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) >FitnessBrowser__Koxy:BWI76_RS13985 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:
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