Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS32750 RR42_RS32750 acetyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__Cup4G11:RR42_RS32750 Length = 539 Score = 404 bits (1037), Expect = e-117 Identities = 236/541 (43%), Positives = 310/541 (57%), Gaps = 16/541 (2%) Query: 4 IHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63 I S I P SP F + A Q+L LR L Q R RG L R+R+ L Sbjct: 4 IESRIDPASPAFASQRAGMQALIERLRA-LEQRAVAASERARPSFARRGALLPRERLARL 62 Query: 64 IDPDSSFLEIGALAAYNV----YDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFP 119 +DP ++FL I LA Y + +D +P +V GIG V G M++A D+ + G Sbjct: 63 LDPATAFLPIANLAGYGMDDPDHDTAIPGGSLVAGIGFVRGVRAMVVATDSGIDAGAMTE 122 Query: 120 LTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHF---GRIFYNQAQMSAE 176 K +R QEIA ENRLP I+LV+S GA L D F G IFYN A++SA Sbjct: 123 GGNLKLMRCQEIALENRLPFIHLVESAGANLRKYRV-----DKFVRGGGIFYNLARLSAA 177 Query: 177 GIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGAD 236 G+P I V GS TAGGAY+P +SD VV+V+G FL GPPL+KAATGE T EELGGAD Sbjct: 178 GLPVITVVHGSSTAGGAYMPGLSDYVVMVRGRARAFLAGPPLLKAATGEIATDEELGGAD 237 Query: 237 VHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRD 296 +H +SG+A++ A DD A+A+ RD+VA L A + +PPR D E+ G++ D Sbjct: 238 LHATVSGLAEFLAEDDEHAIALARDVVASLDWPGVAPRLPQPAQPPRLDAGELDGVMTLD 297 Query: 297 FRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKG 356 ++ D+ E+I R+ D S FK YGT VCG IEG VG ++NNG + A K Sbjct: 298 VKKPVDMLEIIGRLTDDSAWLAFKPDYGTATVCGRGRIEGHAVGFISNNGPIDPAGATKA 357 Query: 357 AHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGS 416 A FI+ C P+VFLQN TGF+VG+ E G+ K GAK++ A+S + VP+ T+ G S Sbjct: 358 AQFIQACNQSGTPIVFLQNTTGFIVGRASEEAGMIKHGAKMIQALSNSTVPQVTIYCGAS 417 Query: 417 FGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQER 476 FGAGN+GMCGR ++PR + WPNAR +VMGG QAA L + R +G + + Sbjct: 418 FGAGNFGMCGRGFRPRFCFSWPNARTAVMGGEQAAMTLEIVARQQAERKGAAVDEARLAQ 477 Query: 477 FMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTR---FGVF 533 I+A +E++ + S L DDGVIDP +TR VLA LA A EA + R FGV Sbjct: 478 QTGEIVANFERQASAFVTSGLLLDDGVIDPRDTRAVLAFVLATAREAEARTPRAMQFGVA 537 Query: 534 R 534 R Sbjct: 538 R 538 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: 730 Number of extensions: 35 Number of successful extensions: 8 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: 539 Length adjustment: 35 Effective length of query: 500 Effective length of database: 504 Effective search space: 252000 Effective search space used: 252000 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