GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisQ in Pseudomonas stutzeri RCH2

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo5_N2C3_1:AO356_05500
         (242 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 =  111 bits (278), Expect = 1e-29
 Identities = 69/213 (32%), Positives = 105/213 (49%), Gaps = 6/213 (2%)

Query: 21  PLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGVPDLVLML 80
           P  + G W+T++L  +S++  +++ +    A+ SR   +R     Y    RG P LV + 
Sbjct: 11  PSFIDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLF 70

Query: 81  LIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAVPRGQVEA 140
           L++Y +  +       + W Y+  DP+   +IT+     AY  E  RGAI  VP G++EA
Sbjct: 71  LVYYGMAQFDVVRQSAL-WPYLR-DPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEA 128

Query: 141 ATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKS 200
           A A G+ R Q    ++ P+  R  LP   N  ++MLKA+AL S I L +L   A+     
Sbjct: 129 ARALGMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMARKIAAR 188

Query: 201 TYQLFYFLVLAALIYLLIT----SASNFILRWL 229
           TY      + A LIYLLI          + RWL
Sbjct: 189 TYLHEEMFLTAGLIYLLIAFILMQGFKLLERWL 221


Lambda     K      H
   0.329    0.142    0.423 

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: 166
Number of extensions: 7
Number of successful extensions: 2
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: 242
Length of database: 229
Length adjustment: 23
Effective length of query: 219
Effective length of database: 206
Effective search space:    45114
Effective search space used:    45114
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: 46 (22.3 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 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