVDFHNGGFN 94 (107)
Q Consensus 52 ~~~G~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a~~yG~~g~~ 94 (107)
|.+|.+.++++++++|.+|+.|+++++.+||+++ ||..+..
T Consensus 1 ~~~g~~~vi~gm~~~~~g~c~ge~rkvv~pp~l~--fg~~~~~ 41 (188)
T KOG0549|consen 1 FTLGQGFVIPGMDQALEGMCNGEKRKVVIPPHLG--FGEGGRG 41 (188)
T ss_pred CcccceEEecCHHHHhhhhhccccceeccCCccc--ccccccc
Confidence 3567889999999999999999999999999999 9966554
No 19
>PHA02122 hypothetical protein
Probab=70.00 E-value=12 Score=20.38 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=15.7
Q ss_pred CCCCEEEEEEEEEEeCCCceeEE
Q 033973 17 VAGQKVTVHCTGYGKNGDLSQKF 39 (107)
Q Consensus 17 ~~gd~V~v~y~~~~~~gg~~~~~ 39 (107)
..||.|.++|.... +| +.|
T Consensus 39 ~~gd~v~vn~e~~~-ng---~l~ 57 (65)
T PHA02122 39 DDGDEVIVNFELVV-NG---KLI 57 (65)
T ss_pred cCCCEEEEEEEEEE-CC---EEE
Confidence 47999999999986 77 665
No 20
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=64.98 E-value=8.8 Score=21.80 Aligned_cols=25 Identities=12% Similarity=0.288 Sum_probs=19.2
Q ss_pred CcccHHHHhcCCCCCcEEEEEECCc
Q 033973 59 VIKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 59 ~i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
...-+-.||.+.++|+.+.+.+|..
T Consensus 42 ~~SPLG~ALlG~~~Gd~v~~~~~~g 66 (77)
T PF01272_consen 42 IDSPLGKALLGKKVGDEVEVELPGG 66 (77)
T ss_dssp TTSHHHHHHTT-BTT-EEEEEETTB
T ss_pred ecCHHHHHhcCCCCCCEEEEEeCCc
Confidence 3445889999999999999999864
No 21
>PF09122 DUF1930: Domain of unknown function (DUF1930); InterPro: IPR015206 This entry represents a domain found in 3-mercaptopyruvate sulphurtransferase which has no known function. This domain adopts a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase []. ; PDB: 1OKG_A.
Probab=50.38 E-value=25 Score=19.66 Aligned_cols=23 Identities=13% Similarity=0.290 Sum_probs=17.8
Q ss_pred ccHHHHhcCCCCCcEEEEEECCc
Q 033973 61 KGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 61 ~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
+.+..|+.-|..||++.++..+.
T Consensus 35 ~El~sA~~HlH~GEkA~V~FkS~ 57 (68)
T PF09122_consen 35 AELKSALVHLHIGEKAQVFFKSQ 57 (68)
T ss_dssp HHHHHHHTT-BTT-EEEEEETTS
T ss_pred HHHHHHHHHhhcCceeEEEEecC
Confidence 56889999999999999988654
No 22
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=39.54 E-value=42 Score=21.67 Aligned_cols=26 Identities=19% Similarity=0.353 Sum_probs=21.8
Q ss_pred CCcccHHHHhcCCCCCcEEEEEECCc
Q 033973 58 SVIKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 58 ~~i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
+...-+-.+|.|.++|+.+.+.+|..
T Consensus 116 S~~SPlG~ALlG~~~Gd~v~v~~p~g 141 (151)
T TIGR01462 116 SIDSPLGKALIGKKVGDVVEVQTPKG 141 (151)
T ss_pred cCCCHHHHHHcCCCCCCEEEEEeCCC
Confidence 44556889999999999999998854
No 23
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=39.19 E-value=36 Score=22.08 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=21.1
Q ss_pred CcccHHHHhcCCCCCcEEEEEECCc
Q 033973 59 VIKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 59 ~i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
...-+-.+|.|.++|+.+.+.+|..
T Consensus 122 ~~SPlG~aLlGk~~Gd~v~~~~p~g 146 (157)
T PRK00226 122 IESPIARALIGKKVGDTVEVTTPGG 146 (157)
T ss_pred cCChHHHHHhCCCCCCEEEEEcCCC
Confidence 4455889999999999999999864
No 24
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=38.09 E-value=38 Score=21.62 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=21.6
Q ss_pred CCcccHHHHhcCCCCCcEEEEEECCc
Q 033973 58 SVIKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 58 ~~i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
++..-+-.||.|.++|+.+.+..|..
