Query psy2439
Match_columns 146
No_of_seqs 176 out of 508
Neff 7.5
Searched_HMMs 46136
Date Sat Aug 17 00:56:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2439.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2439hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07700 HNOB: Heme NO binding 99.8 7.8E-23 1.7E-27 152.6 -1.1 103 1-118 15-124 (171)
2 PF07700 HNOB: Heme NO binding 99.7 2E-17 4.3E-22 123.4 7.1 77 67-145 1-80 (171)
3 KOG4171|consensus 99.6 5.4E-16 1.2E-20 134.2 3.4 101 1-117 15-122 (671)
4 KOG4171|consensus 99.4 1.1E-12 2.5E-17 113.8 7.0 77 67-145 1-80 (671)
5 TIGR02019 BchJ bacteriochlorop 80.7 4.6 9.9E-05 30.8 5.2 63 1-65 16-80 (188)
6 PRK02866 cyanate hydratase; Va 78.5 3.2 6.9E-05 30.4 3.6 81 7-91 20-118 (147)
7 TIGR00673 cynS cyanate hydrata 76.5 3.8 8.3E-05 30.1 3.5 79 7-90 23-120 (150)
8 PF14842 FliG_N: FliG N-termin 75.5 6 0.00013 27.0 4.2 70 25-96 27-101 (108)
9 TIGR02019 BchJ bacteriochlorop 67.8 28 0.00061 26.5 6.6 68 74-143 11-80 (188)
10 PF13443 HTH_26: Cro/C1-type H 59.5 5.9 0.00013 23.8 1.3 47 7-55 12-59 (63)
11 PF12651 RHH_3: Ribbon-helix-h 53.7 30 0.00064 19.8 3.6 30 26-57 6-35 (44)
12 PF01402 RHH_1: Ribbon-helix-h 51.7 25 0.00053 19.0 3.0 26 30-57 7-32 (39)
13 PF11264 ThylakoidFormat: Thyl 50.2 1.2E+02 0.0026 23.6 8.5 110 25-139 59-187 (216)
14 cd08308 Death_Tube Death domai 47.0 45 0.00098 23.7 4.3 53 6-60 23-75 (125)
15 PF01381 HTH_3: Helix-turn-hel 45.5 16 0.00035 21.0 1.6 42 10-53 14-55 (55)
16 PF07061 Swi5: Swi5; InterPro 42.5 34 0.00073 22.5 2.9 27 31-59 53-79 (83)
17 PF12668 DUF3791: Protein of u 41.4 81 0.0018 19.1 6.7 39 33-73 4-44 (62)
18 PLN03060 inositol phosphatase- 39.6 1.8E+02 0.0038 22.5 8.9 109 25-139 62-182 (206)
19 COG1093 SUI2 Translation initi 37.3 97 0.0021 25.0 5.2 58 33-92 103-166 (269)
20 PF12844 HTH_19: Helix-turn-he 36.9 14 0.0003 22.1 0.4 43 10-57 17-62 (64)
21 PF02954 HTH_8: Bacterial regu 34.9 55 0.0012 18.1 2.7 21 37-59 21-41 (42)
22 PLN03169 chalcone synthase fam 34.8 87 0.0019 26.2 4.9 49 6-61 285-344 (391)
23 TIGR03060 PS_II_psb29 photosys 34.8 2.2E+02 0.0047 22.2 8.3 110 25-139 64-190 (214)
24 PRK07194 fliG flagellar motor 34.6 1.1E+02 0.0024 25.1 5.5 68 24-93 28-100 (334)
25 PF09536 DUF2378: Protein of u 34.2 1.5E+02 0.0032 22.3 5.6 60 9-70 26-88 (178)
26 COG0062 Uncharacterized conser 34.0 77 0.0017 24.4 4.1 43 26-70 3-46 (203)
27 PHA01976 helix-turn-helix prot 32.0 38 0.00083 20.3 1.9 21 34-56 44-64 (67)
28 PRK13280 N-glycosylase/DNA lya 31.7 2E+02 0.0043 23.2 6.2 122 3-130 17-149 (269)
29 smart00530 HTH_XRE Helix-turn- 31.6 45 0.00097 17.7 2.0 43 8-52 13-55 (56)
30 smart00760 Bac_DnaA_C Bacteria 31.3 71 0.0015 19.1 3.0 21 33-55 2-22 (60)
31 PLN00047 photosystem II biogen 30.9 2.9E+02 0.0063 22.5 8.3 109 25-139 115-235 (283)
32 PF12085 DUF3562: Protein of u 30.3 1.5E+02 0.0032 18.8 4.5 32 32-65 5-36 (66)
33 COG1536 FliG Flagellar motor s 28.2 1.8E+02 0.0038 24.2 5.6 71 23-95 31-106 (339)
34 PF08299 Bac_DnaA_C: Bacterial 27.5 83 0.0018 19.6 2.9 20 33-54 2-21 (70)
35 TIGR00207 fliG flagellar motor 27.3 2.6E+02 0.0057 23.0 6.5 72 23-96 29-105 (338)
36 KOG1759|consensus 26.9 45 0.00098 23.4 1.6 25 28-54 15-39 (115)
37 PF09840 DUF2067: Uncharacteri 26.7 52 0.0011 25.0 2.1 20 34-55 142-161 (190)
38 PF07739 TipAS: TipAS antibiot 26.6 1.4E+02 0.0031 19.7 4.2 59 1-61 8-67 (118)
39 PF09171 DUF1886: Domain of un 26.3 39 0.00085 26.8 1.4 134 2-143 7-152 (246)
40 TIGR00197 yjeF_nterm yjeF N-te 25.9 1.2E+02 0.0026 23.0 4.0 37 27-66 3-39 (205)
41 KOG3157|consensus 25.9 2.5E+02 0.0054 22.1 5.6 63 6-70 150-224 (244)
42 PF05186 Dpy-30: Dpy-30 motif; 25.8 38 0.00081 19.3 0.9 33 30-64 8-40 (42)
43 PF10885 DUF2684: Protein of u 25.8 43 0.00094 22.1 1.3 26 66-103 20-46 (89)
44 PTZ00098 phosphoethanolamine N 25.2 2.9E+02 0.0064 21.5 6.2 54 5-64 183-236 (263)
45 PRK12880 3-oxoacyl-(acyl carri 24.6 1.8E+02 0.0039 23.8 5.1 40 87-128 69-111 (353)
46 PF07704 PSK_trans_fac: Rv0623 24.1 1.2E+02 0.0027 19.5 3.3 25 29-55 6-30 (82)
47 PLN02377 3-ketoacyl-CoA syntha 23.3 3.5E+02 0.0076 23.7 6.8 43 84-128 178-222 (502)
48 PF05379 Peptidase_C23: Carlav 23.0 1.1E+02 0.0025 20.2 3.0 24 36-61 6-29 (89)
49 PF11080 DUF2622: Protein of u 22.5 28 0.0006 23.7 -0.1 40 21-61 53-92 (96)
50 PRK13890 conjugal transfer pro 22.5 90 0.0019 21.7 2.5 44 10-55 23-66 (120)
51 PF07796 DUF1638: Protein of u 22.4 1.1E+02 0.0024 22.2 3.2 50 2-53 101-152 (166)
52 PF10076 DUF2313: Uncharacteri 21.7 1.4E+02 0.003 21.9 3.6 53 26-94 10-65 (179)
53 PLN03050 pyridoxine (pyridoxam 21.5 1.7E+02 0.0037 22.9 4.2 40 25-66 6-45 (246)
54 PF11638 DnaA_N: DnaA N-termin 21.5 44 0.00096 20.1 0.7 18 5-22 1-20 (65)
55 PRK11187 replication initiatio 21.2 74 0.0016 24.2 1.9 25 30-56 7-31 (182)
56 PF11569 Homez: Homeodomain le 20.4 1.4E+02 0.0029 18.3 2.7 34 21-60 16-49 (56)
57 COG0015 PurB Adenylosuccinate 20.1 1.8E+02 0.004 25.1 4.3 40 6-47 200-239 (438)
No 1
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=99.84 E-value=7.8e-23 Score=152.57 Aligned_cols=103 Identities=29% Similarity=0.501 Sum_probs=83.2
Q ss_pred CcchHHHHHHHHHHhCCC-CccceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHH
Q psy2439 1 LEYGDDVWLKVLKKAGCK-VSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKL 79 (146)
Q Consensus 1 ~~~G~~~W~~i~~~a~~~-~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~ 79 (146)
++||+++|++|++++|++ +..|+++++|||+++++|+.|+|+ ++|+ |.+++++.||++|+.++...|+
T Consensus 15 ~~~G~~~w~~i~~~~~~~~~~~f~~~~~Y~D~~~~~lv~a~a~-~~g~-~~~~~l~~fG~~~~~~~~~~~~--------- 83 (171)
T PF07700_consen 15 EKYGEEVWDEILERAGLDSDGIFTSHGNYDDEETYKLVEAAAE-VTGI-SVEELLEEFGEYFFDFLSESGY--------- 83 (171)
T ss_dssp HHHHHHHHHHHHHHTTSSTTSS--TTSBTTHHHHHHHHHHHHH-HHTS--HHHHHHHHHHHHHHHHHHHCC---------
T ss_pred HHcCHHHHHHHHHHhCCCcCCccccccccCHHHHHHHHHHHHH-HhCC-CHHHHHHHHHHHHHHHHHHhCc---------
Confidence 479999999999999999 789999999999999999999999 9999 9999999999999999988887
Q ss_pred hhcHHHHHHHHHHhCCCC--ccceee----ccCCCCChHHHHHHH
Q psy2439 80 EYGDDVWLKVLKKAGCKV--SCFNTH----HIYPDIYMPDLATAC 118 (146)
Q Consensus 80 ~~G~~~w~~il~~~~~~~--~~~~~h----~~Ypd~~~p~f~~~~ 118 (146)
+...+.++++..++ +.+++| ++||++.+|+|.|..
