Query 026384
Match_columns 239
No_of_seqs 27 out of 29
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 07:20:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026384.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026384hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02744 dihydrolipoyllysine-r 85.6 0.31 6.6E-06 48.9 0.6 47 2-48 1-47 (539)
2 COG0749 PolA DNA polymerase I 77.2 30 0.00064 35.7 11.1 170 41-218 382-574 (593)
3 KOG0005 Ubiquitin-like protein 70.2 4.4 9.6E-05 31.0 2.6 36 66-106 11-46 (70)
4 PF02436 PYC_OADA: Conserved c 56.8 33 0.00073 30.3 6.0 87 8-107 47-146 (196)
5 PF03732 Retrotrans_gag: Retro 56.4 33 0.00072 24.2 5.0 52 80-131 26-78 (96)
6 KOG4077 Cytochrome c oxidase, 56.2 13 0.00028 32.2 3.2 46 56-102 98-143 (149)
7 TIGR02990 ectoine_eutA ectoine 47.3 12 0.00026 33.7 1.7 23 142-164 194-216 (239)
8 COG2012 RPB5 DNA-directed RNA 44.4 11 0.00023 29.8 0.9 21 170-190 24-44 (80)
9 cd00923 Cyt_c_Oxidase_Va Cytoc 41.2 39 0.00084 27.9 3.6 46 56-102 56-101 (103)
10 PF12244 DUF3606: Protein of u 39.1 46 0.001 23.9 3.4 43 71-122 14-56 (57)
11 KOG0787 Dehydrogenase kinase [ 38.6 2.1E+02 0.0045 28.7 8.7 41 50-92 104-144 (414)
12 PF03564 DUF1759: Protein of u 37.5 1.3E+02 0.0028 23.7 6.1 66 44-110 60-128 (145)
13 PF13310 Virulence_RhuM: Virul 37.3 49 0.0011 31.1 4.1 186 5-206 15-248 (260)
14 PF05119 Terminase_4: Phage te 37.1 22 0.00048 26.5 1.6 75 56-137 3-87 (100)
15 COG3473 Maleate cis-trans isom 37.0 28 0.0006 32.3 2.5 33 143-182 193-225 (238)
16 PF14559 TPR_19: Tetratricopep 34.1 43 0.00093 22.4 2.5 56 55-118 4-59 (68)
17 PLN03060 inositol phosphatase- 34.0 3.6E+02 0.0079 24.5 12.2 43 171-219 159-201 (206)
18 PF11791 Aconitase_B_N: Aconit 33.2 1.1E+02 0.0024 26.8 5.4 68 90-159 8-79 (154)
19 PF13371 TPR_9: Tetratricopept 33.0 69 0.0015 21.7 3.4 32 54-86 7-38 (73)
20 PF13438 DUF4113: Domain of un 32.8 38 0.00083 23.8 2.1 16 167-182 3-18 (52)
21 COG5016 Pyruvate/oxaloacetate 32.6 35 0.00077 34.3 2.6 125 17-167 80-214 (472)
22 PF02630 SCO1-SenC: SCO1/SenC; 32.4 63 0.0014 27.1 3.7 40 48-87 72-113 (174)
23 cd07599 BAR_Rvs167p The Bin/Am 31.2 3.4E+02 0.0074 23.3 12.4 20 192-211 155-174 (216)
24 PF02284 COX5A: Cytochrome c o 30.8 38 0.00083 28.1 2.1 45 56-101 59-103 (108)
25 COG1938 Archaeal enzymes of AT 30.6 1.4E+02 0.0031 27.7 5.9 59 157-221 181-239 (244)
26 PF07498 Rho_N: Rho terminatio 28.6 84 0.0018 21.2 3.2 32 169-202 7-39 (43)
27 PF13428 TPR_14: Tetratricopep 28.2 53 0.0012 21.2 2.1 33 52-85 11-43 (44)
28 cd07631 BAR_APPL1 The Bin/Amph 27.7 2.8E+02 0.006 25.5 7.2 24 158-181 100-123 (215)
29 PRK14182 bifunctional 5,10-met 27.5 2.2E+02 0.0048 26.7 6.7 71 41-112 4-85 (282)
30 PF03704 BTAD: Bacterial trans 27.5 1.1E+02 0.0023 23.8 4.1 48 57-106 77-141 (146)
31 PRK09841 cryptic autophosphory 26.7 7.3E+02 0.016 25.7 11.8 84 69-152 231-319 (726)
32 PF04977 DivIC: Septum formati 26.7 29 0.00062 24.7 0.6 23 75-103 52-74 (80)
33 PRK14574 hmsH outer membrane p 26.5 8E+02 0.017 26.3 11.3 120 19-155 77-198 (822)
34 COG3046 Uncharacterized protei 26.2 1.5E+02 0.0032 30.3 5.6 89 40-128 193-307 (505)
35 PRK11519 tyrosine kinase; Prov 26.1 7.4E+02 0.016 25.6 12.3 101 53-153 209-320 (719)
36 PF03114 BAR: BAR domain; Int 25.5 3.6E+02 0.0078 21.8 7.2 153 48-216 25-191 (229)
37 PRK10455 periplasmic protein; 25.5 2.3E+02 0.0049 24.3 6.0 37 70-106 91-139 (161)
38 COG1529 CoxL Aerobic-type carb 25.5 91 0.002 32.4 4.2 58 75-132 349-410 (731)
39 smart00503 SynN Syntaxin N-ter 25.3 3E+02 0.0064 20.7 7.9 25 194-218 83-107 (117)
40 PRK14178 bifunctional 5,10-met 24.7 1.2E+02 0.0026 28.4 4.4 69 41-111 3-80 (279)
41 PF05130 FlgN: FlgN protein; 24.5 3.1E+02 0.0068 20.7 6.2 78 45-126 4-95 (143)
42 PF00763 THF_DHG_CYH: Tetrahyd 24.0 2E+02 0.0044 22.9 5.1 58 41-99 3-62 (117)
43 PRK04778 septation ring format 23.6 7.6E+02 0.016 24.8 10.1 100 44-150 443-550 (569)
44 PF13431 TPR_17: Tetratricopep 22.8 81 0.0018 19.8 2.1 19 70-88 6-24 (34)
45 cd04865 LigD_Pol_like_2 LigD_P 22.7 96 0.0021 28.4 3.4 32 68-99 102-136 (228)
46 PRK14194 bifunctional 5,10-met 22.4 2.9E+02 0.0063 26.1 6.6 71 41-112 7-88 (301)
47 TIGR02778 ligD_pol DNA polymer 22.2 99 0.0021 28.6 3.4 32 68-99 117-151 (245)
48 PRK08045 cystathionine gamma-s 22.0 37 0.00081 31.9 0.6 25 127-151 360-385 (386)
49 cd04863 MtLigD_Pol_like MtLigD 21.8 1E+02 0.0022 28.3 3.4 31 69-99 106-139 (231)
50 COG0783 Dps DNA-binding ferrit 21.8 5.2E+02 0.011 22.2 7.5 72 71-153 73-148 (156)
51 KOG2004 Mitochondrial ATP-depe 21.6 8.6E+02 0.019 26.8 10.3 69 148-219 296-366 (906)
52 PRK14041 oxaloacetate decarbox 20.9 2.4E+02 0.0052 28.2 5.9 82 8-107 336-428 (467)
53 PF08328 ASL_C: Adenylosuccina 20.3 46 0.00099 27.8 0.7 67 57-125 26-97 (115)
54 cd08643 DNA_pol_A_pol_I_B Poly 20.3 1.6E+02 0.0034 29.1 4.5 117 104-223 291-412 (429)
55 PRK14186 bifunctional 5,10-met 20.2 3.4E+02 0.0075 25.6 6.5 71 41-112 5-87 (297)
No 1
>PLN02744 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Probab=85.59 E-value=0.31 Score=48.91 Aligned_cols=47 Identities=40% Similarity=0.632 Sum_probs=43.6
Q ss_pred hhhhhhhhhhhhhhhhHHHHhhccchhHHhhhhhcCCccCcchHHHH
Q 026384 2 AFASRLASKSKQLCSSQVILQRQHAISVRFFANEAAPQALKGDEMLK 48 (239)
Q Consensus 2 a~~~r~~srs~~~~~~~~~~~~~~~~~vR~fA~~Aap~~~kGdd~lK 48 (239)
+++||++..|+.|+....+|...|+..||+|+....+...+||++.+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (539)
T PLN02744 1 AYASRIINHSKKLRNVSNLLRREHAALVRYFSNSTRSSLGKGDDIAK 47 (539)
T ss_pred CchHHHhhhchhhcchHHHhcccccceEEEecCCCccCcccccchhh
Confidence 57899999999999999999999999999999998888889999855
No 2
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=77.24 E-value=30 Score=35.73 Aligned_cols=170 Identities=22% Similarity=0.240 Sum_probs=123.3
Q ss_pred CcchHHHHHHHHHHHH-HHHHHHhchhccccccCCCCHHHHHHHHHHH----------HHHHHhcCCCChHHHHHHHHHh
Q 026384 41 LKGDEMLKNIFLDVKK-KFETALGVLRKEKITIAPEDPAAVSQYANVM----------KTVREKADLFSESQRIAYTIET 109 (239)
Q Consensus 41 ~kGdd~lK~iF~~vqk-kF~~~l~~lkk~kI~idp~DpaAVk~YA~~~----------~~~r~k~gl~s~~e~I~~tie~ 109 (239)
+++|+.|++-|.+=+- -=.|+..+|-.....++|+ ..+.|+.| ..+-+.+|||- .-.+..|+.