T Consensus 90 Si~SPlG~ALlG~~~Gd~v~v~~p~G 115 (137)
T PRK05753 90 SVLAPVGAALLGLSVGQSIDWPLPGG 115 (137)
T ss_pred cccCHHHHHHcCCCCCCEEEEECCCC
Confidence 34566889999999999999988753
No 25
>COG0024 Map Methionine aminopeptidase [Translation, ribosomal structure and biogenesis]
Probab=36.49 E-value=1.4e+02 Score=21.30 Aligned_cols=51 Identities=18% Similarity=0.200 Sum_probs=34.8
Q ss_pred CCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCC------Cc----ccHHHHhcCCCCCcEE
Q 033973 15 KPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGS------VI----KGWDEGVMGMQVGEVA 76 (107)
Q Consensus 15 ~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~------~i----~g~~~~l~~m~~Ge~~ 76 (107)
.+++||.|.|+..... || -.-|+ ..+|.+|... ++ .+|+.++..+++|-+.
T Consensus 86 vlk~GDiv~IDvg~~~-dG---~~~Ds-------a~T~~vg~~~~~~~~~L~~~t~eal~~~I~~vkpG~~l 146 (255)
T COG0024 86 VLKEGDIVKIDVGAHI-DG---YIGDT-------AITFVVGEVSDEDAKRLLEATKEALYAGIEAVKPGARL 146 (255)
T ss_pred ccCCCCEEEEEEEEEE-CC---eeeeE-------EEEEECCCCChHHHHHHHHHHHHHHHHHHHhccCCCCH
Confidence 4899999999999886 77 45553 4667777321 33 4566777777777654
No 26
>cd01090 Creatinase Creatine amidinohydrolase. E.C.3.5.3.3. Hydrolyzes creatine to sarcosine and urea.
Probab=35.88 E-value=1.4e+02 Score=20.41 Aligned_cols=52 Identities=13% Similarity=0.109 Sum_probs=32.2
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC---------CCcccHHHHhcCCCCCcEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG---------SVIKGWDEGVMGMQVGEVA 76 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~---------~~i~g~~~~l~~m~~Ge~~ 76 (107)
..+++||.|.+++-... ++ -.-|. ..+|.+|+- .+..+.+.++..+++|-++
T Consensus 75 r~l~~GD~v~~d~g~~~-~G---Y~ad~-------~RT~~vG~~~~~~~~~~~~~~ea~~~~~~~~rpG~~~ 135 (228)
T cd01090 75 RKVQRGDILSLNCFPMI-AG---YYTAL-------ERTLFLDEVSDAHLKIWEANVAVHERGLELIKPGARC 135 (228)
T ss_pred cccCCCCEEEEEEeEEE-CC---Eeeee-------EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCCCcH
Confidence 44899999999988764 55 33332 344556532 2345566667777777654
No 27
>PF00639 Rotamase: PPIC-type PPIASE domain; InterPro: IPR000297 Peptidylprolyl isomerase (5.2.1.8 from EC) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides []. It has been reported in bacteria and eukayotes. Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.; GO: 0016853 isomerase activity; PDB: 2JZV_A 2PV3_B 1M5Y_A 2PV2_B 2PV1_A 1JNS_A 1JNT_A 3KAB_A 2ZR6_A 2XPB_A ....
Probab=35.14 E-value=46 Score=19.32 Aligned_cols=26 Identities=19% Similarity=0.498 Sum_probs=21.9
Q ss_pred eCCCCCcccHHHHhcCCCCCcEEEEE
Q 033973 54 IGKGSVIKGWDEGVMGMQVGEVARLR 79 (107)
Q Consensus 54 ~G~~~~i~g~~~~l~~m~~Ge~~~v~ 79 (107)
+..+.+.+.|+++|..|++|+....+
T Consensus 57 ~~~~~l~~~~~~~~~~l~~Gevs~pi 82 (95)
T PF00639_consen 57 ISRGQLPPEFEKALFALKPGEVSKPI 82 (95)
T ss_dssp EETTSSBHHHHHHHHTSTTTSBEEEE
T ss_pred ccCCcccHHHHHHHHhCCCCCcCCCE
Confidence 44578999999999999999987544
No 28
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=34.95 E-value=51 Score=21.53 Aligned_cols=25 Identities=8% Similarity=0.120 Sum_probs=21.1
Q ss_pred CcccHHHHhcCCCCCcEEEEEECCc
Q 033973 59 VIKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 59 ~i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
...=+-.||.|.++|+.+.+.+|..
T Consensus 119 ~~SPlG~ALlGk~~GD~v~v~~p~g 143 (156)
T TIGR01461 119 IDSPLARALLKKEVGDEVVVNTPAG 143 (156)
T ss_pred CCCHHHHHHcCCCCCCEEEEEcCCC
Confidence 4455889999999999999998864
No 29
>cd01088 MetAP2 Methionine Aminopeptidase 2. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Probab=34.29 E-value=1.1e+02 Score=21.97 Aligned_cols=52 Identities=12% Similarity=0.029 Sum_probs=33.1
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC------CCcccHHHHhcCCCCCcEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG------SVIKGWDEGVMGMQVGEVA 76 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~------~~i~g~~~~l~~m~~Ge~~ 76 (107)
..+++||.|.++.-+.. +| -.-|. ..+|.+|.. ....+++.++..|++|-+.
