Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_046007987.1 OLEAN_RS02925 acyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000967895.1:WP_046007987.1 Length = 538 Score = 407 bits (1047), Expect = e-118 Identities = 228/542 (42%), Positives = 326/542 (60%), Gaps = 13/542 (2%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQ-RRRHEERGKLFVRDR 59 M+I+ S I +S +F N A Q + R ++ + AEQ + + +RGKL R+R Sbjct: 1 MAILTSEIATHSEEFANNCAAMQIAIDEFRSVETKVLEK--AEQAKEKFRKRGKLLPRER 58 Query: 60 IDTLIDPDSSFLEIGALAAYNVYDEEVPAA---GIVCGIGRVAGRPVMIIANDATVKGGT 116 ++ L+D S+FLE+ +LA ++D++ + GI+ GIG VAG MI N++ +KGGT Sbjct: 59 LNLLLDGGSNFLELCSLAGLKMHDDKDGSGAGGGIIAGIGYVAGARCMIQVNNSAIKGGT 118 Query: 117 YFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAE 176 P + K LR QEIAR N+LP I L +SGGA L ++VF + F NQA++SA Sbjct: 119 ISPAGLDKTLRIQEIARANKLPIITLAESGGANLQYATDVFVPG---AQAFANQARLSAA 175 Query: 177 GIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGAD 236 GIPQI V G+ TAGGAY P +SD ++ V+ +FL GPPL+KAATGE T EELGGA+ Sbjct: 176 GIPQITVVHGNATAGGAYQPGLSDFIIAVRNKTKMFLAGPPLLKAATGEIATDEELGGAE 235 Query: 237 VHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDP-EPPRYDPREIYGILPR 295 +H +G ADY A DD + + I R+++A L + + E P Y+ E+ G++P Sbjct: 236 LHAYEAGTADYLAEDDADGVRIAREVMAGLPWNDQVSPRTEKVYEEPLYNADELLGVVPC 295 Query: 296 DFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALK 355 D ++ YDVREV+ARI DGS +FK + VCGF + G VGI+ NNG + ++ A K Sbjct: 296 DSKKPYDVREVVARIADGSEFQDFKPDFDIQTVCGFIKVAGHAVGIIGNNGPITAKGANK 355 Query: 356 GAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGG 415 A FI+LC + L+FL N TGFMVG + E GI K G+K++ +V+ A VPK +++IGG Sbjct: 356 AAQFIQLCDQNQVSLLFLHNTTGFMVGTESEKSGIIKHGSKMLQSVANARVPKISIVIGG 415 Query: 416 SFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQE 475 S+GAGNY MCGR PR ++ WPN++ +VMGG QA VL + + GQ + + Sbjct: 416 SYGAGNYAMCGRGLDPRFIFAWPNSKTAVMGGAQAGKVLRIVTEEKQLKMGQVPDEKMLD 475 Query: 476 RFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAP---VQPTRFGV 532 + AK E + +AR+WDDG+IDP +TR++L + L E +Q FGV Sbjct: 476 QIEQMTAAKLEAGSTALFGTARIWDDGLIDPRDTRKLLVMLLDMCDEEKHRCLQGNSFGV 535 Query: 533 FR 534 R Sbjct: 536 SR 537 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: 794 Number of extensions: 44 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: 535 Length of database: 538 Length adjustment: 35 Effective length of query: 500 Effective length of database: 503 Effective search space: 251500 Effective search space used: 251500 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