GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Marivita geojedonensis DPG-138

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_085641408.1 MGEO_RS19475 3-deoxy-8-phosphooctulonate synthase

Query= BRENDA::P39912
         (358 letters)



>NCBI__GCF_002115805.1:WP_085641408.1
          Length = 272

 Score = 96.7 bits (239), Expect = 6e-25
 Identities = 80/255 (31%), Positives = 124/255 (48%), Gaps = 25/255 (9%)

Query: 122 IVGPCAVESYEQV----AEVAAAAKKQGIKILRGGAFKP--RTSPYDFQGLGV-EGLQIL 174
           I GPC +ES +        +AAAA+      +   ++    R+S    +GLG+ EGL IL
Sbjct: 20  IAGPCQLESLDHARMLATRIAAAAEATDTPWIFKASYDKANRSSLKGKRGLGMDEGLTIL 79

Query: 175 KRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGL 234
            R+  EF + V+++I T          +DV+QI A   +  +LL AAG     + +K+G 
Sbjct: 80  DRIKAEFGVPVLTDIHTAEQCAPVAQVVDVLQIPAFLSRQTDLLLAAGETGAAINVKKGQ 139

Query: 235 AATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTL--DISAVPILKQETHLPVFV 292
                +  N A  I S GN++I+LCERG     +   N L  D+ ++PI+ Q T  PV  
Sbjct: 140 FLAPWDMENVAAKIASTGNERILLCERG----ASFGYNMLVSDMRSLPIMAQ-TGYPVVF 194

Query: 293 DVTHST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIP 341
           D THS            G+R+ +   A+AA+A+G   V  E H  P  A SD    + I 
Sbjct: 195 DATHSVQLPGGQGTSSGGQREFVPHLARAAVAVGCAAVFIETHDAPDNAPSDGPNMVPID 254

Query: 342 EFEKWLNELKPMVKV 356
           + +  L  ++ + +V
Sbjct: 255 QLKGLLLVMRRIDRV 269


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: 193
Number of extensions: 11
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: 272
Length adjustment: 27
Effective length of query: 331
Effective length of database: 245
Effective search space:    81095
Effective search space used:    81095
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 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