Align L-lactate permease (characterized, see rationale)
to candidate 207586 DVU2110 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >MicrobesOnline__882:207586 Length = 545 Score = 550 bits (1416), Expect = e-161 Identities = 273/542 (50%), Positives = 373/542 (68%), Gaps = 2/542 (0%) Query: 1 MTWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMP 60 M WTQ Y P ++ L+A+VA+LP+ F L V + KGH+A A L A A + + MP Sbjct: 1 MLWTQVYDPFSNITLSAMVAMLPLAILFYMLAVRRAKGHVAAACGLAGAFAATVAVWGMP 60 Query: 61 VSIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLV 120 +A+ + +YG + GL+PI WI++TAV+LY +TV++G+FEII+SS+ +T+D+RLQ L + Sbjct: 61 AGLAVNATLYGVAMGLFPIIWIVLTAVWLYNMTVESGEFEIIKSSLARLTDDRRLQALFI 120 Query: 121 GFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAG 180 F+FGAFLEG AGFG PVAITAA+L+GLGF+P+YA G+CLIANTAPVAFGA+GIP+IVA Sbjct: 121 AFAFGAFLEGTAGFGTPVAITAAMLMGLGFSPVYAGGICLIANTAPVAFGALGIPVIVAS 180 Query: 181 QVSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLT 240 QVS LD + Q GRQLP+ S+IVP W+ +M G + + PA +VA V F+ TQF+ Sbjct: 181 QVSGLDTLTLSQYVGRQLPVFSLIVPLWMTVVMCGFKRTMEVMPAIVVASVCFSGTQFIF 240 Query: 241 SNFIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWS 300 +++ GP LPD+ +A+V+++ L + L+ W+P + F+ K A T ++ S G++ +AW+ Sbjct: 241 ADWHGPTLPDVMAAIVTIVGLLVLLRFWKPARTWHFADEKPEAATGETRHSTGEVLRAWA 300 Query: 301 PFIILTAIVTLWSIKDVQLAL-SFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLL 359 P+ IL V W + V+ L + +S E P LH + KTAPIV + PYAA + NL+ Sbjct: 301 PYAILAVFVFFWGLGSVKTFLNNIFIMSFEWPGLHAAIAKTAPIVKADAPYAAKFTFNLI 360 Query: 360 GAVGTAILIAAMISIVVLK-MSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLS 418 A GTAIL A ++S+ V+ A T +LRFPIL+I ++L A + NYSG+S Sbjct: 361 SAGGTAILFAGLLSVPVMPGYGYGRAFGCLARTCYQLRFPILTIVMILGLAQLMNYSGMS 420 Query: 419 STLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAA 478 STL + TG FPFF+P +GWLGVFLTGS+TSSNALFG++Q TA+ +GV P L VAA Sbjct: 421 STLGIAFTHTGALFPFFAPIMGWLGVFLTGSNTSSNALFGSMQHATASAVGVDPYLTVAA 480 Query: 479 NTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAYIVPW 538 N TGGVTGKMISPQSI+VA A+T G+E LFRF LKHS+ I VL LQAY++PW Sbjct: 481 NATGGVTGKMISPQSISVATASTHTVGQEGALFRFALKHSIAMTLVICVLVTLQAYVIPW 540 Query: 539 TL 540 L Sbjct: 541 ML 542 Lambda K H 0.327 0.140 0.419 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: 917 Number of extensions: 41 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: 545 Length of database: 545 Length adjustment: 35 Effective length of query: 510 Effective length of database: 510 Effective search space: 260100 Effective search space used: 260100 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: 52 (24.6 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