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

GapMind for catabolism of small carbon sources

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

Align L-lactate permease (characterized, see rationale)
to candidate Pf6N2E2_329 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_329
          Length = 587

 Score =  467 bits (1201), Expect = e-136
 Identities = 240/580 (41%), Positives = 348/580 (60%), Gaps = 41/580 (7%)

Query: 1   MTWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMP 60
           M W Q Y P G+  L+ ++A +P+V    +L    +K H+A  + L  AL +AI  + MP
Sbjct: 1   MVWQQVYDPFGNAVLSTLLAAVPVVVMLASLAFFHVKAHLAALMALASALLIAIFAFGMP 60

Query: 61  VSIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLV 120
             +A ++A+YG + GL PI WI++  +FL+++T + G F++++ S+  +T+D+RLQ+LL+
Sbjct: 61  AGMAGSAALYGAANGLLPIGWIVLNIIFLHRLTTENGSFKVLQDSLARITDDRRLQLLLI 120

Query: 121 GFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAG 180
            F FGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGA+G PII   
Sbjct: 121 AFCFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLA 180

Query: 181 QVSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLT 240
           +V+ LD   +  + GRQLP  S++VPFWLI    G R + + WPA LVAGVSFA+ QFL 
Sbjct: 181 KVTGLDEMELSMMVGRQLPFFSVLVPFWLIWAFAGWRKMLEVWPAILVAGVSFAIPQFLV 240

Query: 241 SNFIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPK------------- 287
           SN+ GP L D+ +AL+S+ CLT FLKVW+P  + T + +  R    K             
Sbjct: 241 SNYHGPMLVDVIAALISMACLTGFLKVWKPATVHTSAALSGRVDNSKIDASEDEKPVASA 300

Query: 288 --STFSNGQIFKAWSPFIILTAIVTLW------SIKDVQLALSFATIS------------ 327
             S+ +   + +AW P+IILT  V  W      ++ D + A+   T S            
Sbjct: 301 AFSSDTRSAVGRAWMPWIILTVFVFAWGTQGFKNLFDTRPAIDPQTQSARLDPQGKPMRE 360

Query: 328 --------IEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKM 379
                   +    +H  + K  P+V +     A+YK N   A G+ I +AA++  +++  
Sbjct: 361 ANPIFSPLVTFGTIHQQIEKVPPVVPQPKTEEAVYKFNWFTATGSGIFLAAILGGLLMGY 420

Query: 380 SISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFL 439
           SI   L  +  TL  +R+ +++I  +LA  F+  YSGL +T+ L  A TG+ +P F   L
Sbjct: 421 SIPQLLHHYLRTLWVVRYSLITIVAMLALGFLTRYSGLDATMGLAFAATGIFYPMFGTLL 480

Query: 440 GWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACA 499
           GWLGV LTGSDT+SN LFG LQ  T+ Q+G++P L+ AAN++GGV GKM+  QSI VA  
Sbjct: 481 GWLGVALTGSDTASNVLFGGLQRVTSEQLGISPVLMAAANSSGGVMGKMVDAQSIVVAST 540

Query: 500 ATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAYIVPWT 539
           AT   G E ++ R+   HS+     +G L  LQAY+ P+T
Sbjct: 541 ATRWYGHEGEILRYVFFHSVVLAILVGGLVTLQAYVAPFT 580


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: 949
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: 587
Length adjustment: 36
Effective length of query: 509
Effective length of database: 551
Effective search space:   280459
Effective search space used:   280459
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.

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 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