Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 3607987 Dshi_1395 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >FitnessBrowser__Dino:3607987 Length = 448 Score = 399 bits (1025), Expect = e-115 Identities = 210/432 (48%), Positives = 278/432 (64%), Gaps = 3/432 (0%) Query: 9 LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +L+ANRGEIA RV+R + +G+ +VAVHS D DA H R AD V +G + SYL I Sbjct: 5 ILIANRGEIALRVIRACRELGIQSVAVHSTADTDAMHVRMADEAVCIGPPPSPQSYLSIP 64 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALME 128 +I+A + +GA+AIHPGYGFLSENA F + +++ GL F+GP A I MG K AK M+ Sbjct: 65 AIISACEITGAEAIHPGYGFLSENANFVQIVQDHGLTFIGPTAEHIRVMGDKITAKETMK 124 Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 GVP VPG G DLET R A IGYPV++KATAGGGG+GMK+ + L EA +A Sbjct: 125 NLGVPCVPGSDGGVPDLETARRVAGEIGYPVIVKATAGGGGRGMKLAKTAEDLDEAFQTA 184 Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 + E +++FG+ + +EKYL PRH+E+QVF D G ++L ERDCS+QRRHQKV EEAP+ Sbjct: 185 RSEGKAAFGNPDVYLEKYLSTPRHIEVQVFGDGKGGAVHLGERDCSLQRRHQKVFEEAPS 244 Query: 249 PGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308 P + A+ R +G+ A I Y GAGT+EFL + GEF+F+EMNTRLQVEHPVTEAI Sbjct: 245 PVIDAETRARIGKTCAEAVARIDYAGAGTIEFLYE-NGEFYFIEMNTRLQVEHPVTEAIF 303 Query: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLALYRESAKG 368 G+DLV QIRVA G P+ Q + + GHAIEVR+ AE V F P G + + + G Sbjct: 304 GVDLVKEQIRVAAGYPMTFKQENLQVRGHAIEVRINAE-KVPAFTPCPGMVTTF-HTPGG 361 Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTNIGFLR 428 G R+DS + G I P+YD ++GKLI ++R A RL L E + G+ T + Sbjct: 362 LGVRMDSALYGGYSIPPYYDSLIGKLIVLAQDRPAALARLNRALGELIVDGIDTTVPLFH 421 Query: 429 RIVAHPAFAAAE 440 ++A A + Sbjct: 422 ALLAEEAIQTGD 433 Lambda K H 0.319 0.134 0.389 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: 739 Number of extensions: 34 Number of successful extensions: 3 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