Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate AZOBR_RS21100 AZOBR_RS21100 methylmalonyl-CoA carboxyltransferase
Query= reanno::SB2B:6937191 (535 letters) >FitnessBrowser__azobra:AZOBR_RS21100 Length = 510 Score = 243 bits (621), Expect = 1e-68 Identities = 175/520 (33%), Positives = 261/520 (50%), Gaps = 36/520 (6%) Query: 22 MAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFAAFEV 81 M ++A L + GGG + ++GKL R R+E LD GS F E F Sbjct: 1 MQEILAKLDAMRSGARLGGGEKRVAGQHAKGKLTARERIELFLDEGS-FEEFDMFVQHRC 59 Query: 82 YD-----EDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIAERCH 136 D + VP G++ G G V+G + + D TV GG+ +K + A + Sbjct: 60 NDFGMEGQKVPGDGVVTGHGTVNGRLVFVFSQDFTVFGGSLSEAHAEKICKIMDQAMKVG 119 Query: 137 LPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKG-IPQIAVVMGLCTAGGAYV 195 P I L DSGGA + E + +F Q ++A G IPQI+++MG C G Y Sbjct: 120 APVIGLNDSGGARI---QEGVASLGGYAEVF--QRNVNASGVIPQISLIMGPCAGGAVYS 174 Query: 196 PAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQNDEHA 255 PAM D +V++ +F+ GP +VK T E V+AEELGG H+ SGVAD +ND A Sbjct: 175 PAMTDFIFMVKDSSYMFVTGPDVVKTVTHEVVTAEELGGAITHSSKSGVADMAFENDVEA 234 Query: 256 LELARKAVSRL---NHQKQVELQLSKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIVD 312 L R+ + L N ++ E + P D L +V + KP+D+KE+I + VD Sbjct: 235 LLQLRRFIDFLPASNRERAPERPTAD--PIDRDDLSLDTLVPENPNKPYDMKELILKTVD 292 Query: 313 DSDFDEFKANYGTTLVCGFARIHGYPVGIVANN-----GILFSESAQKGAHFIELCCQRK 367 + DF E + +Y ++ GF R++G VGIVAN G L +S++K A F+ C + Sbjct: 293 EGDFFELQPDYAKNIIIGFGRMNGGTVGIVANQPMVLAGCLDIDSSKKAARFVRFCDAFE 352 Query: 368 IPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCGR 427 IP++ L ++ GFM G E+ GI KHGAK++ A + ATVPK TV+ +YG M + Sbjct: 353 IPILTLVDVPGFMPGTSQEYGGIIKHGAKLLFAYAEATVPKITVITRKAYGGAYDVMASK 412 Query: 428 AFEPTLMWMWPNARISVMGGEQAAGVLATVRKD-GLARKGETMSAEEEAKFKAPIIAQYD 486 + + WP+A I+VMG + A ++ R D G K E + E KF Sbjct: 413 HLRGDINYAWPSAEIAVMGPKGAVEII--FRGDIGDTAKIEARTEEYRQKF--------- 461 Query: 487 KEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIE 526 +P+ A++R + D +I P TR + A+S N ++ Sbjct: 462 --ANPFVAASRGYIDDVIMPHGTRRRVIKALSMLKNKQLQ 499 Lambda K H 0.320 0.137 0.405 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: 676 Number of extensions: 38 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: 510 Length adjustment: 35 Effective length of query: 500 Effective length of database: 475 Effective search space: 237500 Effective search space used: 237500 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