Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 5210426 Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__PV4:5210426 Length = 1094 Score = 296 bits (757), Expect = 3e-84 Identities = 173/448 (38%), Positives = 259/448 (57%), Gaps = 7/448 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+R+L+ANRGEIA R+ + +MG+ ++A+Y+E D ++HTK AD+A + K + +YL Sbjct: 5 FNRILIANRGEIAIRIAQTCADMGIDSLAIYAEDDSQSLHTKKADQAVAL-KGRGVKAYL 63 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 +IE +I A+ DA+HPGYGFLSEN+ F++ + GI FIG S+E++ + +K + Sbjct: 64 DIEQLIAVAKAHGCDAVHPGYGFLSENSSFSKRCHEEGICFIGSSAELLDLLGNKATARE 123 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIG--YPIMVKAASGGGGVGITRVDNQDQLMD 181 A + P G + P S++E +G +M+KA +GGGG G+ V + L + Sbjct: 124 TALRSDTPLTGGINKPC-SLEEVQAFFTSLGDGAAVMIKALAGGGGRGMRPVSRYEDLAE 182 Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241 + + + A AFG +L++E+ + RHIE Q++GD G V AWERECT+QRRNQKL+ Sbjct: 183 AYRQCREEAIIAFGSGELYVEQLVQHARHIEVQILGDGTGAAVHAWERECTLQRRNQKLL 242 Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAF-SDVSRDFYFLELNKRLQVEH 300 E APSP+L R + E ++ + Y LGTFE +D FYF+E+N R+QVEH Sbjct: 243 EIAPSPSLDDATRMPIIESALQLASDVKYQGLGTFEFLLDADDHSKFYFMEINPRIQVEH 302 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDAL--NNFTGSSG 358 TE I ++LVKLQI L AG+ L RG AI+ RIN E L + +SG Sbjct: 303 TITEEITGLNLVKLQILLGAGKTLAELSLTEAPIKRGCAIQARINLEQMLPDGSTKPASG 362 Query: 359 FVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418 + Y+ P G VRVD + +G V P YDSL +K+I GE A+ +L I Sbjct: 363 VIKAYQVPNGHNVRVDDYLYAGYKVSPSYDSLGAKIIAKGEDFSAALNKVYLSLKALNID 422 Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYI 446 G+++ L ++Q + Q + ST ++ Sbjct: 423 GVQSNKALLMNLLQREEVQHNRLSTRFV 450 Lambda K H 0.317 0.135 0.385 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: 1151 Number of extensions: 56 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 509 Length of database: 1094 Length adjustment: 40 Effective length of query: 469 Effective length of database: 1054 Effective search space: 494326 Effective search space used: 494326 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 55 (25.8 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