Alignments for a candidate for garR in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Pseudomonas fluorescens FW300-N1B4

Align tartronate semialdehyde reductase 2 (characterized)
to candidate Pf1N1B4_3659 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659
          Length = 256

 Score =  338 bits (868), Expect = 6e-98
 Identities = 167/253 (66%), Positives = 204/253 (80%)

Query: 39  LSLGAVSVETARQVTEASDIIFIMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPI 98
           ++ GAV++   ++V + ++ I +MVPDTPQV++VLF  +G      KGK ++DMSSISP 
Sbjct: 1   VAAGAVALANPKEVAQEAEFIIVMVPDTPQVDDVLFRADGVAAGVSKGKVVIDMSSISPT 60

Query: 99  ETKRFARQVNELGGDYLDAPVSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITL 158
            TK FA ++NE G  YLDAPVSGGE+GA+  TLSIMVGGD   FER  PLF+ +GKNITL
Sbjct: 61  ATKAFAAKINEKGAQYLDAPVSGGEVGAKAATLSIMVGGDADAFERALPLFQAMGKNITL 120

Query: 159 VGGNGDGQTCKVANQIIVALNIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHG 218
           VGGNGDGQT KVANQIIVALNI+AV+EALLFASK GADP +VR+ALMGGFASS+ILEVHG
Sbjct: 121 VGGNGDGQTAKVANQIIVALNIQAVAEALLFASKNGADPAKVREALMGGFASSKILEVHG 180

Query: 219 ERMIKRTFNPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSA 278
           ERMIK TF+PGF+I+LHQKDLNLAL  A+ L +NLPNTA  Q++F+TCAA GGS  DHSA
Sbjct: 181 ERMIKGTFDPGFRISLHQKDLNLALAGARELGINLPNTANTQQVFSTCAAIGGSNWDHSA 240

Query: 279 LVQALELMANHKL 291
           L++ LE MAN  +
Sbjct: 241 LIKGLEHMANFSI 253


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: 287
Number of extensions: 5
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: 292
Length of database: 256
Length adjustment: 25
Effective length of query: 267
Effective length of database: 231
Effective search space:    61677
Effective search space used:    61677
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: 47 (22.7 bits)

Align candidate Pf1N1B4_3659 (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.31315.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.5e-109  351.0   8.1   2.8e-109  350.8   8.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659  2-hydroxy-3-oxopropionate reduct


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659  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 !  350.8   8.1  2.8e-109  2.8e-109      39     289 ..       1     251 [.       1     253 [. 0.99

  Alignments for each domain:
  == domain 1  score: 350.8 bits;  conditional E-value: 2.8e-109
                                      TIGR01505  39 laaGaesaetakevvedadvivtmvPdsPqveevalGenGileaakkGkvlvdmssiaPleske 102
                                                    +aaGa++    kev+++a+ i++mvPd+Pqv++v++  +G+  +  kGkv++dmssi+P ++k 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659   1 VAAGAVALANPKEVAQEAEFIIVMVPDTPQVDDVLFRADGVAAGVSKGKVVIDMSSISPTATKA 64 
                                                    699************************************************************* PP

                                      TIGR01505 103 lakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkpllealgksivlvGenGaGq 166
                                                    +a +++ekG ++ldaPvsGGe+ga+ +tlsimvGGd   f+++ pl++a+gk+i+lvG+nG+Gq
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659  65 FAAKINEKGAQYLDAPVSGGEVGAKAATLSIMVGGDADAFERALPLFQAMGKNITLVGGNGDGQ 128
                                                    **************************************************************** PP

                                      TIGR01505 167 tvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlldrdfkPGf 230
                                                    t+kvanq+ivalni+av+eal++a+k G+dp +v++al+GG+a+s++le+++er+++ +f+PGf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659 129 TAKVANQIIVALNIQAVAEALLFASKNGADPAKVREALMGGFASSKILEVHGERMIKGTFDPGF 192
                                                    **************************************************************** PP

                                      TIGR01505 231 ridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakd 289
                                                    ri lhqkdl+lal  a+++g++lP+ta  ++++++++a G+++ dhsal++ le++a+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3659 193 RISLHQKDLNLALAGARELGINLPNTANTQQVFSTCAAIGGSNWDHSALIKGLEHMANF 251
                                                    *********************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (256 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: 9.86
//
[ok]

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

Downloads

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

Related tools

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