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_045586135.1 AL072_RS14875 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_001305595.1:WP_045586135.1 Length = 666 Score = 380 bits (976), Expect = e-110 Identities = 199/447 (44%), Positives = 281/447 (62%), Gaps = 4/447 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV++ + MG+ +AVYS+ADK A+H + ADEA +IG + SYL Sbjct: 2 FEKILIANRGEIACRVIRTARRMGIKTVAVYSDADKNALHVEMADEAVHIGPPASAQSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 I+ I+DA ++ A+HPGYGFLSE F EA+ AGI FIGP + MR + DK++ K+ Sbjct: 62 LIDRIVDACKRTGAQAVHPGYGFLSEKPGFQEALAAAGIAFIGPDAHAMRAMGDKIESKK 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 LA AGV T PG G + +EA+ +A IGYP+M+KA++GGGG G+ N ++ + + Sbjct: 122 LAKAAGVSTVPGYLGVIADDEEAVMIARDIGYPVMIKASAGGGGKGMRVAWNDEEAREGF 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 A +F +F+EKY PRHIE QL+ D G + EREC+IQRR+QK+IEE Sbjct: 182 RSATNEARSSFADDRVFVEKYIQQPRHIEIQLLADGQGTCLYLHERECSIQRRHQKVIEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 APSP L R++M E + + Y + GT E D R+FYFLE+N RLQVEHP T Sbjct: 242 APSPFLDAATRKAMGEQAVALANAVQYKSAGTVE-FIVDAERNFYFLEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 ELI +DLV+L I++AAGE L Q+D+ + G AIE R+ AED NF S+G +T Y Sbjct: 301 ELITGLDLVELMIRVAAGEKLTIGQDDVT--LNGWAIEARVYAEDPFRNFLPSTGRLTNY 358 Query: 364 REPTG-PGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 R P P VRVD+G+ G + YYD +++KL +G +R+ AI AL Y I G+ Sbjct: 359 RPPAADPHVRVDTGVFEGGEISMYYDPMIAKLCTWGSTRDAAIGGMREALDQYYIRGVSH 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQK 449 I +M + F +G+ +T++I+++ Sbjct: 419 NIPFLASLMANQRFVDGRLTTNFIAEE 445 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: 755 Number of extensions: 29 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: 666 Length adjustment: 36 Effective length of query: 473 Effective length of database: 630 Effective search space: 297990 Effective search space used: 297990 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