T Consensus 84 ----~~~l~~~g~~~~~FL~~ld~iH~~v~~~~p~~~~P~f~~~~ 124 (171)
T PF07700_consen 84 ----ERLLRFLGRDLFDFLNNLDNIHEEVRKLYPDAKPPSFRCEE 124 (171)
T ss_dssp ----HHHHHCTCSSHHHHHHHHHHHHHHHHHHSTTSS--EEEEEE
T ss_pred ----HHHHHhcCCCHHHHHHhHHHHHHHHHHhCCCCcCCeEEEEE
Confidence 44445555554444 444455 699999999998654
No 2
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=99.71 E-value=2e-17 Score=123.42 Aligned_cols=77 Identities=32% Similarity=0.579 Sum_probs=70.8
Q ss_pred hhhhHHH--HHHHHHhhcHHHHHHHHHHhCCC-CccceeeccCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhh
Q psy2439 67 NLGIILA--IAFQKLEYGDDVWLKVLKKAGCK-VSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYF 143 (146)
Q Consensus 67 myG~i~~--~~~v~~~~G~~~w~~il~~~~~~-~~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~v~~~ 143 (146)
|||+|++ +++|+++||++.|.+++.+++++ ...|..++.|||..+++++.++|+ ++|+ |.+++++.||+|||+++
T Consensus 1 M~Gii~~~~~~~v~~~~G~~~w~~i~~~~~~~~~~~f~~~~~Y~D~~~~~lv~a~a~-~~g~-~~~~~l~~fG~~~~~~~ 78 (171)
T PF07700_consen 1 MYGIIFKALQEFVEEKYGEEVWDEILERAGLDSDGIFTSHGNYDDEETYKLVEAAAE-VTGI-SVEELLEEFGEYFFDFL 78 (171)
T ss_dssp -BHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTTSS--TTSBTTHHHHHHHHHHHHH-HHTS--HHHHHHHHHHHHHHHH
T ss_pred CeehHHHHHHHHHHHHcCHHHHHHHHHHhCCCcCCccccccccCHHHHHHHHHHHHH-HhCC-CHHHHHHHHHHHHHHHH
Confidence 8999999 99999999999999999999999 589999999999999999999999 9999 99999999999999998
Q ss_pred hc
Q psy2439 144 SN 145 (146)
Q Consensus 144 ~~ 145 (146)
.+
T Consensus 79 ~~ 80 (171)
T PF07700_consen 79 SE 80 (171)
T ss_dssp HH
T ss_pred HH
Confidence 64
No 3
>KOG4171|consensus
Probab=99.59 E-value=5.4e-16 Score=134.23 Aligned_cols=101 Identities=32% Similarity=0.592 Sum_probs=95.6
Q ss_pred CcchHHHHHHHHHHhCCCCc-cceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHH
Q psy2439 1 LEYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKL 79 (146)
Q Consensus 1 ~~~G~~~W~~i~~~a~~~~~-~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~ 79 (146)
++||+++|.++...+++... .|.+++.|||..+++|+.|++. ++|. |.|++++.||++|++|+++.||
T Consensus 15 ~~yg~~~w~~v~~~~~~~~~~~~~~~~~y~d~~t~~l~~a~~~-v~~~-~~d~i~~~~G~~~i~f~~~~g~--------- 83 (671)
T KOG4171|consen 15 RNYGEDIWEKVKKPAGLLEGKQFPIHHYYSDTLTPDLVKALSP-VLGD-SADEIWEMYGRFFITFCSEFGY--------- 83 (671)
T ss_pred HHhccchHHhhhhhhccccCCcCccccccCcchhHHHHHHHHh-hhCC-CHHHHHHHHhHHHHHHhhhhCH---------
Confidence 47999999999999999955 5999999999999999999999 9999 9999999999999999999999
Q ss_pred hhcHHHHHHHHHHhCCCC--ccceeec----cCCCCChHHHHHH
Q psy2439 80 EYGDDVWLKVLKKAGCKV--SCFNTHH----IYPDIYMPDLATA 117 (146)
Q Consensus 80 ~~G~~~w~~il~~~~~~~--~~~~~h~----~Ypd~~~p~f~~~ 117 (146)
+...+.++++..+| +++++|. .|| +..|+|.|+
T Consensus 84 ----d~llrsmg~~l~~FL~~LD~lHd~~~~~y~-mr~PSf~c~ 122 (671)
T KOG4171|consen 84 ----DKLLRSMGRNLQEFLQNLDNLHDHLRFKYP-MRGPSFRCE 122 (671)
T ss_pred ----HHHHHHhhhhHHHHHHHHHHHHHHHhhccc-cCCCceeee
Confidence 99999999998888 8888886 899 999999987
No 4
>KOG4171|consensus
Probab=99.36 E-value=1.1e-12 Score=113.79 Aligned_cols=77 Identities=34% Similarity=0.625 Sum_probs=74.2
Q ss_pred hhhhHHH--HHHHHHhhcHHHHHHHHHHhCCCC-ccceeeccCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhh
Q psy2439 67 NLGIILA--IAFQKLEYGDDVWLKVLKKAGCKV-SCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYF 143 (146)
Q Consensus 67 myG~i~~--~~~v~~~~G~~~w~~il~~~~~~~-~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~v~~~ 143 (146)
|||+|++ +.+++++||++.|.++...+++.. +.+.+|+.|||..+|+++.+++. ++|. |.|++|+.||++|++|+
T Consensus 1 myg~i~es~~~lv~~~yg~~~w~~v~~~~~~~~~~~~~~~~~y~d~~t~~l~~a~~~-v~~~-~~d~i~~~~G~~~i~f~ 78 (671)
T KOG4171|consen 1 MYGFIHESLRQLVIRNYGEDIWEKVKKPAGLLEGKQFPIHHYYSDTLTPDLVKALSP-VLGD-SADEIWEMYGRFFITFC 78 (671)
T ss_pred CccHHHHHHHHHHHHHhccchHHhhhhhhccccCCcCccccccCcchhHHHHHHHHh-hhCC-CHHHHHHHHhHHHHHHh
Confidence 8999999 999999999999999999999988 55999999999999999999999 9999 99999999999999999
Q ss_pred hc
Q psy2439 144 SN 145 (146)
Q Consensus 144 ~~ 145 (146)
++
T Consensus 79 ~~ 80 (671)
T KOG4171|consen 79 SE 80 (671)
T ss_pred hh
Confidence 86
No 5
>TIGR02019 BchJ bacteriochlorophyll 4-vinyl reductase. This model represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the "dark" protochlorophyllide reductase enzymes BchN, BchB and BchL. This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll.
Probab=80.72 E-value=4.6 Score=30.76 Aligned_cols=63 Identities=17% Similarity=0.157 Sum_probs=50.3
Q ss_pred CcchHHHHHHHHHHhCCCCc-cceeccccCCchHHHHHHHHHHHhhC-CCCHHHHHHHHhhHHHHHh
Q psy2439 1 LEYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASVIEG-DLTSEYFMEFFGKCFVRYF 65 (146)
Q Consensus 1 ~~~G~~~W~~i~~~a~~~~~-~f~~~~~Y~d~~~~~Lv~a~~~~~~g-~~~~~~~l~~fG~~~v~~~ 65 (146)
+.||++.-++|+.++|.+.- .=-....=|++.+..|..++-+ .+| . ....+|+..|+..-+++
T Consensus 16 ~~~g~~~~~~~~~~~g~~~~~~~~p~~mv~E~~~~aL~~aL~~-elG~~-aa~~vl~~~G~~ta~y~ 80 (188)
T TIGR02019 16 AAYGPGAADRALAAAGQGVLRPGPPSGMLPESQFSTLHRWLRD-TLGET-AAARLLRESGLATADYI 80 (188)
T ss_pred HhcCHHHHHHHHHHcCcccccCCCchhcCCHHHHHHHHHHHHH-HhCHH-HHHHHHHHHhHHHHHHH
Confidence 36899999999999998741 2233556788899999999999 999 5 77789999998775555
No 6
>PRK02866 cyanate hydratase; Validated
Probab=78.52 E-value=3.2 Score=30.42 Aligned_cols=81 Identities=14% Similarity=0.186 Sum_probs=52.1
Q ss_pred HHHHHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHH-----hh---H------HHHH---hhhhh
Q psy2439 7 VWLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFF-----GK---C------FVRY---FSNLG 69 (146)
Q Consensus 7 ~W~~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~f-----G~---~------~v~~---~~myG 69 (146)
+|++|-+.+|++...+++...=-.+....-+.++|+ .+|. |.+.+...- |. . .-|| +.-||
T Consensus 20 Tw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~-~LgL-~~~~~~~l~~~P~rg~~~~~~ptdP~iYR~yE~v~vYG 97 (147)
T PRK02866 20 TWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAE-LLGL-DEDAVALLQEVPYRGSLPPAVPTDPLIYRFYEMVQVYG 97 (147)
T ss_pred CHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHH-HhCC-CHHHHHHHhcCCcCCCCCCCCCCCcHHHHHHHHHHHhh
Confidence 599999999999844444444446667888999999 9999 988654311 11 1 0111 12233
Q ss_pred hHHH-HHHHHHhhcHHHHHHHHH
Q psy2439 70 IILA-IAFQKLEYGDDVWLKVLK 91 (146)
Q Consensus 70 ~i~~-~~~v~~~~G~~~w~~il~ 91 (146)
. . ++.+.|+||+.....|--
T Consensus 98 ~--~~K~~i~E~FGDGIMSAIdf 118 (147)
T PRK02866 98 T--TLKALIHEKFGDGIMSAIDF 118 (147)
T ss_pred H--HHHHHHHHHhCCceeeeeee
Confidence 2 2 788889998877665533
No 7
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=76.54 E-value=3.8 Score=30.08 Aligned_cols=79 Identities=15% Similarity=0.222 Sum_probs=51.4
Q ss_pred HHHHHHHHhCCCCccceeccccC-CchHHHHHHHHHHHhhCCCCHHHHHHHH-----h---hHH------HHH---hhhh
Q psy2439 7 VWLKVLKKAGCKVSCFNTHHIYP-DIYMPDLATACASVIEGDLTSEYFMEFF-----G---KCF------VRY---FSNL 68 (146)
Q Consensus 7 ~W~~i~~~a~~~~~~f~~~~~Y~-d~~~~~Lv~a~~~~~~g~~~~~~~l~~f-----G---~~~------v~~---~~my 68 (146)
+|++|-+++|++. +|++.--|= ......-+.++|+ .+|. |.+.+...- | ... -|| +.-|
T Consensus 23 Twe~IAe~iG~se-vwvaaa~lGQ~~ls~e~A~kla~-lLgL-~~e~~~~l~~~P~rg~~~~~~ptdP~iYR~yE~v~vY 99 (150)
T TIGR00673 23 TFADIADGLGLAE-VFVAAALYGQAAAPADEARLVGA-KLDL-DEDSILELQMAPLRGCIDPVIPTDPTMYRFYEMLQVY 99 (150)
T ss_pred CHHHHHHHHCCCH-HHHHHHHhCCCCCCHHHHHHHHH-HhCc-CHHHHHHHhcCCCCCCCCCCCCCCchHHHHHHHHHHh
Confidence 5999999999987 555544443 5667888999999 9999 988754421 1 100 111 1222
Q ss_pred hhHHH-HHHHHHhhcHHHHHHHH
Q psy2439 69 GIILA-IAFQKLEYGDDVWLKVL 90 (146)
Q Consensus 69 G~i~~-~~~v~~~~G~~~w~~il 90 (146)
|. . ++.+.|+||+.....|-
T Consensus 100 G~--~~K~~i~E~FGDGIMSAId 120 (150)
T TIGR00673 100 GT--TLKAVVHEKFGDGIMSAID 120 (150)
T ss_pred hH--HHHHHHHHHhCcceeeeee
Confidence 22 2 78888888887765543
No 8
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=75.49 E-value=6 Score=27.04 Aligned_cols=70 Identities=10% Similarity=0.086 Sum_probs=35.1
Q ss_pred ccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhH----HH-HHHHHHhhcHHHHHHHHHHhCCC
Q psy2439 25 HHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGII----LA-IAFQKLEYGDDVWLKVLKKAGCK 96 (146)
Q Consensus 25 ~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i----~~-~~~v~~~~G~~~w~~il~~~~~~ 96 (146)
.+.-+++++.+|..++++ .-.+ |++++-.-.-+|.-.....-+.+ .. +.++...+|++.-.+++.+....
