Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate PP_0558 PP_0558 acetyl-CoA carboxylase - biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Putida:PP_0558 Length = 451 Score = 376 bits (965), Expect = e-108 Identities = 200/445 (44%), Positives = 289/445 (64%), Gaps = 6/445 (1%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 +VL+ANRGEIA R+L+A KE+G+ +AV+S AD+ +H ADE+ IG A + DSYL+I Sbjct: 7 KVLIANRGEIALRILRACKELGIKTVAVHSTADRELMHLGLADESVCIGPASSKDSYLHI 66 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 II AAE AIHPGYGFL+ENA+FAE VEK+G FIGP ++ +R + DK+ K Sbjct: 67 PAIIAAAEVTGATAIHPGYGFLAENADFAEQVEKSGFAFIGPKADTIRLMGDKVSAKDAM 126 Query: 126 NMAGVPTAPGSDGPVTSIDE-ALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWE 184 +GVPT PGSDGP+ +E AL +A +GYP+++KAA GGGG G+ V ++ L+ + Sbjct: 127 IKSGVPTVPGSDGPLPEDEEVALAIARDVGYPVIIKAAGGGGGRGMRVVHKEEDLISSAK 186 Query: 185 RNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEA 244 + A AFG +++EK+ NPRH+E Q++ D GN + +R+C++QRR+QK++EEA Sbjct: 187 LTRTEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGNAIHLGDRDCSLQRRHQKVLEEA 246 Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304 P+P + + R+ +F+ + I Y GTFE + + FYF+E+N R+QVEHP +E Sbjct: 247 PAPGIDEKARQEVFKRCVDACIEIGYRGAGTFEFLYE--NGRFYFIEMNTRVQVEHPVSE 304 Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364 ++ ID+VK + +AAG L F QED+ +RG ++E RINAED F S G V ++ Sbjct: 305 MVTGIDIVKEMLSIAAGNKLSFRQEDV--VIRGHSLECRINAEDP-KKFIPSPGKVKHFH 361 Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424 P G GVRVDS + SG VPP YDSL+ KLI YG+ R+ A+ AL + + GIKT I Sbjct: 362 APGGNGVRVDSHLYSGYSVPPNYDSLIGKLITYGKDRDEAMARMRNALDEIVVDGIKTNI 421 Query: 425 ELYKWIMQDPDFQEGKFSTSYISQK 449 L++ +++D F +G + Y+ K Sbjct: 422 PLHRDLVRDEGFCKGGVNIHYLEHK 446 Lambda K H 0.317 0.135 0.385 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: 534 Number of extensions: 18 Number of successful extensions: 5 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: 509 Length of database: 451 Length adjustment: 34 Effective length of query: 475 Effective length of database: 417 Effective search space: 198075 Effective search space used: 198075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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