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 4567888887753211 1135555555433344432 23333321 34778999998 557889999
Q ss_pred hhcCCCcHHHHHHHHHHHH-HcC-----------CCchhhhHHHHHHHHHHHHHhhCCccccccHhhHHHHHHHHHHHHH
Q 026384 110 RTAGIPDARTYLLTLKEIR-ERG-----------LIDEHGAEAMMMDALEKVEKEIKKPLMRNDKKGMALLTAEFDKINK 177 (239)
Q Consensus 110 ~~~~~~dvR~yL~~l~EiR-~~G-----------l~D~~g~~a~mm~ALdkvEK~igkpL~rsDkkGM~~L~ae~~kinK 177 (239)
.|...|.|+.|++...+.- +.| +.+-..-...+-.+-+ =-.++.|+--+-+-=+++-+=.+++.-+
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 9999999999999877654 656 3343333333333433 3478999999999999999999999999
Q ss_pred HcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026384 178 KLGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKK 218 (239)
Q Consensus 178 klGi~~eDl~K~eee~ele~aK~ql~elK~~a~e~m~~~kk 218 (239)
+-|++.-.+=-+--|+.+|+-+.+++++++-.-+.|+..-.
T Consensus 534 ~~~~~~rllLQVHDELvfEv~~~e~e~~~~~v~~~Me~a~~ 574 (593)
T COG0749 534 EEKLKARLLLQVHDELVFEVPKEELEEVKKLLKAIMENAVN 574 (593)
T ss_pred hcchhhhhHHhhhhhhhhcCcHhHHHHHHHHHHHHHHHhhc
Confidence 99888777888899999999999999999999999999855
No 3
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=70.21 E-value=4.4 Score=30.98 Aligned_cols=36 Identities=28% Similarity=0.509 Sum_probs=27.4
Q ss_pred hccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHH
Q 026384 66 RKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYT 106 (239)
Q Consensus 66 kk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~t 106 (239)
+.+.|.|+|.|.- ....+.+-++-|||++.||+-++
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 4
>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=56.80 E-value=33 Score=30.28 Aligned_cols=87 Identities=21% Similarity=0.255 Sum_probs=50.5
Q ss_pred hhhhhhhhhhHHHHhhcc----------chhHHhhhhh--cCCccCcchHHHHHHHHHHHHHHHHHHhchhccccccCCC
Q 026384 8 ASKSKQLCSSQVILQRQH----------AISVRFFANE--AAPQALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPE 75 (239)
Q Consensus 8 ~srs~~~~~~~~~~~~~~----------~~~vR~fA~~--Aap~~~kGdd~lK~iF~~vqkkF~~~l~~lkk~kI~idp~ 75 (239)
+--|+|+.|.||.++=.. .-+|+.|... ..||+.-..++.+.|... ...|+-.|+
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 456889999999887655 2456777775 666654446677766322 344555565
Q ss_pred CHHHHHHHHHHHHHHHHhcCC-CChHHHHHHHH
Q 026384 76 DPAAVSQYANVMKTVREKADL-FSESQRIAYTI 107 (239)
Q Consensus 76 DpaAVk~YA~~~~~~r~k~gl-~s~~e~I~~ti 107 (239)
|.-.=-.+....+.+..+.|- +++++.+++.+
T Consensus 114 ~~l~p~d~~~~r~~l~~~~g~~~~dedvlsyal 146 (196)
T PF02436_consen 114 DLLPPADLDKLRKELEEKAGREPTDEDVLSYAL 146 (196)
T ss_dssp GCS----HHHHHHHHHHHCTSTSCHHHHHHHHH
T ss_pred ccCChhhHHHHHHHHHHHcCCCCCHHHHHHHhc
Confidence 544333456666777777766 57777777766
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=56.43 E-value=33 Score=24.24 Aligned_cols=52 Identities=10% Similarity=0.169 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHH-HcC
Q 026384 80 VSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIR-ERG 131 (239)
Q Consensus 80 Vk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~l~EiR-~~G 131 (239)
+.-|.+....++...+=+.........+....++..+|+.|+....++. ..+
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 4456666777777777767777777777888888889999999998888 666
No 6
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=56.16 E-value=13 Score=32.24 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=33.9
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHH
Q 026384 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQR 102 (239)
Q Consensus 56 kkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~ 102 (239)
+.|-+++-+|-..|+-..|.+. --..|-+.++-++.++|||+++|.
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 5677777788878877743322 355667778888999999999874
No 7
>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=47.35 E-value=12 Score=33.66 Aligned_cols=23 Identities=17% Similarity=0.443 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhhCCccccccHhh
Q 026384 142 MMDALEKVEKEIKKPLMRNDKKG 164 (239)
Q Consensus 142 mm~ALdkvEK~igkpL~rsDkkG 164 (239)
..+.++++|.++|||+++||-.-
T Consensus 194 t~~vi~~lE~~lGkPVlsSNqat 216 (239)
T TIGR02990 194 AATCAQRIEQAIGKPVVTSNQAT 216 (239)
T ss_pred hHHHHHHHHHHHCCCEEEHHHHH
Confidence 56789999999999999999765
No 8
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=44.41 E-value=11 Score=29.83 Aligned_cols=21 Identities=43% Similarity=0.662 Sum_probs=18.6
Q ss_pred HHHHHHHHHcCCCCCChhhHH
Q 026384 170 AEFDKINKKLGIRKEDLPKYE 190 (239)
Q Consensus 170 ae~~kinKklGi~~eDl~K~e 190 (239)
.|...+.|+|||+|++|||+.
T Consensus 24 eE~~~vLk~l~i~~~qLPkI~ 44 (80)
T COG2012 24 EEAKEVLKELGIEPEQLPKIK 44 (80)
T ss_pred HHHHHHHHHhCCCHHHCCccc
Confidence 567889999999999999975
No 9
>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=41.23 E-value=39 Score=27.86 Aligned_cols=46 Identities=11% Similarity=0.094 Sum_probs=35.4
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHH
Q 026384 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQR 102 (239)
Q Consensus 56 kkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~ 102 (239)
+.|-+++-.|-..|.-.. +...-...|-+.++-+++++||+++++.
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 678888877776665553 3455778888889999999999999873
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=39.12 E-value=46 Score=23.92 Aligned_cols=43 Identities=16% Similarity=0.264 Sum_probs=32.0
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHH
Q 026384 71 TIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLL 122 (239)
Q Consensus 71 ~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~ 122 (239)
.|+++|+..|..++ +++|++ .+++...|..---.+.+||.||.
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
>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]
Probab=38.58 E-value=2.1e+02 Score=28.73 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHH
Q 026384 50 IFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVRE 92 (239)
Q Consensus 50 iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~ 92 (239)
.+..|+.-|-..++-|.+.+ ++.| |++..++|.+..-++|.
T Consensus 104 si~~V~s~Y~~sfe~ll~~~-~~~~-~~~~~~qf~d~l~~l~~ 144 (414)
T KOG0787|consen 104 SIQLVQSWYIRSFEDLLEFP-TISP-DLEDLSQFNDLLNTLRN 144 (414)
T ss_pred hHHHHHHHHHHHHHHHHccC-CCCc-chhhHHHHHHHHHHHHh
Confidence 46677777777777777777 7777 89999999988777665
No 12
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=37.49 E-value=1.3e+02 Score=23.74 Aligned_cols=66 Identities=15% Similarity=0.233 Sum_probs=47.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHH---hcCCCChHHHHHHHHHhh
Q 026384 44 DEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVRE---KADLFSESQRIAYTIETR 110 (239)
Q Consensus 44 dd~lK~iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~---k~gl~s~~e~I~~tie~~ 110 (239)
=+.|+.-|-.-..-.+++++.|.+.+ ++..+|+.++..+.+.+..+-. .+|.+..+..+...|-.+
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 35778888777777788888888666 4777999999999888766554 556666655555444433
No 13
>PF13310 Virulence_RhuM: Virulence protein RhuM family
Probab=37.32 E-value=49 Score=31.08 Aligned_cols=186 Identities=18% Similarity=0.234 Sum_probs=114.0
Q ss_pred hhhhhhhhhhhhhHHHHhhc------cchhHHhhhhhcCCc-cCcc----hHHHHHH-------HHHH-----------H
Q 026384 5 SRLASKSKQLCSSQVILQRQ------HAISVRFFANEAAPQ-ALKG----DEMLKNI-------FLDV-----------K 55 (239)
Q Consensus 5 ~r~~srs~~~~~~~~~~~~~------~~~~vR~fA~~Aap~-~~kG----dd~lK~i-------F~~v-----------q 55 (239)
.|.++|.-..|+-.+|++=| .++++|.+|...=.+ -.|| |+-||+- |.++ +
T Consensus 15 ~r~v~r~~~~YnLd~IisVGYRV~S~~~tqFR~WAt~~Lkey~~KGf~~d~erLk~~~~~~~dyf~ell~rIr~IRaSEr 94 (260)
T PF13310_consen 15 KREVSREVKYYNLDAIISVGYRVNSKRGTQFRQWATKVLKEYLIKGFVLDDERLKNGGVFGKDYFDELLERIRDIRASER 94 (260)
T ss_pred CcccccccccccHHHHHHhhheeCcHHHhHHHHHHHHhHHHHHHhhhhhhHHHHHccCcccHHHHHHHHHHHHhhHHHHH
Confidence 35678899999999998755 377899998642221 2222 2333322 2222 2
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhh------h----------cCCCcHHH
Q 026384 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETR------T----------AGIPDART 119 (239)
Q Consensus 56 kkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~------~----------~~~~dvR~ 119 (239)
+=|+...|++. ..++-||.++++-.=||.+.-.+-.-+-=.+..|.|-.-.|.. | .+..-+..
