Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_068001529.1 PsAD2_RS02130 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= SwissProt::Q5LUF3 (681 letters) >NCBI__GCF_001623255.1:WP_068001529.1 Length = 670 Score = 825 bits (2130), Expect = 0.0 Identities = 426/686 (62%), Positives = 514/686 (74%), Gaps = 21/686 (3%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+KILIANRGEIACRVIKTA+ MGI TVA+YSDAD+ ALHV+MADEAVHIG P A +SY Sbjct: 1 MFSKILIANRGEIACRVIKTAKAMGIKTVAVYSDADRDALHVEMADEAVHIGEPTAAKSY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 +VIDK++ A + TGA+AVHPGYGFLSE ++F E L+ EG++F+GP AIE MGDKITSK Sbjct: 61 LVIDKIIDACKQTGAEAVHPGYGFLSERAEFCERLKQEGIVFIGPNPKAIEVMGDKITSK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 + A EANVSTVPGYMGLIE +A +I+ ++GYPVMIKASAGGGGKGMRIAWND+EA +G Sbjct: 121 RFAAEANVSTVPGYMGLIETPQDAKRIAAEVGYPVMIKASAGGGGKGMRIAWNDEEAMDG 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 F +K+EA NSFGDDRIFIEKF+ PRHIEIQV+ D HGN +YLGERECSIQRRNQKV+E Sbjct: 181 FDRAKSEAINSFGDDRIFIEKFIENPRHIEIQVMGDKHGNAVYLGERECSIQRRNQKVIE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAPSP LDE TRR MGEQAVALAKAV Y SAGTVEF+ K+F+FLEMNTRLQVEHPVT Sbjct: 241 EAPSPLLDEKTRRKMGEQAVALAKAVDYDSAGTVEFVAGQDKSFFFLEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 EL+TGVDLVEQMIRVAAGE LSI Q DVKL GW+IE+R+YAEDPYR FLPSIGRLT YRP Sbjct: 301 ELVTGVDLVEQMIRVAAGEALSIKQEDVKLNGWSIESRIYAEDPYRNFLPSIGRLTHYRP 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 P E GK G VRNDTGV EG EISM+YDPMIAKL T A TRA AI Sbjct: 361 PVE---------GK------HGNYLVRNDTGVVEGSEISMFYDPMIAKLVTHAATRAEAI 405 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 E M ALD F+V+GI HN+PFL+++M HP++ SG+++T FIA+EYP+GFE P+ + Sbjct: 406 EGMSTALDEFQVDGIQHNVPFLASLMKHPRWRSGEISTGFIADEYPDGFEPAT-PDAEAN 464 Query: 481 RV-AAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQG----ADFPVTIAADHDGS 535 V A+ A +MH + R + GR+ H V EW V + G A+ +AA Sbjct: 465 SVLASVALSMHLIERERLDHLPGRLRPHHGAVRREWAVRIDGETLKAELVEGLAATPVDL 524 Query: 536 TVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPR 595 + D G++ RV S W PG+ L V + ++V + G+++ +G + V +PR Sbjct: 525 DICVDGGANERVASSWAPGEMLWKGQVGERNVSVQVRAVDNGYQLDWQGFSVVAQVMSPR 584 Query: 596 QAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAE 655 AELA LMPEK+ PDTS +LLCPMPGL+V + V GQEV+ G+ L +EAMKMEN+LRAE Sbjct: 585 IAELAALMPEKVAPDTSNLLLCPMPGLVVSLHVNEGQEVKAGEQLAIVEAMKMENVLRAE 644 Query: 656 KKGVVAKINASAGNSLAVDDVIMEFE 681 + VV+ I A+ G+SLAVD VIMEFE Sbjct: 645 RDCVVSAIKAAPGDSLAVDAVIMEFE 670 Lambda K H 0.317 0.134 0.387 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: 1237 Number of extensions: 40 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: 681 Length of database: 670 Length adjustment: 39 Effective length of query: 642 Effective length of database: 631 Effective search space: 405102 Effective search space used: 405102 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: 54 (25.4 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