Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_097029019.1 CRO07_RS00205 acyl-CoA carboxylase subunit beta
Query= BRENDA::Q9LDD8 (587 letters) >NCBI__GCF_900207575.1:WP_097029019.1 Length = 510 Score = 263 bits (673), Expect = 1e-74 Identities = 172/522 (32%), Positives = 267/522 (51%), Gaps = 32/522 (6%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHEL 127 M+ IL EL AGGG+ V+ R KL RERID LLD GS F E H Sbjct: 1 MKDILQELEDRRAIARAGGGQRRVEAQHKRGKLTARERIDLLLDEGS-FEEFDMFVRHRC 59 Query: 128 ----YEEPLPSG-GIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182 E+ P+G G++TG G I+GR+ + D TV GG+ +K + ++A + Sbjct: 60 TDFGMEDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNG 119 Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242 P I L DSGGA + E + VF ++M+S IPQI++++G C G Y P Sbjct: 120 APVIGLNDSGGARIQ---EGVASLAGYADVF-QRNIMASGVIPQISVIMGPCAGGAVYSP 175 Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302 AM D MV+ +F+ GP +VK T E V+AE+LGGA+ H S V+D ++++ L Sbjct: 176 AMTDFIFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEAL 235 Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362 A R +V L ++ + T + + + L ++ P + Q +D++ +I +I Sbjct: 236 AEIRRLVDFLPLSNR-----TPAPVRPFFDDVARVEDSLDTLIPDNPNQPYDMKELILKI 290 Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417 D +F E +K Y ++TGF R+ GQ+VG++ N G L +S+ K A F+ C Sbjct: 291 ADEGDFYEIQKDYAANIITGFIRLEGQSVGVVANQPMVLAGCLDIDSSRKAARFVRFCDA 350 Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477 IP++ L ++ GF+ G+ E G+ K GAK++ A A VPK+T+IT ++G M Sbjct: 351 FNIPILTLVDVPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMS 410 Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537 + DF + WP A I +MG A +L + E A K++ + T+E E+ F Sbjct: 411 SKHLRGDFNYAWPTAEIAVMGAKGATEILYRAELADKEKIAAR-TKEYEDRF-------- 461 Query: 538 EREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLED 579 ANP+ + R + D VI P TR+ + ++ N+ L + Sbjct: 462 ---ANPFVAAERGFIDEVIMPHSTRRRVSRAFASLRNKKLSN 500 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: 700 Number of extensions: 31 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: 510 Length adjustment: 36 Effective length of query: 551 Effective length of database: 474 Effective search space: 261174 Effective search space used: 261174 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: 52 (24.6 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