T Consensus 95 ~fYqki~di~a-~s~DYd~~~~~t~~Ffa~vQNKlh~Av~g~TAAElI~~Rad~~kp~MGLTtwkg~g~v~k~Dv~iAKN 173 (260)
T PF13310_consen 95 RFYQKITDIYA-TSIDYDPKSEETKQFFATVQNKLHYAVTGHTAAELIYERADAEKPNMGLTTWKGAGRVRKSDVTIAKN 173 (260)
T ss_pred HHHHHHHHHHh-hhhccCcCCHHHHHHHHHHHHHHHHHHhccChHHHHHhhcccCCCCCCccccCCCCCCcccchhHHhc
Confidence 33455556665 7789999999999999999888877766667777776544321 1 23334556
Q ss_pred HHHHHHHHHHcCCCchhhhHHHHHHHHHHHHHh--hCCccccccHhhHHHHHHHHHHHHHHcCCCCCC-hhhHHHHHHHH
Q 026384 120 YLLTLKEIRERGLIDEHGAEAMMMDALEKVEKE--IKKPLMRNDKKGMALLTAEFDKINKKLGIRKED-LPKYEEQLELK 196 (239)
Q Consensus 120 yL~~l~EiR~~Gl~D~~g~~a~mm~ALdkvEK~--igkpL~rsDkkGM~~L~ae~~kinKklGi~~eD-l~K~eee~ele 196 (239)
||+. .|+..+. .+.--=||=.|-. -.+|+ .|+-|...+|.+..--|-+-.. .+++--+.--+
T Consensus 174 YL~e-~El~~LN--------RlVs~yLD~AE~qA~~~~~m------tM~DW~~~LD~fL~fn~~~iL~~aGkIS~e~A~~ 238 (260)
T PF13310_consen 174 YLNE-DELDSLN--------RLVSMYLDFAEDQAERRKPM------TMKDWIEKLDAFLQFNEREILQGAGKISHEQAKE 238 (260)
T ss_pred cccH-HHHHHHH--------HHHHHHHHHHHHHHHccCCC------cHHHHHHHHHHHHHhCCCcccCCCChhhHHHHHH
Confidence 6643 4444332 2222235555543 33444 4889999999998887766433 57775555555
Q ss_pred HHHHHHHHHH
Q 026384 197 IAKAQLEELK 206 (239)
Q Consensus 197 ~aK~ql~elK 206 (239)
.|..+.+.-+
T Consensus 239 kA~~EYekf~ 248 (260)
T PF13310_consen 239 KAEAEYEKFR 248 (260)
T ss_pred HHHHHHHHHH
Confidence 6666555544
No 14
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=37.07 E-value=22 Score=26.54 Aligned_cols=75 Identities=19% Similarity=0.257 Sum_probs=43.4
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHH------hcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHH-
Q 026384 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVRE------KADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIR- 128 (239)
Q Consensus 56 kkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~------k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~l~EiR- 128 (239)
+-|+.+...|.+.. .++|-|...+..|.......++ +-|+. -.+-.+....-|.+...-....+++
T Consensus 3 ~~w~~i~~~L~~~~-~l~~~D~~~l~~yc~~~~~~~~~~~~l~~~G~~------~~~~~G~~~~nP~~~~~~~~~~~~~~ 75 (100)
T PF05119_consen 3 KEWKRIVPELKELG-ILSNLDVPLLERYCEAYSRYREAEKELKKEGFV------VETKNGNPKKNPAVSILNKAMKQMRS 75 (100)
T ss_pred HHHHHHHHHHHHcC-CCcHhHHHHHHHHHHHHHHHHHHHHHHHHcCce------eeCCCCCcccCHHHHHHHHHHHHHHH
Confidence 45677777777666 4778888888888766444333 33333 1111223455666666666666655
Q ss_pred ---HcCCCchhh
Q 026384 129 ---ERGLIDEHG 137 (239)
Q Consensus 129 ---~~Gl~D~~g 137 (239)
++||+..+-
T Consensus 76 l~~~lGLtP~sR 87 (100)
T PF05119_consen 76 LASELGLTPASR 87 (100)
T ss_pred HHHHcCCCHHHH
Confidence 456665543
No 15
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=36.96 E-value=28 Score=32.30 Aligned_cols=33 Identities=18% Similarity=0.507 Sum_probs=25.4
Q ss_pred HHHHHHHHHhhCCccccccHhhHHHHHHHHHHHHHHcCCC
Q 026384 143 MDALEKVEKEIKKPLMRNDKKGMALLTAEFDKINKKLGIR 182 (239)
Q Consensus 143 m~ALdkvEK~igkpL~rsDkkGM~~L~ae~~kinKklGi~ 182 (239)
.+.++++|.++|+|+.+||-.-|-. ..+.+|++
T Consensus 193 ~eii~~lE~~~G~PVvsSN~AT~W~-------~Lr~~g~~ 225 (238)
T COG3473 193 FEIIEKLERDTGVPVVSSNQATLWM-------ALRLIGLR 225 (238)
T ss_pred HHHHHHHHHHhCCceeeccHHHHHH-------HHHHcCCc
Confidence 5789999999999999999765432 34667766
No 16
>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=34.08 E-value=43 Score=22.42 Aligned_cols=56 Identities=21% Similarity=0.322 Sum_probs=33.2
Q ss_pred HHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHH
Q 026384 55 KKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDAR 118 (239)
Q Consensus 55 qkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR 118 (239)
+++|..++..+++. +..+|+++.+.-.++... -+.|=+.. ...+++......|+-.
T Consensus 4 ~~~~~~A~~~~~~~-l~~~p~~~~~~~~la~~~----~~~g~~~~---A~~~l~~~~~~~~~~~ 59 (68)
T PF14559_consen 4 QGDYDEAIELLEKA-LQRNPDNPEARLLLAQCY----LKQGQYDE---AEELLERLLKQDPDNP 59 (68)
T ss_dssp TTHHHHHHHHHHHH-HHHTTTSHHHHHHHHHHH----HHTT-HHH---HHHHHHCCHGGGTTHH
T ss_pred ccCHHHHHHHHHHH-HHHCCCCHHHHHHHHHHH----HHcCCHHH---HHHHHHHHHHHCcCHH
Confidence 45677777777765 477899999888888543 33343333 3344444444444433
No 17
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=34.03 E-value=3.6e+02 Score=24.47 Aligned_cols=43 Identities=23% Similarity=0.348 Sum_probs=32.6
Q ss_pred HHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 026384 171 EFDKINKKLGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKKR 219 (239)
Q Consensus 171 e~~kinKklGi~~eDl~K~eee~ele~aK~ql~elK~~a~e~m~~~kkr 219 (239)
.+.+|.+.+|+. +-.-+-+|++|+.-|+.|. +|.|.|+-...+
T Consensus 159 ~l~~l~~~L~ls-----~~kv~kDL~lYrsnLeKm~-qa~el~ee~~~~ 201 (206)
T PLN03060 159 VLEKLSKALNVS-----KRSVDRDLDVYRNLLSKLA-QAKELIKEYIDR 201 (206)
T ss_pred HHHHHHHHcCCC-----HHHHHhhHHHHHhHHHHHH-HHHHHHHHHHHH
Confidence 677888999988 4455668899999999885 577777665444
No 18
>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=33.18 E-value=1.1e+02 Score=26.79 Aligned_cols=68 Identities=24% Similarity=0.284 Sum_probs=46.0
Q ss_pred HHHhcCCCC---hHHHHHHHHHhhhcCCCcHHHHHHHHHHHH-HcCCCchhhhHHHHHHHHHHHHHhhCCcccc
Q 026384 90 VREKADLFS---ESQRIAYTIETRTAGIPDARTYLLTLKEIR-ERGLIDEHGAEAMMMDALEKVEKEIKKPLMR 159 (239)
Q Consensus 90 ~r~k~gl~s---~~e~I~~tie~~~~~~~dvR~yL~~l~EiR-~~Gl~D~~g~~a~mm~ALdkvEK~igkpL~r 159 (239)
=|...|||| ..++....++-...+...=+.||..+-..| .-|..+...++|..+.++-+ +++.-|+.+
T Consensus 8 eRa~~GipPlPL~a~Qt~~lielLk~~~~~~~~~lldLL~~RV~PGVD~AA~VKA~FL~~ia~--g~~~~~~Is 79 (154)
T PF11791_consen 8 ERAALGIPPLPLNAEQTAELIELLKNPPAGEEAFLLDLLTNRVPPGVDEAAYVKAEFLAAIAK--GEISSPLIS 79 (154)
T ss_dssp HHHCTT-------HHHHHHHHHHHHS--TT-HHHHHHHHHHSS--TT-HHHHHHHHHHHHHHT--TSS-BTTB-
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHc--CCccCCCcC
Confidence 478889987 467888888888877777789999999999 99999999999988887754 345556655
No 19
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=33.02 E-value=69 Score=21.70 Aligned_cols=32 Identities=31% Similarity=0.541 Sum_probs=21.4
Q ss_pred HHHHHHHHHhchhccccccCCCCHHHHHHHHHH
Q 026384 54 VKKKFETALGVLRKEKITIAPEDPAAVSQYANV 86 (239)
Q Consensus 54 vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~ 86 (239)
.+++|+.++..+... |.++|+|+.++-.|+..