T Consensus 69 ~~l~~GDvV~iD~G~~~-dG---Y~sD~-------arT~~vg~~~~~l~ea~~~A~~~ai~~ikPG~~~ 126 (291)
T cd01088 69 TVLKEGDVVKLDFGAHV-DG---YIADS-------AFTVDFDPKYDDLLEAAKEALNAAIKEAGPDVRL 126 (291)
T ss_pred cccCCCCEEEEEEEEEE-CC---EEEEE-------EEEEecChhHHHHHHHHHHHHHHHHHHhcCCCcH
Confidence 45899999999987654 66 44443 234555532 1345567777777877654
No 30
>TIGR00501 met_pdase_II methionine aminopeptidase, type II. Methionine aminopeptidase (map) is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. The role of this protein in general is to produce the mature amino end of cytosolic proteins by removing the N-terminal methionine. This model describes type II, among which the eukaryotic members typically have an N-terminal extension not present in archaeal members. It can act cotranslationally. The enzyme from rat has been shown to associate with translation initiation factor 2 (IF-2) and may have a role in translational regulation.
Probab=33.60 E-value=1.2e+02 Score=21.75 Aligned_cols=52 Identities=12% Similarity=0.091 Sum_probs=32.6
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC--C----CcccHHHHhcCCCCCcEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG--S----VIKGWDEGVMGMQVGEVA 76 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~--~----~i~g~~~~l~~m~~Ge~~ 76 (107)
..+++||.|.+++-+.. || -.-|. ..+|.+|.. . ...+++.++..+++|-+.
T Consensus 73 ~~l~~GDvV~iD~G~~~-dG---Y~aD~-------arT~~vG~~~~~l~~a~~~A~~aai~~~kPGv~~ 130 (295)
T TIGR00501 73 TVFKDGDVVKLDLGAHV-DG---YIADT-------AITVDLGDQYDNLVKAAKDALYTAIKEIRAGVRV 130 (295)
T ss_pred ccCCCCCEEEEEEeEEE-CC---EEEEE-------EEEEEeCcHHHHHHHHHHHHHHHHHHHhcCCCCH
Confidence 45899999999987665 66 54443 344556542 1 234566666777776544
No 31
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=33.55 E-value=66 Score=18.43 Aligned_cols=23 Identities=9% Similarity=0.120 Sum_probs=19.8
Q ss_pred HHHHhcCCCCCcEEEEEECCchh
Q 033973 63 WDEGVMGMQVGEVARLRITPMVL 85 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~a 85 (107)
...+|..|++|+..+|......+
T Consensus 22 ~kk~l~~m~~Ge~LeV~~ddp~~ 44 (78)
T COG0425 22 TKKALAKLKPGEILEVIADDPAA 44 (78)
T ss_pred HHHHHHcCCCCCEEEEEecCcch
Confidence 67899999999999999876554
No 32
>PRK11536 6-N-hydroxylaminopurine resistance protein; Provisional
Probab=32.67 E-value=44 Score=23.31 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=18.5
Q ss_pred CeEEEEecccCCCCCCCCCEEEEEEE
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVHCT 27 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~y~ 27 (107)
|.+++++++|. +..||.|.+--.
T Consensus 143 G~Y~RVL~~G~---V~~GD~v~l~~r 165 (223)
T PRK11536 143 GWLYRVIAPGK---VSADAPLELVSR 165 (223)
T ss_pred EEEEEEECCcE---EcCCCEEEEEeC
Confidence 78999999875 788998877544
No 33
>PRK08671 methionine aminopeptidase; Provisional
Probab=31.94 E-value=1.4e+02 Score=21.35 Aligned_cols=51 Identities=12% Similarity=0.065 Sum_probs=32.2
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC--C----CcccHHHHhcCCCCCcE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG--S----VIKGWDEGVMGMQVGEV 75 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~--~----~i~g~~~~l~~m~~Ge~ 75 (107)
..+++||.|.+++-+.. +| -.-|. ..++.+|.. . ...+++.++..+++|-+
T Consensus 70 ~~l~~GDvV~iD~G~~~-dG---Y~aD~-------arT~~vG~~~~~l~~a~~~a~~aai~~ikpG~~ 126 (291)
T PRK08671 70 RVFPEGDVVKLDLGAHV-DG---YIADT-------AVTVDLGGKYEDLVEASEEALEAAIEVVRPGVS 126 (291)
T ss_pred cccCCCCEEEEEEeEEE-CC---EEEEE-------EEEEEeChhHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 34899999999987654 66 54443 344556532 1 23456667777777754
No 34
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=31.89 E-value=80 Score=17.31 Aligned_cols=23 Identities=13% Similarity=0.154 Sum_probs=19.0
Q ss_pred HHHHhcCCCCCcEEEEEECCchh
Q 033973 63 WDEGVMGMQVGEVARLRITPMVL 85 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~a 85 (107)
..++|..|+.|+..++...-.-+
T Consensus 16 ~kkal~~l~~G~~l~V~~d~~~a 38 (69)
T cd03420 16 LKKEIDKLQDGEQLEVKASDPGF 38 (69)
T ss_pred HHHHHHcCCCCCEEEEEECCccH
Confidence 78899999999999998874433
No 35
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=31.41 E-value=83 Score=17.29 Aligned_cols=23 Identities=13% Similarity=0.001 Sum_probs=18.7
Q ss_pred HHHHhcCCCCCcEEEEEECCchh
Q 033973 63 WDEGVMGMQVGEVARLRITPMVL 85 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~a 85 (107)
..++|..|..|+..++.+.-..+
T Consensus 16 ~kkal~~l~~G~~l~V~~d~~~s 38 (69)
T cd03422 16 TLEALPSLKPGEILEVISDCPQS 38 (69)
T ss_pred HHHHHHcCCCCCEEEEEecCchH
Confidence 57899999999999998874443
No 36
>cd01089 PA2G4-like Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control.
Probab=31.35 E-value=1.7e+02 Score=19.87 Aligned_cols=52 Identities=12% Similarity=0.052 Sum_probs=32.5
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCCC--------------CcccHHHHhcCCCCCcEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKGS--------------VIKGWDEGVMGMQVGEVA 76 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~~--------------~i~g~~~~l~~m~~Ge~~ 76 (107)
..+++||.|.+++-+.. +| -.-|. ..+|.+|... ...+.+.++..+++|-+.
T Consensus 81 ~~l~~Gd~v~iD~g~~~-~G---Y~sD~-------tRT~~vG~~~~~~~~~~~~~~~~~~~ea~~~~~~~~kpG~~~ 146 (228)
T cd01089 81 YTLKDGDVVKIDLGCHI-DG---YIAVV-------AHTIVVGAEAETPVTGKKADVIAAAHYALEAALRLLRPGNQN 146 (228)
T ss_pred cccCCCCEEEEEEEEEE-CC---EEEEE-------EEEEEeCCcCccccchHHHHHHHHHHHHHHHHHHHhCCCCcH
Confidence 34899999999987765 66 43332 3445555321 124456677788888654
No 37
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=30.13 E-value=64 Score=21.12 Aligned_cols=25 Identities=12% Similarity=0.141 Sum_probs=20.8
Q ss_pred CcccHHHHhcCCCCCcEEEEEECCc
Q 033973 59 VIKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 59 ~i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
...-+-.||.|.++||.+.+..|..
T Consensus 121 ~~SPlG~ALlGk~vGD~v~v~~p~g 145 (158)
T PRK05892 121 ADSPLGQALAGHQAGDTVTYSTPQG 145 (158)
T ss_pred cCCHHHHHHhCCCCCCEEEEEcCCC
Confidence 3345889999999999999998864
No 38
>PTZ00053 methionine aminopeptidase 2; Provisional
Probab=29.55 E-value=97 Score=24.18 Aligned_cols=52 Identities=10% Similarity=0.029 Sum_probs=33.3
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC--C----CcccHHHHhcCCCCCcEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG--S----VIKGWDEGVMGMQVGEVA 76 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~--~----~i~g~~~~l~~m~~Ge~~ 76 (107)
..++.||.|.|++-+.. +| -..|.+ .+|.+|.. . +..+.+.|+..+++|-+.
T Consensus 232 ~vLk~GDvVkID~G~~v-dG---YiaD~A-------rTv~vg~~~~~L~eAv~eA~~aaI~~~kpGv~~ 289 (470)
T PTZ00053 232 TVLTYDDVCKLDFGTHV-NG---RIIDCA-------FTVAFNPKYDPLLQATKDATNTGIKEAGIDVRL 289 (470)
T ss_pred cEecCCCeEEEEEeEEE-CC---EEEeEE-------EEEEeCHHHHHHHHHHHHHHHHHHHHhcCCCcH
Confidence 34899999999999876 77 666653 33445521 1 234566666666666543
No 39
>TIGR00495 crvDNA_42K 42K curved DNA binding protein. Proteins identified by this model have been identified in a number of species as a nuclear (but not nucleolar) protein with a cell cycle dependence. Various names given to members of this family have included cell cycle protein p38-2G4, DNA-binding protein GBP16, and proliferation-associated protein 1. This protein is closely related to methionine aminopeptidase, a cobolt-binding protein.
Probab=29.16 E-value=1.7e+02 Score=22.01 Aligned_cols=53 Identities=13% Similarity=0.062 Sum_probs=34.6
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC----------C----CcccHHHHhcCCCCCcEEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG----------S----VIKGWDEGVMGMQVGEVAR 77 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~----------~----~i~g~~~~l~~m~~Ge~~~ 77 (107)
..++.||.|.|++-+.. || -.-|. ..+|.+|.. . ...+++.++..+++|-+..
