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_268802025.1 B5D49_RS04650 biotin carboxylase N-terminal domain-containing protein
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_900167125.1:WP_268802025.1 Length = 470 Score = 202 bits (514), Expect = 2e-56 Identities = 146/449 (32%), Positives = 234/449 (52%), Gaps = 37/449 (8%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 +VL+ANRGEIA R+++A ++G +AVY+ D+ + H + A A + SY + Sbjct: 5 KVLIANRGEIAVRIMEACHDLGHDFVAVYTAEDQASGHVETARTLGGEHCAYRISSYNDA 64 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAV--EKAGITFIGPSSEVMRKIKDKLDGKR 123 I A+ A AIHPGYGF SEN FA V + + FIGPS V+R + DK++ KR Sbjct: 65 GEIFSVADAAQATAIHPGYGFFSENYRFARRVVQRQRPMIFIGPSWWVIRDLGDKINTKR 124 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEK---------IGYPI-MVKAASGGGGVGITRV 173 LA VPT PGSD + EA ++AE I P+ +VKA++GGGG+GI V Sbjct: 125 LARSLNVPTVPGSDRAIYDELEAEEIAENLFDFQEAQGISCPVVLVKASAGGGGMGIDEV 184 Query: 174 DNQDQLMDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYG-NYVVAWERECT 232 + D+ ++ R + + + F + IE+ + H+E Q++ ++ G +V R C+ Sbjct: 185 PDMDRFRQIYRRIRNYSMRQFNDEGVLIEQRVFDFNHLEVQIVSERSGQRHVTFGTRNCS 244 Query: 233 IQR-RNQKLIEEAPS----------PALKMEERESMFEPIIKFGKLINYFTLGTFETAFS 281 +Q QK IE AP A K+ + + + ++ + I Y ++GT+E + Sbjct: 245 VQSPGRQKRIETAPGFYPDGITYSFDAQKV--LDDITDYSLRMAEAIKYDSVGTWEWIVT 302 Query: 282 DVSRDFYFLELNKRLQVEHPTTELIFRI------DLVKLQIKLAAGEHLPFSQEDLNKRV 335 D + LE+N R+QVE+ + I RI +L++ QI+LA G+ + +SQ+D+ Sbjct: 303 P-KGDPFLLEVNTRIQVENGVSAAIARIHGKDGVNLLREQIRLALGDPMGYSQKDIT--F 359 Query: 336 RGTAIEYRINAEDALNNFTGSSGFVTYYREPTGPGVRVDSGI--ESGSYVPPYYDSLVSK 393 G +IEYRI AED N F G + ++ + P + + + + + +P YD ++ Sbjct: 360 EGVSIEYRIIAEDTTNRFQPWVGQIDTFQWKSAPWLTMHTHVPTDRAYQIPTEYDPNLAL 419 Query: 394 LIVYGESREYAIQAGIRALADYKIGGIKT 422 IV+G E A G+ AL + G T Sbjct: 420 AIVWGADLEEAKARGMVALDGVDLQGNDT 448 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: 507 Number of extensions: 25 Number of successful extensions: 9 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: 470 Length adjustment: 34 Effective length of query: 475 Effective length of database: 436 Effective search space: 207100 Effective search space used: 207100 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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