Align L-lactate permease (characterized, see rationale)
to candidate WP_086511817.1 BZY95_RS20890 L-lactate permease
Query= uniprot:L0GFN1 (564 letters) >NCBI__GCF_002151265.1:WP_086511817.1 Length = 610 Score = 733 bits (1892), Expect = 0.0 Identities = 353/565 (62%), Positives = 442/565 (78%), Gaps = 1/565 (0%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 M++ LAL AFTP++LA ++LIG R A AMP+V+L TA I LF W+MS NR++AST Q Sbjct: 1 MTDTTLALLAFTPLILAGVLLIGFRMAAKTAMPIVYLVTAVIALFAWEMSFNRVLASTFQ 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 GL++T +LWIIFGAILLLNTLKHSGGITAIR GF+ ISPDRR+QAII+AWLFGCFIEGA Sbjct: 61 GLILTASILWIIFGAILLLNTLKHSGGITAIRNGFSGISPDRRVQAIIVAWLFGCFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATIGA 180 SGFGTPAA+AAPL+VA+GFPA+AAV++GM++QSTPVSFGAVGTPIVVG+ G++ + I Sbjct: 121 SGFGTPAAVAAPLMVALGFPALAAVVVGMMIQSTPVSFGAVGTPIVVGVTGGINQSAITE 180 Query: 181 QLVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLPFAI 240 QL A G +W Y + I + VAI H I+G +MPL+MV+++ +FFG KSWK G + PFA+ Sbjct: 181 QLEAGGYTWLEYFRLIAAEVAIVHGIIGILMPLIMVVIMVKFFGANKSWKEGLSITPFAL 240 Query: 241 FAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADAKEWPAE 300 FAG+AF +PY G+ LGPEFPS++G +VGLAIV AAR FL PK TWDF + WP Sbjct: 241 FAGVAFVVPYMLAGVLLGPEFPSMIGAMVGLAIVVPAARRGFLIPKDTWDFPERSSWPDN 300 Query: 301 WLGTIEMKLDEMAAR-PMSAFRAWLPYVLVGAILVISRVFPQVTAALKSVSIAFANILGE 359 W+G IE+K+D++A + P+S + WLPYVL+ LV SR + AL + + + NILGE Sbjct: 301 WIGKIEIKIDDIAGKTPLSTWMGWLPYVLLAVFLVASRTIEPLREALNAWTFGWNNILGE 360 Query: 360 TGINAGIEPLYLPGGILVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLFTVPMV 419 G++ + PLYLPGGIL+MVVL+T LH MR ELKAA ESS + AGFVL+FT+PMV Sbjct: 361 AGVSGSLAPLYLPGGILLMVVLVTAVLHRMRAGELKAAFGESSRTIFGAGFVLIFTIPMV 420 Query: 420 RILINSGVNGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSNTVSNMMFSQF 479 RILINSGVN +L SMP+ MA++VAD VG +YP APAVG LGAF+AGSNT +N+M ++F Sbjct: 421 RILINSGVNAGDLVSMPVAMAQFVADGVGDVYPFFAPAVGGLGAFIAGSNTAANLMLAEF 480 Query: 480 QFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGSTLRKTIWPTLY 539 QF VAQ LG+S A +VA QAVGAAAGNM+AIHNVVAASATVGLLGREG T+RKTI PT+Y Sbjct: 481 QFNVAQQLGLSTAFMVALQAVGAAAGNMIAIHNVVAASATVGLLGREGETIRKTILPTIY 540 Query: 540 YVLFTGVIGLIAIYVLGVTDPLVGV 564 Y++F G I +I YVL V+DPL+ V Sbjct: 541 YLVFAGAIAMIGFYVLNVSDPLMEV 565 Lambda K H 0.326 0.140 0.415 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: 1143 Number of extensions: 56 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: 564 Length of database: 610 Length adjustment: 37 Effective length of query: 527 Effective length of database: 573 Effective search space: 301971 Effective search space used: 301971 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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