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_101586891.1 BJEO58_RS00855 acetyl/propionyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_900169175.1:WP_101586891.1 Length = 699 Score = 343 bits (879), Expect = 2e-98 Identities = 188/496 (37%), Positives = 287/496 (57%), Gaps = 6/496 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+R+L+ANRGEIA RV++ + +G+ +AVYS+AD A HT+ AD A+ +G APA SYL Sbjct: 2 FTRILIANRGEIALRVIRTCRALGIETVAVYSDADADAAHTRAADVAHRLGPAPAAQSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 +IE ++ A A+HPGYGFLSENA FA +E+ GI F+GP++ + + DK+ KR Sbjct: 62 DIERVVAAVRATGAQAVHPGYGFLSENAAFARRLEEEGIVFLGPTAASIDVMGDKISAKR 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 GVP PG P + ++ + A+++G+PI+VK ++GGGG G+ V + L + Sbjct: 122 AVAARGVPLVPGVAEPGLTDEQLIARADEVGFPILVKPSAGGGGKGMREVHDPADLAEAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A +FG LF+E+ + PRHIE Q++ D++GN + EREC++QRR+QK+IEE Sbjct: 182 ASARREAAGSFGDDTLFLERLVLTPRHIEVQVLADEHGNVIHLGERECSLQRRHQKVIEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFS-DVSRDFYFLELNKRLQVEHPT 302 APS L R + + + K ++Y GT E S D +F+F+E+N RLQVEHP Sbjct: 242 APSALLDEATRARIGQAAVDTAKSVDYRGAGTVEFIVSADNPDEFFFMEMNTRLQVEHPV 301 Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362 TE + +DLV+ Q+++ AG+ L +Q+D+ + G +IE RI AED F + G Sbjct: 302 TEQVTGVDLVEWQLRIGAGQQLALAQDDVT--LTGHSIEARIYAEDPARGFLPTGGTALD 359 Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 PTG G+RVD+G+E G + YD +++KLIV R+ A+ ALA + GI T Sbjct: 360 VSFPTGEGIRVDAGLEPGQRIVSDYDPMIAKLIVTARDRQEAVARTRTALAGSAVPGIVT 419 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAA---IAAEIQSRGLLRT 479 I + +++ P+ G T I T+ + + ++ A +AA R Sbjct: 420 NIGFLQTLLEMPEVVAGDLHTGLIDAMTEDDLAEAVDPAALQLAAAHVAAAEADRATDSH 479 Query: 480 SSTDNKGKAQSKSGWK 495 + + G SGW+ Sbjct: 480 IAGEPVGMWADGSGWR 495 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: 742 Number of extensions: 33 Number of successful extensions: 3 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: 699 Length adjustment: 37 Effective length of query: 472 Effective length of database: 662 Effective search space: 312464 Effective search space used: 312464 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