GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Burkholderia phytofirmans PsJN

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate BPHYT_RS19370 BPHYT_RS19370 arogenate dehydratase

Query= BRENDA::Q01269
         (268 letters)



>FitnessBrowser__BFirm:BPHYT_RS19370
          Length = 265

 Score =  257 bits (657), Expect = 2e-73
 Identities = 124/241 (51%), Positives = 169/241 (70%), Gaps = 2/241 (0%)

Query: 20  SASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESLGAKLV 79
           +++  A  SRLD IL  G LR  TTGDYKP+S+   +G + G D+DM + LA+SLG K  
Sbjct: 26  TSATTATPSRLDEILARGTLRACTTGDYKPYSFYKADGQFEGIDIDMTESLAKSLGVKTE 85

Query: 80  VVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQT 139
            + TSW NLM DF   + D+ + G+S  LERQ++A+F+  Y+ DGKTPI  C +  ++QT
Sbjct: 86  YIKTSWSNLMNDFVA-KCDVGVGGVSPTLERQKRAFFTQAYMVDGKTPIVRCDDVNKYQT 144

Query: 140 LEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDAIEA 199
           + QIDQP    IVNPGGTNE+FA+     A + V+PDNVTIF+QI+ GKAD+M+TDA E 
Sbjct: 145 VAQIDQPATRVIVNPGGTNERFAKQYFPHANLTVYPDNVTIFKQILAGKADVMVTDASET 204

Query: 200 RLQSRLHPELCAVHPQQPFDFAEKAYLLPR-DEAFKRYVDQWLHIAEQSGLLRQRMEHWL 258
            LQ +L+P LC+VHP +PF + EKA+LLPR D AF++YVDQWLH+A  +G  +   + WL
Sbjct: 205 LLQQKLNPGLCSVHPDKPFQYGEKAWLLPRGDVAFQQYVDQWLHLARATGEYQAISDKWL 264

Query: 259 E 259
           +
Sbjct: 265 K 265


Lambda     K      H
   0.322    0.135    0.406 

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: 219
Number of extensions: 12
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: 268
Length of database: 265
Length adjustment: 25
Effective length of query: 243
Effective length of database: 240
Effective search space:    58320
Effective search space used:    58320
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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