GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Enterococcus termitis LMG 8895

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_069663042.1 BCR25_RS07715 indole-3-glycerol phosphate synthase TrpC

Query= BRENDA::P00909
         (453 letters)



>NCBI__GCF_001730305.1:WP_069663042.1
          Length = 252

 Score =  124 bits (310), Expect = 4e-33
 Identities = 88/239 (36%), Positives = 126/239 (52%), Gaps = 9/239 (3%)

Query: 6   LAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQG--ARTAFILECKKASPSKG 63
           L KI+ +K    +   Q+ PL   Q   Q  T  FY+ ++    +   I E K+ASPSKG
Sbjct: 4   LEKIITEK----KQEIQKMPLEKLQPLRQ--TTSFYERVKKNPEKIHIIGEVKRASPSKG 57

Query: 64  VIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDPY 122
            I    +    A  Y K   +AISVLTD  +F+GS   L  V+     P+LCKDFIID  
Sbjct: 58  AINLSVNVIEQAKAYEKAGVTAISVLTDPTFFKGSIEDLRQVAAEVSIPVLCKDFIIDEK 117

Query: 123 QIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAKVV 182
           Q+  AR   A   LL++S L   + ++L   A +L + VL EV +E+EQ  A  LGA ++
Sbjct: 118 QLIRARNAGATIVLLIVSALSRSRLKKLYEQARTLGLEVLVEVHDEQEQTIAEELGASLI 177

Query: 183 GINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALM 241
           G+NNR+L+   + LN ++ L  K   +   ISESG +   QV ++       L+G  LM
Sbjct: 178 GVNNRNLKTFDVSLNVSQLLGEKQRTDAVYISESGFSDATQVEQVKDKYQAILVGEGLM 236


Lambda     K      H
   0.320    0.135    0.389 

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: 220
Number of extensions: 15
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: 453
Length of database: 252
Length adjustment: 28
Effective length of query: 425
Effective length of database: 224
Effective search space:    95200
Effective search space used:    95200
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: 49 (23.5 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