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 Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate AO353_23340 AO353_23340 lactate permease

Query= TCDB::Q46839
         (560 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_23340
          Length = 587

 Score =  497 bits (1280), Expect = e-145
 Identities = 258/578 (44%), Positives = 357/578 (61%), Gaps = 28/578 (4%)

Query: 2   VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61
           + W Q+Y P G   +S L+A +P++    +LA   LK H+A  + L  ++LIAIFAF MP
Sbjct: 1   MVWQQVYDPFGNPLVSTLMAALPVVVMLTSLAFFHLKAHIAALLALSTALLIAIFAFGMP 60

Query: 62  IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121
            +MA +AA  G   GL PI WI++  ++L++LT  +G F +++ S+  ITDD+RLQ+LLI
Sbjct: 61  ANMAGSAALLGAATGLVPIGWIVLNIIYLHRLTTENGSFKVLQDSLARITDDRRLQLLLI 120

Query: 122 GFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAG 181
            F FGA  EGAAGFG PVA+TGA+L+GLGF PL A+GL LIANTAPVAFGALG PI+   
Sbjct: 121 AFCFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLA 180

Query: 182 QVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFT 241
           +VTG+D   +  M GRQLPF SVLVPFWL+    GW+ + E WPA LVAG SFAV QFF 
Sbjct: 181 KVTGLDEMQLSMMVGRQLPFFSVLVPFWLIWAFAGWRKMLEIWPAILVAGVSFAVPQFFV 240

Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISM-GQSAGAMVVNKPSSGGPVPS 300
           SNY GP L D+ +AL+S+  L  FLKVW+P    T+ ++ G+   + V   P       +
Sbjct: 241 SNYHGPMLVDVIAALISMACLTGFLKVWKPARVHTSAALSGRVDDSKVEESPDEKTAASA 300

Query: 301 EYSLG---QIIRAWSPFLILTVLVTIWTMKPFKALF----------------------AP 335
            ++      ++RAW P++ILTV V  W  + FK +F                      + 
Sbjct: 301 TFASDARPTVMRAWMPWIILTVFVFAWGTQGFKNMFDIRPAMDPQTHSAKLDPQGKPVSE 360

Query: 336 GGAFYSLVINFQIPHLHQQVLKAAPIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFIL 395
               ++  + F    LH QV K  P+V QP P +A++KF  L++ G+ I +AAI    ++
Sbjct: 361 ANPIFAPALTFTT--LHLQVEKVPPVVPQPKPEEAIYKFTWLTSTGSGILLAAIFGGLLM 418

Query: 396 GVGIKKGIGVFAETLISLKWPILSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSP 455
           G  I + +  +  TL  +++ + +I  +LA  F+T YSG+  T+ L  A TG+ +P F  
Sbjct: 419 GYSIPQLVSQYLRTLWVVRYSLTTIAAMLALGFITRYSGLDATMGLAFAATGIFYPMFGT 478

Query: 456 FLGWLGVFLTGSDTSSNALFGSLQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVA 515
            LGWLGV LTGSDT+SN LFG LQ  T++Q+ +S  L+ AAN+SGGV GKM+  QSI VA
Sbjct: 479 LLGWLGVALTGSDTASNVLFGGLQRVTSEQLGISPILMAAANSSGGVMGKMVDAQSIVVA 538

Query: 516 CAATGMVGRESELFRYTVKHSLIFASVIGIITLLQAYV 553
             AT   G E E+ RY   HS++ A ++G +  LQAYV
Sbjct: 539 STATRWYGHEGEILRYVFFHSIVLAILVGGLVTLQAYV 576


Lambda     K      H
   0.327    0.141    0.424 

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: 988
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: 560
Length of database: 587
Length adjustment: 36
Effective length of query: 524
Effective length of database: 551
Effective search space:   288724
Effective search space used:   288724
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