Query 026758
Match_columns 233
No_of_seqs 26 out of 28
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 12:17:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026758.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026758hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02744 dihydrolipoyllysine-r 87.7 0.21 4.5E-06 49.9 0.7 47 2-48 1-47 (539)
2 KOG0005 Ubiquitin-like protein 68.9 4.9 0.00011 30.6 2.6 36 66-106 11-46 (70)
3 TIGR02990 ectoine_eutA ectoine 67.5 6.3 0.00014 35.2 3.5 35 143-177 194-228 (239)
4 COG3473 Maleate cis-trans isom 67.1 6.9 0.00015 36.0 3.7 34 144-177 193-226 (238)
5 PF03732 Retrotrans_gag: Retro 61.3 25 0.00054 24.8 5.0 53 80-132 26-78 (96)
6 KOG4077 Cytochrome c oxidase, 57.8 12 0.00025 32.4 3.2 46 56-102 98-143 (149)
7 PF13348 Y_phosphatase3C: Tyro 44.8 33 0.00072 24.2 3.4 38 140-186 28-66 (68)
8 cd00923 Cyt_c_Oxidase_Va Cytoc 43.3 35 0.00075 28.0 3.7 46 56-102 56-101 (103)
9 PF02436 PYC_OADA: Conserved c 42.8 66 0.0014 28.4 5.6 107 8-136 47-166 (196)
10 PF12244 DUF3606: Protein of u 40.3 44 0.00095 24.0 3.5 43 71-122 14-56 (57)
11 PF03564 DUF1759: Protein of u 39.6 1.2E+02 0.0025 23.9 6.2 66 44-110 60-128 (145)
12 PRK14574 hmsH outer membrane p 36.3 4.1E+02 0.009 28.2 11.1 118 21-156 79-198 (822)
13 COG0783 Dps DNA-binding ferrit 35.9 2.3E+02 0.005 24.3 7.7 73 71-154 73-148 (156)
14 COG1529 CoxL Aerobic-type carb 35.9 50 0.0011 34.1 4.3 60 75-134 349-411 (731)
15 PF11791 Aconitase_B_N: Aconit 34.8 81 0.0018 27.5 4.8 70 90-161 8-80 (154)
16 PF05511 ATP-synt_F6: Mitochon 34.5 73 0.0016 25.9 4.2 67 27-97 18-84 (99)
17 PF02630 SCO1-SenC: SCO1/SenC; 34.5 56 0.0012 27.2 3.8 40 48-87 72-113 (174)
18 PF06456 Arfaptin: Arfaptin-li 33.3 3.6E+02 0.0078 24.2 10.3 29 180-208 168-197 (229)
19 PF14559 TPR_19: Tetratricopep 33.3 45 0.00098 22.2 2.5 58 55-120 4-61 (68)
20 PF13371 TPR_9: Tetratricopept 32.5 71 0.0015 21.5 3.4 32 54-86 7-38 (73)
21 PF02284 COX5A: Cytochrome c o 32.3 35 0.00075 28.2 2.1 45 56-101 59-103 (108)
22 PF13428 TPR_14: Tetratricopep 29.2 51 0.0011 21.2 2.1 34 51-85 10-43 (44)
23 PRK08045 cystathionine gamma-s 28.0 21 0.00045 33.5 0.1 26 127-152 360-385 (386)
24 PF04977 DivIC: Septum formati 27.7 27 0.00058 24.7 0.7 23 75-103 52-74 (80)
25 PRK14182 bifunctional 5,10-met 27.3 2.3E+02 0.005 26.5 6.8 71 41-112 4-85 (282)
26 PF03704 BTAD: Bacterial trans 27.3 1.1E+02 0.0024 23.6 4.1 27 79-106 115-141 (146)
27 PLN03060 inositol phosphatase- 27.0 4.8E+02 0.01 23.6 10.1 114 75-213 84-201 (206)
28 COG5185 HEC1 Protein involved 26.9 1.6E+02 0.0035 30.4 6.1 151 44-206 226-401 (622)
29 PF13310 Virulence_RhuM: Virul 25.6 92 0.002 29.2 3.9 102 6-108 16-146 (260)
30 KOG0787 Dehydrogenase kinase [ 25.2 2.5E+02 0.0054 28.1 6.8 78 50-130 104-186 (414)
31 PRK14178 bifunctional 5,10-met 24.6 1.2E+02 0.0027 28.2 4.5 69 41-111 3-80 (279)
32 PRK10455 periplasmic protein; 24.5 2.5E+02 0.0053 24.0 6.0 36 70-105 91-138 (161)
33 PF13431 TPR_17: Tetratricopep 24.4 73 0.0016 20.0 2.2 19 70-88 6-24 (34)
34 PF00763 THF_DHG_CYH: Tetrahyd 24.4 2.1E+02 0.0045 22.7 5.2 57 41-98 3-61 (117)
35 cd04865 LigD_Pol_like_2 LigD_P 23.9 90 0.0019 28.5 3.4 32 68-99 102-136 (228)
36 PF05130 FlgN: FlgN protein; 23.6 3.2E+02 0.007 20.5 6.2 77 45-125 4-94 (143)
37 TIGR02778 ligD_pol DNA polymer 23.3 92 0.002 28.7 3.4 32 68-99 117-151 (245)
38 cd04863 MtLigD_Pol_like MtLigD 22.9 95 0.0021 28.4 3.4 31 69-99 106-139 (231)
39 PRK14194 bifunctional 5,10-met 22.6 3E+02 0.0065 26.0 6.6 71 41-112 7-88 (301)
40 PF08745 UPF0278: UPF0278 fami 21.7 53 0.0011 29.8 1.5 34 152-186 165-201 (205)
41 PF08328 ASL_C: Adenylosuccina 21.6 38 0.00083 28.2 0.6 67 57-125 26-97 (115)
42 TIGR02215 phage_chp_gp8 phage 21.2 1.4E+02 0.0031 25.9 4.0 39 123-161 15-56 (188)
43 COG0749 PolA DNA polymerase I 21.2 9.5E+02 0.021 25.1 10.4 164 41-212 382-574 (593)
44 PF10553 MSV199: MSV199 domain 21.2 4.6E+02 0.0099 22.4 6.9 74 50-127 52-137 (139)
45 TIGR02684 dnstrm_HI1420 probab 21.1 2.3E+02 0.0051 21.9 4.8 52 105-157 19-70 (89)
46 PF05227 CHASE3: CHASE3 domain 20.7 2.9E+02 0.0062 20.9 5.2 54 27-91 27-80 (138)
47 KOG1962 B-cell receptor-associ 20.2 4.8E+02 0.01 23.8 7.2 38 169-206 149-191 (216)
48 cd01043 DPS DPS protein, ferri 20.0 4.3E+02 0.0094 20.6 8.2 99 44-154 33-132 (139)
No 1
>PLN02744 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Probab=87.65 E-value=0.21 Score=49.85 Aligned_cols=47 Identities=40% Similarity=0.632 Sum_probs=43.9
Q ss_pred hhhhhHhhhhhhhhhhHHHHhhccchhHHhhhhhcCCccCchhHHHH
Q 026758 2 AFASRLASKSKQLCSSQVILQRQHAISVRFFANEAAPQALKGDEMLK 48 (233)
Q Consensus 2 a~~~r~~sr~~~~~~~~~~~~~~~~~~vR~fA~~Aap~~~kGdd~lK 48 (233)
+++||++..|+.|+....+|..+|+.-||+|+....+...+||++.+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (539)
T PLN02744 1 AYASRIINHSKKLRNVSNLLRREHAALVRYFSNSTRSSLGKGDDIAK 47 (539)
T ss_pred CchHHHhhhchhhcchHHHhcccccceEEEecCCCccCcccccchhh
Confidence 57899999999999999999999999999999998888889999855
No 2
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=68.87 E-value=4.9 Score=30.64 Aligned_cols=36 Identities=28% Similarity=0.509 Sum_probs=27.3
Q ss_pred hccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHH
Q 026758 66 RKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYT 106 (233)
Q Consensus 66 kk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~t 106 (233)
+.+.|.|+|.|.- ....+.+-++-||||+.||+-++
T Consensus 11 KeIeidIep~Dkv-----erIKErvEEkeGIPp~qqrli~~ 46 (70)
T KOG0005|consen 11 KEIEIDIEPTDKV-----ERIKERVEEKEGIPPQQQRLIYA 46 (70)
T ss_pred ceEEEeeCcchHH-----HHHHHHhhhhcCCCchhhhhhhc
Confidence 4567888888742 33446688899999999999775
No 3
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=67.50 E-value=6.3 Score=35.22 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhCCccccccHhhHHHHHHHhCCCC
Q 026758 143 MMDALEKVEKEIKKPLMRNDKKGMALLTAELGIRK 177 (233)
Q Consensus 143 mm~ALdkvEK~igkpL~rsDkkGM~~L~aelGI~k 177 (233)
..+.++++|.++|||+++||-.-+--....+|++.
