GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Enterococcus termitis LMG 8895

Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_069663045.1 BCR25_RS07730 anthranilate synthase component I

Query= BRENDA::P9WFX1
         (450 letters)



>NCBI__GCF_001730305.1:WP_069663045.1
          Length = 454

 Score =  120 bits (301), Expect = 9e-32
 Identities = 71/219 (32%), Positives = 113/219 (51%), Gaps = 1/219 (0%)

Query: 224 YRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRL 283
           YR  R  N     + L  G    +G SPE + +V+ +G+V T P+AGTR  G     D  
Sbjct: 232 YRRLRVTNPSTYLYFLDFGETYVIGSSPESLVSVK-EGIVTTNPIAGTRKRGMTAEQDVA 290

Query: 284 ARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARL 343
             ++L  + KE  EH + +     ++  ++E GS  V  +MT+ +   V H+ S +  +L
Sbjct: 291 LANELIHDEKERAEHLMLIDLGRNDVGKVSEIGSVEVPVYMTIEKYRFVMHIVSVVTGKL 350

Query: 344 DPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALT 403
                 M AL+A  PA T SG PK   ++ I+  +   R +Y+GAV  LS +   D A+ 
Sbjct: 351 KHGLSAMDALKATLPAGTVSGAPKIRAMQRIYEFEPVKRNIYAGAVGYLSKNDQADFAIA 410

Query: 404 LRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEKLSTL 442
           +R         +++AGAGI+ +S+P +E+EET +K   L
Sbjct: 411 IRTMVIHKNYAYVQAGAGIVYDSDPTKEYEETLQKAKAL 449


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: 358
Number of extensions: 13
Number of successful extensions: 1
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: 454
Length adjustment: 33
Effective length of query: 417
Effective length of database: 421
Effective search space:   175557
Effective search space used:   175557
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