Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_034270915.1 AMYHA_RS11770 acetyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000504245.1:WP_034270915.1 Length = 532 Score = 466 bits (1198), Expect = e-135 Identities = 257/543 (47%), Positives = 343/543 (63%), Gaps = 19/543 (3%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M+++ + + + DF + +L A+ +GGG + RH +RGKL R+RI Sbjct: 1 MTVVRTSVDAAAEDFAEYRDAMLTKLDELETEHAKAIEGGGEKYTERHRKRGKLLARERI 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120 + LID DS FLE+ LAA+ D +V A +V GIG V G MIIA+D TVKGG+ P Sbjct: 61 ELLIDEDSPFLELSPLAAWGS-DYKV-GASMVTGIGVVEGVECMIIASDPTVKGGSMNPW 118 Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180 +VKK RA +IA +NRLP I LV+SGGA LP Q E+F GR F + + S E +P Sbjct: 119 SVKKGFRAADIAAQNRLPTINLVESGGADLPTQKEIFIPG---GRTFRDLTRASKERVPT 175 Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240 +A V G+ TAGGAY+P MSD VV+VK +FLGGPPLVK ATGEE E LGGA++H R Sbjct: 176 VALVFGNSTAGGAYLPGMSDYVVMVKEQAKVFLGGPPLVKMATGEESDDESLGGAEMHAR 235 Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEP------PRYDPREIYGILP 294 SG+ADY A D+ +A+ + R I+ +R NW + P P PRYD ++ GI+P Sbjct: 236 TSGLADYLAVDEEDAIRLGRSII------KRLNWNKQGPSPKPSYSEPRYDAEDLLGIVP 289 Query: 295 RDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILAN-NGILFSESA 353 D + +D REVIAR+VDGS EFK YG++LV G+A I G+PVGILAN G+LFSE + Sbjct: 290 TDLKVPFDPREVIARVVDGSDFDEFKPLYGSSLVTGWADIHGYPVGILANARGVLFSEES 349 Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413 K FI+L + PL+FL N TG+MVGK YE GI K GA ++ AVS + VP +V++ Sbjct: 350 QKATQFIQLANQSDTPLLFLHNTTGYMVGKNYEQNGIIKHGAMMINAVSNSTVPHISVLM 409 Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473 G S+GAG+YGMCGRAY PR L+ WP+A+ +VMGG Q A VL + R + +RGQ ++ Sbjct: 410 GASYGAGHYGMCGRAYDPRFLFAWPSAKSAVMGGQQLAGVLSIVARASAESRGQAYDEDQ 469 Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTR-FGV 532 A + + E E P + S L+DDG+IDP +TR VL + L+A PV+ R +GV Sbjct: 470 DAAMRAMVEGQIEAESVPTFLSGMLYDDGIIDPRDTRTVLGMSLSAIHNGPVEGARGYGV 529 Query: 533 FRM 535 FRM Sbjct: 530 FRM 532 Lambda K H 0.322 0.139 0.423 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: 780 Number of extensions: 44 Number of successful extensions: 6 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: 535 Length of database: 532 Length adjustment: 35 Effective length of query: 500 Effective length of database: 497 Effective search space: 248500 Effective search space used: 248500 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 (21.9 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