GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Lentibacillus jeotgali Grbi

Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate WP_010529210.1 ON01_RS01340 histidine phosphatase family protein

Query= SwissProt::F4KI56
         (238 letters)



>NCBI__GCF_000224785.1:WP_010529210.1
          Length = 197

 Score = 80.9 bits (198), Expect = 2e-20
 Identities = 61/200 (30%), Positives = 100/200 (50%), Gaps = 12/200 (6%)

Query: 24  VTEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPVAVYSSDLKRA 83
           +T+I  VRHG T WN  GR QG  +  L+E GL QA  +AERL   E  V VYSSDL RA
Sbjct: 1   MTKIGFVRHGVTQWNKEGRAQGTSDIPLDEEGLGQARLLAERLEFGEWDV-VYSSDLLRA 59

Query: 84  KDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLEIPG 143
           K TA  I       ++     L+ER+ G  +G   +E  ++    +          E+  
Sbjct: 60  KQTA-EILNAKLGTQLYLDSRLRERNCGLAEGTTEEERVQRWGPGWR---------ELDM 109

Query: 144 GGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYLRITQASSAGK-LLNASVN 202
             ES+D +  R    +++I++KH  + V++V+HG  ++ +   +   S+  + L N S+ 
Sbjct: 110 QFESYDSIISRGDALIDEISEKHMDQNVLIVSHGAFIKVVLNALIPDSNMDESLKNTSLT 169

Query: 203 VVHLRDQKWIIDSWSDVSHL 222
            +   +  W  + ++   H+
Sbjct: 170 SLIKCEGGWDCNLYNWTEHI 189


Lambda     K      H
   0.315    0.132    0.387 

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: 143
Number of extensions: 9
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: 238
Length of database: 197
Length adjustment: 22
Effective length of query: 216
Effective length of database: 175
Effective search space:    37800
Effective search space used:    37800
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: 45 (21.9 bits)

This GapMind analysis is from Jul 26 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