Alignments for a candidate for maiA in Shewanella amazonensis SB2B

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.5733.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.83
//
[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