T Consensus 27 lk~l~~~ei~~i~~~ma~-l~~v-~~~~~~~Vl~EF~~~~~~~~~~~~gg~~~~~~lL~~alg~~~a~~il~~~~~~ 101 (108)
T PF14842_consen 27 LKHLDEEEIERISREMAK-LGSV-SPEEVEEVLEEFYDEIRAQGGIVSGGRDFARRLLEKALGEEKAKEILDRLEQS 101 (108)
T ss_dssp HHHS-HHHHHHHHHHHHT-------HHHHHHHHHHHHHHHHHTT---S-HHHHHHH-HHHHS---HHHHH-------
T ss_pred HccCCHHHHHHHHHHHHc-cCCC-CHHHHHHHHHHHHHHHHHccccccChHHHHHHHHHHHCCHHHHHHHHHHHhcc
Confidence 445678889999999999 8888 88876555555554333322222 22 88888899999998888776543
No 9
>TIGR02019 BchJ bacteriochlorophyll 4-vinyl reductase. This model represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the "dark" protochlorophyllide reductase enzymes BchN, BchB and BchL. This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll.
Probab=67.79 E-value=28 Score=26.49 Aligned_cols=68 Identities=16% Similarity=0.158 Sum_probs=53.0
Q ss_pred HHHHHHhhcHHHHHHHHHHhCCCC-ccceeeccCCCCChHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhh
Q psy2439 74 IAFQKLEYGDDVWLKVLKKAGCKV-SCFNTHHIYPDIYMPDLATACASVIEG-DLTSEYFMEFFGKCFVRYF 143 (146)
Q Consensus 74 ~~~v~~~~G~~~w~~il~~~~~~~-~~~~~h~~Ypd~~~p~f~~~~s~~~~g-~~~~~~~~~~fG~~~v~~~ 143 (146)
-.-+.+.||++.-.+++.+++... ...--...-|+...-.+..+..+ .+| . ....+++..|+-+-+|+
T Consensus 11 ~~al~~~~g~~~~~~~~~~~g~~~~~~~~p~~mv~E~~~~aL~~aL~~-elG~~-aa~~vl~~~G~~ta~y~ 80 (188)
T TIGR02019 11 VPALEAAYGPGAADRALAAAGQGVLRPGPPSGMLPESQFSTLHRWLRD-TLGET-AAARLLRESGLATADYI 80 (188)
T ss_pred HHHHHHhcCHHHHHHHHHHcCcccccCCCchhcCCHHHHHHHHHHHHH-HhCHH-HHHHHHHHHhHHHHHHH
Confidence 556778999999999999999883 12222346777888888888888 888 5 77889999998877776
No 10
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=59.49 E-value=5.9 Score=23.75 Aligned_cols=47 Identities=17% Similarity=0.039 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCccceecccc-CCchHHHHHHHHHHHhhCCCCHHHHHH
Q psy2439 7 VWLKVLKKAGCKVSCFNTHHIY-PDIYMPDLATACASVIEGDLTSEYFME 55 (146)
Q Consensus 7 ~W~~i~~~a~~~~~~f~~~~~Y-~d~~~~~Lv~a~~~~~~g~~~~~~~l~ 55 (146)
...++.+.+|++...+.....= .......-+.++|+ .+|. +++++++
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~-~l~~-~~~el~~ 59 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAK-ALNC-SPEELFE 59 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHH-HHT---HHHCTE
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHH-HcCC-CHHHHhh
Confidence 3456777788875444333332 25778889999999 9999 9998764
No 11
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=53.68 E-value=30 Score=19.78 Aligned_cols=30 Identities=7% Similarity=-0.078 Sum_probs=24.7
Q ss_pred cccCCchHHHHHHHHHHHhhCCCCHHHHHHHH
Q psy2439 26 HIYPDIYMPDLATACASVIEGDLTSEYFMEFF 57 (146)
Q Consensus 26 ~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~f 57 (146)
..+=|.++.+-+..+|+ .+|+ |...+++..
T Consensus 6 t~~l~~el~~~L~~ls~-~t~i-~~S~Ll~eA 35 (44)
T PF12651_consen 6 TFSLDKELYEKLKELSE-ETGI-PKSKLLREA 35 (44)
T ss_pred EEecCHHHHHHHHHHHH-HHCC-CHHHHHHHH
Confidence 44556778888999999 9999 999998854
No 12
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=51.71 E-value=25 Score=18.96 Aligned_cols=26 Identities=8% Similarity=-0.111 Sum_probs=21.9
Q ss_pred CchHHHHHHHHHHHhhCCCCHHHHHHHH
Q psy2439 30 DIYMPDLATACASVIEGDLTSEYFMEFF 57 (146)
Q Consensus 30 d~~~~~Lv~a~~~~~~g~~~~~~~l~~f 57 (146)
++.+.+.+...|+ ..|. |..++++..
T Consensus 7 ~~~~~~~l~~~a~-~~g~-s~s~~ir~a 32 (39)
T PF01402_consen 7 PDELYERLDELAK-ELGR-SRSELIREA 32 (39)
T ss_dssp EHHHHHHHHHHHH-HHTS-SHHHHHHHH
T ss_pred CHHHHHHHHHHHH-HHCc-CHHHHHHHH
Confidence 4567888999999 9999 999988754
No 13
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=50.24 E-value=1.2e+02 Score=23.61 Aligned_cols=110 Identities=13% Similarity=0.091 Sum_probs=67.3
Q ss_pred cccc-CCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHHh--hcHHHHHHHHHHhCCC--C--
Q psy2439 25 HHIY-PDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKLE--YGDDVWLKVLKKAGCK--V-- 97 (146)
Q Consensus 25 ~~~Y-~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~~--~G~~~w~~il~~~~~~--~-- 97 (146)
++-| |++.-..|..|+|. .+|. +++++-+.-=+ +..+....+.---.+.+..+ =|++....++.++... +
T Consensus 59 m~GY~p~~~~~~If~Alc~-a~~~-dp~~~r~dA~~-l~~~a~~~s~~~l~~~l~~~~~~~~~~l~~~~~~ia~~~~f~Y 135 (216)
T PF11264_consen 59 MQGYPPEEDKDSIFNALCQ-ALGF-DPEQYRQDAEK-LEEWAKGKSIEDLLSWLSQKGGEGDNPLAAILQAIASNPKFKY 135 (216)
T ss_pred hcCCCChhHHHHHHHHHHH-HcCC-CHHHHHHHHHH-HHHHHHcCCHHHHHHHHhccccccchHHHHHHHHHhcCCCCch
Confidence 5667 89999999999999 9999 99887665433 33333333321112222221 1223333344333222 1
Q ss_pred ------ccceeec------cCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q psy2439 98 ------SCFNTHH------IYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 139 (146)
Q Consensus 98 ------~~~~~h~------~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~ 139 (146)
++|.+.. .=++...|......++ .+|. |.+-+-.+.+-|.
