Alignments for a candidate for maiA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for maiA in Shewanella loihica PV-4

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate 5208938 Shew_1439 maleylacetoacetate isomerase (RefSeq)

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



>FitnessBrowser__PV4:5208938
          Length = 214

 Score =  298 bits (764), Expect = 4e-86
 Identities = 145/215 (67%), Positives = 172/215 (80%), Gaps = 2/215 (0%)

Query: 1   MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60
           M L GYWRSSAAYRVRIALNLKG+ AE  SVHLV++GGEQH  +Y ALNPQELVPTL+  
Sbjct: 1   MKLLGYWRSSAAYRVRIALNLKGLDAELESVHLVKNGGEQHLPEYAALNPQELVPTLIEG 60

Query: 61  DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120
           D +    L+QSLAIIEYLDE Y    +LP +   RA VRAMAL+IACE+HPLNNL+VLQY
Sbjct: 61  DNEF--VLSQSLAIIEYLDEQYGGAMMLPTAPKARAEVRAMALSIACEVHPLNNLKVLQY 118

Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQR 180
           LT  L ++E+AK+AWYHHW+  GF+A E QL +H+G YC+GD+VT+ADLCL+PQVYNA R
Sbjct: 119 LTNTLELDEDAKNAWYHHWIHQGFSAFEKQLEKHAGSYCYGDEVTLADLCLIPQVYNANR 178

Query: 181 FNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215
           F VDL+ YPNI R+W  C+QL AF  AAPERQADA
Sbjct: 179 FKVDLSTYPNIRRIWDNCHQLEAFVLAAPERQADA 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: 183
Number of extensions: 3
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: 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 5208938 Shew_1439 (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.24607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    1.4e-91  291.9   0.1    1.5e-91  291.7   0.1    1.0  1  lcl|FitnessBrowser__PV4:5208938  Shew_1439 maleylacetoacetate iso


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208938  Shew_1439 maleylacetoacetate isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.7   0.1   1.5e-91   1.5e-91       2     210 ..       3     213 ..       2     214 .] 0.98

  Alignments for each domain:
  == domain 1  score: 291.7 bits;  conditional E-value: 1.5e-91
                        TIGR01262   2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkide.gevltqSlAiieyLeety 77 
                                      l +y+rSsa+yRvRiaL+Lkg+d e ++v+L+k+ Geq+ +e++alNPqelvPtL+ ++ + vl+qSlAiieyL+e+y
  lcl|FitnessBrowser__PV4:5208938   3 LLGYWRSSAAYRVRIALNLKGLDAELESVHLVKNgGEQHLPEYAALNPQELVPTLIEGDnEFVLSQSLAIIEYLDEQY 80 
                                      789*******************************9********************99773679*************** PP

                        TIGR01262  78 pepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellkekagafcv 155
                                          +lp+ p++ra+vra+al iac++hPl+Nl+vlq+l+++l+ de++k++w++hwi++G++a+E+ l+++ag++c 
  lcl|FitnessBrowser__PV4:5208938  81 GGAMMLPTAPKARAEVRAMALSIACEVHPLNNLKVLQYLTNTLELDEDAKNAWYHHWIHQGFSAFEKQLEKHAGSYCY 158
                                      ****************************************************************************** PP

                        TIGR01262 156 GdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210
                                      Gdevtlad+cL+pqvynA+rf+vdl++yP ++ri +++++l+af  a+pe+q d+
  lcl|FitnessBrowser__PV4:5208938 159 GDEVTLADLCLIPQVYNANRFKVDLSTYPNIRRIWDNCHQLEAFVLAAPERQADA 213
                                      ****************************************************996 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: 8.56
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources