Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_041672188.1 SUDEN_RS03245 acetyl-CoA carboxylase biotin carboxylase subunit
Query= BRENDA::Q9I299 (655 letters) >NCBI__GCF_000012965.1:WP_041672188.1 Length = 483 Score = 377 bits (969), Expect = e-109 Identities = 197/448 (43%), Positives = 281/448 (62%), Gaps = 2/448 (0%) Query: 6 RSIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADS 65 + I ++LVANRGEIA R++R+ + L I SVA+ S++D V +AD + G + Sbjct: 2 KKISKILVANRGEIALRIIRACKELEIKSVAIFSEVDVEGIWVKKADECYPITG-DALQA 60 Query: 66 YLRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAA 125 YL DRII AL +G AIHPGYGFLSENA+FA++CE+ G++F+GP A I G K A+ Sbjct: 61 YLDYDRIITLALKAGCDAIHPGYGFLSENAEFAQSCEDRGIIFIGPKPAHIALFGDKMAS 120 Query: 126 KALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAE 185 K M E GVP++ G D + A +IG+P+++KAA GGGG+GM++V+ E Sbjct: 121 KVAMREIGVPVLEGTDEPIVDKAEGGKIAAKIGFPIIIKAAFGGGGRGMRIVKSAKLFDE 180 Query: 186 ALSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVV 245 SA EAK FG + +EKY+ PRH+EIQV AD++G+ ++L ERDCSIQRRHQKV+ Sbjct: 181 MFDSATNEAKKYFGKGDVFIEKYVENPRHIEIQVVADKYGNVVHLGERDCSIQRRHQKVI 240 Query: 246 EEAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPV 305 E AP+P L R+ + + +A +GY GTVE+LLDE +F+EMNTR+QVEHPV Sbjct: 241 EIAPSPRLNPAARKELYRISTKAMLKLGYESVGTVEYLLDENDNIYFIEMNTRVQVEHPV 300 Query: 306 TEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYR 365 TE I+G+D++ I +A G+ L QE++ G+AIE R+ AE+P+ +F+P+ G + Y Sbjct: 301 TEIISGIDIIQRMIEIAEGDKLKYLQEEINFRGYAIEFRINAENPQNNFMPSIGTITNY- 359 Query: 366 EAAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTN 425 GPG R+DS V G + P YD M+ KLI W E A ++ L E + G+ TN Sbjct: 360 ITPGGPGVRLDSSVYTGYTIPPNYDSMVGKLIVWALDWEGAVKKASRALDEFYIDGVITN 419 Query: 426 LAFLRRILGHPAFAAAELDTGFIARHQD 453 L+ R I+ F A L+T ++ + + Sbjct: 420 LSLHREIVKDADFIAGNLNTSYLDKKME 447 Lambda K H 0.319 0.135 0.397 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: 595 Number of extensions: 21 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: 655 Length of database: 483 Length adjustment: 36 Effective length of query: 619 Effective length of database: 447 Effective search space: 276693 Effective search space used: 276693 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: 53 (25.0 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