Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 350978 BT1450 propionyl-CoA carboxylase beta chain (NCBI ptt file)
Query= BRENDA::Q9LDD8 (587 letters) >FitnessBrowser__Btheta:350978 Length = 514 Score = 252 bits (644), Expect = 2e-71 Identities = 162/505 (32%), Positives = 255/505 (50%), Gaps = 28/505 (5%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126 M+ ++ L +K GGG+ +++ S KL RERID LL+ GS F+EL +L H Sbjct: 1 MKELIKNLEELNRKAEKGGGDARIEKQHSVGKLTARERIDLLLEKGS-FIELDKLVTHRC 59 Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182 + ++ G++TG G I R+ A D TV GG KK + ++A + Sbjct: 60 TDFGMEKQKFSGDGVVTGYGMIGKRLVYVFAQDFTVFGGALSETHAKKICKVMDMAMQMG 119 Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242 P I L DSGGA + + + +F S M+S IPQI+ ++G C G Y P Sbjct: 120 APIIGLNDSGGARIQEGVRSLA---GYAEIFLRNS-MASGVIPQISAIMGPCAGGAVYSP 175 Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302 A+ D +MVK +G +F+ GP +VK+ T EEVS EDLGG +H T SGV+ A++++ + Sbjct: 176 ALTDFILMVKNSGYMFITGPDVVKSVTQEEVSKEDLGGVGIHMTKSGVAHLSAENDIECI 235 Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362 R ++ ++ E F N P EL + P + Q ++++ +I + Sbjct: 236 NYIRELIS--YLPGNNMEEPPFVVTN---DSPTRLTPELSDLVPTNPNQPYNIKEMIEAV 290 Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417 D + F E + ++ +VTG+ R+ G+T+G++ N G L +++K A F+ C Sbjct: 291 ADDNNFFELQAEFAANIVTGYIRLNGKTIGVVANQPLVLAGTLDINASIKAARFVRFCDA 350 Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477 IPL+ L ++ GF+ G E GI + GAK++ A A VPK+T+IT ++G M Sbjct: 351 FNIPLLTLVDVPGFLPGVDQEYGGIIRNGAKLLYAYCEATVPKVTVITRKAYGGAYDVMS 410 Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537 + D +P A I +MG A +L + E I+ ++ EE K+ D Sbjct: 411 SKHIRGDVNLAFPTAEIAVMGPDGAVNILFKKE--------IEKSQTPEERRKELQSDYR 462 Query: 538 EREANPYYSTARLWDDGVIDPCDTR 562 E+ ANPY + + D VIDP TR Sbjct: 463 EKFANPYRAAELGYVDEVIDPAVTR 487 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: 690 Number of extensions: 28 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: 514 Length adjustment: 36 Effective length of query: 551 Effective length of database: 478 Effective search space: 263378 Effective search space used: 263378 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