Align L-lactate permease (characterized, see rationale)
to candidate WP_043745478.1 AMB_RS20875 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >NCBI__GCF_000009985.1:WP_043745478.1 Length = 547 Score = 734 bits (1894), Expect = 0.0 Identities = 365/546 (66%), Positives = 446/546 (81%), Gaps = 11/546 (2%) Query: 3 WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62 W Q Y P G+LWL++++A +PI+FFF+AL +LKLKGH+AG +T+L+++AVAI+ YKMPV+ Sbjct: 4 WMQVYDPAGNLWLSSLIAAIPIIFFFVALAILKLKGHVAGTITVLLSIAVAIVFYKMPVA 63 Query: 63 IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122 A+ + + GF +GLWPIAWIII AVFLYK+TVKTGQFEIIRSSV+S+T DQRLQML++GF Sbjct: 64 AAVMAGVQGFLFGLWPIAWIIIGAVFLYKVTVKTGQFEIIRSSVVSITADQRLQMLMIGF 123 Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV Sbjct: 124 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 183 Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242 S LD F IG +AGRQLP+L++ VPFW+I +MDG +G+R+TWPA LVAG SFA + TSN Sbjct: 184 SGLDAFKIGAMAGRQLPLLAVFVPFWIIFIMDGFKGVRETWPAILVAGGSFAFGVWFTSN 243 Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKST--FSNGQIFKAWS 300 +IGPELPDITSAL+SL+C+T+FLK WQPK IF F K+ K + ++ GQ+ +AW+ Sbjct: 244 YIGPELPDITSALISLVCITVFLKFWQPKNIFRF---KEEGEDEKHSHDYTTGQVARAWA 300 Query: 301 PFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIY 354 PF+ILTA+VT+WS+K + L F I+ EVP LHNLV K PIVA A+Y Sbjct: 301 PFLILTAVVTVWSLKPFKAMFAKGGELVFTNINWEVPALHNLVAKVPPIVAAAKAVPAVY 360 Query: 355 KLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANY 414 LNL+ A GTAILI+A+I+I++L M S L +F +TL EL+ PI +IG VLAFA+VAN Sbjct: 361 TLNLVSATGTAILISAIITIIMLGMKGSEGLKTFGETLNELKRPIYTIGTVLAFAYVANA 420 Query: 415 SGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPEL 474 SGLS+TLAL+L G G +PFFSP LGWLGVFLTGSDTSSNALFGALQA TA+Q+G++ L Sbjct: 421 SGLSTTLALLLTGAGDFYPFFSPVLGWLGVFLTGSDTSSNALFGALQATTAHQLGISDIL 480 Query: 475 LVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAY 534 +VAANTTGGVTGKMISPQSIAVACAA GL G E++LFRFTLKHS+FF IGV+T LQAY Sbjct: 481 MVAANTTGGVTGKMISPQSIAVACAAVGLVGHEANLFRFTLKHSVFFVCIIGVITTLQAY 540 Query: 535 IVPWTL 540 ++ W + Sbjct: 541 VLTWMI 546 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: 1052 Number of extensions: 36 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: 547 Length adjustment: 35 Effective length of query: 510 Effective length of database: 512 Effective search space: 261120 Effective search space used: 261120 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