T Consensus 136 SRl~AIGL~~LLe~a~~~~~~~~~~~~~~l~~l~~-~l~l-s~~kv~kDL~lYr 187 (216)
T PF11264_consen 136 SRLFAIGLFRLLELAGADLVKDEEKRPEALEKLSE-ALGL-SKEKVEKDLDLYR 187 (216)
T ss_pred HHHHHHHHHHHHHhcCcccccChhhHHHHHHHHHH-HcCC-CHHHHHhhHHHHH
Confidence 2222221 2345578888899999 9999 9999999988774
No 14
>cd08308 Death_Tube Death domain of Tube. Death domains (DDs) similar to the DD in the protein Tube from Drosophila melanogaster. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in mediating innate immune response to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Some members of this subfamily contain a C-terminal kinase domain, like Pelle, in addition to the DD. Tube has no counterpart in vertebrates. It contains an N-terminal DD and a C-terminal region with five copies of the Tube repeat, an 8-amino acid motif. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (D
Probab=47.02 E-value=45 Score=23.74 Aligned_cols=53 Identities=21% Similarity=0.245 Sum_probs=38.8
Q ss_pred HHHHHHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhH
Q psy2439 6 DVWLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKC 60 (146)
Q Consensus 6 ~~W~~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~ 60 (146)
+.|.++.....-+.+.+..+..|+.+ -.+.+.++++ ..|+-|.+++|+.-|++
T Consensus 23 d~Wk~L~~~Ip~~~~~~~~~~~Y~~~-hv~~ie~~~~-~~grSpte~LL~eWGT~ 75 (125)
T cd08308 23 DGWKKLMAIIPSDDDDFNNLAKYNAE-HFKLIEQAAN-KQRRSCSEILLDEWGTS 75 (125)
T ss_pred ccHHHHHHhcCCcccccccccccCHH-HHHHHHHHHH-hcCCChHHHHHHHHhhc
Confidence 67998888765554457778888777 6788888888 78872445577777766
No 15
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=45.49 E-value=16 Score=21.05 Aligned_cols=42 Identities=19% Similarity=0.094 Sum_probs=25.6
Q ss_pred HHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHH
Q psy2439 10 KVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYF 53 (146)
Q Consensus 10 ~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~ 53 (146)
++-+.+|++........+-.-....+.+..+|+ .+|. |++++
T Consensus 14 ~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~-~l~~-~~~~l 55 (55)
T PF01381_consen 14 ELAEKLGISRSTISRIENGKRNPSLDTLKKIAK-ALGV-SPEYL 55 (55)
T ss_dssp HHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHH-HHTS-EHHHH
T ss_pred HHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHH-HHCC-CHHHC
Confidence 455555666444444444445566777888888 8888 87764
No 16
>PF07061 Swi5: Swi5; InterPro: IPR010760 This entry represents Swi5 and is involved in meiotic DNA repair synthesis and meiotic joint molecule formation []. It is known to interact with Swi2, Rhp51 and Swi6 [].
Probab=42.48 E-value=34 Score=22.49 Aligned_cols=27 Identities=26% Similarity=0.099 Sum_probs=24.0
Q ss_pred chHHHHHHHHHHHhhCCCCHHHHHHHHhh
Q psy2439 31 IYMPDLATACASVIEGDLTSEYFMEFFGK 59 (146)
Q Consensus 31 ~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~ 59 (146)
+....|++.+|. .-|. +.-++.+.||-
T Consensus 53 D~gQ~Lig~iA~-~rgv-t~~~v~~e~gl 79 (83)
T PF07061_consen 53 DIGQGLIGLIAD-QRGV-TVKDVYEEFGL 79 (83)
T ss_pred HHHHHHHHHHHH-HcCC-cHHHHHHHcCC
Confidence 467889999999 9999 99999999983
No 17
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=41.39 E-value=81 Score=19.12 Aligned_cols=39 Identities=10% Similarity=0.097 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhhCCCCHHHHHHHHhhHH-HHHh-hhhhhHHH
Q psy2439 33 MPDLATACASVIEGDLTSEYFMEFFGKCF-VRYF-SNLGIILA 73 (146)
Q Consensus 33 ~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~-v~~~-~myG~i~~ 73 (146)
+..++...|+ ..|+ |+++++..|-++= ..++ ..|...+.
T Consensus 4 ~v~~Ie~~A~-~~~~-s~~ea~~~~~~~~~~~~i~~~Yd~lHt 44 (62)
T PF12668_consen 4 VVFCIEEFAK-KLNI-SGEEAYNYFKRSGVIDYIIDCYDVLHT 44 (62)
T ss_pred HHHHHHHHHH-HHCc-CHHHHHHHHHHcCcHHHHHHcchHHHH
Confidence 4568999999 9999 9999999888776 5555 47777666
No 18
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=39.63 E-value=1.8e+02 Score=22.53 Aligned_cols=109 Identities=10% Similarity=-0.014 Sum_probs=61.7
Q ss_pred cccc-CCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHH-hhcHHHHHHHHHHhCC--CC---
Q psy2439 25 HHIY-PDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKL-EYGDDVWLKVLKKAGC--KV--- 97 (146)
Q Consensus 25 ~~~Y-~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~-~~G~~~w~~il~~~~~--~~--- 97 (146)
++-| |++....|..|+|+ .+|. +++++-+.-=+ +..+....+.---.+++.. .=|++....++.++.. .+
T Consensus 62 m~GY~Pee~~~~IF~Alc~-a~~~-dp~~~r~dA~~-l~~~a~~~s~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~f~YS 138 (206)
T PLN03060 62 MDGYPNATDRDAIFKAYIE-ALGE-DPDQYRKDAKK-LEEWASSQSASGIADFNSGDGEVEAVLKDIAERAAGKTKFHYS 138 (206)
T ss_pred HcCCCChHHHHHHHHHHHH-HcCC-CHHHHHHHHHH-HHHHHhcCCHHHHHHHHhcccccchHHHHHHHHhhcCCCcchH
Confidence 4556 88999999999999 9999 99887665433 3333333322100222211 1112223333333321 11
Q ss_pred -----ccceeeccCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q psy2439 98 -----SCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 139 (146)
Q Consensus 98 -----~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~ 139 (146)
++|.+-..=.+. =|......|+ .+|. +.+-+-.+.+-|.
T Consensus 139 Rl~AIGL~~LLe~a~~~-d~~~l~~l~~-~L~l-s~~kv~kDL~lYr 182 (206)
T PLN03060 139 RFFAIGLFRLLECAKAS-DPAVLEKLSK-ALNV-SKRSVDRDLDVYR 182 (206)
T ss_pred HHHHHHHHHHHHHcCCC-CHHHHHHHHH-HcCC-CHHHHHhhHHHHH
Confidence 223322222222 3457777889 9999 9999999888763
No 19
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=37.32 E-value=97 Score=24.96 Aligned_cols=58 Identities=24% Similarity=0.107 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHh-hhhhhHHH-----HHHHHHhhcHHHHHHHHHH
Q psy2439 33 MPDLATACASVIEGDLTSEYFMEFFGKCFVRYF-SNLGIILA-----IAFQKLEYGDDVWLKVLKK 92 (146)
Q Consensus 33 ~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~-~myG~i~~-----~~~v~~~~G~~~w~~il~~ 92 (146)
..+|+.-+|+ .+|+ |.+++++.+|-.+..-+ +-|.-+-. .+.+...-+++.|...+..
T Consensus 103 a~klle~aae-kl~~-~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~~~l~e 166 (269)
T COG1093 103 ADKLLELAAE-KLGK-DLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWKEVLKE 166 (269)
T ss_pred HHHHHHHHHH-HhCC-CHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHHHHHHH
Confidence 5678999999 9999 99999999998885533 33333221 3344444566777774433
No 20
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=36.87 E-value=14 Score=22.15 Aligned_cols=43 Identities=12% Similarity=-0.044 Sum_probs=24.1
Q ss_pred HHHHHhCCCCc---cceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHH
Q psy2439 10 KVLKKAGCKVS---CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFF 57 (146)
Q Consensus 10 ~i~~~a~~~~~---~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~f 57 (146)
++.+.+|++.. .+..... ......+..+|+ .+|+ |+++++...
T Consensus 17 ~~a~~~~i~~~~i~~~e~g~~---~~~~~~l~~i~~-~~~v-~~~~l~~~~ 62 (64)
T PF12844_consen 17 DLAEKLGISRSTISKIENGKR---KPSVSTLKKIAE-ALGV-SLDELFDGE 62 (64)
T ss_dssp HHHHHHTS-HHHHHHHHTTSS-----BHHHHHHHHH-HHTS--HHHHCCCH
T ss_pred HHHHHHCcCHHHHHHHHCCCc---CCCHHHHHHHHH-HhCC-CHHHHhccC
Confidence 44555566422 3333333 223667788899 9999 988876543
No 21
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=34.85 E-value=55 Score=18.14 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=15.2
Q ss_pred HHHHHHHhhCCCCHHHHHHHHhh
Q psy2439 37 ATACASVIEGDLTSEYFMEFFGK 59 (146)
Q Consensus 37 v~a~~~~~~g~~~~~~~l~~fG~ 59 (146)
+..+|+ .+|+ |+..+.+..-+
T Consensus 21 ~~~aA~-~Lgi-sr~tL~~klkk 41 (42)
T PF02954_consen 21 VSKAAR-LLGI-SRRTLYRKLKK 41 (42)
T ss_dssp HHHHHH-HHTS--HHHHHHHHHH
T ss_pred HHHHHH-HHCC-CHHHHHHHHHh
Confidence 357888 9999 99998876543
No 22
>PLN03169 chalcone synthase family protein; Provisional
Probab=34.84 E-value=87 Score=26.19 Aligned_cols=49 Identities=18% Similarity=0.159 Sum_probs=34.6
Q ss_pred HHHHHHHHHhCCCCc-----cceeccccCCchHHHHHHHHHHHhhCCCCHHHH------HHHHhhHH
Q psy2439 6 DVWLKVLKKAGCKVS-----CFNTHHIYPDIYMPDLATACASVIEGDLTSEYF------MEFFGKCF 61 (146)
Q Consensus 6 ~~W~~i~~~a~~~~~-----~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~------l~~fG~~~ 61 (146)
...+++++++|++.. .|..|+ --.+++.++.+ .+|. |.+.+ ++.||.--
T Consensus 285 ~~i~~~L~~~gl~~~did~~~~v~Hq-----~n~~il~~v~~-~Lgl-~~ek~~~s~~~l~~~GNts 344 (391)
T PLN03169 285 GFCKKLMKKAGLVEKDYNDLFWAVHP-----GGPAILNRLEK-KLKL-APEKLECSRRALMDYGNVS 344 (391)
T ss_pred HHHHHHHHHcCCCCCCCCcceEEecC-----CCHHHHHHHHH-HcCC-CHHHHHHHHHHHHHhCCch
Confidence 456778888888732 233333 35899999999 9999 99876 56666544
No 23
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=34.79 E-value=2.2e+02 Score=22.17 Aligned_cols=110 Identities=9% Similarity=0.030 Sum_probs=60.0
Q ss_pred cccc-CCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHHh-hcHH---HHHHHHHHhCCCC--
Q psy2439 25 HHIY-PDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKLE-YGDD---VWLKVLKKAGCKV-- 97 (146)
Q Consensus 25 ~~~Y-~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~~-~G~~---~w~~il~~~~~~~-- 97 (146)
++-| |++....|..|+|. .+|. +++++-+.-=+. ..+....+.---.+++..+ -+.. ....+..+....-
T Consensus 64 m~GY~Pee~~~~IF~Alc~-a~~~-dp~~~r~dA~~l-~~~a~~~s~~~i~~~l~~~~~~~~~~l~l~~ia~n~~f~YSR 140 (214)
T TIGR03060 64 MEGYRPEEHLDALFDALCN-SNGF-DPEQLREDAKQL-LEQAKGKGLDEILSWLTQANLSNGGGDTLQGIAGRHKFKYSR 140 (214)
T ss_pred HcCCCChHHHHHHHHHHHH-hcCC-CHHHHHHHHHHH-HHHHhcCCHHHHHHHHhccccCCcchhHHHHHhcCCCcchHH
Confidence 4556 88999999999999 9999 998876654333 3333333321001111110 0000 0111110000000
Q ss_pred ----ccceeec------cCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q psy2439 98 ----SCFNTHH------IYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 139 (146)
Q Consensus 98 ----~~~~~h~------~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~ 139 (146)
++|.+-. .=++...+.....+|+ .+|. |.+-+-.+.+-|.
