Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate AO353_19320 AO353_19320 acetyl-CoA carboxylase carboxyltransferase subunit
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19320 Length = 538 Score = 425 bits (1092), Expect = e-123 Identities = 233/544 (42%), Positives = 323/544 (59%), Gaps = 30/544 (5%) Query: 13 PDFQANFAYHQSLAADLRE----RLAQIRQ------GGGAEQRRRHEERGKLFVRDRIDT 62 P ++ H A RE + Q RQ AE + + ++RG+L R R++ Sbjct: 2 PQIESQLDIHSRQFAQNREAMLSNIEQFRQLERNLLAKAAEAKPKFDKRGQLLPRARLNL 61 Query: 63 LIDPDSSFLEIGALAAYNVYDEE---VPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFP 119 L+DP + FLE+ +LA Y ++D++ G++ GIG V+G V+++AN++ +KGGT P Sbjct: 62 LLDPGAPFLELASLAGYKLHDDKDGSQAGGGLIAGIGYVSGVRVLVVANNSAIKGGTISP 121 Query: 120 LTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIP 179 +KK LR Q+IA EN+LP I L +SGGA L +E+F + R F NQA+MSA G+P Sbjct: 122 SGLKKSLRLQQIAMENKLPVITLAESGGANLNYAAEIFVEG---ARSFANQARMSAMGLP 178 Query: 180 QIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHT 239 QI V GS TAGGAY P +SD VV+V+G +FL GPPL+KAATGE T EELGGA++H Sbjct: 179 QITVVHGSATAGGAYQPGLSDYVVVVRGKAKLFLAGPPLLKAATGEVATDEELGGAEMHA 238 Query: 240 RISGVADYFANDDREALAIVRDIV------AHLGPRQRANWELRDPEPPRYDPREIYGIL 293 +I+G A+Y A +D + + +VR+IV A L R +W+ P Y ++ G++ Sbjct: 239 QIAGTAEYLAENDADGVRLVREIVSLLPWNAQLPQRSAEHWD-----EPLYPIDDLLGLI 293 Query: 294 PRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESA 353 P D ++ YDVRE+IARI DGSR EFK + +CG I+G P G + NNG + + A Sbjct: 294 PDDPKKPYDVREIIARIADGSRFLEFKGEFDQQTMCGHLKIQGRPCGFIGNNGPITPQGA 353 Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413 K A FI+LC PL+F N TGFMVG + E G+ K GAK++ AV+ A VPK T+++ Sbjct: 354 SKAAQFIQLCDQSQTPLLFFHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTMVV 413 Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473 GGS+GAGNY MCGR PR ++ WPN+R +VMGG QA VL + G P+ Sbjct: 414 GGSYGAGNYAMCGRGLDPRFIFAWPNSRTAVMGGAQAGKVLRIVSEARQAKDGLVPDPKM 473 Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPV---QPTRF 530 + K + + Y SA LWDDG+IDP +TR +L L EA V QP F Sbjct: 474 LDTLEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGYLLDICHEAEVRQLQPNSF 533 Query: 531 GVFR 534 G+ R Sbjct: 534 GIAR 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: 771 Number of extensions: 44 Number of successful extensions: 4 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 17 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