Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_055436809.1 ASC41_RS11575 acyl-CoA carboxylase subunit beta
Query= BRENDA::Q9LDD8 (587 letters) >NCBI__GCF_001418085.1:WP_055436809.1 Length = 513 Score = 268 bits (684), Expect = 5e-76 Identities = 173/521 (33%), Positives = 266/521 (51%), Gaps = 29/521 (5%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126 ME + L + + GGG+ + + + KL RER+ LLD GS F E+ L H Sbjct: 1 MESKIKNLNEKLAQAYLGGGQARIDKQHEKKKLTARERVMYLLDEGS-FEEIGALVTHRT 59 Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182 + ++ G++TG G ++GR+ A D TV GG+ +K + ++A + Sbjct: 60 KDFGMDKQQFYGDGVVTGYGTVNGRLIYVFAQDFTVFGGSLSETHAEKICKVMDLALKVG 119 Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242 P I L DSGGA + + + +FY ++V SS IPQI+ ++G C G Y P Sbjct: 120 APIIGLNDSGGARIQEGVRSLG---GYADIFY-KNVQSSGVIPQISAIMGPCAGGAVYSP 175 Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302 AM D ++MV+ +F+ GP +VK T EEV++E+LGGA+ H T SGV+ + +++ L Sbjct: 176 AMTDFTIMVEDTSYMFVTGPNVVKTVTNEEVTSEELGGASTHSTKSGVAHKTSSNDIECL 235 Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362 VK L Q T K+ + + L +I P + Q +D+ S+IA I Sbjct: 236 ----EDVKKLLSYLPQNNTETPTLLPFKLKDEVRE--SLSTIIPANANQPYDMHSVIAGI 289 Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417 +D F E K Y ++ GFAR+ G+++GI+ N G+L S+ K A F+ C Sbjct: 290 IDEDSFYEIHKNYAENILVGFARLGGRSIGIVANQPMYLAGVLDVNSSKKAARFVRFCDA 349 Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477 IPL+ L+++ GF+ G+ E NGI GAK++ A S A VP+IT+IT ++G M Sbjct: 350 FNIPLLTLEDVPGFLPGTDQEWNGIIVHGAKLLYAFSEATVPRITVITRKAYGGAYDVMN 409 Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537 + D F WP+A I +MG AA ++ + E + +KW E+E E Sbjct: 410 SKHIGSDMNFAWPSAEIAVMGAKGAAEIIFKKEINAADDKEVKWKEKEAE--------YA 461 Query: 538 EREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLE 578 E ANPY + R + D VI P DTR+ L + N+ +E Sbjct: 462 ELFANPYSAAERGFIDEVILPKDTRRKLIKAFAMLENKEVE 502 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: 770 Number of extensions: 36 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: 513 Length adjustment: 36 Effective length of query: 551 Effective length of database: 477 Effective search space: 262827 Effective search space used: 262827 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