GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltJ in Desulfovibrio vulgaris Miyazaki F

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 8502447 DvMF_3153 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q9I403
         (248 letters)



>lcl|FitnessBrowser__Miya:8502447 DvMF_3153 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 233

 Score =  174 bits (440), Expect = 2e-48
 Identities = 93/225 (41%), Positives = 139/225 (61%), Gaps = 12/225 (5%)

Query: 1   MNYNWDWGVFFKSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRL 60
           M YN+DW +        S  YL W I G+  T  I+ +  ++A+ALG+L+ VMR    R 
Sbjct: 1   MQYNFDWKLVL------SGEYLQWIIDGVVVTCQISALSLVLAMALGTLIAVMRLSAVRP 54

Query: 61  VSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTW-FKQDLNPTTSAYLSVVVCLG 119
           +   +  + E FRN PLLVQ+F WYF    +LP  +  W +KQ+       + + V+ L 
Sbjct: 55  LVWFSAGFTEFFRNTPLLVQIFFWYFGSDAVLPTAVNQWLYKQNFE-----FAAGVISLA 109

Query: 120 LFTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNI 179
           ++TAA + E++R+GI ++P  Q  A+RA G    Q  R+V+LPQAFRII+PPL S+ LN+
Sbjct: 110 VYTAAFIAEEIRSGIFSIPRTQLEASRACGLTFLQAMRYVVLPQAFRIIVPPLISQALNL 169

Query: 180 FKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNM 224
           FKNSS+   IG+MEL    +Q   ++ + FEAFT++TLIY T+++
Sbjct: 170 FKNSSLCMTIGVMELTYMARQIESYTFHGFEAFTVSTLIYLTISL 214


Lambda     K      H
   0.327    0.141    0.433 

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: 194
Number of extensions: 11
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: 248
Length of database: 233
Length adjustment: 23
Effective length of query: 225
Effective length of database: 210
Effective search space:    47250
Effective search space used:    47250
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 (21.7 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