Alignments for a candidate for garR in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Cupriavidus basilensis 4G11

Align tartronate semialdehyde reductase 2 (characterized)
to candidate RR42_RS23235 RR42_RS23235 tartronate semialdehyde reductase

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



>FitnessBrowser__Cup4G11:RR42_RS23235
          Length = 286

 Score =  387 bits (994), Expect = e-112
 Identities = 194/282 (68%), Positives = 227/282 (80%)

Query: 11  MGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIFIMVPDTPQVE 70
           MGTPMA NL   GH++ +++   V   LL  G V+  + ++V E +D+IF+MVPDTP VE
Sbjct: 1   MGTPMAANLIAGGHEVSLSSRSGVPQSLLDSGGVACSSGKEVAERADVIFLMVPDTPHVE 60

Query: 71  EVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSGGEIGAREGT 130
             LF   G       GK +VDMSSISPI TK FA +VN LG  YLDAPVSGGE+GAR  T
Sbjct: 61  AALFNNGGIAAGLSAGKIVVDMSSISPIATKAFAERVNALGCQYLDAPVSGGEVGARNAT 120

Query: 131 LSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALLFA 190
           LSIMVGG +A FE V+PLFEL+GKNITLVG NG GQT KVANQIIVALNIEAV+EALLFA
Sbjct: 121 LSIMVGGPQATFETVRPLFELMGKNITLVGDNGAGQTAKVANQIIVALNIEAVAEALLFA 180

Query: 191 SKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNLALQSAKALA 250
           SKAGADP RVRQALMGGFASS++LEVHGERMIKRTF+PGF+I LHQKDLNLAL +A+ + 
Sbjct: 181 SKAGADPARVRQALMGGFASSKVLEVHGERMIKRTFDPGFRIGLHQKDLNLALSNAREMG 240

Query: 251 LNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           ++LPNTATCQELFN CA++GGS  DHSALV+ALELMANH++A
Sbjct: 241 VSLPNTATCQELFNACASHGGSDWDHSALVRALELMANHEVA 282


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: 341
Number of extensions: 7
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: 286
Length adjustment: 26
Effective length of query: 266
Effective length of database: 260
Effective search space:    69160
Effective search space used:    69160
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 RR42_RS23235 RR42_RS23235 (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.10084.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-124  400.9   4.3   1.7e-124  400.8   4.3    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS23235  RR42_RS23235 tartronate semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS23235  RR42_RS23235 tartronate semialdehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.8   4.3  1.7e-124  1.7e-124      10     291 .]       1     281 [.       1     281 [. 0.99

  Alignments for each domain:
  == domain 1  score: 400.8 bits;  conditional E-value: 1.7e-124
                                 TIGR01505  10 mGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalGenG 78 
                                               mG+Pm+ nl+  G+++   ++   + + ll  G+++ ++ kev+e advi+ mvPd+P+ve+ ++ + G
  lcl|FitnessBrowser__Cup4G11:RR42_RS23235   1 MGTPMAANLIAGGHEVSLSSRS-GVPQSLLDSGGVACSSGKEVAERADVIFLMVPDTPHVEAALFNNGG 68 
                                               9****************99998.999******************************************* PP

                                 TIGR01505  79 ileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkp 147
                                               i  +   Gk++vdmssi+P+++k +a+ v+++G ++ldaPvsGGe+ga+++tlsimvGG +a f+ v+p
  lcl|FitnessBrowser__Cup4G11:RR42_RS23235  69 IAAGLSAGKIVVDMSSISPIATKAFAERVNALGCQYLDAPVSGGEVGARNATLSIMVGGPQATFETVRP 137
                                               ********************************************************************* PP

                                 TIGR01505 148 llealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvlea 216
                                               l+e++gk+i+lvG+nGaGqt+kvanq+ivalnieav+eal++a+kaG+dp +v+qal+GG+a+s+vle+
  lcl|FitnessBrowser__Cup4G11:RR42_RS23235 138 LFELMGKNITLVGDNGAGQTAKVANQIIVALNIEAVAEALLFASKAGADPARVRQALMGGFASSKVLEV 206
                                               ********************************************************************* PP

                                 TIGR01505 217 kkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvralek 285
                                               ++er+++r+f+PGfri lhqkdl+lal  a+++g++lP+ta+++el++a++++G+++ dhsalvrale+
  lcl|FitnessBrowser__Cup4G11:RR42_RS23235 207 HGERMIKRTFDPGFRIGLHQKDLNLALSNAREMGVSLPNTATCQELFNACASHGGSDWDHSALVRALEL 275
                                               ********************************************************************* PP

                                 TIGR01505 286 lakdkv 291
                                               +a+++v
  lcl|FitnessBrowser__Cup4G11:RR42_RS23235 276 MANHEV 281
                                               ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (286 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: 9.45
//
[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, or view the source code.

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