Align L-lactate permease (characterized, see rationale)
to candidate WP_005811125.1 DHAF_RS16920 L-lactate permease
Query= uniprot:L0GFN1 (564 letters) >NCBI__GCF_000021925.1:WP_005811125.1 Length = 601 Score = 567 bits (1461), Expect = e-166 Identities = 297/557 (53%), Positives = 379/557 (68%), Gaps = 6/557 (1%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 MS GLLA+ + PIL+ AI L+GL+WPAS+AMP+ F+ + LFVW + ++ A+T+ Sbjct: 1 MSTGLLAILSLMPILVVAIFLVGLKWPASKAMPISFVVAVVLALFVWKVPGAQVGAATVN 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 G+V + LL+IIFG+ILLLNTL+ SGG+ IR GFT I+PDRRIQ II+AWLFG FIEG+ Sbjct: 61 GIVTAITLLYIIFGSILLLNTLQESGGLQTIRNGFTDITPDRRIQVIIVAWLFGSFIEGS 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATIGA 180 SGFGTPAA+A PL+V +GFPAMAAV+ GM++QSTPVSFGAVGTP++ G++SGL T + A Sbjct: 121 SGFGTPAAVAVPLMVGLGFPAMAAVVAGMMIQSTPVSFGAVGTPMLTGVSSGLKTVELEA 180 Query: 181 QLVAQG-SSWNAYLQ-QITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLPF 238 + G S W+ ++ I + VA+ H G +MPL +V +TRFFGK KS+ G V PF Sbjct: 181 YASSLGFSDWHNFIAFGIANKVALLHVTAGILMPLFVVAFMTRFFGKNKSFSEGLAVWPF 240 Query: 239 AIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPK-TTWDFADAKEW 297 AIFA LA T+PY LGPEFPS+LGGL+GLAIV AA+ FL PK WDF + K W Sbjct: 241 AIFAALAMTVPYLIVANLLGPEFPSMLGGLIGLAIVVPAAKKGFLMPKGEAWDFDEKKNW 300 Query: 298 PAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRV-FPQVTAALKSVSIAFANI 356 W G++E++ + A MS AW+PYVL+G LV +RV F + LK I NI Sbjct: 301 DPSWTGSVEIQ-NIAAKNKMSGLVAWMPYVLIGLTLVATRVSFLPLATLLKKAKIVIPNI 359 Query: 357 LGETGINAGIEPLYLPGGILVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLFTV 416 G T I+A E L+ PG + V +ITFFLH M + A K S +L AG L+FTV Sbjct: 360 FG-TSISASWEILFSPGSAFIFVTIITFFLHKMDGAAYGRAWKSSFKTMLGAGSALIFTV 418 Query: 417 PMVRILINSGVNGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSNTVSNMMF 476 PMV++ +NSG A MPIV+A VA GS +PL AP +G LGAF+AGSNTVSNMMF Sbjct: 419 PMVQVFMNSGGGLAGFEKMPIVLAEAVAGLAGSAWPLFAPTIGGLGAFVAGSNTVSNMMF 478 Query: 477 SQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGSTLRKTIWP 536 S FQFGV + + + +VA QAVG AAGN++ +HNVVAASA VGLLG+EG +RKT +P Sbjct: 479 SLFQFGVGERIAVDPTWIVALQAVGGAAGNIICVHNVVAASAVVGLLGKEGLVIRKTFFP 538 Query: 537 TLYYVLFTGVIGLIAIY 553 LYY IG IY Sbjct: 539 FLYYAFLPAAIGYSIIY 555 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: 1132 Number of extensions: 57 Number of successful extensions: 6 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: 601 Length adjustment: 36 Effective length of query: 528 Effective length of database: 565 Effective search space: 298320 Effective search space used: 298320 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