GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sinorhizobium fredii NGR234

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012707834.1 NGR_RS17645 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000018545.1:WP_012707834.1
          Length = 256

 Score =  297 bits (761), Expect = 1e-85
 Identities = 149/254 (58%), Positives = 186/254 (73%)

Query: 1   MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60
           M+P+IRP +AGNWKMNGT  SL +++A+A G+   L    E LIC PATLL  A  +   
Sbjct: 1   MTPDIRPLVAGNWKMNGTRASLDQIKAMAEGVKGALSAKVETLICPPATLLYVATALCDD 60

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

Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180
             A LVA++C+GET EERKS K LDVL RQL  SLPD ATAEN +IAYEPVWA+GTG T 
Sbjct: 121 HAAALVAIVCIGETEEERKSGKTLDVLKRQLAESLPDAATAENTVIAYEPVWAIGTGLTP 180

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

Query: 241 AIDFLTICDVYRKL 254
           A DFL I   Y +L
Sbjct: 241 AEDFLAIYGAYEEL 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: 243
Number of extensions: 9
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 WP_012707834.1 NGR_RS17645 (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.2539757.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-55  174.2   1.5    2.1e-55  174.1   1.5    1.0  1  NCBI__GCF_000018545.1:WP_012707834.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012707834.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   1.5   2.1e-55   2.1e-55       1     228 []       8     242 ..       8     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 2.1e-55
                             TIGR00419   1 lviinfKlnesvgkvelevaklae.evaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 
                                           lv +n+K+n+++ + +++ a  +  + a +a+ve  + pp   l v++   + s ++++Aq+++ ++sGa+tG
  NCBI__GCF_000018545.1:WP_012707834.1   8 LVAGNWKMNGTRASLDQIKAMAEGvKGALSAKVETLICPPATLLYVATALCDdSPLMIGAQDCHQKQSGAHTG 80 
                                           799*********999876554444556778999999*****99999998888899****************** PP

                             TIGR00419  72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa. 143
                                           eisAem++d+   +v++gHsErR+ ++e+d l+ +k   +++  l ++vC+get+eer++++t+++++++ a 
  NCBI__GCF_000018545.1:WP_012707834.1  81 EISAEMIADCFGTHVIVGHSERRTDHAETDALVRAKTEAAHAAALVAIVCIGETEEERKSGKTLDVLKRQLAe 153
                                           *****************************************************************99988653 PP

                             TIGR00419 144 ....aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaq 212
                                               aa  e+ v+A+EPv++iGtG + +  + e+ ++++r  l         ++r+lyG+sv+ ++++el+  
  NCBI__GCF_000018545.1:WP_012707834.1 154 slpdAATAENTVIAYEPVWAIGTGLTPTVGDVEEAHAFMRRELVSRFGSEGGKMRILYGGSVKPSNATELMGV 226
                                           33336779********************************87777666667889******************* PP

                             TIGR00419 213 ldvdGvLlasavlkae 228
                                            +vdG+L+++a+lkae
  NCBI__GCF_000018545.1:WP_012707834.1 227 ANVDGALIGGASLKAE 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: 18.03
//
[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:

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