GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Sphingomonas koreensis DSMZ 15582

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Ga0059261_0290 Ga0059261_0290 3-dehydroquinate dehydratase (EC 4.2.1.10)

Query= BRENDA::A0A124C1Y7
         (157 letters)



>FitnessBrowser__Korea:Ga0059261_0290
          Length = 144

 Score =  152 bits (383), Expect = 3e-42
 Identities = 77/141 (54%), Positives = 95/141 (67%), Gaps = 2/141 (1%)

Query: 10  IMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAATHGGTVDFRQSNHEGELVDWIHE 69
           I +LNGPNLNLLG R+PEIYGSDTL D+  +        G T+D RQSNHEG L+DW+HE
Sbjct: 5   IYVLNGPNLNLLGMREPEIYGSDTLDDIAGMLEDRGRELGLTIDMRQSNHEGHLIDWMHE 64

Query: 70  AR-MDHCGIVINPGAYSHTSVAILDALNTCDGLPVIEVHISNIHKREAFRHHSYVSLRAD 128
           A+  D   I++N GAY+HTS+A+ D + +    PVIEVHISN H RE +R HSYV + A 
Sbjct: 65  AQARDAKAILLNSGAYTHTSLALYDCIRSI-RTPVIEVHISNPHAREEYRRHSYVGMAAK 123

Query: 129 GVIAGCGVQGYVFGVERVAAL 149
           G IAG G   YV  +E  A L
Sbjct: 124 GTIAGFGALSYVLALEAAARL 144


Lambda     K      H
   0.321    0.137    0.416 

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: 96
Number of extensions: 4
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: 157
Length of database: 144
Length adjustment: 16
Effective length of query: 141
Effective length of database: 128
Effective search space:    18048
Effective search space used:    18048
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 (21.8 bits)
S2: 42 (20.8 bits)

Align candidate Ga0059261_0290 Ga0059261_0290 (3-dehydroquinate dehydratase (EC 4.2.1.10))
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.2471940.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-57  179.6   0.0    1.4e-57  179.4   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0290  Ga0059261_0290 3-dehydroquinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0290  Ga0059261_0290 3-dehydroquinate dehydratase (EC 4.2.1.10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   0.0   1.4e-57   1.4e-57       2     138 ..       5     142 ..       4     144 .] 0.98

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 1.4e-57
                                 TIGR01088   2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdgi 69 
                                               i vlnGPnlnlLG rep++yGs tl++i  +le+ ++el++ ++++qsn+eg+lid++hea+ + +++i
  lcl|FitnessBrowser__Korea:Ga0059261_0290   5 IYVLNGPNLNLLGMREPEIYGSDTLDDIAGMLEDRGRELGLTIDMRQSNHEGHLIDWMHEAQARdAKAI 73 
                                               88***********************************************************98879*** PP

                                 TIGR01088  70 vinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138
                                               ++n++a+thts+al D + +++ Pv+evh+sn haree+r++s+++ +akG+i G+Ga +y lalea++
  lcl|FitnessBrowser__Korea:Ga0059261_0290  74 LLNSGAYTHTSLALYDCIRSIRTPVIEVHISNPHAREEYRRHSYVGMAAKGTIAGFGALSYVLALEAAA 142
                                               *****************************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (144 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: 11.53
//
[ok]

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