Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_010960346.1 MCA_RS05120 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::Smeli:SM_b21124 (662 letters) >NCBI__GCF_000008325.1:WP_010960346.1 Length = 448 Score = 429 bits (1103), Expect = e-124 Identities = 224/455 (49%), Positives = 300/455 (65%), Gaps = 17/455 (3%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 M K++IANRGEIA RI+R R LGI+ VAV+S+AD D HV LADE++ IG AP+ +SY Sbjct: 1 MLGKVVIANRGEIALRILRACRELGIKAVAVHSEADRDLKHVRLADESVCIGPAPSRDSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I+ AA A AIHPGYGFLSENADFAE V ++G IF+GP P IR MG K AA Sbjct: 61 LNVPAIISAAEVTDALAIHPGYGFLSENADFAEKVIQSGFIFIGPRPETIRMMGDKVAAI 120 Query: 121 ALMERSGVPVVPGYHG-----EEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQE 175 M+++G+P +PG G EE++ + AR IG+P++IKA GGGG+GMR V + Sbjct: 121 EAMKKAGIPTLPGSDGPLGDDEEENLAI----ARRIGFPIIIKAAGGGGGRGMRVVHSEA 176 Query: 176 DFGPALEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRH 235 ++E R EA +AFG+ V +E++L PRHIE QV D HGN+VHL ERDCS QRRH Sbjct: 177 SLAASIELTRSEAGAAFGNDMVYMEKFLENPRHIEFQVIADSHGNVVHLGERDCSTQRRH 236 Query: 236 QKVIEEAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMN 295 QKV+EEAPAPG+T R MG V+A + IGY+GAGT EF+ FYF+EMN Sbjct: 237 QKVVEEAPAPGITQAQRDEMGMRCVQACREIGYLGAGTFEFLYQ------DGQFYFIEMN 290 Query: 296 TRLQVEHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLP 355 TR+QVEHPVTE +TG D+V+ QLR+A+GEPL +QA++ M G A E R+ AEDP F+P Sbjct: 291 TRVQVEHPVTEMVTGFDIVKEQLRIAAGEPLSIRQAEVEMRGHAIECRINAEDPV-NFMP 349 Query: 356 ATGRLTELSFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKEC 414 + G + + P G RV++ + G + PYYD +I KLI HG+ R+ A+ R++ AL E Sbjct: 350 SPGLIEQFHMPGGPGIRVETHIYNGYRVPPYYDSMIGKLIAHGETRAGAIARMRTALNEM 409 Query: 415 RIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREI 449 IGG N L+ + + F +G + +++++ Sbjct: 410 VIGGIKCNIPLLLDIVNDSAFEAGGQNIHYLEQKL 444 Lambda K H 0.319 0.135 0.394 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: 765 Number of extensions: 25 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: 662 Length of database: 448 Length adjustment: 35 Effective length of query: 627 Effective length of database: 413 Effective search space: 258951 Effective search space used: 258951 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 (21.8 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