GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gly1 in Pseudomonas fluorescens GW456-L13

Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate PfGW456L13_1114 Low-specificity L-threonine aldolase (EC 4.1.2.48)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1114
         (346 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1114
          Length = 346

 Score =  714 bits (1843), Expect = 0.0
 Identities = 346/346 (100%), Positives = 346/346 (100%)

Query: 1   MTDKSQQFASDNYSGICPEAWAAMEQANHGHQRAYGDDEWTARASDGFRKLFETDCEVFF 60
           MTDKSQQFASDNYSGICPEAWAAMEQANHGHQRAYGDDEWTARASDGFRKLFETDCEVFF
Sbjct: 1   MTDKSQQFASDNYSGICPEAWAAMEQANHGHQRAYGDDEWTARASDGFRKLFETDCEVFF 60

Query: 61  AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPD 120
           AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPD
Sbjct: 61  AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPD 120

Query: 121 SIREVALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSN 180
           SIREVALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSN
Sbjct: 121 SIREVALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSN 180

Query: 181 ACAFLGCTPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASK 240
           ACAFLGCTPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASK
Sbjct: 181 ACAFLGCTPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASK 240

Query: 241 MRFLSAPWVGILENDAWLKYANHANHCAQLLAELVSDIPGVELMFPVQANGVFLQLSEPA 300
           MRFLSAPWVGILENDAWLKYANHANHCAQLLAELVSDIPGVELMFPVQANGVFLQLSEPA
Sbjct: 241 MRFLSAPWVGILENDAWLKYANHANHCAQLLAELVSDIPGVELMFPVQANGVFLQLSEPA 300

Query: 301 IAALTAKGWRFYTFIGNGGARFMCSWDTEQERVRELAKDIREVMSH 346
           IAALTAKGWRFYTFIGNGGARFMCSWDTEQERVRELAKDIREVMSH
Sbjct: 301 IAALTAKGWRFYTFIGNGGARFMCSWDTEQERVRELAKDIREVMSH 346


Lambda     K      H
   0.320    0.133    0.416 

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: 570
Number of extensions: 3
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: 346
Length of database: 346
Length adjustment: 29
Effective length of query: 317
Effective length of database: 317
Effective search space:   100489
Effective search space used:   100489
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 (21.9 bits)
S2: 49 (23.5 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