GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapM in Pseudomonas fluorescens FW300-N2E3

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_12325 AO353_12325 ABC
           transporter permease
          Length = 319

 Score =  120 bits (301), Expect = 5e-32
 Identities = 75/213 (35%), Positives = 114/213 (53%), Gaps = 17/213 (7%)

Query: 170 PLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFM 229
           PL  GL  TL LS V   + L +G+   L R S  P +R L   +IE++RG PL+  +F+
Sbjct: 116 PLLWGLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPLLVQIFI 175

Query: 230 ASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYW 289
                  F+ T  N+ +    +  +S+FT AY+AE+IR G+Q+I +GQ E A SLGL   
Sbjct: 176 ----FYFFIGTVLNLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARSLGLSAG 231

Query: 290 QKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL----GIVKLNFSDANWAS 345
           Q  R +++PQA K V+P +   FI   KDTSLV++I + +LL     ++  +FS      
Sbjct: 232 QSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFS------ 285

Query: 346 AVTPITGLIFAGFIFWLFCFGMSRYSGFMERHL 378
              P   L     ++ L    +S+ +  +ER L
Sbjct: 286 ---PFEILFCVAGLYLLINLPLSKIASRLERRL 315


Lambda     K      H
   0.330    0.145    0.469 

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: 269
Number of extensions: 18
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: 384
Length of database: 319
Length adjustment: 29
Effective length of query: 355
Effective length of database: 290
Effective search space:   102950
Effective search space used:   102950
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: 49 (23.5 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, 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