Align L-lactate permease (characterized, see rationale)
to candidate WP_004303509.1 C665_RS06635 L-lactate permease
Query= uniprot:L0GFN1 (564 letters) >NCBI__GCF_000310185.1:WP_004303509.1 Length = 566 Score = 897 bits (2318), Expect = 0.0 Identities = 446/563 (79%), Positives = 507/563 (90%), Gaps = 1/563 (0%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 M G LA AF+PILLAA++L+GLRWPA RAMP+V+ TA IGL+VW+MS+NR++ASTLQ Sbjct: 1 MQPGTLAFLAFSPILLAAVLLVGLRWPAKRAMPVVYFLTAGIGLYVWEMSLNRVLASTLQ 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 GLVIT+G+LWIIFGAILLLNTLK+SGGITAIRAGF ISPDRRIQAIII WLFGCFIEGA Sbjct: 61 GLVITIGVLWIIFGAILLLNTLKYSGGITAIRAGFAKISPDRRIQAIIIGWLFGCFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATIGA 180 SGFGTPAAIAAPLLVA+GFPA+AAVLLGMLVQSTPVSFGAVGTPI++G+NSGLD+ATIGA Sbjct: 121 SGFGTPAAIAAPLLVAIGFPALAAVLLGMLVQSTPVSFGAVGTPIIIGVNSGLDSATIGA 180 Query: 181 QLVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLPFAI 240 QL A+GSSW+ +LQ ITS+VAI HA+VGTV+PL+MV+MLTRFFG+EKSWKAGFEVLPFAI Sbjct: 181 QLAARGSSWDVFLQVITSNVAIIHAMVGTVIPLIMVMMLTRFFGREKSWKAGFEVLPFAI 240 Query: 241 FAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADAKEWPAE 300 FAGLAFT+PYA TG+FLGPEFPSLLGGLVGLA+VTTAARF FL PK TWDFAD KEWP+E Sbjct: 241 FAGLAFTVPYAFTGVFLGPEFPSLLGGLVGLALVTTAARFGFLVPKKTWDFADPKEWPSE 300 Query: 301 WLGTIEMKLDEMAA-RPMSAFRAWLPYVLVGAILVISRVFPQVTAALKSVSIAFANILGE 359 W+G++EMKLD++ +P+S FRAWLPYVLVGA+LV+SRVFP++ A+KSV I FA+ILGE Sbjct: 301 WMGSVEMKLDQLPRHQPISIFRAWLPYVLVGALLVLSRVFPEIGGAMKSVVIVFADILGE 360 Query: 360 TGINAGIEPLYLPGGILVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLFTVPMV 419 GI A +PLYLPGGILV VVLIT FLHGM L AV ESS VLL AGFVLLFTVPMV Sbjct: 361 KGIKADFQPLYLPGGILVAVVLITVFLHGMHARSLVKAVGESSRVLLGAGFVLLFTVPMV 420 Query: 420 RILINSGVNGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSNTVSNMMFSQF 479 RILINSGVN A+L SMPI MA++VADSVG++YPLLAP+VGALGAF+AGSNTVSNMM SQF Sbjct: 421 RILINSGVNAADLPSMPIAMAKWVADSVGNVYPLLAPSVGALGAFIAGSNTVSNMMLSQF 480 Query: 480 QFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGSTLRKTIWPTLY 539 QFGVA SLGIS AMVVA QA+GAAAGNMVAIHNVVAASATVGLLGREG+ LRKT WPT+Y Sbjct: 481 QFGVATSLGISTAMVVAVQAIGAAAGNMVAIHNVVAASATVGLLGREGAILRKTFWPTVY 540 Query: 540 YVLFTGVIGLIAIYVLGVTDPLV 562 YVL TG + +IAIYVLGV+DPL+ Sbjct: 541 YVLMTGTVAMIAIYVLGVSDPLL 563 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: 1250 Number of extensions: 59 Number of successful extensions: 3 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: 566 Length adjustment: 36 Effective length of query: 528 Effective length of database: 530 Effective search space: 279840 Effective search space used: 279840 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