GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00870 in Pseudomonas simiae WCS417

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF521 PS417_02655 amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__WCS417:GFF521
          Length = 378

 Score =  205 bits (521), Expect = 2e-57
 Identities = 129/362 (35%), Positives = 195/362 (53%), Gaps = 7/362 (1%)

Query: 12  AIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKF 71
           A+AAA GV++  +  VKIG   P++GA A +G+    GA+ A + +N  G  I G+KI  
Sbjct: 14  AVAAALGVSTFVQADVKIGVAGPMTGANAAFGEQYMKGAQAAADVINKAG-GINGEKIV- 71

Query: 72  ELVAEDDAADPKQGTAAAQKLCDA-KVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130
            LVA DDA +PKQ  A A +L D  KV GVVGH  S  TIPAS+VY++ GI  +T  +TN
Sbjct: 72  -LVAGDDACEPKQAVAVANRLADQDKVIGVVGHFCSSNTIPASEVYDEAGIIAITPGSTN 130

Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190
           P +T+ G    FR+   D+  G     Y VD LK K VA+I+D+  YG+G+AD      T
Sbjct: 131 PQVTERGLGAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVINDKDTYGKGLADATAAQLT 190

Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250
            +G+K V E+  T    DF A++T I++   D +++GG+ P+ GP++RQ+ + G+ +VK+
Sbjct: 191 KRGVKPVLEEGLTRGEKDFSALVTKIRSTGADVVYFGGLHPEAGPLVRQIREAGLKDVKF 250

Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310
              DG+ T E+   A GA+ +  V    G      +P   A   ++  K   + + Y+ Y
Sbjct: 251 MSDDGVVTDELVATAGGAQYVDGVYMTFGADP-RLLPDSKAVVEEF-RKNGTEPEGYTLY 308

Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVY-KD 369
            Y +   +      A S   +     L     K V    A++  G++K     +Y + KD
Sbjct: 309 AYASVQALAAGFNGAKSNKGEDAAKWLKAHPVKTVMGEKAWDSKGDLKISDYVVYQWDKD 368

Query: 370 GK 371
           GK
Sbjct: 369 GK 370


Lambda     K      H
   0.315    0.131    0.375 

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: 387
Number of extensions: 19
Number of successful extensions: 3
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: 375
Length of database: 378
Length adjustment: 30
Effective length of query: 345
Effective length of database: 348
Effective search space:   120060
Effective search space used:   120060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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