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

GapMind for catabolism of small carbon sources

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

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate Pf6N2E2_1294 Carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1294
          Length = 686

 Score =  976 bits (2524), Expect = 0.0
 Identities = 487/707 (68%), Positives = 578/707 (81%), Gaps = 25/707 (3%)

Query: 3   TKKIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKV 62
           T ++ KH+ W  + ++G   L+VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA  V
Sbjct: 2   TTRLVKHLAWFAVAVLGGCALSVVALRRGEPINALWIVVAAVAIYLVAYRYYSLFIANNV 61

Query: 63  MKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL 122
           M+LD  RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL
Sbjct: 62  MQLDARRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL 121

Query: 123 LAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLAL 182
           +AGVVLAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLAL
Sbjct: 122 IAGVVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLAL 181

Query: 183 IVVKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIA 242
           IVVKALAESPWG+FTV +T+PIA+FMGIYMR+IRPGR+GE+SVIG++LL+ SI+ GG IA
Sbjct: 182 IVVKALAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVLLLLGSIWLGGQIA 241

Query: 243 HDPYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVV 302
            DP W  A TF    IT+ LIGY FV+A+LPVWLILAPRDYL+TFLKIG IV LA+GI+V
Sbjct: 242 ADPVWAKAFTFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILV 301

Query: 303 LNPELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDA 362
             PELKMPA+TQ+ DGTGP+WKG LFPFLFITIACGAVSGFHALISSGTTPKLL NET+A
Sbjct: 302 TMPELKMPALTQFTDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNA 361

Query: 363 RFIGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMA 422
           R+IGYG MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +G                   
Sbjct: 362 RYIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVG------------------- 402

Query: 423 QLKDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLP 482
              DV A  A TVSSWGF I+PE +   AKDIGE +VL RAGGAPTLAVGIA + H VLP
Sbjct: 403 --GDVVA-VAQTVSSWGFAITPEALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLP 459

Query: 483 MAD-MGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTA 541
             + M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S  A +I TA
Sbjct: 460 GENTMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATA 519

Query: 542 GCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTV 601
           GCV LWGYLLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+L TVVLIKMKR +Y+WVT+
Sbjct: 520 GCVALWGYLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLATVVLIKMKRQRYVWVTL 579

Query: 602 VPAVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVN 660
           +PA WLLICTT A  +KLF  NP + GF  +A +Y + +A G  L  A+ I  M H+V N
Sbjct: 580 LPASWLLICTTTAGLIKLFDANPAI-GFLALARKYNDALAAGQVLAPAKSIEQMQHVVFN 638

Query: 661 NYTNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707
            YTNA L++LFL VV+SI+FY  K  +A   + +RTDKE P+  +P+
Sbjct: 639 AYTNATLTVLFLFVVFSILFYALKVGIAAWGTKERTDKEAPFQAVPD 685


Lambda     K      H
   0.327    0.142    0.440 

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: 1518
Number of extensions: 67
Number of successful extensions: 6
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: 716
Length of database: 686
Length adjustment: 39
Effective length of query: 677
Effective length of database: 647
Effective search space:   438019
Effective search space used:   438019
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: 54 (25.4 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