Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 5210939 Shew_3365 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >FitnessBrowser__PV4:5210939 Length = 450 Score = 428 bits (1100), Expect = e-124 Identities = 225/450 (50%), Positives = 308/450 (68%), Gaps = 17/450 (3%) Query: 9 LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +LVANRGEIA R++R R +G+ TVA++S+ D+D+ H R AD ++ +G + A +SYL I Sbjct: 7 VLVANRGEIALRIIRACRQLGIKTVALYSSADKDSGHLRLADQQICIGPAPAKESYLNIA 66 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128 ++ AA + AIHPGYGFL+ENA FA+ + ++G F+GP A I MG K +A M+ Sbjct: 67 AILGAADLARVDAIHPGYGFLAENADFAQQVTDSGFHFIGPKADTIRLMGDKVSAIAAMK 126 Query: 129 TAGVPLVPGYHG-----EAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183 AGVP VPG G EAQ LE A +IGYP+++KATAGGGGKGM+VVED +QL Sbjct: 127 AAGVPTVPGSDGLLGDNEAQSLEI----AAQIGYPLIIKATAGGGGKGMRVVEDEAQLLG 182 Query: 184 ALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243 A+A ++EA+++FG+ + +EKYL +PRH+E+QV D G+C+ L ERDCS+QR QKV+ Sbjct: 183 AIALTRQEAEAAFGNGGVYLEKYLTRPRHIEVQVLCDHQGHCISLGERDCSLQRAQQKVI 242 Query: 244 EEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPV 303 E APAPGLTP+ R+ + E+ +RA QAIGY GAGT+EFL GEF+FMEMNTR+QVEH + Sbjct: 243 ESAPAPGLTPEQRQQISESCIRACQAIGYRGAGTLEFLYQ-DGEFYFMEMNTRIQVEHTI 301 Query: 304 TEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYR 363 +E +TG+DL+ Q+RVAQGEPL + ++ + GHAIE R+ AEDP + F P+ GR+ Sbjct: 302 SEMVTGVDLLVLQLRVAQGEPLALQESLIQPKGHAIECRINAEDPAS-FAPSPGRIDRLV 360 Query: 364 ESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTN 423 G G R +S + G + P YD M+ KLIAWG+DR QA R+ + LDE I G+KTN Sbjct: 361 VPG-GLGVRWESHLSPGAHVPPQYDAMIAKLIAWGDDRAQAIARMRTALDELTITGIKTN 419 Query: 424 IGFLRRIVAHPAFAAAE-----LDTGFIPR 448 + LR ++A P E L+ F+PR Sbjct: 420 VPLLRALLADPQVQQGETSIHYLEETFLPR 449 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: 761 Number of extensions: 31 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: 450 Length adjustment: 35 Effective length of query: 614 Effective length of database: 415 Effective search space: 254810 Effective search space used: 254810 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