Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_086508686.1 BZY95_RS03995 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::SB2B:6937189 (673 letters) >NCBI__GCF_002151265.1:WP_086508686.1 Length = 446 Score = 421 bits (1081), Expect = e-122 Identities = 224/445 (50%), Positives = 300/445 (67%), Gaps = 8/445 (1%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 M +K+LIANRGEIA R++R +++GIKTVAV+S ADR+ HV LADE+ +G + A SY Sbjct: 1 MLDKVLIANRGEIALRILRACKELGIKTVAVHSKADRELMHVRLADEAVCIGPAPSAQSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L +I A+ + AIHPGYGFLSENA FA E SG F+GP ++ I MG K +A Sbjct: 61 LNIPALISAAEVTDSSAIHPGYGFLSENANFAEQVERSGFVFIGPRAETIRLMGDKVSAI 120 Query: 121 LIMEKAGVPLVPGYHG---DDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESEL 177 M+KAGVP VPG G DD+ D LA A++IGYP++IKAA GGGG+GMR+V +E L Sbjct: 121 EAMKKAGVPTVPGSDGPLGDDEGDN--LAIARRIGYPVIIKAAAGGGGRGMRVVHTEGHL 178 Query: 178 KAAIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQK 237 +AI+ R EA ++FG+ + ME++L +PRHVEVQV AD QGN ++L DRDCS+QRRHQK Sbjct: 179 LSAINVTRTEAHAAFGDGTVYMEKFLERPRHVEVQVLADGQGNAIHLFDRDCSLQRRHQK 238 Query: 238 VVEEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEH 297 V+EEAPAPG+ R ++ EA A IDYRGAGT EFL + D FFF+EMNTR+QVEH Sbjct: 239 VLEEAPAPGIDPEARAKVLEACRQACIEIDYRGAGTFEFLYE-DGRFFFIEMNTRVQVEH 297 Query: 298 PVTEMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTF 357 PVTEMVTG D+V+ QL +A+G L + Q +++++GHAFE RI AEDP F+P+ GK+T Sbjct: 298 PVTEMVTGVDIVREQLRIASGLPLSIRQEDVKVNGHAFECRINAEDPRT-FMPSPGKVT- 355 Query: 358 LREPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLK 417 L P +R+DS + + +YD +I KLI W +SR AL R+ L + V G+K Sbjct: 356 LYHPPGGLGIRMDSHLYTGYTVPPHYDSLIGKLITWGDSREIALTRMRNGLDELLVEGIK 415 Query: 418 HNIEFLSNIAEHPAFAQANFSTDFI 442 N + ++ F Q + ++ Sbjct: 416 TNTDLHKDLVRDGHFQQGGVNIHYL 440 Lambda K H 0.317 0.134 0.380 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: 763 Number of extensions: 32 Number of successful extensions: 4 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: 673 Length of database: 446 Length adjustment: 36 Effective length of query: 637 Effective length of database: 410 Effective search space: 261170 Effective search space used: 261170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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