GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Haloglycomyces albus DSM 45210

Align Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_025273081.1 HALAL_RS0105715 HAD family hydrolase

Query= SwissProt::P9WGJ3
         (308 letters)



>NCBI__GCF_000527155.1:WP_025273081.1
          Length = 258

 Score =  112 bits (281), Expect = 7e-30
 Identities = 83/247 (33%), Positives = 118/247 (47%), Gaps = 6/247 (2%)

Query: 57  AAAFFDVDNTLVQGSSAVHFGRGLAARHYFTYRDVLGFLYAQAKFQLLGKENSNDVAAGR 116
           +AAFFD+D T+V  SSA+ FGR L        RDVL   Y Q  +++ G  +   +   R
Sbjct: 5   SAAFFDLDKTIVSKSSALAFGRPLYHLGLLGRRDVLRAAYGQLVYRI-GGGDGRQMERTR 63

Query: 117 RKALAFIEGRSVAELVALGEEIYDEIIADKIWDGTRELTQMHLDAGQQVWLITATPYELA 176
                   G S   +  +  E  D +I   I+    +L + HLDAG+ V LI+A+ Y++ 
Sbjct: 64  NYLADLSRGWSAETVRDVVMETLDHLIQPFIYTEALDLVRGHLDAGRNVVLISASGYDIV 123

Query: 177 ATIARRLGLTGALGT-VAESVDGIFTGRLVGEILHGTGKAHAVRSLAIREGLNLKRCTAY 235
           + IA  LG+   + T +    +G++TG  V     G  KA A+R  A    ++L    AY
Sbjct: 124 SPIADSLGIPEVIATRLRTDGNGMYTGE-VEFYAAGQAKAEAIRDYARNRDIDLSASFAY 182

Query: 236 SDSYNDVPMLSLVGTAVAINPDARLRSLARERGWEIRDFRIARKAARIGVPSALALGAAG 295
           SDS  D PML  VG    +N D  LR L +  GW +  F       R G P    +    
Sbjct: 183 SDSITDEPMLRAVGNPRVVNGDKSLRKLGKSEGWPLLSF---NDPTREGKPCGKEMRTGF 239

Query: 296 GALAALA 302
            A+AALA
Sbjct: 240 VAVAALA 246


Lambda     K      H
   0.319    0.134    0.388 

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: 179
Number of extensions: 11
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: 308
Length of database: 258
Length adjustment: 26
Effective length of query: 282
Effective length of database: 232
Effective search space:    65424
Effective search space used:    65424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 25 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