Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate PP_4735 PP_4735 L-lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >FitnessBrowser__Putida:PP_4735 Length = 556 Score = 987 bits (2551), Expect = 0.0 Identities = 510/564 (90%), Positives = 524/564 (92%), Gaps = 9/564 (1%) Query: 1 MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60 MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLAL+I VAIFAF M Sbjct: 1 MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALSILVAIFAFQM 60 Query: 61 PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120 P DMA AAAGYGF YGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL Sbjct: 61 PVDMALAAAGYGFLYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120 Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA Sbjct: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180 Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240 GQVTGIDAF IGAMTGRQLPLLSLFVPFWLVFMMDGLRGV+ETWPAALVAGLSFA+TQYF Sbjct: 181 GQVTGIDAFHIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVKETWPAALVAGLSFAVTQYF 240 Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRS 300 TSNFIGPELPDITSALASLI LTLFLKVWQPKR A ++ G+ +A V QP Sbjct: 241 TSNFIGPELPDITSALASLICLTLFLKVWQPKR-AFSEAKGSVGAAVV--------QPSG 291 Query: 301 TVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVI 360 + SPYS GEI KAWSPFLILTVLVTIWTLKPFKA FA GG+MY +VFNFAIPHLDQ+VI Sbjct: 292 SQPSPYSFGEIFKAWSPFLILTVLVTIWTLKPFKAAFAPGGAMYNFVFNFAIPHLDQLVI 351 Query: 361 KVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWP 420 K APIV PTA+PAVFKLDPISATGTAIF SALISM VLKIN KTGLTTFKET +ELRWP Sbjct: 352 KTAPIVAAPTAMPAVFKLDPISATGTAIFLSALISMAVLKINFKTGLTTFKETFWELRWP 411 Query: 421 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS 480 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS Sbjct: 412 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS 471 Query: 481 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS 540 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFT+KHS Sbjct: 472 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTVKHS 531 Query: 541 LFFATIVGLITLAQAYWFTGMLVH 564 LFFATIVGLITL QAYW TGMLVH Sbjct: 532 LFFATIVGLITLVQAYWLTGMLVH 555 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: 1093 Number of extensions: 40 Number of successful extensions: 2 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: 556 Length adjustment: 36 Effective length of query: 528 Effective length of database: 520 Effective search space: 274560 Effective search space used: 274560 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