Alignments for a candidate for tpiA in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for tpiA in Pyrolobus fumarii 1A

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_014026435.1 PYRFU_RS04420 triose-phosphate isomerase

Query= BRENDA::P62002
         (228 letters)



>NCBI__GCF_000223395.1:WP_014026435.1
          Length = 230

 Score =  225 bits (574), Expect = 5e-64
 Identities = 115/221 (52%), Positives = 160/221 (72%), Gaps = 3/221 (1%)

Query: 8   IIAINFKTYIEATGKRALEIAKAAEKVYKETG--VTIVVAPQLVDLRMIAESVE-IPVFA 64
           I+A+NFK Y  A G+RALE+ KAAE+V +E    V++++AP   ++  I+ SVE + V+A
Sbjct: 6   ILAVNFKVYPSAFGRRALEVVKAAERVAREFEGTVSVIIAPPHTEIARISSSVERVIVYA 65

Query: 65  QHIDPIKPGSHTGHVLPEAVKEAGAVGTLLNHSENRMILADLEAAIRRAEEVGLMTMVCS 124
           QH+DP++PG+HTG V  EAVKEAGA G+L+NHSE ++ L ++E  + R + VGL  +VC+
Sbjct: 66  QHVDPVEPGAHTGSVPVEAVKEAGARGSLVNHSERKLRLDEIERVVERLKVVGLEQLVCA 125

Query: 125 NNPAVSAAVAALNPDYVAVEPPELIGTGIPVSKAKPEVITNTVELVKKVNPEVKVLCGAG 184
           + P  +AA+A   P YVAVEPPELIGTGI VS+AKPEV+T  VE V +V+P V VL GAG
Sbjct: 126 DTPRAAAAIAVFEPTYVAVEPPELIGTGIAVSRAKPEVVTKAVESVTRVSPNVPVLVGAG 185

Query: 185 ISTGEDVKKAIELGTVGVLLASGVTKAKDPEKAIWDLVSGI 225
           I + ED ++++ELG  GVL+AS V KA DP   + +L  G+
Sbjct: 186 IVSREDARRSVELGARGVLVASAVMKAADPYAKMRELAEGL 226


Lambda     K      H
   0.314    0.132    0.362 

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: 190
Number of extensions: 9
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: 228
Length of database: 230
Length adjustment: 23
Effective length of query: 205
Effective length of database: 207
Effective search space:    42435
Effective search space used:    42435
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate WP_014026435.1 PYRFU_RS04420 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.8920.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.5e-56  175.5   5.5    1.3e-55  174.7   5.5    1.3  1  lcl|NCBI__GCF_000223395.1:WP_014026435.1  PYRFU_RS04420 triose-phosphate i


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_014026435.1  PYRFU_RS04420 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   5.5   1.3e-55   1.3e-55       2     227 ..       7     212 ..       6     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 1.3e-55
                                 TIGR00419   2 viinfK.lnesvgkvelevaklaeevasea..gvevavappfvdldvvkdeveseiqvaAqnvdavksG 67 
                                               + +nfK +  ++g+++lev k ae va e    v+v +app+  + +++  ve ++ v+Aq+vd v++G
  lcl|NCBI__GCF_000223395.1:WP_014026435.1   7 LAVNFKvYPSAFGRRALEVVKAAERVAREFegTVSVIIAPPHTEIARISSSVE-RVIVYAQHVDPVEPG 74 
                                               679***9********************97522688999***************.999************ PP

                                 TIGR00419  68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136
                                               a+tG++  e++k++Ga+g+l++HsEr+  l++ +  ie +v rlk  gl+ +vC              +
  lcl|NCBI__GCF_000223395.1:WP_014026435.1  75 AHTGSVPVEAVKEAGARGSLVNHSERK--LRLDE--IERVVERLKVVGLEQLVCA-------------D 126
                                               ***************************..99999..*******************.............4 PP

                                 TIGR00419 137 nvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaae 205
                                               +    aa+a +ep +vAvEP+eliGtG++vs+A++evv+k v+      +  v+++v vl+Ga++ + e
  lcl|NCBI__GCF_000223395.1:WP_014026435.1 127 TPRAAAAIAVFEPTYVAVEPPELIGTGIAVSRAKPEVVTKAVE-----SVTRVSPNVPVLVGAGIVSRE 190
                                               4444455555*********************************.....9999***************** PP

                                 TIGR00419 206 daelaaqldvdGvLlasavlka 227
                                               da+  ++l++ GvL+asav+ka
  lcl|NCBI__GCF_000223395.1:WP_014026435.1 191 DARRSVELGARGVLVASAVMKA 212
                                               *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (230 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 2.59
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis