Alignments for a candidate for btsT in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for btsT in Pseudomonas fluorescens FW300-N2E3

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate AO353_13990 AO353_13990 carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13990
          Length = 688

 Score =  983 bits (2542), Expect = 0.0
 Identities = 483/708 (68%), Positives = 582/708 (82%), Gaps = 25/708 (3%)

Query: 2   DTKKIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQK 61
           +   + +H+PW++L ++GA  L VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA  
Sbjct: 3   NNNSLLRHLPWLVLAVVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANN 62

Query: 62  VMKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW 121
           VM+L+P RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW
Sbjct: 63  VMQLNPLRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW 122

Query: 122 LLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLA 181
           L+AGVVLAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLA
Sbjct: 123 LIAGVVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGQIPGTIALFGCFLIMIIILAVLA 182

Query: 182 LIVVKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVI 241
           LIVVKALAESPWG+FTV +T+PIA+FMG+YMR+IRPGR+GE+S++G++LL+ SI+ GG I
Sbjct: 183 LIVVKALAESPWGIFTVMATIPIAMFMGVYMRYIRPGRIGEISIVGVLLLLGSIWLGGQI 242

Query: 242 AHDPYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIV 301
           A DP W  A +F    IT+ LIGY FV+A+LPVWLILAPRDYL+TFLKIG IV LA+GI+
Sbjct: 243 AADPVWAKAFSFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGIL 302

Query: 302 VLNPELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETD 361
           +  P LKMPA+TQ+IDGTGP+WKG LFPFLFITIACGAVSGFHALI+SGTTPKLL NE++
Sbjct: 303 ITMPVLKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLDNESN 362

Query: 362 ARFIGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIM 421
           AR+IGYG MLMESFVAIMA+VAAS+IEPG+YFAMN+P A           +GGE      
Sbjct: 363 ARYIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAA----------IVGGE------ 406

Query: 422 AQLKDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL 481
                     A TVSSWGF I+PE +   AKDIGE +VL RAGGAPTLAVGIA + H VL
Sbjct: 407 ------VMQVAQTVSSWGFAITPEALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVL 460

Query: 482 PMAD-MGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGT 540
           P  + M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S  A +I T
Sbjct: 461 PGENTMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIAT 520

Query: 541 AGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVT 600
           AGCV +WGYLLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+LGTVVLIKMKR +YIWVT
Sbjct: 521 AGCVAMWGYLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLGTVVLIKMKRQRYIWVT 580

Query: 601 VVPAVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVV 659
           ++PA WLLICTT A  +KLF  NP + GF  +A +Y + +ANG  L  A+ I  M H++ 
Sbjct: 581 LLPAAWLLICTTTAGFIKLFDANPAI-GFLSLAKKYSDALANGQILAPAKDITQMQHVIY 639

Query: 660 NNYTNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707
           N YTNA L+ LFL VV+SI+FY  K  ++   S +RTDKE+P+  IPE
Sbjct: 640 NAYTNATLTALFLFVVFSILFYAIKVGISAWGSKERTDKESPFQAIPE 687


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: 1536
Number of extensions: 66
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: 688
Length adjustment: 39
Effective length of query: 677
Effective length of database: 649
Effective search space:   439373
Effective search space used:   439373
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)
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Protein sequences (fasta format)
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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, or view the source code.

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