GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Streptacidiphilus oryzae TH49

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_051939384.1 BS73_RS02730 hydroxyacid dehydrogenase

Query= BRENDA::P9WNX3
         (528 letters)



>NCBI__GCF_000744815.1:WP_051939384.1
          Length = 325

 Score =  137 bits (344), Expect = 8e-37
 Identities = 100/304 (32%), Positives = 155/304 (50%), Gaps = 13/304 (4%)

Query: 14  PSTVAALGDQVEV---RWVDGPDRDKLLAAVPEADALLVR-SATTVDAEVLAAAPKLKIV 69
           P+ +A L + VE+     + G    +   A+ EA+ L+       VDAE LAAAP+L+ V
Sbjct: 12  PTELARLRELVELTSEEALSGFGTPEARKALGEAELLITGWGCPPVDAEALAAAPRLRAV 71

Query: 70  ARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLR-EH- 127
                 + N   +A   RG+ V  A  +N    AE+ LA++L + +++  +  +LR EH 
Sbjct: 72  VHVAGTVRNHITEACWERGLRVSTAAAANGVPVAEYTLAMILLSQKRVLESARALRTEHR 131

Query: 128 --TWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIE 185
              W      G   F +TVG++    IG+ V   +      V+ +DP+VSP  A +LG  
Sbjct: 132 RPAWTADPRLGN--FRRTVGILSASGIGRRVIGLLRPHDLEVLLHDPFVSPEEAERLGAR 189

Query: 186 LLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAI 245
            + +++L A +D +SVH P  P+T GL+ +E LA    G  ++N ARG +VD+ AL   +
Sbjct: 190 AVGIEELFAVSDTVSVHTPLLPQTVGLVSRELLALMPDGATLINTARGAVVDQEALTAEL 249

Query: 246 TGGHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHL-GASTAEAQDRAGTDVAESVRLAL 303
             G +RA  LDV   +P    SPL+    V++TPH+ G+   E        + E  RLA 
Sbjct: 250 LSGRLRAV-LDVTVPDPLPPGSPLYGCPNVLLTPHVAGSLGGELLRMTELALGEIERLAR 308

Query: 304 AGEF 307
             EF
Sbjct: 309 GEEF 312


Lambda     K      H
   0.317    0.133    0.370 

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: 377
Number of extensions: 17
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: 528
Length of database: 325
Length adjustment: 31
Effective length of query: 497
Effective length of database: 294
Effective search space:   146118
Effective search space used:   146118
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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