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 GFF926 PGA1_c09420 pyruvate carboxylase Pyc
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Phaeo:GFF926 Length = 1188 Score = 340 bits (873), Expect = 1e-97 Identities = 182/460 (39%), Positives = 279/460 (60%), Gaps = 9/460 (1%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPA-L 59 M F ++L+ANRGEIA RV++A EMG +AVY+E DK +H ADEAY IG+ + Sbjct: 43 MTDFKKILIANRGEIAIRVMRAANEMGKKTVAVYAEEDKLGLHRFKADEAYRIGEGMGPV 102 Query: 60 DSYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKL 119 +YL+I+ II A++ DAIHPGYG LSEN +F +A + GITFIGP +E MR + DK Sbjct: 103 AAYLSIDEIIRVAKECGADAIHPGYGLLSENPDFVDACARNGITFIGPKAETMRALGDKA 162 Query: 120 DGKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179 +R+A A VP P ++ +D K A ++GYP+M+KA+ GGGG G+ + ++D+L Sbjct: 163 SARRVAIDADVPVIPATEVLGNDMDAIRKEAAEVGYPLMLKASWGGGGRGMRPIHSEDEL 222 Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239 + +R A AFG + ++EK RH+E Q++GDK+G +ER+C++QRRNQK Sbjct: 223 EEKVLEGRREAEAAFGNGEGYLEKMITRARHVEVQILGDKHGEIYHLYERDCSVQRRNQK 282 Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299 ++E AP+P L E+R + + K + +NY GT E FYF+E+N R+QVE Sbjct: 283 VVERAPAPYLTEEQRTEICDLGRKICQHVNYECAGTVEFLMDMNDGKFYFIEVNPRVQVE 342 Query: 300 HPTTELIFRIDLVKLQIKLAAGEHL-----PFSQEDLNKRVRGTAIEYRINAEDALNNFT 354 H TE + ID+V+ QI +A G+ + SQ+++ ++ G A++ R+ ED LNNF Sbjct: 343 HTVTEEVTGIDIVQAQILIAEGKTIAEATGKASQDEI--QLNGHALQTRVTTEDPLNNFI 400 Query: 355 GSSGFVTYYREPTGPGVRVDSGIE-SGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALA 413 G +T YR TG G+R+D G +G + YYDSL++K+ + E AI RAL Sbjct: 401 PDYGRITAYRSATGMGIRLDGGTAYAGGVITRYYDSLLTKVTAKAPTPEKAIARMDRALR 460 Query: 414 DYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQF 453 ++++ G+ T I + +++ P F +++T +I + + F Sbjct: 461 EFRVRGVSTNIAFVENLLKHPTFLSNEYTTKFIDETPELF 500 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: 1242 Number of extensions: 52 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: 1188 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1147 Effective search space: 536796 Effective search space used: 536796 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