GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Shewanella amazonensis SB2B

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate 6938097 Sama_2218 maleylacetoacetate isomerase (RefSeq)

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



>FitnessBrowser__SB2B:6938097
          Length = 213

 Score =  297 bits (760), Expect = 1e-85
 Identities = 145/215 (67%), Positives = 167/215 (77%), Gaps = 3/215 (1%)

Query: 1   MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60
           M LYGYWRSSAAYRVRIALNLKG+ AEQLSVHLV++GGEQH  DY+ALNPQ LVP+LV+D
Sbjct: 1   MKLYGYWRSSAAYRVRIALNLKGLDAEQLSVHLVKNGGEQHSDDYVALNPQHLVPSLVLD 60

Query: 61  DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120
           D   G  LTQSLAI+EY ++     PLLP SA +RA VRAM L IACEIHPLNNLRVLQY
Sbjct: 61  D---GTVLTQSLAIMEYFEDAGLGLPLLPESATDRATVRAMCLAIACEIHPLNNLRVLQY 117

Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQR 180
           L+  + +++E K+ WYHHW+  GFTA E  L RHSG YCFGD  T+AD CL+PQVYNA+R
Sbjct: 118 LSGDMGLSDEVKNTWYHHWIHEGFTAFEKLLARHSGEYCFGDSPTLADACLIPQVYNARR 177

Query: 181 FNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215
           FNV L  YPNI+R+ A CN   AF DA PE Q DA
Sbjct: 178 FNVPLDNYPNILRIEAHCNATQAFIDALPENQPDA 212


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: 201
Number of extensions: 5
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: 216
Length of database: 213
Length adjustment: 22
Effective length of query: 194
Effective length of database: 191
Effective search space:    37054
Effective search space used:    37054
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 6938097 Sama_2218 (maleylacetoacetate isomerase (RefSeq))
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.14476.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.8e-89  284.9   0.0    2.1e-89  284.8   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6938097  Sama_2218 maleylacetoacetate iso


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938097  Sama_2218 maleylacetoacetate isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.8   0.0   2.1e-89   2.1e-89       1     210 [.       2     212 ..       2     213 .] 0.99

  Alignments for each domain:
  == domain 1  score: 284.8 bits;  conditional E-value: 2.1e-89
                         TIGR01262   1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlAiieyLeet 76 
                                       klY+y+rSsa+yRvRiaL+Lkg+d e  +v+L+k+ Geq+++++ alNPq+lvP L+ d+g+vltqSlAi+ey e++
  lcl|FitnessBrowser__SB2B:6938097   2 KLYGYWRSSAAYRVRIALNLKGLDAEQLSVHLVKNgGEQHSDDYVALNPQHLVPSLVLDDGTVLTQSLAIMEYFEDA 78 
                                       69*********************************9***************************************** PP

                         TIGR01262  77 ypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellkekagaf 153
                                           +Llp+ +++ra vra+ l+iac+ihPl+Nlrvlq+l+  +g ++e k++w++hwi++G++a+E+ll++++g++
  lcl|FitnessBrowser__SB2B:6938097  79 GLGLPLLPESATDRATVRAMCLAIACEIHPLNNLRVLQYLSGDMGLSDEVKNTWYHHWIHEGFTAFEKLLARHSGEY 155
                                       ***************************************************************************** PP

                         TIGR01262 154 cvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210
                                       c+Gd++tlad cL+pqvynA+rf+v l++yP + rie+++++++af +a penqpd+
  lcl|FitnessBrowser__SB2B:6938097 156 CFGDSPTLADACLIPQVYNARRFNVPLDNYPNILRIEAHCNATQAFIDALPENQPDA 212
                                       ********************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (213 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: 7.12
//
[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