GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Burkholderia phytofirmans PsJN

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate BPHYT_RS02805 BPHYT_RS02805 maleylacetoacetate isomerase

Query= reanno::MR1:200836
         (216 letters)



>FitnessBrowser__BFirm:BPHYT_RS02805
          Length = 214

 Score =  238 bits (608), Expect = 5e-68
 Identities = 124/218 (56%), Positives = 153/218 (70%), Gaps = 8/218 (3%)

Query: 1   MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60
           M LY Y+RSSA+YRVRIALN+K +  + + VHLVRDGGEQ K +Y  +N   +VPT V  
Sbjct: 1   MKLYSYFRSSASYRVRIALNVKNLPYDYVPVHLVRDGGEQLKPEYRKVNADGIVPTFV-- 58

Query: 61  DEQDG-DALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQ 119
              DG D + QSLAIIEYL+E++P+  LLP +  +RA+VRA+AL +ACEIHPLNNLRVL+
Sbjct: 59  ---DGNDVMPQSLAIIEYLEEVHPEPALLPKAPADRAYVRALALQVACEIHPLNNLRVLK 115

Query: 120 YLTQKLTVNEEAKSAWYHHWVATGFTALETQLV--RHSGRYCFGDKVTIADLCLVPQVYN 177
           YL   L V++ AK AWY HWV  GF   ET L     +G+ CFGD  TIAD CL+PQV+N
Sbjct: 116 YLKHTLGVDDYAKDAWYRHWVEAGFATFETHLAGDPRTGKLCFGDTPTIADTCLIPQVFN 175

Query: 178 AQRFNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215
           AQRF VD T +P I R++    QL AFA AAP  Q DA
Sbjct: 176 AQRFKVDTTKFPTIQRIYDHAMQLDAFARAAPGAQPDA 213


Lambda     K      H
   0.321    0.134    0.408 

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: 174
Number of extensions: 6
Number of successful extensions: 3
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: 216
Length of database: 214
Length adjustment: 22
Effective length of query: 194
Effective length of database: 192
Effective search space:    37248
Effective search space used:    37248
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate BPHYT_RS02805 BPHYT_RS02805 (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.21732.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    5.5e-90  286.6   0.0    6.1e-90  286.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS02805  BPHYT_RS02805 maleylacetoacetate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS02805  BPHYT_RS02805 maleylacetoacetate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.5   0.0   6.1e-90   6.1e-90       1     210 [.       2     213 ..       2     214 .] 0.99

  Alignments for each domain:
  == domain 1  score: 286.5 bits;  conditional E-value: 6.1e-90
                                TIGR01262   1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlAi 69 
                                              klYsyfrSsasyRvRiaL++k++ y +vpv+L++d Geq k+e++++N  + vPt++++ ++v+ qSlAi
  lcl|FitnessBrowser__BFirm:BPHYT_RS02805   2 KLYSYFRSSASYRVRIALNVKNLPYDYVPVHLVRDgGEQLKPEYRKVNADGIVPTFVDG-NDVMPQSLAI 70 
                                              69********************************************************9.5********* PP

                                TIGR01262  70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGl 139
                                              ieyLee +pepaLlpk pa+ra vralal +ac+ihPl+Nlrvl++l+++lgvd+ +k++w++hw+e+G+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02805  71 IEYLEEVHPEPALLPKAPADRAYVRALALQVACEIHPLNNLRVLKYLKHTLGVDDYAKDAWYRHWVEAGF 140
                                              ********************************************************************** PP

                                TIGR01262 140 aalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenq 207
                                              a++E++l+  +++g+ c+Gd++t+ad cL+pqv nA+rf+vd +++Pt++ri +++ +l+af++a+p  q
  lcl|FitnessBrowser__BFirm:BPHYT_RS02805 141 ATFETHLAgdPRTGKLCFGDTPTIADTCLIPQVFNAQRFKVDTTKFPTIQRIYDHAMQLDAFARAAPGAQ 210
                                              *******99999********************************************************** PP

                                TIGR01262 208 pdt 210
                                              pd+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02805 211 PDA 213
                                              **7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (214 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.07
//
[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