Align L-lactate permease (characterized, see rationale)
to candidate WP_015944586.1 DHAF_RS16925 L-lactate permease
Query= uniprot:L0GFN1 (564 letters) >NCBI__GCF_000021925.1:WP_015944586.1 Length = 623 Score = 510 bits (1313), Expect = e-149 Identities = 280/583 (48%), Positives = 358/583 (61%), Gaps = 35/583 (6%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 MS L A PIL+ AI L+GL+WPAS+AMPL ++ +GL VW + V +I+ T++ Sbjct: 1 MSILLQGFLALLPILVVAIFLVGLKWPASKAMPLSYITVVIVGLLVWKLPVIQIVGGTVK 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 GLV+ L LL+IIFG++L+L T+ SGG+ IR +S DRRIQ II+AWLFG FIEGA Sbjct: 61 GLVVALSLLYIIFGSVLVLYTIMESGGLAQIRQSLIGVSADRRIQVIIVAWLFGSFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTAT--- 177 SGFGTPAA+A PL++ +GFPA AAV+ GM++QSTPVSFGAVGTPI G+ +GL T Sbjct: 121 SGFGTPAAVACPLMLGLGFPAFAAVIAGMMIQSTPVSFGAVGTPIRTGVGTGLGAGTDPG 180 Query: 178 -------IGAQLVAQGSSWN--AYLQQ----ITSSVAITHAIVGTVMPLVMVLMLTRFFG 224 +G +V + N AY Q I +VAI H + G + PL +V LTR+FG Sbjct: 181 INEFASNLGINIVDAAGTLNPIAYYDQFIALIAHNVAILHFVGGFLTPLFVVAFLTRYFG 240 Query: 225 KEKSWKAGFEVLPFAIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLT 284 K KSW G + PFA+F+ LAFT+PY F+ E S+LG L+GL IV AA+ KFLT Sbjct: 241 KNKSWSEGIAIWPFALFSALAFTIPYVLINRFVNYELTSMLGALIGLVIVIFAAKNKFLT 300 Query: 285 PK--TTWDFADAKEWPAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQV 342 PK TWDF D K+W W G IE+ E MS AWLPY+ V +++I+R P + Sbjct: 301 PKEEDTWDFIDKKDWDPSWTGNIEVHYVEKPG-GMSTLVAWLPYIFVAGLILITRFIPPL 359 Query: 343 TAALKSVSIAFANILGETGINAGIEPLYLPGGILVMVVLITFFLHGMRVSELKAAVKESS 402 A L V+I + I G+ LY PG I ++V L+TF +HGM+ A K++ Sbjct: 360 KAFLNDVAITYPAI---GGLTEKWVILYSPGTIFIIVSLLTFLVHGMKTDSYVKAWKQAG 416 Query: 403 GVLLSAGFVLLFTVPMVRILINSGVNGAELASMPIVMARYVADSVGSIYPLLAPAVGALG 462 V A L+FTVPMV++ INSG AEL MP +A G ++PL AP +G LG Sbjct: 417 KVTAGASVALIFTVPMVQVFINSGGGAAELLKMPYALAEATYQLAGGLWPLFAPIIGGLG 476 Query: 463 AFLAGSNTVSNMMFSQFQFGVAQSLGISG------------AMVVATQAVGAAAGNMVAI 510 AF+AGSNTVSNM FS FQF AQ L + G VVA QA+G AAGN++ I Sbjct: 477 AFVAGSNTVSNMTFSLFQFQTAQ-LIVDGNPALAPMAMQWPLWVVALQAIGGAAGNVICI 535 Query: 511 HNVVAASATVGLLGREGSTLRKTIWPTLYYVLFTGVIGLIAIY 553 HNVVAASA VG LGREG T+RKT LYY G G +Y Sbjct: 536 HNVVAASAVVGFLGREGETIRKTFMFFLYYAFIPGAFGYSLLY 578 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: 1084 Number of extensions: 50 Number of successful extensions: 7 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: 623 Length adjustment: 37 Effective length of query: 527 Effective length of database: 586 Effective search space: 308822 Effective search space used: 308822 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