GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Pseudomonas fluorescens FW300-N2C3

Align tartronate semialdehyde reductase 2 (characterized)
to candidate AO356_19610 AO356_19610 2-hydroxy-3-oxopropionate reductase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_19610
          Length = 296

 Score =  373 bits (958), Expect = e-108
 Identities = 189/291 (64%), Positives = 230/291 (79%), Gaps = 1/291 (0%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVAD-ELLSLGAVSVETARQVTEASDIIF 60
           K+GFIG GIMG PMA+NL +AGH L ++     A  +LL+ GAV++   ++V + ++ I 
Sbjct: 3   KIGFIGTGIMGHPMALNLQKAGHSLFLSQHHDAAPADLLAGGAVALANPKEVAQEAEFII 62

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           +MVPDTPQVE+VL   +G       GK ++DMSSISP  TK FA ++NE G  YLDAPVS
Sbjct: 63  VMVPDTPQVEDVLLRADGIAAGVGAGKVVIDMSSISPTATKAFAAKINEKGAQYLDAPVS 122

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GA+  TLSIMVGGD A FER  PLF+ +GKNITLVGGNGDGQT KVANQIIVALNI
Sbjct: 123 GGEVGAKAATLSIMVGGDSAAFERALPLFQAMGKNITLVGGNGDGQTAKVANQIIVALNI 182

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           +AV+EALLFA+K GADP +VR+ALMGGFASS+ILEVHGERMIK TF+PGF+I+LHQKDLN
Sbjct: 183 QAVAEALLFAAKNGADPAKVREALMGGFASSKILEVHGERMIKGTFDPGFRISLHQKDLN 242

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291
           LALQ AK L +NLPNTA  Q++F+TCAA GGS  DHSAL++ LE MAN  +
Sbjct: 243 LALQGAKELNINLPNTANAQQVFSTCAAIGGSHWDHSALIKGLEHMANFSI 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: 326
Number of extensions: 5
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 AO356_19610 AO356_19610 (2-hydroxy-3-oxopropionate 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.1403935.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.9e-123  397.3   9.9   2.2e-123  397.1   9.9    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610  AO356_19610 2-hydroxy-3-oxopropi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610  AO356_19610 2-hydroxy-3-oxopropionate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.1   9.9  2.2e-123  2.2e-123       1     289 [.       3     291 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 397.1 bits;  conditional E-value: 2.2e-123
                                       TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmv 63 
                                                     k+gfiG GimG+Pm+ nl kaG++l   + ++ a ++lla Ga++    kev+++a+ i++mv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610   3 KIGFIGTGIMGHPMALNLQKAGHSLFLSQHHDAAPADLLAGGAVALANPKEVAQEAEFIIVMV 65 
                                                     89************************************************************* PP

                                       TIGR01505  64 PdsPqveevalGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeaga 126
                                                     Pd+Pqve+v+l  +Gi  +   Gkv++dmssi+P ++k +a +++ekG ++ldaPvsGGe+ga
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610  66 PDTPQVEDVLLRADGIAAGVGAGKVVIDMSSISPTATKAFAAKINEKGAQYLDAPVSGGEVGA 128
                                                     *************************************************************** PP

                                       TIGR01505 127 iegtlsimvGGdkavfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvl 189
                                                     + +tlsimvGGd a f+++ pl++a+gk+i+lvG+nG+Gqt+kvanq+ivalni+av+eal++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610 129 KAATLSIMVGGDSAAFERALPLFQAMGKNITLVGGNGDGQTAKVANQIIVALNIQAVAEALLF 191
                                                     *************************************************************** PP

                                       TIGR01505 190 aekaGvdpkavlqalrGGlagstvleakkerlldrdfkPGfridlhqkdlalaldaakavgaa 252
                                                     a k G+dp +v++al+GG+a+s++le+++er+++ +f+PGfri lhqkdl+lal+ ak++ ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610 192 AAKNGADPAKVREALMGGFASSKILEVHGERMIKGTFDPGFRISLHQKDLNLALQGAKELNIN 254
                                                     *************************************************************** PP

                                       TIGR01505 253 lPvtavvaellaalradGdgtldhsalvraleklakd 289
                                                     lP+ta  ++++++++a G+++ dhsal++ le++a+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19610 255 LPNTANAQQVFSTCAAIGGSHWDHSALIKGLEHMANF 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.90
//
[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