GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydratase in Thiohalomonas denitrificans HLD2

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_092991511.1 BLP65_RS00430 prephenate dehydratase

Query= BRENDA::O22241
         (424 letters)



>NCBI__GCF_900102855.1:WP_092991511.1
          Length = 360

 Score =  150 bits (378), Expect = 8e-41
 Identities = 104/291 (35%), Positives = 151/291 (51%), Gaps = 30/291 (10%)

Query: 125 LRVAYQGVPGAYSEAAAGKAYPNC-DAIPCDQFDVAFQAVELWIADRAVLPVENSLGGSI 183
           + +A+ G  G +S+ A  K + +     P    D  F+ VE   AD  V+PVENS  G++
Sbjct: 91  MTIAFLGPEGTFSQEAVLKHFGHAIKGAPQAAIDEVFREVEAGSADYGVVPVENSTEGAV 150

Query: 184 HRNYDLLLRHRLHIVGEVQIPVHHCLL----ALPGVRTDCVSRVISHPQALAQTEHSLDV 239
           +   DLLLR  L I GEV++ +H  L+    +L G+RT     + SH Q+ AQ    LD 
Sbjct: 151 NITLDLLLRTSLKICGEVELRIHDHLMSRERSLEGIRT-----IYSHAQSFAQCREWLDS 205

Query: 240 LTPHAAREAFHDTAAAAEYISANDLHDTAAVASARAAELYNLQILADGIQDDPGNVTRFL 299
             P+  R A    + AA   +A   +  AAVA A AAEL+ L  LA+ I+D P N TRFL
Sbjct: 206 HLPNVRRVAVSSNSEAARMAAAE--NGAAAVAGATAAELFGLNRLAENIEDIPDNTTRFL 263

Query: 300 MLAREPIIPRTDRPFKTSIVFAAQEHKGTSVLFKVLSAFAFRDISLTKIESRPHHNRPLR 359
           +L RE   P  +   KTS++ +++   G   LF++L   A   +S+T+IESRP       
Sbjct: 264 ILGREDTPPSGED--KTSLLVSSRNESG--ALFQLLKPLADNGVSMTRIESRP------- 312

Query: 360 VVGDGSFGTSKNFEYMFYVDFEASMAEPRAQNALAEVQEYTSFLRVLGSYP 410
                       +EY+F+VD E     P   +AL E++   S  +VLGS+P
Sbjct: 313 -------SRQGMWEYVFFVDLEGHREMPAVASALVELERNASLFKVLGSFP 356


Lambda     K      H
   0.318    0.131    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: 316
Number of extensions: 17
Number of successful extensions: 4
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: 424
Length of database: 360
Length adjustment: 31
Effective length of query: 393
Effective length of database: 329
Effective search space:   129297
Effective search space used:   129297
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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