T Consensus 99 ~~Lk~GDvVkIDlG~~i-dG---Y~aD~-------arTv~vG~~~~~~~t~~~~~l~~aa~~A~~aai~~vkPG~~~~ 165 (389)
T TIGR00495 99 YILKEGDVVKIDLGCHI-DG---FIALV-------AHTFVVGVAQEEPVTGRKADVIAAAHLAAEAALRLVKPGNTNT 165 (389)
T ss_pred cCcCCCCEEEEEEEEEE-CC---EEEEE-------EEEEEECCcccccCCHHHHHHHHHHHHHHHHHHHHhCCCCcHH
Confidence 34899999999998876 77 55443 345666631 1 1244667888888876543
No 40
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=28.32 E-value=74 Score=20.80 Aligned_cols=24 Identities=8% Similarity=0.102 Sum_probs=20.6
Q ss_pred cccHHHHhcCCCCCcEEEEEECCc
Q 033973 60 IKGWDEGVMGMQVGEVARLRITPM 83 (107)
Q Consensus 60 i~g~~~~l~~m~~Ge~~~v~ip~~ 83 (107)
..=+-.+|.|.++|+.+.+.+|..
T Consensus 122 ~SPlG~ALlGk~vGd~v~v~~p~g 145 (157)
T PRK01885 122 DSPMARALLKKEVGDEVTVNTPAG 145 (157)
T ss_pred cCHHHHHHhCCCCCCEEEEEcCCC
Confidence 445889999999999999998864
No 41
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=26.68 E-value=59 Score=18.72 Aligned_cols=19 Identities=11% Similarity=-0.039 Sum_probs=10.3
Q ss_pred cccCCCCCCCCccCCCCCCC
Q 033973 88 FHNGGFNLTQSWILRYKSCR 107 (107)
Q Consensus 88 yG~~g~~~~~~~~ipp~s~l 107 (107)
||.+|.....+ .|||...+
T Consensus 41 fGTEgR~~~~~-~ipp~~~v 59 (74)
T cd01736 41 FGTEGRPTDGP-EIPPSDEV 59 (74)
T ss_pred ecccCCCCCCC-ccCCCCcc
Confidence 67766653223 27776543
No 42
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=25.68 E-value=84 Score=19.10 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=21.2
Q ss_pred HHHHhcCCCCCcEEEEEECCchh
Q 033973 63 WDEGVMGMQVGEVARLRITPMVL 85 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~a 85 (107)
+...|...++|+.+.|.|.|+.-
T Consensus 26 lsr~l~ey~~Gd~V~I~IdpSv~ 48 (98)
T COG2139 26 LSRYLQEYKVGDKVHIDIDPSVH 48 (98)
T ss_pred hhhHHhhccCCCEEEEEeCcccc
Confidence 78899999999999999999876
No 43
>TIGR02925 cis_trans_EpsD peptidyl-prolyl cis-trans isomerase, EpsD family. Members of this family belong to the peptidyl-prolyl cis-trans isomerase family and are found in loci associated with exopolysaccharide biosynthesis. All members are encoded near a homolog of EpsH, as detected by TIGR02602.
Probab=25.30 E-value=56 Score=22.20 Aligned_cols=28 Identities=4% Similarity=-0.120 Sum_probs=22.2
Q ss_pred CCCCcccHHHHhcCCCCCcEEEEEECCchh
Q 033973 56 KGSVIKGWDEGVMGMQVGEVARLRITPMVL 85 (107)
Q Consensus 56 ~~~~i~g~~~~l~~m~~Ge~~~v~ip~~~a 85 (107)
.+++.+.|.+++..|++|+.. . |....+
T Consensus 189 ~~~l~~~~~~a~~~l~~G~is-~-v~s~~G 216 (232)
T TIGR02925 189 AEQLPAEILAVLAKLKPGAPL-V-VQGPNN 216 (232)
T ss_pred hhhCCHHHHHHHHhCCCCCeE-E-eecCCc
Confidence 467899999999999999985 3 555444
No 44
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=25.11 E-value=1e+02 Score=16.60 Aligned_cols=23 Identities=13% Similarity=0.151 Sum_probs=18.4
Q ss_pred HHHHhcCCCCCcEEEEEECCchh
Q 033973 63 WDEGVMGMQVGEVARLRITPMVL 85 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~a 85 (107)
+..+|..|..|+..++...-..+
T Consensus 17 ~~~~l~~l~~G~~l~v~~d~~~~ 39 (70)
T PF01206_consen 17 AKKALKELPPGEVLEVLVDDPAA 39 (70)
T ss_dssp HHHHHHTSGTT-EEEEEESSTTH
T ss_pred HHHHHHhcCCCCEEEEEECCccH
Confidence 67889999999999999876554
No 45
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=24.24 E-value=1.4e+02 Score=19.01 Aligned_cols=24 Identities=25% Similarity=0.396 Sum_probs=15.7
Q ss_pred CeEEEEecccCCCCCCCCCEEEEE
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVH 25 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~ 25 (107)
|.+..-..+|.|..++++|.|.|.