T Consensus 141 l~AIGL~~LLe~a~~~~~~d~~~~~~~l~~l~~-~L~l-s~~kv~KDL~lYr 190 (214)
T TIGR03060 141 LFAIGLYSLLEEAAPDKDIDEEDLNEILKELSE-ALGL-SYDRVEKDLDLYK 190 (214)
T ss_pred HHHHHHHHHHHhcCcccccCHHHHHHHHHHHHH-HcCC-CHHHHHhhHHHHH
Confidence 2222211 1123447888899999 9999 9999999888763
No 24
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=34.58 E-value=1.1e+02 Score=25.09 Aligned_cols=68 Identities=15% Similarity=0.127 Sum_probs=50.5
Q ss_pred eccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHH-----HHHHHHhhcHHHHHHHHHHh
Q psy2439 24 THHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILA-----IAFQKLEYGDDVWLKVLKKA 93 (146)
Q Consensus 24 ~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~-----~~~v~~~~G~~~w~~il~~~ 93 (146)
-.+.-+++++.+|..++++ .-.+ |++++-.-.-+|.-.+-...|+... +..+....|++.-..++++.
T Consensus 28 vl~~L~~~ei~~l~~~m~~-l~~v-~~~~~~~vl~eF~~~~~~~~~~~~g~~~~~~~~L~~alg~~~a~~il~~i 100 (334)
T PRK07194 28 VMQQLSREEVQRLSQKMAR-LSGI-KVDQARQVLQRFFDDYREQSGINGASRSYLQRTLNKALGGDIAKSLINSI 100 (334)
T ss_pred HHhcCCHHHHHHHHHHHHh-CCCC-CHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHcCHHHHHHHHHHH
Confidence 3566788999999999999 8888 9999887777766555444333312 66777888998888877664
No 25
>PF09536 DUF2378: Protein of unknown function (DUF2378); InterPro: IPR011751 This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus (strain DK 1622). Members are about 200 amino acids in length. No other homologs are known; the function is unknown.
Probab=34.22 E-value=1.5e+02 Score=22.27 Aligned_cols=60 Identities=25% Similarity=0.253 Sum_probs=45.7
Q ss_pred HHHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhC-CCCHHHHHHHHhhHHHH-Hh-hhhhh
Q psy2439 9 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEG-DLTSEYFMEFFGKCFVR-YF-SNLGI 70 (146)
Q Consensus 9 ~~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g-~~~~~~~l~~fG~~~v~-~~-~myG~ 70 (146)
.+-+..+|++- .+.-...||=+...++..++++ .+. .+|.++-++..|+.++. |. ++-|=
T Consensus 26 ~~rlr~~g~d~-~~~~~~~YP~~~flr~l~~aa~-~l~p~~~~e~a~r~lG~~~v~gf~~T~~Gr 88 (178)
T PF09536_consen 26 AERLRAAGLDL-DRPLFPAYPLEVFLRLLAAAAR-ELYPGLPREEAYRRLGRRFVEGFFETLVGR 88 (178)
T ss_pred HHHHHHhccCc-cccccccCCHHHHHHHHHHHHH-HHcCCCCHHHHHHHHHHHHHHHHHHhHHHH
Confidence 34455667654 6777889999999999999999 553 23999999999999966 43 45554
No 26
>COG0062 Uncharacterized conserved protein [Function unknown]
Probab=33.96 E-value=77 Score=24.38 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=35.9
Q ss_pred cccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHh-hhhhh
Q psy2439 26 HIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYF-SNLGI 70 (146)
Q Consensus 26 ~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~-~myG~ 70 (146)
..|.-..++++....++ .+|. |...|||.-|.-..+-+ .+|+-
T Consensus 3 ~~~~~~~~~~~~~~~~~-~lg~-~~~~LMEnAG~aVa~~i~~~~~~ 46 (203)
T COG0062 3 VVSSAAEMMAIDDLNAE-ALGL-PLDILMENAGLAVARAILREYPL 46 (203)
T ss_pred chhhHHHHHHHHHHHHH-HcCC-CHHHHHHHHHHHHHHHHHHHcCc
Confidence 34566778899999999 9999 99999999999997655 57765
No 27
>PHA01976 helix-turn-helix protein
Probab=32.00 E-value=38 Score=20.29 Aligned_cols=21 Identities=14% Similarity=-0.004 Sum_probs=15.8
Q ss_pred HHHHHHHHHHhhCCCCHHHHHHH
Q psy2439 34 PDLATACASVIEGDLTSEYFMEF 56 (146)
Q Consensus 34 ~~Lv~a~~~~~~g~~~~~~~l~~ 56 (146)
...+..+|+ .+|+ +++.++..
T Consensus 44 ~~~l~~ia~-~l~v-~~~~l~~g 64 (67)
T PHA01976 44 LKTLLRLAD-ALGV-TLDWLCGR 64 (67)
T ss_pred HHHHHHHHH-HHCc-CHHHHhcC
Confidence 455678888 8898 98888653
No 28
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=31.66 E-value=2e+02 Score=23.21 Aligned_cols=122 Identities=19% Similarity=0.113 Sum_probs=70.6
Q ss_pred chHHHHHHHHHHhCCCCc-cceeccccCCchHHHHHHHHHH--HhhCCCCHHHHHHHHhhHHHHHhhhhhhHHH-HHHHH
Q psy2439 3 YGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACAS--VIEGDLTSEYFMEFFGKCFVRYFSNLGIILA-IAFQK 78 (146)
Q Consensus 3 ~G~~~W~~i~~~a~~~~~-~f~~~~~Y~d~~~~~Lv~a~~~--~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~-~~~v~ 78 (146)
+|-+.|.+|.++.+.+-. .=.-...|.......|+-+.|- -.+-. .-++=+..|++||.. -.-.++... ..|+.
T Consensus 17 l~i~~~~~iee~~DpQy~av~~L~~~~g~~~~~~Lvi~NaLvSYqLsg-kGEe~W~eFs~yf~~-~~~~~~~~~~~~Fl~ 94 (269)
T PRK13280 17 LGIEGALEIEERVDPQYKAVENLVESLGEDLFAKLVIANALVSYQLSG-KGEEWWWEFSKYFSE-KGVEDIVEAYIEFLK 94 (269)
T ss_pred cCHHHHHHHHhccCHHHHHHHHHHHHcCccHHHHHHHHHHHHHHhcCC-cHHHHHHHHHHHhcc-cCchhHHHHHHHHHh
Confidence 456667777777665521 2233456777777777765442 13333 567799999999822 122333333 66666
Q ss_pred Hhhc-----HHHHHHHHHHhCCCC--ccceeeccCCCCChHHHHHHHHHHHhCCCCHHH
Q psy2439 79 LEYG-----DDVWLKVLKKAGCKV--SCFNTHHIYPDIYMPDLATACASVIEGDLTSEY 130 (146)
Q Consensus 79 ~~~G-----~~~w~~il~~~~~~~--~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~~~ 130 (146)
...| +.+..++..-..... ........| ..+..+....++ .+|. ..++
T Consensus 95 ~s~~nrrl~e~KikRi~r~~~fl~~L~l~~~~~~y--~~l~~l~~~La~-~L~s-~~~~ 149 (269)
T PRK13280 95 NSKGNRRLLEQKIKRIEKVEPFLESLTLLDLPLYY--EDLEELLEQLAK-ILGA-KKES 149 (269)
T ss_pred cCchhHHHHHHHHHHHHHHHHHhhhhccchhhhhH--hhHHHHHHHHHH-HhCC-CCCc
Confidence 5533 344445544432222 222333456 558999999999 9988 6554
No 29
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=31.60 E-value=45 Score=17.73 Aligned_cols=43 Identities=12% Similarity=-0.070 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHH
Q psy2439 8 WLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEY 52 (146)
Q Consensus 8 W~~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~ 52 (146)
+.++-+.+|++...+.....=......+.+..+++ .+|. +++.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~-~~~~-~~~~ 55 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAK-ALGV-SLDE 55 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHH-HhCC-Chhh
Confidence 34555556665322221111111225566667777 7777 6654
No 30
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=31.32 E-value=71 Score=19.08 Aligned_cols=21 Identities=19% Similarity=0.205 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHhhCCCCHHHHHH
Q psy2439 33 MPDLATACASVIEGDLTSEYFME 55 (146)
Q Consensus 33 ~~~Lv~a~~~~~~g~~~~~~~l~ 55 (146)
+..++.++|+ ..|+ +++++..
