GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09275
          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:

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