GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Paraburkholderia bryophila 376MFSha3.1

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate H281DRAFT_05213 H281DRAFT_05213 gluconate 2-dehydrogenase

Query= curated2:Q58424
         (524 letters)



>FitnessBrowser__Burk376:H281DRAFT_05213
          Length = 321

 Score =  219 bits (557), Expect = 2e-61
 Identities = 127/324 (39%), Positives = 189/324 (58%), Gaps = 9/324 (2%)

Query: 1   MVKILVTDPLHEDAIKILEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEK 60
           M KI+    L ED +  L++  EV        +  +  ++DAD  +  S  K+T  ++E 
Sbjct: 1   MKKIVAWKSLPEDVLAYLQQHVEVVQVDPAQHDAFVAALRDADGGIGAS-VKITPAMLEG 59

Query: 61  AEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATA 120
           A +LK +    VG D  DV   T +GI++ + PD  + S A+    L+LA+AR + +  A
Sbjct: 60  ATRLKALSTISVGFDQFDVADLTRRGIVLAHTPDVLTESTADTVFSLILASARRVVELAA 119

Query: 121 SLKRGEWDRK----RFKGIELYGKTLGVIGLGRIGQQVVKRAK-AFGMNIIGYDPYIPKE 175
            +K G+W +     +F G+++ GKTLG++GLGRIG  V +RA   F M ++  +    +E
Sbjct: 120 WVKAGQWQQSIGPAQF-GVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANRE 178

Query: 176 VAESMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLI 235
             E+ G   V+ + EL   ADF+ L VPLTP+TRH+IG ++++ MKK+AI++N +RG  +
Sbjct: 179 AEEAYGARRVE-LPELLANADFVCLQVPLTPQTRHMIGAKELSSMKKSAILINASRGATV 237

Query: 236 DEKALYEALKEGKIRAAALDVFEEEP-PKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIV 294
           DEKAL EAL+ G I  A LDVFE EP P D+PLL L NV+  PH G++T E + A     
Sbjct: 238 DEKALIEALQNGTIHGAGLDVFETEPLPADSPLLKLANVVALPHIGSATRETRHAMARNA 297

Query: 295 AEQIKKVLRGELAENVVNMPNIPQ 318
           AE +   L G L  N+VN   + Q
Sbjct: 298 AENLVAALNGTLTTNIVNREVLQQ 321


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: 354
Number of extensions: 15
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: 524
Length of database: 321
Length adjustment: 31
Effective length of query: 493
Effective length of database: 290
Effective search space:   142970
Effective search space used:   142970
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