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 BPHYT_RS25975 BPHYT_RS25975 urea carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__BFirm:BPHYT_RS25975 Length = 1203 Score = 342 bits (876), Expect = 6e-98 Identities = 189/445 (42%), Positives = 273/445 (61%), Gaps = 5/445 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F +VL+ANRGEIA RV++ +K +G+ ++AVYSEAD++A+H ADEA IG A A SYL Sbjct: 3 FRKVLIANRGEIACRVIRTLKRLGIASVAVYSEADRHAMHVMLADEAVCIGPALAAQSYL 62 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 N I+DAA DA+HPGYGFLSENA FA+A + AGI FIGP+ + MR+ K + Sbjct: 63 NSAAILDAARACGADAVHPGYGFLSENAAFAQACDDAGIRFIGPTPQHMREFGLKHTARE 122 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 LA V PG+ G + + AL+ AE IGYP+M+K+ +GGGG+G++ + QL V+ Sbjct: 123 LAQANDVALLPGT-GLLPDVSAALREAESIGYPVMLKSTAGGGGIGMSLCRDAAQLEGVF 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 RL F A +++EK+ N RHIE Q+ GD G + ER+C++QRRNQK+IEE Sbjct: 182 ASVARLGEANFANAGVYVEKFVENARHIEVQVFGDGKGGVISLGERDCSVQRRNQKVIEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 P+P L ER ++ ++ + + Y + GT E F +R FYFLE+N RLQVEH T Sbjct: 242 TPAPGLTHAERSALHASAVRLAQAVKYKSAGTVEFVFDADTRRFYFLEVNTRLQVEHCVT 301 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E I IDLV+ I+ A GE P + L +G +I+ R+ AED F S+G +T+ Sbjct: 302 EEITGIDLVEWMIREAEGELAPL--DTLATVPQGASIQVRLYAEDPHKQFQPSAGVLTHV 359 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 RVD+ ++SG+ V +YD L++KLIV GE+RE + A AL ++ GI+T Sbjct: 360 --AFAADARVDTWVDSGTEVSAFYDPLLAKLIVKGETREAGLAALRAALEQTQLYGIETN 417 Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448 ++ + I F G+ +T+++ + Sbjct: 418 LDYLRAIAGSATFARGEQTTAFLGR 442 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: 1279 Number of extensions: 56 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 509 Length of database: 1203 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1162 Effective search space: 543816 Effective search space used: 543816 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