T Consensus 7 ~~~~~~~A~~~~~~~-l~~~p~~~~~~~~~a~~ 38 (73)
T PF13371_consen 7 QQEDYEEALEVLERA-LELDPDDPELWLQRARC 38 (73)
T ss_pred hCCCHHHHHHHHHHH-HHhCcccchhhHHHHHH
Confidence 455677777766543 36778888888777743
No 20
>PF13438 DUF4113: Domain of unknown function (DUF4113)
Probab=32.85 E-value=38 Score=23.82 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHcCCC
Q 026384 167 LLTAEFDKINKKLGIR 182 (239)
Q Consensus 167 ~L~ae~~kinKklGi~ 182 (239)
.|+..+|+||.++|-.
T Consensus 3 ~LM~~iD~iN~r~G~~ 18 (52)
T PF13438_consen 3 RLMQAIDAINRRFGRG 18 (52)
T ss_pred HHHHHHHHHHHhcCCC
Confidence 5888999999999954
No 21
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]
Probab=32.56 E-value=35 Score=34.32 Aligned_cols=125 Identities=24% Similarity=0.373 Sum_probs=85.1
Q ss_pred hHHHHhhccchhHHhhhhhcCCccCcchHHHHHHHHHHHHHHHHHHhchhccccccCC-CCHHHHHHHHHHHHHHHHhcC
Q 026384 17 SQVILQRQHAISVRFFANEAAPQALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAP-EDPAAVSQYANVMKTVREKAD 95 (239)
Q Consensus 17 ~~~~~~~~~~~~vR~fA~~Aap~~~kGdd~lK~iF~~vqkkF~~~l~~lkk~kI~idp-~DpaAVk~YA~~~~~~r~k~g 95 (239)
-|-++.+|+.+.-|||| ||+|..- |++-.+.=++++| ..|. +|+--.+. -++ +-++.|
T Consensus 80 LQMLlRGQNlvGYrhya----------DDvVe~F---v~ka~~nGidvfR----iFDAlND~RNl~~---ai~-a~kk~G 138 (472)
T COG5016 80 LQMLLRGQNLVGYRHYA----------DDVVEKF---VEKAAENGIDVFR----IFDALNDVRNLKT---AIK-AAKKHG 138 (472)
T ss_pred HHHHHccCccccccCCc----------hHHHHHH---HHHHHhcCCcEEE----echhccchhHHHH---HHH-HHHhcC
Confidence 57889999999999986 7787766 8888888899888 4444 56543322 122 234566
Q ss_pred CCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHcC-----CCchhhhHH--HHHHHHHHHHHhhCCccc--cccHhhHH
Q 026384 96 LFSESQRIAYTIETRTAGIPDARTYLLTLKEIRERG-----LIDEHGAEA--MMMDALEKVEKEIKKPLM--RNDKKGMA 166 (239)
Q Consensus 96 l~s~~e~I~~tie~~~~~~~dvR~yL~~l~EiR~~G-----l~D~~g~~a--~mm~ALdkvEK~igkpL~--rsDkkGM~ 166 (239)
. -++.+|-|-+.+.-++-.|+..+.|+-..| ++|++|.-. ..-+-+-.+-+.++-|+- +-.-.||+
T Consensus 139 ~-----h~q~~i~YT~sPvHt~e~yv~~akel~~~g~DSIciKDmaGlltP~~ayelVk~iK~~~~~pv~lHtH~TsG~a 213 (472)
T COG5016 139 A-----HVQGTISYTTSPVHTLEYYVELAKELLEMGVDSICIKDMAGLLTPYEAYELVKAIKKELPVPVELHTHATSGMA 213 (472)
T ss_pred c-----eeEEEEEeccCCcccHHHHHHHHHHHHHcCCCEEEeecccccCChHHHHHHHHHHHHhcCCeeEEecccccchH
Confidence 5 345667777889999999999999999776 567777531 233445556667777764 34455665
Q ss_pred H
Q 026384 167 L 167 (239)
Q Consensus 167 ~ 167 (239)
.
T Consensus 214 ~ 214 (472)
T COG5016 214 E 214 (472)
T ss_pred H
Confidence 3
No 22
>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=32.42 E-value=63 Score=27.05 Aligned_cols=40 Identities=15% Similarity=0.266 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHhchhccccccCC--CCHHHHHHHHHHH
Q 026384 48 KNIFLDVKKKFETALGVLRKEKITIAP--EDPAAVSQYANVM 87 (239)
Q Consensus 48 K~iF~~vqkkF~~~l~~lkk~kI~idp--~DpaAVk~YA~~~ 87 (239)
...+.++++++..--.-++=.-|++|| +.|+..++|++..
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 5699999999754
No 23
>cd07599 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains fo
Probab=31.19 E-value=3.4e+02 Score=23.34 Aligned_cols=20 Identities=25% Similarity=0.219 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 026384 192 QLELKIAKAQLEELKKDALE 211 (239)
Q Consensus 192 e~ele~aK~ql~elK~~a~e 211 (239)
|.+|+.|+...+.+.....+
T Consensus 155 e~~l~~a~~~y~~lN~~Lk~ 174 (216)
T cd07599 155 ERKLEEAKEEYEALNELLKS 174 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444333
No 24
>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=30.77 E-value=38 Score=28.09 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=25.0
Q ss_pred HHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCChHH
Q 026384 56 KKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSESQ 101 (239)
Q Consensus 56 kkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e 101 (239)
+.|-+++-+|-.+|.-.. +...-...|-+.++-+++++||+++++
T Consensus 59 ND~a~AVR~lE~iK~K~~-~~~~~Y~~~lqElkPtl~ELGI~t~Ee 103 (108)
T PF02284_consen 59 NDFALAVRILEGIKDKCG-NKKEIYPYILQELKPTLEELGIPTPEE 103 (108)
T ss_dssp T-HHHHHHHHHHHHHHTT-T-TTHHHHHHHHHHHHHHHHT---TTT
T ss_pred hhHHHHHHHHHHHHHHcc-ChHHHHHHHHHHHhhHHHHhCCCCHHH
Confidence 456666666665555553 222256666677777777888887765
No 25
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=30.55 E-value=1.4e+02 Score=27.69 Aligned_cols=59 Identities=31% Similarity=0.374 Sum_probs=42.0
Q ss_pred cccccHhhHHHHHHHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 026384 157 LMRNDKKGMALLTAEFDKINKKLGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKKREE 221 (239)
Q Consensus 157 L~rsDkkGM~~L~ae~~kinKklGi~~eDl~K~eee~ele~aK~ql~elK~~a~e~m~~~kkree 221 (239)
..+-|-.+-+.+ ++.+|+-+|+. =|-+++++|++ +...||+++-.+..+.++.+++..+
T Consensus 181 ~~~PDP~AAa~v---ve~lnk~~~l~-V~td~L~keAe--~i~~~lekl~eq~~~~~~~~~~~~e 239 (244)
T COG1938 181 GDRPDPRAAARV---VEALNKMLGLN-VDTDKLEKEAE--EIEEQLEKLAEQLEKEEERVEREEE 239 (244)
T ss_pred CCCCChHHHHHH---HHHHHHHhcCc-cCHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhcccc
Confidence 344577766655 45888999987 36778887774 6778888888888887777655543
No 26
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=28.59 E-value=84 Score=21.19 Aligned_cols=32 Identities=38% Similarity=0.525 Sum_probs=24.3
Q ss_pred HHHHHHHHHHcCCCCCChhhH-HHHHHHHHHHHHH
Q 026384 169 TAEFDKINKKLGIRKEDLPKY-EEQLELKIAKAQL 202 (239)
Q Consensus 169 ~ae~~kinKklGi~~eDl~K~-eee~ele~aK~ql 202 (239)
..++-++.+.+||. ...++ ..|+.+.|.++|-
T Consensus 7 ~~eL~~iAk~lgI~--~~~~~~K~eLI~~Il~~q~ 39 (43)
T PF07498_consen 7 LSELREIAKELGIE--GYSKMRKQELIFAILKAQA 39 (43)
T ss_dssp HHHHHHHHHCTT-T--TGCCS-HHHHHHHHHHHHC
T ss_pred HHHHHHHHHHcCCC--CCCcCCHHHHHHHHHHHHH
Confidence 46788999999997 66555 7788888888763
No 27
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=28.23 E-value=53 Score=21.16 Aligned_cols=33 Identities=24% Similarity=0.381 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhchhccccccCCCCHHHHHHHHH
Q 026384 52 LDVKKKFETALGVLRKEKITIAPEDPAAVSQYAN 85 (239)
Q Consensus 52 ~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~ 85 (239)
...+.+|..+...+++. |-.+|+|+.|+-.|+.