T Consensus 194 t~~vi~~lE~~lGkPVlsSNqat~W~~Lr~~G~~~ 228 (239)
T TIGR02990 194 AATCAQRIEQAIGKPVVTSNQATAWRCLRLCGDPD 228 (239)
T ss_pred hHHHHHHHHHHHCCCEEEHHHHHHHHHHHHcCCCC
Confidence 46789999999999999999988766666777653
No 4
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=67.06 E-value=6.9 Score=36.00 Aligned_cols=34 Identities=18% Similarity=0.477 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhCCccccccHhhHHHHHHHhCCCC
Q 026758 144 MDALEKVEKEIKKPLMRNDKKGMALLTAELGIRK 177 (233)
Q Consensus 144 m~ALdkvEK~igkpL~rsDkkGM~~L~aelGI~k 177 (233)
.+.++++|.++|+|+.+||-.-|-.-...+|++-
T Consensus 193 ~eii~~lE~~~G~PVvsSN~AT~W~~Lr~~g~~~ 226 (238)
T COG3473 193 FEIIEKLERDTGVPVVSSNQATLWMALRLIGLRE 226 (238)
T ss_pred HHHHHHHHHHhCCceeeccHHHHHHHHHHcCCcc
Confidence 5789999999999999999998877777888653
No 5
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=61.31 E-value=25 Score=24.76 Aligned_cols=53 Identities=11% Similarity=0.196 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHcC
Q 026758 80 VSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRG 132 (233)
Q Consensus 80 Vk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~G 132 (233)
+.-|.+....++...+=+.........+....|+..+|+.|+....++....+
T Consensus 26 ~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~ 78 (96)
T PF03732_consen 26 FITWEEFKDAFRKRFFPPDRKEQARQELNSLRQGNESVREYVNRFRELARRAP 78 (96)
T ss_pred CCCHHHHHHHHHHHHhhhhccccchhhhhhhhccCCcHHHHHHHHHHHHHHCC
Confidence 44567777777777777777777777788888888999999999999988888
No 6
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=57.81 E-value=12 Score=32.40 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=33.4
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHH
Q 026758 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQR 102 (233)
Q Consensus 56 kkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~ 102 (233)
+.|-+++-+|-..|+-..|.+. .-..|-+.++-++.++|||+++|.
T Consensus 98 NDfa~aVRilE~iK~K~g~~k~-~Y~y~v~elkpvl~ELGI~t~EeL 143 (149)
T KOG4077|consen 98 NDFATAVRILEAIKDKCGAQKQ-VYPYYVKELKPVLNELGIPTPEEL 143 (149)
T ss_pred ccHHHHHHHHHHHHHhcccHHH-HHHHHHHHHHHHHHHhCCCCHHHh
Confidence 5677777778777777743222 355667778888899999999874
No 7
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=44.76 E-value=33 Score=24.18 Aligned_cols=38 Identities=21% Similarity=0.427 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhhCCccccccHhhHHHHH-HHhCCCCCChhhHHHH
Q 026758 140 EAMMMDALEKVEKEIKKPLMRNDKKGMALLT-AELGIRKEDLPKYEEQ 186 (233)
Q Consensus 140 ~a~mm~ALdkvEK~igkpL~rsDkkGM~~L~-aelGI~keDl~K~eee 186 (233)
.+.|..+++.|+..-| |+.-|. ..+|+.++|..++++.
T Consensus 28 ~e~l~~~l~~i~~~yG---------s~e~Yl~~~lgl~~~~i~~Lr~~ 66 (68)
T PF13348_consen 28 PEYLEAALDAIDERYG---------SVENYLREELGLSEEDIERLRER 66 (68)
T ss_dssp HHHHHHHHHHHHHHHS---------SHHHHHHHT-T--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcC---------CHHHHHHHcCCCCHHHHHHHHHH
Confidence 4578899999999988 677777 5599999999888764
No 8
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=43.31 E-value=35 Score=28.04 Aligned_cols=46 Identities=11% Similarity=0.094 Sum_probs=34.6
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHH
Q 026758 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQR 102 (233)
Q Consensus 56 kkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~ 102 (233)
+.|-+++-.|-..|.-.. +...-...|-+.++-+++++||+++++.
T Consensus 56 ND~alAVR~lE~vK~K~~-~~~~~y~~~lqeikp~l~ELGI~t~EeL 101 (103)
T cd00923 56 NDFALAVRILEAIKDKCG-AHKEIYPYILQEIKPTLKELGISTPEEL 101 (103)
T ss_pred hhHHHHHHHHHHHHHHcc-CchhhHHHHHHHHhHHHHHHCCCCHHHh
Confidence 577777777776665553 3455678888889999999999999873
No 9
>PF02436 PYC_OADA: Conserved carboxylase domain; InterPro: IPR003379 This domain represents a conserved region in pyruvate carboxylase (PYC) (6.4.1.1 from EC), oxaloacetate decarboxylase alpha chain (OADA) (4.1.1.3 from EC), and transcarboxylase 5s subunit (2.1.3.1 from EC). The domain is found adjacent to the HMGL-like domain (IPR000891 from INTERPRO) and often close to the biotin_lipoyl domain (IPR000089 from INTERPRO) of biotin requiring enzymes.; PDB: 2NX9_B 3HBL_A 3HB9_C 3HO8_A 3BG5_C 1S3H_A 1RQE_A 1U5J_A 1RQB_A 2QF7_B ....
Probab=42.85 E-value=66 Score=28.35 Aligned_cols=107 Identities=21% Similarity=0.259 Sum_probs=58.6
Q ss_pred hhhhhhhhhhHHHHhhcc----------chhHHhhhhh--cCCccCchhHHHHHHHHHHHHHHHHHHhchhccccccCCC
Q 026758 8 ASKSKQLCSSQVILQRQH----------AISVRFFANE--AAPQALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPE 75 (233)
Q Consensus 8 ~sr~~~~~~~~~~~~~~~----------~~~vR~fA~~--Aap~~~kGdd~lK~iF~evqkkF~~~l~~lkk~kI~ldp~ 75 (233)
+--|+|+.|.||++.=.. .-+|+.|... ..||+.-..++.+.|... ...|+-.|+
T Consensus 47 VTPsSqiVg~qA~~nV~~~~~g~r~~~~p~~v~~~~~G~~G~pp~~~~~~l~~~vl~~-------------~~~i~~RP~ 113 (196)
T PF02436_consen 47 VTPSSQIVGDQAVFNVLNGLLGERYKDFPDSVVDYLLGKYGKPPGGFPEELRKKVLKG-------------EEPITGRPG 113 (196)
T ss_dssp STTHHHHHHHHHHHHHHTT-HHTTTSS-BHHHHHHHTTTT---TTSS-HHHHHHHHTT-------------S---SSSGG
T ss_pred cCcHHHHHHHHHHHHHHhhhcCccccchhHHHHHHhCcccCCCCCCCCHHHHHHHhcC-------------CCCCCCCcc
Confidence 456889999999875443 3467778886 666665557777766422 344555565
Q ss_pred CHHHHHHHHHHHHHHHHhcCC-CChHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHcCCcch
Q 026758 76 DPAAVSQYANVMKTVREKADL-FSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDE 136 (233)
Q Consensus 76 DpaAVk~YA~~~~~vr~k~gl-~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~ 136 (233)
|.-.=-.+....+.+..+.|- +++++.+++.+=-. .++.|+. .|.+.|.-..
T Consensus 114 ~~l~p~d~~~~r~~l~~~~g~~~~dedvlsyal~P~-----v~~~f~~----~~~~~g~~~~ 166 (196)
T PF02436_consen 114 DLLPPADLDKLRKELEEKAGREPTDEDVLSYALFPK-----VAEDFLK----FRAKYGDVSV 166 (196)
T ss_dssp GCS----HHHHHHHHHHHCTSTSCHHHHHHHHHCHH-----HHHHHHH----HHHHHS-GGC
T ss_pred ccCChhhHHHHHHHHHHHcCCCCCHHHHHHHhcCch-----hHHHHHH----HHHhcCCCCc
Confidence 443333455566677777766 57777777766321 2355554 3555664333
No 10
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=40.29 E-value=44 Score=23.95 Aligned_cols=43 Identities=16% Similarity=0.264 Sum_probs=32.0
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHH
Q 026758 71 TIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLL 122 (233)
Q Consensus 71 ~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~ 122 (233)
.|+++|+..|..++ +++|++ .+++...|..---.+.+||.||.
