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 WP_012277981.1 SHAL_RS15030 ATP-grasp domain-containing protein
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_000019185.1:WP_012277981.1 Length = 702 Score = 360 bits (923), Expect = e-103 Identities = 192/449 (42%), Positives = 275/449 (61%), Gaps = 4/449 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA R++ K MG+ +A+YS+AD A H ADEA+Y+G + DSYL Sbjct: 2 FTKLLIANRGEIACRIINTAKVMGVRTVALYSDADIDARHVAMADEAFYLGGSAPADSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E II+ A++A +AIHPGYGFLSENA+FA E+A I F+GPS+ + + K K Sbjct: 62 KGELIIEIAKRAGAEAIHPGYGFLSENADFALKCEQANIAFVGPSAAAIDSMGSKSAAKE 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 + A VP PG G + + + A K+G+P+++KAA GGGG G+ V++ ++++D Sbjct: 122 IMGAANVPLVPGYHGDAQNDELLVSEANKMGFPLLIKAAFGGGGKGMRIVESNNEVLDAI 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A +FG L +E+Y PRH+E Q+ D +GN + +R+C+IQRR+QK++EE Sbjct: 182 HSARREAISSFGNDKLLMERYLRQPRHVEVQVFADSHGNCIYLSDRDCSIQRRHQKVVEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P L R M E + K INY GT E D FYF+E+N RLQVEHP T Sbjct: 242 APAPGLSDALRVKMGEAAVAAAKAINYEGAGTVEFLL-DTDDSFYFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 EL+ DLVK Q+ +A+G LP Q ++ R+ G A E RI AED N+F +SG + + Sbjct: 301 ELVTGQDLVKWQLMVASGSPLPLKQNEV--RIVGHAFEARIYAEDPHNDFLPASGKLDFL 358 Query: 364 REP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 REP VR+DSG+ + +YD ++SKLI + ESR A+Q + AL DY+I G+K Sbjct: 359 REPEQSQFVRIDSGVRENDVISNFYDPMISKLITWDESRPRALQRLVHALDDYQISGLKH 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTD 451 IE I + F + FST +I + D Sbjct: 419 NIEFLANIAKHQAFSDANFSTDFIERYGD 447 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: 768 Number of extensions: 30 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: 702 Length adjustment: 37 Effective length of query: 472 Effective length of database: 665 Effective search space: 313880 Effective search space used: 313880 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 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