GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Pseudomonas putida KT2440

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate PP_0560 PP_0560 3-dehydroquinate dehydratase 1, type II

Query= BRENDA::O30557
         (147 letters)



>FitnessBrowser__Putida:PP_0560
          Length = 151

 Score =  270 bits (690), Expect = 7e-78
 Identities = 134/144 (93%), Positives = 140/144 (97%)

Query: 1   MATLLVLHGPNLNLLGTREPGTYGSTTLGQINQDLERRAREAGHHLLHLQSNAEYELIDR 60
           MATLLVLHGPNLNLLGTREPG YG+ TL QINQDLE+RAR AGHHLL+LQSNAEYELIDR
Sbjct: 1   MATLLVLHGPNLNLLGTREPGHYGAVTLAQINQDLEQRARAAGHHLLYLQSNAEYELIDR 60

Query: 61  IHAARDEGVDFIIINPAAFTHTSVALRDALLAVSIPFIEVHLSNVHKREPFRHHSYFSDV 120
           IHAAR+EGVDFI+INPAAFTHTSVALRDALLAVSIPFIEVHLSNVHKREPFRHHSYFSDV
Sbjct: 61  IHAARNEGVDFILINPAAFTHTSVALRDALLAVSIPFIEVHLSNVHKREPFRHHSYFSDV 120

Query: 121 AVGVICGLGATGYRLALESALEQL 144
           AVGVICGLGA+GYRLALESALEQL
Sbjct: 121 AVGVICGLGASGYRLALESALEQL 144


Lambda     K      H
   0.322    0.138    0.402 

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: 141
Number of extensions: 1
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: 147
Length of database: 151
Length adjustment: 16
Effective length of query: 131
Effective length of database: 135
Effective search space:    17685
Effective search space used:    17685
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: 42 (20.8 bits)

Align candidate PP_0560 PP_0560 (3-dehydroquinate dehydratase 1, type II)
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.2471334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    8.6e-65  202.8   0.1    9.8e-65  202.6   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_0560  PP_0560 3-dehydroquinate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0560  PP_0560 3-dehydroquinate dehydratase 1, type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.6   0.1   9.8e-65   9.8e-65       2     140 ..       4     143 ..       3     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 9.8e-65
                           TIGR01088   2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdgivinpaa 75 
                                         +lvl+GPnlnlLG+rep++yG++tl +i++ le+ a++++ ++ ++qsn e+elid+ih a ++ vd+i+inpaa
  lcl|FitnessBrowser__Putida:PP_0560   4 LLVLHGPNLNLLGTREPGHYGAVTLAQINQDLEQRARAAGHHLLYLQSNAEYELIDRIHAARNEgVDFILINPAA 78 
                                         79***********************************************************9999********** PP

                           TIGR01088  76 lthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealvea 140
                                         +thtsvalrDal+avs+P++evhlsnvh+re+fr++s++++va Gvi+GlGa+gy+lale ++e+
  lcl|FitnessBrowser__Putida:PP_0560  79 FTHTSVALRDALLAVSIPFIEVHLSNVHKREPFRHHSYFSDVAVGVICGLGASGYRLALESALEQ 143
                                         ***********************************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (151 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: 12.11
//
[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