Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011386591.1 AMB_RS21445 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Smeli:SM_b21124 (662 letters) >NCBI__GCF_000009985.1:WP_011386591.1 Length = 663 Score = 505 bits (1300), Expect = e-147 Identities = 303/660 (45%), Positives = 393/660 (59%), Gaps = 27/660 (4%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF+K+LIANRGEIACR+I+TA+++GI+TVAVYSDAD DALHV++ADEA+ IG A +A+SY Sbjct: 1 MFTKILIANRGEIACRVIKTAKKMGIKTVAVYSDADKDALHVSMADEAVHIGPAASAQSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L IV A + GAQA+HPGYGFLSE +F EA+ +AG+ F+GP AI AMG K +K Sbjct: 61 LVIDKIVDACKQTGAQAVHPGYGFLSEKREFQEALGKAGIAFIGPDAHAIFAMGDKIESK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 L +GV VPGY G +DA AREIGYPV++KA AGGGGKGMR + Sbjct: 121 KLAREAGVNTVPGYLGVIKDADEAVKIAREIGYPVMLKASAGGGGKGMRLAWNDAEAHEG 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 +A EA+++FGD V +E+++ +PRHIE+QV D G ++L ER+CS+QRRHQKVIE Sbjct: 181 FTSATNEAKTSFGDDRVFVEKFIEQPRHIEIQVLADGQGTTLYLGERECSIQRRHQKVIE 240 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAP+P +T E R+AMG+ A A+ + Y AGTVEFI G FYF+EMNTRLQV Sbjct: 241 EAPSPFLTPETRKAMGEQACALARIVNYKSAGTVEFIVGGATG----EFYFLEMNTRLQV 296 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTE ITG+DLVE +RVASGE L Q D+ +NGW+ EAR+YAEDP R FLP+TGRL Sbjct: 297 EHPVTEMITGLDLVEQMIRVASGEKLSITQDDVKLNGWSMEARVYAEDPFRNFLPSTGRL 356 Query: 361 TELSFPEGTS--RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGG 418 T P ++ RVD+GV +G I+ +YDP+IAKLI +G R AA+ ++ AL E I G Sbjct: 357 TRYQPPAESAHVRVDTGVYEGGEISMFYDPMIAKLITYGPTRDAAIAHMRQALDEYYIRG 416 Query: 419 TVTNRDFLIRLTEEHDFRSGHPDTGLIDREIER-LTAPVAPGDEALALAAIFSTGALDPN 477 N FL L + F G T I E A P D+ L A+ A N Sbjct: 417 LSHNIPFLASLFSKERFVKGALTTNFIAEEYANGFHANDLPADDPTVLIAV----AAAAN 472 Query: 478 RSTDPWSSLGSWQIWGDAHR-----MVVIEHADVRATVTLASRGRDQFAVRAGASTLPVL 532 R + S Q G + +VV+ TV A G +AV G T+ V Sbjct: 473 RRIHERDTRISGQFPGHEMKAGDEWVVVMSGQYHDITVRPAENG---YAVALGGETVDVR 529 Query: 533 VLDRF-EGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHV-------PDGLTGGQSS 584 + E R V G+ ++ R L L H G + V + L ++ Sbjct: 530 TDWQIGEPLFRANVDGRAVAVQIERVGSGLRLAHAGSRVDVLVLTPHAAKMNKLMPFKAP 589 Query: 585 EIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEG 644 L++PMPGL+ + V AG V G+ L V+EAMKME L A R+ T+A H A G Sbjct: 590 PDMSKYLLSPMPGLLVKLLVEAGQEVKAGEPLAVVEAMKMENILKAERDATVAKTHAASG 649 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: 1102 Number of extensions: 60 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: 663 Length adjustment: 38 Effective length of query: 624 Effective length of database: 625 Effective search space: 390000 Effective search space used: 390000 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