Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ac3H11_2276 Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3)
Query= BRENDA::Q9LDD8 (587 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2276 Length = 510 Score = 251 bits (642), Expect = 4e-71 Identities = 170/530 (32%), Positives = 266/530 (50%), Gaps = 48/530 (9%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126 M+ IL +L GGG++ + ++ KL RERI+ LLD G+ F E H Sbjct: 1 MQDILEQLEKKRALARLGGGQKRIDAQHAKGKLTARERIELLLDDGT-FEEWDMFVEHRC 59 Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182 + + +P G++TG G I+GR+ + D TV GG +K + + A + Sbjct: 60 TDFGMEDNKIPGDGVVTGYGMINGRLVFVFSQDFTVFGGALSETHAEKICKVMDQAMKVG 119 Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242 P I L DSGGA + E + VF ++V++S IPQI++++G G Y P Sbjct: 120 APVIGLNDSGGARIQ---EGVASLGGYADVF-QKNVLASGVIPQISMIMGPSAGGAVYSP 175 Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302 AM D MVK + +F+ GP +VK T EEV+AE+LGGA H T SGV+D ++++ L Sbjct: 176 AMTDFIFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADMAFENDVEAL 235 Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINE--------LRSIAPVDHKQQFD 354 + R + L + ++ K P+ N+ L ++ P + + +D Sbjct: 236 MMLRRLYNYLPLNNRE-------------KAPVRKSNDPADRMDLSLDTLVPENPNKPYD 282 Query: 355 VRSIIARIVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGA 409 ++ +I + VD +F E + +Y ++ GFAR+ GQTVGI+ N G L +S++K A Sbjct: 283 MKELILKTVDDGDFFELQPEYAKNILIGFARMEGQTVGIVANQPLVLAGCLDIKSSIKAA 342 Query: 410 HFIELCSQRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASF 469 F+ C IP+V ++ GFM G+ E GI K GAK++ A + VPKIT+IT ++ Sbjct: 343 RFVRFCDAFNIPVVTFVDVPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKITVITRKAY 402 Query: 470 GAGNYAMCGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAF 529 G M + D WPNA I +MG A ++ + + K +K E E + Sbjct: 403 GGAYDVMSSKHLRGDVNLAWPNAEIAVMGAKGAVEIIFRED----KNDPVKLAAREAE-Y 457 Query: 530 KKKTVDAYEREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLED 579 K +R ANP+ + AR + D VI P +TRK + L ++ LE+ Sbjct: 458 K-------QRFANPFVAGARGFIDDVILPHETRKRICRSLVMLRDKKLEN 500 Lambda K H 0.320 0.138 0.408 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: 734 Number of extensions: 37 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: 587 Length of database: 510 Length adjustment: 36 Effective length of query: 551 Effective length of database: 474 Effective search space: 261174 Effective search space used: 261174 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: 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