T Consensus 11 ~~~~G~~~~A~~~~~~~-l~~~P~~~~a~~~La~ 43 (44)
T PF13428_consen 11 YRRLGQPDEAERLLRRA-LALDPDDPEAWRALAQ 43 (44)
T ss_pred HHHcCCHHHHHHHHHHH-HHHCcCCHHHHHHhhh
Confidence 33445566666666543 3688999999988874
No 28
>cd07631 BAR_APPL1 The Bin/Amphiphysin/Rvs (BAR) domain of Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing (APPL) proteins are effectors of the small GTPase Rab5 that function in endosome-mediated signaling. They contain BAR, pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. They form homo- and hetero-oligomers that are mediated by their BAR domains. Vertebrates contain two APPL proteins, APPL1 and APPL2. APPL1 interacts with diverse receptors (e.g. NGF receptor TrkA, FSHR, adiponectin receptors) and signaling proteins (e.g. Akt, PI3K), and may function as an adaptor linked to many distinct signaling pathways. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be invo
Probab=27.70 E-value=2.8e+02 Score=25.45 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=17.5
Q ss_pred ccccHhhHHHHHHHHHHHHHHcCC
Q 026384 158 MRNDKKGMALLTAEFDKINKKLGI 181 (239)
Q Consensus 158 ~rsDkkGM~~L~ae~~kinKklGi 181 (239)
...|=.+.+-....|+++..++..
T Consensus 100 ~kedL~~~Ke~KK~FdK~Se~~d~ 123 (215)
T cd07631 100 KERDLKEILTLKEVFQIASNDHDA 123 (215)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHH
Confidence 456667788888888888776643
No 29
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.49 E-value=2.2e+02 Score=26.73 Aligned_cols=71 Identities=15% Similarity=0.171 Sum_probs=50.5
Q ss_pred CcchHHHHHHHHHHHHHHHHHH--hchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHh
Q 026384 41 LKGDEMLKNIFLDVKKKFETAL--GVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIET 109 (239)
Q Consensus 41 ~kGdd~lK~iF~~vqkkF~~~l--~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s---------~~e~I~~tie~ 109 (239)
+.|..+-+.|..+.++..+.+- +...+.-|.+- ||..|-..|.+.....-+++||.+ .++.+..+|+.
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 4577777888888888887764 23344444444 666677889999999999999875 34557778876
Q ss_pred hhc
Q 026384 110 RTA 112 (239)
Q Consensus 110 ~~~ 112 (239)
.-+
T Consensus 83 lN~ 85 (282)
T PRK14182 83 LNA 85 (282)
T ss_pred HhC
Confidence 644
No 30
>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=27.46 E-value=1.1e+02 Score=23.81 Aligned_cols=48 Identities=23% Similarity=0.372 Sum_probs=27.5
Q ss_pred HHHHHHhchhccccccCCCCHH-----------------HHHHHHHHHHHHHHhcCCCChHHHHHHH
Q 026384 57 KFETALGVLRKEKITIAPEDPA-----------------AVSQYANVMKTVREKADLFSESQRIAYT 106 (239)
Q Consensus 57 kF~~~l~~lkk~kI~idp~Dpa-----------------AVk~YA~~~~~~r~k~gl~s~~e~I~~t 106 (239)
.|..++..++ .=|.++|-|+. |+..|......+++++|+. |+..+...
T Consensus 77 ~~~~a~~~~~-~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~-Ps~~~~~l 141 (146)
T PF03704_consen 77 DYEEALRLLQ-RALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIE-PSPETRAL 141 (146)
T ss_dssp -HHHHHHHHH-HHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS-----HHHHHH
T ss_pred CHHHHHHHHH-HHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcC-cCHHHHHH
Confidence 3444444443 23467785553 7888998899999999995 44444443
No 31
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=26.74 E-value=7.3e+02 Score=25.66 Aligned_cols=84 Identities=14% Similarity=0.281 Sum_probs=49.8
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHH----HHHH-HcCCCchhhhHHHHH
Q 026384 69 KITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTL----KEIR-ERGLIDEHGAEAMMM 143 (239)
Q Consensus 69 kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~l----~EiR-~~Gl~D~~g~~a~mm 143 (239)
.|+....||.-..+.+|.+-++=-+-.+-.-.+....+++...+..+.+++=|..+ ..+| +.|+.|...--....
T Consensus 231 ~Is~~~~dP~~Aa~ilN~la~~Yi~~~l~~k~~~a~~a~~fL~~qL~~l~~~L~~aE~~l~~fr~~~~~~d~~~ea~~~l 310 (726)
T PRK09841 231 ELTMTGDDPQLITRILNSIANNYLQQNIARQAAQDSQSLEFLQRQLPEVRSELDQAEEKLNVYRQQRDSVDLNLEAKAVL 310 (726)
T ss_pred EEEEeCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence 45566689987777666644433333333335555666666667777777766654 7788 778877442223344
Q ss_pred HHHHHHHHh
Q 026384 144 DALEKVEKE 152 (239)
Q Consensus 144 ~ALdkvEK~ 152 (239)
+-+.+++.+
T Consensus 311 ~~~~~l~~q 319 (726)
T PRK09841 311 EQIVNVDNQ 319 (726)
T ss_pred HHHHHHHHH
Confidence 555555544
No 32
>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=26.68 E-value=29 Score=24.71 Aligned_cols=23 Identities=26% Similarity=0.472 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCChHHHH
Q 026384 75 EDPAAVSQYANVMKTVREKADLFSESQRI 103 (239)
Q Consensus 75 ~DpaAVk~YA~~~~~~r~k~gl~s~~e~I 103 (239)
+||..|.++| |+++||-.|+|.|
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 33
>PRK14574 hmsH outer membrane protein; Provisional
Probab=26.55 E-value=8e+02 Score=26.27 Aligned_cols=120 Identities=14% Similarity=0.146 Sum_probs=70.2
Q ss_pred HHHhhccchhHHhhhhhcCCccCcchHHHH--HHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCC
Q 026384 19 VILQRQHAISVRFFANEAAPQALKGDEMLK--NIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADL 96 (239)
Q Consensus 19 ~~~~~~~~~~vR~fA~~Aap~~~kGdd~lK--~iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl 96 (239)
+....|.-...+.+...+..|.-.-.-.+. ......+++|..++..+++. +.++|++|++....+ ..-+..
T Consensus 77 l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~ka-L~~dP~n~~~l~gLa------~~y~~~ 149 (822)
T PRK14574 77 IAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSS-LKKDPTNPDLISGMI------MTQADA 149 (822)
T ss_pred HHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhhCCCCHHHHHHHH------HHHhhc
Confidence 334445555666666654433112233334 34666778999999999987 699999998885332 222222
Q ss_pred CChHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHcCCCchhhhHHHHHHHHHHHHHhhCC
Q 026384 97 FSESQRIAYTIETRTAGIPDARTYLLTLKEIRERGLIDEHGAEAMMMDALEKVEKEIKK 155 (239)
Q Consensus 97 ~s~~e~I~~tie~~~~~~~dvR~yL~~l~EiR~~Gl~D~~g~~a~mm~ALdkvEK~igk 155 (239)
...+.....++.....-|+.+.|+. +..+. .|..+.. +||...++-+..
T Consensus 150 -~q~~eAl~~l~~l~~~dp~~~~~l~-layL~-~~~~~~~-------~AL~~~ekll~~ 198 (822)
T PRK14574 150 -GRGGVVLKQATELAERDPTVQNYMT-LSYLN-RATDRNY-------DALQASSEAVRL 198 (822)
T ss_pred -CCHHHHHHHHHHhcccCcchHHHHH-HHHHH-HhcchHH-------HHHHHHHHHHHh
Confidence 4455666677777777888888844 33333 2222322 256666665543
No 34
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=26.18 E-value=1.5e+02 Score=30.31 Aligned_cols=89 Identities=12% Similarity=0.213 Sum_probs=66.1
Q ss_pred cCcchHHHHHHHHHHHHHHHHHHhchhccccccCCCCHH-HHHHHHHHHH----------------------HHHHhcCC
Q 026384 40 ALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPA-AVSQYANVMK----------------------TVREKADL 96 (239)
Q Consensus 40 ~~kGdd~lK~iF~~vqkkF~~~l~~lkk~kI~idp~Dpa-AVk~YA~~~~----------------------~~r~k~gl 96 (239)
.+..|++|..|--.|-+.|-.-.|-+...--|+++.+.- +.+++-+.+. .--=++||
T Consensus 193 ~fppd~~vq~v~e~Ve~~f~~~~G~~e~F~wpvtr~~A~~~L~~Fi~~~L~nFG~yQDam~~d~~~L~HSllS~alNigL 272 (505)
T COG3046 193 KFPPDEIVQEVKERVERLFPDNFGQVEGFGWPVTRTQALRALKHFIADRLPNFGSYQDAMSADDPHLWHSLLSFALNIGL 272 (505)
T ss_pred CCCCcchhHHHHHHHHhhCCCCCCccccCCCCCCHHHHHHHHHHHHHHhhhcCCcHHHHHhcCCchhHHHHHHHHhhccC
Confidence 344599999999999999999888888888888876654 5565554421 11228999
Q ss_pred CChHHHHHHHHHhhh-cCCC--cHHHHHHHHHHHH
Q 026384 97 FSESQRIAYTIETRT-AGIP--DARTYLLTLKEIR 128 (239)
Q Consensus 97 ~s~~e~I~~tie~~~-~~~~--dvR~yL~~l~EiR 128 (239)
.+|.|+|.+++.... .+|| +|-+|.-.+-=-|
T Consensus 273 L~PleVi~Aa~~Ay~~g~ipLN~VEGFvRQiiGWR 307 (505)
T COG3046 273 LTPLEVIRAALKAYREGDIPLNSVEGFVRQIIGWR 307 (505)
T ss_pred CCHHHHHHHHHHhhccCCCchHHHHHHHHHHhhHH
Confidence 999999999999877 4554 6777776665555
No 35
>PRK11519 tyrosine kinase; Provisional
Probab=26.15 E-value=7.4e+02 Score=25.56 Aligned_cols=101 Identities=15% Similarity=0.261 Sum_probs=59.3
Q ss_pred HHHHHHHHHHhchh--c----cccccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHH---
Q 026384 53 DVKKKFETALGVLR--K----EKITIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLT--- 123 (239)
Q Consensus 53 ~vqkkF~~~l~~lk--k----~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~--- 123 (239)
.+-..+..-|.+.+ + ..|.....||.-....+|.+-..--+-.+-.-.+....+++-..+..+.+|+=|..
