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 permease (characterized, see rationale)
to candidate AO353_05700 AO353_05700 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05700
          Length = 562

 Score =  758 bits (1958), Expect = 0.0
 Identities = 378/552 (68%), Positives = 454/552 (82%), Gaps = 19/552 (3%)

Query: 2   TWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPV 61
           TW Q Y+PLGSL L+A+ A++PIVFFFLAL V +LKGH+AG++TL +++ VAI  ++MPV
Sbjct: 3   TWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALSILVAIFAFQMPV 62

Query: 62  SIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVG 121
            +A A+A YGF+YGLWPIAWII+ AVFLYK+TVK+GQFE+IRSSV+S+T+DQRLQ+LL+G
Sbjct: 63  DMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIG 122

Query: 122 FSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQ 181
           F FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVAGQ
Sbjct: 123 FCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQ 182

Query: 182 VSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTS 241
           V+ +D F IG +AGRQLP+LS+ VPFWL+ MMDG+RG+++TWPA LVAG+SFAVTQF TS
Sbjct: 183 VTGIDAFKIGAMAGRQLPLLSVFVPFWLVFMMDGLRGVKETWPAALVAGLSFAVTQFFTS 242

Query: 242 NFIGPELPDITSALVSLICLTLFLKVWQPKEIF-------------TFSGMKQRAVTPKS 288
           NFIGPELPDITSALVSL+ LTLFLKVWQPK  F             +  G  Q   T  S
Sbjct: 243 NFIGPELPDITSALVSLVSLTLFLKVWQPKRSFAEATASVGAATVRSAGGFGQPRTTQPS 302

Query: 289 TFSNGQIFKAWSPFIILTAIVTLWSIKDVQLALSFA------TISIEVPYLHNLVIKTAP 342
            +S G+IFKAWSPF+ILTA+VT+W++K  +   +          +  +P+L  LVIKTAP
Sbjct: 303 PYSFGEIFKAWSPFLILTALVTIWTLKPFKAMFAAGGSMYSWVFNFAIPHLDQLVIKTAP 362

Query: 343 IVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSI 402
           IVA  T   A++KL+ + A GTAI  +A+IS+++LK++    LT+ K+T  ELR+PILSI
Sbjct: 363 IVAAPTAIPAVFKLDPISATGTAIFFSALISMLILKINFKIGLTTLKETFFELRWPILSI 422

Query: 403 GLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQA 462
           G+VLAFAFV NYSG+SST+ALVLA TG AFPFFSPFLGWLGVFLTGSDTSSNALF +LQA
Sbjct: 423 GMVLAFAFVTNYSGMSSTMALVLAATGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSLQA 482

Query: 463 NTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFC 522
            TA+QIGV   LLVAANT+GGVTGKMISPQSIAVACAATGL GKESDLFRFTLKHSLFF 
Sbjct: 483 TTAHQIGVNDVLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLFFA 542

Query: 523 TFIGVLTVLQAY 534
           T +G++T+ QAY
Sbjct: 543 TIVGLITLAQAY 554


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: 1134
Number of extensions: 46
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: 562
Length adjustment: 36
Effective length of query: 509
Effective length of database: 526
Effective search space:   267734
Effective search space used:   267734
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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