Align L-lactate permease (characterized, see rationale)
to candidate 8501125 DvMF_1861 L-lactate permease (RefSeq)
Query= uniprot:A0KZB2 (547 letters) >FitnessBrowser__Miya:8501125 Length = 569 Score = 383 bits (984), Expect = e-111 Identities = 220/562 (39%), Positives = 333/562 (59%), Gaps = 29/562 (5%) Query: 4 LQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGLLS 63 L L +L P++ ++ +V +R P+++AMP++ ++ L A+ W + +AA L+G+++ Sbjct: 5 LLALVALLPILVALVLMVGMRWPSTRAMPLAWLVCVLGAIGAWNLPAGYIAALSLQGVVT 64 Query: 64 AITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAGFG 123 AI L I+FGA+ +L TLKYSG M+TI+ G NIS D R+Q III ++F AFIEG+AGFG Sbjct: 65 AIGVLIIVFGAIIILYTLKYSGGMETIQYGMQNISRDKRIQAIIIGYMFAAFIEGAAGFG 124 Query: 124 TPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAAEQ 183 TPAA+ APLL+ LG PP+AAAV+ L+ +S CVSFGA+G P+L G+ + L + Sbjct: 125 TPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGL-----KFLAPLVKDA 179 Query: 184 FAAHGG-SYVGYARFIVMHMITIDLITGTLI---PLVMVTILTGFFGRNKSFKEGLAIWK 239 AA+ G ++ + F + + L+ G +I P+ M+ LT F+G+ KS+ EG A W+ Sbjct: 180 AAANPGLNFTDFGSFAKVIGQWVTLMHGPMIFILPIFMLGFLTRFYGQKKSWAEGFAAWQ 239 Query: 240 FAIFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAENDS 299 F +FA +AF VP +L GPEFPS+IG LVG+ +++ A+KG+ +PK W DF + Sbjct: 240 FCVFAAVAFIVPYLTFAWLVGPEFPSLIGGLVGLGIIVAGAKKGFCVPKETW-DFGPQST 298 Query: 300 QEGAKIETTA---------KFSQIAAWTPYIIMAALLVLSR-TVAPLKAWLSSFNISWTG 349 E T A SQ AW PYI++ +LVL+R LK W+S+ + Sbjct: 299 WEAEWTGTIATSTNTEFKPHMSQFMAWLPYILIGVILVLTRIPELGLKGWMSAQKLPIND 358 Query: 350 LMGTE-LKASFATLYAPGAF-FVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGA 407 ++G + + AS LY PG F V +L L MK A+K++ S M I+L A Sbjct: 359 ILGYKGVSASIDYLYLPGTIPFTLVALLTIMLHGMKGDAVKKAWSESFSKMKAPTIALFA 418 Query: 408 SVPMVKIFLNSGVNGAGL-----ASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSA 462 +V +V IF SGV A L SMP+A+A + G W +A VG GAF++GS Sbjct: 419 AVALVSIFRGSGVADAALNPNNYPSMPLAMAKTVAAFAGNAWPMLASYVGGLGAFITGSN 478 Query: 463 TFSNMMFSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEI 522 T S+++F+ Q+ VA + + +++A Q G GNM+C+ N+VA V G+ GRE I Sbjct: 479 TVSDLLFAEFQWGVAQQLSLPRQIIVAAQVAGGAMGNMVCIHNIVAVCAVTGLIGREGMI 538 Query: 523 IRKTM-PVAIGYALLAGTIATL 543 +++T P A+ Y ++ G IA++ Sbjct: 539 LKRTFWPFAL-YGIVVGIIASI 559 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: 970 Number of extensions: 60 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: 569 Length adjustment: 36 Effective length of query: 511 Effective length of database: 533 Effective search space: 272363 Effective search space used: 272363 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 17 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