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 5210129 Shew_2573 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__PV4:5210129 Length = 677 Score = 365 bits (938), Expect = e-105 Identities = 193/456 (42%), Positives = 283/456 (62%), Gaps = 7/456 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA R++K + MG+ +A+YS+ADK A H ADE++Y+G + +SYL Sbjct: 2 FTKLLIANRGEIACRIIKTAQVMGIKTVALYSDADKDARHVAMADESFYLGGSAPSESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E I++ A+++ AIHPGYGFLSENA+FA E+AGI F+GPS++ + + K K Sbjct: 62 KGELILEIAKRSGAQAIHPGYGFLSENADFARQCEQAGIAFVGPSADAIDAMGSKSAAKI 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 + A VP PG G S + LK +++IG+P ++KAA GGGG G+ V+++ + ++ Sbjct: 122 IMEQANVPLVPGYHGDDQSDEVLLKASKEIGFPQLIKAAYGGGGKGMRIVESESEALEAI 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A +FG L IE+Y PRH+E Q+ D GN + +R+C+IQRR+QK++EE Sbjct: 182 NSARREAASSFGNDKLLIERYLRQPRHVEVQVFADTQGNCIYLSDRDCSIQRRHQKVVEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFE----TAFSDVSRDFYFLELNKRLQVE 299 AP+P L R +M E + K I+Y GT E T ++ S FYF+E+N RLQVE Sbjct: 242 APAPGLSDSLRRAMGEAAVAAAKAIDYVGAGTVEFLLDTHATEESNSFYFMEMNTRLQVE 301 Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359 HP TE++ DLVK Q+ +A+G LP SQED+ R+ G + E RI AED N F +SG Sbjct: 302 HPVTEMVTGQDLVKWQLMVASGSELPLSQEDV--RIHGHSFEVRIYAEDPQNEFLPASGK 359 Query: 360 VTYYREP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418 + + REP VR+DSGI + +YD +++KLIV+ ESR A+Q + AL Y+I Sbjct: 360 LNFLREPEQNRYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQIS 419 Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454 G+K IE I + F + FST +I + D + Sbjct: 420 GLKHNIEFLANIAEHKAFSQADFSTDFIERYGDTLI 455 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: 757 Number of extensions: 39 Number of successful extensions: 4 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: 677 Length adjustment: 37 Effective length of query: 472 Effective length of database: 640 Effective search space: 302080 Effective search space used: 302080 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: 53 (25.0 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