Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_111394452.1 CLV31_RS17930 acyl-CoA carboxylase subunit beta
Query= reanno::SB2B:6937191 (535 letters) >NCBI__GCF_003253485.1:WP_111394452.1 Length = 538 Score = 487 bits (1254), Expect = e-142 Identities = 250/521 (47%), Positives = 343/521 (65%), Gaps = 17/521 (3%) Query: 28 DLKDKLAHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFAAFEVYDED-- 85 +L+ K+ ++ GGG + +GKL R R++ L+D S FLE+ FAA +Y E+ Sbjct: 14 ELRSKMTQVKLGGGPKRIAAEHEKGKLTARERIDYLIDEDSEFLEIGIFAADGMYQEEGG 73 Query: 86 VPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIAERCHLPCIYLVDS 145 P+AG++ GIG VSG C+I+ANDATVK G ++P+T KK+LRAQ IA LP IYLVDS Sbjct: 74 CPSAGVVTGIGMVSGRMCVIVANDATVKAGAWFPMTAKKNLRAQEIAMENRLPIIYLVDS 133 Query: 146 GGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQIAVVMGLCTAGGAYVPAMADESIIV 205 G LP Q+E+FPD++HFGR F N A+MSA GI Q+A +MG C AGGAY+P M+DE++IV Sbjct: 134 AGVFLPMQNEIFPDKEHFGRQFRNNAKMSAMGIVQVAAIMGSCVAGGAYLPIMSDEALIV 193 Query: 206 REQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQNDEHALELARKAVSR 265 + G+IFLAG LV+AA GE V E LGG H +ISGV D+ ND+ L+ R+ Sbjct: 194 DKTGSIFLAGSYLVRAAIGENVDNETLGGATTHCEISGVTDNKYANDQECLDAIRRIFET 253 Query: 266 LNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIVDDSDFDEFKANYGT 325 L Q + K P +L I D KP+D+ +V+ ++D+ +E+K +YG Sbjct: 254 LGDQPKAGFDRIGTKQPSLSQEKLLEIFPIDRAKPYDMHQVLEGLIDEGSLEEYKKDYGK 313 Query: 326 TLVCGFARIHGYPVGIVAN--------------NGILFSESAQKGAHFIELCCQRKIPLV 371 TL+CG ARI G+ VGIVAN G+++S+SA K A FI C QRKIPLV Sbjct: 314 TLICGTARIDGWAVGIVANQRKIVKTAKGEMQMGGVIYSDSADKAARFIMNCNQRKIPLV 373 Query: 372 FLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCGRAFEP 431 FLQ+++GFMVG K EH GI K GAKMV A++ + VPKFT+++G SYGAGNY MCG+A++P Sbjct: 374 FLQDVSGFMVGSKAEHGGIIKDGAKMVNAMANSVVPKFTLVVGNSYGAGNYAMCGKAYDP 433 Query: 432 TLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAPIIAQYDKEGHP 491 L++ WP A+++VM G AA L ++ L + G+ +S EEE + I+A+Y++E P Sbjct: 434 RLIFSWPTAQMAVMSGASAAKTLLQIKVASLKKSGKEISPEEEKQLLDEIVAKYNEELSP 493 Query: 492 YHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGV 532 Y+A+ARLW DG+IDP +TR V+ I+AA +API E RF V Sbjct: 494 YYAAARLWVDGVIDPRETRKVISAGIAAANHAPITE-RFNV 533 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: 795 Number of extensions: 37 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: 538 Length adjustment: 35 Effective length of query: 500 Effective length of database: 503 Effective search space: 251500 Effective search space used: 251500 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 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