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_013536981.1 THEAM_RS01140 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000185805.1:WP_013536981.1 Length = 448 Score = 421 bits (1081), Expect = e-122 Identities = 225/449 (50%), Positives = 301/449 (67%), Gaps = 5/449 (1%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF KVL+ANRGEIAVR++R C ELG++TVAVYS AD+ HV ADE+ IG + + SY Sbjct: 1 MFKKVLIANRGEIAVRIIRTCRELGIKTVAVYSTADRDSLHVYLADESVCIGGPQPSQSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA ADA+HPGYGFL+EN FA + ++GPS + M +G+K KAR Sbjct: 61 LNVPAIIAAAELTGADAVHPGYGFLSENPGFAEICQACGIKFIGPSPETMLLMGDKAKAR 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + + A VPVVPG+ + ++ A+ G+PV +KA GGGGRG++++ S + + Q Sbjct: 121 EVAKKAGVPVVPGSGV-VKTVQEALREAERIGFPVLVKAAHGGGGRGMRLIESARDAETQ 179 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA E EA F + VYVEK++E PRHIEVQ++AD GNV L ER+CSLQRRHQKV+E Sbjct: 180 IATAMAEAEAAFGSGEVYVEKFVENPRHIEVQVIADSKGNVFTLFERECSLQRRHQKVVE 239 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 EAPSP ++ +LR + +AA R Y AGTVEFLV+ G FYF+E+NTRIQVEH VT Sbjct: 240 EAPSPFVTPELRRELSKAAASIARYINYEGAGTVEFLVDGKGNFYFIEMNTRIQVEHPVT 299 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E VT D++ Q+ AAGEELDFSQ V++ GH++EFRI E F P G + Sbjct: 300 EMVTSKDLIAQQIAAAAGEELDFSQ--VKLNGHAVEFRITCEDYRSGFRPVPGKVEKLLL 357 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEG-LRTVI 418 PGG G+R+D + +G ++ YDS++AKL+V G REE L RA+RAL+EF I+G L+T I Sbjct: 358 PGGFGVRVDTHLYEGYKVPVYYDSLLAKLVVWGETREEALKRAKRALSEFVIKGDLKTTI 417 Query: 419 PFHRLMLTDEAFREGSHTTKYLDEVLDPE 447 PFH +L +E F G TK L++ + PE Sbjct: 418 PFHLKLLENELFLRGEIDTKTLEDKILPE 446 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: 611 Number of extensions: 22 Number of successful extensions: 5 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: 448 Length adjustment: 35 Effective length of query: 566 Effective length of database: 413 Effective search space: 233758 Effective search space used: 233758 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