GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Mycolicibacterium vanbaalenii PYR-1

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_011781954.1 MVAN_RS24155 aminodeoxychorismate synthase, component I

Query= curated2:P96556
         (531 letters)



>NCBI__GCF_000015305.1:WP_011781954.1
          Length = 420

 Score =  139 bits (351), Expect = 2e-37
 Identities = 101/281 (35%), Positives = 139/281 (49%), Gaps = 26/281 (9%)

Query: 232 WNEPE-------YLAALDRGKEAIVDGEVFQVVISRRFEMECGASPLDVY-RVLRNTNPS 283
           W EP+        LA L    EAI  GEV+Q  +  +F      +P+D +      T P+
Sbjct: 145 WGEPDRHAHRRGVLACL----EAIAAGEVYQACVCTQFAGVLAGAPVDFFAEAAARTVPA 200

Query: 284 PYMYIFSLEDAAGRQYSIVGSSPEALVTVTGEDVITHPIAGSRPRGKTVDADKALAEELL 343
              ++      AG   ++   SPE  +   GE V + PI G+ P       D A    L 
Sbjct: 201 RAAFV------AGDWGAVASLSPELFLRRCGEAVTSSPIKGTLP-------DFADPATLR 247

Query: 344 ADQKERAEHLMLVDLSRNDLSKVCVAGSVDVTQFMEVERFSHIMHLVSTVVGRLAPTAKA 403
           A  K+ AE++M+VDL RNDL +V   GSV V + + V     + HLVSTV  R+      
Sbjct: 248 ASVKDVAENIMIVDLVRNDLGRVARTGSVSVPELLAVRPAPGVWHLVSTVSARVPEDTPT 307

Query: 404 YDVLKATFPAGTLSGAPKPRALRLLDELEPHRRGIYGGVVGYLDFAGDMDMAIAIRSALL 463
             +L ATFP  +++G PK RA  LL   EPHRRGIY G VG        ++ +AIR+   
Sbjct: 308 AVLLDATFPPASVTGTPKSRARGLLTGWEPHRRGIYCGTVGLASPVAGCELNVAIRTVEF 367

Query: 464 -REGRAYVQAGGGIVADSSNPAEAQETVNKAAAPLRAVHTA 503
             +G A +  GGGI ADS    E +E ++KAA  + AV  A
Sbjct: 368 GADGSAVLGVGGGITADSDPDLEWEECLHKAAPIVNAVPVA 408


Lambda     K      H
   0.317    0.133    0.387 

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: 575
Number of extensions: 29
Number of successful extensions: 3
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: 531
Length of database: 420
Length adjustment: 33
Effective length of query: 498
Effective length of database: 387
Effective search space:   192726
Effective search space used:   192726
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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