Alignments for a candidate for lctP in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Pseudomonas fluorescens FW300-N2E3

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate AO353_05700 AO353_05700 L-lactate permease

Query= reanno::pseudo5_N2C3_1:AO356_07550
         (564 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05700
          Length = 562

 Score = 1017 bits (2630), Expect = 0.0
 Identities = 521/564 (92%), Positives = 534/564 (94%), Gaps = 2/564 (0%)

Query: 1   MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60
           MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLAL+I VAIFAF M
Sbjct: 1   MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALSILVAIFAFQM 60

Query: 61  PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120
           P DMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL
Sbjct: 61  PVDMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120

Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180
           IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA
Sbjct: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180

Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240
           GQVTGIDAFKIGAM GRQLPLLS+FVPFWLVFMMDGLRGV+ETWPAALVAGLSFA+TQ+F
Sbjct: 181 GQVTGIDAFKIGAMAGRQLPLLSVFVPFWLVFMMDGLRGVKETWPAALVAGLSFAVTQFF 240

Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRS 300
           TSNFIGPELPDITSAL SL+SLTLFLKVWQPKR+  A+   +  +ATV  S GGFGQPR+
Sbjct: 241 TSNFIGPELPDITSALVSLVSLTLFLKVWQPKRSF-AEATASVGAATV-RSAGGFGQPRT 298

Query: 301 TVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVI 360
           T  SPYS GEI KAWSPFLILT LVTIWTLKPFKAMFAAGGSMY WVFNFAIPHLDQ+VI
Sbjct: 299 TQPSPYSFGEIFKAWSPFLILTALVTIWTLKPFKAMFAAGGSMYSWVFNFAIPHLDQLVI 358

Query: 361 KVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWP 420
           K APIV  PTAIPAVFKLDPISATGTAIFFSALISML+LKIN K GLTT KET FELRWP
Sbjct: 359 KTAPIVAAPTAIPAVFKLDPISATGTAIFFSALISMLILKINFKIGLTTLKETFFELRWP 418

Query: 421 ILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFS 480
           ILSIGMVLAFAFVTNYSGMSSTMALVLA TGAAFPFFSPFLGWLGVFLTGSDTSSNALFS
Sbjct: 419 ILSIGMVLAFAFVTNYSGMSSTMALVLAATGAAFPFFSPFLGWLGVFLTGSDTSSNALFS 478

Query: 481 SLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS 540
           SLQATTAHQIGVND LLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS
Sbjct: 479 SLQATTAHQIGVNDVLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHS 538

Query: 541 LFFATIVGLITLAQAYWFTGMLVH 564
           LFFATIVGLITLAQAYWFTGMLVH
Sbjct: 539 LFFATIVGLITLAQAYWFTGMLVH 562


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: 1150
Number of extensions: 42
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: 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources