Alignments for a candidate for iolE in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Sinorhizobium meliloti 1021

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate SMc00433 SMc00433 myo-inositol catabolism protein

Query= reanno::Smeli:SMc00433
         (300 letters)



>FitnessBrowser__Smeli:SMc00433
          Length = 300

 Score =  622 bits (1603), Expect = 0.0
 Identities = 300/300 (100%), Positives = 300/300 (100%)

Query: 1   MIRYGTNPIAWSNDDDHSIGAHLTLEDCLSDCRKIGFDGIEKGHKMPSDPEALKQKLSSY 60
           MIRYGTNPIAWSNDDDHSIGAHLTLEDCLSDCRKIGFDGIEKGHKMPSDPEALKQKLSSY
Sbjct: 1   MIRYGTNPIAWSNDDDHSIGAHLTLEDCLSDCRKIGFDGIEKGHKMPSDPEALKQKLSSY 60

Query: 61  DLVFVSGWHSTNLLTHDVEAEKKAIQPHLDLLKHNGCKVAIVCETSNAIHGDDSKSLVKD 120
           DLVFVSGWHSTNLLTHDVEAEKKAIQPHLDLLKHNGCKVAIVCETSNAIHGDDSKSLVKD
Sbjct: 61  DLVFVSGWHSTNLLTHDVEAEKKAIQPHLDLLKHNGCKVAIVCETSNAIHGDDSKSLVKD 120

Query: 121 KPVLPADKWEKFGTDLEAIAEYCAGQGVDLVYHHHMGTIVQTGEEIDLLMRNTGPATKLL 180
           KPVLPADKWEKFGTDLEAIAEYCAGQGVDLVYHHHMGTIVQTGEEIDLLMRNTGPATKLL
Sbjct: 121 KPVLPADKWEKFGTDLEAIAEYCAGQGVDLVYHHHMGTIVQTGEEIDLLMRNTGPATKLL 180

Query: 181 LDTGHAWFGGSDPAEVARKYMGRVRHIHCKNVRPAVRKVVEGEGLSFLEGVRRGVFTVPG 240
           LDTGHAWFGGSDPAEVARKYMGRVRHIHCKNVRPAVRKVVEGEGLSFLEGVRRGVFTVPG
Sbjct: 181 LDTGHAWFGGSDPAEVARKYMGRVRHIHCKNVRPAVRKVVEGEGLSFLEGVRRGVFTVPG 240

Query: 241 DEEGGVDFLPVLKTAAEHGYDGWLVIEAEQDSAVRNPFEYQSLGLKSLKTFAREAGLDRA 300
           DEEGGVDFLPVLKTAAEHGYDGWLVIEAEQDSAVRNPFEYQSLGLKSLKTFAREAGLDRA
Sbjct: 241 DEEGGVDFLPVLKTAAEHGYDGWLVIEAEQDSAVRNPFEYQSLGLKSLKTFAREAGLDRA 300


Lambda     K      H
   0.318    0.137    0.420 

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: 536
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: 300
Length of database: 300
Length adjustment: 27
Effective length of query: 273
Effective length of database: 273
Effective search space:    74529
Effective search space used:    74529
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate SMc00433 SMc00433 (myo-inositol catabolism protein)
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))

# 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/TIGR04379.hmm
# target sequence database:        /tmp/gapView.14644.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04379  [M=290]
Accession:   TIGR04379
Description: myo_inos_iolE: myo-inosose-2 dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.1e-111  356.6   0.0   6.9e-111  356.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00433  SMc00433 myo-inositol catabolism


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00433  SMc00433 myo-inositol catabolism protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.4   0.0  6.9e-111  6.9e-111       2     288 ..       2     290 ..       1     292 [. 0.98

  Alignments for each domain:
  == domain 1  score: 356.4 bits;  conditional E-value: 6.9e-111
                           TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsalllek 76 
                                         +++g +PiaW+ndD +++g++ tle++ls+++++gf g+E g+k+p dp++Lk++l++++l  vsgw s++ll++
  lcl|FitnessBrowser__Smeli:SMc00433   2 IRYGTNPIAWSNDDDHSIGAHLTLEDCLSDCRKIGFDGIEKGHKMPSDPEALKQKLSSYDLVFVSGWHSTNLLTH 76 
                                         89************************************************************************* PP

                           TIGR04379  77 sveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaer.pklteeeweelaeklnklgeilkekglkla 150
                                         +ve+e++a++ hl+llk+ g+kv++v+E++++i+gd +++l ++ p+l +++we++++ l++++e+++ +g+ l+
  lcl|FitnessBrowser__Smeli:SMc00433  77 DVEAEKKAIQPHLDLLKHNGCKVAIVCETSNAIHGDDSKSLVKDkPVLPADKWEKFGTDLEAIAEYCAGQGVDLV 151
                                         ************************************999886655****************************** PP

                           TIGR04379 151 yHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDvRkevleevrkekk 225
                                         yHhH+gt+v+t eeid lm +t+p+  +ll+DtGH+ f+g dp++v++ky+ R++h+H+K+vR++v + v+ e  
  lcl|FitnessBrowser__Smeli:SMc00433 152 YHHHMGTIVQTGEEIDLLMRNTGPA-TKLLLDTGHAWFGGSDPAEVARKYMGRVRHIHCKNVRPAVRKVVEGEGL 225
                                         *************************.9************************************************ PP

                           TIGR04379 226 sFldavlkGvftvPGd..GcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkakkylee 288
                                         sFl++v++GvftvPGd  G +df ++l++ ++++Y+GWlv+EaEqD a+ +p+ey + + k l++
  lcl|FitnessBrowser__Smeli:SMc00433 226 SFLEGVRRGVFTVPGDeeGGVDFLPVLKTAAEHGYDGWLVIEAEQDSAVRNPFEYQSLGLKSLKT 290
                                         ***************9779****************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (300 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.39
//
[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