Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_026608369.1 METAC_RS0119920 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000427445.1:WP_026608369.1 Length = 453 Score = 427 bits (1099), Expect = e-124 Identities = 213/444 (47%), Positives = 295/444 (66%), Gaps = 1/444 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+R++RA +ELG+ TVAV+S AD HV+ ADE+ +GP A DSY Sbjct: 1 MFDKILIANRGEIALRILRAAKELGISTVAVHSTADSEAMHVKLADESVCVGPPSARDSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +++ A A+A+HPGYGFLAENA FA + D +VGP A+ + +G+K +A+ Sbjct: 61 LNIPALLAACEITGAEALHPGYGFLAENARFAEILADHHIVFVGPKAEHIRMMGDKIEAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 +++ +P VPG+ + AVA + GYPV +KA GGGGRG+KV S+ E+ Sbjct: 121 RTVKELGIPCVPGSDGAISGDHEAAAVARELGYPVIVKASAGGGGRGMKVARSQSELSVA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA+ E + F + +VY+EK+LE PRHIEVQIL D G HLGER+CSLQRRHQKV E Sbjct: 181 LATARLEAKTAFGDDAVYLEKFLEKPRHIEVQILGDGRGKAIHLGERECSLQRRHQKVWE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 E+PSPAL+ R IGE +R Y GT+EFL EDG+FYF+E+NTRIQVEH VTE Sbjct: 241 ESPSPALNASQRGHIGEVCASAMRKLGYVGLGTIEFLYEDGQFYFIEMNTRIQVEHPVTE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TG+D+V Q+++AAG L +Q+ V GH++E RINAE P F P+ G ++ Y PP Sbjct: 301 MITGVDLVNEQIKIAAGSPLSLTQEQVIFHGHAIECRINAEHP-ATFRPSPGEIAYYHPP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+R+D AV G I YDS++ KLIV G R E L+R R+L+EF I+G+ T IP Sbjct: 360 GGLGVRVDSAVYAGYVIPPTYDSLVGKLIVHGRTRNEALMRLRRSLDEFIIDGIDTTIPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLDEVL 444 + ++ + + + +L++ L Sbjct: 420 FQTLVRNADIQNALYDIHWLEKFL 443 Lambda K H 0.312 0.132 0.371 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: 617 Number of extensions: 20 Number of successful extensions: 2 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: 601 Length of database: 453 Length adjustment: 35 Effective length of query: 566 Effective length of database: 418 Effective search space: 236588 Effective search space used: 236588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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