GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Pseudomonas stutzeri RCH2

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate GFF3446 Psest_3511 maleylacetoacetate isomerase

Query= reanno::psRCH2:GFF3446
         (219 letters)



>FitnessBrowser__psRCH2:GFF3446
          Length = 219

 Score =  441 bits (1135), Expect = e-129
 Identities = 219/219 (100%), Positives = 219/219 (100%)

Query: 1   MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL 60
           MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL
Sbjct: 1   MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL 60

Query: 61  LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV 120
           LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV
Sbjct: 61  LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV 120

Query: 121 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLETFGDKLSLNDRPGYLEACLVPQVYN 180
           LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLETFGDKLSLNDRPGYLEACLVPQVYN
Sbjct: 121 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLETFGDKLSLNDRPGYLEACLVPQVYN 180

Query: 181 ARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDAQ 219
           ARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDAQ
Sbjct: 181 ARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDAQ 219


Lambda     K      H
   0.321    0.137    0.412 

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: 327
Number of extensions: 7
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: 219
Length of database: 219
Length adjustment: 22
Effective length of query: 197
Effective length of database: 197
Effective search space:    38809
Effective search space used:    38809
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: 45 (21.9 bits)

Align candidate GFF3446 Psest_3511 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))

# 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/TIGR01262.hmm
# target sequence database:        /tmp/gapView.7584.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01262  [M=211]
Accession:   TIGR01262
Description: maiA: maleylacetoacetate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      2e-89  284.8   0.1    2.2e-89  284.7   0.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3446  Psest_3511 maleylacetoacetate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3446  Psest_3511 maleylacetoacetate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.7   0.1   2.2e-89   2.2e-89       1     210 [.       6     218 ..       6     219 .] 0.98

  Alignments for each domain:
  == domain 1  score: 284.7 bits;  conditional E-value: 2.2e-89
                           TIGR01262   1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkide..gevltqSlAiiey 72 
                                         +lY+y+rSsa+yRvRiaL+Lkg++y+ vpv+L+kd G+q++++++alNPq+lvP L++++  g++++qSlAi+ey
  lcl|FitnessBrowser__psRCH2:GFF3446   6 TLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDgGQQRAADYRALNPQQLVPLLVDEGngGARISQSLAILEY 80 
                                         59*********************************9********************99876689*********** PP

                           TIGR01262  73 LeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellk 147
                                         L+e +p paLlp+dp +ra+vr+la++iac+ihPl+Nlrvlq+l+++lgvd+e+k++w++hw+++Glaa+E+ l+
  lcl|FitnessBrowser__psRCH2:GFF3446  81 LDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGLE 155
                                         *************************************************************************** PP

                           TIGR01262 148 ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210
                                         +   + +  d+++  + cLvpqvynA+rf++dla+yP++ +i +++++lpafq+a+pe qpd+
  lcl|FitnessBrowser__psRCH2:GFF3446 156 TFGDKLSLNDRPGYLEACLVPQVYNARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218
                                         **************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (219 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.45
//
[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:

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