GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapA in Pedobacter sp. GW460-11-11-14-LB5

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate CA265_RS08390 CA265_RS08390 dihydrodipicolinate synthase family protein

Query= BRENDA::A9CL94
         (309 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS08390 CA265_RS08390
           dihydrodipicolinate synthase family protein
          Length = 310

 Score =  134 bits (337), Expect = 3e-36
 Identities = 72/221 (32%), Positives = 120/221 (54%), Gaps = 2/221 (0%)

Query: 6   EGIIPVMITPF-RDGKIDFEGVANLVEWYIANGSDALFAVCQSSEMMFLTLEERVELAAF 64
           +G IPVM+TPF  +G ID+  +  L E Y+  GS  LFA C SSEM  L+ +ER++    
Sbjct: 6   KGFIPVMLTPFLSNGNIDYPALTQLTEIYLQAGSSGLFANCLSSEMFELSGKERIQAIKH 65

Query: 65  VKRAAAGRIPVIASGHISEALEDQQKELNAIARTGVDGIVLVTNRMDARQEGGSKFLDDL 124
           V +   G +PV+A+G     +  Q   +  ++  GV+ ++ +T+ +    E    F D +
Sbjct: 66  VIKVVDGAVPVVATGTFGGEISKQADFVKEVSDAGVEAVIAITSLLADESESDEVFNDRV 125

Query: 125 GWLLDRLPPNLPLGLYECPAPYRRLMTDAEISFCANSGRFVILKDVSCDLETVKRRVALT 184
             LL +    +PLG YECP PY+R++   +++    + R +  KD   DL  +K ++ LT
Sbjct: 126 FDLLHQTD-KIPLGFYECPVPYKRVLKPQQLADFVATDRVIYHKDTCLDLGQIKEKLKLT 184

Query: 185 ANTPLAIVNANAAIAFDAMKAGSRGFTGVFTNFHPDLYKWL 225
           A     + +A    A +++KAG+ G + +  N+ P+L  WL
Sbjct: 185 AGKTFGLYDAYIVHAVESLKAGASGLSCIQGNYFPELIVWL 225


Lambda     K      H
   0.323    0.138    0.406 

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: 211
Number of extensions: 7
Number of successful extensions: 3
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: 309
Length of database: 310
Length adjustment: 27
Effective length of query: 282
Effective length of database: 283
Effective search space:    79806
Effective search space used:    79806
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: 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