T Consensus 14 ~I~~~e~~ev~ywa-------~~~gvt--~~~L~~AV~~vG~~~~~V~~~L~ 56 (57)
T PF12244_consen 14 RIDLSEPYEVRYWA-------KRFGVT--EEQLREAVRAVGNSRAAVRAYLG 56 (57)
T ss_pred hcCCCCHHHHHHHH-------HHHCcC--HHHHHHHHHHHCcCHHHHHHHHc
Confidence 46668888888877 667775 45677777777777888888885
No 11
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=39.61 E-value=1.2e+02 Score=23.90 Aligned_cols=66 Identities=15% Similarity=0.233 Sum_probs=47.4
Q ss_pred hHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHH---hcCCCChHHHHHHHHHhh
Q 026758 44 DEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVRE---KADLFSESQRIAYTIETR 110 (233)
Q Consensus 44 dd~lK~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~---k~gl~s~~e~I~~tie~~ 110 (233)
=+.|+.-|-.-..-.+++++.|.+.+ ++..+|+.++..+.+.+..+-. .+|.+..+..+...|-.+
T Consensus 60 ~~~L~~~yg~~~~i~~~~~~~l~~l~-~~~~~d~~~L~~~~~~v~~~i~~L~~lg~~~~~~~l~~~i~~K 128 (145)
T PF03564_consen 60 WELLEERYGNPRRIIQALLEELRNLP-PISNDDPEALRSLVDKVNNCIRALKALGVNVDDPLLISIILSK 128 (145)
T ss_pred HHHHHHHhCCchHHHHHHHHHHhccc-cccchhHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 35788888887777888888888666 4777999999999988766554 556666655554444433
No 12
>PRK14574 hmsH outer membrane protein; Provisional
Probab=36.29 E-value=4.1e+02 Score=28.23 Aligned_cols=118 Identities=13% Similarity=0.114 Sum_probs=70.2
Q ss_pred HhhccchhHHhhhhhcCCccCchhHHHH--HHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC
Q 026758 21 LQRQHAISVRFFANEAAPQALKGDEMLK--NIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS 98 (233)
Q Consensus 21 ~~~~~~~~vR~fA~~Aap~~~kGdd~lK--~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s 98 (233)
...|.-...+.+...+..|.-.-.-.+. ......+++|..++..+++. +.++|++|++....+ ..-+.. .
T Consensus 79 ~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~ka-L~~dP~n~~~l~gLa------~~y~~~-~ 150 (822)
T PRK14574 79 GWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSS-LKKDPTNPDLISGMI------MTQADA-G 150 (822)
T ss_pred HHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhhCCCCHHHHHHHH------HHHhhc-C
Confidence 3445555666666654432222233344 34667788999999999987 689999998885332 222222 4
Q ss_pred hHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHcCCcchhhhHHHHHHHHHHHHHhhCC
Q 026758 99 ESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKVEKEIKK 156 (233)
Q Consensus 99 ~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK~igk 156 (233)
..+.....++.....-|+.+.|+.. ..+ ..|..+... ||...++-+..
T Consensus 151 q~~eAl~~l~~l~~~dp~~~~~l~l-ayL--~~~~~~~~~-------AL~~~ekll~~ 198 (822)
T PRK14574 151 RGGVVLKQATELAERDPTVQNYMTL-SYL--NRATDRNYD-------ALQASSEAVRL 198 (822)
T ss_pred CHHHHHHHHHHhcccCcchHHHHHH-HHH--HHhcchHHH-------HHHHHHHHHHh
Confidence 4556666777777778888888443 332 333433322 55556655544
No 13
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=35.93 E-value=2.3e+02 Score=24.28 Aligned_cols=73 Identities=16% Similarity=0.363 Sum_probs=46.3
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHcCC---cchhhhHHHHHHHH
Q 026758 71 TIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGL---IDEHGAEAMMMDAL 147 (233)
Q Consensus 71 ~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl---~D~~g~~a~mm~AL 147 (233)
.|+.--+...+.|... -.|.+.-|-++..+.+...++. |-.-+.++|...++ ..+.++-.+|-+.+
T Consensus 73 ~LGg~p~~t~~~~~~~-s~ike~~~~~~~~~~l~~l~~~----------~~~l~~~~r~~~~~a~e~gD~~Tadl~~~~~ 141 (156)
T COG0783 73 ALGGVPLGTLSEYLKL-SSIKEEPGDYTAREMLKELVED----------YEYLIKELRKGIELADEAGDEVTADLLTDII 141 (156)
T ss_pred HcCCCCcccHHHHHHh-CCCcccCCCCCHHHHHHHHHHH----------HHHHHHHHHHHHHhhhhcCChhHHHHHHHHH
Confidence 5553333466666633 2344444447777777777654 44555666777776 44567788888999
Q ss_pred HHHHHhh
Q 026758 148 EKVEKEI 154 (233)
Q Consensus 148 dkvEK~i 154 (233)
.++||.+
T Consensus 142 ~~~EK~~ 148 (156)
T COG0783 142 RELEKTL 148 (156)
T ss_pred HHHHHHH
Confidence 9999864
No 14
>COG1529 CoxL Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]
Probab=35.91 E-value=50 Score=34.08 Aligned_cols=60 Identities=20% Similarity=0.218 Sum_probs=51.5
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcC---CCcHHHHHHHHHHHHHHcCCc
Q 026758 75 EDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAG---IPDARTYLLTLKEIRERRGLI 134 (233)
Q Consensus 75 ~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~---~~dvR~yL~~~~EiR~~~Gl~ 134 (233)
++|.+.-..--.|..+.++|||.+.+-|+.+++.+.--+ ..+.+.|...+.+..+++|..
T Consensus 349 g~~~~~~a~E~~~d~lA~~Lgidp~eiR~~n~~~~g~~~~~~~~~~~~~~~~~~~~ak~~~~~ 411 (731)
T COG1529 349 GRPEGTFALERAVDELAEELGIDPVEIRLRNLIRGGPFGLGRRYDSGDYLEELDEAAKRFGWS 411 (731)
T ss_pred CCchhHHHHHHHHHHHHHHhCCCHHHHhhhhccccCCCCCcccccCccHHHHHHHHHHhcCcc
Confidence 777776666677999999999999999999999966655 888999999999999888863
No 15
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=34.82 E-value=81 Score=27.48 Aligned_cols=70 Identities=23% Similarity=0.260 Sum_probs=47.7
Q ss_pred HHHhcCCCC---hHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHcCCcchhhhHHHHHHHHHHHHHhhCCccccc
Q 026758 90 VREKADLFS---ESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKVEKEIKKPLMRN 161 (233)
Q Consensus 90 vr~k~gl~s---~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK~igkpL~rs 161 (233)
=|...|||| ..++....++-...+...=+.||..+-..|..-|..+...++|..+.++-+ +++.-|+.+.
T Consensus 8 eRa~~GipPlPL~a~Qt~~lielLk~~~~~~~~~lldLL~~RV~PGVD~AA~VKA~FL~~ia~--g~~~~~~Is~ 80 (154)
T PF11791_consen 8 ERAALGIPPLPLNAEQTAELIELLKNPPAGEEAFLLDLLTNRVPPGVDEAAYVKAEFLAAIAK--GEISSPLISP 80 (154)
T ss_dssp HHHCTT-------HHHHHHHHHHHHS--TT-HHHHHHHHHHSS--TT-HHHHHHHHHHHHHHT--TSS-BTTB-H
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHc--CCccCCCcCH
Confidence 478889987 467888888888877777789999999999999999999999988887754 3455566653
No 16
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=34.49 E-value=73 Score=25.86 Aligned_cols=67 Identities=12% Similarity=0.101 Sum_probs=37.0
Q ss_pred hhHHhhhhhcCCccCchhHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCC
Q 026758 27 ISVRFFANEAAPQALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLF 97 (233)
Q Consensus 27 ~~vR~fA~~Aap~~~kGdd~lK~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~ 97 (233)
...|+++-+| +...+..|.+..+|.+-=+.|.+.... ..-+ ++| -.|+--+.|...+..+.+..|.-
T Consensus 18 ~~~Rni~~sa-~~~~k~~DPIQklFldKIREY~~Ksks-~gGk-lVD-~~Pe~~kel~eel~kL~r~YG~g 84 (99)
T PF05511_consen 18 HLRRNIGTSA-VAFNKALDPIQKLFLDKIREYNQKSKS-SGGK-LVD-AGPEYEKELNEELEKLARQYGGG 84 (99)
T ss_dssp ----------------S--TTTHHHHHHHHHHHHHHTT-TSS--STT---THHHHHHHHHHHHHHHHHHSS
T ss_pred HHHHHhhhhH-HHHhcccChHHHHHHHHHHHHHHHhcc-CCCC-CCC-CCHHHHHHHHHHHHHHHHHhCCc
Confidence 3456665553 322267899999999988888776653 2222 455 56889999999999998877765
No 17
>PF02630 SCO1-SenC: SCO1/SenC; InterPro: IPR003782 This family is involved in biogenesis of respiratory and photosynthetic systems. In yeast the SCO1 protein is specifically required for a post-translational step in the accumulation of subunits 1 and 2 of cytochrome c oxidase (COXI and COX-II) []. It is a mitochondrion-associated cytochrome c oxidase assembly factor. The purple nonsulphur photosynthetic eubacterium Rhodobacter capsulatus is a versatile organism that can obtain cellular energy by several means, including the capture of light energy for photosynthesis as well as the use of light-independent respiration, in which molecular oxygen serves as a terminal electron acceptor. The SenC protein is required for optimal cytochrome c oxidase activity in aerobically grown R. capsulatus cells and is involved in the induction of structural polypeptides of the light-harvesting and reaction centre complexes [].; PDB: 2K6V_A 3ME8_A 3ME7_A 2GT6_A 2GQL_A 2GQK_A 2GGT_B 1WP0_C 2HRN_A 2GQM_A ....
