Align L-lactate permease (characterized, see rationale)
to candidate 8499614 DvMF_0381 L-lactate transport (RefSeq)
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__Miya:8499614 Length = 506 Score = 303 bits (777), Expect = 8e-87 Identities = 190/517 (36%), Positives = 285/517 (55%), Gaps = 29/517 (5%) Query: 14 WLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITY-KMPVSIALASAIYGF 72 +L AL PIV+ +L VLKL + ALTL+ LA+A+ + KMP +AL++A+ G Sbjct: 6 YLQLAAALAPIVWLIFSLVVLKLPAYRTCALTLVCTLALAVFGWWKMPAFMALSAALEGA 65 Query: 73 SYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGFSFGAFLEGAA 132 + LWPI +II AVF Y + TG ++I + S+T D+RL +L+V + FG FLEG A Sbjct: 66 AMALWPIMIVIIAAVFTYNLARHTGSMDVITRMLSSITTDKRLLVLIVAWGFGGFLEGVA 125 Query: 133 GFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQVSSLDPFHIGQ 192 G+G VAI A++L +GF P++AA +CL+ANT P AFGA+GIPI+ V+ L I Sbjct: 126 GYGTAVAIPASILAAMGFQPMFAAVICLVANTVPTAFGAIGIPIVTMAGVTGLPVETISY 185 Query: 193 LAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSNFIGPELPDIT 252 QL + I++ + L+ + G +GI+ + ATLV+G++FA Q T+ ++G ELP Sbjct: 186 YTALQLFVFIILITYLLVILTAGFKGIKGVFWATLVSGLAFAFPQLYTAKYMGAELP--- 242 Query: 253 SALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWSPFIILTAIVTLW 312 L+ +C + VW +F Q P + + KAW P+I++ A + L Sbjct: 243 -CLIGSVCSMIATIVW--ARLFHRDTAAQVDPIPAA-----EKVKAWLPYILVFAFIILC 294 Query: 313 SIKDVQLALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAVGTAILIAAMI 372 S ++ A+ A S +KT + + P+ + G I+IA I Sbjct: 295 S--NLFPAIRDALGS----------VKTTVRIYGDNPFT----FKWIATPGALIIIATYI 338 Query: 373 SIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLALVLA-GTGVA 431 ++ + + T +L + +++ ++A A V + SG+ +T+A+ +A T Sbjct: 339 GGMIQGVKVREITGVLGSTAKKLVYSGVTVVSIVALAKVMSTSGMINTIAIAVADSTSSY 398 Query: 432 FPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTGGVTGKMISP 491 FPF SP LG LG F+TGSDTSSN LFG LQ AN+I + +V+A+ G GKMISP Sbjct: 399 FPFISPLLGALGTFVTGSDTSSNVLFGQLQMEVANRISIDSTWIVSASAAGATAGKMISP 458 Query: 492 QSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVL 528 QSIAVA AATGL G E + TL + + +G L Sbjct: 459 QSIAVATAATGLTGYEGRIMNRTLAVCVGYVLVLGTL 495 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: 789 Number of extensions: 46 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: 545 Length of database: 506 Length adjustment: 35 Effective length of query: 510 Effective length of database: 471 Effective search space: 240210 Effective search space used: 240210 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