GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_12325
          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 (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