Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF3280 HP15_3222 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >FitnessBrowser__Marino:GFF3280 Length = 448 Score = 415 bits (1066), Expect = e-120 Identities = 216/445 (48%), Positives = 297/445 (66%), Gaps = 6/445 (1%) Query: 6 LTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65 L +L+ANRGEIA R++R + +G+ TVAVHS DRD H R AD V +G + A DSYL Sbjct: 4 LEKVLIANRGEIALRILRACKELGIKTVAVHSQVDRDLMHVRLADESVCIGPNSATDSYL 63 Query: 66 QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKT 125 I +I+AA+ + + IHPGYGFL+ENA FA +E +G F+GP A I MG+K +A Sbjct: 64 NIPTIISAAEVTDSVGIHPGYGFLAENADFAEQVEKSGFRFIGPKAETIRLMGNKVSAIN 123 Query: 126 LMETAGVPLVPGYHGEAQDLE--TFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183 M AGVP VPG G D E T R A E IGYPV++KA +GGGG+GM+VV + L + Sbjct: 124 AMIKAGVPTVPGSDGPLDDDEERTLRIAKE-IGYPVMIKAASGGGGRGMQVVHSEAALLK 182 Query: 184 ALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243 + Q EA+++FGD + +EK+L PRHVE+QV AD HGNC++L +RDCS+QRR+QKV+ Sbjct: 183 GVQITQSEAKNAFGDPTVYLEKFLEAPRHVEVQVLADMHGNCIHLGDRDCSMQRRNQKVI 242 Query: 244 EEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPV 303 EEAPAP + P+ R +A A + IGYVGAGT EFL GEF+F+EMNTR+QVEHPV Sbjct: 243 EEAPAPNINPESRERTLKACTDACKEIGYVGAGTFEFLYQ-DGEFYFIEMNTRVQVEHPV 301 Query: 304 TEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYR 363 +E +TG+D+V Q+R+A G PL TQ + + GHA+E R+ AEDP F+P+ G++ + Sbjct: 302 SEMVTGVDIVREQLRIASGLPLQYTQDDIRISGHAMECRINAEDP-KTFIPSPGKVKHF- 359 Query: 364 ESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTN 423 + G G RVDS + G + P+YD ++ KLI WG+DR+ AR R+ + LDE V+ G+KTN Sbjct: 360 HAPGGNGVRVDSHLYSGYTVPPYYDSLVAKLITWGDDRDIARRRMKNALDELVVEGIKTN 419 Query: 424 IGFLRRIVAHPAFAAAELDTGFIPR 448 R++V F + ++ + Sbjct: 420 QPLHRKLVRDGGFKQVDFTIHYLEK 444 Lambda K H 0.319 0.134 0.390 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: 677 Number of extensions: 27 Number of successful extensions: 4 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: 649 Length of database: 448 Length adjustment: 35 Effective length of query: 614 Effective length of database: 413 Effective search space: 253582 Effective search space used: 253582 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 (21.7 bits) S2: 52 (24.6 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