Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_101589300.1 BJEO58_RS09820 ATP-grasp domain-containing protein
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >NCBI__GCF_900169175.1:WP_101589300.1 Length = 600 Score = 399 bits (1024), Expect = e-115 Identities = 205/457 (44%), Positives = 286/457 (62%), Gaps = 10/457 (2%) Query: 9 LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +L+ANRGEIA R++R R +G+ +VA ++A D DA AD L GS AA++YL I Sbjct: 23 VLIANRGEIALRIVRACRDLGIASVAAYTAADADALFVSLADDAYRLDGSGAAETYLSIP 82 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128 ++ A +GA A+HPGYG+L+E+ FA A+ AGL ++GP ASAIDA+G K+ A+ + + Sbjct: 83 TMVELAHRAGADAVHPGYGYLAESGEFATAVAEAGLTWVGPTASAIDALGDKAGARAVAQ 142 Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 G P+ G G + + D AE IGYPV +KA GGGG+G + D L A +A Sbjct: 143 AVGAPVPQGSAGPVESIPEALDVAEEIGYPVAIKAVHGGGGRGFRTAADAQALPAAFEAA 202 Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 REA+++FG L+E+ +++PRHVE Q AD HG L ++ RDC++QRR+QKV+EEAPA Sbjct: 203 SREAKAAFGRGDCLIEQQIIRPRHVETQCLADAHGRVLVVSTRDCTMQRRNQKVLEEAPA 262 Query: 249 PGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308 PGLT + + +A+V + +GYVGA T EFL+ A G FME N R+QVEH +TE + Sbjct: 263 PGLTDEQEHLLEDASVNILRHVGYVGAATCEFLVGADGRITFMEANARIQVEHTITEEVA 322 Query: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAEG 368 G+DLVAWQ+R+A G LP ++ GHA + R+ AEDP + F+P G + YRE + G Sbjct: 323 GVDLVAWQLRIAAGAALP--ESFPAPRGHAFQFRINAEDPTHGFVPVCGTITRYREPS-G 379 Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFLR 428 PG R+DSG+ G + +DPML KLI WG DRE A R +DEF + GL T + R Sbjct: 380 PGVRMDSGIATGTVVGTDFDPMLAKLIVWGPDRESALARSRRAIDEFALEGLPTLLPLHR 439 Query: 429 RIVAHPAFAAAE-------LDTGFIPRYQAQLLPEPS 458 + FA E L+ F+P + A+ LP+PS Sbjct: 440 SLTDSAEFAGPELRVSTRWLEEDFMPAWSAERLPQPS 476 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: 958 Number of extensions: 46 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 649 Length of database: 600 Length adjustment: 37 Effective length of query: 612 Effective length of database: 563 Effective search space: 344556 Effective search space used: 344556 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: 54 (25.4 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