Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_055436809.1 ASC41_RS11575 acyl-CoA carboxylase subunit beta
Query= SwissProt::Q3J4E3 (510 letters) >NCBI__GCF_001418085.1:WP_055436809.1 Length = 513 Score = 669 bits (1725), Expect = 0.0 Identities = 331/514 (64%), Positives = 403/514 (78%), Gaps = 5/514 (0%) Query: 1 MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60 M+ ++ L + A A GGGQ R++ QH++ KLTARER+ LLDEGSFEE V HR Sbjct: 1 MESKIKNLNEKLAQAYLGGGQARIDKQHEKKKLTARERVMYLLDEGSFEEIGALVTHRTK 60 Query: 61 DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120 DFGM + GDGVVTG+GT+NGR++YVF+QDFTVFGGSLSETHA+KICK+MD+A++ GA Sbjct: 61 DFGMDKQQFYGDGVVTGYGTVNGRLIYVFAQDFTVFGGSLSETHAEKICKVMDLALKVGA 120 Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180 P+IGLNDSGGARIQEGV SL GYAD+F +N+ +SGVIPQIS IMGPCAGGAVYSPAMTDF Sbjct: 121 PIIGLNDSGGARIQEGVRSLGGYADIFYKNVQSSGVIPQISAIMGPCAGGAVYSPAMTDF 180 Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240 MV DTSYMFVTGP+VVKTVTNE VT+EELGGASTH+ KS VA ND+E L ++++ Sbjct: 181 TIMVEDTSYMFVTGPNVVKTVTNEEVTSEELGGASTHSTKSGVAHKTSSNDIECLEDVKK 240 Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300 L+ +LP N T P F + +SL T+IP N NQPYDM +I I DE FYEI Sbjct: 241 LLSYLP-QNNTETPTLLPFKLKDEVRESLSTIIPANANQPYDMHSVIAGIIDEDSFYEIH 299 Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360 K++A NI+ GF RL G+++G+VANQPM LAG LD++SS+KAARFVRFCDAFNIP+LTL D Sbjct: 300 KNYAENILVGFARLGGRSIGIVANQPMYLAGVLDVNSSKKAARFVRFCDAFNIPLLTLED 359 Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420 VPGFLPGT QE+ G+I HGAKLL+A+ EATVP++TVITRKAYGGAYDVM SKH+ D N+ Sbjct: 360 VPGFLPGTDQEWNGIIVHGAKLLYAFSEATVPRITVITRKAYGGAYDVMNSKHIGSDMNF 419 Query: 421 AWPTAEIAVMGAKGATEILYRSELG---DKE-KIAARAKEYEDRFANPFVAAERGFIDEV 476 AWP+AEIAVMGAKGA EI+++ E+ DKE K + EY + FANP+ AAERGFIDEV Sbjct: 420 AWPSAEIAVMGAKGAAEIIFKKEINAADDKEVKWKEKEAEYAELFANPYSAAERGFIDEV 479 Query: 477 IMPHSTRRRVSKAFASLRNKKLANPWKKHDNIPL 510 I+P TRR++ KAFA L NK++ P +KH NIPL Sbjct: 480 ILPKDTRRKLIKAFAMLENKEVERPKRKHGNIPL 513 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: 794 Number of extensions: 27 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: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 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 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