GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Klebsiella michiganensis M5al

Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate BWI76_RS13025 BWI76_RS13025 histidine phosphatase family protein

Query= BRENDA::D3DFG8
         (211 letters)



>FitnessBrowser__Koxy:BWI76_RS13025
          Length = 206

 Score = 88.2 bits (217), Expect = 1e-22
 Identities = 65/202 (32%), Positives = 98/202 (48%), Gaps = 3/202 (1%)

Query: 2   VKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLL--AQELSREHLDVIYSSPLKRT 59
           +KLILVRHAE+EWN  G  QG  D  L+ RG ++  +L  A   S   ++ +Y+SPL R 
Sbjct: 1   MKLILVRHAETEWNLEGIIQGHSDSSLTCRGLRETSVLLAAFSASEYQIERVYASPLGRA 60

Query: 60  YLTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGG 119
           +     +AE  +  +  E  + E   G + GM +E + +K+P           +    GG
Sbjct: 61  WQMGQSLAEHFHCSLTAEPALKEQAFGQFEGMPLELLRQKHPNYANALFRLDAEYCPPGG 120

Query: 120 ESLASVYNRVKGFLEEVR-KRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNAS 178
           ESLA    RV  FL+ +       QT+ +VSH    +     L    ++ F  +   +AS
Sbjct: 121 ESLAHASQRVMRFLQNLEDTSSHQQTICIVSHGHVSQGTLAILKEGTVNSFPRYAHPHAS 180

Query: 179 YSVIHMEERRNVILKLNITCHL 200
           YSVI +   + + LK  I  HL
Sbjct: 181 YSVIDLINGKCIGLKWGIATHL 202


Lambda     K      H
   0.320    0.136    0.408 

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: 120
Number of extensions: 7
Number of successful extensions: 4
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: 211
Length of database: 206
Length adjustment: 21
Effective length of query: 190
Effective length of database: 185
Effective search space:    35150
Effective search space used:    35150
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: 45 (21.9 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