GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Methanobacterium veterum MK4

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_048080437.1 EJ01_RS03090 triose-phosphate isomerase

Query= SwissProt::O74025
         (226 letters)



>NCBI__GCF_000745485.1:WP_048080437.1
          Length = 226

 Score =  426 bits (1094), Expect = e-124
 Identities = 221/226 (97%), Positives = 222/226 (98%)

Query: 1   MNEIKETPIVILNFKTYLESTGENALKLAKGSEMVAEETGVNIMVHPQYADIYRIAHEVN 60
           MNEIKETPIVILNFKTYLESTGENALKLAK SEMVAEETGVNIMV PQYADIYRIA EVN
Sbjct: 1   MNEIKETPIVILNFKTYLESTGENALKLAKSSEMVAEETGVNIMVAPQYADIYRIAREVN 60

Query: 61  IPVLAQHIDTIDAGGHTGSILPECVKEAGAVGTLINHSERRVELFEIDAAIKKADSLGLS 120
           IPVLAQHIDTIDAGGHTGSILPECVKEAGAVGTLINHSERRVELFEIDAAIKKADSLGLS
Sbjct: 61  IPVLAQHIDTIDAGGHTGSILPECVKEAGAVGTLINHSERRVELFEIDAAIKKADSLGLS 120

Query: 121 TVVCTNNIETSSAAATLNPDFVAIEPPELIGSGIPVSKPEPEIVEKTVESIHNINPEVRV 180
           TVVCTNNIETSSAAATLNP+FVAIEPPELIGSGIPVSK EPEIVEKTVESIHNINPEVRV
Sbjct: 121 TVVCTNNIETSSAAATLNPNFVAIEPPELIGSGIPVSKAEPEIVEKTVESIHNINPEVRV 180

Query: 181 LCGAGISTGDDLKAAIDLGSEGVLLASGIILADDPKKALLDLVSKI 226
           LCGAGISTGDDLKAAIDLGSEGVLLASGIILADDPKKALLDLVSKI
Sbjct: 181 LCGAGISTGDDLKAAIDLGSEGVLLASGIILADDPKKALLDLVSKI 226


Lambda     K      H
   0.313    0.133    0.368 

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: 303
Number of extensions: 8
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: 226
Length of database: 226
Length adjustment: 22
Effective length of query: 204
Effective length of database: 204
Effective search space:    41616
Effective search space used:    41616
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_048080437.1 EJ01_RS03090 (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.2006679.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.7e-72  229.9   2.5      2e-72  229.7   2.5    1.0  1  NCBI__GCF_000745485.1:WP_048080437.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745485.1:WP_048080437.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.7   2.5     2e-72     2e-72       1     228 []       9     213 ..       9     213 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 2e-72
                             TIGR00419   1 lviinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGe 72 
                                           +vi+nfK + es+g+ +l +ak +e va+e+gv++ vap++ d+ ++++ev+  i+v+Aq++d++++G++tG+
  NCBI__GCF_000745485.1:WP_048080437.1   9 IVILNFKtYLESTGENALKLAKSSEMVAEETGVNIMVAPQYADIYRIAREVN--IPVLAQHIDTIDAGGHTGS 79 
                                           79**************************************************..******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145
                                           i+ e++k++Ga g+li+HsErR  +++ +  i++ + ++  lgl +vvC+             nn+ t+ aaa
  NCBI__GCF_000745485.1:WP_048080437.1  80 ILPECVKEAGAVGTLINHSERR--VELFE--IDAAIKKADSLGLSTVVCT-------------NNIETSSAAA 135
                                           **********************..88888..99*****************.............********** PP

                             TIGR00419 146 AlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGv 218
                                            l+p++vA+EP+eliG+G+pvskAe+e vek+v+       ++++++vrvl+Ga++++++d ++a++l+ +Gv
  NCBI__GCF_000745485.1:WP_048080437.1 136 TLNPNFVAIEPPELIGSGIPVSKAEPEIVEKTVE-----SIHNINPEVRVLCGAGISTGDDLKAAIDLGSEGV 203
                                           **********************************.....999******************************* PP

                             TIGR00419 219 Llasavlkae 228
                                           Llas+++ a+
  NCBI__GCF_000745485.1:WP_048080437.1 204 LLASGIILAD 213
                                           *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (226 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: 11.76
//
[ok]

This GapMind analysis is from Sep 24 2021. 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:

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