T Consensus 2 ~~~I~~~Va~-~~~i-~~~~i~s 22 (60)
T smart00760 2 IEEIIEAVAE-YFGV-KPEDLKS 22 (60)
T ss_pred HHHHHHHHHH-HhCC-CHHHHhc
Confidence 3567888888 8888 8888754
No 31
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=30.95 E-value=2.9e+02 Score=22.45 Aligned_cols=109 Identities=11% Similarity=0.016 Sum_probs=60.0
Q ss_pred cccc-CCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHHh-hcHHHHHHHHHHh--CCCC---
Q psy2439 25 HHIY-PDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKLE-YGDDVWLKVLKKA--GCKV--- 97 (146)
Q Consensus 25 ~~~Y-~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~~-~G~~~w~~il~~~--~~~~--- 97 (146)
++-| |++....|..|+|+ .+|. +++++-+.-=+ +..+....+..--.+++... -.......|..++ ...+
T Consensus 115 m~GY~Pee~~~~IF~Alc~-a~g~-Dp~qyr~dA~~-l~~~A~~~s~~~l~~~l~~~~~l~~~l~~IA~~a~~~~~f~YS 191 (283)
T PLN00047 115 MEGYPSDEDRDAIFKAYIK-ALGE-DPEQYRKDAAK-LEEWARSQTGSSLVDFSSKEGEIEGILKDIAERAGSKGKFSYS 191 (283)
T ss_pred HccCCChHHHHHHHHHHHH-HcCC-CHHHHHHHHHH-HHHHHhcCCHHHHHHHHhcchHHHHHHHHHHHhhccCCCcchH
Confidence 5667 69999999999999 9999 99887665433 33333322221001111111 0001111222121 1221
Q ss_pred -----ccceeeccCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q psy2439 98 -----SCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 139 (146)
Q Consensus 98 -----~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~ 139 (146)
++|.+-..=... -|......++ .+|. +.+-+-.+.+-|.
T Consensus 192 RlfAIGLf~LLe~a~~~-d~~~l~~l~e-~Lgl-s~~kv~KDLdlYr 235 (283)
T PLN00047 192 RFFAIGLFRLLELANAT-EPTALEKLCA-ALNI-NKRSVDRDLDVYR 235 (283)
T ss_pred HHHHHHHHHHHHhcCCC-CHHHHHHHHH-HcCC-CHHHHHhhHHHHH
Confidence 233332222222 3567777999 9999 9999999888774
No 32
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=30.33 E-value=1.5e+02 Score=18.77 Aligned_cols=32 Identities=9% Similarity=0.159 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHh
Q psy2439 32 YMPDLATACASVIEGDLTSEYFMEFFGKCFVRYF 65 (146)
Q Consensus 32 ~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~ 65 (146)
....++.++++ .+|. |.+++...|=.-+..+-
T Consensus 5 ~~~e~i~~iA~-~t~~-P~e~V~~my~dt~~~l~ 36 (66)
T PF12085_consen 5 NVDEVIRSIAE-ETGT-PAETVRRMYDDTMRELS 36 (66)
T ss_pred cHHHHHHHHHH-HHCC-CHHHHHHHHHHHHHHHH
Confidence 36788999999 9999 99999998877765554
No 33
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=28.24 E-value=1.8e+02 Score=24.25 Aligned_cols=71 Identities=11% Similarity=0.047 Sum_probs=54.7
Q ss_pred eeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhH----HH-HHHHHHhhcHHHHHHHHHHhCC
Q psy2439 23 NTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGII----LA-IAFQKLEYGDDVWLKVLKKAGC 95 (146)
Q Consensus 23 ~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i----~~-~~~v~~~~G~~~w~~il~~~~~ 95 (146)
.-...++++++.++..+++. .-.. |+++..+..++|.-.+...-++. .- +.+.....|+++=..++++...
T Consensus 31 ~vlk~l~~~eiq~l~~~~a~-lk~v-~~~~~~~il~eF~~~~~~~~~i~~~~~~~~~~lL~kalg~~~a~~i~~~i~~ 106 (339)
T COG1536 31 EVLKHLSPEEIQRLSTEMAT-LKTV-SPEEKEQVLEEFEELFTEQAGINKGADEYARELLEKALGEEKAESLLERITG 106 (339)
T ss_pred HHHHhCCHHHHHHHHHHHHh-ccCC-CHHHHHHHHHHHHHHHHhccccccChHHHHHHHHHHhCcHhHHHHHHHHhhh
Confidence 34567899999999999999 9999 99999999998775555433222 22 7778888898888887777655
No 34
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=27.54 E-value=83 Score=19.58 Aligned_cols=20 Identities=25% Similarity=0.223 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhCCCCHHHHH
Q psy2439 33 MPDLATACASVIEGDLTSEYFM 54 (146)
Q Consensus 33 ~~~Lv~a~~~~~~g~~~~~~~l 54 (146)
..+++.++|+ ..|+ |.+++.
T Consensus 2 ~~~Ii~~Va~-~~~v-~~~~i~ 21 (70)
T PF08299_consen 2 IEDIIEAVAE-YFGV-SVEDIR 21 (70)
T ss_dssp HHHHHHHHHH-HTT---HHHHH
T ss_pred HHHHHHHHHH-HHCC-CHHHHh
Confidence 4578899999 9999 999988
No 35
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=27.26 E-value=2.6e+02 Score=22.98 Aligned_cols=72 Identities=7% Similarity=-0.014 Sum_probs=51.6
Q ss_pred eeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHH-----HHHHHHhhcHHHHHHHHHHhCCC
Q psy2439 23 NTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILA-----IAFQKLEYGDDVWLKVLKKAGCK 96 (146)
Q Consensus 23 ~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~-----~~~v~~~~G~~~w~~il~~~~~~ 96 (146)
.-.+.-+++++.+|..+.++ .-.+ |++++-.-.-+|.-.+-..-|+... +..+....|++.-..++++....
T Consensus 29 ~vlk~L~~~ei~~l~~~m~~-l~~v-~~~~~~~vl~eF~~~~~~~~~~~~g~~~~~~~~L~~alg~~~a~~il~~i~~~ 105 (338)
T TIGR00207 29 EVFKHLSQEEIETLSAEIAN-VTQI-DNQQKDDVLEEFEQIAEAQAYINIGGLDYAREVLEKALGEEKAASILNDLTSS 105 (338)
T ss_pred HHHHcCCHHHHHHHHHHHHh-cCCC-CHHHHHHHHHHHHHHHHhcCCccCChHHHHHHHHHHhcCHHHHHHHHHHHhcc
Confidence 34567788999999999999 9999 9998777766665444333332211 66777889998888877766443
No 36
>KOG1759|consensus
Probab=26.87 E-value=45 Score=23.40 Aligned_cols=25 Identities=36% Similarity=0.603 Sum_probs=21.5
Q ss_pred cCCchHHHHHHHHHHHhhCCCCHHHHH
Q psy2439 28 YPDIYMPDLATACASVIEGDLTSEYFM 54 (146)
Q Consensus 28 Y~d~~~~~Lv~a~~~~~~g~~~~~~~l 54 (146)
=|+....+|..++|+ ++|+ |.+.++
T Consensus 15 V~~~fe~elt~~lAk-imgk-P~~~i~ 39 (115)
T KOG1759|consen 15 VPDGFEKELTKALAK-IMGK-PEDYIM 39 (115)
T ss_pred CCccHHHHHHHHHHH-HhCC-ChhhEE
Confidence 456688999999999 9999 999865
No 37
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=26.72 E-value=52 Score=25.01 Aligned_cols=20 Identities=20% Similarity=0.194 Sum_probs=11.2
Q ss_pred HHHHHHHHHHhhCCCCHHHHHH
Q psy2439 34 PDLATACASVIEGDLTSEYFME 55 (146)
Q Consensus 34 ~~Lv~a~~~~~~g~~~~~~~l~ 55 (146)
-+++.++|- .+|. +++++++
T Consensus 142 K~vi~~~s~-~~g~-~p~evie 161 (190)
T PF09840_consen 142 KRVIAAVSY-ATGL-DPEEVIE 161 (190)
T ss_pred HHHHHHHHH-HhCC-CHHHHHH
Confidence 355555555 6666 6666544
No 38
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=26.60 E-value=1.4e+02 Score=19.72 Aligned_cols=59 Identities=14% Similarity=0.111 Sum_probs=17.7
Q ss_pred CcchHHHHHHHHHHh-CCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHH
Q psy2439 1 LEYGDDVWLKVLKKA-GCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 61 (146)
Q Consensus 1 ~~~G~~~W~~i~~~a-~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~ 61 (146)
++||.+.|.+..++. .++.........--+++..+|..+..+ -..- +.+++.....++.
T Consensus 8 e~yg~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~l~~~~~~-g~~p-~s~evq~l~~~~~ 67 (118)
T PF07739_consen 8 ERYGDEAYAESEERLASLSKEEWQELQKEWDELFAELAALMEE-GVDP-DSPEVQELAERWM 67 (118)
T ss_dssp HH-----------------------TTHHHHHHHHHHHHHHHH-T--T-T-HHHHHHHHHHH
T ss_pred HHHChHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHc-CCCc-CCHHHHHHHHHHH
Confidence 368888888887776 444444555554444455555555444 2233 4455666666655
No 39
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=26.28 E-value=39 Score=26.82 Aligned_cols=134 Identities=18% Similarity=0.102 Sum_probs=75.4
Q ss_pred cchHHHHHHHHHHhCCCCc-cceeccccCCchHHHHHHHHHHH---hhCCCCHHHHHHHHhhHHHHHhhhhhhHHH-HHH
Q psy2439 2 EYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASV---IEGDLTSEYFMEFFGKCFVRYFSNLGIILA-IAF 76 (146)
Q Consensus 2 ~~G~~~W~~i~~~a~~~~~-~f~~~~~Y~d~~~~~Lv~a~~~~---~~g~~~~~~~l~~fG~~~v~~~~myG~i~~-~~~ 76 (146)
+.|-+.|+.|-++ +.+-. .=.-...|+++...+|+-+-|=| .+| .-|+-+..|++||.+. .-..+.-. ..|
T Consensus 7 ~l~i~~~~~iEe~-DpQy~av~~L~~~~g~~~~~~Lvi~NaLvSYqLs~--kGEe~W~~Fs~yfs~~-~~~~~~~~~~~F 82 (246)
T PF09171_consen 7 ELGIEAARYIEER-DPQYKAVKNLVESYGEELFAKLVIANALVSYQLSG--KGEEYWWEFSEYFSKR-PIEDICEAFIEF 82 (246)
T ss_dssp CCHHHHHHHHHCC-SHHHHHHHHHHCCC-HHHHHHHHHHHHHT-SS-TT---HHHHHHHHHHHHCTS---SSHHHHHHHH
T ss_pred hcCHHHHHHHHHh-ChHHHHHHHHHHHcCchHHHHHHHHHHHHHHhcCC--chHHHHHHHHHHHhcC-CchhHHHHHHHH
Confidence 4677778777666 44311 22334567777777788877741 334 4578999999998544 22222222 444
Q ss_pred HHHhh-----cHHHHHHHHHHhCCCCc--cceeeccCCCCChHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhh
Q psy2439 77 QKLEY-----GDDVWLKVLKKAGCKVS--CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYF 143 (146)
Q Consensus 77 v~~~~-----G~~~w~~il~~~~~~~~--~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~~~~~~~fG~~~v~~~ 143 (146)
+.... -+.+..++..-...-.. ..+....| ..+..+....++ .+|. ..++=.--|-..++.|.