Probab=34.46 E-value=56 Score=27.22 Aligned_cols=40 Identities=15% Similarity=0.266 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHhchhccccccCC--CCHHHHHHHHHHH
Q 026758 48 KNIFLDVKKKFETALGVLRKEKITIAP--EDPAAVSQYANVM 87 (233)
Q Consensus 48 K~iF~evqkkF~~~l~~lkk~kI~ldp--~DpaAVk~YA~~~ 87 (233)
...+.++++++..--.-++=.-|++|| +.|++.++|++..
T Consensus 72 l~~l~~~~~~l~~~~~~v~~v~ISvDP~~DTp~~L~~Y~~~~ 113 (174)
T PF02630_consen 72 LANLSQLQKQLGEEGKDVQFVFISVDPERDTPEVLKKYAKKF 113 (174)
T ss_dssp HHHHHHHHHHHHHTTTTEEEEEEESSTTTC-HHHHHHHHHCH
T ss_pred HHHHHHHHHHhhhccCceEEEEEEeCCCCCCHHHHHHHHHhc
Confidence 344566666666552234555699999 5699999999654
No 18
>PF06456 Arfaptin: Arfaptin-like domain; InterPro: IPR010504 Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms a an elongated, crescent-shaped dimer of three-helix coiled-coils []. The N-terminal region of ICA69 is similar to arfaptin [].; PDB: 1I4D_B 1I4L_B 1I49_B 1I4T_A 4DCN_D.
Probab=33.32 E-value=3.6e+02 Score=24.21 Aligned_cols=29 Identities=28% Similarity=0.499 Sum_probs=22.8
Q ss_pred hhhHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q 026758 180 LPKYE-EQLELKIAKAQLEELKKDALEAME 208 (233)
Q Consensus 180 l~K~e-ee~ele~aK~qL~elK~~a~e~m~ 208 (233)
.|+++ ++..+..+|...+.||.|++.-|+
T Consensus 168 ~~~~r~~q~~~~~~k~rf~kLr~Dv~~Kl~ 197 (229)
T PF06456_consen 168 EPKFRVAQGNYQEAKERFDKLRSDVLVKLD 197 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45533 456789999999999999988776
No 19
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=33.30 E-value=45 Score=22.18 Aligned_cols=58 Identities=21% Similarity=0.337 Sum_probs=33.9
Q ss_pred HHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHH
Q 026758 55 KKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTY 120 (233)
Q Consensus 55 qkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~y 120 (233)
+++|..++..+++. +..+|+++.+.-.++... -+.|=+. ....+++......|+-..|
T Consensus 4 ~~~~~~A~~~~~~~-l~~~p~~~~~~~~la~~~----~~~g~~~---~A~~~l~~~~~~~~~~~~~ 61 (68)
T PF14559_consen 4 QGDYDEAIELLEKA-LQRNPDNPEARLLLAQCY----LKQGQYD---EAEELLERLLKQDPDNPEY 61 (68)
T ss_dssp TTHHHHHHHHHHHH-HHHTTTSHHHHHHHHHHH----HHTT-HH---HHHHHHHCCHGGGTTHHHH
T ss_pred ccCHHHHHHHHHHH-HHHCCCCHHHHHHHHHHH----HHcCCHH---HHHHHHHHHHHHCcCHHHH
Confidence 45677777777765 477899999888888543 2334333 3334444444444443333
No 20
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=32.52 E-value=71 Score=21.52 Aligned_cols=32 Identities=31% Similarity=0.541 Sum_probs=21.7
Q ss_pred HHHHHHHHHhchhccccccCCCCHHHHHHHHHH
Q 026758 54 VKKKFETALGVLRKEKITIAPEDPAAVSQYANV 86 (233)
Q Consensus 54 vqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~ 86 (233)
.+++|+.++..+... |.++|+|+.++-.|+..
T Consensus 7 ~~~~~~~A~~~~~~~-l~~~p~~~~~~~~~a~~ 38 (73)
T PF13371_consen 7 QQEDYEEALEVLERA-LELDPDDPELWLQRARC 38 (73)
T ss_pred hCCCHHHHHHHHHHH-HHhCcccchhhHHHHHH
Confidence 455677777766543 36778888888877743
No 21
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=32.31 E-value=35 Score=28.23 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=22.7
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHH
Q 026758 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQ 101 (233)
Q Consensus 56 kkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e 101 (233)
+.|-+++-+|-.+|.-..+ ...-...|-+.++-+++++||+++++
T Consensus 59 ND~a~AVR~lE~iK~K~~~-~~~~Y~~~lqElkPtl~ELGI~t~Ee 103 (108)
T PF02284_consen 59 NDFALAVRILEGIKDKCGN-KKEIYPYILQELKPTLEELGIPTPEE 103 (108)
T ss_dssp T-HHHHHHHHHHHHHHTTT--TTHHHHHHHHHHHHHHHHT---TTT
T ss_pred hhHHHHHHHHHHHHHHccC-hHHHHHHHHHHHhhHHHHhCCCCHHH
Confidence 3455555555555544432 22255566666667777777777664
No 22
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=29.20 E-value=51 Score=21.18 Aligned_cols=34 Identities=24% Similarity=0.347 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhchhccccccCCCCHHHHHHHHH
Q 026758 51 FLDVKKKFETALGVLRKEKITIAPEDPAAVSQYAN 85 (233)
Q Consensus 51 F~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~ 85 (233)
....+.+|..+...+++. |..+|+|+.|+..|+.
T Consensus 10 ~~~~~G~~~~A~~~~~~~-l~~~P~~~~a~~~La~ 43 (44)
T PF13428_consen 10 AYRRLGQPDEAERLLRRA-LALDPDDPEAWRALAQ 43 (44)
T ss_pred HHHHcCCHHHHHHHHHHH-HHHCcCCHHHHHHhhh
Confidence 334455666666666643 3688999999998874
No 23
>PRK08045 cystathionine gamma-synthase; Provisional
Probab=27.96 E-value=21 Score=33.45 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=24.1
Q ss_pred HHHHcCCcchhhhHHHHHHHHHHHHH
Q 026758 127 IRERRGLIDEHGAEAMMMDALEKVEK 152 (233)
Q Consensus 127 iR~~~Gl~D~~g~~a~mm~ALdkvEK 152 (233)
||-+.||+|.+..-+-+.+||+++||
T Consensus 360 iR~svGlE~~~dl~~dl~~al~~~~~ 385 (386)
T PRK08045 360 LRISTGIEDGEDLIADLENGFRAANK 385 (386)
T ss_pred EEEEeCcCCHHHHHHHHHHHHHHhhc
Confidence 67889999999999999999999987
No 24
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=27.73 E-value=27 Score=24.74 Aligned_cols=23 Identities=26% Similarity=0.472 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCChHHHH
Q 026758 75 EDPAAVSQYANVMKTVREKADLFSESQRI 103 (233)
Q Consensus 75 ~DpaAVk~YA~~~~~vr~k~gl~s~~e~I 103 (233)
+||..|.++| |+++||-.|+|.|
T Consensus 52 ~~~~~ie~~A------R~~lgm~~~~E~v 74 (80)
T PF04977_consen 52 NDPDYIEKVA------REKLGMVKPGEIV 74 (80)
T ss_pred CCHHHHHHHH------HHHcCCcCCCCEE
Confidence 5899999987 8999999988764
No 25
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.27 E-value=2.3e+02 Score=26.49 Aligned_cols=71 Identities=14% Similarity=0.143 Sum_probs=50.5
Q ss_pred CchhHHHHHHHHHHHHHHHHHHh--chhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHh
Q 026758 41 LKGDEMLKNIFLDVKKKFETALG--VLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIET 109 (233)
Q Consensus 41 ~kGdd~lK~iF~evqkkF~~~l~--~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s---------~~e~I~~tie~ 109 (233)
+.|..+-+.+..+.++..+.+-. ..++.-|.+- ||..|-..|.+.....-+++||.+ .++.+..+|+.