T Consensus 66 G~~VtAyiPg~Gh~lqEH~~Vli~ 89 (129)
T COG0048 66 GKEVTAYIPGEGHNLQEHSEVLIR 89 (129)
T ss_pred CcEEEEEcCCCCccccccCEEEEe
Confidence 344555567777777777777664
No 46
>PF03894 XFP: D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; InterPro: IPR005593 Phosphoketolases (PK) are key enzymes of the pentose phosphate pathway of heterofermentative and facultative homofermentative lactic acid bacteria and of the D-fructose 6-phosphate shunt of bifidobacteria. PK activity has been sporadically reported in other microorganisms including eukaryotic yeasts. Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase is a thiamine diphosphate (ThdP)-dependent enzyme found in bacteria such as Bifidobacterium sp [, ]. This enzyme has dual-specificity with the following catalytic activities: 4.1.2.9 from EC: xylose 5-P + Pi = acetyl-P + glyeraldehyde-3-P 4.1.2.22 from EC: fructose-6-P + Pi = acetyl-P + erythrose-4-P Phosphoketolases are distantly related to transketolases, e.g. IPR005475 from INTERPRO.; GO: 0016832 aldehyde-lyase activity, 0005975 carbohydrate metabolic process; PDB: 3AI7_B 3AHC_A 3AHJ_A 3AHG_A 3AHE_A 3AHI_A 3AHD_A 3AHF_A 3AHH_A.
Probab=23.27 E-value=84 Score=21.27 Aligned_cols=26 Identities=19% Similarity=0.325 Sum_probs=16.1
Q ss_pred CCcccHHHHhcCCCCCcEEEEEECCch
Q 033973 58 SVIKGWDEGVMGMQVGEVARLRITPMV 84 (107)
Q Consensus 58 ~~i~g~~~~l~~m~~Ge~~~v~ip~~~ 84 (107)
..=|||.+.|...+ .+.+++++||+.
T Consensus 141 HQdPgfi~~~~~k~-~~~~RvylPpDA 166 (179)
T PF03894_consen 141 HQDPGFIDHVLNKK-PDVVRVYLPPDA 166 (179)
T ss_dssp G---THHHHHHCC---T-EEEEE-SSH
T ss_pred cCCChHHHHHHhcC-cccceeecCCcH
Confidence 34589999999887 569999999864
No 47
>COG2258 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.15 E-value=79 Score=21.95 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=20.0
Q ss_pred CeEEEEecccCCCCCCCCCEEEEEEEEE
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVHCTGY 29 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~y~~~ 29 (107)
|+++++|++|. +..||.+.+-+...
T Consensus 140 G~y~RVL~~G~---v~~gD~l~l~~r~~ 164 (210)
T COG2258 140 GWYARVLEEGK---VRAGDPLKLIPRPS 164 (210)
T ss_pred cEEEEEcccce---ecCCCceEEecCCC
Confidence 68999998875 78888888877654
No 48
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.12 E-value=1.4e+02 Score=16.24 Aligned_cols=22 Identities=18% Similarity=0.116 Sum_probs=18.4
Q ss_pred HHHHhcCCCCCcEEEEEECCch
Q 033973 63 WDEGVMGMQVGEVARLRITPMV 84 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~ 84 (107)
...+|..|..|+..++.+.-..
T Consensus 16 ~k~~l~~l~~G~~l~V~~dd~~ 37 (69)
T cd03423 16 LHKKVRKMKPGDTLLVLATDPS 37 (69)
T ss_pred HHHHHHcCCCCCEEEEEeCCCc
Confidence 7789999999999999886433
No 49
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=23.11 E-value=96 Score=19.24 Aligned_cols=24 Identities=21% Similarity=0.079 Sum_probs=19.0
Q ss_pred EecccCCCCCCCCCEEEEEEEEEE
Q 033973 7 ILTPGNGPKPVAGQKVTVHCTGYG 30 (107)
Q Consensus 7 ~~~~G~g~~~~~gd~V~v~y~~~~ 30 (107)
+++..+|...++||.|++-=.+..
T Consensus 42 ~~kDsnG~~L~dGDsV~liKDLkV 65 (109)
T TIGR00686 42 IVKDCNGNLLANGDSVILIKDLKV 65 (109)
T ss_pred eEEcCCCCCccCCCEEEEEeeccc
Confidence 467778888999999998666655
No 50
>PRK11018 hypothetical protein; Provisional
Probab=22.90 E-value=1.4e+02 Score=16.92 Aligned_cols=22 Identities=14% Similarity=0.019 Sum_probs=18.4
Q ss_pred HHHHhcCCCCCcEEEEEECCch
Q 033973 63 WDEGVMGMQVGEVARLRITPMV 84 (107)
Q Consensus 63 ~~~~l~~m~~Ge~~~v~ip~~~ 84 (107)
...+|..|+.|+..+|.+.-..
T Consensus 25 ~kk~l~~l~~G~~L~V~~d~~~ 46 (78)
T PRK11018 25 TLEALPQLKKGEILEVVSDCPQ 46 (78)
T ss_pred HHHHHHhCCCCCEEEEEeCCcc
Confidence 6789999999999999887433
No 51
>TIGR00500 met_pdase_I methionine aminopeptidase, type I. Methionine aminopeptidase is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. This model describes type I. The role of this protein in general is to produce the mature form of cytosolic proteins by removing the N-terminal methionine.
