Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate 3607892 Dshi_1300 Propionyl-CoA carboxylase (RefSeq)
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__Dino:3607892 Length = 534 Score = 668 bits (1723), Expect = 0.0 Identities = 327/519 (63%), Positives = 389/519 (74%) Query: 17 ANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSSFLEIGAL 76 AN A H + A + + A GGG R RH RGK+ RDR+ L+DP S FLE+GA Sbjct: 16 ANRAAHLAALAQVSQVAALAAAGGGEAARARHVARGKMLPRDRVANLLDPGSPFLEVGAT 75 Query: 77 AAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQEIARENR 136 A + ++D P G + G+GRV G+ VM++ NDATVKGGTY+P+TVKKHLRAQEIA E Sbjct: 76 AGHGLHDGAAPCGGAIAGVGRVHGQDVMVVCNDATVKGGTYYPITVKKHLRAQEIAAECH 135 Query: 137 LPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCTAGGAYVP 196 LPCIYLVDSGGA LP Q EVFPDRDHFGRIFYNQA+MSA GIPQIA VMGSCTAGGAYVP Sbjct: 136 LPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQARMSAAGIPQIAVVMGSCTAGGAYVP 195 Query: 197 AMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFANDDREAL 256 AMSD +IVK GTIFL GPPLVKAATGE V+AE+LGG DVHTR+SGVAD A DD AL Sbjct: 196 AMSDVTIIVKAQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADALAEDDAHAL 255 Query: 257 AIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIARIVDGSRL 316 A+ R VA L ++ + PE P YDP E+ ++P YD+ EVIARIVDGSR Sbjct: 256 ALARQAVASLNRAAPSSVVWQSPEAPAYDPEELLELVPASLSVPYDIHEVIARIVDGSRF 315 Query: 317 HEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCARNIPLVFLQNI 376 FK R+G TLV GFAHIEG PVGI+ANNG+LFSE+A KGAHF+ELC R IPLVFLQNI Sbjct: 316 DAFKPRFGETLVTGFAHIEGCPVGIVANNGVLFSEAAQKGAHFVELCSQRKIPLVFLQNI 375 Query: 377 TGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMCGRAYQPRQLWM 436 TGFMVG+QYEN GIA+ GAK+VTAV+ VPK T+++GGSFGAGNYGM GRAYQPR +W Sbjct: 376 TGFMVGRQYENEGIARHGAKMVTAVATTAVPKITMVVGGSFGAGNYGMAGRAYQPRFMWS 435 Query: 437 WPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKYEQEGHPYYASA 496 WP++RISVMGG QAA VL T++RD + +G + +E+ F P + +E + HP YASA Sbjct: 436 WPSSRISVMGGAQAAGVLATVKRDAIERKGGSWSAQEEAAFKQPTIEMFEAQSHPLYASA 495 Query: 497 RLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 RLWDDG++DP ++R VL+L L AA AP++ TRFGVFRM Sbjct: 496 RLWDDGIVDPRKSRAVLSLSLRAALNAPIEETRFGVFRM 534 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: 951 Number of extensions: 36 Number of successful extensions: 3 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: 534 Length adjustment: 35 Effective length of query: 500 Effective length of database: 499 Effective search space: 249500 Effective search space used: 249500 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 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