Align propionyl-CoA carboxylase (EC 6.4.1.3) (characterized)
to candidate WP_013075719.1 BTUS_RS08590 acyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-16260 (572 letters) >NCBI__GCF_000092905.1:WP_013075719.1 Length = 509 Score = 521 bits (1342), Expect = e-152 Identities = 261/510 (51%), Positives = 349/510 (68%), Gaps = 4/510 (0%) Query: 64 EREEALREEIAEILEGGPEKYKEQLPEEGKLFVRDRIDLWFGDDFLF-EDGKFAEFDADD 122 ERE+ + E I GGP + ++ E GK FVRDR+ L+F D + E G+FA + D+ Sbjct: 3 EREQRVIRERQRIQRGGPPRGHQKQAEAGKKFVRDRLALFFDDQEPYTEFGQFARWP-DE 61 Query: 123 QLPADGLITGAAEFEGRDLHFMANDYTVKRGSMAAKGVEKFLRMQQRALKTGRPVLYLMD 182 +LP DG++TG +GR + F AND+TVK GS+ EK +R Q+ AL+ +P+LYL+D Sbjct: 62 ELPGDGVVTGTGRIDGRTVFFAANDFTVKAGSIGRYHGEKLVRAQEAALRARKPMLYLVD 121 Query: 183 SSGGRIDQQTGFFANREGIGKFYYNHSMLSGRVPQICVLYGPCIAGAAYTPVFADFTVMV 242 SSG RID+ G ++ G+ +Y HS++SG VPQ+ VLYG C AG AYTPVF D VM+ Sbjct: 122 SSGARIDETGGHHVDKGSAGRLFYMHSIMSGSVPQVGVLYGTCFAGTAYTPVFTDLLVMM 181 Query: 243 RDMSAMAIASPRMVEMVTGEEISLEELGGPDIHAQHSGSADLIADDEEHARELVAQLISY 302 +D +AMAIASPRMVEM G+++ ELGG +H ++ GSA + D EE A LV ++ SY Sbjct: 182 KD-AAMAIASPRMVEMAIGQKVGPRELGGAQVHLKN-GSAHFVVDSEEEAGALVRRIFSY 239 Query: 303 LPDNADEDPPQTSGTAPKRSPEGIDSVVPEKPNKGYDMFDVIERVVDAGSTLELRPEYGK 362 LPD+++ PP P P ID ++P PN+ YD+ +I+ VVD S LE++ Y Sbjct: 240 LPDSSENSPPPGELREPALDPAAIDEIIPADPNRPYDVHRLIDAVVDRDSFLEVKAGYAD 299 Query: 363 EIITSFARIDGRPIGVIANQPAQRAGAIFPDAAEKAAQFIWTCDAYNIPLLYLCDTPGFM 422 E++T FAR+ GR IGV+ANQPA + G +FP++++K A+F+W CDAYNIPLL+L DTPGFM Sbjct: 300 ELVTGFARLGGRVIGVVANQPAVKGGTLFPESSDKGAEFVWMCDAYNIPLLFLVDTPGFM 359 Query: 423 AGSGVEKEGILEQGKKMIYATSSATVPKQSVVVRKAYGAGIYAMSGPAYDPESTIGLPSG 482 G+ VEK IL +G+K I+ATS ATVP+ VVVRKAYGAGIYAMSGPAYDPE T+ LPS Sbjct: 360 VGTAVEKNAILRRGRKFIFATSCATVPRICVVVRKAYGAGIYAMSGPAYDPELTLALPSA 419 Query: 483 EIAIMGPEAAINAVYARKLSEIDDEDERQQKEQELREAYREDIDIHRMASEVVVDDIVPP 542 EIA+MGPEAAINAVY KL ++D ER + LRE YR DI ++A ++VVD+++PP Sbjct: 420 EIAVMGPEAAINAVYFNKLQAVEDPVERDRLVARLREEYRAGYDIFKLAGQMVVDELIPP 479 Query: 543 SDLRTELTNRFAFYETVEKDLPDKKHGTIL 572 +LR EL F Y + LP +KH TIL Sbjct: 480 RELRNELLRYFEIYADKKISLPPRKHATIL 509 Lambda K H 0.315 0.135 0.385 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: 851 Number of extensions: 49 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: 572 Length of database: 509 Length adjustment: 35 Effective length of query: 537 Effective length of database: 474 Effective search space: 254538 Effective search space used: 254538 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: 42 (22.0 bits) S2: 52 (24.6 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