GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Xanthobacter autotrophicus Py2

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_012112958.1 XAUT_RS04725 4-hydroxy-2-oxovalerate aldolase

Query= metacyc::MONOMER-3404
         (345 letters)



>NCBI__GCF_000017645.1:WP_012112958.1
          Length = 344

 Score =  474 bits (1220), Expect = e-138
 Identities = 233/333 (69%), Positives = 269/333 (80%)

Query: 8   KLYISDVTLRDGSHAIRHQYSIQNVQDIARALDKARVDSIEVTHGDGLQGSSFNYGFGAH 67
           KLYI DVTLRDG HA+RHQY +   + IARALD+ARVD+IE++HGDGL GS+FNYGFGAH
Sbjct: 8   KLYIQDVTLRDGMHALRHQYDLAATRAIARALDRARVDAIEISHGDGLTGSTFNYGFGAH 67

Query: 68  SDLEWIEAAADVIQHARVTVLLVPGIGTVHDLKAAYDAGARSVRVATHCTEADVSRQHIE 127
            D EWI A A+   HA VTVLL+PGIGTVHDLK AY+AGARSVRV THCTEADVSRQHIE
Sbjct: 68  DDAEWIAAVAEECSHAVVTVLLIPGIGTVHDLKHAYEAGARSVRVCTHCTEADVSRQHIE 127

Query: 128 YARELGMDTVGFLMMSHMIPAEQLAAQGKLMETYGAQCIYMADSGGAMNMNDIRDRMRAF 187
            ARELGMDT  FLMM+HMIP E LA Q +LME+YGA+C+Y+ DS GA+   D   R++  
Sbjct: 128 AARELGMDTATFLMMAHMIPPEALAEQARLMESYGAECVYVTDSAGALLPEDYTARVKTL 187

Query: 188 KAVLNPQTQTGMHAHHNLSLGVANSIIAVEEGCDRIDASLAGMGAGAGNAPLEVFIAAAE 247
           +  L P+T+ G+H HHNL+LG+AN++  +E G  R+DASLAGMGAGAGNAPLE  IA   
Sbjct: 188 RDALRPETEIGVHTHHNLTLGIANAVAGIEAGAVRVDASLAGMGAGAGNAPLEALIAVLN 247

Query: 248 RLGWNHGTDLYTLMDAADDIVRPLQDRPVRVDRETLGLGYAGVYSSFLRHAEVAAAKYGL 307
           R G + G DLY LMDAADD+VRPLQDRPVRVDRE+L LGYAGVYSSFLRHAE AA  YG+
Sbjct: 248 RKGIDTGCDLYALMDAADDLVRPLQDRPVRVDRESLSLGYAGVYSSFLRHAENAAQTYGV 307

Query: 308 KTLDILVELGRRRMVGGQEDMIVDVALDLLAAR 340
            T +IL ELGRRRMVGGQEDMIVDVALDL  A+
Sbjct: 308 DTREILSELGRRRMVGGQEDMIVDVALDLAEAK 340


Lambda     K      H
   0.320    0.135    0.389 

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: 467
Number of extensions: 21
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: 345
Length of database: 344
Length adjustment: 29
Effective length of query: 316
Effective length of database: 315
Effective search space:    99540
Effective search space used:    99540
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: 49 (23.5 bits)

Align candidate WP_012112958.1 XAUT_RS04725 (4-hydroxy-2-oxovalerate aldolase)
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))

# 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/TIGR03217.hmm
# target sequence database:        /tmp/gapView.297740.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03217  [M=334]
Accession:   TIGR03217
Description: 4OH_2_O_val_ald: 4-hydroxy-2-oxovalerate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-172  559.8   8.2   1.2e-172  559.6   8.2    1.0  1  NCBI__GCF_000017645.1:WP_012112958.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_012112958.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.6   8.2  1.2e-172  1.2e-172       2     333 ..       8     339 ..       7     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 559.6 bits;  conditional E-value: 1.2e-172
                             TIGR03217   2 kltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaeav 74 
                                           kl+i+dvtLrdG+ha rhq++    raia+aLd+a+vdaie++hGdGL+gs++nyGf+a++d+e+i+a+ae++
  NCBI__GCF_000017645.1:WP_012112958.1   8 KLYIQDVTLRDGMHALRHQYDLAATRAIARALDRARVDAIEISHGDGLTGSTFNYGFGAHDDAEWIAAVAEEC 80 
                                           789********************************************************************** PP

                             TIGR03217  75 kkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspeklae 147
                                            +a v+vll+PGigtv++lk+a++aG+++vrv thcteadvs+qhie+arelg++t +fLmm+hm++pe+lae
  NCBI__GCF_000017645.1:WP_012112958.1  81 SHAVVTVLLIPGIGTVHDLKHAYEAGARSVRVCTHCTEADVSRQHIEAARELGMDTATFLMMAHMIPPEALAE 153
                                           ************************************************************************* PP

                             TIGR03217 148 qakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridas 220
                                           qa+l+esyGa++vyv+dsaGallped ++rvk+l++al+pete+G+h+h+nl+l++an+++ +e+Ga r+das
  NCBI__GCF_000017645.1:WP_012112958.1 154 QARLMESYGAECVYVTDSAGALLPEDYTARVKTLRDALRPETEIGVHTHHNLTLGIANAVAGIEAGAVRVDAS 226
                                           ************************************************************************* PP

                             TIGR03217 221 laglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrhae 293
                                           lag+GagaGnaple+l+avl+r G++tg+dl++l+daa+d+vrPl+drpvrvdre+l+lGyaGvyssflrhae
  NCBI__GCF_000017645.1:WP_012112958.1 227 LAGMGAGAGNAPLEALIAVLNRKGIDTGCDLYALMDAADDLVRPLQDRPVRVDRESLSLGYAGVYSSFLRHAE 299
                                           ************************************************************************* PP

                             TIGR03217 294 raaekygvdardilvelGrrklvgGqedmivdvaldlake 333
                                           +aa+ ygvd+r+il elGrr++vgGqedmivdvaldla++
  NCBI__GCF_000017645.1:WP_012112958.1 300 NAAQTYGVDTREILSELGRRRMVGGQEDMIVDVALDLAEA 339
                                           *************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (344 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: 13.62
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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