GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Desulfuromusa kysingii DSM 7343

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_092344854.1 BLU87_RS03700 tryptophan synthase subunit alpha

Query= uniprot:M4NLA4
         (266 letters)



>NCBI__GCF_900107645.1:WP_092344854.1
          Length = 268

 Score =  240 bits (612), Expect = 3e-68
 Identities = 134/266 (50%), Positives = 169/266 (63%), Gaps = 2/266 (0%)

Query: 1   MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60
           MSRI+  FAAL+    T LIPF+TAGDP  +    ++  LVDAGADLIELGVPFSDPMAD
Sbjct: 1   MSRIEATFAALRQRQETALIPFITAGDPDLKVAAEIILTLVDAGADLIELGVPFSDPMAD 60

Query: 61  GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120
           GP IQ +SERA+A G  L+ VL  VA  R+  A  P++LMGY NP+  +G  RF  +AV 
Sbjct: 61  GPTIQASSERALAAGTTLSGVLQLVAEVRKKTA-VPLILMGYYNPVFCYGVERFVRDAVA 119

Query: 121 AGVDGVLLVDCPLEESAVLQP-LRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179
           AGVDG+LLVD P EE+A + P L ++G+  I L APTT   RM +L   AEG+LYYVS  
Sbjct: 120 AGVDGLLLVDLPPEEAAEISPLLHESGVALITLLAPTTPRERMQRLAAVAEGYLYYVSMT 179

Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239
           G+TG   +S  DI   V D++     PV VGFGI   A A A+  FAD VV+GSALV  +
Sbjct: 180 GVTGGQKISPEDIRLAVDDLKGMTNVPVGVGFGITTVADACAVGTFADGVVVGSALVKII 239

Query: 240 AGATDAGEITRRTQAFLAPIRAALDA 265
                + E+      F+A ++  L A
Sbjct: 240 EKYGKSEELLPEVAKFVAELKGGLTA 265


Lambda     K      H
   0.322    0.136    0.394 

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: 220
Number of extensions: 10
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: 266
Length of database: 268
Length adjustment: 25
Effective length of query: 241
Effective length of database: 243
Effective search space:    58563
Effective search space used:    58563
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: 47 (22.7 bits)

Align candidate WP_092344854.1 BLU87_RS03700 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

# 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.22590.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.2e-87  278.2   0.1    2.4e-87  278.0   0.1    1.0  1  lcl|NCBI__GCF_900107645.1:WP_092344854.1  BLU87_RS03700 tryptophan synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900107645.1:WP_092344854.1  BLU87_RS03700 tryptophan synthase subunit alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.0   0.1   2.4e-87   2.4e-87       1     256 []       8     260 ..       8     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 278.0 bits;  conditional E-value: 2.4e-87
                                 TIGR00262   1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 
                                               f++l++++e+a++pF+tagdPdl++++eii tlv+aGad++ElGvpfsDP+aDGptiqa++ RAl+ag+
  lcl|NCBI__GCF_900107645.1:WP_092344854.1   8 FAALRQRQETALIPFITAGDPDLKVAAEIILTLVDAGADLIELGVPFSDPMADGPTIQASSERALAAGT 76 
                                               789****************************************************************** PP

                                 TIGR00262  70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138
                                               +++ +l+l+++vr+k +++P++l+ yyn++f +gve F++ a +agvdg+l++DlP eea+++    ++
  lcl|NCBI__GCF_900107645.1:WP_092344854.1  77 TLSGVLQLVAEVRKK-TAVPLILMGYYNPVFCYGVERFVRDAVAAGVDGLLLVDLPPEEAAEISPLLHE 144
                                               ***************.***************************************************** PP

                                 TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207
                                                gv+ i l aPt++ er++++a  +eG+ Y vs++Gvtg ++   e+++ ++  +k ++++Pv vGFGi
  lcl|NCBI__GCF_900107645.1:WP_092344854.1 145 SGVALITLLAPTTPRERMQRLAAVAEGYLYYVSMTGVTGGQKISPEDIRLAVDDLKGMTNVPVGVGFGI 213
                                               ********************************************************************* PP

                                 TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkelk 256
                                               +    + ++  + adgv+vGsAlvkiie+  +++e++l e+++fv elk
  lcl|NCBI__GCF_900107645.1:WP_092344854.1 214 TTVADACAVGTF-ADGVVVGSALVKIIEKY-GKSEELLPEVAKFVAELK 260
                                               **9999999888.9**************99.99************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (268 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: 7.97
//
[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