T Consensus 4 ldGk~iA~~i~~~ik~~v~~l~~~g~~P~LaiI~v-g~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~ 82 (282)
T PRK14182 4 IDGKQIAAKVKGEVATEVRALAARGVQTGLTVVRV-GDDPASAIYVRGKRKDCEEVGITSVEHHLPATTTQAELLALIAR 82 (282)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEEEe-CCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHH
Confidence 45777788888888888877642 3344444443 666677889999999999999875 34557788876
Q ss_pred hhc
Q 026758 110 RTA 112 (233)
Q Consensus 110 ~~~ 112 (233)
.-+
T Consensus 83 lN~ 85 (282)
T PRK14182 83 LNA 85 (282)
T ss_pred HhC
Confidence 644
No 26
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=27.26 E-value=1.1e+02 Score=23.63 Aligned_cols=27 Identities=19% Similarity=0.218 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHhcCCCChHHHHHHH
Q 026758 79 AVSQYANVMKTVREKADLFSESQRIAYT 106 (233)
Q Consensus 79 AVk~YA~~~~~vr~k~gl~s~~e~I~~t 106 (233)
|+..|......+++++|+.| +..+...
T Consensus 115 A~~~Y~~~~~~l~~elg~~P-s~~~~~l 141 (146)
T PF03704_consen 115 ALRVYERYRRRLREELGIEP-SPETRAL 141 (146)
T ss_dssp HHHHHHHHHHHHHHHHS-----HHHHHH
T ss_pred HHHHHHHHHHHHHHHhCcCc-CHHHHHH
Confidence 78888888899999999954 4444433
No 27
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=27.01 E-value=4.8e+02 Score=23.64 Aligned_cols=114 Identities=15% Similarity=0.122 Sum_probs=62.1
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHcCC----cchhhhHHHHHHHHHHH
Q 026758 75 EDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERRGL----IDEHGAEAMMMDALEKV 150 (233)
Q Consensus 75 ~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~EiR~~~Gl----~D~~g~~a~mm~ALdkv 150 (233)
.||..+++.|+.........+. .+ .++-.+.++...-.....+..+-..-++ --..|.-.+|..|=+
T Consensus 84 ~dp~~~r~dA~~l~~~a~~~s~---~~----l~~~l~~~~~~~~~l~~~~~~~~~~~~f~YSRl~AIGL~~LLe~a~~-- 154 (206)
T PLN03060 84 EDPDQYRKDAKKLEEWASSQSA---SG----IADFNSGDGEVEAVLKDIAERAAGKTKFHYSRFFAIGLFRLLECAKA-- 154 (206)
T ss_pred CCHHHHHHHHHHHHHHHhcCCH---HH----HHHHHhcccccchHHHHHHHHhhcCCCcchHHHHHHHHHHHHHHcCC--
Confidence 8999999999887776654332 21 1112222221112222222222211111 123455555544411
Q ss_pred HHhhCCccccccHhhHHHHHHHhCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 026758 151 EKEIKKPLMRNDKKGMALLTAELGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKKR 213 (233)
Q Consensus 151 EK~igkpL~rsDkkGM~~L~aelGI~keDl~K~eee~ele~aK~qL~elK~~a~e~m~~~kkr 213 (233)
+|.+=+..|.+.||+.++ .-+-+|++|++-|+.|. +|.|.|+-...+
T Consensus 155 ----------~d~~~l~~l~~~L~ls~~-----kv~kDL~lYrsnLeKm~-qa~el~ee~~~~ 201 (206)
T PLN03060 155 ----------SDPAVLEKLSKALNVSKR-----SVDRDLDVYRNLLSKLA-QAKELIKEYIDR 201 (206)
T ss_pred ----------CCHHHHHHHHHHcCCCHH-----HHHhhHHHHHhHHHHHH-HHHHHHHHHHHH
Confidence 156677778877997764 34557889999998885 567776665444
No 28
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=26.90 E-value=1.6e+02 Score=30.40 Aligned_cols=151 Identities=15% Similarity=0.198 Sum_probs=93.2
Q ss_pred hHHHHHHHHH-HHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHH
Q 026758 44 DEMLKNIFLD-VKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLL 122 (233)
Q Consensus 44 dd~lK~iF~e-vqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~ 122 (233)
+-+|-.+|++ +-.-|-..|+ .+|++.+--+.+-.-.... --||...-+..+.+.+..-.-+..|+.-=.
T Consensus 226 e~~Vek~lfdY~~~~Y~~fl~--------~~~~~~~~e~Elk~~f~~~--~~~i~~~i~~lk~~n~~l~e~i~ea~k~s~ 295 (622)
T COG5185 226 ELMVEKLLFDYFTESYKSFLK--------LEDNYEPSEQELKLGFEKF--VHIINTDIANLKTQNDNLYEKIQEAMKISQ 295 (622)
T ss_pred HHHHHHHHHHHHHHHHHHHhc--------CCCccCchHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566666665 3344444443 4555555333332221111 124555555666666666666666666666
Q ss_pred HHHHHHHHc-CCcc------------------hhhhHHHHHHHHHHHHHhhCCccccccHhhHHHHHHHhCCCCCChhhH
Q 026758 123 TLKEIRERR-GLID------------------EHGAEAMMMDALEKVEKEIKKPLMRNDKKGMALLTAELGIRKEDLPKY 183 (233)
Q Consensus 123 ~~~EiR~~~-Gl~D------------------~~g~~a~mm~ALdkvEK~igkpL~rsDkkGM~~L~aelGI~keDl~K~ 183 (233)
...++|.+. -|.+ ..|+..-|-.-++++|.+|. +++++.-|...-...-||.++++.++
T Consensus 296 ~i~~l~ek~r~l~~D~nk~~~~~~~mk~K~~~~~g~l~kl~~eie~kEeei~--~L~~~~d~L~~q~~kq~Is~e~fe~m 373 (622)
T COG5185 296 KIKTLREKWRALKSDSNKYENYVNAMKQKSQEWPGKLEKLKSEIELKEEEIK--ALQSNIDELHKQLRKQGISTEQFELM 373 (622)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHH--HHHhhHHHHHHHHHhcCCCHHHHHHH
Confidence 666655442 2333 33555556666777777774 68888888887777789999998885
Q ss_pred HH-----HHHHHHHHHHHHHHHHHHHHH
Q 026758 184 EE-----QLELKIAKAQLEELKKDALEA 206 (233)
Q Consensus 184 ee-----e~ele~aK~qL~elK~~a~e~ 206 (233)
.- ..||++.+-|.++|.+.+-++
T Consensus 374 n~Ere~L~reL~~i~~~~~~L~k~V~~~ 401 (622)
T COG5185 374 NQEREKLTRELDKINIQSDKLTKSVKSR 401 (622)
T ss_pred HHHHHHHHHHHHHhcchHHHHHHHHHhH
Confidence 43 357999999999999877553
No 29
>PF13310 Virulence_RhuM: Virulence protein RhuM family
Probab=25.60 E-value=92 Score=29.19 Aligned_cols=102 Identities=18% Similarity=0.242 Sum_probs=67.1
Q ss_pred hHhhhhhhhhhhHHHHhhcc------chhHHhhhhhcCC-ccCch----hHHHHHH-------HHHH-----------HH
Q 026758 6 RLASKSKQLCSSQVILQRQH------AISVRFFANEAAP-QALKG----DEMLKNI-------FLDV-----------KK 56 (233)
Q Consensus 6 r~~sr~~~~~~~~~~~~~~~------~~~vR~fA~~Aap-~~~kG----dd~lK~i-------F~ev-----------qk 56 (233)
|-++|.-..|+-.+|++=|. ++++|.+|...=. =-.|| |+-||+- |.++ ++
T Consensus 16 r~v~r~~~~YnLd~IisVGYRV~S~~~tqFR~WAt~~Lkey~~KGf~~d~erLk~~~~~~~dyf~ell~rIr~IRaSEr~ 95 (260)
T PF13310_consen 16 REVSREVKYYNLDAIISVGYRVNSKRGTQFRQWATKVLKEYLIKGFVLDDERLKNGGVFGKDYFDELLERIRDIRASERR 95 (260)
T ss_pred cccccccccccHHHHHHhhheeCcHHHhHHHHHHHHhHHHHHHhhhhhhHHHHHccCcccHHHHHHHHHHHHhhHHHHHH
Confidence 45678889999999988553 7889999864211 11122 2233222 2211 23
Q ss_pred HHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHH
Q 026758 57 KFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIE 108 (233)
Q Consensus 57 kF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie 108 (233)
=|+...|++. ..++-||.++++-.=||.+.-.+-.-+-=.+..|.|-.-.|
T Consensus 96 fYqki~di~a-~s~DYd~~~~~t~~Ffa~vQNKlh~Av~g~TAAElI~~Rad 146 (260)
T PF13310_consen 96 FYQKITDIYA-TSIDYDPKSEETKQFFATVQNKLHYAVTGHTAAELIYERAD 146 (260)
T ss_pred HHHHHHHHHh-hhhccCcCCHHHHHHHHHHHHHHHHHHhccChHHHHHhhcc
Confidence 3455566666 77899999999999999998888877666677777765443
No 30
>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]
Probab=25.22 E-value=2.5e+02 Score=28.10 Aligned_cols=78 Identities=19% Similarity=0.175 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCC-----CcHHHHHHHH
Q 026758 50 IFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGI-----PDARTYLLTL 124 (233)
Q Consensus 50 iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~-----~dvR~yL~~~ 124 (233)
.+..|+.-|-..++-|.+.+ ++.| |++..++|.+..-++|.--.-- .-.-++-.+|+.-+.+ ..+++||+..
