Align L-lactate permease (characterized, see rationale)
to candidate AZOBR_RS25125 AZOBR_RS25125 L-lactate permease
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__azobra:AZOBR_RS25125 Length = 562 Score = 764 bits (1972), Expect = 0.0 Identities = 384/558 (68%), Positives = 459/558 (82%), Gaps = 20/558 (3%) Query: 3 WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62 WTQ Y P G+LWL+A+VA LPI+FFF+ALT+L++KGH+AG +T+ I+LAVAI+ YKMPV Sbjct: 4 WTQVYDPAGNLWLSALVAALPIIFFFIALTMLRMKGHVAGTITVAISLAVAILFYKMPVG 63 Query: 63 IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122 +ALASA YGF YGLWPIAWII+ AVFLYKITVKTGQFEIIRSSV+S+TEDQRLQML+VGF Sbjct: 64 MALASAGYGFLYGLWPIAWIIVAAVFLYKITVKTGQFEIIRSSVVSITEDQRLQMLMVGF 123 Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV Sbjct: 124 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 183 Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242 +SLDPF IG +AGRQLP+LS+ VPFW+I +MDG +G+R+TWPA LVAG +FAVTQ+ T+N Sbjct: 184 TSLDPFRIGAMAGRQLPLLSVFVPFWIIMIMDGWKGVRETWPAILVAGGTFAVTQYFTAN 243 Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFS--------------GMKQRAVTPKS 288 FIGPELPDITSALVSL+ +T+FLK W+PK IF F+ M + Sbjct: 244 FIGPELPDITSALVSLVSITVFLKFWKPKAIFRFANSPLASGPVPQSVGAMASSEFNAQR 303 Query: 289 TFSNGQIFKAWSPFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAP 342 ++S G+I KAWSPF+ILT IVT+WS+K + AL+ + + L LV+K AP Sbjct: 304 SYSAGEIAKAWSPFLILTVIVTIWSLKPFKALFVKGGALADTVLYFPIAGLDKLVLKAAP 363 Query: 343 IVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSI 402 IVA P A+YKL+LL A GTAILI+A+I++V+LKM ++ + +F +T+ EL+ PI SI Sbjct: 364 IVASPKPIDAVYKLDLLAATGTAILISAIITMVMLKMRPADGVKTFVETVSELKRPIYSI 423 Query: 403 GLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQA 462 G+VLAFAF+ANYSGLSSTLAL+LAGTG FPFFSP LGWLGVFLTGSDTSSNALF LQA Sbjct: 424 GMVLAFAFIANYSGLSSTLALLLAGTGFLFPFFSPILGWLGVFLTGSDTSSNALFCGLQA 483 Query: 463 NTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFC 522 TA Q+GV+ L+VAANTTGGVTGKMISPQSIAVACAA GL G+ES+LFRFT+KHSLFF Sbjct: 484 TTAQQVGVSDVLMVAANTTGGVTGKMISPQSIAVACAAVGLVGRESELFRFTVKHSLFFV 543 Query: 523 TFIGVLTVLQAYIVPWTL 540 IGV+T++QAYI+PW + Sbjct: 544 AIIGVITMIQAYILPWMI 561 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: 1086 Number of extensions: 31 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: 562 Length adjustment: 36 Effective length of query: 509 Effective length of database: 526 Effective search space: 267734 Effective search space used: 267734 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 Apr 09 2024. 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