Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_090448441.1 BLS63_RS24635 hypothetical protein
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_900100495.1:WP_090448441.1 Length = 521 Score = 152 bits (385), Expect = 2e-41 Identities = 111/364 (30%), Positives = 182/364 (50%), Gaps = 23/364 (6%) Query: 211 YSSGTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALV 270 Y+SGT+GLPKGV ++ NV + +N T+ S +V L LP +H+ A Sbjct: 161 YTSGTTGLPKGVRLTSENVFKGPMTAL---ENRGISPCTEIGSKDVILLCLPHAHV-AGS 216 Query: 271 VIGHAGAYRGDQTIVLPKFELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSS 330 ++G G G + I+ F ++ I++ +++ +VP ++ ++ + S Sbjct: 217 ILGIYGLVMGAKLIICRDFVPADIVSTIEREQVTLTLMVPVMVRGLIAAMEKTG-IACKS 275 Query: 331 VTSLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHD---IWLG----- 382 + ++ GAAP+ D +K P+ Q YGLTET V+ P D I G Sbjct: 276 LKTILYGAAPMATSLLKDAMKALPHSGFGQIYGLTETSGPVTFLTPDDHRSIAAGNNDLA 335 Query: 383 -SSGALLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFVDGWMRT 441 S G+ GVE +++ + + GE++ RSP ++ GY N + T DGW T Sbjct: 336 LSCGSATAGVELQVINHYGQPVPP-GGIGEIICRSPQIMKGYWNRTEDTLSAIQDGWFYT 394 Query: 442 GDEAVIRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDR 501 GD I KG +V+I DR +++I G V PAE+E + HP ++D A+I +PD + Sbjct: 395 GDVGYI--DDKG--YVYIYDRKRDMIITGGENVYPAEVENVLYEHPAIADVAIIGVPDAQ 450 Query: 502 AGEVPKAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRR 561 GE KA+ V A ++ L+ Y + A K + + FV+ +P++ +GK+LRR Sbjct: 451 WGEAVKAVAVLKPGAVLS---AEDLIAYAKGKIAGFK-IPKSVDFVEELPRNATGKVLRR 506 Query: 562 LIRD 565 LIR+ Sbjct: 507 LIRE 510 Lambda K H 0.316 0.134 0.392 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: 654 Number of extensions: 32 Number of successful extensions: 6 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: 578 Length of database: 521 Length adjustment: 36 Effective length of query: 542 Effective length of database: 485 Effective search space: 262870 Effective search space used: 262870 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 (21.6 bits) S2: 53 (25.0 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