Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011781994.1 MVAN_RS24360 acyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000015305.1:WP_011781994.1 Length = 549 Score = 482 bits (1240), Expect = e-140 Identities = 266/541 (49%), Positives = 344/541 (63%), Gaps = 18/541 (3%) Query: 2 SIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRID 61 SI+ + I SP F + A+L + GGG + RH RGK+ R+RI+ Sbjct: 20 SILQTAIDTASPAFLEAAEVMTAKLAELEAEHTKALAGGGEKYVARHHARGKMTARERIE 79 Query: 62 TLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLT 121 L+DPDS FLE+ LAA+ + A IV GIG V+G +++AND TVKGGT P T Sbjct: 80 ALLDPDSPFLELSPLAAWGT--DFTVGASIVVGIGAVSGVECLLVANDPTVKGGTSNPWT 137 Query: 122 VKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQI 181 ++K LRA +IA +NRLP I LV+SGGA LP Q E+F G++F + ++SA GIP I Sbjct: 138 LRKILRANQIALQNRLPVISLVESGGADLPTQKEIFIPG---GQMFRDLTRLSAAGIPTI 194 Query: 182 ACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRI 241 A V G+ TAGGAY+P MSD VV+++ +FL GPPLVK ATGEE E LGGA++H R Sbjct: 195 ALVFGNSTAGGAYIPGMSDHVVMIRERSKVFLAGPPLVKMATGEESDDESLGGAEMHART 254 Query: 242 SGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEP-----PRYDPREIYGILPRD 296 SG+ADYFA D+ +AL I R IVA L NW + P P PRYD E+ G++P D Sbjct: 255 SGLADYFAVDELDALRIGRRIVARL------NWRKQGPAPRPVVVPRYDENELIGVVPPD 308 Query: 297 FRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILAN-NGILFSESALK 355 R +D REVIARIVDGS EFK YG +LV G+A + G+P+GILAN G+LFS + K Sbjct: 309 LRIPFDPREVIARIVDGSEFDEFKPLYGGSLVTGWATLHGYPLGILANARGVLFSAESQK 368 Query: 356 GAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGG 415 FI+L N PL+FL N TG+MVGK YE GG+ K GA ++ AVS + VP +++IG Sbjct: 369 ATQFIQLANRSNTPLLFLHNTTGYMVGKDYEEGGMIKHGAMMINAVSNSTVPHISLLIGA 428 Query: 416 SFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQE 475 S+GAG+YGMCGRAY PR L+ WP+A+ +VMGGTQ A VL + R ARG + Sbjct: 429 SYGAGHYGMCGRAYDPRFLFAWPSAKSAVMGGTQLAGVLSIVNRAATEARGGQVDEAADA 488 Query: 476 RFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPT-RFGVFR 534 A + A+ E E P + S RL+DDGVIDP +TR VL + L+A A P++ T FGVFR Sbjct: 489 ALRAAVEAQIEAESLPMFLSGRLYDDGVIDPRDTRTVLGMCLSAIANGPIEGTSNFGVFR 548 Query: 535 M 535 M Sbjct: 549 M 549 Lambda K H 0.322 0.139 0.423 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: 820 Number of extensions: 36 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: 535 Length of database: 549 Length adjustment: 35 Effective length of query: 500 Effective length of database: 514 Effective search space: 257000 Effective search space used: 257000 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 (21.9 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