Align Propionyl-CoA carboxylase beta chain; EC 6.4.1.3 (characterized)
to candidate GFF2128 PGA1_c21600 propionyl-CoA carboxylase beta chain
Query= SwissProt::Q168G2 (510 letters) >FitnessBrowser__Phaeo:GFF2128 Length = 510 Score = 926 bits (2393), Expect = 0.0 Identities = 450/510 (88%), Positives = 485/510 (95%) Query: 1 MKDILEQLEDRRAAARLGGGQKRIDAQHGRGKLTARERVDLLLDEGSFEEFDMFVTHRCT 60 MKDIL +LEDRR AARLGGGQKRIDAQHGRGKLTARER++LLLDEGSFEEFDMFV HRCT Sbjct: 1 MKDILSELEDRRNAARLGGGQKRIDAQHGRGKLTARERIELLLDEGSFEEFDMFVAHRCT 60 Query: 61 DFNMQDQKPAGDGVVTGWGTINGRVVYVFSQDFTVLGGSVSETHSKKICKIMDMAMQNGA 120 DF M++Q+PAGDGVVTGWGTINGR+VYVFSQDFTV GGS+SETH++KICKIMDMA+QNGA Sbjct: 61 DFGMENQRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAVQNGA 120 Query: 121 PVIGINDSGGARIQEGVDSLAGYGEVFQRNIMASGVVPQISMIMGPCAGGAVYSPAMTDF 180 PVIGINDSGGARIQEGV SLAGY EVFQRNIMASGVVPQIS+IMGPCAGGAVYSPAMTDF Sbjct: 121 PVIGINDSGGARIQEGVASLAGYAEVFQRNIMASGVVPQISVIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVKDSSYMFVTGPDVVKTVTNEQVSAEELGGATTHTRKSSVADAAFENDVEALAEVRR 240 IFMVKD+SYMFVTGPDVVKTVTNE V+AEELGGA+THT+KSSVAD AFENDVEALAEVRR Sbjct: 181 IFMVKDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALAEVRR 240 Query: 241 LVDFLPLNNREKPPVRPFFDDPDRIEPSLDTLVPDNPNTPYDMKELIHKLADEGDFYEIQ 300 LVDFLPLNNREKPPVRPFFD+P R+E SLDTL+P NPNTPYDMKELIHK+ADEGDFYEIQ Sbjct: 241 LVDFLPLNNREKPPVRPFFDEPGRVETSLDTLIPANPNTPYDMKELIHKVADEGDFYEIQ 300 Query: 301 EEFAKNIITGFIRLEGRTVGVVANQPLVLAGCLDIDSSRKAARFVRFCDAFEIPLLTLID 360 E+FAKNIITGFIRLEG+TVGVVANQP VLAGCLDIDSSRKAARFVRFCD FEIP+LTL+D Sbjct: 301 EDFAKNIITGFIRLEGQTVGVVANQPTVLAGCLDIDSSRKAARFVRFCDCFEIPILTLVD 360 Query: 361 VPGFLPGTSQEYGGVIKHGAKLLYAYGEATVPMVTVITRKAYGGAYVVMSSKHLRADFNY 420 VPGFLPGTSQEYGGVIKHGAKLL+AYGEATVP VTVITRKAYGGAY VM+SKHLR DFNY Sbjct: 361 VPGFLPGTSQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420 Query: 421 AWPTAEVAVMGAKGATEIIHRGDLGDPEKIAQHTADYEERFANPFVASERGFVDEVIQPR 480 AWPTAE+AVMGAKGATEIIHR DL D +KIA+HT DYEERFANPFVA+ERGF+DEVI P+ Sbjct: 421 AWPTAEIAVMGAKGATEIIHRADLADADKIAEHTKDYEERFANPFVAAERGFIDEVIMPQ 480 Query: 481 STRKRVARAFASLRNKSVQMPWKKHDNIPL 510 STRKRV+RAFASLR K ++ PWKKHDNIPL Sbjct: 481 STRKRVSRAFASLRGKQLKNPWKKHDNIPL 510 Lambda K H 0.319 0.137 0.402 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: 978 Number of extensions: 30 Number of successful extensions: 3 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: 510 Length of database: 510 Length adjustment: 34 Effective length of query: 476 Effective length of database: 476 Effective search space: 226576 Effective search space used: 226576 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 (21.8 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