Alignments for a candidate for garR in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Acidovorax sp. GW101-3H11

Align tartronate semialdehyde reductase 2 (characterized)
to candidate Ac3H11_1088 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)

Query= ecocyc::G6278-MONOMER
         (292 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1088
          Length = 322

 Score =  391 bits (1005), Expect = e-114
 Identities = 202/294 (68%), Positives = 237/294 (80%), Gaps = 4/294 (1%)

Query: 1   MKLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIF 60
           +KLGFIGLGIMG PM  +L  AGHQL+V T G VA ++    A    TAR V E +DI+F
Sbjct: 24  LKLGFIGLGIMGAPMCGHLIAAGHQLYVHTRGRVAPQIAQSSATQCTTARGVAERADIVF 83

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKG---KTIVDMSSISPIETKRFARQVNELGGDYLDA 117
           +M+PDTP VE+VLFG +G  +  LKG   K +VDMSSISP+ TK FA ++  +G  YLDA
Sbjct: 84  LMLPDTPDVEKVLFGADGVAQG-LKGSVGKVVVDMSSISPVATKDFAARIEAVGAQYLDA 142

Query: 118 PVSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVA 177
           PVSGGE+GA+  TLSIMVGG EAVFER++PLFE LGKNITLVGGNGDGQT KVANQIIVA
Sbjct: 143 PVSGGELGAKNATLSIMVGGPEAVFERIRPLFERLGKNITLVGGNGDGQTAKVANQIIVA 202

Query: 178 LNIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQK 237
           LNIEAV+EALLFA++AGADP RVRQAL+GGFASS+ILEVH ERMIKRTF+PGF+I LHQK
Sbjct: 203 LNIEAVAEALLFAARAGADPARVRQALLGGFASSKILEVHAERMIKRTFDPGFRIGLHQK 262

Query: 238 DLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291
           DLNLAL SA+AL + LPNTA  QELFN C A+GG   DHSA+V+ALE MAN ++
Sbjct: 263 DLNLALSSARALGVPLPNTAMAQELFNACVAHGGQGWDHSAMVRALEKMANFEM 316


Lambda     K      H
   0.318    0.135    0.376 

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: 346
Number of extensions: 6
Number of successful extensions: 2
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: 292
Length of database: 322
Length adjustment: 27
Effective length of query: 265
Effective length of database: 295
Effective search space:    78175
Effective search space used:    78175
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 Ac3H11_1088 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))
to HMM TIGR01505 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))

# 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/TIGR01505.hmm
# target sequence database:        /tmp/gapView.13073.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01505  [M=291]
Accession:   TIGR01505
Description: tartro_sem_red: 2-hydroxy-3-oxopropionate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.3e-127  409.3   4.3   4.8e-127  409.1   4.3    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088  2-hydroxy-3-oxopropionate reduct


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088  2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.1   4.3  4.8e-127  4.8e-127       1     290 [.      25     315 ..      25     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 409.1 bits;  conditional E-value: 4.8e-127
                                        TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtm 62 
                                                      k+gfiGlGimG Pm+  l+ aG+ql v t++  ++ +++   a+   ta+ v+e ad+++ m
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088  25 KLGFIGLGIMGAPMCGHLIAAGHQLYVHTRG-RVAPQIAQSSATQCTTARGVAERADIVFLM 85 
                                                      89*****************************.89999************************* PP

                                        TIGR01505  63 vPdsPqveevalGenGileaak..kGkvlvdmssiaPleskelakavkekGidvldaPvsGG 122
                                                      +Pd+P+ve+v++G +G+ ++ k   Gkv+vdmssi+P+++k++a  +++ G ++ldaPvsGG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088  86 LPDTPDVEKVLFGADGVAQGLKgsVGKVVVDMSSISPVATKDFAARIEAVGAQYLDAPVSGG 147
                                                      ******************98763369************************************ PP

                                        TIGR01505 123 eagaiegtlsimvGGdkavfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavs 184
                                                      e ga+++tlsimvGG +avf++++pl+e lgk+i+lvG+nG+Gqt+kvanq+ivalnieav+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088 148 ELGAKNATLSIMVGGPEAVFERIRPLFERLGKNITLVGGNGDGQTAKVANQIIVALNIEAVA 209
                                                      ************************************************************** PP

                                        TIGR01505 185 ealvlaekaGvdpkavlqalrGGlagstvleakkerlldrdfkPGfridlhqkdlalaldaa 246
                                                      eal++a +aG+dp +v+qal GG+a+s++le+++er+++r+f+PGfri lhqkdl+lal +a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088 210 EALLFAARAGADPARVRQALLGGFASSKILEVHAERMIKRTFDPGFRIGLHQKDLNLALSSA 271
                                                      ************************************************************** PP

                                        TIGR01505 247 kavgaalPvtavvaellaalradGdgtldhsalvraleklakdk 290
                                                      +a+g+ lP+ta+ +el++a+ a+G+ + dhsa+vralek+a+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1088 272 RALGVPLPNTAMAQELFNACVAHGGQGWDHSAMVRALEKMANFE 315
                                                      *****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (322 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.80
//
[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