GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Marinobacter adhaerens HP15

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 GFF2975 HP15_2919 amino acid ABC transporter, permease protein

Query= TCDB::Q9I403
         (248 letters)



>FitnessBrowser__Marino:GFF2975
          Length = 223

 Score =  118 bits (296), Expect = 9e-32
 Identities = 75/243 (30%), Positives = 129/243 (53%), Gaps = 24/243 (9%)

Query: 3   YNWDWGVFFKSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVS 62
           + +DW     S        + + I G+ +T+ I+  G +I  ALG   G++       + 
Sbjct: 5   FQFDWQAAIDS--------IPFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLR 56

Query: 63  GIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFT 122
             ATAY+EIFR  P+LVQ+   ++ +PDL+           ++P T+     +  + L +
Sbjct: 57  WPATAYIEIFRGTPILVQVLFIFYGLPDLIGG--------PIDPLTAG----IAAIALNS 104

Query: 123 AARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKN 182
            A + E VR G+Q++  GQT A  ++G    Q +  V+ PQAFR +IPPL ++ +   K+
Sbjct: 105 GAYISEVVRGGVQSIDKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKD 164

Query: 183 SSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLIMRLVERKVAVPGL 242
           +S+ S+IG+ EL+ Q +     +   FE + +  ++Y  + +SL +I+R VER+    GL
Sbjct: 165 TSLFSVIGVGELVRQGQIYIANTFTAFEVYFVVAILYLAITLSLSIILRFVERR----GL 220

Query: 243 ISV 245
            SV
Sbjct: 221 ASV 223


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: 175
Number of extensions: 10
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: 223
Length adjustment: 23
Effective length of query: 225
Effective length of database: 200
Effective search space:    45000
Effective search space used:    45000
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