Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate HSERO_RS04625 HSERO_RS04625 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__HerbieS:HSERO_RS04625 Length = 556 Score = 295 bits (754), Expect = 4e-84 Identities = 194/553 (35%), Positives = 289/553 (52%), Gaps = 14/553 (2%) Query: 17 NYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRD-EKYT 75 +Y + Y F + F +NA E DRH + + +AL + + ++Y+ Sbjct: 12 DYADVYAGFRIETLREQFQGDFETGINACVECCDRHVKG---DNIALEFVSLHGEHQQYS 68 Query: 76 FKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFME 135 F +++ + R N+LR+ G ++ G V +PR+PEL +LG ++ GA+ PLF AF Sbjct: 69 FAQVRSMAARVANLLRQQG-IQPGQIVAGMLPRTPELLATVLGTLRAGAVYQPLFTAFGP 127 Query: 136 GAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAES-GTNIINYDEAAKQE 194 A++ RL S A ++VT + R +D++ + V V + I++ A + Sbjct: 128 KAIEHRLALSGASLIVTN--VANRDKLDEIANCPQVCTVRESNDPLRAGDIDFRAAVDAQ 185 Query: 195 STRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWCTA 254 S D L+ TSG+TG KGV A+ + + L +D +W A Sbjct: 186 SDDFAPVLRSGADLMLMMSTSGTTGAAKGVPVPLSALQAFSVYMREAVGLLPQDKFWNMA 245 Query: 255 DPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAG 314 DPGW G Y I P G F+ Y TI +LG+ APTA+RM+M AG Sbjct: 246 DPGWAYGLYYAIIGPLAIGHGITFNEAAFTVSGTYETIRRLGITSLAGAPTAYRMMMAAG 305 Query: 315 DEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCM-- 372 +E AA LR V S GEPLN EV+RW + IHD + TE G ++ N+ + Sbjct: 306 EEAAASVK-GRLRAVSSAGEPLNAEVVRWFASALDVPIHDHYGQTELG-MVVNNHHALRH 363 Query: 373 DIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMP 432 ++ PGS G +PG ++D EL + G LAI + ++ K ++ + Sbjct: 364 EVVPGSAGFAMPGYRVVVLDENHQELGANQPGELAIDIARSPLYW--FSGYWKQDTPAIA 421 Query: 433 GGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPD 492 G+Y +GD+ ++ G F GR DDVI ++G R+GPF+VES L+EHPA+A+ VIG PD Sbjct: 422 HGYYSTGDNVELEPNGSISFIGRSDDVITSAGYRIGPFDVESALLEHPAVADVAVIGLPD 481 Query: 493 PVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMR 552 P R EI+KAF+ L + F+ SD L+E++ VK+ L+AHA PR IEF D LPKT SGK+ R Sbjct: 482 PERTEIVKAFVVLSDQFKASDALREQLAQHVKRRLSAHAYPRAIEFLDALPKTPSGKLQR 541 Query: 553 RVLKAWELNLPAG 565 VL+ E + AG Sbjct: 542 FVLRKMEADRRAG 554 Lambda K H 0.318 0.136 0.425 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 784 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 572 Length of database: 556 Length adjustment: 36 Effective length of query: 536 Effective length of database: 520 Effective search space: 278720 Effective search space used: 278720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory