Aligments for a candidate for aroG in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Aligments for a candidate for aroG in Bacteroides thetaiotaomicron VPI-5482

Align 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (characterized, see rationale)
to candidate 353460 BT3934 putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCBI ptt file)

Query= uniprot:L0FSZ3_ECHVK
         (367 letters)



>FitnessBrowser__Btheta:353460
          Length = 353

 Score =  343 bits (881), Expect = 3e-99
 Identities = 171/344 (49%), Positives = 238/344 (69%), Gaps = 7/344 (2%)

Query: 11  GLGLKGHVIIAGPCSAETPEQVEKVCLEMKEQNIIPSMFRAGIWKPRTRPGSFEGIGEDG 70
           G+  K  ++IAGPCSAET EQV +   ++  +     ++RAGIWKPRT+PG FEGIG +G
Sbjct: 10  GIEAKRPIVIAGPCSAETEEQVMETAKQLAAKG--QKIYRAGIWKPRTKPGGFEGIGVEG 67

Query: 71  LKWMEIVRHHLNIPITTEVGNTAHVELALKHKVDVLWIGARTTVNPFAVQEIAEALKGTD 130
           L W++ V+    + ++TEV    HV   LK  +D+LW+GARTT NPFAVQEIA+ALKG D
Sbjct: 68  LAWLKEVKKETGMYVSTEVATAKHVYECLKAGIDILWVGARTTANPFAVQEIADALKGVD 127

Query: 131 IPVMVKNPMNPDLQLWIGALERLHAVGINKLAAIHRGFSDAYDKR-FRNKPNWSMPIHLK 189
           IPV+VKNP+NPDL+LWIGALER+H  G+ +L AIHRGFS +YDK+ +RN P W +PI L+
Sbjct: 128 IPVLVKNPVNPDLELWIGALERIHNAGLKRLGAIHRGFS-SYDKKIYRNLPQWHIPIELR 186

Query: 190 REWKGMEVINDPSHIVGKRDGILEISQRAINFGLDGLMIETHHDPDNAWSDAKQQVTPAQ 249
           R    + +  DPSHI GKR+ +  + Q+A++   DGL++E+H +PD AWSDA QQVTP  
Sbjct: 187 RRLPNLPIFCDPSHIGGKRELVAPLCQQAMDLNFDGLIVESHCNPDCAWSDASQQVTPDV 246

Query: 250 LKDILSKIDFKTPLDSEKPSEKLHDLRSAIDHMDDQLIDLLAERFAVIDQIGAHKREHKL 309
           L  IL+ +  +T     + +E L  LR  ID  DD +I  LA+R  V  +IG +K+EH +
Sbjct: 247 LDYILNLLVIRT---ETQTTESLSQLRKQIDECDDNIIQELAKRMRVAREIGTYKKEHGI 303

Query: 310 TVFQSDRWKEVMDSRTDKGVKKGLSEKFMKELLFSIHEESVKRQ 353
           TV Q+ R+ E+++ R  +G + G+S  FMK +  +IHEESV++Q
Sbjct: 304 TVLQAGRYNEILEKRGAQGEQCGMSADFMKLIFEAIHEESVRQQ 347


Lambda     K      H
   0.318    0.135    0.409 

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: 406
Number of extensions: 18
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: 367
Length of database: 353
Length adjustment: 29
Effective length of query: 338
Effective length of database: 324
Effective search space:   109512
Effective search space used:   109512
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 (21.7 bits)
S2: 49 (23.5 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis