GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Salinicoccus carnicancri Crm

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_017549807.1 C792_RS0112560 dihydrodipicolinate synthase family protein

Query= BRENDA::A9CFV4
         (303 letters)



>NCBI__GCF_000330705.1:WP_017549807.1
          Length = 293

 Score =  138 bits (348), Expect = 1e-37
 Identities = 93/291 (31%), Positives = 144/291 (49%), Gaps = 5/291 (1%)

Query: 2   KFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLA 61
           +FEG +   ITP+  D  ++ +   A ++  ++ +  GI+I GSTGE+ +    E+  + 
Sbjct: 4   QFEGAFPVLITPMHGDYSVNYEGMKANVQYYLDQQAAGIVIVGSTGEFASLDEAEKKKIV 63

Query: 62  AYARQVI-GTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHA 120
                ++  T   L+VG    RT   IEYA+ A+   AD +L+ +  Y  PTE E     
Sbjct: 64  ELVGPMVKDTDTALLVGIADERTSKVIEYARHAEANHADGLLLINSFYQTPTEEEAFHQF 123

Query: 121 LAVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVA-IKESSGDMGNLHLLARKFP 179
             V+     P+M+YN P    V + +    R+ +  + V  IKESSGD+  +  +A    
Sbjct: 124 KDVNDVVTQPLMMYNNPFTANVNLEDATICRIDRELDKVQYIKESSGDIRKVRAVADN-T 182

Query: 180 QIALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLP 239
            + L CG DD A E F  GA  WV   +N  P     LYE     K +D+ + +   +LP
Sbjct: 183 DLVLFCGSDDLAFESFVQGATGWVSVAANIAPNSAAQLYELVKAGK-YDEAKTLNKDLLP 241

Query: 240 LMDFLE-CGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTL 289
           L +FLE  GK+VQ +K   ++ GL  G  R P   L  DE   L++++  L
Sbjct: 242 LCEFLEDSGKYVQIVKKAMDLKGLAGGPSRKPRLGLTDDEVSQLKSLMEKL 292


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: 197
Number of extensions: 8
Number of successful extensions: 5
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: 293
Length adjustment: 26
Effective length of query: 277
Effective length of database: 267
Effective search space:    73959
Effective search space used:    73959
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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