T Consensus 104 si~~V~s~Y~~sfe~ll~~~-~~~~-~~~~~~qf~d~l~~l~~rH~dv-v~~lA~Gl~E~~~~~~dp~~~~~iqyFLdr~ 180 (414)
T KOG0787|consen 104 SIQLVQSWYIRSFEDLLEFP-TISP-DLEDLSQFNDLLNTLRNRHNDV-VPTLAQGLIEYREKDGDPVTEKNIQYFLDRF 180 (414)
T ss_pred hHHHHHHHHHHHHHHHHccC-CCCc-chhhHHHHHHHHHHHHhccchh-HHHHHHHHHHHHHhcCCcchHHHHHHHHHHH
Confidence 46677777777777777777 7777 8999999999877776532211 1122333344444332 3456666665
Q ss_pred HHHHHH
Q 026758 125 KEIRER 130 (233)
Q Consensus 125 ~EiR~~ 130 (233)
--=|++
T Consensus 181 y~sRIs 186 (414)
T KOG0787|consen 181 YMSRIS 186 (414)
T ss_pred HHHHHH
Confidence 444443
No 31
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.63 E-value=1.2e+02 Score=28.21 Aligned_cols=69 Identities=16% Similarity=0.216 Sum_probs=51.5
Q ss_pred CchhHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHhhh
Q 026758 41 LKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRT 111 (233)
Q Consensus 41 ~kGdd~lK~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s---------~~e~I~~tie~~~ 111 (233)
+.|-.+-+.+..+++++...+ +...+.-|.+- ||..|-..|.+.....-+++||.+ .++.+...|+..-
T Consensus 3 l~Gk~~a~~i~~~~~~~v~~l-g~~P~Laii~v-g~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN 80 (279)
T PRK14178 3 LDGKAVSEKRLELLKEEIIES-GLYPRLATVIV-GDDPASQMYVRMKHRACERVGIGSVGIELPGDATTRTVLERIRRLN 80 (279)
T ss_pred eeHHHHHHHHHHHHHHHHHHh-CCCCeEEEEEe-CCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence 457778888999999998876 76666666665 555566789999999999999874 3345667777653
No 32
>PRK10455 periplasmic protein; Reviewed
Probab=24.52 E-value=2.5e+02 Score=24.01 Aligned_cols=36 Identities=17% Similarity=0.213 Sum_probs=25.2
Q ss_pred cccCCCCHHHHHHHHHHHHHHHH------------hcCCCChHHHHHH
Q 026758 70 ITIAPEDPAAVSQYANVMKTVRE------------KADLFSESQRIAY 105 (233)
Q Consensus 70 I~ldp~DpaAVk~YA~~~~~vr~------------k~gl~s~~e~I~~ 105 (233)
|+-+|=|+++|..+++.+-.+.. =..+.+|+|+-..
T Consensus 91 i~ad~FDeaavra~~~k~~~~~~~~~~~~~~~~~qiy~vLTPEQr~q~ 138 (161)
T PRK10455 91 IASDTFDKAKAEAQITKMEAQRKARMLAHMETQNKIYNVLTPEQKKQF 138 (161)
T ss_pred HccCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 55667899999999886443332 2468888888654
No 33
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=24.45 E-value=73 Score=19.97 Aligned_cols=19 Identities=26% Similarity=0.457 Sum_probs=15.7
Q ss_pred cccCCCCHHHHHHHHHHHH
Q 026758 70 ITIAPEDPAAVSQYANVMK 88 (233)
Q Consensus 70 I~ldp~DpaAVk~YA~~~~ 88 (233)
|.++|+++.|+-.|+....
T Consensus 6 ie~~P~n~~a~~nla~~~~ 24 (34)
T PF13431_consen 6 IELNPNNAEAYNNLANLYL 24 (34)
T ss_pred HHHCCCCHHHHHHHHHHHH
Confidence 5689999999999997543
No 34
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=24.36 E-value=2.1e+02 Score=22.70 Aligned_cols=57 Identities=23% Similarity=0.228 Sum_probs=37.2
Q ss_pred CchhHHHHHHHHHHHHHHHHHHhc--hhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC
Q 026758 41 LKGDEMLKNIFLDVKKKFETALGV--LRKEKITIAPEDPAAVSQYANVMKTVREKADLFS 98 (233)
Q Consensus 41 ~kGdd~lK~iF~evqkkF~~~l~~--lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s 98 (233)
+.|..+-+.+..++++....+-.. ..+.-|.+- ||..|-..|.+.....-+++||..
T Consensus 3 L~Gk~va~~i~~~l~~~i~~l~~~~~~P~Laii~v-g~d~~S~~Y~~~k~k~~~~~Gi~~ 61 (117)
T PF00763_consen 3 LDGKPVAKEIKEELKEEIEKLKEKGITPKLAIILV-GDDPASISYVRSKQKAAEKLGIEF 61 (117)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHCT---EEEEEEE-S--HHHHHHHHHHHHHHHHHT-EE
T ss_pred eeHHHHHHHHHHHHHHHHHHHHhcCCCcEEEEEec-CCChhHHHHHHHHHHHHHHcCCce
Confidence 468888888888888887766433 444444444 444556789999999999999864
No 35
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=23.88 E-value=90 Score=28.50 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=26.4
Q ss_pred cccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 026758 68 EKITIAPEDP---AAVSQYANVMKTVREKADLFSE 99 (233)
Q Consensus 68 ~kI~ldp~Dp---aAVk~YA~~~~~vr~k~gl~s~ 99 (233)
.-++|||+++ +.|..=|..++.+-.++||.|.
T Consensus 102 lvfDLDP~~~~~f~~v~~~A~~vr~~L~~lgL~sf 136 (228)
T cd04865 102 LVIDLDPQPGTSFEDVVEVALLVREVLDELGLRGY 136 (228)
T ss_pred EEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccc
Confidence 3478999866 6888888889999999999874
No 36
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=23.58 E-value=3.2e+02 Score=20.51 Aligned_cols=77 Identities=14% Similarity=0.173 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHH--------------HhcCCCChHHHHHHHHHhh
Q 026758 45 EMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVR--------------EKADLFSESQRIAYTIETR 110 (233)
Q Consensus 45 d~lK~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr--------------~k~gl~s~~e~I~~tie~~ 110 (233)
+-|..+..+...-|+.+++.+.++.=-|-.+|+..+..+......+- .+++..+....+...++
T Consensus 4 ~~L~~~L~~~~~~~~~L~~ll~~e~~~l~~~d~~~l~~~~~~k~~l~~~l~~le~~r~~~~~~~~~~~~~~~l~~~~~-- 81 (143)
T PF05130_consen 4 EELIELLEEQIELLQELLELLEEEREALISGDIDELEELVEEKQELLEELRELEKQRQQLLAKLGAEPEEATLSELIE-- 81 (143)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHC--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccccHHHHHh--
Confidence 34678888889999999999888876666688887777666544333 35555555555555555
Q ss_pred hcCCCcHHHHHHHHH
Q 026758 111 TAGIPDARTYLLTLK 125 (233)
Q Consensus 111 ~~~~~dvR~yL~~~~ 125 (233)
..+..+.....+.
T Consensus 82 --~~~~l~~~~~~l~ 94 (143)
T PF05130_consen 82 --EREELQALWRELR 94 (143)
T ss_dssp --CCHHHHHHHHHHH
T ss_pred --ccHHHHHHHHHHH
Confidence 4444444444333
No 37
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=23.35 E-value=92 Score=28.72 Aligned_cols=32 Identities=16% Similarity=0.155 Sum_probs=26.4
Q ss_pred cccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 026758 68 EKITIAPEDP---AAVSQYANVMKTVREKADLFSE 99 (233)
Q Consensus 68 ~kI~ldp~Dp---aAVk~YA~~~~~vr~k~gl~s~ 99 (233)
.-++|||+++ +.|.+=|..++.+-.++||.|.
