GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Echinicola vietnamensis KMM 6221, DSM 17526

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Echvi_0181 Echvi_0181 Phosphoglycerate dehydrogenase and related dehydrogenases

Query= curated2:Q58424
         (524 letters)



>FitnessBrowser__Cola:Echvi_0181
          Length = 311

 Score =  181 bits (458), Expect = 4e-50
 Identities = 102/309 (33%), Positives = 175/309 (56%), Gaps = 13/309 (4%)

Query: 2   VKILVTDPLHEDAIKILEEVG-EVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEK 60
           + IL+ D +H   I +LEE G +V  +  +T+EE+   I D + L++RS T + + ++EK
Sbjct: 1   MNILIIDEMHSSIIPLLEEKGFKVNYSPKITREEIEAIIADYEGLIIRSKTPMDKPLLEK 60

Query: 61  AEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATA 120
           A+KLK IGRAG G+D ID++   ++GI + +AP+ +  +V E  + ++L    N+ +A +
Sbjct: 61  AKKLKFIGRAGAGLDKIDLDFIQKQGIKLFHAPEGNRDAVGEHAVAMLLMLFNNLKKADS 120

Query: 121 SLKRGEWDRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESM 180
            +++G WDR+  +G EL GKT+G+ G G +G+   +R   FG+ ++ YD Y+ K   E  
Sbjct: 121 EVRQGVWDREGNRGEELQGKTVGIFGYGNMGKAFARRLSGFGVKVVAYDKYLDKYSDEYA 180

Query: 181 GVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKAL 240
                D   +L ++AD +++HVPLT +TR+    E +A   K   ++N ARG +I  + L
Sbjct: 181 AQVTFD---QLQQQADVLSIHVPLTEETRNFFTEEVLAGFSKPFYLINTARGEVISMETL 237

Query: 241 YEALKEGKIRAAALDVFEEE---------PPKDNPLLTLDNVIGTPHQGASTEEAQKAAG 291
             AL++G ++ A LDV E E               L   D+V+ +PH    T ++ K   
Sbjct: 238 NAALEKGILKGALLDVLENEKLHTLNDVQKTAFEKLSVRDDVLFSPHIAGWTFQSYKKIN 297

Query: 292 TIVAEQIKK 300
            ++  +I +
Sbjct: 298 EVLVSKISE 306


Lambda     K      H
   0.316    0.137    0.372 

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: 365
Number of extensions: 21
Number of successful extensions: 3
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: 524
Length of database: 311
Length adjustment: 31
Effective length of query: 493
Effective length of database: 280
Effective search space:   138040
Effective search space used:   138040
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 (21.5 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