Aligments for a candidate for lctP in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for lctP in Pseudomonas fluorescens FW300-N2E2

Align L-lactate permease (characterized, see rationale)
to candidate Pf6N2E2_3380 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3380
          Length = 565

 Score =  752 bits (1942), Expect = 0.0
 Identities = 375/554 (67%), Positives = 450/554 (81%), Gaps = 21/554 (3%)

Query: 2   TWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPV 61
           TW Q Y+PLGSL L+A+ A++PIVFFFLAL V +LKGH+AG++TL +A+AVAI  + MP 
Sbjct: 4   TWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPA 63

Query: 62  SIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVG 121
            +A A+A YGF+YGLWPIAWII+ AVFLYK+TVK+GQFE+IRSSV+S+T+DQRLQ+LL+G
Sbjct: 64  DMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIG 123

Query: 122 FSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQ 181
           F FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVAGQ
Sbjct: 124 FCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQ 183

Query: 182 VSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTS 241
           V+ +D F IG + GRQLP+LS+ VPFWL+ MMDG+RG+R+TWPA LVAG+SFA+TQ+ TS
Sbjct: 184 VTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTS 243

Query: 242 NFIGPELPDITSALVSLICLTLFLKVWQPKE---------------IFTFSGMKQRAVTP 286
           NFIGPELPDITSAL SLI LTLFLKVWQPK                  +  G  Q   T 
Sbjct: 244 NFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASAGGFGQPRSTV 303

Query: 287 KSTFSNGQIFKAWSPFIILTAIVTLWSIKDVQLALSFA------TISIEVPYLHNLVIKT 340
            S +S G+I KAWSPF+ILT +VT+W++K  +   +          +  +P+L  +VIK 
Sbjct: 304 ASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVIKV 363

Query: 341 APIVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPIL 400
           APIV   T   A++KL+ + A GTAI  +A+IS++VLK++I   LT+FK+TL ELR+PIL
Sbjct: 364 APIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWPIL 423

Query: 401 SIGLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGAL 460
           SIG+VLAFAFV NYSG+SST+ALVLAGTG AFPFFSPFLGWLGVFLTGSDTSSNALF +L
Sbjct: 424 SIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSL 483

Query: 461 QANTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLF 520
           QA TA+Q+GV   LLVAANT+GGVTGKMISPQSIAVACAATGL GKESDLFRFTLKHSLF
Sbjct: 484 QATTAHQLGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLF 543

Query: 521 FCTFIGVLTVLQAY 534
           F T +G++T+ QAY
Sbjct: 544 FATIVGLITLAQAY 557


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: 1116
Number of extensions: 40
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: 565
Length adjustment: 36
Effective length of query: 509
Effective length of database: 529
Effective search space:   269261
Effective search space used:   269261
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code.

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