GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Chlorobaculum parvum NCIB 8327

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_012503218.1 CPAR_RS10115 3-deoxy-8-phosphooctulonate synthase

Query= BRENDA::P39912
         (358 letters)



>NCBI__GCF_000020505.1:WP_012503218.1
          Length = 286

 Score =  122 bits (307), Expect = 9e-33
 Identities = 81/247 (32%), Positives = 132/247 (53%), Gaps = 21/247 (8%)

Query: 122 IVGPCAVESYEQVAEVAAAA----KKQGIKILRGGAFKP--RTSPYDFQGLGV-EGLQIL 174
           + GPC +E+ +    VA       +++GI ++  G+++   R+S   + G+G  E L+IL
Sbjct: 20  VAGPCLIENRQMAVAVATELDRIRQEEGISVIFKGSYRKANRSSASSYTGIGDREALEIL 79

Query: 175 KRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGL 234
             + D FD+ V++++   + +E A  Y+DV+QI A   +  EL+ AA +    + +K+G 
Sbjct: 80  CEIRDVFDMPVLTDVHETSDVELAASYVDVLQIPAFLSRQTELIVAAASTGLAINIKKGQ 139

Query: 235 AATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDV 294
                +   AAE   S GN +I+L ERG  T        +D   +PI+  ++  PV  D 
Sbjct: 140 FMAPEDMALAAEKAASTGNRKIMLTERG--TTFGYHNLVVDYRGLPIM-ADSGWPVIFDA 196

Query: 295 THST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEF 343
           THS            G R  L+P A+AA+A G DG+  EVHP+PS A+SD+A Q+ + +F
Sbjct: 197 THSVQLPSASSGVSGGDRRFLMPLARAAVAAGVDGLFFEVHPEPSNAMSDAATQVPLDQF 256

Query: 344 EKWLNEL 350
              + EL
Sbjct: 257 HAMVREL 263


Lambda     K      H
   0.316    0.134    0.369 

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: 209
Number of extensions: 10
Number of successful extensions: 2
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: 358
Length of database: 286
Length adjustment: 28
Effective length of query: 330
Effective length of database: 258
Effective search space:    85140
Effective search space used:    85140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Jul 25 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