Align L-lactate permease (characterized, see rationale)
to candidate 208810 DVU3284 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >MicrobesOnline__882:208810 Length = 543 Score = 580 bits (1494), Expect = e-170 Identities = 288/536 (53%), Positives = 383/536 (71%), Gaps = 2/536 (0%) Query: 1 MTWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMP 60 M W Q Y PL S +A+VA +P+ F L V + KGH+A L A+ +AI + MP Sbjct: 1 MNWIQNYDPLSSALGSALVAAIPLFILFYMLAVKRAKGHVAAFLGTTSAIVLAIAVWGMP 60 Query: 61 VSIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLV 120 VS+A ++ +YG +YGL+PI WI+ITAV++Y +TV++G+FEII+ S+ +T+D+RLQ + + Sbjct: 61 VSLAASATLYGAAYGLFPIVWIVITAVWVYNMTVESGEFEIIKDSLARLTDDRRLQAIFI 120 Query: 121 GFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAG 180 F+FG+F+EG AGFG PVAITA++LVGLGFNPLYAAG+CLIANTAPVAFGA+GIPIIVAG Sbjct: 121 AFAFGSFIEGTAGFGTPVAITASMLVGLGFNPLYAAGICLIANTAPVAFGAIGIPIIVAG 180 Query: 181 QVSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLT 240 QV+ LD HI Q+ GRQLP LS+IVP WL M G + + PA VAGV FA +QF+ Sbjct: 181 QVTGLDTMHISQIVGRQLPFLSVIVPMWLCVTMCGFKRAMEVLPAVAVAGVCFAGSQFVF 240 Query: 241 SNFIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWS 300 SN+ GP LPDI SA+V++I L L L+VW+P + F G + ++ S +S G + +AW Sbjct: 241 SNYHGPTLPDIMSAIVTIIGLVLLLRVWKPATTWRFPGEAEVELSAVSQYSAGDVIRAWM 300 Query: 301 PFIILTAIVTLWSIKDVQLAL-SFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLL 359 P+IIL +V W + V+ L ++S++ P LHNL+ KTAPI AK PYAA YKLNL+ Sbjct: 301 PYIILAVMVFFWGLDGVKKVLDGIFSVSVDWPGLHNLIEKTAPIAAKNAPYAAKYKLNLI 360 Query: 360 GAVGTAILIAAMISIVVL-KMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLS 418 A GTAIL++ ++++ V+ K A+ T +LRFP+++I ++L A + NYSG+S Sbjct: 361 SAGGTAILLSGLLAVPVMPKYGFDKAIACLFRTFYQLRFPVVTIAMILGLAQIMNYSGMS 420 Query: 419 STLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAA 478 STL + TG FPFF+P LGWLGVFLTGSDTSSNALFG +Q TA +GV P L VAA Sbjct: 421 STLGIAFTKTGWLFPFFAPLLGWLGVFLTGSDTSSNALFGGMQRATAEAVGVDPHLTVAA 480 Query: 479 NTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAY 534 N++GGVTGKMISPQSI+VA A+T + G+E LFRFTL HS+ F+ VLT+LQAY Sbjct: 481 NSSGGVTGKMISPQSISVATASTNMVGQEGSLFRFTLGHSIAMTLFVCVLTLLQAY 536 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: 912 Number of extensions: 29 Number of successful extensions: 4 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: 543 Length adjustment: 35 Effective length of query: 510 Effective length of database: 508 Effective search space: 259080 Effective search space used: 259080 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