T Consensus 83 L~~s~~n~r~~~~KikRl~k~~~~~~~l~l~~~~~~y--~~l~~l~~~La~-~L~~-~~~~KTiVFAvKM~~Ya 152 (246)
T PF09171_consen 83 LSNSKYNRRLLEQKIKRLRKFCPFLENLSLQDNPLYY--EDLEELWRELAK-ILNS-KPESKTIVFAVKMFGYA 152 (246)
T ss_dssp CCC-TTS-TTHHHHHHHHHHHCCHHHTT-HHHHHHHH--CTHHHHHHHHHH-HHTS--TTSHHHHHHHHHHHHH
T ss_pred HhhCcchHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh--hhHHHHHHHHHH-HhCC-CCccchhhHHHHHHHHH
Confidence 44332 24455555544333212 22333466 778999999999 9988 76665555555555443
No 40
>TIGR00197 yjeF_nterm yjeF N-terminal region. This model is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO match the yjeF C-terminal domain but lack this region.
Probab=25.90 E-value=1.2e+02 Score=22.97 Aligned_cols=37 Identities=19% Similarity=0.074 Sum_probs=28.2
Q ss_pred ccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhh
Q psy2439 27 IYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFS 66 (146)
Q Consensus 27 ~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~ 66 (146)
.|+-+++.++=..+ + ..|+ |...+||..|+...+++.
T Consensus 3 i~t~~qm~~~d~~~-~-~~gi-~~~~LME~Ag~~va~~i~ 39 (205)
T TIGR00197 3 VVSPKDMAIDKENA-E-YLGL-TLDLLMENAGKAVAQAVL 39 (205)
T ss_pred cCCHHHHHHHHHHH-H-hcCC-CHHHHHHHHHHHHHHHHH
Confidence 34555666655555 8 8899 999999999999977663
No 41
>KOG3157|consensus
Probab=25.88 E-value=2.5e+02 Score=22.10 Aligned_cols=63 Identities=11% Similarity=-0.055 Sum_probs=41.1
Q ss_pred HHHHHHHHHh-CCCCccceecc----------ccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHH-HHHhhhhhh
Q psy2439 6 DVWLKVLKKA-GCKVSCFNTHH----------IYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF-VRYFSNLGI 70 (146)
Q Consensus 6 ~~W~~i~~~a-~~~~~~f~~~~----------~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~-v~~~~myG~ 70 (146)
+.-+.|..++ .+....++|-+ +-|-..++++-..+|+ .+|+ |+|++.-..|-.- +.....+|-
T Consensus 150 ~l~~~i~~~c~nL~f~GlMTIGs~~~s~ss~eNpDF~~L~~~r~~ic~-~lg~-~~dq~eLSMGMS~DF~~AIe~Gs 224 (244)
T KOG3157|consen 150 ELAEHIKSECKNLKFSGLMTIGSFDNSHSSGENPDFQVLVKLRESICK-KLGI-PADQVELSMGMSADFLLAIEQGS 224 (244)
T ss_pred HHHHHHHHhCCcceeeeeEEeccccccccCCCCccHHHHHHHHHHHHH-HhCC-ChHHhhhhcccchhHHHHHHhCC
Confidence 3445566655 23323344443 3445578999999999 9999 9999988877665 444455554
No 42
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=25.77 E-value=38 Score=19.27 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=22.9
Q ss_pred CchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHH
Q psy2439 30 DIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRY 64 (146)
Q Consensus 30 d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~ 64 (146)
+.++.-|..++++ +.-. -+++=.+..|.|+.++
T Consensus 8 ~~v~p~L~~gL~~-l~~~-rP~DPi~~La~~Ll~~ 40 (42)
T PF05186_consen 8 ETVGPVLTEGLAE-LAKE-RPEDPIEFLAEYLLKH 40 (42)
T ss_dssp HHTHHHHHHHHHH-HHHH---SSHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHH-HHHH-CCCChHHHHHHHHHHh
Confidence 4567778888888 5556 6678888888888654
No 43
>PF10885 DUF2684: Protein of unknown function (DUF2684); InterPro: IPR020263 This entry contains proteins with no known function.
Probab=25.76 E-value=43 Score=22.08 Aligned_cols=26 Identities=19% Similarity=0.428 Sum_probs=18.8
Q ss_pred hhhhhHHHHHHHHHhhcHHHHHHHHHHhCCCC-ccceee
Q psy2439 66 SNLGIILAIAFQKLEYGDDVWLKVLKKAGCKV-SCFNTH 103 (146)
Q Consensus 66 ~myG~i~~~~~v~~~~G~~~w~~il~~~~~~~-~~~~~h 103 (146)
.+||+||- |..+++.....+ ..|++.
T Consensus 20 n~y~wini------------w~AILgq~f~~fP~fF~~~ 46 (89)
T PF10885_consen 20 NRYGWINI------------WMAILGQFFTRFPVFFESR 46 (89)
T ss_pred eccceehH------------HHHHHHhHhhcCceeeeee
Confidence 57888855 999999987776 444443
No 44
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=25.21 E-value=2.9e+02 Score=21.49 Aligned_cols=54 Identities=9% Similarity=0.054 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHH
Q psy2439 5 DDVWLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRY 64 (146)
Q Consensus 5 ~~~W~~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~ 64 (146)
.+.+.++++++|+....+.-...| .........+ .+-. -.+++.+.||+-....
T Consensus 183 ~~~~~~~l~~aGF~~v~~~d~~~~----~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~ 236 (263)
T PTZ00098 183 IQEYGDLIKSCNFQNVVAKDISDY----WLELLQVELK-KLEE-KKEEFLKLYSEKEYNS 236 (263)
T ss_pred HHHHHHHHHHCCCCeeeEEeCcHH----HHHHHHHHHH-HHHH-hHHHHHHhcCHHHHHH
Confidence 355666777777765333322222 2222222223 3333 5666777777655444
No 45
>PRK12880 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=24.62 E-value=1.8e+02 Score=23.84 Aligned_cols=40 Identities=18% Similarity=0.181 Sum_probs=27.3
Q ss_pred HHHHHHhCCCC---ccceeeccCCCCChHHHHHHHHHHHhCCCCH
Q psy2439 87 LKVLKKAGCKV---SCFNTHHIYPDIYMPDLATACASVIEGDLTS 128 (146)
Q Consensus 87 ~~il~~~~~~~---~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~ 128 (146)
.+.+.+++++. .........||...|+....+.+ .||. +.
T Consensus 69 ~~aL~~a~~~~~dId~lI~~t~t~d~~~P~~a~~v~~-~Lg~-~~ 111 (353)
T PRK12880 69 NTLLQGLNIDKNSLDALIVVTQSPDFFMPSTACYLHQ-LLNL-SS 111 (353)
T ss_pred HHHHHHcCCCHHHCCEEEEEcCCCCCCCCcHHHHHHH-HhCC-CC
Confidence 34555555443 23334457789999999999999 9988 64
No 46
>PF07704 PSK_trans_fac: Rv0623-like transcription factor; InterPro: IPR011660 This entry represents the Rv0623 (P96913 from SWISSPROT)-like group of transcription factors associated with the PSK operon [].
Probab=24.12 E-value=1.2e+02 Score=19.55 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=21.2
Q ss_pred CCchHHHHHHHHHHHhhCCCCHHHHHH
Q psy2439 29 PDIYMPDLATACASVIEGDLTSEYFME 55 (146)
Q Consensus 29 ~d~~~~~Lv~a~~~~~~g~~~~~~~l~ 55 (146)
-|.++.+|+..+++ .+|. |..+..+
T Consensus 6 kd~ev~~LareLA~-~tG~-s~TeAVr 30 (82)
T PF07704_consen 6 KDPEVDRLARELAR-LTGE-SKTEAVR 30 (82)
T ss_pred CCHHHHHHHHHHHH-HHCC-CHHHHHH
Confidence 46789999999999 9999 8877555
No 47
>PLN02377 3-ketoacyl-CoA synthase
Probab=23.29 E-value=3.5e+02 Score=23.73 Aligned_cols=43 Identities=5% Similarity=-0.145 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCC--ccceeeccCCCCChHHHHHHHHHHHhCCCCH
Q psy2439 84 DVWLKVLKKAGCKV--SCFNTHHIYPDIYMPDLATACASVIEGDLTS 128 (146)
Q Consensus 84 ~~w~~il~~~~~~~--~~~~~h~~Ypd~~~p~f~~~~s~~~~g~~~~ 128 (146)
+...+.+.+++++. +...+...-|+.-+|++...+.+ .+|. ..
