Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate Echvi_0160 Echvi_0160 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= SwissProt::Q3J4E3 (510 letters) >FitnessBrowser__Cola:Echvi_0160 Length = 527 Score = 650 bits (1677), Expect = 0.0 Identities = 319/515 (61%), Positives = 400/515 (77%), Gaps = 8/515 (1%) Query: 2 KDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCTD 61 K+ L+ L+ + A GGGQ+R+ QH++GKLTARERI LL+DEG+F+E D F HRC D Sbjct: 15 KEKLELLKKKNEEALMGGGQQRIATQHEKGKLTARERIHLLIDEGTFQEIDKFKMHRCKD 74 Query: 62 FGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGAP 121 FG+ + GDGVVTG+G +NGR+VYV+SQDFTVFGGSLSETHA+KICKIMDMAM+NGAP Sbjct: 75 FGLDKEYYLGDGVVTGYGEVNGRLVYVYSQDFTVFGGSLSETHAEKICKIMDMAMKNGAP 134 Query: 122 VIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDFI 181 VIGLNDSGGARIQEGV SL GYAD+F RN ASGVIPQ+S IMGPCAGGAVYSPA+TDFI Sbjct: 135 VIGLNDSGGARIQEGVNSLGGYADIFYRNTRASGVIPQLSAIMGPCAGGAVYSPAITDFI 194 Query: 182 FMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRRL 241 MV +TSYMFVTGP+VVKTVT E V++EELGGASTH+ KS V A +N+VE + I+ + Sbjct: 195 LMVEETSYMFVTGPNVVKTVTQEHVSSEELGGASTHSTKSGVTHFACQNEVECIKTIKDI 254 Query: 242 VDFLPLSNRTPAPVRPF--FDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEI 299 + ++P + AP P+ +D +R LDT++P+NPN PYDM+E++ I DEA F E+ Sbjct: 255 LSYIPQNCEDDAPSYPYDMLEDESR--PVLDTMVPENPNHPYDMREVVRGIVDEASFLEV 312 Query: 300 QKDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLV 359 ++FA N++ GF R+ G+++GVV NQP LAG LD D+S KAARFVRFCD FN+P+L LV Sbjct: 313 HQNFADNMVVGFARIAGRSIGVVGNQPQSLAGVLDNDASIKAARFVRFCDCFNVPLLVLV 372 Query: 360 DVPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFN 419 DVPGFLPGT QE+ G+I +GAKLL+A+ EATVP++TVITRKAYGGAYDVM SKH+ D N Sbjct: 373 DVPGFLPGTDQEWNGIITNGAKLLYAFSEATVPRITVITRKAYGGAYDVMNSKHIGADLN 432 Query: 420 YAWPTAEIAVMGAKGATEILYRSELGDKE----KIAARAKEYEDRFANPFVAAERGFIDE 475 +AWPTAEIAVMGAKGA EI+++ E+ E K+ + +Y +FANP+ AA RG+IDE Sbjct: 433 FAWPTAEIAVMGAKGAAEIIFKKEIAQAEDSEAKLQEKIDQYTRKFANPYKAAHRGYIDE 492 Query: 476 VIMPHSTRRRVSKAFASLRNKKLANPWKKHDNIPL 510 VI+P TR+++ F L+NK P KKH NIPL Sbjct: 493 VILPSQTRKKLISGFKMLKNKVDNLPKKKHGNIPL 527 Lambda K H 0.321 0.138 0.404 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: 822 Number of extensions: 26 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: 527 Length adjustment: 35 Effective length of query: 475 Effective length of database: 492 Effective search space: 233700 Effective search space used: 233700 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 Apr 09 2024. 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