GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Burkholderia phytofirmans PsJN

Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate BPHYT_RS16630 BPHYT_RS16630 phosphoglycerate mutase

Query= SwissProt::F4KI56
         (238 letters)



>FitnessBrowser__BFirm:BPHYT_RS16630
          Length = 223

 Score =  114 bits (284), Expect = 2e-30
 Identities = 81/208 (38%), Positives = 107/208 (51%), Gaps = 10/208 (4%)

Query: 25  TEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKE----ERPVAVYSSDL 80
           T+I+ +RHGET WN   RIQG I+  L   GL QA  +A R+  E     R  A+YSSDL
Sbjct: 3   TQILFIRHGETDWNRIKRIQGHIDIPLATTGLAQAQRLARRMADEAKQGARLDAIYSSDL 62

Query: 81  KRAKDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLE 140
           +RA+ TA  IA     P  +    L+ER  G+ QG    E A + P+ Y A + +++   
Sbjct: 63  QRAQQTAQPIADALALPLQLR-EGLRERSYGAFQGHDSDEIALRFPDEY-AHWQTRDAGF 120

Query: 141 IPGGGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYLRI----TQASSAGKL 196
            P  GES   L  R + A+E +   H G R+  V HGGVL  +          A     L
Sbjct: 121 APPEGESLRTLYHRVLHAIEPLVAAHPGGRIACVAHGGVLDCVRRFACGLPLDAPRNYPL 180

Query: 197 LNASVNVVHLRDQKWIIDSWSDVSHLSS 224
           LN SVN V   + K  I SW+DVSHL +
Sbjct: 181 LNTSVNAVDFDNGKATIVSWADVSHLDA 208


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: 157
Number of extensions: 6
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: 238
Length of database: 223
Length adjustment: 23
Effective length of query: 215
Effective length of database: 200
Effective search space:    43000
Effective search space used:    43000
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: 46 (22.3 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