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_092349757.1 BLU87_RS13655 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_900107645.1:WP_092349757.1 Length = 445 Score = 480 bits (1235), Expect = e-140 Identities = 232/444 (52%), Positives = 323/444 (72%), Gaps = 2/444 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+R++RAC+E+G+++VAV+S+ D HV ADE+ IGPA +ADSY Sbjct: 1 MFHKILIANRGEIALRIIRACKEMGIKSVAVHSDVDHDALHVSLADESICIGPAASADSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +++I AA ADADAIHPGYGFL+ENAEFA E T++GP+AD M R+G+K AR Sbjct: 61 LNMKAIISAAEIADADAIHPGYGFLSENAEFAEICEQCGITFIGPTADNMRRMGDKISAR 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + A VP++PGT + ++ E+ + +A+D GYP+ IKA GGGGRG+K+VHS + Sbjct: 121 QTVTAAGVPILPGTNQSIETIEEAQKIANDIGYPIIIKASAGGGGRGMKIVHSPASLANS 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA+ E +A F A VY+EK+ + PRH+E+QIL D+HGNV HLGERDCS+QRRHQK+IE Sbjct: 181 LATARTEAQAGFGKADVYIEKFCQHPRHVEIQILGDKHGNVIHLGERDCSIQRRHQKLIE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 EAP P L+ +LRE++G A +A Y +AGTVE+L++ DG FYFME+NTRIQVEH VT Sbjct: 241 EAPCPVLTPELREKMGACAVAAAKAVNYASAGTVEYLLDSDGSFYFMEMNTRIQVEHPVT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E VTG+D+VK Q+ AAG L + Q+D++I GH++E RINAE PEK F P G ++ Y Sbjct: 301 EMVTGVDIVKEQINSAAGLPLRYKQEDIKITGHAIECRINAEDPEK-FTPFPGKITGYHT 359 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG+GIR++ A+ + +YDSMI KLIV RE+ + + AL+E+ I+G++T IP Sbjct: 360 PGGMGIRIESAMYDQYTVLPNYDSMIGKLIVHAETREQAIQKMACALDEYIIQGIKTTIP 419 Query: 420 FHRLMLTDEAFREGSHTTKYLDEV 443 FH+ M+ ++ F +G+ T +L+ V Sbjct: 420 FHQKMMANKQFNDGNFDTNFLERV 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: 600 Number of extensions: 19 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: 601 Length of database: 445 Length adjustment: 35 Effective length of query: 566 Effective length of database: 410 Effective search space: 232060 Effective search space used: 232060 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