Alignments for a candidate for tpiA in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for tpiA in Malonomonas rubra DSM 5091

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_072909215.1 BUB13_RS13070 triose-phosphate isomerase

Query= BRENDA::Q6GIL6
         (253 letters)



>NCBI__GCF_900142125.1:WP_072909215.1
          Length = 252

 Score =  243 bits (619), Expect = 4e-69
 Identities = 125/253 (49%), Positives = 169/253 (66%), Gaps = 2/253 (0%)

Query: 1   MRTPIIAGNWKMNKTVQEAKDFVNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQG 60
           MR P+IAGNWK+NKT+ EA++    L     + E   ++ AP     A    + +G A  
Sbjct: 1   MRKPMIAGNWKLNKTIAEARELSGDLAKCLANFEAVDIVVAPVFTSLAAVQEMIKGTA-- 58

Query: 61  LEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFK 120
           +++  QN Y E+ GAFTGE SP+ L D G +YV+IGHSERR+L  E+D  IN+K     +
Sbjct: 59  IKLAGQNCYPEETGAFTGEVSPLMLKDAGCEYVIIGHSERRQLLEESDTFINQKIIKALE 118

Query: 121 HGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIGTGKSS 180
            G+ PI+C+GET +ERE+G   DV+  QVK  +A LS   +  VVIAYEP+WAIGTGK++
Sbjct: 119 AGLKPILCIGETLQERENGDMLDVLANQVKGGLANLSATHMADVVIAYEPVWAIGTGKTA 178

Query: 181 TSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASL 240
           + E A E  +F+R  +  + +KEV+ ATRI YGGSVKP+N+   MAQ DIDGALVGGASL
Sbjct: 179 SDEQAQEAHSFIRGLLQGMFTKEVAFATRILYGGSVKPSNVDGLMAQDDIDGALVGGASL 238

Query: 241 KVEDFVQLLEGAK 253
           K EDF++L+   K
Sbjct: 239 KAEDFIRLVRFEK 251


Lambda     K      H
   0.311    0.129    0.359 

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: 195
Number of extensions: 8
Number of successful extensions: 2
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: 253
Length of database: 252
Length adjustment: 24
Effective length of query: 229
Effective length of database: 228
Effective search space:    52212
Effective search space used:    52212
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 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate WP_072909215.1 BUB13_RS13070 (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.4190788.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      5e-71  225.1   0.4    5.7e-71  225.0   0.4    1.0  1  NCBI__GCF_900142125.1:WP_072909215.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072909215.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0   0.4   5.7e-71   5.7e-71       1     228 []       5     241 ..       5     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 5.7e-71
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           ++ +n+Kln ++ +  ++  +la+ +a+ + v ++vap f  l  v++ ++ + i++a qn+   ++GaftGe
  NCBI__GCF_900142125.1:WP_072909215.1   5 MIAGNWKLNKTIAEARELSGDLAKCLANFEAVDIVVAPVFTSLAAVQEMIKgTAIKLAGQNCYPEETGAFTGE 77 
                                           5899***********************************************99******************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa.a 144
                                           +s  mlkd+G+++v+igHsErR ll+e+d +i++k+ ++ e glk+++C+getl+ere +  ++++a++ +  
  NCBI__GCF_900142125.1:WP_072909215.1  78 VSPLMLKDAGCEYVIIGHSERRQLLEESDTFINQKIIKALEAGLKPILCIGETLQERENGDMLDVLANQVKgG 150
                                           ****************************************************************999886524 PP

                             TIGR00419 145 aA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210
                                            A      + ++v+A+EPv++iGtGk++s  +a++ ++++r  l+   +keva  +r+lyG+sv+ ++   l+
  NCBI__GCF_900142125.1:WP_072909215.1 151 LAnlsathMADVVIAYEPVWAIGTGKTASDEQAQEAHSFIRGLLQGmFTKEVAFATRILYGGSVKPSNVDGLM 223
                                           55677788999*******************************999989************************* PP

                             TIGR00419 211 aqldvdGvLlasavlkae 228
                                           aq d+dG+L+++a+lkae
  NCBI__GCF_900142125.1:WP_072909215.1 224 AQDDIDGALVGGASLKAE 241
                                           ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (252 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: 19.86
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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