Alignments for a candidate for tpi in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Sinorhizobium fredii NGR234

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_015887814.1 NGR_RS08355 triose-phosphate isomerase

Query= BRENDA::A0A1D3TX75
         (262 letters)



>NCBI__GCF_000018545.1:WP_015887814.1
          Length = 255

 Score =  206 bits (523), Expect = 5e-58
 Identities = 111/255 (43%), Positives = 158/255 (61%), Gaps = 10/255 (3%)

Query: 5   NKLYLGTNTKMYKTISETTGFIERLQELTKDISRE-KLQLFVLPSYTALESVGKISDPEL 63
           ++L++GT+ KM KT+SE   F + L     D  R+ ++Q FV+P +T +  + +      
Sbjct: 4   SRLWVGTSWKMNKTLSEAIAFADGLA--AADAKRDDRIQRFVIPPFTVVREMKERLKETS 61

Query: 64  IAFGSQNISWDDQGQFTGEVSPIMIKETGASIAMIGHSERRHIFRENDLEENLKIRCSLR 123
           +  G+QN+ W+D G +TGE+SP+M+K+ G  +  +GHSERR  F E D    LK   ++R
Sbjct: 62  VKIGAQNMHWEDAGAWTGEISPLMLKDCGLDLVELGHSERREHFGETDRSVGLKTAAAVR 121

Query: 124 HGFTTLLCIGETEEEKEKNISDEVLKEQLK--IGLYKVAKEQAHGLWIAYEPVWAIGVNG 181
           HG   L+CIGET  E+E   +D VLK Q++    L   A +QA  + +AYEPVWAIGVNG
Sbjct: 122 HGLVPLICIGETLAEREAGEADAVLKRQVEGAFALLDGAAKQA-PILLAYEPVWAIGVNG 180

Query: 182 KPASKQYASEKHKVIKQTLNEIFGEELGEKIPVLYGGSVNNENAEELISMEGIDGLFIGR 241
            PA+  YA  +H    Q + E+    LG  +PVLYGGSVN  N EELI+   +DGLFIGR
Sbjct: 181 IPATADYADARH----QRIAEVAEAALGVAVPVLYGGSVNPGNCEELIAQPHVDGLFIGR 236

Query: 242 SAWDADNFNKIIRKV 256
           SAW+ D +  I+ +V
Sbjct: 237 SAWEVDGYLDILERV 251


Lambda     K      H
   0.315    0.134    0.380 

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: 194
Number of extensions: 9
Number of successful extensions: 4
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: 262
Length of database: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate WP_015887814.1 NGR_RS08355 (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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.3415129.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.5e-45  140.6   0.0    4.4e-45  140.3   0.0    1.0  1  NCBI__GCF_000018545.1:WP_015887814.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_015887814.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.3   0.0   4.4e-45   4.4e-45       2     222 ..       8     236 ..       7     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 4.4e-45
                             TIGR00419   2 viinfKlnesvgkvelevaklae.evaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           v+  +K+n ++++       la+ +    + ++  v ppf  ++ +k++++ + ++++Aqn++  ++Ga+tGe
  NCBI__GCF_000018545.1:WP_015887814.1   8 VGTSWKMNKTLSEAIAFADGLAAaDAKRDDRIQRFVIPPFTVVREMKERLKeTSVKIGAQNMHWEDAGAWTGE 80 
                                           6789*************99**99555566779999**************99899******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145
                                           is  mlkd+G   v +gHsErR ++ e+d  ++ k a +   gl +++C+getl+erea++  ++v++ +   
  NCBI__GCF_000018545.1:WP_015887814.1  81 ISPLMLKDCGLDLVELGHSERREHFGETDRSVGLKTAAAVRHGLVPLICIGETLAEREAGEA-DAVLKRQVEG 152
                                           **********************************************************9876.6666655433 PP

                             TIGR00419 146 A.........lepdvvAvEPveliG.tGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedae 208
                                           A           p ++A+EPv++iG  G+p++   a++ ++ +    + +++ +   v vlyG+sv+ +++ e
  NCBI__GCF_000018545.1:WP_015887814.1 153 AfalldgaakQAPILLAYEPVWAIGvNGIPATADYADARHQRIA---EVAEAALGVAVPVLYGGSVNPGNCEE 222
                                           33377777668899***********56****************9...45666777789*************** PP

                             TIGR00419 209 laaqldvdGvLlas 222
                                           l+aq+ vdG+ ++ 
  NCBI__GCF_000018545.1:WP_015887814.1 223 LIAQPHVDGLFIGR 236
                                           **********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (255 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: 17.26
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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 (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 2024 update 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

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 catabolism of small carbon sources