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_078718056.1 B5D49_RS12550 pyruvate carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_900167125.1:WP_078718056.1 Length = 1233 Score = 305 bits (781), Expect = 6e-87 Identities = 185/474 (39%), Positives = 276/474 (58%), Gaps = 11/474 (2%) Query: 7 VLVANRGEIATRVLKAIKEMGMT-AIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 +LVANRG A R+ + I EM ++ ++ DK + T A+E +G P +YL+I Sbjct: 18 ILVANRGIPARRICRTISEMSEAISVMTATDVDKTSPATSGANELMLLGDDPR--AYLDI 75 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 + II A+ V AIHPG+GF +E+ F E ++AGI FIGP ++ MR + +K+ +RLA Sbjct: 76 DTIIQRAKDRGVIAIHPGWGFAAEDESFPEKCKEAGIIFIGPPTDAMRTLGNKVAVRRLA 135 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 GVP PGS+ V I +A ++A++IG PIM+KA GGGG GI V ++DQL + + Sbjct: 136 QEIGVPVVPGSEEAV-DIPKAREIAKQIGLPIMLKAEGGGGGRGIYEVYSEDQLEKAFHK 194 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 LA +FG L+IEK + RHIE Q+I D++GN ER+C++QR +QKLIE P Sbjct: 195 ASALAQASFGNPRLYIEKLLTSVRHIEIQVIADQHGNVFAFDERDCSVQRNHQKLIEITP 254 Query: 246 SPALKM--EERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 SP +M E RE + E K + Y+++ T E + Y +E+N RLQVEH T Sbjct: 255 SPWPQMTPELREQLKEYSRNLVKAVGYYSVCTVEFLVEEDGTP-YLIEVNTRLQVEHGIT 313 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E + IDLV+ Q+ +A G L F++E N + A++ RIN ED N+F+ ++ + Y Sbjct: 314 ECRYGIDLVEEQVAIAFGSKLRFTEE--NCKPFQHALQVRINFEDPQNSFSPNAARIERY 371 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 P G GVR+DS I G P YDS + LI YG S E + RAL +Y IGG+KTT Sbjct: 372 FAPGGQGVRLDSCIGEGYTFPSQYDSAAALLITYGRSWEKTVLLMRRALREYVIGGVKTT 431 Query: 424 IELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEI--KAAIAAEIQSRG 475 I ++ +++ PDF ++T ++ ++ + Y E ++ + AEI ++G Sbjct: 432 IPFHRQVLKHPDFFYANYNTKFVDMHKNELLAYSDEAKDSFRLCRLIAEISAKG 485 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: 1294 Number of extensions: 65 Number of successful extensions: 6 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: 1233 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1192 Effective search space: 557856 Effective search space used: 557856 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: 55 (25.8 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