GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Pseudomonas stutzeri RCH2

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 GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__psRCH2:GFF136
          Length = 229

 Score = 82.8 bits (203), Expect = 9e-21
 Identities = 64/213 (30%), Positives = 105/213 (49%), Gaps = 15/213 (7%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233
           G  +TL L  V +   L V + L + R SR   +R L   +I   RG PL+  LF+    
Sbjct: 16  GAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLFLVYYG 75

Query: 234 LPLFLPTGWNV------DKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLG 287
           +  F     +       D    A+I +++ T+AY+AE+IRG +Q +P G+ E A +LG+ 
Sbjct: 76  MAQFDVVRQSALWPYLRDPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEAARALGMS 135

Query: 288 YWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAV 347
             Q    II+P+A ++ +P+  N  I   K ++L + I + +L G+       A   +A 
Sbjct: 136 RSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGM-------ARKIAAR 188

Query: 348 TPITGLIF--AGFIFWLFCFGMSRYSGFMERHL 378
           T +   +F  AG I+ L  F + +    +ER L
Sbjct: 189 TYLHEEMFLTAGLIYLLIAFILMQGFKLLERWL 221


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: 257
Number of extensions: 16
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: 229
Length adjustment: 26
Effective length of query: 358
Effective length of database: 203
Effective search space:    72674
Effective search space used:    72674
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: 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