Align L-lactate permease (characterized, see rationale)
to candidate BWI76_RS27185 BWI76_RS27185 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__Koxy:BWI76_RS27185 Length = 551 Score = 730 bits (1884), Expect = 0.0 Identities = 366/547 (66%), Positives = 440/547 (80%), Gaps = 9/547 (1%) Query: 3 WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62 W Q Y P G++WL++++A LPI+FFF AL LKLKG++A T++IAL+VA++ YKMPV Sbjct: 4 WQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAATWTVVIALSVALLFYKMPVD 63 Query: 63 IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122 ALAS +YGF YGLWPIAWIII AVF+YKI+VKTGQF+IIRSS++S+T DQRLQML+VGF Sbjct: 64 HALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVGF 123 Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLI NTAPVAFGAMGIPI+VAGQV Sbjct: 124 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIVNTAPVAFGAMGIPILVAGQV 183 Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242 + LD F IGQ+ GRQLP L+IIV FW++A+MDG RGI++TWPA +VAG SFA+ Q+L+SN Sbjct: 184 TGLDSFEIGQMVGRQLPFLTIIVLFWIMAIMDGWRGIKETWPAVMVAGGSFAIAQYLSSN 243 Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAV---TPKSTFSNGQIFKAW 299 F+GPELPDI S+LVSL+CLTLFLK WQP IF F M V ++ ++ GQ+ +AW Sbjct: 244 FLGPELPDIISSLVSLVCLTLFLKRWQPVRIFRFGDMGASQVDMNLARTRYTPGQVIRAW 303 Query: 300 SPFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAPIVAKETPYAAI 353 SPF+ LTA VTLWS+ + A+ I+I VP+L +V + P+V + TPYAA+ Sbjct: 304 SPFLFLTATVTLWSVPPFKALFAPGGAMYDFVINISVPFLDKMVARMPPVVNEATPYAAV 363 Query: 354 YKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVAN 413 YK + L A GTAIL AA++SIV L+M +A+++F L EL PI SIG+VLAFAF++N Sbjct: 364 YKFDWLSATGTAILFAALLSIVWLRMKPKDAISTFGSMLKELALPIYSIGMVLAFAFISN 423 Query: 414 YSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPE 473 YSGLSSTLAL LA TG AF FFSPFLGWLGVFLTGSDTSSNALF ALQA A QIGV+ Sbjct: 424 YSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGVSDI 483 Query: 474 LLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQA 533 LLVAANTTGGVTGKMISPQSIA+ACAA GL GKESDLFRFT+KHSL F +GV+T LQA Sbjct: 484 LLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCMVGVITTLQA 543 Query: 534 YIVPWTL 540 Y++ W + Sbjct: 544 YVLTWMI 550 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: 1051 Number of extensions: 42 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: 551 Length adjustment: 36 Effective length of query: 509 Effective length of database: 515 Effective search space: 262135 Effective search space used: 262135 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