GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Sinorhizobium meliloti 1021

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate SMc01023 SMc01023 triosephosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>lcl|FitnessBrowser__Smeli:SMc01023 SMc01023 triosephosphate
           isomerase
          Length = 256

 Score =  295 bits (754), Expect = 8e-85
 Identities = 147/254 (57%), Positives = 188/254 (74%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M+P+IRP +AGNWKMNGT  SL +++A+A G+  DL    +ALIC PATLL  A  +   
Sbjct: 1   MTPDIRPLVAGNWKMNGTRASLDQIKAMAEGVKGDLSARVDALICPPATLLYVATALCDD 60

Query: 61  ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120
             +++G Q+CH    G +TG++SA M+ +   +HVI+GHSERRT + E DA+VRAK +AA
Sbjct: 61  SPLMIGAQDCHQKQSGAHTGEVSAEMVADCFGTHVIVGHSERRTDHGEGDALVRAKTEAA 120

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
             A LVA++CVGET EERK+ + LD+L RQL  SLPD ATAEN +IAYEPVWA+GTG T 
Sbjct: 121 HGADLVAIVCVGETEEERKAGRTLDILKRQLSESLPDQATAENTVIAYEPVWAIGTGLTP 180

Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240
           T +DV E HAF+  ++ SRFG EG K+R+LYGGSVKPSNA EL+  A+V+GALIGGASLK
Sbjct: 181 TVSDVEEAHAFMRRELVSRFGAEGGKMRILYGGSVKPSNAKELMGVANVDGALIGGASLK 240

Query: 241 AIDFLTICDVYRKL 254
           A DFL I   Y +L
Sbjct: 241 ADDFLAIYRAYEEL 254


Lambda     K      H
   0.320    0.137    0.403 

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: 252
Number of extensions: 12
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: 254
Length of database: 256
Length adjustment: 24
Effective length of query: 230
Effective length of database: 232
Effective search space:    53360
Effective search space used:    53360
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate SMc01023 SMc01023 (triosephosphate 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.20094.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    9.4e-54  168.6   0.4    1.1e-53  168.4   0.4    1.0  1  lcl|FitnessBrowser__Smeli:SMc01023  SMc01023 triosephosphate isomera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01023  SMc01023 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   0.4   1.1e-53   1.1e-53       1     228 []       8     242 ..       8     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 1.1e-53
                           TIGR00419   1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                         lv +n+K+n+++ + ++ +  +ae v +   a v   + pp   l v++   + s ++++Aq+++ ++sGa+tGe
  lcl|FitnessBrowser__Smeli:SMc01023   8 LVAGNWKMNGTRASLDQ-IKAMAEGVKGDlsARVDALICPPATLLYVATALCDdSPLMIGAQDCHQKQSGAHTGE 81 
                                         799*******9998775.55666666664114566679999988888888877789******************* PP

                           TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA. 146
                                         +sAem++d+   +v++gHsErR+ + e d l+ +k   ++  +l ++vCvget+eer+a+rt++ ++++ +    
  lcl|FitnessBrowser__Smeli:SMc01023  82 VSAEMVADCFGTHVIVGHSERRTDHGEGDALVRAKTEAAHGADLVAIVCVGETEEERKAGRTLDILKRQLSESLp 156
                                         ****************************************************************99888653223 PP

                           TIGR00419 147 ....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdG 217
                                              e+ v+A+EPv++iGtG + +  + e+ ++++r  l         ++r+lyG+sv+ ++++el+   +vdG
  lcl|FitnessBrowser__Smeli:SMc01023 157 dqatAENTVIAYEPVWAIGTGLTPTVSDVEEAHAFMRRELVSRFGAEGGKMRILYGGSVKPSNAKELMGVANVDG 231
                                         33349********************************77666444446689************************ PP

                           TIGR00419 218 vLlasavlkae 228
                                         +L+++a+lka+
  lcl|FitnessBrowser__Smeli:SMc01023 232 ALIGGASLKAD 242
                                         *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (256 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: 9.79
//
[ok]

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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