T Consensus 117 lvfDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~~f 151 (245)
T TIGR02778 117 IVFDLDPGPGVAWKLVVEAAQLIRELLDELGLESF 151 (245)
T ss_pred EEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccc
Confidence 3468999877 6788888899999999999874
No 38
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=22.89 E-value=95 Score=28.37 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=26.0
Q ss_pred ccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 026758 69 KITIAPEDP---AAVSQYANVMKTVREKADLFSE 99 (233)
Q Consensus 69 kI~ldp~Dp---aAVk~YA~~~~~vr~k~gl~s~ 99 (233)
-++|||++. +.|.+=|..++.+-.++||.|.
T Consensus 106 vfDLDP~~~~~f~~v~~~A~~~r~~L~~lgL~s~ 139 (231)
T cd04863 106 VFDLDPGEPAGLVECARVALWLRDRLAALGLASF 139 (231)
T ss_pred EEECCCCCCCCHHHHHHHHHHHHHHHHHcCCccc
Confidence 368999776 6888889999999999999874
No 39
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.57 E-value=3e+02 Score=25.97 Aligned_cols=71 Identities=15% Similarity=0.184 Sum_probs=50.9
Q ss_pred CchhHHHHHHHHHHHHHHHHHHh--chhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHh
Q 026758 41 LKGDEMLKNIFLDVKKKFETALG--VLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIET 109 (233)
Q Consensus 41 ~kGdd~lK~iF~evqkkF~~~l~--~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~gl~s---------~~e~I~~tie~ 109 (233)
+.|..+-+.|..++++..+.+-. .-++.-|.+- ||..|-..|.+.....-+++||.+ .++.+...|+.
T Consensus 7 l~Gk~iA~~i~~~lk~~i~~l~~~g~~P~LaiI~v-g~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~ 85 (301)
T PRK14194 7 IDGKAAAARVLAQVREDVRTLKAAGIEPALAVILV-GNDPASQVYVRNKILRAEEAGIRSLEHRLPADTSQARLLALIAE 85 (301)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEEEe-CCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHH
Confidence 57888888888888888877542 2333333333 666688899999999999999876 35567777777
Q ss_pred hhc
Q 026758 110 RTA 112 (233)
Q Consensus 110 ~~~ 112 (233)
.-+
T Consensus 86 lN~ 88 (301)
T PRK14194 86 LNA 88 (301)
T ss_pred HcC
Confidence 644
No 40
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=21.75 E-value=53 Score=29.78 Aligned_cols=34 Identities=29% Similarity=0.524 Sum_probs=14.9
Q ss_pred HhhCCccccccHhhHHHHHHHhCC---CCCChhhHHHH
Q 026758 152 KEIKKPLMRNDKKGMALLTAELGI---RKEDLPKYEEQ 186 (233)
Q Consensus 152 K~igkpL~rsDkkGM~~L~aelGI---~keDl~K~eee 186 (233)
++++..|.++| .|+..|...||| ++.++|.+-++
T Consensus 165 ~El~a~lvt~D-~gi~~~A~~lGi~~i~~~~F~~~Lee 201 (205)
T PF08745_consen 165 LELDAVLVTDD-YGIQNWAEKLGIRFIDARDFPRMLEE 201 (205)
T ss_dssp HHHT--EE----HHHHHHHHHTT--EE-----------
T ss_pred HHcCCEEEeCC-HhHHHHHHHCCCEEEecccccccccc
Confidence 46888888877 599999999994 56778776554
No 41
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=21.63 E-value=38 Score=28.16 Aligned_cols=67 Identities=15% Similarity=0.195 Sum_probs=43.1
Q ss_pred HHHHHHhchhccccccCCC-----CHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHH
Q 026758 57 KFETALGVLRKEKITIAPE-----DPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLK 125 (233)
Q Consensus 57 kF~~~l~~lkk~kI~ldp~-----DpaAVk~YA~~~~~vr~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~~~ 125 (233)
-|..++.+|.| |.++|. =.+.|.=.|--+.|+.+..|+|.|=|++++.-.+..-+..+.+.|.+.+.
T Consensus 26 A~~s~lkGl~K--l~vn~~~l~~dL~~nWeVlaEpIQTvmRr~g~~~pYE~LK~lTRg~~it~~~l~~fI~~L~ 97 (115)
T PF08328_consen 26 AYKSLLKGLGK--LEVNEERLAEDLDENWEVLAEPIQTVMRRYGIPNPYEKLKELTRGKKITKEDLREFIESLD 97 (115)
T ss_dssp HHHHHHHHHHT--EEE-HHHHHHHHCT-GGGGHHHHHHHHHHTT-SSHHHHHHHHHTTS---HHHHHHHHHTSS
T ss_pred HHHHHHHHHhc--ccCCHHHHHHHHHHCHHHHHHHHHHHHHHcCCCCHHHHHHHHHcCCCCCHHHHHHHHHhCC
Confidence 35566666764 344420 01133334556889999999999999999999988888888888887654
No 42
>TIGR02215 phage_chp_gp8 phage conserved hypothetical protein, phiE125 gp8 family. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. Members of this family show some similarity to members of pfam05135, a putative DNA packaging protein family.
Probab=21.23 E-value=1.4e+02 Score=25.87 Aligned_cols=39 Identities=15% Similarity=0.201 Sum_probs=29.2
Q ss_pred HHHHHHHHcCC--c-chhhhHHHHHHHHHHHHHhhCCccccc
Q 026758 123 TLKEIRERRGL--I-DEHGAEAMMMDALEKVEKEIKKPLMRN 161 (233)
Q Consensus 123 ~~~EiR~~~Gl--~-D~~g~~a~mm~ALdkvEK~igkpL~rs 161 (233)
++.|.+.-.++ . |+.=....+..|.+.+|..+|++|++.
T Consensus 15 tl~e~K~~LRi~~~~eDa~l~~li~aA~~~iE~~tgr~l~~q 56 (188)
T TIGR02215 15 TVADFKAFLRLGTEVQDEVLRSLLTAARAAIEARTGKILISQ 56 (188)
T ss_pred CHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHHhCceeeee
Confidence 35666666777 2 344466788899999999999999874
No 43
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=21.20 E-value=9.5e+02 Score=25.07 Aligned_cols=164 Identities=21% Similarity=0.245 Sum_probs=102.6
Q ss_pred CchhHHHHHHHHHHHH-HHHHHHhchhccccccCCCCHHHHHHHHHHH----------HHHHHhcCCCChHHHHHHHHHh
Q 026758 41 LKGDEMLKNIFLDVKK-KFETALGVLRKEKITIAPEDPAAVSQYANVM----------KTVREKADLFSESQRIAYTIET 109 (233)
Q Consensus 41 ~kGdd~lK~iF~evqk-kF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~----------~~vr~k~gl~s~~e~I~~tie~ 109 (233)
+++|+.|++-|.+=+- -=.|+..++-.....++|+ ..+.|+-| ..+-+.+|||- .-.+..|+.
T Consensus 382 ls~D~~Ll~AF~~g~DiH~~TA~~vFgv~~~~Vt~e----~Rr~AKaINFGiiYG~safgLa~~L~I~~--~eA~~~I~~ 455 (593)
T COG0749 382 LSQDEGLLRAFTEGEDIHTATAAEVFGVPIEEVTSE----QRRKAKAINFGLIYGMSAFGLAQQLGIPR--KEAKEYIDR 455 (593)
T ss_pred hcCCHHHHHHHhcCccHHHHHHHHHhCCChhhCCHH----HhhhhhhhccceeeccchhhHHHHcCCCh--HHHHHHHHH
Confidence 4567888877753111 0124555554333344432 23333221 34778999998 557889999
Q ss_pred hhcCCCcHHHHHHHHHHHHHHcC-----------CcchhhhHHHHHHHHHHHHHhhCCccccccHhhHHH----HHHHhC
Q 026758 110 RTAGIPDARTYLLTLKEIRERRG-----------LIDEHGAEAMMMDALEKVEKEIKKPLMRNDKKGMAL----LTAELG 174 (233)
Q Consensus 110 ~~~~~~dvR~yL~~~~EiR~~~G-----------l~D~~g~~a~mm~ALdkvEK~igkpL~rsDkkGM~~----L~aelG 174 (233)
.|...|.|+.|++...+.=++-| +.+-..-....-.+-+ =-.++.|+--+-+-=+++ +-..|.
