Alignments for a candidate for lctP in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Pseudomonas simiae WCS417

Align L-lactate permease (characterized, see rationale)
to candidate GFF4712 PS417_24105 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__WCS417:GFF4712
          Length = 564

 Score =  751 bits (1939), Expect = 0.0
 Identities = 379/554 (68%), Positives = 452/554 (81%), Gaps = 21/554 (3%)

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

Query: 62  SIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVG 121
            +ALA+A YGF+YGLWPIAWII+ AVFLYK+TVK+GQFEIIRSSV+S+T+DQRLQ+LL+G
Sbjct: 63  DMALAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEIIRSSVLSITDDQRLQVLLIG 122

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

Query: 182 VSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTS 241
           V+ +D F IG + GRQLP+LS+ VPFWL+ MMDG+RG+R+TWPA LVAG+SFA+TQ+ TS
Sbjct: 183 VTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGVRGVRETWPAALVAGLSFAITQYFTS 242

Query: 242 NFIGPELPDITSALVSLICLTLFLKVWQPKEIF---TFSGMKQRAVT--------PKST- 289
           NFIGPELPDITSAL SLI LTLFLKVWQPK              AVT        P++T 
Sbjct: 243 NFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSAAVTASAGGFGLPRNTI 302

Query: 290 ---FSNGQIFKAWSPFIILTAIVTLWSIKDVQLALSFA------TISIEVPYLHNLVIKT 340
              +S GQIFKAWSPF+ILT +VT+W++K  +   +          +  +P+L  LVIK 
Sbjct: 303 VSPYSLGQIFKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYSWVFNFAIPHLDQLVIKV 362

Query: 341 APIVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPIL 400
           APIV   T   A++KL+ + A GTAI  +A+IS++VLK+ I   LT+ K+T  ELR+PIL
Sbjct: 363 APIVTNPTAIPAVFKLDPISATGTAIFFSALISMLVLKIDIKTGLTTLKETFYELRWPIL 422

Query: 401 SIGLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGAL 460
           SIG+VLAFAFV NYSG+SST+ALVLAGTG AFPFFSPFLGWLGVFLTGSDTSSNALF +L
Sbjct: 423 SIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSL 482

Query: 461 QANTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLF 520
           QA TA+QIGV   LLVAANT+GGVTGKMISPQSIAVACAATGL GKESDLFRFTLKHSLF
Sbjct: 483 QATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLF 542

Query: 521 FCTFIGVLTVLQAY 534
           F T +G++T+ QAY
Sbjct: 543 FATIVGLITLAQAY 556


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: 1113
Number of extensions: 41
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: 564
Length adjustment: 36
Effective length of query: 509
Effective length of database: 528
Effective search space:   268752
Effective search space used:   268752
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
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