Alignments for a candidate for iolG in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolG in Sinorhizobium meliloti 1021

Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate SM_b20899 SM_b20899 myo-inositol dehydrogenase

Query= BRENDA::O68965
         (330 letters)



>FitnessBrowser__Smeli:SM_b20899
          Length = 330

 Score =  640 bits (1652), Expect = 0.0
 Identities = 330/330 (100%), Positives = 330/330 (100%)

Query: 1   MTVRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRTIDAIEAA 60
           MTVRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRTIDAIEAA
Sbjct: 1   MTVRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRTIDAIEAA 60

Query: 61  ADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGF 120
           ADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGF
Sbjct: 61  ADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGF 120

Query: 121 NRRFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMAR 180
           NRRFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMAR
Sbjct: 121 NRRFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMAR 180

Query: 181 FLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIE 240
           FLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIE
Sbjct: 181 FLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIE 240

Query: 241 VHGSKGAVAAENQRPVSIEIATGDGYTRPPLHDFFMTRYTEAYANEIESFIAAIEKGAEI 300
           VHGSKGAVAAENQRPVSIEIATGDGYTRPPLHDFFMTRYTEAYANEIESFIAAIEKGAEI
Sbjct: 241 VHGSKGAVAAENQRPVSIEIATGDGYTRPPLHDFFMTRYTEAYANEIESFIAAIEKGAEI 300

Query: 301 APSGNDGLAALALADAAVRSVAEKRQISIA 330
           APSGNDGLAALALADAAVRSVAEKRQISIA
Sbjct: 301 APSGNDGLAALALADAAVRSVAEKRQISIA 330


Lambda     K      H
   0.320    0.134    0.379 

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: 495
Number of extensions: 13
Number of successful extensions: 1
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: 330
Length of database: 330
Length adjustment: 28
Effective length of query: 302
Effective length of database: 302
Effective search space:    91204
Effective search space used:    91204
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate SM_b20899 SM_b20899 (myo-inositol dehydrogenase)
to HMM TIGR04380 (iolG: inositol 2-dehydrogenase (EC 1.1.1.18))

# 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/TIGR04380.hmm
# target sequence database:        /tmp/gapView.22284.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04380  [M=330]
Accession:   TIGR04380
Description: myo_inos_iolG: inositol 2-dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.2e-130  421.2   3.5   1.4e-130  421.0   3.5    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20899  SM_b20899 myo-inositol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20899  SM_b20899 myo-inositol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.0   3.5  1.4e-130  1.4e-130       2     329 ..       3     327 ..       2     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 421.0 bits;  conditional E-value: 1.4e-130
                            TIGR04380   2 lkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAvliasptd 75 
                                          +++g++GaGRigkvHa+ ++ +  +a+l+av+d++ +aa+++a ++g    v++++ai + +++dAv+i++ptd
  lcl|FitnessBrowser__Smeli:SM_b20899   3 VRFGLLGAGRIGKVHAKAVSGN-ADARLVAVADAFPAAAEAIAGAYGC--EVRTIDAIEAAADIDAVVICTPTD 73 
                                          689*******************.*************************..8999******************** PP

                            TIGR04380  76 tHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkklveagkiGklellr 149
                                          tHa+li++ a+agk+ifcEKPidld e+++++lk+v++++ kl++GfnRRFD++f++v+k++++g+iG++e+++
  lcl|FitnessBrowser__Smeli:SM_b20899  74 THADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGFNRRFDPHFMAVRKAIDDGRIGEVEMVT 147
                                          ************************************************************************** PP

                            TIGR04380 150 itsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpeleeagdvdtavvvlkfenga 223
                                          itsrDP++ppv+y+k sGg+f+DmtiHDfDmarfllg+e+++v+a+++vl+d+++++agd+d++ v+l++++g+
  lcl|FitnessBrowser__Smeli:SM_b20899 148 ITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMARFLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGK 221
                                          ************************************************************************** PP

                            TIGR04380 224 laviensrraayGYdqrvEvfGskGslraendtestvvlsdeegvraekpenfFleRyaeayraeikafvdail 297
                                           a+i+nsrra+yGYdqr+Ev+GskG+++aen+++ ++++++ +g+++   + fF+ Ry+eay++ei++f+ ai+
  lcl|FitnessBrowser__Smeli:SM_b20899 222 QAIISNSRRATYGYDQRIEVHGSKGAVAAENQRPVSIEIATGDGYTRPPLHDFFMTRYTEAYANEIESFIAAIE 295
                                          ************************************************************************** PP

                            TIGR04380 298 edkevsvtaeDglkalklalaakrsleegrav 329
                                          +++e +++++Dgl+al+la+aa rs++e+r++
  lcl|FitnessBrowser__Smeli:SM_b20899 296 KGAEIAPSGNDGLAALALADAAVRSVAEKRQI 327
                                          ***************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (330 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.13
//
[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