GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Pseudomonas stutzeri RCH2

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__psRCH2:GFF136
          Length = 229

 Score =  108 bits (269), Expect = 2e-28
 Identities = 75/210 (35%), Positives = 113/210 (53%), Gaps = 9/210 (4%)

Query: 176 NGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQV 235
           +G  LTL +  +S++    + V L + R+S    VR     YI   RG PL+  LFL   
Sbjct: 15  DGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLFLVYY 74

Query: 236 MLPLF-FAADVRLDRVLR-----AIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGL 289
            +  F       L   LR     AI  + L +AAY+AE +RG +Q V  G++EAA+ALG+
Sbjct: 75  GMAQFDVVRQSALWPYLRDPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEAARALGM 134

Query: 290 NTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGR 349
           +    +L I+LP+A R  +PA   + I + K ++L S + L+ELTG+AR I A+      
Sbjct: 135 SRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMARKIAARTYL--- 191

Query: 350 YAEVYLFIGLIYWLFCYSMSLASRRLERQL 379
           + E++L  GLIY L  + +    + LER L
Sbjct: 192 HEEMFLTAGLIYLLIAFILMQGFKLLERWL 221


Lambda     K      H
   0.332    0.145    0.452 

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: 246
Number of extensions: 12
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: 381
Length of database: 229
Length adjustment: 26
Effective length of query: 355
Effective length of database: 203
Effective search space:    72065
Effective search space used:    72065
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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