Alignments for a candidate for iolC in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Sinorhizobium meliloti 1021

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate SMc01165 SMc01165 sugar kinase

Query= reanno::Smeli:SMc01165
         (650 letters)



>FitnessBrowser__Smeli:SMc01165
          Length = 650

 Score = 1292 bits (3343), Expect = 0.0
 Identities = 650/650 (100%), Positives = 650/650 (100%)

Query: 1   MSQIPSAQVPSGAGAKPLDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGT 60
           MSQIPSAQVPSGAGAKPLDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGT
Sbjct: 1   MSQIPSAQVPSGAGAKPLDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGT 60

Query: 61  ARLGLKSALLTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLL 120
           ARLGLKSALLTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLL
Sbjct: 61  ARLGLKSALLTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLL 120

Query: 121 FYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFD 180
           FYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFD
Sbjct: 121 FYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFD 180

Query: 181 IDYRPNLWGLAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAAL 240
           IDYRPNLWGLAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAAL
Sbjct: 181 IDYRPNLWGLAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAAL 240

Query: 241 KTIRSLSKATIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLR 300
           KTIRSLSKATIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLR
Sbjct: 241 KTIRSLSKATIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLR 300

Query: 301 GWLTGEPHATSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHV 360
           GWLTGEPHATSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHV
Sbjct: 301 GWLTGEPHATSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHV 360

Query: 361 HWATTRRRDIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFG 420
           HWATTRRRDIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFG
Sbjct: 361 HWATTRRRDIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFG 420

Query: 421 MLIDDKYGRDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLS 480
           MLIDDKYGRDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLS
Sbjct: 421 MLIDDKYGRDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLS 480

Query: 481 FYHPDDPAELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAG 540
           FYHPDDPAELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAG
Sbjct: 481 FYHPDDPAELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAG 540

Query: 541 LKPDWWKLEPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVK 600
           LKPDWWKLEPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVK
Sbjct: 541 LKPDWWKLEPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVK 600

Query: 601 GFAVGRTIFADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQLGETKAA 650
           GFAVGRTIFADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQLGETKAA
Sbjct: 601 GFAVGRTIFADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQLGETKAA 650


Lambda     K      H
   0.320    0.136    0.407 

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: 1522
Number of extensions: 40
Number of successful extensions: 3
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: 650
Length of database: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space:   374544
Effective search space used:   374544
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: 54 (25.4 bits)

Align candidate SMc01165 SMc01165 (sugar kinase)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))

# 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/TIGR04382.hmm
# target sequence database:        /tmp/gapView.18344.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04382  [M=309]
Accession:   TIGR04382
Description: myo_inos_iolC_N: 5-dehydro-2-deoxygluconokinase
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-126  407.4   0.0     3e-126  406.8   0.0    1.3  1  lcl|FitnessBrowser__Smeli:SMc01165  SMc01165 sugar kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01165  SMc01165 sugar kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.8   0.0    3e-126    3e-126       2     309 .]      18     342 ..      17     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: 406.8 bits;  conditional E-value: 3e-126
                           TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreeleregvd 76 
                                         ldlitiGR++vDly+qqig++ledv sfak++GG+p+Ni+vg+arlGlk+al+t+vgd+q+Grf+re+l+regv+
  lcl|FitnessBrowser__Smeli:SMc01165  18 LDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGTARLGLKSALLTRVGDEQMGRFIREQLQREGVE 92 
                                         8************************************************************************** PP

                           TIGR04382  77 tshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreavlkal 151
                                         t+++vtd+e++t+l++l+++++++fpllfYR+n+aD al+ dd++e++i++a+a+lv+gt+++k+++++a+ ka+
  lcl|FitnessBrowser__Smeli:SMc01165  93 TRGIVTDPERLTALAILSVENDKSFPLLFYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAI 167
                                         *************************************************************************** PP

                           TIGR04382 152 elakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEfeiaagekddeaaaka 214
                                         ++ak++g+++v+DiDYRp+lW+            +++++sa+l++vl ++d+i+GteeE+ ia+ge+d  aa+k+
  lcl|FitnessBrowser__Smeli:SMc01165 168 RIAKESGARIVFDIDYRPNLWGlaghdagesryiASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAALKT 242
                                         *************************************************************************** PP

                           TIGR04382 215 llelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanA 284
                                         +++l+++++v+KrG+ G++vy++      e+ +  kgf++ev++vlGaGDaF+sg+l+g+l+ge++++++++anA
  lcl|FitnessBrowser__Smeli:SMc01165 243 IRSLSKATIVLKRGPMGCIVYDGPisddlEDGIVGKGFPIEVYNVLGAGDAFMSGFLRGWLTGEPHATSATWANA 317
                                         **********************99999999********************************************* PP

                           TIGR04382 285 agaivvsrlscaeamptleeleefl 309
                                         +ga++vsrl ca+++pt++el+ fl
  lcl|FitnessBrowser__Smeli:SMc01165 318 CGAFAVSRLLCAPEIPTWTELQYFL 342
                                         **********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (650 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: 15.10
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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