Probab=22.14 E-value=2.3e+02 Score=19.29 Aligned_cols=51 Identities=16% Similarity=0.076 Sum_probs=32.3
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC---------CCcccHHHHhcCCCCCcE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG---------SVIKGWDEGVMGMQVGEV 75 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~---------~~i~g~~~~l~~m~~Ge~ 75 (107)
..+++||.|.+++-... ++ -.-|. ..+|.+|.- .+..+++.++..+++|-+
T Consensus 82 ~~l~~Gd~v~iD~g~~~-~g---Y~aD~-------~RT~~vG~~~~~~~~~~~~~~~a~~~~~~~~kpG~~ 141 (247)
T TIGR00500 82 KVLKDGDIVNIDVGVIY-DG---YHGDT-------AKTFLVGKISPEAEKLLECTEESLYKAIEEAKPGNR 141 (247)
T ss_pred cccCCCCEEEEEEEEEE-CC---EEEEE-------EEEEEcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 45899999999988765 55 33332 345556531 124556677777788754
No 52
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=22.13 E-value=1.5e+02 Score=16.92 Aligned_cols=28 Identities=21% Similarity=0.096 Sum_probs=22.6
Q ss_pred CCCccc----HHHHhcCCCCCcEEEEEECCch
Q 033973 57 GSVIKG----WDEGVMGMQVGEVARLRITPMV 84 (107)
Q Consensus 57 ~~~i~g----~~~~l~~m~~Ge~~~v~ip~~~ 84 (107)
+..+|. ..++|..|+.|+...+...-..
T Consensus 16 Gl~CP~Pll~~kk~l~~l~~G~~l~V~~dd~~ 47 (81)
T PRK00299 16 GLRCPEPVMMVRKTVRNMQPGETLLIIADDPA 47 (81)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCEEEEEeCCcc
Confidence 556666 8999999999999999886433
No 53
>PF03831 PhnA: PhnA protein; InterPro: IPR013988 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the C-terminal domain of PhnA.; PDB: 2AKK_A 2AKL_A.
Probab=21.75 E-value=43 Score=18.23 Aligned_cols=23 Identities=22% Similarity=0.128 Sum_probs=12.9
Q ss_pred ecccCCCCCCCCCEEEEEEEEEE
Q 033973 8 LTPGNGPKPVAGQKVTVHCTGYG 30 (107)
Q Consensus 8 ~~~G~g~~~~~gd~V~v~y~~~~ 30 (107)
++..+|...+.||.|++-=.+..
T Consensus 2 v~DsnGn~L~dGDsV~~iKDLkV 24 (56)
T PF03831_consen 2 VKDSNGNELQDGDSVTLIKDLKV 24 (56)
T ss_dssp -B-TTS-B--TTEEEEESS-EEE
T ss_pred eEcCCCCCccCCCEEEEEeeeee
Confidence 35567888999999988655555
No 54
>PRK02268 hypothetical protein; Provisional
Probab=21.64 E-value=70 Score=20.74 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=20.3
Q ss_pred CcccHHHHhcCCCCCcEEEEEECCch
Q 033973 59 VIKGWDEGVMGMQVGEVARLRITPMV 84 (107)
Q Consensus 59 ~i~g~~~~l~~m~~Ge~~~v~ip~~~ 84 (107)
+.-|=...|..|++||...++.|.+.
T Consensus 25 v~hgK~apl~RmkpGD~ivyYsp~~~ 50 (141)
T PRK02268 25 VCHGKAAPLRRMKPGDWIIYYSPKTT 50 (141)
T ss_pred eCCCccchhhcCCCCCEEEEEeceEe
Confidence 34444567889999999999998765
No 55
>COG4922 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.53 E-value=1.1e+02 Score=19.43 Aligned_cols=17 Identities=29% Similarity=0.235 Sum_probs=14.7
Q ss_pred CCCCCEEEEEEEEEEeC
Q 033973 16 PVAGQKVTVHCTGYGKN 32 (107)
Q Consensus 16 ~~~gd~V~v~y~~~~~~ 32 (107)
+.+||+|.+||.-+...
