Alignments for a candidate for garR in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Phyllobacterium brassicacearum STM 196

Align tartronate semialdehyde reductase 2 (characterized)
to candidate WP_106711239.1 CU102_RS11545 2-hydroxy-3-oxopropionate reductase

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



>NCBI__GCF_003010955.1:WP_106711239.1
          Length = 294

 Score =  374 bits (961), Expect = e-108
 Identities = 191/292 (65%), Positives = 235/292 (80%), Gaps = 3/292 (1%)

Query: 3   LGFIGLGIMGTPMAINLARAGHQLHVTT--IGPVADELLSLGAVSVETARQVTEASDIIF 60
           +GFIGLGIMGTPMA +L  AGH +  +   I P   EL+  G   VE+ + + E +DII 
Sbjct: 4   IGFIGLGIMGTPMARHLQDAGHDVSTSKFFIAP-KQELIDNGLKIVESPKALAEKTDIII 62

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           +M+PDTP+V++VLFGENG       GK ++DMSSISPI+TK FAR+V E G +Y+DAPVS
Sbjct: 63  LMLPDTPEVKDVLFGENGVVFGLKPGKLVIDMSSISPIDTKEFARKVRETGSEYIDAPVS 122

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GA+  +LSIM GG ++ F+R  PLF+L+GKNITLVG  GDGQ  KVANQIIVAL I
Sbjct: 123 GGEVGAKNASLSIMAGGTQSAFDRALPLFKLMGKNITLVGDCGDGQVTKVANQIIVALTI 182

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           EA+SEAL+ ASKAGA+P RVR+ALMGGFASSRILE+HG+RMIKRTF PGF+I+LHQKDLN
Sbjct: 183 EAISEALVLASKAGANPARVREALMGGFASSRILELHGDRMIKRTFEPGFRISLHQKDLN 242

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           LALQSAK L ++LPNTA+ QELFN+CAANG S LDHS LV+ALE +ANH++A
Sbjct: 243 LALQSAKTLGVSLPNTASTQELFNSCAANGESGLDHSGLVRALERIANHEVA 294


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: 308
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: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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 WP_106711239.1 CU102_RS11545 (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.2808091.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-129  416.8   1.5   2.5e-129  416.6   1.5    1.0  1  NCBI__GCF_003010955.1:WP_106711239.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106711239.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.6   1.5  2.5e-129  2.5e-129       2     291 .]       4     293 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 416.6 bits;  conditional E-value: 2.5e-129
                             TIGR01505   2 vgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveeval 74 
                                           +gfiGlGimG+Pm++ l  aG+++ + +      +el+  G + +e+ k+++e++d+i+ m+Pd+P+v++v++
  NCBI__GCF_003010955.1:WP_106711239.1   4 IGFIGLGIMGTPMARHLQDAGHDVSTSKFFIAPKQELIDNGLKIVESPKALAEKTDIIILMLPDTPEVKDVLF 76 
                                           89************************99999999*************************************** PP

                             TIGR01505  75 GenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkp 147
                                           GenG++ + k+Gk+++dmssi+P+++ke+a++v+e G +++daPvsGGe+ga+++ lsim GG ++ fd++ p
  NCBI__GCF_003010955.1:WP_106711239.1  77 GENGVVFGLKPGKLVIDMSSISPIDTKEFARKVRETGSEYIDAPVSGGEVGAKNASLSIMAGGTQSAFDRALP 149
                                           ************************************************************************* PP

                             TIGR01505 148 llealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakker 220
                                           l++++gk+i+lvG+ G+Gq++kvanq+ival iea+sealvla+kaG++p +v++al+GG+a+s++le +++r
  NCBI__GCF_003010955.1:WP_106711239.1 150 LFKLMGKNITLVGDCGDGQVTKVANQIIVALTIEAISEALVLASKAGANPARVREALMGGFASSRILELHGDR 222
                                           ************************************************************************* PP

                             TIGR01505 221 lldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakdkv 291
                                           +++r+f+PGfri lhqkdl+lal++ak++g++lP+ta+ +el+++++a+G+++ldhs lvrale++a+++v
  NCBI__GCF_003010955.1:WP_106711239.1 223 MIKRTFEPGFRISLHQKDLNLALQSAKTLGVSLPNTASTQELFNSCAANGESGLDHSGLVRALERIANHEV 293
                                           *********************************************************************97 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: 10.47
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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