Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 8500054 DvMF_0817 Biotin carboxylase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >FitnessBrowser__Miya:8500054 Length = 472 Score = 229 bits (585), Expect = 2e-64 Identities = 168/462 (36%), Positives = 239/462 (51%), Gaps = 48/462 (10%) Query: 9 LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA---ADSYL 65 +LVANRGEIA R+++ R +GL V++A D + H R I +LGG K+ SY Sbjct: 8 VLVANRGEIAIRIVQACRKLGLAFTCVYTAEDAASGHVR---IARELGGDKSLCRVSSYH 64 Query: 66 QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAG--LIFLGPPASAIDAMGSKSAA 123 ++L+A A +GA A+HPGYGF +E+ FAR + LIF+GP I +G K Sbjct: 65 DANELMAVADDAGATAVHPGYGFFAEDYRFARRVSQRDRKLIFIGPSWRVIRELGDKINT 124 Query: 124 KTLMETAGVPLVPGYHGE----------AQDLETFRDAAERIGYPVLLKATAGGGGKGMK 173 K L + GVP VPG AQ L F++ VL+KA+AGGGG G++ Sbjct: 125 KRLARSLGVPTVPGSDRPIYDEMEAEKVAQSLFEFQEQQGIRKPLVLVKASAGGGGMGIE 184 Query: 174 VVEDVSQLAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHG-NCLYLNERD 232 V D+ + A F D +L+E+ + H+E+QV +D+ G N ++ R+ Sbjct: 185 EVYDIDLFRSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQVVSDRSGRNPVHFGTRN 244 Query: 233 CSIQRRH-QKVVEEAPAPGLTP----------QLRRAMGEAAVRAAQAIGYVGAGTVEFL 281 CSIQ QK +E AP G P Q+ R + + ++ A+ +GY GT E++ Sbjct: 245 CSIQSTGLQKRIEIAP--GFDPSSIEYGFDAAQVLRDITQHSLAMARKVGYDNVGTWEWI 302 Query: 282 LDARGEFFFMEMNTRLQVEHPVTEAIT------GLDLVAWQIRVAQGEPLPITQAQVPLL 335 + G F ME+NTR+QVE+ V+ I G+DL+A QIR+ GEPL Q V Sbjct: 303 VTRDGRPFLMEVNTRIQVENGVSATIARVRGQKGVDLIAEQIRIGLGEPLGYGQEDVTFE 362 Query: 336 GHAIEVRLYAEDPGNDFLPATGRLALYRESAEGPGRRVDSGVEEGD--EISPFYDPMLGK 393 G IE RL AEDP N F P GR+ + E P + + V D +I +DP L Sbjct: 363 GVGIEYRLIAEDPDNRFTPWVGRVDGF-GWPERPWLAMHTHVPSDDPYDIPTEFDPNLAL 421 Query: 394 LIAWGEDREQARLRLLSMLDEFVIGG-------LKTNIGFLR 428 I WG+D +AR R + LD V+ G L++N+ FLR Sbjct: 422 AIIWGKDLAEARERGVEFLDTLVLEGANNAGEPLRSNVRFLR 463 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: 668 Number of extensions: 41 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: 649 Length of database: 472 Length adjustment: 36 Effective length of query: 613 Effective length of database: 436 Effective search space: 267268 Effective search space used: 267268 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: 53 (25.0 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