GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Phaeobacter inhibens BS107

Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC

Query= TCDB::Q9I404
         (222 letters)



>FitnessBrowser__Phaeo:GFF196
          Length = 432

 Score =  113 bits (283), Expect = 5e-30
 Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 12/210 (5%)

Query: 17  GMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLVITWFYFA 76
           G ++ + L V  V   V LG  LAL R S+  L+  I   ++ + R +PL+ ++    F 
Sbjct: 224 GFMLNMMLGVTCVSLSVPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLL----FV 279

Query: 77  VPFILRWITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQMGAAQALGMTYG 136
              +L +    D  V  F   ++   +F AAY  E++R G+ A+PKGQ  AA +LG+ Y 
Sbjct: 280 ASVMLSYFFPPDATVDLFLRVVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYP 339

Query: 137 QTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNSARSRGDIIGQAN---- 192
           Q MRL+ILPQA +   P ++  ++ LF+DT+LV  + + D +     RG I+        
Sbjct: 340 QAMRLIILPQALKISIPGIVNVAVGLFKDTTLVSVISMFDLVGMI--RGPILASTEWNGV 397

Query: 193 --EFLIFAGLVYFVVSFTASFAVKRLQKRL 220
             E L FA  ++F+V +  S   + L++RL
Sbjct: 398 YWELLGFAAFLFFIVCYGISQYSQWLERRL 427


Lambda     K      H
   0.331    0.143    0.426 

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: 247
Number of extensions: 9
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: 222
Length of database: 432
Length adjustment: 27
Effective length of query: 195
Effective length of database: 405
Effective search space:    78975
Effective search space used:    78975
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 (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