Alignments for a candidate for kdgD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kdgD in Herbaspirillum seropedicae SmR1

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate HSERO_RS15785 HSERO_RS15785 5-dehydro-4-deoxyglucarate dehydratase

Query= reanno::HerbieS:HSERO_RS15785
         (306 letters)



>FitnessBrowser__HerbieS:HSERO_RS15785
          Length = 306

 Score =  614 bits (1584), Expect = 0.0
 Identities = 306/306 (100%), Positives = 306/306 (100%)

Query: 1   MSQYTPQDLKQILSSGLLSFPLTDFDEQGDFRPKTYIERLEWLAPYGASALFAAGGTGEF 60
           MSQYTPQDLKQILSSGLLSFPLTDFDEQGDFRPKTYIERLEWLAPYGASALFAAGGTGEF
Sbjct: 1   MSQYTPQDLKQILSSGLLSFPLTDFDEQGDFRPKTYIERLEWLAPYGASALFAAGGTGEF 60

Query: 61  FSLVPGEYSDIIRTAVDTCRGKVPIIAGAGGSTRAAIAYAQEAERLGAHGILLMPHYLTE 120
           FSLVPGEYSDIIRTAVDTCRGKVPIIAGAGGSTRAAIAYAQEAERLGAHGILLMPHYLTE
Sbjct: 61  FSLVPGEYSDIIRTAVDTCRGKVPIIAGAGGSTRAAIAYAQEAERLGAHGILLMPHYLTE 120

Query: 121 ASQDGIAAHVEAVCKSVKFGVIIYNRAVCKLNADTLQKLADRCPNLIGFKDGIGEIEPMV 180
           ASQDGIAAHVEAVCKSVKFGVIIYNRAVCKLNADTLQKLADRCPNLIGFKDGIGEIEPMV
Sbjct: 121 ASQDGIAAHVEAVCKSVKFGVIIYNRAVCKLNADTLQKLADRCPNLIGFKDGIGEIEPMV 180

Query: 181 HIRRKLGDRFTYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAVEFYQAIAKEDHDT 240
           HIRRKLGDRFTYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAVEFYQAIAKEDHDT
Sbjct: 181 HIRRKLGDRFTYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAVEFYQAIAKEDHDT 240

Query: 241 VGKLIDEFFLPYLAIRNRKAGYAVSIVKAGARIAGHDAGPVRTPLTDCTPEEHEELAALM 300
           VGKLIDEFFLPYLAIRNRKAGYAVSIVKAGARIAGHDAGPVRTPLTDCTPEEHEELAALM
Sbjct: 241 VGKLIDEFFLPYLAIRNRKAGYAVSIVKAGARIAGHDAGPVRTPLTDCTPEEHEELAALM 300

Query: 301 NKLGPQ 306
           NKLGPQ
Sbjct: 301 NKLGPQ 306


Lambda     K      H
   0.321    0.138    0.410 

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: 498
Number of extensions: 15
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
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: 48 (23.1 bits)

Align candidate HSERO_RS15785 HSERO_RS15785 (5-dehydro-4-deoxyglucarate dehydratase)
to HMM TIGR03249 (kdgD: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))

# 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/TIGR03249.hmm
# target sequence database:        /tmp/gapView.6494.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03249  [M=299]
Accession:   TIGR03249
Description: KdgD: 5-dehydro-4-deoxyglucarate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.6e-138  446.1   0.0   2.9e-138  445.9   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15785  HSERO_RS15785 5-dehydro-4-deoxyg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15785  HSERO_RS15785 5-dehydro-4-deoxyglucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.9   0.0  2.9e-138  2.9e-138       1     298 [.       6     303 ..       6     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 445.9 bits;  conditional E-value: 2.9e-138
                                  TIGR03249   1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvve 68 
                                                pq+lk+ ++sGllsfP+t+fd++g+++++++ e++e+l++++++alf+agGtGeffsl + e++++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15785   6 PQDLKQILSSGLLSFPLTDFDEQGDFRPKTYIERLEWLAPYGASALFAAGGTGEFFSLVPGEYSDIIR 73 
                                                89****************************************************************** PP

                                  TIGR03249  69 vaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesvdlgv 136
                                                 av++++gkvP++ag+Gg+++ ai +a++ae+ Ga+G+ll+P+yl+ea+q+G+aa+v+av++sv++gv
  lcl|FitnessBrowser__HerbieS:HSERO_RS15785  74 TAVDTCRGKVPIIAGAGGSTRAAIAYAQEAERLGAHGILLMPHYLTEASQDGIAAHVEAVCKSVKFGV 141
                                                ******************************************************************** PP

                                  TIGR03249 137 ivyqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylal 204
                                                i+y+r+ ++l+adtl++la+r+pnl+GfkdGiG+ie +++i++klGdr++ylgGlPtaev+a+ay+al
  lcl|FitnessBrowser__HerbieS:HSERO_RS15785 142 IIYNRAVCKLNADTLQKLADRCPNLIGFKDGIGEIEPMVHIRRKLGDRFTYLGGLPTAEVYAAAYKAL 209
                                                ******************************************************************** PP

                                  TIGR03249 205 GvtsyssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrd 272
                                                Gv +yssa+fnfiPk+a +fy+a++k+d+ tv ++++e++lP+++irnrk+Gyavs++kaG+++ G+d
  lcl|FitnessBrowser__HerbieS:HSERO_RS15785 210 GVPVYSSAVFNFIPKTAVEFYQAIAKEDHDTVGKLIDEFFLPYLAIRNRKAGYAVSIVKAGARIAGHD 277
                                                ******************************************************************** PP

                                  TIGR03249 273 vgpvraPlvdlekeelaeleellkka 298
                                                +gpvr+Pl+d + ee +el++l++k+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15785 278 AGPVRTPLTDCTPEEHEELAALMNKL 303
                                                **********************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (306 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: 00:00:00.00
# Mc/sec: 9.44
//
[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