Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ac3H11_4479 Biotin carboxylase (EC 6.3.4.14)
Query= BRENDA::Q9I297 (535 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4479 Length = 1095 Score = 180 bits (457), Expect = 2e-49 Identities = 155/502 (30%), Positives = 227/502 (45%), Gaps = 40/502 (7%) Query: 44 AQARHSARGKLLVRERINRLLDPGSPFLELSALA--------AHEVYGEEVAAAGIVAGI 95 A A+ A+G RE I L D GS F+E ALA + E A G+V GI Sbjct: 604 AIAKRHAQGGRTARENIADLCDNGS-FIEYGALAIAAQARRRSKEDLIANTPADGMVTGI 662 Query: 96 GRVEGV-------ECMIVGNDATVKGGTYYPLTVKKHLRAQAIALENRLPCIYLVDSGGA 148 G + G +++ DATV GT K R IAL +LP + + GG Sbjct: 663 GGINGALFGDEKSRAVVMSYDATVLAGTQGARNHAKTDRMLGIALAQKLPVVLFAEGGGG 722 Query: 149 NLPRQDEVFPDREHFGRIFFNQANMSARGIPQIAVVMGSCTAGGAYVPAMSDETVMVREQ 208 D H F + A +S + +P I + G C AG A + SD + R Sbjct: 723 RPGDTDMPIVAGLHV-HTFASYAALSGQ-VPVIGIAAGRCFAGNAALLGCSDVIIATRG- 779 Query: 209 ATIFLAGPPLVKAATGEVVSAEELGGADVHCKVSGVADHYAEDDDHALAIARRCVANLNW 268 + I + GP +++ V E++G + V +GV D +D+ A+ AR ++ Sbjct: 780 SNIGMGGPAMIEGGGLGVFKPEQIGPSRVQ-HANGVIDVLVDDEAGAVQAARHYLSFF-- 836 Query: 269 RKQGQLQCRAPRAPLYPAEELYGVIPADSKQPYDVREVIARLVDGSEFDEFKALFGTTLV 328 Q R P L V+P + + YD R +A LVD + + FG + Sbjct: 837 ------QGRTPEWSAPDQRLLRAVVPENRLRVYDTRTAMAGLVDDASLLPLRTGFGAGIH 890 Query: 329 CGFAHLHGYPIAILANN-----GILFAEAAQKGAHFIELACQRGIPLLFLQNITGFMVGQ 383 A + G P+ +LANN G + A+AA KGA F++L G+P++ L + GFMVG Sbjct: 891 TALARIEGRPVGLLANNPQHLGGAIDADAADKGARFMQLCNAHGLPIVSLVDTPGFMVGP 950 Query: 384 KYEAGGIAKHGAKLVTAVACARVPKFTVLIGGSFGAGNYGM-CGRAYDPRFLWMWPNARI 442 + EA +H ++L A RVP F+V++ +G G GM G + P F WP Sbjct: 951 EVEATAQVRHVSRLFVTAASLRVPTFSVVLRKGYGLGAMGMTAGGFHAPVFTVAWPTGEF 1010 Query: 443 GVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAKIKAPILEQYEHQGHPYYSSARLWDDG 502 G MG E G + R++ E + G E +A + A +L + G + +A L D Sbjct: 1011 GAMGLE---GAVRLGFRKELEALPE--GAERDA-LFAKLLAKSYANGEAMHMAATLEIDA 1064 Query: 503 VIDPAQTREVLALALSAALNAP 524 VIDPA TR LA L++A AP Sbjct: 1065 VIDPADTRAWLARGLASAQVAP 1086 Lambda K H 0.321 0.137 0.409 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: 1235 Number of extensions: 72 Number of successful extensions: 6 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: 1095 Length adjustment: 40 Effective length of query: 495 Effective length of database: 1055 Effective search space: 522225 Effective search space used: 522225 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 (21.9 bits) S2: 55 (25.8 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