T Consensus 456 YF~rypgv~~ym~~~~~~ar~~GyV~Tl~gRRry~p~i~s~n~~~R~~aE--R~AiNaPIQGTAADiiK~AMI~vd~~l~ 533 (593)
T COG0749 456 YFERYPGVKEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRAAAE--RAAINAPIQGTAADIIKLAMIKVDKALK 533 (593)
T ss_pred HHHhChHHHHHHHHHHHHHHHcCceeecccccccCcccccCCHHHHHHHH--HHHhcCcCcccHHHHHHHHHHhHHHHHh
Confidence 99999999999998887655555 3333322222333333 346777877665543333 233332
Q ss_pred ---CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026758 175 ---IRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKK 212 (233)
Q Consensus 175 ---I~keDl~K~eee~ele~aK~qL~elK~~a~e~m~~~kk 212 (233)
++.-.+=-+--|+.+|+-+.+++++++-.-+.|+..-.
T Consensus 534 ~~~~~~rllLQVHDELvfEv~~~e~e~~~~~v~~~Me~a~~ 574 (593)
T COG0749 534 EEKLKARLLLQVHDELVFEVPKEELEEVKKLLKAIMENAVN 574 (593)
T ss_pred hcchhhhhHHhhhhhhhhcCcHhHHHHHHHHHHHHHHHhhc
Confidence 23333445788999999999999999999999999855
No 44
>PF10553 MSV199: MSV199 domain; InterPro: IPR018879 This entry represents ORF MSV199 (Q9YVP3 from SWISSPROT), an MTG motif gene family protein from Melanoplus sanguinipes entomopoxvirus (MsEPV) [].
Probab=21.18 E-value=4.6e+02 Score=22.43 Aligned_cols=74 Identities=20% Similarity=0.301 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHhchhcccc---ccCCCCHHHHHHHHHHHHHHH---------HhcCCCChHHHHHHHHHhhhcCCCcH
Q 026758 50 IFLDVKKKFETALGVLRKEKI---TIAPEDPAAVSQYANVMKTVR---------EKADLFSESQRIAYTIETRTAGIPDA 117 (233)
Q Consensus 50 iF~evqkkF~~~l~~lkk~kI---~ldp~DpaAVk~YA~~~~~vr---------~k~gl~s~~e~I~~tie~~~~~~~dv 117 (233)
=|..||++|..+|. +-.| .|+-.||..- .|--..+.+. ++-=+.+|.+-=.+.+.=-|+.+-.+
T Consensus 52 ~~~~qk~~F~k~Lk---~nnI~y~ei~y~d~~i~-~yp~iq~Ei~~l~~~~~~~skwlIm~~~~fK~aIm~LnTkn~~~I 127 (139)
T PF10553_consen 52 NYKEQKKNFKKMLK---NNNIEYKEIKYNDPEIE-LYPTIQEEIKNLSPNNIAKSKWLIMEPDDFKMAIMRLNTKNGDII 127 (139)
T ss_pred HHHHHHHHHHHHHH---hCCCChhccccCChHHH-hhHHHHHHHHhCCcchhhhceeEEeeHHHHHHHHHHcCCcchhHH
Confidence 38999999999887 4444 3433566543 3664433322 12233445555556677778999999
Q ss_pred HHHHHHHHHH
Q 026758 118 RTYLLTLKEI 127 (233)
Q Consensus 118 R~yL~~~~Ei 127 (233)
|+|+..+.|+
T Consensus 128 R~YYi~lEel 137 (139)
T PF10553_consen 128 REYYIDLEEL 137 (139)
T ss_pred HHHHHHHHHH
Confidence 9999998875
No 45
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=21.08 E-value=2.3e+02 Score=21.85 Aligned_cols=52 Identities=15% Similarity=0.093 Sum_probs=29.8
Q ss_pred HHHHhhhcCCCcHHHHHHHHHHHHHHcCCcchhhhHHHHHHHHHHHHHhhCCc
Q 026758 105 YTIETRTAGIPDARTYLLTLKEIRERRGLIDEHGAEAMMMDALEKVEKEIKKP 157 (233)
Q Consensus 105 ~tie~~~~~~~dvR~yL~~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK~igkp 157 (233)
.-|+...+++ ....++..+.++|+..|++.-.-.--+=-..|-.+|+--+.|
T Consensus 19 ~~l~~~le~~-~~~~~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~g~~~P 70 (89)
T TIGR02684 19 EYLAQALEDG-DPAYIAHALGYIARARGMTQLARKTGLSRESLYKALSGKGNP 70 (89)
T ss_pred HHHHHHHHcC-CHHHHHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHcCCCCC
Confidence 3344444443 555788889999999998631111111135677777655554
No 46
>PF05227 CHASE3: CHASE3 domain; InterPro: IPR007891 CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE3 domains are not known at this time [].; PDB: 3VA9_A.
Probab=20.74 E-value=2.9e+02 Score=20.89 Aligned_cols=54 Identities=17% Similarity=0.358 Sum_probs=36.3
Q ss_pred hhHHhhhhhcCCccCchhHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHH
Q 026758 27 ISVRFFANEAAPQALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVR 91 (233)
Q Consensus 27 ~~vR~fA~~Aap~~~kGdd~lK~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr 91 (233)
..+|-|-- .||+-....|.+-...|...++.|+ .+..++|.-.......-..+.
T Consensus 27 ~~~RgYll-------tgd~~~l~~y~~~~~~~~~~l~~L~----~l~~~~p~q~~~l~~l~~~~~ 80 (138)
T PF05227_consen 27 SALRGYLL-------TGDPEFLEPYQEARARLEKALAQLR----QLVQDNPEQQERLDQLEELID 80 (138)
T ss_dssp HHHHHHHH-------H--HHHHHHHHHHHHHHHHHHHHHH----HHTTT-HHHHHHHHHHHHHHH
T ss_pred HHhhHHHH-------cCCHhhhchHHHHHHHHHHHHHHHH----HHhcCCHHHHHHHHHHHHHHH
Confidence 35566654 4666778899999999999999998 555688886665554444433
No 47
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=20.16 E-value=4.8e+02 Score=23.83 Aligned_cols=38 Identities=37% Similarity=0.421 Sum_probs=24.8
Q ss_pred HHHHhCCCCCChhhHHHHHH-----HHHHHHHHHHHHHHHHHH
Q 026758 169 LTAELGIRKEDLPKYEEQLE-----LKIAKAQLEELKKDALEA 206 (233)
Q Consensus 169 L~aelGI~keDl~K~eee~e-----le~aK~qL~elK~~a~e~ 206 (233)
|.++..--++|+.|+++|++ |+-+..+-+.|+|++-+-
T Consensus 149 ~~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~ 191 (216)
T KOG1962|consen 149 LEEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGL 191 (216)
T ss_pred hhhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 55555555677777777664 666777777777766543
No 48
>cd01043 DPS DPS protein, ferritin-like diiron-binding domain. DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) disp
Probab=20.02 E-value=4.3e+02 Score=20.63 Aligned_cols=99 Identities=11% Similarity=0.224 Sum_probs=58.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhc-CCCChHHHHHHHHHhhhcCCCcHHHHHH
Q 026758 44 DEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKA-DLFSESQRIAYTIETRTAGIPDARTYLL 122 (233)
Q Consensus 44 dd~lK~iF~evqkkF~~~l~~lkk~kI~ldp~DpaAVk~YA~~~~~vr~k~-gl~s~~e~I~~tie~~~~~~~dvR~yL~ 122 (233)
-+.+...+.+..+.+..+-+-+....-.- ++.|+-+.+|+. +.+.- +-.++.+.+...++...+-+...|.=..
T Consensus 33 h~~l~e~~~~~~~~~D~lAERi~~lgg~P-~~~~~~~~~~s~----l~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~i~ 107 (139)
T cd01043 33 HELFEELYDELREAIDEIAERIRALGGKP-LGTLKEYAELST----IKEEPAGVLSAKEMVAELLEDYETLIEELREAIE 107 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCCC-CCCHHHHHhHCC----CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666777777777776665444222 366776766653 22222 4556777777776665544433333322
Q ss_pred HHHHHHHHcCCcchhhhHHHHHHHHHHHHHhh
Q 026758 123 TLKEIRERRGLIDEHGAEAMMMDALEKVEKEI 154 (233)
Q Consensus 123 ~~~EiR~~~Gl~D~~g~~a~mm~ALdkvEK~i 154 (233)
.+.+ ..+-++..+|.+-+...||.+
T Consensus 108 ~a~~-------~~D~~t~~ll~~il~~~ek~~ 132 (139)
T cd01043 108 LADE-------AGDPATADLLTEIIRELEKQA 132 (139)
T ss_pred HHHH-------cCCHHHHHHHHHHHHHHHHHH
Confidence 2222 456778888888888888864
Done!