GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpD_1 in Pedobacter sp. GW460-11-11-14-LB5

Align Aminodeoxychorismate/anthranilate synthase component II (characterized, see rationale)
to candidate CA265_RS22895 CA265_RS22895 aminodeoxychorismate/anthranilate synthase component II

Query= uniprot:A0A1X9ZDE4_9SPHI
         (198 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS22895 CA265_RS22895
           aminodeoxychorismate/anthranilate synthase component II
          Length = 198

 Score =  409 bits (1051), Expect = e-119
 Identities = 198/198 (100%), Positives = 198/198 (100%)

Query: 1   MEDINKKTVLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYDKILLSPGPGI 60
           MEDINKKTVLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYDKILLSPGPGI
Sbjct: 1   MEDINKKTVLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYDKILLSPGPGI 60

Query: 61  PEEAGLLLDVIRTYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVDGDEP 120
           PEEAGLLLDVIRTYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVDGDEP
Sbjct: 61  PEEAGLLLDVIRTYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVDGDEP 120

Query: 121 LFWECPQTINVGRYHSWVVSKDNFPSCLKITARDHKSEIMALRHETLDVRGVQFHPESVL 180
           LFWECPQTINVGRYHSWVVSKDNFPSCLKITARDHKSEIMALRHETLDVRGVQFHPESVL
Sbjct: 121 LFWECPQTINVGRYHSWVVSKDNFPSCLKITARDHKSEIMALRHETLDVRGVQFHPESVL 180

Query: 181 TEYGKQMMENWLSSSTTV 198
           TEYGKQMMENWLSSSTTV
Sbjct: 181 TEYGKQMMENWLSSSTTV 198


Lambda     K      H
   0.319    0.137    0.420 

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: 254
Number of extensions: 3
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: 198
Length of database: 198
Length adjustment: 20
Effective length of query: 178
Effective length of database: 178
Effective search space:    31684
Effective search space used:    31684
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: 45 (21.9 bits)

Align candidate CA265_RS22895 CA265_RS22895 (aminodeoxychorismate/anthranilate synthase component II)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)

# 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/TIGR00566.hmm
# target sequence database:        /tmp/gapView.27231.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00566  [M=192]
Accession:   TIGR00566
Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    1.8e-58  183.5   0.0    2.1e-58  183.3   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS22895  CA265_RS22895 aminodeoxychorisma


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS22895  CA265_RS22895 aminodeoxychorismate/anthranilate synthase component II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   2.1e-58   2.1e-58       2     191 ..       9     193 ..       8     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 2.1e-58
                                  TIGR00566   2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 
                                                vl+idnydsftynlv+l++e g e  v rnd++ l+++e+    + i++sPGP+ P+ea++  l++i+
  lcl|FitnessBrowser__Pedo557:CA265_RS22895   9 VLVIDNYDSFTYNLVHLINEVGYEAEVWRNDKFDLADVEKYD--K-ILLSPGPGIPEEAGLL-LDVIR 72 
                                                9**************************************864..4.88*************9.***** PP

                                  TIGR00566  70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfn..Pdalkatryhslv 135
                                                 +a    i+GvClG+qa+a +fG+ + ++ + +hG    ++  +    ++lf   P++++++ryhs v
  lcl|FitnessBrowser__Pedo557:CA265_RS22895  73 TYAPTKSIFGVCLGQQAIAEVFGGTLLNLGRPMHGIATPVTVVD--GDEPLFWecPQTINVGRYHSWV 138
                                                *****************************************998..456666556************* PP

                                  TIGR00566 136 veaetldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191
                                                v  ++ +++l++ta ++++ eima+rh+ l++ GvqfhPes+l+e Gk++++n+l 
  lcl|FitnessBrowser__Pedo557:CA265_RS22895 139 VSKDNFPSCLKITARDHKS-EIMALRHETLDVRGVQFHPESVLTEYGKQMMENWLS 193
                                                **************99988.*********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (198 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.37
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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