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 Ga0059261_0292 Ga0059261_0292 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Korea:Ga0059261_0292 Length = 454 Score = 447 bits (1149), Expect = e-130 Identities = 230/446 (51%), Positives = 307/446 (68%), Gaps = 3/446 (0%) Query: 4 KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63 K+L+ANRGEIA+R+ RAC E+G++TVAV+S AD HVR AD+A IGP AADSYL+ Sbjct: 6 KLLIANRGEIALRIHRACHEMGIKTVAVHSTADADAMHVRLADQAVCIGPPAAADSYLNI 65 Query: 64 ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123 ++I AA + ADAIHPGYGFL+ENA+FA VE +VGP + + +G+K +A+ Sbjct: 66 PNIISAAEISGADAIHPGYGFLSENAKFAEIVELHNLIFVGPKPEHIRVMGDKVEAKRTA 125 Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFET 183 +P+VPG+ E+ K +A + GYPV IKA GGGGRG+KV D+ + + Sbjct: 126 GALGLPLVPGSDGAISDVEEAKKLAAEIGYPVIIKAASGGGGRGMKVCTDPDQFETLMQQ 185 Query: 184 AKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAP 243 A E +A F +A+VY+EKYL PRHIE+Q+ D +GN HLGERDCSLQRRHQKV+EEAP Sbjct: 186 AGSEAKAAFGDATVYLEKYLGNPRHIEIQVFGDGNGNAIHLGERDCSLQRRHQKVLEEAP 245 Query: 244 SPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEEVT 303 SP LS + R RIGE + + Y AGT+EFL E+GEFYF+E+NTR+QVEH VTE +T Sbjct: 246 SPVLSTEERNRIGEICAKAMADMGYRGAGTIEFLWENGEFYFIEMNTRLQVEHPVTEAIT 305 Query: 304 GLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGGI 363 GLD+V+ Q+RVA G L Q+DV+ GH++E RINAE P + FAP+ G +S Y PGG+ Sbjct: 306 GLDLVREQIRVAEGHGLTLRQEDVQFRGHAIECRINAEDP-RTFAPSPGRVSQYHAPGGM 364 Query: 364 GIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE--GLRTVIPFH 421 +R+D + G ++ YDSMIAKLIV G+ R+ L R RAL EF IE G++T IP H Sbjct: 365 NVRVDSGLYSGYKVPPYYDSMIAKLIVYGTTRQGALRRLRRALEEFVIEGDGMKTTIPLH 424 Query: 422 RLMLTDEAFREGSHTTKYLDEVLDPE 447 + +L + F++G +T K+L+E L E Sbjct: 425 QALLDNPQFQQGDYTIKWLEEWLARE 450 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: 691 Number of extensions: 26 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: 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 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