Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1016 PGA1_c10330 methylcrotonoyl-CoA carboxylase subunit alpha
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__Phaeo:GFF1016 Length = 645 Score = 642 bits (1656), Expect = 0.0 Identities = 364/662 (54%), Positives = 445/662 (67%), Gaps = 24/662 (3%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF K+LIANRGEIACR++ TAR +G+RTVAVYSDAD A HV +ADEA+ IGG+ A+SY Sbjct: 1 MFDKILIANRGEIACRVMETARAMGVRTVAVYSDADVTAKHVQMADEAVHIGGSAPADSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I++ A+ GAQAIHPGYGFLSEN F +AV AG+ F+GP AIR MGLKDAAK Sbjct: 61 LKGDVIIRVAQESGAQAIHPGYGFLSENPAFVDAVEAAGLSFIGPSADAIRKMGLKDAAK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 ALME++GVPVVPGYHG QDA FLA A +IGYPVLIKA AGGGGKGMR VE +F A Sbjct: 121 ALMEKAGVPVVPGYHGANQDAEFLAGEAEKIGYPVLIKAVAGGGGKGMRLVEAPAEFSDA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 L++A+ EA +AFG+ VL+E+Y+ +PRHIE+QVFGD + VHLFERDCSLQRRHQKVIE Sbjct: 181 LKSAQGEATTAFGNPDVLIEKYIQQPRHIEVQVFGD-GTHAVHLFERDCSLQRRHQKVIE 239 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAPAPGMTAE+R AMG+A VRAA+AIGY GAGTVEFI D ++GL D F+FMEMNTRLQV Sbjct: 240 EAPAPGMTAEMREAMGEAGVRAAEAIGYKGAGTVEFIVDGSDGLRTDGFWFMEMNTRLQV 299 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTE ITG+DLVEWQLRVASGE LP +Q D+++ G AFEARLYAED +GFLPATG L Sbjct: 300 EHPVTELITGVDLVEWQLRVASGESLPAQQDDLTITGHAFEARLYAEDVPKGFLPATGTL 359 Query: 361 TELSFPEGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTV 420 T LSFP R DSGVR GDTI+P+YDP+I+K+IVHG RS AL +L+ AL+ + GTV Sbjct: 360 THLSFP-AECRADSGVRAGDTISPWYDPMISKVIVHGATRSVALSKLRRALERTEVAGTV 418 Query: 421 TNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAIFSTGALDPNRST 480 TN FL L F G DTGLI R++E LT A GD +A + AL ++S Sbjct: 419 TNLAFLGALASHQGFGRGEVDTGLIARDLEALT---AVGDMPVAHWIAAAQRALCLHKS- 474 Query: 481 DPWSSLGSWQIWGDAHRMVVIEHADVRATVTLASRGRDQFAVRAGASTLPVL---VLDRF 537 + +W HR V + H + +T+ G + S+ V R Sbjct: 475 ---GGDSGFTLWAPLHRAVQLTHGEESLEITVEVLGPQAQRWQLDDSSHEVTFDGTCWRH 531 Query: 538 EGGARLEVA-GQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMP 596 +G VA RL F+R + +F D L ++ + + APMP Sbjct: 532 DGHPLPNVAEADGRLTVFAR-----------ISSIFDCIDPLDRAGTAGGDTNVIEAPMP 580 Query: 597 GLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLVTL 656 GLVK V AG V +G L ++EAMKME +L A+R+G +A V + G QV G LV L Sbjct: 581 GLVKAVFAEAGAEVKEGDRLAILEAMKMEHSLLAARDGVVAEVLASAGDQVEAGAALVRL 640 Query: 657 ME 658 E Sbjct: 641 EE 642 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: 1218 Number of extensions: 62 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: 662 Length of database: 645 Length adjustment: 38 Effective length of query: 624 Effective length of database: 607 Effective search space: 378768 Effective search space used: 378768 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: 54 (25.4 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