Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_034275130.1 AMYHA_RS25160 acyl-CoA carboxylase subunit beta
Query= BRENDA::Q9LDD8 (587 letters) >NCBI__GCF_000504245.1:WP_034275130.1 Length = 549 Score = 240 bits (612), Expect = 1e-67 Identities = 162/527 (30%), Positives = 265/527 (50%), Gaps = 26/527 (4%) Query: 51 PDGVDRNSEAFSSNSIAMEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLL 110 P G S S + G L++L + + G AV++ ++ K RERID LL Sbjct: 7 PLGGQHGSAEESIDIHTTAGKLADLYRRNDEAVHAGSARAVEKQHAKGKKTARERIDMLL 66 Query: 111 DPGSSFLELSQLAGHEL----YEEPLPSG-GIITGIGPIHGR-ICMFMANDPTVKGGTYY 164 DPGS F+EL +LA H + P G G++TG G I GR +C+F + D T+ GG+ Sbjct: 67 DPGS-FVELDELARHRSTNFGQDANRPYGDGVVTGYGTIDGRPVCVF-SQDVTIFGGSLG 124 Query: 165 PITIKKHLRAQEIAARCRLPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGI 224 + +K ++ ++A + P I + + GGA + E +G +F +V +S + Sbjct: 125 EVYGEKIVKVMDLAIKTGRPIIGINEGGGARIQ---EGVVSLGLYGEIF-TRNVKASGVV 180 Query: 225 PQIAIVLGSCTAGGAYIPAMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVH 284 PQI++++G+ G Y PA+ D VMV +F+ GP ++K TGEEV+ E+LGG H Sbjct: 181 PQISLIMGANAGGHVYSPALTDFVVMVDQTSHMFITGPDVIKTVTGEEVTFEELGGGRSH 240 Query: 285 CTVSGVSDYFAQDELHGLAIGRNIVKNL---HMAAKQGMEGTFGSKNLVYKEPLYDINEL 341 T SG + Y DE ++ + ++ L ++A E + N V + D EL Sbjct: 241 NTKSGNAHYLGADEEDAISYVKELLSFLPPNNLAEPPVFEAPPHTGNSVADDITDDDREL 300 Query: 342 RSIAPVDHKQQFDVRSIIARIVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN---- 397 ++ P +D+ +I +VD EF E + + ++ GF R+ GQ+VGI+ N Sbjct: 301 DTLIPDSPNVPYDMHEVITHVVDDGEFLEVHELFAPNVLVGFGRVDGQSVGIVANQPTQF 360 Query: 398 -GILFNESALKGAHFIELCSQRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCA 456 G L +++ K A F+ C +P++ ++ GF+ G+ E NGI + GAK++ A + A Sbjct: 361 AGCLDIDASEKAARFVRTCDAFNVPVLTFVDVPGFLPGTDQEWNGIIRRGAKLIYAYAEA 420 Query: 457 KVPKITIITGASFGAGNYAMCGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKR 516 VP +T+IT ++G M + D WP A+I +MG AA ++ + A + Sbjct: 421 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANIVYRKTLANAEA 480 Query: 517 QGIKWTEEEEEAFKKKTVDAYERE-ANPYYSTARLWDDGVIDPCDTR 562 +G ++ E + + + YE NPY + R + D VI P TR Sbjct: 481 EG-----QDIEKLRGELIQEYEDTLCNPYVAAERGYVDSVIPPSHTR 522 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: 756 Number of extensions: 45 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: 549 Length adjustment: 36 Effective length of query: 551 Effective length of database: 513 Effective search space: 282663 Effective search space used: 282663 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 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