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.903956.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.18
//
[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:

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:

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:

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:

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