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_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_002893965.1:WP_050656086.1 Length = 679 Score = 366 bits (940), Expect = e-105 Identities = 203/490 (41%), Positives = 294/490 (60%), Gaps = 7/490 (1%) Query: 7 VLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNIE 66 VLVANRGEIA RV++ ++E+G+ ++AVYS+AD A H + AD A IG A A +SYL I+ Sbjct: 10 VLVANRGEIAVRVIRTLRELGIRSVAVYSDADANARHVREADTAVNIGPAAARESYLVID 69 Query: 67 HIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLAN 126 +IDAA+ IHPGYGFLSEN+ F+ A AGI F+GPS + + DK+ K Sbjct: 70 KVIDAAKSTGAQGIHPGYGFLSENSAFSAACAAAGIAFLGPSEHAIEVMGDKITAKNSVA 129 Query: 127 MAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWERN 186 VP PG P + +E + AE IGYP++VK ++GGGG G+ V++ L + Sbjct: 130 AFDVPVVPGIARPNLTDEELIAAAEDIGYPVLVKPSAGGGGKGMRLVEDPANLAEALRSA 189 Query: 187 KRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAPS 246 +R A +FG LF+E++ + PRHIE Q++ D++GN V EREC++QRR+QK+IEEAPS Sbjct: 190 RREAASSFGDDTLFLERFVLRPRHIEVQVLADQHGNVVHLGERECSLQRRHQKVIEEAPS 249 Query: 247 PALKMEERESMFEPIIKFGKLINYFTLGTFETAFS-DVSRDFYFLELNKRLQVEHPTTEL 305 P L R+ + + ++Y GT E S D +F+F+E+N RLQVEHP TE+ Sbjct: 250 PLLDQVTRDRIGAAACNTARSVDYTGAGTVEFIVSADKPDEFFFMEMNTRLQVEHPVTEM 309 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 + +DLV+ Q+++AAGE L FSQ D+ + G AIE R+ AED F + G V E Sbjct: 310 VTGLDLVEWQVRVAAGEKLAFSQSDIT--LTGHAIEARVYAEDPGRGFLPTGGRVVDLVE 367 Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 P+G GVRVDSG+ +G+ V YD ++SK+I + R A++ RAL D + G+ T IE Sbjct: 368 PSGSGVRVDSGLLAGTVVGSDYDPMLSKVIAHAPDRAGALRKLDRALGDTAVLGVVTNIE 427 Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSSTDNK 485 ++++ DPD G T + ++ + FV E + AA A R L R ++++ Sbjct: 428 FARFLLADPDVIAGNLDTGLLDRRVEDFVAADASDEVLIAAAA----YRWLSRWTTSERF 483 Query: 486 GKAQSKSGWK 495 SGW+ Sbjct: 484 DPWDVPSGWR 493 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: 671 Number of extensions: 26 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: 679 Length adjustment: 37 Effective length of query: 472 Effective length of database: 642 Effective search space: 303024 Effective search space used: 303024 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