T Consensus 178 ~A~~~aL~kaGi~p~dID~LVv~cS~~~~~PSlaa~V~~-~LGl-r~ 222 (502)
T PLN02377 178 GALDNLFANTNVNPKDIGILVVNCSLFNPTPSLSAMIVN-KYKL-RG 222 (502)
T ss_pred HHHHHHHHHcCCCHHHCCEEEEECCCCCCCCcHHHHHHH-HhCC-CC
Confidence 44566677776654 21222347777789999999999 9987 64
No 48
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=23.01 E-value=1.1e+02 Score=20.19 Aligned_cols=24 Identities=13% Similarity=0.152 Sum_probs=19.9
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHhhHH
Q psy2439 36 LATACASVIEGDLTSEYFMEFFGKCF 61 (146)
Q Consensus 36 Lv~a~~~~~~g~~~~~~~l~~fG~~~ 61 (146)
.++|+|+ .+|+ +..+++....+-.
T Consensus 6 vi~AiA~-aL~R-~~~dVl~Vl~~~~ 29 (89)
T PF05379_consen 6 VIRAIAE-ALGR-REQDVLAVLSRKC 29 (89)
T ss_pred hhHHHHH-HhCC-CHHHHHHHHHhcc
Confidence 4789999 9999 9999998766643
No 49
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=22.55 E-value=28 Score=23.69 Aligned_cols=40 Identities=18% Similarity=0.135 Sum_probs=29.7
Q ss_pred cceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHH
Q psy2439 21 CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCF 61 (146)
Q Consensus 21 ~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~ 61 (146)
.|--...=+.+++.+|+.++++..+|+ +++-....+.+|+
T Consensus 53 tfgl~S~l~~~eV~~la~~lae~algk-~p~V~V~t~~e~~ 92 (96)
T PF11080_consen 53 TFGLISALSAEEVAQLARGLAESALGK-TPEVEVTTWEEWL 92 (96)
T ss_pred eEEEEecCCHHHHHHHHHHHhhhhcCC-CCceEEEEHHHHH
Confidence 455455558899999999999769999 8876655555554
No 50
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=22.52 E-value=90 Score=21.65 Aligned_cols=44 Identities=11% Similarity=0.077 Sum_probs=24.5
Q ss_pred HHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHHHH
Q psy2439 10 KVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYFME 55 (146)
Q Consensus 10 ~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~ 55 (146)
++-+++|++...+....+=...-....+..+|+ .+|. ++++++.
T Consensus 23 eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~-aL~v-~~~~L~~ 66 (120)
T PRK13890 23 ELSERSGVSISFLSDLTTGKANPSLKVMEAIAD-ALET-PLPLLLE 66 (120)
T ss_pred HHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHH-HHCC-CHHHHhc
Confidence 455556666433222111111335566788888 8888 8887764
No 51
>PF07796 DUF1638: Protein of unknown function (DUF1638); InterPro: IPR012437 This entry contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins and are confined to Bacteria and Archaea.
Probab=22.43 E-value=1.1e+02 Score=22.18 Aligned_cols=50 Identities=16% Similarity=0.185 Sum_probs=38.1
Q ss_pred cchHHHHHHHHHH--hCCCCccceeccccCCchHHHHHHHHHHHhhCCCCHHHH
Q psy2439 2 EYGDDVWLKVLKK--AGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSEYF 53 (146)
Q Consensus 2 ~~G~~~W~~i~~~--a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~ 53 (146)
+||++.=+.+.+. .+.+.-.+.-.+.|+.+...+-+.++|+ .+|. |.+.+
T Consensus 101 ~~G~~~~~~~~~~~~~~y~~~~~Idtg~~~~~~~~~~~~~~a~-~~~l-~~~~~ 152 (166)
T PF07796_consen 101 RYGEDRADAIMRMMFGHYKRVVLIDTGVYDEEDFEEKVREFAE-FLGL-PIEEI 152 (166)
T ss_pred hcCccchHHHHHHHHhCCCeEEEEecccccchHHHHHHHHHHH-HhCC-CEEEE
Confidence 4676666666433 3566668888899999999999999999 9999 76554
No 52
>PF10076 DUF2313: Uncharacterized protein conserved in bacteria (DUF2313); InterPro: IPR018755 Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins, including Gp48 from Bacteriophage Mu and other Mu-like prophages such as FluMu.
Probab=21.70 E-value=1.4e+02 Score=21.89 Aligned_cols=53 Identities=11% Similarity=0.055 Sum_probs=35.4
Q ss_pred cccCCc---hHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhhhhhhHHHHHHHHHhhcHHHHHHHHHHhC
Q psy2439 26 HIYPDI---YMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKLEYGDDVWLKVLKKAG 94 (146)
Q Consensus 26 ~~Y~d~---~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~myG~i~~~~~v~~~~G~~~w~~il~~~~ 94 (146)
..|+.. ++.+++.|.+. .+.. --+.+-...-+.++.-.. .|+ +.|+++++-..
T Consensus 10 ~~~~~~~~~~~~~l~~a~~~-el~~-~~~~~~~l~~e~f~~Tat-~~L-------------~~wE~~lgi~~ 65 (179)
T PF10076_consen 10 GYAWSREPSEFQALLEAEGP-ELDR-LDDRADDLLDEQFPSTAT-WGL-------------PRWERMLGIPP 65 (179)
T ss_pred ccccccchHHHHHHHHHHHH-HHHH-HHHHHHHHHHcCCHHHHH-HHH-------------HHHHHHcCCCC
Confidence 445555 78888888888 6655 455555555555566555 777 89999987554
No 53
>PLN03050 pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional
Probab=21.50 E-value=1.7e+02 Score=22.93 Aligned_cols=40 Identities=18% Similarity=0.066 Sum_probs=32.8
Q ss_pred ccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhHHHHHhh
Q psy2439 25 HHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKCFVRYFS 66 (146)
Q Consensus 25 ~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~~v~~~~ 66 (146)
++.|+-+++.++=..+.+ ..|. |...+||.-|+...+++.
T Consensus 6 ~~i~t~~qmr~~d~~~i~-~~Gi-~~~~LME~AG~ava~~i~ 45 (246)
T PLN03050 6 TGYLNAQDAAALDEELMS-TPGF-SLEQLMELAGLSVAEAVY 45 (246)
T ss_pred eEeeCHHHHHHHHHHHHH-hcCC-CHHHHHHHHHHHHHHHHH
Confidence 456677778888777777 7899 999999999999977663
No 54
>PF11638 DnaA_N: DnaA N-terminal domain; InterPro: IPR024633 The bacterial DnaA protein [, , ] plays an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) []. This entry represents the N-terminal domain of DnaA. This domain is monomeric in solution and has a hydrophobic cleft flanked by several negative residues on one side and positive residues on the other [].; GO: 0005524 ATP binding; PDB: 2JMP_A 2E0G_A.
Probab=21.48 E-value=44 Score=20.07 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=10.3
Q ss_pred HHHHHHHHHHh--CCCCccc
Q psy2439 5 DDVWLKVLKKA--GCKVSCF 22 (146)
Q Consensus 5 ~~~W~~i~~~a--~~~~~~f 22 (146)
++.|++|+++. .++...|
T Consensus 1 ~~~W~~vl~~lk~~l~~~~f 20 (65)
T PF11638_consen 1 EEIWEKVLERLKKELSEQSF 20 (65)
T ss_dssp -HHHHHHHHHHHHHTSS-HH
T ss_pred CcHHHHHHHHHHHHCCHHHH
Confidence 46788888777 3444344
No 55
>PRK11187 replication initiation regulator SeqA; Provisional
Probab=21.17 E-value=74 Score=24.16 Aligned_cols=25 Identities=8% Similarity=0.062 Sum_probs=22.2
Q ss_pred CchHHHHHHHHHHHhhCCCCHHHHHHH
Q psy2439 30 DIYMPDLATACASVIEGDLTSEYFMEF 56 (146)
Q Consensus 30 d~~~~~Lv~a~~~~~~g~~~~~~~l~~ 56 (146)
|+++++-+.+=.+ ..|. |+.|+|+.
T Consensus 7 DeELYryIAS~Tq-~IGE-SASDILRR 31 (182)
T PRK11187 7 DEELYRYIASHTQ-HIGE-SASDILRR 31 (182)
T ss_pred cHHHHHHHHHccC-ccCC-CHHHHHHH
Confidence 7889999988889 9999 99999984
No 56
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=20.36 E-value=1.4e+02 Score=18.27 Aligned_cols=34 Identities=6% Similarity=0.126 Sum_probs=20.7
Q ss_pred cceeccccCCchHHHHHHHHHHHhhCCCCHHHHHHHHhhH
Q psy2439 21 CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKC 60 (146)
Q Consensus 21 ~f~~~~~Y~d~~~~~Lv~a~~~~~~g~~~~~~~l~~fG~~ 60 (146)
.|.+|+.-.+..+.. +|+ .+|+ +.+++...|-+.
T Consensus 16 Yy~~h~~L~E~DL~~----L~~-kS~m-s~qqVr~WFa~~ 49 (56)
T PF11569_consen 16 YYLKHKQLQEEDLDE----LCD-KSRM-SYQQVRDWFAER 49 (56)
T ss_dssp HHHHT----TTHHHH----HHH-HTT---HHHHHHHHHHH
T ss_pred HHHHcCCccHhhHHH----HHH-HHCC-CHHHHHHHHHHh
Confidence 566677666666655 467 8888 999999988654
No 57
>COG0015 PurB Adenylosuccinate lyase [Nucleotide transport and metabolism]
Probab=20.08 E-value=1.8e+02 Score=25.09 Aligned_cols=40 Identities=23% Similarity=0.294 Sum_probs=31.2
Q ss_pred HHHHHHHHHhCCCCccceeccccCCchHHHHHHHHHHHhhCC
Q psy2439 6 DVWLKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGD 47 (146)
Q Consensus 6 ~~W~~i~~~a~~~~~~f~~~~~Y~d~~~~~Lv~a~~~~~~g~ 47 (146)
++=+.+.+++|+.....+ .++||.+..-.++.+++. +.+.
T Consensus 200 ~ve~~v~e~LGL~~~p~s-tq~~~RD~~ae~~~~La~-i~~s 239 (438)
T COG0015 200 EVEERVAEKLGLKPAPIS-TQVSPRDRIAEFFSALAL-LAGS 239 (438)
T ss_pred HHHHHHHHHcCCCCCCCC-cccccchHHHHHHHHHHH-HHHH
Confidence 666778888899873444 499999999999888888 6665
Done!