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 GFF3994 HP15_3934 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Marino:GFF3994 Length = 473 Score = 414 bits (1064), Expect = e-120 Identities = 219/471 (46%), Positives = 307/471 (65%), Gaps = 7/471 (1%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++L+ANRGEIA R+ +A E+G+ ++A++SEAD+Y++H K ADEAY I K P L YLN Sbjct: 5 KLLIANRGEIAVRIARACSELGIRSVAIHSEADEYSLHVKKADEAYQISKDP-LSGYLNP 63 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 HI++ A + DA+HPGYGFLSENAE A E+ GITF+GPS+ + + DK ++ A Sbjct: 64 HHIVNMAVETGCDALHPGYGFLSENAELAAICEQRGITFVGPSANAISSMGDKTQARQTA 123 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 AGVP PGS+G + +++A+ A IGYP+M+KA SGGGG GI R DN+ +L +ER Sbjct: 124 LAAGVPVTPGSEGNLADVEDAVVQAADIGYPVMLKATSGGGGRGIRRCDNEKELRQNFER 183 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 A +AFG A++F+EK + PRHIE Q++ D +GN V +ER+C+IQRRNQKLIE AP Sbjct: 184 VISEATKAFGSAEVFLEKCIIEPRHIEVQILADTHGNVVHLYERDCSIQRRNQKLIELAP 243 Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305 SP L+ +RE + + + K Y GT E D FYF+E+N R+QVEH TE Sbjct: 244 SPQLEESQREYIGDLAKRVAKQCGYVNAGTVEFLL-DHDGSFYFMEMNTRVQVEHTITEE 302 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 I +D++K QI++AAGE L QED++ RG A ++RINAED N F S G ++ Y Sbjct: 303 ITGVDIIKAQIRIAAGEPLGLKQEDIS--YRGFAAQFRINAEDPKNGFLPSFGRISRYYS 360 Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 GPGVR D+ + +G +PPYYDS+ +KLIV+ + I RAL D I G++TTI Sbjct: 361 AGGPGVRTDANMYTGYEIPPYYDSMCAKLIVWAMDWDELIARSRRALGDMGIYGVQTTIP 420 Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLRE--QEEIKAAIAAEIQSR 474 YK I++ PDFQ F+T ++ ++ Q ++Y + E I AIAA I ++ Sbjct: 421 YYKQILEHPDFQAADFNTGFV-ERNPQLLEYSSKTRPESIATAIAAAIAAQ 470 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: 595 Number of extensions: 27 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: 473 Length adjustment: 34 Effective length of query: 475 Effective length of database: 439 Effective search space: 208525 Effective search space used: 208525 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 Sep 17 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