GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sphingopyxis indica DS15

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_089214123.1 CHB69_RS00990 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_900188185.1:WP_089214123.1
          Length = 247

 Score =  202 bits (513), Expect = 7e-57
 Identities = 111/244 (45%), Positives = 145/244 (59%), Gaps = 6/244 (2%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R ++ GNWKMNG   +L E  AI AG  +      +  +C P TL+      LGG     
Sbjct: 4   RKYVVGNWKMNGLSGALAEAEAIFAGARAH--EAVDVALCPPFTLIG-PMAALGGAT--- 57

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           GGQ+CH    G +TG +SA ML +AGA+ VI+GHSERR  + E DA V+AK  AA  AGL
Sbjct: 58  GGQDCHPQPSGAFTGSVSAPMLADAGAALVIVGHSERREGFAERDADVKAKAGAALTAGL 117

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
             ++CVGE L  R+S   +D +  Q++GSLP       + +AYEP+WA+GTG   T  DV
Sbjct: 118 SVILCVGEPLGVRESGGAIDYVLAQVQGSLPGDFDPARLAVAYEPIWAIGTGRVPTIEDV 177

Query: 186 AEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDFL 245
           A +H  I   +  R G+  A +RLLYGGSV   NA +LL    V+GAL+GGASL A  FL
Sbjct: 178 AAMHGAIRAALSDRIGEGAAAVRLLYGGSVNGDNAADLLGARDVDGALVGGASLTAAKFL 237

Query: 246 TICD 249
            I +
Sbjct: 238 PIVE 241


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: 241
Number of extensions: 11
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: 254
Length of database: 247
Length adjustment: 24
Effective length of query: 230
Effective length of database: 223
Effective search space:    51290
Effective search space used:    51290
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: 46 (22.3 bits)

Align candidate WP_089214123.1 CHB69_RS00990 (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.1979331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.1e-45  140.4   0.1    4.9e-45  140.1   0.1    1.0  1  NCBI__GCF_900188185.1:WP_089214123.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188185.1:WP_089214123.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.1   0.1   4.9e-45   4.9e-45       2     227 ..       7     233 ..       6     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 4.9e-45
                             TIGR00419   2 viinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeis 74 
                                           v++n+K+n+  g  ++  a  a   a+ + v va+ ppf  +  ++         + q+++ + sGaftG++s
  NCBI__GCF_900188185.1:WP_089214123.1   7 VVGNWKMNGLSGALAEAEAIFAGARAH-EAVDVALCPPFTLIGPMAALGG---ATGGQDCHPQPSGAFTGSVS 75 
                                           89*******999998877766666665.5689*******99977665544...789***************** PP

                             TIGR00419  75 AemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA. 146
                                           A ml+d+Ga+ v++gHsErR  ++e d  +++k   +   gl +++Cvge l  re++  i+ v+ + +    
  NCBI__GCF_900188185.1:WP_089214123.1  76 APMLADAGAALVIVGHSERREGFAERDADVKAKAGAALTAGLSVILCVGEPLGVRESGGAIDYVLAQVQGSLp 148
                                           ***********************999999***********************************988776655 PP

                             TIGR00419 147 ..lepd..vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldv 215
                                             ++p+   vA+EP+++iGtG++ +  +  ++++ +r  l+    e a  vr+lyG+sv++ ++a+l    dv
  NCBI__GCF_900188185.1:WP_089214123.1 149 gdFDPArlAVAYEPIWAIGTGRVPTIEDVAAMHGAIRAALSDRIGEGAAAVRLLYGGSVNGDNAADLLGARDV 221
                                           78887643699**************************9999999999************************** PP

                             TIGR00419 216 dGvLlasavlka 227
                                           dG+L+++a+l a
  NCBI__GCF_900188185.1:WP_089214123.1 222 DGALVGGASLTA 233
                                           *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (247 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: 20.58
//
[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