Alignments for a candidate for btsT in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for btsT in Pseudomonas fluorescens FW300-N1B4

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate Pf1N1B4_4835 Carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4835
          Length = 685

 Score =  978 bits (2527), Expect = 0.0
 Identities = 481/705 (68%), Positives = 580/705 (82%), Gaps = 25/705 (3%)

Query: 5   KIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMK 64
           ++ KH+ W  + ++GAF L+VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA KVM+
Sbjct: 3   RLAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIATKVMQ 62

Query: 65  LDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLA 124
           LDP RATPAV+NNDGL+YVPTN++VLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL+A
Sbjct: 63  LDPNRATPAVLNNDGLDYVPTNKHVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIA 122

Query: 125 GVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIV 184
           GVVLAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLALIV
Sbjct: 123 GVVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIV 182

Query: 185 VKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHD 244
           VKALAESPWG+FTV +T+PIA+FMGIYMR+IRPGR+GE+SVIG+ LL+ SI+ GG IA D
Sbjct: 183 VKALAESPWGMFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVALLLGSIWLGGQIAAD 242

Query: 245 PYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLN 304
           P W  A TF    IT+ LIGY FV+A+LPVWLILAPRDYL+TFLKIG IV LA+GI++  
Sbjct: 243 PVWAKAFTFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILITM 302

Query: 305 PELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARF 364
           P+LKMPA+TQ+IDGTGP+WKG LFPFLFITIACGAVSGFH+LI+SGTTPKLLA+E  AR+
Sbjct: 303 PDLKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHSLIASGTTPKLLASEGHARY 362

Query: 365 IGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQL 424
           IGYG MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +G                     
Sbjct: 363 IGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAALVGAD------------------- 403

Query: 425 KDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLPMA 484
                  A TVSSWGF I+PE +   AKDIGE ++L RAGGAPTLAVGIA + H++LP  
Sbjct: 404 ---AVSVAQTVSSWGFAITPEALQAVAKDIGEATILARAGGAPTLAVGIAQILHQLLPGE 460

Query: 485 D-MGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGC 543
           + M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S  A +I TAGC
Sbjct: 461 NTMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGC 520

Query: 544 VGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVP 603
           V +WGYLLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+L TVVLIKMKR +Y+WVT++P
Sbjct: 521 VAMWGYLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLATVVLIKMKRQRYVWVTMLP 580

Query: 604 AVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNY 662
           AVWLLICTT A  +KLF  NP + GF  +A +Y + +ANG  L  A+ I  M H++ N Y
Sbjct: 581 AVWLLICTTTAGFIKLFDANPAI-GFLALAKKYSDALANGQVLAPAKSIEQMQHVIYNAY 639

Query: 663 TNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707
           TNA L+ LFL+VV+SI+F+  K  +A   + +RTDKE P+  +P+
Sbjct: 640 TNATLTALFLLVVFSILFFALKVGIAAWGTKERTDKEAPFQALPD 684


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: 1506
Number of extensions: 71
Number of successful extensions: 7
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: 685
Length adjustment: 39
Effective length of query: 677
Effective length of database: 646
Effective search space:   437342
Effective search space used:   437342
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