GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metA in Pseudomonas putida KT2440

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate PP_5097 PP_5097 homoserine O-acetyltransferase

Query= SwissProt::Q88CT3
         (379 letters)



>FitnessBrowser__Putida:PP_5097
          Length = 379

 Score =  782 bits (2019), Expect = 0.0
 Identities = 379/379 (100%), Positives = 379/379 (100%)

Query: 1   MSTVFPEDSVGLVVPQTARFDEPLALACGRSLASYELVYETYGTLNASASNAVLICHALS 60
           MSTVFPEDSVGLVVPQTARFDEPLALACGRSLASYELVYETYGTLNASASNAVLICHALS
Sbjct: 1   MSTVFPEDSVGLVVPQTARFDEPLALACGRSLASYELVYETYGTLNASASNAVLICHALS 60

Query: 61  GHHHAAGYHAATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGK 120
           GHHHAAGYHAATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGK
Sbjct: 61  GHHHAAGYHAATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGK 120

Query: 121 PYGADFPVLTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDI 180
           PYGADFPVLTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDI
Sbjct: 121 PYGADFPVLTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDI 180

Query: 181 ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSM 240
           ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSM
Sbjct: 181 ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSM 240

Query: 241 GEKFGRELKSDKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAATH 300
           GEKFGRELKSDKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAATH
Sbjct: 241 GEKFGRELKSDKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAATH 300

Query: 301 GGDLAATLAHVTADYCIMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAFL 360
           GGDLAATLAHVTADYCIMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAFL
Sbjct: 301 GGDLAATLAHVTADYCIMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAFL 360

Query: 361 IPTPRYMQGFSNYMNRIAI 379
           IPTPRYMQGFSNYMNRIAI
Sbjct: 361 IPTPRYMQGFSNYMNRIAI 379


Lambda     K      H
   0.320    0.136    0.421 

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: 656
Number of extensions: 15
Number of successful extensions: 1
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: 379
Length of database: 379
Length adjustment: 30
Effective length of query: 349
Effective length of database: 349
Effective search space:   121801
Effective search space used:   121801
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: 50 (23.9 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