GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Dechlorosoma suillum PS

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Dsui_2908 Dsui_2908 aspartate/tyrosine/aromatic aminotransferase

Query= curated2:Q2N7G6
         (367 letters)



>FitnessBrowser__PS:Dsui_2908
          Length = 408

 Score = 72.0 bits (175), Expect = 3e-17
 Identities = 53/174 (30%), Positives = 79/174 (45%), Gaps = 18/174 (10%)

Query: 70  AKLAEVHGLDAGRIVCGTGSDELLNLAAQAFAGPGDEVLFSTYSFSVYDIAARRCGATP- 128
           A+  +V G+    I  G G  EL+ ++  A   PGDEVL     + ++  A      TP 
Sbjct: 85  AQQKKVKGVGLEDIYVGNGVSELIVMSMNALLNPGDEVLVPAPDYPLWTAAVSLSSGTPR 144

Query: 129 --VEAPDADYAADVDALLAAVTDKTRVVFVANPNNPTGSFLPRD------EIARLHAGLP 180
             +    A +  D+D + A +T+ TR + + NPNNPTG+  P D      EIAR H    
Sbjct: 145 HYICDEGAGWLPDLDDIRAKITENTRAIVIINPNNPTGALYPDDLLKEIVEIARQH---- 200

Query: 181 QDVLFVLDQAYAEYLTPEEDDGGFALAAAHENVLVT--RTFSKAYGLAGERIGW 232
             ++   D+ Y + L    +    A+ +  E+VL       SK Y   G R GW
Sbjct: 201 -HLIIYADEVYDKVLYDGVEH--TAIGSLSEDVLTISFNGLSKNYRSCGYRAGW 251


Lambda     K      H
   0.317    0.134    0.393 

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: 18
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: 367
Length of database: 408
Length adjustment: 30
Effective length of query: 337
Effective length of database: 378
Effective search space:   127386
Effective search space used:   127386
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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