T Consensus 209 ~~~~~l~~~l~V~~~~k~S~ii~Is~~~~dP~~Aa~iaN~l~~~Yi~~~~~~k~~~a~~a~~fL~~ql~~l~~~L~~aE~ 288 (719)
T PRK11519 209 GMINNLQNNLTVTENGKDTGVLSLTYTGEDREQIRDILNSITRNYLEQNIERKSEEASKSLAFLAQQLPEVRSRLDVAEN 288 (719)
T ss_pred HHHHHHHhcceEEecCCCceEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555532 2 45666778999777777776444444444444455556666666666666666655
Q ss_pred -HHHHH-HcCCCchhhhHHHHHHHHHHHHHhh
Q 026384 124 -LKEIR-ERGLIDEHGAEAMMMDALEKVEKEI 153 (239)
Q Consensus 124 -l~EiR-~~Gl~D~~g~~a~mm~ALdkvEK~i 153 (239)
+.++| +.|+.|...--....+.+.++++++
T Consensus 289 ~l~~fr~~~~~vd~~~ea~~~l~~~~~l~~ql 320 (719)
T PRK11519 289 KLNAFRQDKDSVDLPLEAKAVLDSMVNIDAQL 320 (719)
T ss_pred HHHHHHHHcCCCCchHHHHHHHHHHHHHHHHH
Confidence 47788 7788775443333555555555443
No 36
>PF03114 BAR: BAR domain; InterPro: IPR004148 Endocytosis and intracellular transport involve several mechanistic steps: (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton; (2) following its formation, the vesicle has to be pinched off the membrane; (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment. Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases. ; GO: 0005515 protein binding, 0005737 cytoplasm; PDB: 4AVM_A 2D4C_C 1X03_A 1X04_A 2RND_A 2RMY_A 2FIC_A 2C08_A 2Z0V_A 3SOG_A ....
Probab=25.55 E-value=3.6e+02 Score=21.76 Aligned_cols=153 Identities=17% Similarity=0.241 Sum_probs=78.2
Q ss_pred HHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHH-hcCCCChHHHHHHHHHhhhcCCCcHH---HHHHH
Q 026384 48 KNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVRE-KADLFSESQRIAYTIETRTAGIPDAR---TYLLT 123 (239)
Q Consensus 48 K~iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~-k~gl~s~~e~I~~tie~~~~~~~dvR---~yL~~ 123 (239)
-..|.+..++|..+=..+++.- ..++.|-+.+..... ...+-++.+.+...+.......++-. ..+..
T Consensus 25 D~~f~~~~~~~~~~~~~~~~l~--------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~l~~ 96 (229)
T PF03114_consen 25 DEEFEELEEKFKQLEESIKKLQ--------KSLKKYLDSIKKLSASQKNMKSPFEELADALIELGSEFSDDSSLGNALEK 96 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHCHTHHHHHHHHHHHHHHHCTSTTCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHhhhhhHHhhhhhHHHHHHHHHHHHHhccccccchhhhHHHH
Confidence 4457777777776666555322 345566665444433 22233777788888887774443333 24444
Q ss_pred HHHHH-HcCCCchhhhHHHHHHHHHHHHHhhCCcccc--ccHhhHHHHHHHHHHHHHHcCCCCCChhhHHH-------HH
Q 026384 124 LKEIR-ERGLIDEHGAEAMMMDALEKVEKEIKKPLMR--NDKKGMALLTAEFDKINKKLGIRKEDLPKYEE-------QL 193 (239)
Q Consensus 124 l~EiR-~~Gl~D~~g~~a~mm~ALdkvEK~igkpL~r--sDkkGM~~L~ae~~kinKklGi~~eDl~K~ee-------e~ 193 (239)
+++.. ..+ ...-+-.+.++..+-.||-+ ++=+.......+.++..-.|.-....+.++.+ +.
T Consensus 97 ~~~~~~~i~--------~~~~~~~~~~~~~vi~pl~~~~~~~~~i~~~~kkr~~~~ldyd~~~~k~~k~~~~~~~~~~~~ 168 (229)
T PF03114_consen 97 FGEAMQEIE--------EARKELESQIESTVIDPLKEFLKEFKEIKKLIKKREKKRLDYDSARSKLEKLRKKKSKSSKEE 168 (229)
T ss_dssp HHHHHHHHH--------HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTSSBTHHHH
T ss_pred HHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccHH
Confidence 44443 221 11222233344444444321 23333333333333332222222122222221 78
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 026384 194 ELKIAKAQLEELKKDALEAMETQ 216 (239)
Q Consensus 194 ele~aK~ql~elK~~a~e~m~~~ 216 (239)
+++.++...+.+.....+.|...
T Consensus 169 ~l~~a~~~f~~~~~~l~~~l~~l 191 (229)
T PF03114_consen 169 KLEEAKEEFEALNEELKEELPKL 191 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 88999999999999998888876
No 37
>PRK10455 periplasmic protein; Reviewed
Probab=25.49 E-value=2.3e+02 Score=24.32 Aligned_cols=37 Identities=16% Similarity=0.212 Sum_probs=25.7
Q ss_pred cccCCCCHHHHHHHHHHHHHHHH------------hcCCCChHHHHHHH
Q 026384 70 ITIAPEDPAAVSQYANVMKTVRE------------KADLFSESQRIAYT 106 (239)
Q Consensus 70 I~idp~DpaAVk~YA~~~~~~r~------------k~gl~s~~e~I~~t 106 (239)
|+-+|=|+++|..+++.+-.+.. =..+++|+|+-+..
T Consensus 91 i~ad~FDeaavra~~~k~~~~~~~~~~~~~~~~~qiy~vLTPEQr~q~~ 139 (161)
T PRK10455 91 IASDTFDKAKAEAQITKMEAQRKARMLAHMETQNKIYNVLTPEQKKQFN 139 (161)
T ss_pred HccCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 55667899999998886443332 24688888886543
No 38
>COG1529 CoxL Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]
Probab=25.48 E-value=91 Score=32.36 Aligned_cols=58 Identities=19% Similarity=0.205 Sum_probs=49.4
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcC---CCcHHHHHHHHHHHH-HcCC
Q 026384 75 EDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAG---IPDARTYLLTLKEIR-ERGL 132 (239)
Q Consensus 75 ~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~---~~dvR~yL~~l~EiR-~~Gl 132 (239)
++|.+.-..--.|..+.++|||.+.+-|+.+++.+.--+ ..+.+.|...+.+.. +.|.
T Consensus 349 g~~~~~~a~E~~~d~lA~~Lgidp~eiR~~n~~~~g~~~~~~~~~~~~~~~~~~~~ak~~~~ 410 (731)
T COG1529 349 GRPEGTFALERAVDELAEELGIDPVEIRLRNLIRGGPFGLGRRYDSGDYLEELDEAAKRFGW 410 (731)
T ss_pred CCchhHHHHHHHHHHHHHHhCCCHHHHhhhhccccCCCCCcccccCccHHHHHHHHHHhcCc
Confidence 777776666667999999999999999999999966655 888899999999988 6674
No 39
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=25.32 E-value=3e+02 Score=20.68 Aligned_cols=25 Identities=32% Similarity=0.347 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 026384 194 ELKIAKAQLEELKKDALEAMETQKK 218 (239)
Q Consensus 194 ele~aK~ql~elK~~a~e~m~~~kk 218 (239)
+-.+-++|.+-|+++-.+.|..+.+
T Consensus 83 ~~r~~~~q~~~L~~~f~~~m~~fq~ 107 (117)
T smart00503 83 SDRTRKAQTEKLRKKFKEVMNEFQR 107 (117)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999998843
No 40
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.70 E-value=1.2e+02 Score=28.43 Aligned_cols=69 Identities=16% Similarity=0.216 Sum_probs=51.3
Q ss_pred CcchHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHhhh
Q 026384 41 LKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIETRT 111 (239)
Q Consensus 41 ~kGdd~lK~iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s---------~~e~I~~tie~~~ 111 (239)
+.|-.+-+.|..+++++...+ +...+.-|.+- ||..|-..|.+.....-+++||.+ .++.+..+|+..-
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 357778888999999998876 76666666665 555566789999999999999875 2345667777653
No 41
>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=24.52 E-value=3.1e+02 Score=20.68 Aligned_cols=78 Identities=15% Similarity=0.186 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHHHHHHHHHHHH--------------HhcCCCChHHHHHHHHHhh
Q 026384 45 EMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVSQYANVMKTVR--------------EKADLFSESQRIAYTIETR 110 (239)
Q Consensus 45 d~lK~iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk~YA~~~~~~r--------------~k~gl~s~~e~I~~tie~~ 110 (239)
+-|..+..+...-|+.+++.+.++.=-|-.+|+..+..+......+- .+++..+....+...++
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 34678888899999999999888876666688887776665544333 35555555555555555
Q ss_pred hcCCCcHHHHHHHHHH
Q 026384 111 TAGIPDARTYLLTLKE 126 (239)
Q Consensus 111 ~~~~~dvR~yL~~l~E 126 (239)
..+..+.....+.+
T Consensus 82 --~~~~l~~~~~~l~~ 95 (143)
T PF05130_consen 82 --EREELQALWRELRE 95 (143)
T ss_dssp --CCHHHHHHHHHHHH
T ss_pred --ccHHHHHHHHHHHH
Confidence 44444444444433
No 42
>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=23.97 E-value=2e+02 Score=22.86 Aligned_cols=58 Identities=24% Similarity=0.272 Sum_probs=37.2
Q ss_pred CcchHHHHHHHHHHHHHHHHHHh--chhccccccCCCCHHHHHHHHHHHHHHHHhcCCCCh
Q 026384 41 LKGDEMLKNIFLDVKKKFETALG--VLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSE 99 (239)
Q Consensus 41 ~kGdd~lK~iF~~vqkkF~~~l~--~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~ 99 (239)
+.|..+-+.+..++++....+-. ...+.-|.+- ||..|-..|.+.....-+++||...
