Align L-lactate permease (characterized)
to candidate BWI76_RS27185 BWI76_RS27185 L-lactate permease
Query= SwissProt::P33231 (551 letters) >FitnessBrowser__Koxy:BWI76_RS27185 Length = 551 Score = 1026 bits (2652), Expect = 0.0 Identities = 514/551 (93%), Positives = 537/551 (97%) Query: 1 MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKM 60 MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAA+WTV IAL+VALLFYKM Sbjct: 1 MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAATWTVVIALSVALLFYKM 60 Query: 61 PVANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLI 120 PV +ALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLI Sbjct: 61 PVDHALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLI 120 Query: 121 VGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVA 180 VGF FGAFLEGAAGFGAPVAITAALLVGLGF PLYAAGLCLIVNTAPVAFGAMGIPILVA Sbjct: 121 VGFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIVNTAPVAFGAMGIPILVA 180 Query: 181 GQVTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYL 240 GQVTG+DSFEIGQMVGRQLPF+TIIVLFWIMAIMDGWRGIKETWPAV+VAGGSFAIAQYL Sbjct: 181 GQVTGLDSFEIGQMVGRQLPFLTIIVLFWIMAIMDGWRGIKETWPAVMVAGGSFAIAQYL 240 Query: 241 SSNFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVL 300 SSNF+GPELPDIISSLVSL+CLTLFLKRWQPVR+FRFGD+GASQVDM LA T YT GQV+ Sbjct: 241 SSNFLGPELPDIISSLVSLVCLTLFLKRWQPVRIFRFGDMGASQVDMNLARTRYTPGQVI 300 Query: 301 RAWTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAY 360 RAW+PFLFLTATVTLWS+PPFKALFA GGA+Y++VINI VP+LDK+VARMPPVV+EAT Y Sbjct: 301 RAWSPFLFLTATVTLWSVPPFKALFAPGGAMYDFVINISVPFLDKMVARMPPVVNEATPY 360 Query: 361 AAVFKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAF 420 AAV+KFDW SATGTAILFAALLSIVWL+MKP DAISTFGS LKELALPIYSIGMVLAFAF Sbjct: 361 AAVYKFDWLSATGTAILFAALLSIVWLRMKPKDAISTFGSMLKELALPIYSIGMVLAFAF 420 Query: 421 ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV 480 ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV Sbjct: 421 ISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGV 480 Query: 481 SDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITT 540 SD+LLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTC+VGVITT Sbjct: 481 SDILLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCMVGVITT 540 Query: 541 LQAYVLTWMIP 551 LQAYVLTWMIP Sbjct: 541 LQAYVLTWMIP 551 Lambda K H 0.328 0.140 0.436 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: 1159 Number of extensions: 37 Number of successful extensions: 2 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: 551 Length of database: 551 Length adjustment: 36 Effective length of query: 515 Effective length of database: 515 Effective search space: 265225 Effective search space used: 265225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 53 (25.0 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