Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 351214 BT1686 propionyl-CoA carboxylase beta chain (NCBI ptt file)
Query= BRENDA::Q9LDD8 (587 letters) >FitnessBrowser__Btheta:351214 Length = 517 Score = 264 bits (675), Expect = 6e-75 Identities = 167/496 (33%), Positives = 251/496 (50%), Gaps = 44/496 (8%) Query: 85 GGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE-----LYEEPLPSGGIIT 139 GGGE+A+ + + K RERI LLD GS F E+ H + ++ P G++T Sbjct: 21 GGGEKAIAKQHEKGKYTARERIAMLLDEGS-FEEMDMFVEHRCTNFGMEKKHYPGDGVVT 79 Query: 140 GIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCRLPCIYLVDSGGAYLPKQ 199 G G I GR+ A D TV G+ K + + A + PCI + DSGGA + + Sbjct: 80 GCGTIEGRLVYLFAQDFTVTAGSLSETMSLKICKIMDQAMKMGAPCIGINDSGGARIQEG 139 Query: 200 AEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIPAMADESVMVKGNGTIFL 259 + +F ++++S IPQI+ + G C G Y PA+ D ++M++G +FL Sbjct: 140 INALA---GYAEIF-QRNILASGVIPQISGIFGPCAGGAVYSPALTDFTLMMEGTSYMFL 195 Query: 260 AGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGLAIGRNIVKNLHMAAKQG 319 GP +VK TGE+VS E+LGGA+VH T SGV+ + A+ E GLA+ R ++ Sbjct: 196 TGPKVVKTVTGEDVSQENLGGASVHSTKSGVTHFTAKTEEEGLALIRTLL---------- 245 Query: 320 MEGTFGSKNLVYKEPLYDINE--------LRSIAPVDHKQQFDVRSIIARIVDGSEFDEF 371 ++ +N + + P D + L I P + +D+ +I+ IVD EF E Sbjct: 246 ---SYIPQNNLEEAPYVDCTDPIDRLEDSLNDIIPDSPNKPYDMYEVISAIVDNGEFLEI 302 Query: 372 KKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQRKIPLVFLQ 426 +K Y ++ GFAR GQ+VGI+ N G+L + ++ KGA F+ C IP+V L Sbjct: 303 QKDYAKNIIIGFARFNGQSVGIVANQPKFLAGVLDSNASRKGARFVRFCDAFNIPIVSLV 362 Query: 427 NITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMCGRAYSPDFM 486 ++ GF+ G+ E NG+ GAK++ A A VPK+TI S+G + M + D Sbjct: 363 DVPGFLPGTGQEYNGVILHGAKLLYAYGEATVPKVTITLRKSYGGSHIVMSCKQLRGDMN 422 Query: 487 FIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAYEREANPYYS 546 + WP A I +MGGA A VL E ++ E+E E K ANPY + Sbjct: 423 YAWPTAEIAVMGGAGAVEVLYAREAKDQENPAQFLAEKEAEYTK--------LFANPYNA 474 Query: 547 TARLWDDGVIDPCDTR 562 + D VI+P +TR Sbjct: 475 AKYGYIDDVIEPRNTR 490 Lambda K H 0.320 0.138 0.408 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: 741 Number of extensions: 35 Number of successful extensions: 7 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: 587 Length of database: 517 Length adjustment: 36 Effective length of query: 551 Effective length of database: 481 Effective search space: 265031 Effective search space used: 265031 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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