GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Dechlorosoma suillum PS

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate Dsui_0664 Dsui_0664 glutamate-1-semialdehyde-2,1-aminomutase

Query= CharProtDB::CH_002469
         (406 letters)



>FitnessBrowser__PS:Dsui_0664
          Length = 427

 Score =  143 bits (360), Expect = 1e-38
 Identities = 105/339 (30%), Positives = 159/339 (46%), Gaps = 23/339 (6%)

Query: 21  APFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTN 80
           AP    RGEG R+WD +GK Y+D+ G      LGHAH    +A+ E A+       G   
Sbjct: 33  APRFFTRGEGPRVWDAEGKSYLDYVGSWGPLILGHAHAPTVKAVQEAAAL--GLSFGAPT 90

Query: 81  EPVLRLAKKLIDATFA-DRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFH 139
           E  + +A  L D   + D V   +SG EA  +A++LAR        + +  +V F+  +H
Sbjct: 91  EAEIEIADLLCDILPSLDMVRLVSSGTEATMSAIRLARGH------TGRDLLVKFEGCYH 144

Query: 140 GRT---LFTVSAGGQPAYSQDFAPLPADI-RHAAYNDINSASALID------DSTCAVIV 189
           G +   L    +G     +     +PAD+ +H    + N+A  L +          AVIV
Sbjct: 145 GHSDSLLVKAGSGLLTFGNPSSGGVPADVAKHTLVLEYNNAEQLAEAFAKQGSEIAAVIV 204

Query: 190 EPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLT 249
           EP+ G   ++     F+Q +RELC++H A+LIFDEV TG  R G   A   +G+TPDL T
Sbjct: 205 EPVAGNMNLIAPKPEFMQAMRELCSKHGAVLIFDEVMTGF-RVGPQCAQGLFGITPDLTT 263

Query: 250 TAKALGGGFPVGALLATEE-CARVMTVGT--HGTTYGGNPLASAVAGKVLELINTPEMLN 306
             K +GGG PV A     E   ++  +G      T  GNP+A A     L+    P   +
Sbjct: 264 LGKVIGGGMPVAAFGGKREIMEKIAPLGPVYQAGTLSGNPVAVAAGLVTLKATRAPGFYD 323

Query: 307 GVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNA 345
            +  R     + L     ++G+    + +G + G   +A
Sbjct: 324 SLAARTKQLTDGLTAAAKKHGVTFCAQSVGGMFGLYFSA 362


Lambda     K      H
   0.319    0.136    0.407 

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: 434
Number of extensions: 27
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: 406
Length of database: 427
Length adjustment: 31
Effective length of query: 375
Effective length of database: 396
Effective search space:   148500
Effective search space used:   148500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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