GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas litoralis 2SM5

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein

Query= curated2:Q4A0N2
         (394 letters)



>NCBI__GCF_900105005.1:WP_090273343.1
          Length = 404

 Score =  269 bits (687), Expect = 1e-76
 Identities = 143/383 (37%), Positives = 231/383 (60%), Gaps = 9/383 (2%)

Query: 9   DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68
           D+    NY+P+++   +G G+++WD +   YID   G +V + GH HP++++AL EQ+Q+
Sbjct: 13  DRLMVPNYAPVEMIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQK 72

Query: 69  ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128
           +  VS  + ++   +  +K+      + VL +N+G EA E A K+AR+W  D    D+  
Sbjct: 73  LWHVSNIMTNEPALRLADKLVAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKH- 131

Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAII 188
            EIIA + +FHGRTL ++S+  Q  Y +GFGP ++ I +  + DI  L+  I+ +T A++
Sbjct: 132 -EIIACSNSFHGRTLFTVSVGGQPKYSQGFGPAISGISHVPYNDIAALEAQISERTCAVV 190

Query: 189 LEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIY 248
           +EP+QGEGGV      +++ VR LC++YN LLI DE+Q G+GRTGK++A       PDI 
Sbjct: 191 VEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSGVAPDIL 250

Query: 249 LLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQN 308
              K +GGG +PI+A+L    V   L+ GTHGST+GGNPL CAV+   LD++N   ++  
Sbjct: 251 TSAKGIGGG-FPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTPQVLDG 309

Query: 309 ALDLGDRLLKHLQQIESELIV--EVRGRGLFIGIELNVAAQDYCEQMI----NKGVLCKE 362
             +   +L   L+ +  EL V  E+RG+GL IG  L    +    Q++     +G+L  +
Sbjct: 310 VGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQAGQVMRLAQEEGLLVLQ 369

Query: 363 TQGNIIRIAPPLVIDKDEIDEVI 385
              +++R+AP L+I + +I E +
Sbjct: 370 AGADVVRLAPSLIIPEADIREAL 392


Lambda     K      H
   0.317    0.136    0.396 

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: 343
Number of extensions: 13
Number of successful extensions: 5
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: 394
Length of database: 404
Length adjustment: 31
Effective length of query: 363
Effective length of database: 373
Effective search space:   135399
Effective search space used:   135399
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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