Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate AZOBR_RS25125 AZOBR_RS25125 L-lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >FitnessBrowser__azobra:AZOBR_RS25125 Length = 562 Score = 787 bits (2032), Expect = 0.0 Identities = 394/565 (69%), Positives = 468/565 (82%), Gaps = 7/565 (1%) Query: 1 MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60 MQ W Q+Y P G+L LSAL A +PI+FFF+AL + R+KGHVAG+IT+A+++AVAI + M Sbjct: 1 MQPWTQVYDPAGNLWLSALVAALPIIFFFIALTMLRMKGHVAGTITVAISLAVAILFYKM 60 Query: 61 PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120 P MA A+AGYGF YGLWPIAWIIVAAVFLYK+TVK+GQFE+IRSSV+SIT+DQRLQ+L+ Sbjct: 61 PVGMALASAGYGFLYGLWPIAWIIVAAVFLYKITVKTGQFEIIRSSVVSITEDQRLQMLM 120 Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180 +GF FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVA Sbjct: 121 VGFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVA 180 Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240 GQVT +D F+IGAM GRQLPLLS+FVPFW++ +MDG +GVRETWPA LVAG +FA+TQYF Sbjct: 181 GQVTSLDPFRIGAMAGRQLPLLSVFVPFWIIMIMDGWKGVRETWPAILVAGGTFAVTQYF 240 Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPK---RTAGAQIAGATSSATVTASVGGFGQ 297 T+NFIGPELPDITSAL SL+S+T+FLK W+PK R A + +A S V SVG Sbjct: 241 TANFIGPELPDITSALVSLVSITVFLKFWKPKAIFRFANSPLA----SGPVPQSVGAMAS 296 Query: 298 PRSTVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQ 357 YS GEI KAWSPFLILTV+VTIW+LKPFKA+F GG++ V F I LD+ Sbjct: 297 SEFNAQRSYSAGEIAKAWSPFLILTVIVTIWSLKPFKALFVKGGALADTVLYFPIAGLDK 356 Query: 358 MVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFEL 417 +V+K APIV +P I AV+KLD ++ATGTAI SA+I+M++LK+ G+ TF ET+ EL Sbjct: 357 LVLKAAPIVASPKPIDAVYKLDLLAATGTAILISAIITMVMLKMRPADGVKTFVETVSEL 416 Query: 418 RWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNA 477 + PI SIGMVLAFAF+ NYSG+SST+AL+LAGTG FPFFSP LGWLGVFLTGSDTSSNA Sbjct: 417 KRPIYSIGMVLAFAFIANYSGLSSTLALLLAGTGFLFPFFSPILGWLGVFLTGSDTSSNA 476 Query: 478 LFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTL 537 LF LQATTA Q+GV+D L+VAANT+GGVTGKMISPQSIAVACAA GLVG+ES+LFRFT+ Sbjct: 477 LFCGLQATTAQQVGVSDVLMVAANTTGGVTGKMISPQSIAVACAAVGLVGRESELFRFTV 536 Query: 538 KHSLFFATIVGLITLAQAYWFTGML 562 KHSLFF I+G+IT+ QAY M+ Sbjct: 537 KHSLFFVAIIGVITMIQAYILPWMI 561 Lambda K H 0.327 0.139 0.422 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: 948 Number of extensions: 34 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: 564 Length of database: 562 Length adjustment: 36 Effective length of query: 528 Effective length of database: 526 Effective search space: 277728 Effective search space used: 277728 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