T Consensus 71 iadGdLV~vh~hqt~~~ 87 (129)
T COG4922 71 IADGDLVTVHYHQTVSE 87 (129)
T ss_pred eccCCEEEEEEeeeeCC
Confidence 78999999999988744
No 56
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.46 E-value=1.8e+02 Score=17.09 Aligned_cols=12 Identities=33% Similarity=0.410 Sum_probs=9.0
Q ss_pred CCCCCCEEEEEE
Q 033973 15 KPVAGQKVTVHC 26 (107)
Q Consensus 15 ~~~~gd~V~v~y 26 (107)
.++.||.|.+|-
T Consensus 38 ~v~~GdyVLVHv 49 (82)
T COG0298 38 EVKVGDYVLVHV 49 (82)
T ss_pred ccccCCEEEEEe
Confidence 577888888774
No 57
>PLN03158 methionine aminopeptidase; Provisional
Probab=21.19 E-value=3.8e+02 Score=20.39 Aligned_cols=52 Identities=21% Similarity=0.120 Sum_probs=34.2
Q ss_pred CCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEEeCCC---------CCcccHHHHhcCCCCCcEE
Q 033973 14 PKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQIGKG---------SVIKGWDEGVMGMQVGEVA 76 (107)
Q Consensus 14 ~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~~G~~---------~~i~g~~~~l~~m~~Ge~~ 76 (107)
..+++||.|.++..++. +| -.-|. ..+|.+|.- ....+++.++..+++|-.+
T Consensus 216 r~L~~GDiV~iDvg~~~-~G---Y~aD~-------tRT~~VG~~~~e~~~l~e~~~eal~~aI~~vkPGv~~ 276 (396)
T PLN03158 216 RKLEDGDIVNVDVTVYY-KG---CHGDL-------NETFFVGNVDEASRQLVKCTYECLEKAIAIVKPGVRY 276 (396)
T ss_pred ccCCCCCEEEEEEeEEE-CC---EEEeE-------EeEEEcCCCCHHHHHHHHHHHHHHHHHHHHcCCCCCH
Confidence 44899999999998876 66 33332 344556531 2446677788888888543
No 58
>PRK04980 hypothetical protein; Provisional
Probab=21.10 E-value=1.6e+02 Score=17.96 Aligned_cols=74 Identities=11% Similarity=0.120 Sum_probs=40.7
Q ss_pred CeEEEEecccCCCCCCCCCEEEEEEEEEEeCCCceeEEecccCCCCccEEEE-e------CCCCCcccHHHHhcCCCCCc
Q 033973 2 GIEKQILTPGNGPKPVAGQKVTVHCTGYGKNGDLSQKFWSTKDPGQQPFTFQ-I------GKGSVIKGWDEGVMGMQVGE 74 (107)
Q Consensus 2 Gl~~~~~~~G~g~~~~~gd~V~v~y~~~~~~gg~~~~~~st~~~~~~p~~~~-~------G~~~~i~g~~~~l~~m~~Ge 74 (107)
|-+..+++.++...+++||.+.+|-- .+| ..|-.-.-..-.|..|. + -.+.-++-|.+.+..+-+|+
T Consensus 18 GkKTiTiRd~se~~~~~G~~~~V~~~---e~g---~~~c~ieI~sV~~i~f~eLte~hA~qEg~sL~elk~~i~~iYp~~ 91 (102)
T PRK04980 18 GRKTITIRDESESHFKPGDVLRVGTF---EDD---RYFCTIEVLSVSPVTFDELNEKHAEQENMTLPELKQVIAEIYPNL 91 (102)
T ss_pred CCceEEeeCCcccCCCCCCEEEEEEC---CCC---cEEEEEEEEEEEEEehhhCCHHHHHHhCCCHHHHHHHHHHHCCCC
Confidence 44566777777666999999999721 122 22211000000122221 0 02335778999999998887
Q ss_pred EEEEEEC
Q 033973 75 VARLRIT 81 (107)
Q Consensus 75 ~~~v~ip 81 (107)
.....|.
T Consensus 92 ~~lyvI~ 98 (102)
T PRK04980 92 DQLYVIE 98 (102)
T ss_pred ceEEEEE
Confidence 7666554
No 59
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=20.82 E-value=87 Score=17.47 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=13.5
Q ss_pred ccHHHHhc--CCCCCcEEEE
Q 033973 61 KGWDEGVM--GMQVGEVARL 78 (107)
Q Consensus 61 ~g~~~~l~--~m~~Ge~~~v 78 (107)
-|++++|. |.+.|+.+.|
T Consensus 43 ~Gv~~~L~~~G~~~GD~V~I 62 (69)
T TIGR03595 43 LGVEDALRKAGAKDGDTVRI 62 (69)
T ss_pred CCHHHHHHHcCCCCCCEEEE
Confidence 47888886 4588888775
No 60
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=20.43 E-value=1.3e+02 Score=15.01 Aligned_cols=23 Identities=17% Similarity=0.388 Sum_probs=16.4
Q ss_pred CcccHHHHhcCCCCCcEEEEEECC
Q 033973 59 VIKGWDEGVMGMQVGEVARLRITP 82 (107)
Q Consensus 59 ~i~g~~~~l~~m~~Ge~~~v~ip~ 82 (107)
++..|.+.+ ++++|+...+.+..
T Consensus 11 iPk~~~~~l-~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 11 IPKEIREKL-GLKPGDEVEIEVEG 33 (47)
T ss_dssp E-HHHHHHT-TSSTTTEEEEEEET
T ss_pred CCHHHHHHc-CCCCCCEEEEEEeC
Confidence 345666666 88999999887754
Done!