GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Caldicellulosiruptor kronotskyensis 2002

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_013430006.1 CALKRO_RS05120 type II 3-dehydroquinate dehydratase

Query= BRENDA::G8M0G7
         (142 letters)



>NCBI__GCF_000166775.1:WP_013430006.1
          Length = 145

 Score =  193 bits (490), Expect = 1e-54
 Identities = 93/139 (66%), Positives = 111/139 (79%), Gaps = 1/139 (0%)

Query: 1   MKKILIINGPNLNLLGTREKEVYGTETLDDIAKKVAEEAAKLNVNIEFFQSNHEGDIIDK 60
           MKK+L+INGPNLNLLG REK +YG+ + +D+ K ++++A +L   +EFFQSNHEG+IIDK
Sbjct: 1   MKKVLVINGPNLNLLGIREKNIYGSVSYEDVLKSISQKAQELGFEVEFFQSNHEGEIIDK 60

Query: 61  IHAAR-GNTDAIIINPGAYTHYSIAIRDAIKAVEIPTIEIHLSNIHAREEFRSHSVIAPV 119
           IH+A     DAIIINPGAYTHYS AI DAIKAV IP IE+H+SNIHAREEFR  SVIAP 
Sbjct: 61  IHSAYFEKVDAIIINPGAYTHYSYAIHDAIKAVNIPAIEVHISNIHAREEFRRKSVIAPA 120

Query: 120 CVGQICGFGSNSYILGLNA 138
           C GQI GFG  SYI+ L A
Sbjct: 121 CTGQISGFGIKSYIIALYA 139


Lambda     K      H
   0.319    0.137    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: 111
Number of extensions: 5
Number of successful extensions: 2
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: 142
Length of database: 145
Length adjustment: 16
Effective length of query: 126
Effective length of database: 129
Effective search space:    16254
Effective search space used:    16254
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 (21.7 bits)
S2: 42 (20.8 bits)

Align candidate WP_013430006.1 CALKRO_RS05120 (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.3528250.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      9e-67  209.2   0.7      1e-66  209.1   0.7    1.0  1  NCBI__GCF_000166775.1:WP_013430006.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430006.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.1   0.7     1e-66     1e-66       1     140 [.       3     143 ..       3     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 1e-66
                             TIGR01088   1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihea.leqvdgivin 72 
                                           k+lv+nGPnlnlLG re+++yGs+++e++ + ++++a+el+ eve+fqsn+ege+idkih+a +e+vd+i+in
  NCBI__GCF_000166775.1:WP_013430006.1   3 KVLVINGPNLNLLGIREKNIYGSVSYEDVLKSISQKAQELGFEVEFFQSNHEGEIIDKIHSAyFEKVDAIIIN 75 
                                           79**********************************************************984578******* PP

                             TIGR01088  73 paalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealvea 140
                                           p+a+th+s+a+ Da++av++P +evh+sn+hareefr+ksv+a++++G+i+G+G+k+y +al al e+
  NCBI__GCF_000166775.1:WP_013430006.1  76 PGAYTHYSYAIHDAIKAVNIPAIEVHISNIHAREEFRRKSVIAPACTGQISGFGIKSYIIALYALKEI 143
                                           **************************************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (145 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 12.30
//
[ok]

This GapMind analysis is from Jul 26 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