GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Sulfurihydrogenibium subterraneum DSM 15120

Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_028950293.1 Q385_RS0103255 hydroxyacid dehydrogenase

Query= uniprot:Q5JGC4
         (304 letters)



>NCBI__GCF_000619805.1:WP_028950293.1
          Length = 342

 Score =  190 bits (482), Expect = 5e-53
 Identities = 114/288 (39%), Positives = 166/288 (57%), Gaps = 21/288 (7%)

Query: 23  EVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAAPKLKVIGRAGVGLDNIDLKAA 82
           EV + + P +D  VEL K++D  IV    K+ + V+     LK+I     G D+ID++  
Sbjct: 28  EVEFTKEPLDDTNVELYKNIDVAIVFIYSKLNKDVLSKMANLKLIITRSTGYDHIDVEYT 87

Query: 83  EERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCMGIELEGKTI 142
            +  I V N PG  + +VAE    LI A+ARK      +  +G++++    GI+L GKTI
Sbjct: 88  SKNSITVCNVPGYGNNTVAEYTFALILALARKFKPMIERTSKGIFSRDGLTGIDLMGKTI 147

Query: 143 GVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKEVGGKFADLETLLKESDVVTLHVP 202
           GV+G GRIG  V +IA   GMK+L YD Y ++E   + G ++  LE LL+ SD+VTLHVP
Sbjct: 148 GVIGAGRIGKHVIRIAYGFGMKILVYDRYKDKELIDKYGVEYVGLEDLLRMSDIVTLHVP 207

Query: 203 LVDATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIA-GAGLDVFEEEPL 261
              +T+HLIN   +KLMK  A+L+N +RG VV+ +A+V+AL+EG +A G GLD FE E +
Sbjct: 208 YNKSTHHLINRFNIKLMKLDAMLVNTSRGPVVEMEAIVQALKEGRLAGGVGLDTFEAEEV 267

Query: 262 --------PADHPLTKL------------DNVVLTPHIGASTVEAQMR 289
                     D P  KL            +NV+++PH   +T +A  R
Sbjct: 268 LIEEEYLKRDDIPAIKLKKALESFYVLHSENVIVSPHNAYNTKDALYR 315


Lambda     K      H
   0.317    0.136    0.378 

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: 258
Number of extensions: 10
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: 304
Length of database: 342
Length adjustment: 28
Effective length of query: 276
Effective length of database: 314
Effective search space:    86664
Effective search space used:    86664
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: 48 (23.1 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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