Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013421126.1 RVAN_RS18025 acetate--CoA ligase
Query= BRENDA::D6EQU8 (658 letters) >NCBI__GCF_000166055.1:WP_013421126.1 Length = 686 Score = 236 bits (602), Expect = 3e-66 Identities = 186/628 (29%), Positives = 282/628 (44%), Gaps = 35/628 (5%) Query: 15 QRIAQARITRFQAWAAEHHGAPAE---------GGYAALHRWSVDELDTFWKAVTEWFD- 64 QRIA + R Q +E + P E Y L+RWS+++ D FWK + D Sbjct: 21 QRIANIQSMR-QMVQSEVYPVPPEFAARAHVDAAAYERLYRWSIEDPDGFWKKEAAFLDW 79 Query: 65 VRFSTPYARVLGDRTMPGAQWFPGATLNYAEHAL-RAAGTRPDEPALLYVDETH-EPAPV 122 ++ T + D +WF TLN + + + R + D+PA+ + +T E V Sbjct: 80 IKPFTEVSDTSFDVNNFRVRWFADGTLNGSVNCIDRHLAAKADKPAVFWEGDTPGESRVV 139 Query: 123 TWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGA 182 TW EL +V LA L++LGV GD V+ YLP IP+ +VA++AT +G V T F A Sbjct: 140 TWGELADKVNRLANVLKSLGVGKGDVVAIYLPVIPEVMVAMMATIRIGAVHTVVFSGFSA 199 Query: 183 RSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAP-- 240 S+ +R + VL T D GG+ + + R P++ VI + G E P Sbjct: 200 ESLENRIADSKAKVLITADEGFRGGRISPLKRNADDAVRNQPSIEHVIVVRRSGAEVPFT 259 Query: 241 DGTLDW--ETLTAAD--AEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQ 296 G W E AAD EPV +V + PL++LY+SG+TG PK +V + G LV Sbjct: 260 PGRDLWYDEATEAADPWCEPV--EVGAEDPLFILYTSGSTGKPKGLVHTTAGYLVHAGTS 317 Query: 297 LGLHCDLGPGDRFFWYTSTGWMMWNF--LVSGLLTGTTIVLYDGSPGFPATDAQWRIAER 354 + D GD F+ GW+ + L LL G T V+++G P +P W I E+ Sbjct: 318 WRIIFDWHEGDVFWSTADVGWVTAHSYKLYGPLLNGATTVMFEGVPSWPDASRWWSIIEK 377 Query: 355 TGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGAD 414 +F T+ + + + G P R DLS+++ + + G P+ P+ +RW H G Sbjct: 378 HRVNIFYTAPTALRSLMREGEAPVRKHDLSSLRVLGSVGEPINPEAWRWFHSVIGGGRCP 437 Query: 415 L----WIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEV-GE 469 + W T V GA+P P G P G + P G L G Sbjct: 438 IVDNYWQTETGAVTLV--PIPGAIPNKP---GMAAKPYFGIRPEVVSPEGVTLEGPAEGN 492 Query: 470 LVVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLN 529 + P +D + R+ +YF +PG + GD +T G I GR D +N Sbjct: 493 MCFRGSWPGQARTILHDHE--RFLKTYFAPFPGRFFSGDGVTRDEDGYYRIAGRVDDVIN 550 Query: 530 RQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKR 589 G R+G+ ++ A+ P + E+ V+G G + +V L + L I++ Sbjct: 551 VSGHRLGTVELESAIASHPAVAEAAVVGYNHDVKGQGVFAYVTLKADMPETEELRAEIRQ 610 Query: 590 TIRVNLSPRHVPDEVIEVPGIPHTLTGK 617 +R +SP PD V P +P GK Sbjct: 611 WVRARISPIASPDIVQWAPALPKNRAGK 638 Lambda K H 0.320 0.138 0.442 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: 1345 Number of extensions: 76 Number of successful extensions: 5 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: 658 Length of database: 686 Length adjustment: 39 Effective length of query: 619 Effective length of database: 647 Effective search space: 400493 Effective search space used: 400493 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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