Align L-lactate permease (characterized, see rationale)
to candidate 8501125 DvMF_1861 L-lactate permease (RefSeq)
Query= uniprot:L0GFN1 (564 letters) >FitnessBrowser__Miya:8501125 Length = 569 Score = 467 bits (1202), Expect = e-136 Identities = 249/563 (44%), Positives = 353/563 (62%), Gaps = 11/563 (1%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 MS LLAL A PIL+A ++++G+RWP++RAMPL +L + W++ I A +LQ Sbjct: 1 MSLELLALVALLPILVALVLMVGMRWPSTRAMPLAWLVCVLGAIGAWNLPAGYIAALSLQ 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 G+V +G+L I+FGAI++L TLK+SGG+ I+ G IS D+RIQAIII ++F FIEGA Sbjct: 61 GVVTAIGVLIIVFGAIIILYTLKYSGGMETIQYGMQNISRDKRIQAIIIGYMFAAFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGIN--SGLDTATI 178 +GFGTPAA+AAPLL+++GFP +AA ++ ++ S VSFGAVGTPI++G+ + L Sbjct: 121 AGFGTPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGLKFLAPLVKDAA 180 Query: 179 GAQLVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLPF 238 A + + ++ + I V + H + ++P+ M+ LTRF+G++KSW GF F Sbjct: 181 AANPGLNFTDFGSFAKVIGQWVTLMHGPMIFILPIFMLGFLTRFYGQKKSWAEGFAAWQF 240 Query: 239 AIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADAKEWP 298 +FA +AF +PY +GPEFPSL+GGLVGL I+ A+ F PK TWDF W Sbjct: 241 CVFAAVAFIVPYLTFAWLVGPEFPSLIGGLVGLGIIVAGAKKGFCVPKETWDFGPQSTWE 300 Query: 299 AEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQ--VTAALKSVSIAFANI 356 AEW GTI + MS F AWLPY+L+G ILV++R+ P+ + + + + +I Sbjct: 301 AEWTGTIATSTNTEFKPHMSQFMAWLPYILIGVILVLTRI-PELGLKGWMSAQKLPINDI 359 Query: 357 LGETGINAGIEPLYLPGGI-LVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLFT 415 LG G++A I+ LYLPG I +V L+T LHGM+ +K A ES + + L Sbjct: 360 LGYKGVSASIDYLYLPGTIPFTLVALLTIMLHGMKGDAVKKAWSESFSKMKAPTIALFAA 419 Query: 416 VPMVRILINSGVNGAEL-----ASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSNT 470 V +V I SGV A L SMP+ MA+ VA G+ +P+LA VG LGAF+ GSNT Sbjct: 420 VALVSIFRGSGVADAALNPNNYPSMPLAMAKTVAAFAGNAWPMLASYVGGLGAFITGSNT 479 Query: 471 VSNMMFSQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGSTL 530 VS+++F++FQ+GVAQ L + ++VA Q G A GNMV IHN+VA A GL+GREG L Sbjct: 480 VSDLLFAEFQWGVAQQLSLPRQIIVAAQVAGGAMGNMVCIHNIVAVCAVTGLIGREGMIL 539 Query: 531 RKTIWPTLYYVLFTGVIGLIAIY 553 ++T WP Y + G+I I + Sbjct: 540 KRTFWPFALYGIVVGIIASILCF 562 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: 1037 Number of extensions: 50 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: 569 Length adjustment: 36 Effective length of query: 528 Effective length of database: 533 Effective search space: 281424 Effective search space used: 281424 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