Aligments for a candidate for Dshi_1194 in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for Dshi_1194 in Pseudomonas stutzeri RCH2

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate GFF84 Psest_0084 TRAP transporter, 4TM/12TM fusion protein

Query= uniprot:E4PQE4
         (729 letters)



>lcl|FitnessBrowser__psRCH2:GFF84 Psest_0084 TRAP transporter,
           4TM/12TM fusion protein
          Length = 674

 Score =  362 bits (928), Expect = e-104
 Identities = 218/562 (38%), Positives = 312/562 (55%), Gaps = 55/562 (9%)

Query: 219 LIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQV-YTDAGILGPT 277
           L+ E  RRV G+AL II  +FLAY   G YLPG L + G  + +  +Q+ +   G+ G  
Sbjct: 114 LVFEAARRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTP 173

Query: 278 TAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTS 337
           T VS+TYI LFI+F +FL+ + +   F +FA    G   GGPAKVS+ +S LMG I G+ 
Sbjct: 174 TYVSATYIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSG 233

Query: 338 AGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTE 397
             NVV+TG  TIPLMK+ GY    AG VEA +S G QIMPP+MGA AFIMAE   +P+ E
Sbjct: 234 VANVVTTGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVE 293

Query: 398 IAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQ-CYLFVPIIILIVA 456
           IA AA+IPA+LYF SV++MV  EA + G++G+ +DE P     +K+  YL +P+++L+  
Sbjct: 294 IAKAALIPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWL 353

Query: 457 LFMGYSVIRAGTLATVSAAVV------------------SWLSPN-------KMGLRHI- 490
           LF G + + AGT+     A+V                   W++         ++G+  I 
Sbjct: 354 LFSGRTPMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIF 413

Query: 491 -----------------------LQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARF 527
                                  L AL   +  A+ + + CA  GVI+GV+SLTGV + F
Sbjct: 414 GVIAALVAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTF 473

Query: 528 SVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFF 587
           +  +L V   +  L+L+  M   ++LGMG+PT   Y + +S+ AP L+ LG+  + +H F
Sbjct: 474 AGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMF 533

Query: 588 VFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEA 647
           VFYF +++ +TPPVALA +AAA I+    ++ S+ + RI IA FIVPFM  YN AL+M+ 
Sbjct: 534 VFYFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQG 593

Query: 648 G-WFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGI 706
           G W      L  A F V +      G+     A W  ++L  AAA  M+     +D  G 
Sbjct: 594 GDWGATLYMLFKAAFAVGLWGAVFTGYLQRPMALW-EKVLAFAAAASMVLAMPISDEIGF 652

Query: 707 ALAVLAFV--IQKQRKTRLATA 726
           AL  L  +  I + R+   ATA
Sbjct: 653 ALGALFLIQHIWRARRAEPATA 674


Lambda     K      H
   0.327    0.139    0.410 

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: 1249
Number of extensions: 67
Number of successful extensions: 5
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: 729
Length of database: 674
Length adjustment: 39
Effective length of query: 690
Effective length of database: 635
Effective search space:   438150
Effective search space used:   438150
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, 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