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 CA265_RS02215 CA265_RS02215 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Pedo557:CA265_RS02215 Length = 503 Score = 419 bits (1076), Expect = e-121 Identities = 222/493 (45%), Positives = 315/493 (63%), Gaps = 5/493 (1%) Query: 3 PFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSY 62 P S++LVANRGEIA R++++ KEMG+ +AV+SEAD+ A+H +YADEA IG AP+ SY Sbjct: 10 PISKLLVANRGEIALRIMRSAKEMGIKTVAVFSEADRNALHVRYADEAVCIGPAPSNQSY 69 Query: 63 LNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGK 122 L E II A + +AIHPGYGFLSENA FA+ V AG+ +GPS + M + +KL K Sbjct: 70 LVGEKIIGACKLTGAEAIHPGYGFLSENAGFAQMVADAGLILVGPSPQAMETMGNKLSAK 129 Query: 123 RLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182 A +P PG++ + ++EA + A ++G+PI++KAA+GGGG G+ V+ + + Sbjct: 130 AAALKYNIPMVPGTEEAIQDVNEAKQRAIEVGFPILIKAAAGGGGKGMRIVERAEDFEEQ 189 Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242 + A AFG +FIE+Y +PRHIE Q++GD +GN V +EREC++QRR+QK+IE Sbjct: 190 MQLAVSEATSAFGDGAVFIERYVTSPRHIEIQVLGDNHGNIVHLFERECSVQRRHQKVIE 249 Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302 EAPS L E R+ M + + + +NY GT E D + DF+FLE+N RLQVEHP Sbjct: 250 EAPSSVLTEEIRQRMGKCAVDVARSVNYTGAGTVEFIL-DENLDFFFLEMNTRLQVEHPV 308 Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362 TELI IDLVK Q+K+A+GE L FSQEDL ++ G A+E R+ AED NNF G + Sbjct: 309 TELITGIDLVKEQLKIASGEKLSFSQEDL--KISGHAVELRVYAEDPANNFLPDIGTLQT 366 Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 Y P G GVRVD G E G +P YYD +++KLI YG+ RE AI+ +RA+ +Y I GI+T Sbjct: 367 YNTPKGNGVRVDDGFEQGMEIPIYYDPMIAKLITYGKDREEAIERMVRAIEEYDITGIET 426 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSST 482 T+ K++MQ F+ G F T ++ + + L+ Q+E +A IAA I ++ + Sbjct: 427 TLGFGKFVMQHEAFKTGNFDTHFVGKYFKP--ESLKVQDETEALIAAVIAAKLFDKKEVK 484 Query: 483 DNKGKAQSKSGWK 495 ++ S W+ Sbjct: 485 LGDAAIKNSSDWR 497 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: 592 Number of extensions: 28 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: 503 Length adjustment: 34 Effective length of query: 475 Effective length of database: 469 Effective search space: 222775 Effective search space used: 222775 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