Align L-lactate permease (characterized, see rationale)
to candidate 350981 BT1453 L-lactate permease (NCBI ptt file)
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__Btheta:350981 Length = 499 Score = 267 bits (683), Expect = 6e-76 Identities = 162/520 (31%), Positives = 283/520 (54%), Gaps = 26/520 (5%) Query: 15 LTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVSIALASAIYGFSY 74 +T I+A++P++ + + K+ G + ++L++ + +A+ + V S +YG Sbjct: 1 MTLILAIIPVLLLIVLMAFFKMSGDKSSIISLIVTMLIALFGFAFSVDNLFYSFLYGALK 60 Query: 75 GLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGFSFGAFLEGAAGF 134 + PI II+ A+F Y + +KT + EII+ S++ D+ +Q+LL+ + FG LE AGF Sbjct: 61 AVSPILIIILMAIFSYNVLLKTEKMEIIKQQFASISTDKSIQVLLLTWGFGGLLEAMAGF 120 Query: 135 GAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQVSSLDPFHIGQLA 194 G VAI AA+L+ LGF P+++A + LIAN+ AFGA+G P++V + ++LD + Sbjct: 121 GTAVAIPAAILISLGFKPIFSATVSLIANSVATAFGAIGTPVLVLAKETNLDVLQLSTNV 180 Query: 195 GRQLPILSIIVPFWLIAMMD-GIRGI-RQTWPATLVAGVSFAVTQFLTSNFIGPELPDIT 252 QL +L ++P L+ + + ++ + + + A LV GVS V Q+L + ++G E P I Sbjct: 181 VLQLSVLMFLIPLVLLFLTNPKLKALPKNIFLALLVGGVSL-VGQYLAARYMGAESPAII 239 Query: 253 SALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWSPFIILTAIVTLW 312 +++S+I + L+ K+ KE K R KST I AWS ++++ ++ L Sbjct: 240 GSILSIIVIVLYGKLTASKE------EKAR----KSTLKTKDILNAWSIYLLILFLIILT 289 Query: 313 SIKDVQLALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAVGTAILIAAMI 372 S L + +N V + + V T Y ++ L G + + I Sbjct: 290 SPLFPSLRSTLE---------NNWVTRISLPVNATT---VNYTISWLTHAGVLLFLGTFI 337 Query: 373 SIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLALVLA-GTGVA 431 ++ + +T+ +L+ +++ ++ + + + SG+ + +A LA TG Sbjct: 338 GGLIQGAKVKELFIVLWNTVKQLKKTFITVICLVGLSTIMDTSGMIAVIATALATATGSL 397 Query: 432 FPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTGGVTGKMISP 491 +P F+P +G LG F+TGSDTSSN LFG LQA+ A QI V+P+ L AANT G GK+ISP Sbjct: 398 YPLFAPVIGCLGTFITGSDTSSNILFGKLQASVAGQIHVSPDWLSAANTVGATGGKIISP 457 Query: 492 QSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVL 531 QSIA+A +A GKE ++ + + ++L + G++ + Sbjct: 458 QSIAIATSAGNQQGKEGEILKAAIPYALAYVVITGIIVYI 497 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: 727 Number of extensions: 32 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: 499 Length adjustment: 35 Effective length of query: 510 Effective length of database: 464 Effective search space: 236640 Effective search space used: 236640 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 Apr 09 2024. 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