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_012281650.1 HM1_RS02300 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000019165.1:WP_012281650.1 Length = 454 Score = 480 bits (1235), Expect = e-140 Identities = 233/441 (52%), Positives = 323/441 (73%), Gaps = 1/441 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 +F+K+L+ANRGEIAVR++RAC+E+G+ TVAVYSEADK HV+ ADEAY +GPA + SY Sbjct: 7 LFNKILIANRGEIAVRIIRACKEMGIGTVAVYSEADKDALHVKLADEAYCVGPAPSNRSY 66 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA + A+AIHPG+GFL+ENA FA E + ++GP + A+E +G K AR Sbjct: 67 LNIPNIISAATVSGAEAIHPGFGFLSENAYFAEICETCKIKFIGPGSKAIESMGSKAVAR 126 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 M A V VVPG+ S E+ + +A++ GYPV IKA GGGGRG+++ HSE ++ Sbjct: 127 ETMIKAGVRVVPGSESIVTSEEEAEKIAEEIGYPVMIKASAGGGGRGMRIAHSEKDLFNA 186 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 +TA+ E EA F N +VY+EK++E PRHIE QI+AD+ GN +LGERDCS+QRR+QK++E Sbjct: 187 LQTAQAEAEAAFGNKAVYIEKFIEEPRHIEFQIMADQFGNTVYLGERDCSIQRRNQKLLE 246 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 EAPSPALS +LR+ +GE A ++ Y NAGTVEFL++ G +YF+E+NTRIQVEH VT Sbjct: 247 EAPSPALSPELRKEMGEQAVLAAKSVNYVNAGTVEFLLDKHGHYYFIEMNTRIQVEHPVT 306 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E +TG+D++K Q+R+AAGE L ++QDD+ I+GH++E RINAE P + F P+ G ++ Y P Sbjct: 307 EMITGIDLIKEQIRIAAGEPLGYTQDDIVIKGHAIECRINAEDPARNFMPSPGKITAYHP 366 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG+G+R+D A G I YDSMI KLIV G DR E + R +RAL+EF IEG++T IP Sbjct: 367 PGGLGVRLDSAAYAGYTIPPTYDSMIGKLIVWGRDRNEAIARMQRALDEFVIEGVKTTIP 426 Query: 420 FHRLMLTDEAFREGSHTTKYL 440 F + +L + F++G T ++ Sbjct: 427 FQQKVLGNAFFQKGEVYTNFI 447 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: 630 Number of extensions: 17 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: 454 Length adjustment: 35 Effective length of query: 566 Effective length of database: 419 Effective search space: 237154 Effective search space used: 237154 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