GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapA in Pseudomonas fluorescens FW300-N2C3

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO356_09275 AO356_09275 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::A9CFV4
         (303 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09275 AO356_09275
           4-hydroxy-tetrahydrodipicolinate synthase
          Length = 303

 Score =  469 bits (1208), Expect = e-137
 Identities = 228/303 (75%), Positives = 266/303 (87%)

Query: 1   MKFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDL 60
           +KFEGIYTPA+TP   DGEID   F+ VLESL+EA+VHGIIIGGSTGEYYAQTA+ER  L
Sbjct: 1   LKFEGIYTPAVTPHTPDGEIDWRVFSEVLESLIEAKVHGIIIGGSTGEYYAQTAEERLKL 60

Query: 61  AAYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHA 120
           AA+AR+VIG+R+ L++GTGA RTED++ +A+ AK I ADAILV++PPYALPT++ENA+HA
Sbjct: 61  AAHAREVIGSRVQLIIGTGAIRTEDAVLFAEDAKRIKADAILVTTPPYALPTDQENAIHA 120

Query: 121 LAVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKFPQ 180
           L +DRAAN+PIMLYNYP RM V M EEY +RVGKSKNV AIKESSGDMG +HLLAR+FP 
Sbjct: 121 LTIDRAANMPIMLYNYPGRMCVQMNEEYLARVGKSKNVKAIKESSGDMGRVHLLAREFPH 180

Query: 181 IALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPL 240
           IALSCGWDDQALEFFAWGA+SWVCAGSNFLP+EHVALYEACVVEKNFDKGR IM+AM+PL
Sbjct: 181 IALSCGWDDQALEFFAWGARSWVCAGSNFLPKEHVALYEACVVEKNFDKGRQIMSAMMPL 240

Query: 241 MDFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTLKRTVAQIASGA 300
           M+ L+ GKFVQ IK GCE+ GL  G VRAPLRPLNSD+KR+LQTV+  +KRTVA I SGA
Sbjct: 241 MNALDGGKFVQCIKFGCELNGLAVGDVRAPLRPLNSDDKRSLQTVIANVKRTVAHITSGA 300

Query: 301 NHA 303
           N+A
Sbjct: 301 NNA 303


Lambda     K      H
   0.320    0.135    0.397 

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: 324
Number of extensions: 5
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: 303
Length of database: 303
Length adjustment: 27
Effective length of query: 276
Effective length of database: 276
Effective search space:    76176
Effective search space used:    76176
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: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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