Align L-lactate permease (characterized, see rationale)
to candidate WP_028583131.1 G494_RS0101675 L-lactate permease
Query= uniprot:A0KZB2 (547 letters) >NCBI__GCF_000429965.1:WP_028583131.1 Length = 563 Score = 451 bits (1160), Expect = e-131 Identities = 240/551 (43%), Positives = 340/551 (61%), Gaps = 12/551 (2%) Query: 2 TILQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGL 61 T +Q L + TP+I I L+ + A +AMP+ + A A+F W M + AS L+G+ Sbjct: 3 TTIQALLAATPIIIAAILLLGVHWSARRAMPVVYLTAAAIALFFWDMSFNRILASTLQGM 62 Query: 62 LSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAG 121 + I L IIFGA+ LLNTL+ SGA+ TIRAGFTNIS D RVQ +II WLFG FIEG++G Sbjct: 63 VVTIAVLWIIFGAIMLLNTLQRSGAITTIRAGFTNISPDRRVQALIIAWLFGCFIEGASG 122 Query: 122 FGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAA 181 FGTPAAI APLLV +G P +AA +V ++ S VSFGA+G P+L G+ GL ++ + Sbjct: 123 FGTPAAIAAPLLVAIGFPALAAVMVGMMIQSTPVSFGAVGTPILIGINNGLDH---AVLS 179 Query: 182 EQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKFA 241 EQ G S+ + R I + I GTL+PL+MV +LT FFGRNKS++EGLA+ FA Sbjct: 180 EQLLQAGSSWELFIRLITSEVAIGHAIVGTLMPLLMVVMLTRFFGRNKSWREGLAMLPFA 239 Query: 242 IFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAENDSQE 301 +F GLAFT+P + GPEFPS++G+L G+A+V+P AR+G+L+PK W+ D + Sbjct: 240 LFTGLAFTIPYALTGIFLGPEFPSIVGALAGLAIVVPAARQGFLVPKESWDFPPSKDWPQ 299 Query: 302 G--------AKIETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSSFNISWTGLMG- 352 G A K AWTPY+++A +LV SR K L + + ++G Sbjct: 300 GWLGNLTLKAPTADERKIPLALAWTPYVLVAVILVASRVFPSFKGLLKGVSFGFANILGE 359 Query: 353 TELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMV 412 + AS LY PG + VC+L FL +MK + + + K+++ L ++PMV Sbjct: 360 AGVSASVQPLYLPGGILLFVCLLTLFLHRMKPAQLLAAATDAGKTLIGAGFVLVFTIPMV 419 Query: 413 KIFLNSGVNGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSL 472 +I +NSG+NGA L SMPVA+A +S G+V+ +AP VG GAF++GS T SNMM S Sbjct: 420 RILINSGINGADLVSMPVAMASFAAESFGSVYPLLAPTVGALGAFIAGSNTVSNMMLSQF 479 Query: 473 QYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVAIG 532 Q+ VA + ++ +++ALQ IGA AGNM+ + NVVAA+ VG+ G+E + +R T+ I Sbjct: 480 QFEVAGALSVSGAILVALQAIGAAAGNMIAIHNVVAASATVGLLGQEGKTLRMTILPTIY 539 Query: 533 YALLAGTIATL 543 Y AG + + Sbjct: 540 YVSAAGVLGLI 550 Lambda K H 0.326 0.138 0.413 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: 919 Number of extensions: 53 Number of successful extensions: 5 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: 547 Length of database: 563 Length adjustment: 36 Effective length of query: 511 Effective length of database: 527 Effective search space: 269297 Effective search space used: 269297 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