Alignments for a candidate for garR in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Pseudomonas simiae WCS417

Align tartronate semialdehyde reductase 2 (characterized)
to candidate GFF1730 PS417_08800 tartronate semialdehyde reductase

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



>FitnessBrowser__WCS417:GFF1730
          Length = 296

 Score =  370 bits (950), Expect = e-107
 Identities = 186/291 (63%), Positives = 226/291 (77%), Gaps = 1/291 (0%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTI-GPVADELLSLGAVSVETARQVTEASDIIF 60
           K+GFIG GIMG PMA NL +AGHQL ++   G  A  L+  GAV++   +QV + ++ I 
Sbjct: 3   KIGFIGTGIMGQPMAANLQKAGHQLFLSEHHGKAAQALVDAGAVALANPQQVAQEAEFII 62

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           +MVPDTPQV++VLF ++G        K ++DMSSISP  TK FA ++NE G  YLDAPVS
Sbjct: 63  VMVPDTPQVDDVLFRKDGVAAGLSPNKVVIDMSSISPTATKAFAAKINETGAQYLDAPVS 122

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GA+ GTLSIM+GG+   FER  PLF+ +GKNITLVGGNGDGQT KVANQIIVALNI
Sbjct: 123 GGEVGAKAGTLSIMIGGEPQTFERALPLFQAMGKNITLVGGNGDGQTAKVANQIIVALNI 182

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           +AV+EALLFASK GADP +VR+ALMGGFASS+ILEVHGERMIK TF+PGF+I LHQKDLN
Sbjct: 183 QAVAEALLFASKNGADPAKVREALMGGFASSKILEVHGERMIKGTFDPGFRINLHQKDLN 242

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291
           LAL  AK L +NLPNTA  Q++F+TC A GG   DHSAL++ LE MAN  +
Sbjct: 243 LALAGAKELGINLPNTAGTQQVFSTCTAIGGGNWDHSALIKGLEHMANFSI 293


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: 338
Number of extensions: 8
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: 296
Length adjustment: 26
Effective length of query: 266
Effective length of database: 270
Effective search space:    71820
Effective search space used:    71820
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 GFF1730 PS417_08800 (tartronate semialdehyde reductase)
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.18344.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-121  390.9   7.9   1.9e-121  390.7   7.9    1.0  1  lcl|FitnessBrowser__WCS417:GFF1730  PS417_08800 tartronate semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1730  PS417_08800 tartronate semialdehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.7   7.9  1.9e-121  1.9e-121       1     289 [.       3     291 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 390.7 bits;  conditional E-value: 1.9e-121
                           TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalG 75 
                                         k+gfiG GimG+Pm+ nl kaG+ql   + + +a++ l+ aGa++    ++v+++a+ i++mvPd+Pqv++v++ 
  lcl|FitnessBrowser__WCS417:GFF1730   3 KIGFIGTGIMGQPMAANLQKAGHQLFLSEHHGKAAQALVDAGAVALANPQQVAQEAEFIIVMVPDTPQVDDVLFR 77 
                                         89************************************************************************* PP

                           TIGR01505  76 enGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkplle 150
                                         ++G+  +  + kv++dmssi+P ++k +a +++e G ++ldaPvsGGe+ga+ gtlsim+GG+   f+++ pl++
  lcl|FitnessBrowser__WCS417:GFF1730  78 KDGVAAGLSPNKVVIDMSSISPTATKAFAAKINETGAQYLDAPVSGGEVGAKAGTLSIMIGGEPQTFERALPLFQ 152
                                         *************************************************************************** PP

                           TIGR01505 151 algksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlldrd 225
                                         a+gk+i+lvG+nG+Gqt+kvanq+ivalni+av+eal++a+k G+dp +v++al+GG+a+s++le+++er+++ +
  lcl|FitnessBrowser__WCS417:GFF1730 153 AMGKNITLVGGNGDGQTAKVANQIIVALNIQAVAEALLFASKNGADPAKVREALMGGFASSKILEVHGERMIKGT 227
                                         *************************************************************************** PP

                           TIGR01505 226 fkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakd 289
                                         f+PGfri+lhqkdl+lal  ak++g++lP+ta  +++++++ a G+g+ dhsal++ le++a+ 
  lcl|FitnessBrowser__WCS417:GFF1730 228 FDPGFRINLHQKDLNLALAGAKELGINLPNTAGTQQVFSTCTAIGGGNWDHSALIKGLEHMANF 291
                                         **************************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (296 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: 8.50
//
[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