Alignments for a candidate for maiA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for maiA in Caulobacter crescentus NA1000

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate CCNA_03683 CCNA_03683 maleylpyruvate isomerase

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



>FitnessBrowser__Caulo:CCNA_03683
          Length = 210

 Score =  196 bits (499), Expect = 2e-55
 Identities = 110/215 (51%), Positives = 139/215 (64%), Gaps = 9/215 (4%)

Query: 1   MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKAD-YIALNPQELVPTLVV 59
           ++L+   R+SA YRVRI LNLKG++ E   V LV +    H+ + Y ALN Q LVPTL  
Sbjct: 3   LVLHSAKRASAPYRVRIGLNLKGLAFELRPVDLVANA---HQGEAYRALNAQALVPTL-- 57

Query: 60  DDEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQ 119
             E DG  LTQSLAI+E+LDE YP  PLLP  A +RA VRAMA  IAC+IHPLNNLR+L+
Sbjct: 58  --EVDGRPLTQSLAILEWLDETYPAHPLLPTDAFDRATVRAMAEIIACDIHPLNNLRILR 115

Query: 120 YLTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQ 179
            LT  L ++E A++AW   W+  GF+ALE  + RH   Y FGD   + D  LVPQV+NA 
Sbjct: 116 QLT-ALEIDEPARNAWVARWIQDGFSALEPMIARHGQGYAFGDAPGLVDCLLVPQVFNAN 174

Query: 180 RFNVDLTPYPNIMRVWAECNQLPAFADAAPERQAD 214
           RFNVDL+P+P +    A     PA A A P+   +
Sbjct: 175 RFNVDLSPFPALEAAAAHARAHPAIAAAHPDHHPE 209


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: 163
Number of extensions: 7
Number of successful extensions: 4
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: 210
Length adjustment: 22
Effective length of query: 194
Effective length of database: 188
Effective search space:    36472
Effective search space used:    36472
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 CCNA_03683 CCNA_03683 (maleylpyruvate 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.17044.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-76  242.3   0.0    2.2e-76  242.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03683  CCNA_03683 maleylpyruvate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03683  CCNA_03683 maleylpyruvate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.2   0.0   2.2e-76   2.2e-76       2     209 ..       5     209 ..       4     210 .] 0.97

  Alignments for each domain:
  == domain 1  score: 242.2 bits;  conditional E-value: 2.2e-76
                             TIGR01262   2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAiieyLe 74 
                                           l+s  r+sa yRvRi+L+Lkg+++e +pv+L+++ +++ e+++alN q+lvPtL++d g+ ltqSlAi+e+L+
  lcl|FitnessBrowser__Caulo:CCNA_03683   5 LHSAKRASAPYRVRIGLNLKGLAFELRPVDLVAN-AHQGEAYRALNAQALVPTLEVD-GRPLTQSLAILEWLD 75 
                                           5666799**************************6.999*******************.6************** PP

                             TIGR01262  75 etypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellk 147
                                           etyp ++Llp+d+ +ra vra+a++iacdihPl+Nlr+l++l+  l++de ++++w+++wi++G++alE +++
  lcl|FitnessBrowser__Caulo:CCNA_03683  76 ETYPAHPLLPTDAFDRATVRAMAEIIACDIHPLNNLRILRQLT-ALEIDEPARNAWVARWIQDGFSALEPMIA 147
                                           *******************************************.568************************** PP

                             TIGR01262 148 ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpd 209
                                           ++ + +++Gd+++l+d++Lvpqv nA+rf+vdl+++P+l++ +++++++pa+++ahp++ p+
  lcl|FitnessBrowser__Caulo:CCNA_03683 148 RHGQGYAFGDAPGLVDCLLVPQVFNANRFNVDLSPFPALEAAAAHARAHPAIAAAHPDHHPE 209
                                           99999*****************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (210 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: 7.44
//
[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