GapMind for catabolism of small carbon sources

 

Alignments for a candidate for phtA in Dechlorosoma suillum PS

Align The threonine uptake permease, PhtA (Sauer et al., 2005) (required for maximal growth in macrophages and Acanthamoeba castellanii) (characterized)
to candidate Dsui_3451 Dsui_3451 sugar phosphate permease

Query= TCDB::Q5ZY33
         (427 letters)



>FitnessBrowser__PS:Dsui_3451
          Length = 427

 Score =  175 bits (443), Expect = 3e-48
 Identities = 121/405 (29%), Positives = 183/405 (45%), Gaps = 15/405 (3%)

Query: 27  AFYFSDYLARVAPGVMHRYLQMDFGINEAGFGILTASFYVPYILMQIPVGLTVDRLSIRW 86
           A Y   +  R AP  +   L + F    A  G L A+++  Y +MQ+P G+ VD L  R 
Sbjct: 24  AAYMLSFFHRFAPAGIAHDLTLAFQTTAASLGALAATYFYVYTIMQVPTGVLVDTLGPRR 83

Query: 87  LLTIMSLVTAFGCCVFGLADGLLTASIGRMLIGFSAAFAFICSLRLATSWFPPTMLGLLS 146
           +L +  LV A G  +FGLAD L  A +GR L+G   +  FI  L++    F       L 
Sbjct: 84  ILFLGGLVAAAGSVLFGLADTLNEALVGRTLVGLGVSVTFIAMLKIIAVNFDERRFATLV 143

Query: 147 GLTQALGMLGAAAGEAPVSFLVSNVGWRHSMLIIAFLFIALSGLLYQFVQDKPGEHRNEI 206
           G +  +G LG+    AP+S L  ++ WR   +    L   L    + FV+D  GE     
Sbjct: 144 GASMLVGNLGSVLAGAPLSLLAQSISWRGIFVGAGALSALLGVACWFFVKDGGGERPRFD 203

Query: 207 RSVNRISILDSLKIILSNKQTWLNAMYAGFLFGPTAVIGEAIGPAYLQFGRGLGAHAAAF 266
           R+V    I   L  +L N+ TW   +    L G            YL     L    A+ 
Sbjct: 204 RTV----IFGGLASVLKNRSTWPAVVVNFGLAGSFFSFAGLWATPYLMRVHELTRAQASS 259

Query: 267 ATGLIFIGWGISGPLSGWISDKMGRRKPLMIISAVCGVILSSLFVFIPEMSQTTAYILFF 326
              L F G+ +     G +SD++G+RKP++I  A    +L   ++    +     Y LF 
Sbjct: 260 HLSLYFAGFALGCFFIGTLSDRLGKRKPVVIAGAFLYCLLWLFWLTNIRLPLAATYCLFG 319

Query: 327 VFGLTNTGVAISYAVSTEIHDRSVVGTSIAFTNMTSIFVGALFQPLVGRIIDMV------ 380
           + GLT    A+++A + E++   + G S + TNM     GAL QPL G  +D V      
Sbjct: 320 LMGLTTASFALTWACAKEVNPPMLSGMSTSVTNMGGFLAGALLQPLAGWAMDQVWDGTLA 379

Query: 381 SGPRAYNVETLLLSDFQAGLKLLPLCSLVALILAFTVKETYCKPI 425
           +G R Y  +T     F+ G+  +   + +  +  F VKET C+ I
Sbjct: 380 NGVRVYGPDT-----FRVGMACMAAAACIGFVACFWVKETGCRNI 419


Lambda     K      H
   0.329    0.143    0.438 

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: 502
Number of extensions: 23
Number of successful extensions: 4
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: 427
Length of database: 427
Length adjustment: 32
Effective length of query: 395
Effective length of database: 395
Effective search space:   156025
Effective search space used:   156025
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 (21.8 bits)
S2: 51 (24.3 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