GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Mycolicibacterium vanbaalenii PYR-1

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_011779024.1 MVAN_RS08980 type II 3-dehydroquinate dehydratase

Query= BRENDA::N1V364
         (155 letters)



>NCBI__GCF_000015305.1:WP_011779024.1
          Length = 147

 Score =  185 bits (470), Expect = 2e-52
 Identities = 90/142 (63%), Positives = 108/142 (76%)

Query: 14  RKLLVLNGPNLNLLGTREPQIYGSDTLEDAETLAARAAEAHGLAVECLQSNHEGVLIDAI 73
           R+LL++NGPNLNLLGTR+P++YG+ TL + E   A  A   GL V  +QSNHEGVL+DAI
Sbjct: 4   RRLLLVNGPNLNLLGTRQPEVYGATTLAEIEARVAEVAAEAGLQVRSVQSNHEGVLVDAI 63

Query: 74  HAARGTAAGIVINPGGYTHTSVALRDALSGVDLPVVEVHISNIHRREEFRHHSYISGIAV 133
           HAAR   AGI+INP  Y+HTSVA+ DAL  V LPV EVH+SNIH REEFRHHSY+S +A 
Sbjct: 64  HAARTDCAGIIINPAAYSHTSVAIADALRSVGLPVAEVHLSNIHAREEFRHHSYVSAVAD 123

Query: 134 AVIAGAGISGYKFAVDLLASRL 155
            V+AGAG  GY+ AV  LA RL
Sbjct: 124 MVVAGAGPLGYEMAVRFLADRL 145


Lambda     K      H
   0.317    0.133    0.375 

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: 68
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: 155
Length of database: 147
Length adjustment: 16
Effective length of query: 139
Effective length of database: 131
Effective search space:    18209
Effective search space used:    18209
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 (21.6 bits)
S2: 43 (21.2 bits)

Align candidate WP_011779024.1 MVAN_RS08980 (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.1000.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.2e-60  186.6   0.3    9.2e-60  186.5   0.3    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779024.1  MVAN_RS08980 type II 3-dehydroqu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779024.1  MVAN_RS08980 type II 3-dehydroquinate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.5   0.3   9.2e-60   9.2e-60       2     140 ..       6     144 ..       5     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 9.2e-60
                                 TIGR01088   2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgiv 70 
                                               +l++nGPnlnlLG+r+p+vyG++tl eie+ + e a+e++++v  +qsn+eg l+d+ih a  +  gi+
  lcl|NCBI__GCF_000015305.1:WP_011779024.1   6 LLLVNGPNLNLLGTRQPEVYGATTLAEIEARVAEVAAEAGLQVRSVQSNHEGVLVDAIHAARTDCAGII 74 
                                               799****************************************************************** PP

                                 TIGR01088  71 inpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealve 139
                                               inpaa++htsva++Dal +v lPv evhlsn+hareefr++s++++va+ v+ G G+ gy++a+++l++
  lcl|NCBI__GCF_000015305.1:WP_011779024.1  75 INPAAYSHTSVAIADALRSVGLPVAEVHLSNIHAREEFRHHSYVSAVADMVVAGAGPLGYEMAVRFLAD 143
                                               ******************************************************************987 PP

                                 TIGR01088 140 a 140
                                                
  lcl|NCBI__GCF_000015305.1:WP_011779024.1 144 R 144
                                               5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (147 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: 5.00
//
[ok]

This GapMind analysis is from Apr 10 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