GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF136 Psest_0136 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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