T Consensus 3 L~Gk~va~~i~~~l~~~i~~l~~~~~~P~Laii~v-g~d~~S~~Y~~~k~k~~~~~Gi~~~ 62 (117)
T PF00763_consen 3 LDGKPVAKEIKEELKEEIEKLKEKGITPKLAIILV-GDDPASISYVRSKQKAAEKLGIEFE 62 (117)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHCT---EEEEEEE-S--HHHHHHHHHHHHHHHHHT-EEE
T ss_pred eeHHHHHHHHHHHHHHHHHHHHhcCCCcEEEEEec-CCChhHHHHHHHHHHHHHHcCCceE
Confidence 46788888888888888766543 3444554554 4445566799999999999998643
No 43
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=23.64 E-value=7.6e+02 Score=24.80 Aligned_cols=100 Identities=21% Similarity=0.233 Sum_probs=67.7
Q ss_pred hHHHHHHHHHHHHHHHHHHhchhccccccCCCCHHHHH-HHHHHHH---HHHHh-cCCCChHHHHHHHHHh---hhcCCC
Q 026384 44 DEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPAAVS-QYANVMK---TVREK-ADLFSESQRIAYTIET---RTAGIP 115 (239)
Q Consensus 44 dd~lK~iF~~vqkkF~~~l~~lkk~kI~idp~DpaAVk-~YA~~~~---~~r~k-~gl~s~~e~I~~tie~---~~~~~~ 115 (239)
.+-...-|..++..-+.+...|.. .|| +..||. .|..+.. .+..+ -+|-.--..+..+|.+ +...-+
T Consensus 443 p~~y~~~~~~~~~~i~~l~~~L~~--g~V---Nm~ai~~e~~e~~~~~~~L~~q~~dL~~~a~~lE~~Iqy~nRfr~~~~ 517 (569)
T PRK04778 443 PEDYLEMFFEVSDEIEALAEELEE--KPI---NMEAVNRLLEEATEDVETLEEETEELVENATLTEQLIQYANRYRSDNE 517 (569)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcc--CCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCH
Confidence 344567788999999999998886 345 466777 7765532 22222 2222222333333333 337889
Q ss_pred cHHHHHHHHHHHHHcCCCchhhhHHHHHHHHHHHH
Q 026384 116 DARTYLLTLKEIRERGLIDEHGAEAMMMDALEKVE 150 (239)
Q Consensus 116 dvR~yL~~l~EiR~~Gl~D~~g~~a~mm~ALdkvE 150 (239)
.|..-+..+..+=.-| ++..+-..+-.||++||
T Consensus 518 ~V~~~f~~Ae~lF~~~--~Y~~al~~~~~alE~ve 550 (569)
T PRK04778 518 EVAEALNEAERLFREY--DYKAALEIIATALEKVE 550 (569)
T ss_pred HHHHHHHHHHHHHHhC--ChHHHHHHHHHHHHhhC
Confidence 9999999888766778 99999998999999987
No 44
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=22.78 E-value=81 Score=19.83 Aligned_cols=19 Identities=26% Similarity=0.457 Sum_probs=15.7
Q ss_pred cccCCCCHHHHHHHHHHHH
Q 026384 70 ITIAPEDPAAVSQYANVMK 88 (239)
Q Consensus 70 I~idp~DpaAVk~YA~~~~ 88 (239)
|.++|+++.|+-.|+....
T Consensus 6 ie~~P~n~~a~~nla~~~~ 24 (34)
T PF13431_consen 6 IELNPNNAEAYNNLANLYL 24 (34)
T ss_pred HHHCCCCHHHHHHHHHHHH
Confidence 5689999999999997543
No 45
>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=22.70 E-value=96 Score=28.40 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=26.3
Q ss_pred cccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 026384 68 EKITIAPEDP---AAVSQYANVMKTVREKADLFSE 99 (239)
Q Consensus 68 ~kI~idp~Dp---aAVk~YA~~~~~~r~k~gl~s~ 99 (239)
.-++|||+++ +.|..=|..++.+-..+||.|.
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 6788888889999999999874
No 46
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.45 E-value=2.9e+02 Score=26.15 Aligned_cols=71 Identities=15% Similarity=0.184 Sum_probs=50.7
Q ss_pred CcchHHHHHHHHHHHHHHHHHHh--chhccccccCCCCHHHHHHHHHHHHHHHHhcCCCC---------hHHHHHHHHHh
Q 026384 41 LKGDEMLKNIFLDVKKKFETALG--VLRKEKITIAPEDPAAVSQYANVMKTVREKADLFS---------ESQRIAYTIET 109 (239)
Q Consensus 41 ~kGdd~lK~iF~~vqkkF~~~l~--~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s---------~~e~I~~tie~ 109 (239)
+.|..+-+.|..++++..+.+-. .-++.-|.+- ||..|-..|.+.....-+++||.+ .++.+...|+.
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 56788888888888888777542 2333334443 666678899999999999999876 35566677777
Q ss_pred hhc
Q 026384 110 RTA 112 (239)
Q Consensus 110 ~~~ 112 (239)
.-+
T Consensus 86 lN~ 88 (301)
T PRK14194 86 LNA 88 (301)
T ss_pred HcC
Confidence 644
No 47
>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=22.22 E-value=99 Score=28.63 Aligned_cols=32 Identities=16% Similarity=0.155 Sum_probs=26.4
Q ss_pred cccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 026384 68 EKITIAPEDP---AAVSQYANVMKTVREKADLFSE 99 (239)
Q Consensus 68 ~kI~idp~Dp---aAVk~YA~~~~~~r~k~gl~s~ 99 (239)
.-++|||+++ +.|.+=|..++.+-.++||.|.
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 5788888889999999999874
No 48
>PRK08045 cystathionine gamma-synthase; Provisional
Probab=22.01 E-value=37 Score=31.90 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=23.1
Q ss_pred HH-HcCCCchhhhHHHHHHHHHHHHH
Q 026384 127 IR-ERGLIDEHGAEAMMMDALEKVEK 151 (239)
Q Consensus 127 iR-~~Gl~D~~g~~a~mm~ALdkvEK 151 (239)
+| +.||||.+..-+-+.+||+++||
T Consensus 360 iR~svGlE~~~dl~~dl~~al~~~~~ 385 (386)
T PRK08045 360 LRISTGIEDGEDLIADLENGFRAANK 385 (386)
T ss_pred EEEEeCcCCHHHHHHHHHHHHHHhhc
Confidence 67 88999999999999999999987
No 49
>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=21.80 E-value=1e+02 Score=28.29 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=26.0
Q ss_pred ccccCCCCH---HHHHHHHHHHHHHHHhcCCCCh
Q 026384 69 KITIAPEDP---AAVSQYANVMKTVREKADLFSE 99 (239)
Q Consensus 69 kI~idp~Dp---aAVk~YA~~~~~~r~k~gl~s~ 99 (239)
-++|||++. +.|.+=|..++.+-.++||.|.
