GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Magnetospirillum magneticum AMB-1

Align periplasmic dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_043744545.1 AMB_RS13610 type II 3-dehydroquinate dehydratase

Query= metacyc::MONOMER-15328
         (160 letters)



>NCBI__GCF_000009985.1:WP_043744545.1
          Length = 155

 Score =  183 bits (465), Expect = 1e-51
 Identities = 86/143 (60%), Positives = 112/143 (78%)

Query: 15  PLITVLNGPNLNMLGLRQPGIYGHATLDDVEQVCIQAAERLDVAIDFRQTNGEGELVSWV 74
           P+I++LNGPNLNMLG RQP +YG  TL D+E  C   A+ L + ++F QTN EGELV+ +
Sbjct: 8   PIISILNGPNLNMLGTRQPELYGTETLADIEAACRTHADSLGLTVEFSQTNMEGELVTSI 67

Query: 75  QECRGRADGIVINPAAYGHTSIALLDALLAVELPVIEVHISNIHRREPFRHHTYVSQAAI 134
           Q+CRGRA GI+IN  AY HTS+A+LDALLA E+P IEVH+SNIH+R+ FRHH+YV++AA 
Sbjct: 68  QKCRGRAVGIIINAGAYTHTSVAILDALLAAEVPAIEVHLSNIHQRDSFRHHSYVAKAAK 127

Query: 135 GVICGLGVRGYAHALQAITDMIE 157
           G+ICGLG  GY  AL A+  +I+
Sbjct: 128 GMICGLGSHGYILALDALARLIK 150


Lambda     K      H
   0.322    0.139    0.414 

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: 117
Number of extensions: 4
Number of successful extensions: 1
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: 160
Length of database: 155
Length adjustment: 17
Effective length of query: 143
Effective length of database: 138
Effective search space:    19734
Effective search space used:    19734
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: 43 (21.2 bits)

Align candidate WP_043744545.1 AMB_RS13610 (type II 3-dehydroquinate dehydratase)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01088.hmm
# target sequence database:        /tmp/gapView.14228.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01088  [M=141]
Accession:   TIGR01088
Description: aroQ: 3-dehydroquinate dehydratase, type II
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.5e-61  190.4   0.2    6.3e-61  190.3   0.2    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043744545.1  AMB_RS13610 type II 3-dehydroqui


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043744545.1  AMB_RS13610 type II 3-dehydroquinate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.2   6.3e-61   6.3e-61       2     139 ..      10     147 ..       9     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 6.3e-61
                                 TIGR01088   2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgiv 70 
                                               i +lnGPnln+LG+r+p++yG+ tl +ie+ ++++a +l++ ve+ q+n+egel++ i+++ +++ gi+
  lcl|NCBI__GCF_000009985.1:WP_043744545.1  10 ISILNGPNLNMLGTRQPELYGTETLADIEAACRTHADSLGLTVEFSQTNMEGELVTSIQKCRGRAVGII 78 
                                               789****************************************************************** PP

                                 TIGR01088  71 inpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealve 139
                                               in++a+thtsva+ Dal+a+++P +evhlsn+h+r++fr++s++a++akG+i+GlG +gy lal al++
  lcl|NCBI__GCF_000009985.1:WP_043744545.1  79 INAGAYTHTSVAILDALLAAEVPAIEVHLSNIHQRDSFRHHSYVAKAAKGMICGLGSHGYILALDALAR 147
                                               ****************************************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (155 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.68
//
[ok]

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

Links

Downloads

Related tools

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