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_012384335.1 BIND_RS06800 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000019845.1:WP_012384335.1 Length = 453 Score = 431 bits (1109), Expect = e-125 Identities = 216/444 (48%), Positives = 301/444 (67%), Gaps = 1/444 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+R++RA +ELG+ TVAV+S AD + HVR ADE+ IGP A DSY Sbjct: 1 MFDKILIANRGEIALRILRAAKELGIATVAVHSTADANAMHVRLADESVCIGPPPARDSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +++ A A+A+HPGYGFL+ENA FA + + ++GP A+ + +G+K +A+ Sbjct: 61 LNIPAILAACEVTGAEAVHPGYGFLSENARFAEILAEHHIAFIGPKAEHIRLMGDKVEAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 +P VPG+ + AVA G+PV IKA GGGGRG+K+ + +++ Sbjct: 121 RTALRLGIPCVPGSDGAIRDEAEALAVAKTLGFPVLIKAAAGGGGRGMKLARTAEDLPLA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TAK E + F + SVY+EKYLE PRHIEVQIL D G HLGERDCSLQRRHQKV E Sbjct: 181 LSTAKMEALSAFGDDSVYLEKYLEKPRHIEVQILGDGKGKAIHLGERDCSLQRRHQKVWE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 E PSPAL+++ R RIGE + +R Y+ AGT+EFL E+GEFYF+E+NTRIQVEH +TE Sbjct: 241 ETPSPALNQEQRPRIGEICAQAMRDLGYSGAGTIEFLYENGEFYFIEMNTRIQVEHPITE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 VTG+D+V Q+++AAG L +Q++V GH++E RINAE P F P+ G ++ Y PP Sbjct: 301 MVTGVDLVNEQIKIAAGSTLSLTQEEVLFSGHAIECRINAENP-STFHPSPGKIAYYHPP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+R+D AV G +I +YDS++ KLIV +R E L+R RAL+E I+G+ T +P Sbjct: 360 GGLGVRVDSAVYAGYKIPPNYDSLVGKLIVHARNRNEALMRLRRALDECVIDGIETTLPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLDEVL 444 R ++ + + GS+ +L++ L Sbjct: 420 FRTLIRNTDIQNGSYDIHWLEKFL 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: 615 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