Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate BWI76_RS13985 BWI76_RS13985 urea carboxylase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS13985 BWI76_RS13985 urea carboxylase Length = 1201 Score = 391 bits (1004), Expect = e-112 Identities = 213/438 (48%), Positives = 285/438 (65%), Gaps = 7/438 (1%) Query: 8 TLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67 TLL+ANRG IACR++RT +AM + VAV+S D + H R+AD + LG AA +YL Sbjct: 4 TLLIANRGAIACRILRTLRAMQVKGVAVYSEADLSSLHIRDADEALSLGDGPAAQTYLAT 63 Query: 68 DKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALM 127 +K+IAAA+ SGA+AIHPGYGFLSENA FA A E AGL F+GP + G K A+AL Sbjct: 64 EKIIAAAQQSGARAIHPGYGFLSENAAFAEACEAAGLAFVGPTPRQLRVFGLKHTARALA 123 Query: 128 ETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187 + GVPL+ G A E R AAE +GYPV+LK+TAGGGG GM+V D +L EA A+ Sbjct: 124 KAEGVPLLEGSELLADSDEACR-AAEAVGYPVMLKSTAGGGGIGMRVCRDARELTEAFAT 182 Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247 QR Q++F D+ + +EKY+ + RH+E+Q+F D G+ + L RDCS+QRR+QKV+EE P Sbjct: 183 VQRLGQNNFSDAGVFLEKYIERARHLEVQIFGDGRGDVIALGVRDCSVQRRNQKVIEETP 242 Query: 248 APGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARG-EFFFMEMNTRLQVEHPVTEA 306 AP L QA+ AA+ +A+ Y AGTVEF+ D+ +F+F+E+NTRLQVEH VTE Sbjct: 243 APNLPEGTAQALCAAAIALGKAVSYRSAGTVEFVYDSTARQFYFLEVNTRLQVEHGVTEQ 302 Query: 307 ITGLDLVAWQIRVAQGE--PLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRL--ALY 362 + G+DLV W I +A G+ PL + A + GHAI+ RLYAEDP F P+ G L A++ Sbjct: 303 VWGVDLVRWMIELAAGDLPPLDVLAAGLRPQGHAIQARLYAEDPGRQFQPSPGLLTEAIF 362 Query: 363 RESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKT 422 A G R+D VE G E+ PF+DPML K IAW +R++A L L E + G++T Sbjct: 363 -PPADGAALRIDRWVEAGCEVPPFFDPMLAKTIAWRPSRDEAIAGLAQALAETRLYGVET 421 Query: 423 NIGFLRRIVAHPAFAAAE 440 N +L +I+ F E Sbjct: 422 NRLYLLQILGFAPFTEGE 439 Score = 49.7 bits (117), Expect = 8e-10 Identities = 27/69 (39%), Positives = 41/69 (59%) Query: 581 GLAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSE 640 G+ +P++G++ +V + G V AG LVVLE+MKME + AP GVI+ ++ Q G V Sbjct: 1130 GVESPISGNLWQVQTAAGSRVRAGDVLVVLESMKMEIPLLAPCDGVIQQVHVQPGSAVRA 1189 Query: 641 GSALVAFEE 649 G + E Sbjct: 1190 GQRVAVIIE 1198 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: 1812 Number of extensions: 79 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 649 Length of database: 1201 Length adjustment: 43 Effective length of query: 606 Effective length of database: 1158 Effective search space: 701748 Effective search space used: 701748 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: 56 (26.2 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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