GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Acidovorax sp. GW101-3H11

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 Ac3H11_1956 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= TCDB::Q9I403
         (248 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1956
          Length = 252

 Score =  211 bits (536), Expect = 1e-59
 Identities = 110/255 (43%), Positives = 159/255 (62%), Gaps = 22/255 (8%)

Query: 4   NWDWGVFFKST----------GIGSE-TYLDWYIAGLGWTIAIALVGWIIALALGSLLGV 52
           +WDW VF + T          G G + TYLDW ++  GWT++++L+  ++AL LGSL+G 
Sbjct: 2   SWDWQVFCQDTMDREVVQSCFGKGGDITYLDWMLSAWGWTVSVSLLALVLALVLGSLIGT 61

Query: 53  MRTVPNR-LVSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAY 111
           +RT+ +R ++  +  A+VE+FRN+PLLVQ+F+WY ++P L P          +      +
Sbjct: 62  LRTLQDRPMIVRLGNAWVELFRNIPLLVQIFLWYHVIPSLFP----------VMKGVPGF 111

Query: 112 LSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPP 171
             VV+ LG FT+AR+ EQVR+GIQALP GQ  A  A+GF   Q YR+VLLP AFRIIIPP
Sbjct: 112 ALVVLALGFFTSARIAEQVRSGIQALPRGQRYAGMAVGFTTFQTYRYVLLPMAFRIIIPP 171

Query: 172 LTSEFLNIFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLIMR 231
           LTSE +NIFKNSSVA  + + EL     Q  E ++   E +   T +Y     ++  IM 
Sbjct: 172 LTSETMNIFKNSSVAFAVSVAELTMFAMQAQEETSRGIEVYLAVTSLYIISAFAINRIMA 231

Query: 232 LVERKVAVPGLISVG 246
            +E++V +PG++  G
Sbjct: 232 FIEKRVRIPGMVVAG 246


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: 237
Number of extensions: 13
Number of successful extensions: 4
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: 252
Length adjustment: 24
Effective length of query: 224
Effective length of database: 228
Effective search space:    51072
Effective search space used:    51072
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 (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