Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate BPHYT_RS23275 BPHYT_RS23275 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__BFirm:BPHYT_RS23275 Length = 692 Score = 625 bits (1613), Expect = 0.0 Identities = 356/702 (50%), Positives = 436/702 (62%), Gaps = 61/702 (8%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF+K+LIANRGEIACR+ T +RLGI +VAVYSDAD +A HVA DEA+ IGG+ AAESY Sbjct: 1 MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADANAKHVAACDEAVHIGGSTAAESY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I++AAR+ GAQA+HPGYGFLSEN DFA A AG++F+GPP AI AMG K AAK Sbjct: 61 LRVERIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 ALM + VP+VPGYHG++QDA L A IGYPVL+KA AGGGGKGMR VER EDF A Sbjct: 121 ALMHTAAVPLVPGYHGDDQDAQLLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFEAA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 L + +REA S+FG+ VL+E+YLT+PRH+E+QVF DRHG V+LF+RDCS+QRRHQKV+E Sbjct: 181 LASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLE 240 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAPAPG+ AE++R MGDAAV AA+A+ YVGAGTVEFI T FYFMEMNTRLQV Sbjct: 241 EAPAPGLAAEIKREMGDAAVAAARAVNYVGAGTVEFIMTGTG-----DFYFMEMNTRLQV 295 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTE +TG DLVEWQLRVA+GE LP Q + ++G A EAR+YAE PARGFLP+TG L Sbjct: 296 EHPVTEMVTGQDLVEWQLRVAAGEALPLTQEQLKIDGHAIEARIYAEHPARGFLPSTGTL 355 Query: 361 TELSFPEGTS----------------------RVDSGVRQGDTITPYYDPLIAKLIVHGQ 398 L PEG R+DSGVR+GDTITP+YDP+IAKLIVHG Sbjct: 356 KHLRMPEGVEFTLDAAGSGAAGLGESGRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGA 415 Query: 399 NRSAALGRLQDALKECRIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAP-VA 457 R AL R+ AL C + G TN +FL + F +G DTGLI+R + L AP Sbjct: 416 TREEALARMSRALHACEVVGPHTNVEFLQSIVASEPFATGDLDTGLIERHHDALFAPRKK 475 Query: 458 PGDEALALA-AIFSTGALDPNRSTDPWSSLGSWQIWG---------------------DA 495 P EALALA A PW +L W++ G D+ Sbjct: 476 PFKEALALACAALLKREGGTAHGASPWDALSHWRLNGGYTQTLGWRDLESGSAGNAGSDS 535 Query: 496 HRMVVIEHADVRATVTLASRG-RDQFAVRAGASTLPVLVLDRFEGGARLEVAGQKRLIRF 554 + A T TL G R+ F+ G+ L + R + + R Sbjct: 536 ESTFTVTFARDGGTQTLEHDGVREDFSWSDGSG------LHEY----RATIGDARATGRV 585 Query: 555 SRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQ 614 D + +F G L F + L +E + L APMPG V V V G V KG Sbjct: 586 FVDGDTFHVFCLGEALSFEWQNLLAHAADAEGGEGRLTAPMPGKVIAVLVEPGTVVEKGT 645 Query: 615 ALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLVTL 656 L+VMEAMKME T+ A GT++ V + G QV++G L+ L Sbjct: 646 PLIVMEAMKMEHTIGAPAAGTVSEVLYSVGDQVADGAQLLVL 687 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: 1305 Number of extensions: 74 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 662 Length of database: 692 Length adjustment: 39 Effective length of query: 623 Effective length of database: 653 Effective search space: 406819 Effective search space used: 406819 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