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 GFF3280 HP15_3222 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Marino:GFF3280 Length = 448 Score = 442 bits (1138), Expect = e-128 Identities = 223/445 (50%), Positives = 308/445 (69%), Gaps = 2/445 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 M KVL+ANRGEIA+R++RAC+ELG++TVAV+S+ D+ HVR ADE+ IGP A DSY Sbjct: 3 MLEKVLIANRGEIALRILRACKELGIKTVAVHSQVDRDLMHVRLADESVCIGPNSATDSY 62 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA D+ IHPGYGFLAENA+FA +VE S F ++GP A+ + +G K A Sbjct: 63 LNIPTIISAAEVTDSVGIHPGYGFLAENADFAEQVEKSGFRFIGPKAETIRLMGNKVSAI 122 Query: 121 SLMQDADVPVVPGTTEPADSAED-VKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179 + M A VP VPG+ P D E+ +A + GYPV IKA GGGGRG++VVHSE + Sbjct: 123 NAMIKAGVPTVPGSDGPLDDDEERTLRIAKEIGYPVMIKAASGGGGRGMQVVHSEAALLK 182 Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239 + + E + F + +VY+EK+LEAPRH+EVQ+LAD HGN HLG+RDCS+QRR+QKVI Sbjct: 183 GVQITQSEAKNAFGDPTVYLEKFLEAPRHVEVQVLADMHGNCIHLGDRDCSMQRRNQKVI 242 Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299 EEAP+P ++ + RER +A + Y AGT EFL +DGEFYF+E+NTR+QVEH V+ Sbjct: 243 EEAPAPNINPESRERTLKACTDACKEIGYVGAGTFEFLYQDGEFYFIEMNTRVQVEHPVS 302 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E VTG+D+V+ QLR+A+G L ++QDD+ I GH+ME RINAE P K F P+ G + + Sbjct: 303 EMVTGVDIVREQLRIASGLPLQYTQDDIRISGHAMECRINAEDP-KTFIPSPGKVKHFHA 361 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D + G + YDS++AKLI G DR+ R + AL+E +EG++T P Sbjct: 362 PGGNGVRVDSHLYSGYTVPPYYDSLVAKLITWGDDRDIARRRMKNALDELVVEGIKTNQP 421 Query: 420 FHRLMLTDEAFREGSHTTKYLDEVL 444 HR ++ D F++ T YL++++ Sbjct: 422 LHRKLVRDGGFKQVDFTIHYLEKLM 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: 639 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: 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 17 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