Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012040994.1 BBTA_RS03150 acyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000015165.1:WP_012040994.1 Length = 538 Score = 424 bits (1091), Expect = e-123 Identities = 238/542 (43%), Positives = 326/542 (60%), Gaps = 13/542 (2%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M+II + I P FQAN L +R+ A+ R A + R H+ RG+L R+R+ Sbjct: 1 MAIIDNTISPTGAAFQANRDGMLGLIGRMRDLEARTRNASAAAKDRFHQ-RGQLLPRERV 59 Query: 61 DTLIDPDSSFLEIGALAAYNVYD-----EEVPAAGIVCGIGRVAGRPVMIIANDATVKGG 115 ++DP + FLE+ LA Y ++D + VP G+V GIG V+G M+ ANDA + G Sbjct: 60 ALVLDPGAPFLELSTLAGY-MFDVPDPAKSVPGGGVVAGIGFVSGVRCMVSANDAGIDAG 118 Query: 116 TYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSA 175 P + K LR QE+A EN+LP + LV+S GA L L+ V D G IF N A++SA Sbjct: 119 ALQPYGLDKTLRVQELALENKLPYVQLVESAGANL-LRYRV-EDFVRGGNIFRNLARLSA 176 Query: 176 EGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGA 235 G+P + GS TAGGAY +SD +V+V+G FL GPPL+KAATGE T EELGGA Sbjct: 177 AGLPVVTVTHGSSTAGGAYQTGLSDYIVMVRGRTRAFLAGPPLLKAATGEIATEEELGGA 236 Query: 236 DVHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPR 295 ++HT +SG+ DY A DDR+AL I R+I+ L R + + +PPRYD E+ GI+P Sbjct: 237 EMHTSVSGLGDYLAEDDRDALRIAREIMGKLN-WDRPSRDATTAKPPRYDQEELLGIMPL 295 Query: 296 DFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALK 355 D ++ D+R+VIARIVD S E YG VCG A IEG +GI+ NNG L A K Sbjct: 296 DHKRPVDMRQVIARIVDDSDFVEMSPNYGPATVCGHARIEGQAIGIVTNNGPLDPAGANK 355 Query: 356 GAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGG 415 HFI+ CC P+++L N TG++VG+ YE G+ K G+K++ AV+ A VP+ T+ G Sbjct: 356 ATHFIQACCQTRTPILYLNNTTGYIVGRAYEEAGMIKHGSKMIQAVTSATVPQITIYCGA 415 Query: 416 SFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQE 475 SFGAGNYGMCGR + PR + WPNA+ +VMGG QAA + + RG+ + E+ + Sbjct: 416 SFGAGNYGMCGRGFHPRFCFSWPNAKTAVMGGEQAAETMAIVTEAAAARRGKPVEREKLD 475 Query: 476 RFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPV---QPTRFGV 532 A I++ ++ + + SAR+ DDGVIDP +TR VL+ LA EA Q +F V Sbjct: 476 AMKAQIVSVFDSQMDVFATSARVLDDGVIDPRDTRAVLSEVLAICREAEAREPQRMQFSV 535 Query: 533 FR 534 R Sbjct: 536 AR 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: 732 Number of extensions: 34 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