Alignments for a candidate for garR in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Escherichia coli BW25113

Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate 17198 b3125 tartronate semialdehyde reductase (RefSeq)

Query= SwissProt::P0ABQ2
         (294 letters)



>FitnessBrowser__Keio:17198
          Length = 294

 Score =  565 bits (1457), Expect = e-166
 Identities = 294/294 (100%), Positives = 294/294 (100%)

Query: 1   MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60
           MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI
Sbjct: 1   MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60

Query: 61  ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120
           ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV
Sbjct: 61  ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120

Query: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALN 180
           SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALN
Sbjct: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALN 180

Query: 181 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL 240
           IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL
Sbjct: 181 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL 240

Query: 241 ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR 294
           ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR
Sbjct: 241 ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR 294


Lambda     K      H
   0.316    0.133    0.366 

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: 430
Number of extensions: 4
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: 294
Length of database: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate 17198 b3125 (tartronate semialdehyde reductase (RefSeq))
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.15590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.5e-160  519.1  11.9   1.7e-160  518.9  11.9    1.0  1  lcl|FitnessBrowser__Keio:17198  b3125 tartronate semialdehyde re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17198  b3125 tartronate semialdehyde reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.9  11.9  1.7e-160  1.7e-160       1     291 []       2     292 ..       2     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 518.9 bits;  conditional E-value: 1.7e-160
                       TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalGenGi 79 
                                     kvgfiGlGimGkPmsknllkaGy+lvva++++ea+++++aaGae+a+tak+++e++dvi+tm+P+sP+v+evalGenGi
  lcl|FitnessBrowser__Keio:17198   2 KVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVIITMLPNSPHVKEVALGENGI 80 
                                     8****************************************************************************** PP

                       TIGR01505  80 leaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkpllealgksivl 158
                                     +e+ak+G+vl+dmssiaPl+s+e+++a+k+kGid+ldaPvsGGe++ai+gtls+mvGGdka+fdk+++l++a+++s+v+
  lcl|FitnessBrowser__Keio:17198  81 IEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVH 159
                                     ******************************************************************************* PP

                       TIGR01505 159 vGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlldrdfkPGfridlhqk 237
                                     +Ge+GaG+++k+anqvivalni+a+seal+la+kaGv+p++v+qa+rGGlagstvl+ak+++++dr+fkPGfridlh+k
  lcl|FitnessBrowser__Keio:17198 160 TGEIGAGNVTKLANQVIVALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIK 238
                                     ******************************************************************************* PP

                       TIGR01505 238 dlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakdkv 291
                                     dla+ald++++vga+lP+ta+v+e+++alradG gt+dhsal++++eklak++v
  lcl|FitnessBrowser__Keio:17198 239 DLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEV 292
                                     ***************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (294 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: 8.66
//
[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