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 50
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=21.75 E-value=5.2e+02 Score=22.23 Aligned_cols=72 Identities=14% Similarity=0.290 Sum_probs=42.8
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHHHHH-HcC---CCchhhhHHHHHHHH
Q 026384 71 TIAPEDPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLKEIR-ERG---LIDEHGAEAMMMDAL 146 (239)
Q Consensus 71 ~idp~DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~l~EiR-~~G---l~D~~g~~a~mm~AL 146 (239)
.|+.--+...+.|... -.+.+.-|-++..+.+...++.... -+..+| -.+ =..+.++-.+|-+.+
T Consensus 73 ~LGg~p~~t~~~~~~~-s~ike~~~~~~~~~~l~~l~~~~~~----------l~~~~r~~~~~a~e~gD~~Tadl~~~~~ 141 (156)
T COG0783 73 ALGGVPLGTLSEYLKL-SSIKEEPGDYTAREMLKELVEDYEY----------LIKELRKGIELADEAGDEVTADLLTDII 141 (156)
T ss_pred HcCCCCcccHHHHHHh-CCCcccCCCCCHHHHHHHHHHHHHH----------HHHHHHHHHHhhhhcCChhHHHHHHHHH
Confidence 5653333466666633 2344444447888888877765433 233333 222 234667888899999
Q ss_pred HHHHHhh
Q 026384 147 EKVEKEI 153 (239)
Q Consensus 147 dkvEK~i 153 (239)
.++||.+
T Consensus 142 ~~~EK~~ 148 (156)
T COG0783 142 RELEKTL 148 (156)
T ss_pred HHHHHHH
Confidence 9999864
No 51
>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]
Probab=21.60 E-value=8.6e+02 Score=26.84 Aligned_cols=69 Identities=23% Similarity=0.371 Sum_probs=43.1
Q ss_pred HHHHhhCCccccccHhhHH--HHHHHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 026384 148 KVEKEIKKPLMRNDKKGMA--LLTAEFDKINKKLGIRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKKR 219 (239)
Q Consensus 148 kvEK~igkpL~rsDkkGM~--~L~ae~~kinKklGi~~eDl~K~eee~ele~aK~ql~elK~~a~e~m~~~kkr 219 (239)
++--+|+|++=...++--. +|..++-.|.++||+.+.|...+.+...= ..+. ..+=..++.-++.-.+|
T Consensus 296 klq~ki~k~vE~k~~~~~r~ylL~eQlk~IKkeLg~e~Ddkd~~~~~~~e-r~~~--~~~P~~v~kv~~eEl~k 366 (906)
T KOG2004|consen 296 KLQQKIGKEVEEKIKQDHREYLLREQLKAIKKELGIEKDDKDALVEKFRE-RIKS--LKMPDHVLKVIDEELTK 366 (906)
T ss_pred HHHHHhhhHHHhhhhHHHHHHHHHHHHHHHHHhhCCCccchhhHHHHHHH-Hhhh--ccCcHHHHHHHHHHHHH
Confidence 4445677777666666555 78889999999999998887655443321 1111 34444555555555444
No 52
>PRK14041 oxaloacetate decarboxylase; Provisional
Probab=20.95 E-value=2.4e+02 Score=28.18 Aligned_cols=82 Identities=18% Similarity=0.327 Sum_probs=49.0
Q ss_pred hhhhhhhhhhHHHHhhccc-------hhHHhhhhh--cCCccCcchHHHHHHHHHHHHHHHHHHhchhccccccCCCCHH
Q 026384 8 ASKSKQLCSSQVILQRQHA-------ISVRFFANE--AAPQALKGDEMLKNIFLDVKKKFETALGVLRKEKITIAPEDPA 78 (239)
Q Consensus 8 ~srs~~~~~~~~~~~~~~~-------~~vR~fA~~--Aap~~~kGdd~lK~iF~~vqkkF~~~l~~lkk~kI~idp~Dpa 78 (239)
+-=|+|++|.||.+|.=.+ -.|+.|... ..||+.-..++.+.|. +. ...|+..|+|.-
T Consensus 336 VTP~Sq~vg~~A~~Nvl~g~r~~~~~~~~~~~~~G~~G~~p~~~~~~~~~~il-----------~~--~~~~~~rp~~~~ 402 (467)
T PRK14041 336 VTPTSQIVGVQAVLNVLTGERYKRVTNETKNYVKGLYGRPPAPIDEELMKKIL-----------GD--EKPIDCRPADLL 402 (467)
T ss_pred CCChhHHHHHHHHHhhcChhheeeCCHHHHHHhCcCCCCCCCCCCHHHHHHHh-----------CC--CCCCcCChhhcc
Confidence 3457899999999874322 346777775 5666444455666552 21 124555565432
Q ss_pred HHHHHHHHHHHHHHhcC--CCChHHHHHHHH
Q 026384 79 AVSQYANVMKTVREKAD--LFSESQRIAYTI 107 (239)
Q Consensus 79 AVk~YA~~~~~~r~k~g--l~s~~e~I~~ti 107 (239)
......+|+++| ..++++.+.|.+
T Consensus 403 -----~p~~~~~~~~~~~~~~~~e~~l~y~~ 428 (467)
T PRK14041 403 -----EPELEKARKELGILAETDEDLLIYVI 428 (467)
T ss_pred -----CchHHHHHHHhcccCCCHHHHHHHHc
Confidence 223456777776 567777777766
No 53
>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=20.29 E-value=46 Score=27.82 Aligned_cols=67 Identities=15% Similarity=0.168 Sum_probs=42.6
Q ss_pred HHHHHHhchhccccccCCC-----CHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHhhhcCCCcHHHHHHHHH
Q 026384 57 KFETALGVLRKEKITIAPE-----DPAAVSQYANVMKTVREKADLFSESQRIAYTIETRTAGIPDARTYLLTLK 125 (239)
Q Consensus 57 kF~~~l~~lkk~kI~idp~-----DpaAVk~YA~~~~~~r~k~gl~s~~e~I~~tie~~~~~~~dvR~yL~~l~ 125 (239)
-|..++.+|.|. .++|. =.+.|.=.|--+.|+.+..|+|.|=|++++.-.+..-+..+.+.|.+.+.
T Consensus 26 A~~s~lkGl~Kl--~vn~~~l~~dL~~nWeVlaEpIQTvmRr~g~~~pYE~LK~lTRg~~it~~~l~~fI~~L~ 97 (115)
T PF08328_consen 26 AYKSLLKGLGKL--EVNEERLAEDLDENWEVLAEPIQTVMRRYGIPNPYEKLKELTRGKKITKEDLREFIESLD 97 (115)
T ss_dssp HHHHHHHHHHTE--EE-HHHHHHHHCT-GGGGHHHHHHHHHHTT-SSHHHHHHHHHTTS---HHHHHHHHHTSS
T ss_pred HHHHHHHHHhcc--cCCHHHHHHHHHHCHHHHHHHHHHHHHHcCCCCHHHHHHHHHcCCCCCHHHHHHHHHhCC
Confidence 355566666643 34320 01133334566889999999999999999999888888888888877654
No 54
>cd08643 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5
Probab=20.28 E-value=1.6e+02 Score=29.07 Aligned_cols=117 Identities=17% Similarity=0.147 Sum_probs=82.0
Q ss_pred HHHHHhhhcCCCcHHHHHHHHHHHH-HcCCCchhhhHHHHHHHHHHHHHhhCCccccccHhhHHHHHHHHHHHHHHcC--
Q 026384 104 AYTIETRTAGIPDARTYLLTLKEIR-ERGLIDEHGAEAMMMDALEKVEKEIKKPLMRNDKKGMALLTAEFDKINKKLG-- 180 (239)
Q Consensus 104 ~~tie~~~~~~~dvR~yL~~l~EiR-~~Gl~D~~g~~a~mm~ALdkvEK~igkpL~rsDkkGM~~L~ae~~kinKklG-- 180 (239)
...++.++...|.++.|.+.+.+.- +.|..........-. ...=..++.|+=-+=+-=|+..+-.+...-.+.|
T Consensus 291 ~~~~~~f~~~~P~v~~~~~~~~~~a~~~Gyv~tl~GRrr~~---~~~r~A~Nt~iQGsAADi~K~Ami~i~~~l~~~g~~ 367 (429)
T cd08643 291 RVVRANFLKGLPALGKLIKKVKEAAKKRGHLVGLDGRRIRV---RSAHAALNTLLQSAGAILMKKWLVLLDDELTAKGGV 367 (429)
T ss_pred HHHHHHHHHhCccHHHHHHHHHHHHHhCCceeCCCCCcccC---chHHHHhChhhhhHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3467888899999999999999887 667554433322111 1234578888888877788888888877766665
Q ss_pred --CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 026384 181 --IRKEDLPKYEEQLELKIAKAQLEELKKDALEAMETQKKREEFK 223 (239)
Q Consensus 181 --i~~eDl~K~eee~ele~aK~ql~elK~~a~e~m~~~kkree~k 223 (239)
.+..-+--+--|+.++.-+.+.++..+-+.++|+..-+.-.|.
T Consensus 368 ~~~~~~lvlqVHDElv~ev~~~~ae~v~~~v~~~Me~a~~~~~l~ 412 (429)
T cd08643 368 WGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAGEHFNFR 412 (429)
T ss_pred cCCCeEEEEEEccceEEEeCHHHHHHHHHHHHHHHHHhhhccCCC
Confidence 3333334456677778888899999999999999986443343
No 55
>PRK14186 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.16 E-value=3.4e+02 Score=25.62 Aligned_cols=71 Identities=15% Similarity=0.165 Sum_probs=50.7
Q ss_pred CcchHHHHHHHHHHHHHHHHHH---hchhccccccCCCCHHHHHHHHHHHHHHHHhcCCCCh---------HHHHHHHHH
Q 026384 41 LKGDEMLKNIFLDVKKKFETAL---GVLRKEKITIAPEDPAAVSQYANVMKTVREKADLFSE---------SQRIAYTIE 108 (239)
Q Consensus 41 ~kGdd~lK~iF~~vqkkF~~~l---~~lkk~kI~idp~DpaAVk~YA~~~~~~r~k~gl~s~---------~e~I~~tie 108 (239)
+.|..+-..|-.++++..+.+. +...+.-|.+- ||..|-..|.+.....-+++||.+. ++.+...|+
T Consensus 5 ldGk~iA~~i~~~lk~~v~~l~~~~g~~p~LaiI~v-gdd~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~ 83 (297)
T PRK14186 5 LDGKALAAEIEQRLQAQIESNLPKAGRPPGLAVLRV-GDDPASAVYVRNKEKACARVGIASFGKHLPADTSQAEVEALIA 83 (297)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEEe-CCChHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHH
Confidence 5677778888888888887754 33344445554 5666778999999999999999773 455667777
Q ss_pred hhhc
Q 026384 109 TRTA 112 (239)
Q Consensus 109 ~~~~ 112 (239)
..-+
T Consensus 84 ~lN~ 87 (297)
T PRK14186 84 QLNQ 87 (297)
T ss_pred HHhC
Confidence 6644
Done!