GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF84
          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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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:

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:

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:

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:

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