GapMind for Amino acid biosynthesis

 

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

Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_085639309.1 MGEO_RS14630 anthranilate synthase component I

Query= BRENDA::P9WFX1
         (450 letters)



>NCBI__GCF_002115805.1:WP_085639309.1
          Length = 504

 Score =  130 bits (327), Expect = 1e-34
 Identities = 83/261 (31%), Positives = 130/261 (49%), Gaps = 9/261 (3%)

Query: 186 GFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLT----YRLGRRHNTPVRSFLLQL 241
           G+++ V  A + I AG   +V+ ++     +  DFPL     YR  RR N     F    
Sbjct: 233 GYKQAVEKAKEYIRAGDIFQVVPAQ----RWTQDFPLPPFALYRSLRRTNPSPFMFYFNF 288

Query: 242 GGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAIS 301
           GG + +G SPE++  V    V I  P+AGTR  G  PA D     DL +++KE  EH + 
Sbjct: 289 GGFQVIGASPEILVRVFGSEVTI-RPIAGTRPRGATPAEDDALEADLLADAKECAEHLML 347

Query: 302 VRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVT 361
           +     ++  +A+ G+    +   +     V H+ S +   L    D ++AL A  PA T
Sbjct: 348 LDLGRNDVGRVAKIGTVRPTEKFIIERYSHVMHIVSNVVGELSDDHDALSALLAGLPAGT 407

Query: 362 ASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAG 421
            SG PK   +E I  L+   RG+Y G V   SA G +D  + LR A     + +++AG G
Sbjct: 408 VSGAPKVRAMEIIDELEPEKRGIYGGGVGYFSAGGDMDMCIALRTALVKDKKLYIQAGGG 467

Query: 422 IIEESEPEREFEETCEKLSTL 442
           ++ +S+PE E++ET  K + +
Sbjct: 468 VVYDSDPEAEYQETVHKSNAI 488


Lambda     K      H
   0.319    0.135    0.386 

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: 450
Number of extensions: 23
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: 450
Length of database: 504
Length adjustment: 33
Effective length of query: 417
Effective length of database: 471
Effective search space:   196407
Effective search space used:   196407
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: 51 (24.3 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