Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate PfGW456L13_5114 L-lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5114 Length = 564 Score = 1056 bits (2730), Expect = 0.0 Identities = 539/564 (95%), Positives = 550/564 (97%) Query: 1 MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60 MQTWQQLY+PLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLAL+I VAIFAF M Sbjct: 1 MQTWQQLYTPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALSILVAIFAFQM 60 Query: 61 PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120 P DMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL Sbjct: 61 PVDMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120 Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA Sbjct: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180 Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFA+TQYF Sbjct: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAVTQYF 240 Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRS 300 TSNFIGPELPDITSALASLISLTLFLKVWQPKR AG I GA S++ V+ASVGGFGQ R+ Sbjct: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPKRAAGQHIVGAVSASVVSASVGGFGQKRT 300 Query: 301 TVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVI 360 TVASPYSLGEI KAWSPFLILTVLVTIWTLKPFKAMFAAGGSMY +VFNFAIPHLDQMVI Sbjct: 301 TVASPYSLGEIFKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYSFVFNFAIPHLDQMVI 360 Query: 361 KVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWP 420 KVAPIV+ PTA+PAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKET +ELRWP Sbjct: 361 KVAPIVVAPTALPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETFYELRWP 420 Query: 421 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS 480 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS Sbjct: 421 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS 480 Query: 481 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS 540 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS Sbjct: 481 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS 540 Query: 541 LFFATIVGLITLAQAYWFTGMLVH 564 LFFATIVGLITLAQAYWFTGMLVH Sbjct: 541 LFFATIVGLITLAQAYWFTGMLVH 564 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: 1123 Number of extensions: 37 Number of successful extensions: 1 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: 564 Length adjustment: 36 Effective length of query: 528 Effective length of database: 528 Effective search space: 278784 Effective search space used: 278784 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 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