Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_073038419.1 BUB04_RS07710 propionyl-CoA carboxylase
Query= reanno::SB2B:6937191 (535 letters) >NCBI__GCF_900129305.1:WP_073038419.1 Length = 533 Score = 440 bits (1131), Expect = e-128 Identities = 232/504 (46%), Positives = 321/504 (63%), Gaps = 10/504 (1%) Query: 40 GGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFAAFEVYD---EDVPAAGIIAGIG 96 GG A++R +GK R ++KL+DPG+ F ELS+ A F ++ EDVP GI+ G+G Sbjct: 30 GGEAAVQRLAKQGKQPVRQLIQKLIDPGTEFYELSRLAGFGMHYPGVEDVPCGGIVTGLG 89 Query: 97 RVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEV 156 ++ G MIIAND+ VK GTY+PIT+KKH+RAQAIAE+C L C+Y+ DSGGA LP Q +V Sbjct: 90 KIYGNWTMIIANDSRVKAGTYFPITLKKHMRAQAIAEQCGLNCVYIADSGGAFLPMQADV 149 Query: 157 FPDRDHFGRIFFNQARMSAKGIPQIAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGP 216 FPD HFG +F+N ARMSAKG+ QI + G TAGGAY+ MA +++++ FL GP Sbjct: 150 FPDDGHFGSMFYNMARMSAKGLKQITLSTGGNTAGGAYIVFMACQAVMIDRMAYSFLGGP 209 Query: 217 PLVKAATGEEVSAEELGGGDVHTKISGVADHLAQNDEHALELARKAVSRLNHQKQVELQL 276 PLVKAATGE +SAE+LGG VHT+ISG ADH + + A+E R+ +S L +++++ Sbjct: 210 PLVKAATGEVISAEDLGGARVHTQISGGADHFCRTQDEAIEKVREILS-LERPQELQIHR 268 Query: 277 SKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIVDDSDFDEFKANY----GTTLVCGFA 332 PP+ + +Y + + + +V+ +I I DDS F E+K NY G +V G Sbjct: 269 YAESPPQVPVETIYEELPAKIHQGINVRNIIRAIADDSHFIEYKRNYAPGRGDNIVTGKI 328 Query: 333 RIHGYPVGIVANN--GILFSESAQKGAHFIELCCQRKIPLVFLQNITGFMVGKKYEHEGI 390 R+ G PVGI+A+N GI+F E+A+K +I C Q K PL+F+Q+ G+MVG + EH GI Sbjct: 329 RLKGIPVGIIASNGLGIIFVEAARKATEWIVRCSQEKTPLLFIQSSPGYMVGSESEHMGI 388 Query: 391 AKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCGRAFEPTLMWMWPNARISVMGGEQA 450 K+GA MV AVSCA VP+ ++IG GA NYGMCGRA+ P ++ AR SVM G A Sbjct: 389 GKYGADMVRAVSCAQVPRIQLVIGPDNGAANYGMCGRAYRPHFLFSTMRARTSVMSGRSA 448 Query: 451 AGVLATVRKDGLARKGETMSAEEEAKFKAPIIAQYDKEGHPYHASARLWDDGIIDPAQTR 510 A VL T+ + +G MS E+ F+ +I +YD E HP+ ARL +D ++ + R Sbjct: 449 AEVLLTIEERKREAEGRPMSEGEKQAFRQQMIEKYDGEAHPFFCGARLLNDRVLKFREIR 508 Query: 511 DVLGLAISAALNAPIEETRFGVFR 534 D L +A +L PI E FG R Sbjct: 509 DWLAVAFEVSLLKPIGEPAFGNLR 532 Lambda K H 0.320 0.137 0.405 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: 780 Number of extensions: 40 Number of successful extensions: 5 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: 535 Length of database: 533 Length adjustment: 35 Effective length of query: 500 Effective length of database: 498 Effective search space: 249000 Effective search space used: 249000 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