Align L-lactate permease (characterized, see rationale)
to candidate Pf1N1B4_4246 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4246 Length = 585 Score = 467 bits (1202), Expect = e-136 Identities = 243/578 (42%), Positives = 348/578 (60%), Gaps = 39/578 (6%) Query: 1 MTWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMP 60 M W Q Y P + L+ I+A +P+V +L +K H+A L L AL +AI + MP Sbjct: 1 MVWQQIYDPFDNPMLSTIMAAVPVVVMLASLAFFHIKAHLAALLALGSALLIAIFAFGMP 60 Query: 61 VSIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLV 120 ++A ++A+YG + GL PI WI++ +FL+++T + G F++++ S+ +T+D+RLQ+LL+ Sbjct: 61 ANMAGSAALYGAANGLLPIGWIVLNIIFLHRLTTENGSFKVLQDSLARITDDRRLQLLLI 120 Query: 121 GFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAG 180 F FGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGA+G PII Sbjct: 121 AFCFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLA 180 Query: 181 QVSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLT 240 +V+ LD + + GRQLP S+IVPFWLI G R + + WPA L+AGVSFAV QFL Sbjct: 181 KVTGLDEMELSMMVGRQLPFFSVIVPFWLIWAFAGWRKMLEIWPAILIAGVSFAVPQFLV 240 Query: 241 SNFIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRA----------VTPKSTF 290 SN+ GP L D+ +AL+S+ CLT FLKVW+P + T + + RA P +TF Sbjct: 241 SNYHGPMLVDVIAALISMACLTGFLKVWKPATVHTSAALSGRADNSRVDVDPDEEPSATF 300 Query: 291 SNG---QIFKAWSPFIILTAIVTLWSI--------------------------KDVQLAL 321 ++ + +AW P+IILT V W K ++ A Sbjct: 301 ASDAKPAVMRAWMPWIILTVFVFAWGTQSFKNLFDTRPVMDPQTHSAKLDPQGKPMREAN 360 Query: 322 SFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSI 381 ++ +H + K P+V AIYK N + G+ IL+AA++ +++ SI Sbjct: 361 PIFAPTLTFTTIHQQIEKVPPVVPVAKTEDAIYKFNWFTSTGSGILLAALLGGLLMGYSI 420 Query: 382 SNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGW 441 L + TL +R+ +++I +LA F+ YSGL +T+ L A TG+ +P F LGW Sbjct: 421 PQLLHHYLRTLWVVRYSLITIVAMLALGFLTRYSGLDATMGLAFAATGIFYPMFGTLLGW 480 Query: 442 LGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAAT 501 LGV LTGSDT+SN LFG LQ TA Q+G++P L+ AAN++GGV GKM+ QSI VA AT Sbjct: 481 LGVALTGSDTASNVLFGGLQRVTAEQLGLSPVLMAAANSSGGVMGKMVDAQSIVVASTAT 540 Query: 502 GLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAYIVPWT 539 G E ++ R+ HS+ +G L LQAY+ P++ Sbjct: 541 RWYGHEGEILRYVFFHSVVLAILVGGLVTLQAYVAPFS 578 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: 933 Number of extensions: 39 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: 585 Length adjustment: 36 Effective length of query: 509 Effective length of database: 549 Effective search space: 279441 Effective search space used: 279441 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