Align L-lactate permease (characterized, see rationale)
to candidate H281DRAFT_00392 H281DRAFT_00392 lactate permease
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__Burk376:H281DRAFT_00392 Length = 532 Score = 397 bits (1020), Expect = e-115 Identities = 220/534 (41%), Positives = 321/534 (60%), Gaps = 13/534 (2%) Query: 5 QTYTPLG-SLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVSI 63 Q TP+G SL + +VA LPI+ L L + A L++ L VAI ++ PV + Sbjct: 4 QLLTPVGNSLLPSFLVAALPIIVVLLLLGWARRPAWQASLAGLIVGLVVAIAVWQFPVRL 63 Query: 64 ALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVI-SVTEDQRLQMLLVGF 122 AL S G + WP+ WI+ TA+ LY I ++G+F R +I ++ D+R+ +++VGF Sbjct: 64 ALDSVAAGVVFACWPVMWIVFTAILLYNIAQRSGRFAAFRMWMIDNLPNDRRVVLVVVGF 123 Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182 SFGA LEG +GFG PVAIT++LL+ LGF L A LI NTAPVAFGA+G+PI V G V Sbjct: 124 SFGALLEGISGFGTPVAITSSLLILLGFPTLEALTFTLIFNTAPVAFGALGVPITVLGAV 183 Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242 + L + ++ GRQLP ++++PF++IA+ G R + + WP LV+G SFA+TQF+ SN Sbjct: 184 THLPADSLAKMVGRQLPFFALLLPFYVIAVYAGFRNMVRVWPVLLVSGASFALTQFVASN 243 Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWSPF 302 ++ L D+ S++VSL+ FL+VW+P F+ R + Q W P+ Sbjct: 244 YVNYSLTDVLSSMVSLVVTIAFLRVWKPAVDPAFAVNIDRVGEVRGKIGGSQ---GWYPW 300 Query: 303 IILTAIVTLWSIKDVQLALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAV 362 II++ +V +W++ + L + + P L V I TPY AI+ L A Sbjct: 301 IIVSVVVIVWTVAKIFL---IGDVKVPWPGLDKAVF----ITLYNTPYGAIWDFQPL-AT 352 Query: 363 GTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLA 422 GTAIL+AA+I+ +V+ +S + + DT ++ R IL++ ++ A++ NYSGL+ TL Sbjct: 353 GTAILVAAIITSLVVGLSARDFGAAIVDTWVQTRIAILTVATIVGLAYLMNYSGLTYTLG 412 Query: 423 LVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTG 482 L +A G FP S FLGW+ VFL+GSDTS NALFG LQ ANQ+ + P L+ A N++G Sbjct: 413 LGVASVGPFFPLVSAFLGWVAVFLSGSDTSGNALFGNLQVVAANQLNLNPVLMAATNSSG 472 Query: 483 GVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAYIV 536 GV GKMISPQ+I+ A T L GKE +F T KHS+ +G+L LQ ++ Sbjct: 473 GVMGKMISPQNISTGVATTDLKGKEGVVFAKTFKHSILLTVLLGILVWLQQNVL 526 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: 882 Number of extensions: 36 Number of successful extensions: 6 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: 532 Length adjustment: 35 Effective length of query: 510 Effective length of database: 497 Effective search space: 253470 Effective search space used: 253470 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