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_011382686.1 AMB_RS01215 pyruvate carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_000009985.1:WP_011382686.1 Length = 1154 Score = 353 bits (905), Expect = e-101 Identities = 183/469 (39%), Positives = 286/469 (60%), Gaps = 6/469 (1%) Query: 2 PPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPA-LD 60 PPF+++LVANRGEIA R+ +A E+G+ +AVYS D++A+H ADE+Y IGK ++ Sbjct: 9 PPFAKLLVANRGEIAIRICRAATELGLATVAVYSTEDRFALHRFKADESYLIGKGKGPIE 68 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 +YL+I+ +I ++A DA+HPGYGFLSEN +FA+AV AG+ F+GPSS+VMR + +K+ Sbjct: 69 AYLSIDEMIRVGKEAGCDAVHPGYGFLSENPDFADAVRAAGMAFVGPSSDVMRLLGNKVA 128 Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180 + LA AGVP P + + E + A +GYP+M+KA+ GGGG G+ ++ + +L Sbjct: 129 ARALAEKAGVPVMPATGPLPADLVECKRQAAAVGYPLMLKASWGGGGRGMRVIEAETELE 188 Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240 ++ +R A AFG ++++EK RH+E Q++GD GN V +ER+C++QRRNQK+ Sbjct: 189 ELLAVARREAKAAFGNDEVYLEKLVRRARHVEVQILGDSQGNLVHLYERDCSVQRRNQKV 248 Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300 +E AP+P L +R + E ++ + Y GT E + FYF+E+N R+QVEH Sbjct: 249 VERAPAPYLDGRQRSELCETAVRLARAAAYENAGTVEFLMDMETGAFYFIEVNPRVQVEH 308 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKR----VRGTAIEYRINAEDALNNFTGS 356 TE++ ID+VK QI++A G + D+ K+ + G AI+ RI ED NNF Sbjct: 309 TVTEVVTGIDIVKAQIRIAGGAPIGAPGSDVPKQAEIPLNGHAIQCRITTEDPANNFIPD 368 Query: 357 SGFVTYYREPTGPGVRVDSGIE-SGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADY 415 G ++ YR G G+R+D G SG+ + YYDSL+ K+ + + E AI RAL ++ Sbjct: 369 YGRISAYRGANGFGIRLDGGTAFSGALITRYYDSLLEKVTAWAPTPEEAIARMDRALREF 428 Query: 416 KIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIK 464 +I G+ T + + +++ P F ++T +I + + F + R K Sbjct: 429 RIRGVATNLTFLEAVIEHPKFVGCAYTTRFIDETPELFARQDRRDRATK 477 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: 1181 Number of extensions: 49 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: 1154 Length adjustment: 40 Effective length of query: 469 Effective length of database: 1114 Effective search space: 522466 Effective search space used: 522466 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 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