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_RS19860 RR42_RS19860 tartronate semialdehyde reductase

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



>FitnessBrowser__Cup4G11:RR42_RS19860
          Length = 308

 Score =  389 bits (1000), Expect = e-113
 Identities = 201/297 (67%), Positives = 234/297 (78%), Gaps = 7/297 (2%)

Query: 3   LGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIFIM 62
           +GFIGLGIMG PMA +L  AGH L V  + P    L+  G     +A +V + +DII IM
Sbjct: 7   VGFIGLGIMGAPMAGHLRAAGHTLFVHDVNPAPQALVDAGVTVCTSAEEVAKRADIIVIM 66

Query: 63  VPDTPQVEEVLFGENGCT-------KASLKGKTIVDMSSISPIETKRFARQVNELGGDYL 115
           VPDTP VE VLF E G         K +  GK +VDMSSISPI TK FA +VN+LG  YL
Sbjct: 67  VPDTPHVEAVLFAEKGVAAALKGAGKQAAHGKIVVDMSSISPIATKDFAARVNKLGAAYL 126

Query: 116 DAPVSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQII 175
           DAPVSGGE+GA+  +L+IMVGG +  F+ VKPLF+LLGKN+TLVGGNGDGQT KVANQII
Sbjct: 127 DAPVSGGEVGAKAASLTIMVGGPQESFDEVKPLFDLLGKNVTLVGGNGDGQTTKVANQII 186

Query: 176 VALNIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALH 235
           VALNI+AVSEALLFASKAGADP RVRQALMGGFA+SRILEVHGERM+KRTF+PGF+I LH
Sbjct: 187 VALNIQAVSEALLFASKAGADPARVRQALMGGFAASRILEVHGERMVKRTFDPGFRIELH 246

Query: 236 QKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           QKDLNLALQ AKAL + LPNTAT QELFNTCAANG  + DHSAL +A+E+M+NH++A
Sbjct: 247 QKDLNLALQGAKALGVALPNTATAQELFNTCAANGLGKQDHSALCRAIEIMSNHEIA 303


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: 365
Number of extensions: 10
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: 308
Length adjustment: 27
Effective length of query: 265
Effective length of database: 281
Effective search space:    74465
Effective search space used:    74465
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_RS19860 RR42_RS19860 (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.23121.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-127  410.5   9.6   2.1e-127  410.3   9.6    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS19860  RR42_RS19860 tartronate semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS19860  RR42_RS19860 tartronate semialdehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.3   9.6  2.1e-127  2.1e-127       2     291 .]       7     302 ..       6     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 410.3 bits;  conditional E-value: 2.1e-127
                                 TIGR01505   2 vgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqve 70 
                                               vgfiGlGimG Pm+  l  aG+ l v +++ +a + l+ aG ++  +a+ev++ ad+iv+mvPd+P+ve
  lcl|FitnessBrowser__Cup4G11:RR42_RS19860   7 VGFIGLGIMGAPMAGHLRAAGHTLFVHDVN-PAPQALVDAGVTVCTSAEEVAKRADIIVIMVPDTPHVE 74 
                                               9*****************************.89999********************************* PP

                                 TIGR01505  71 evalGenGil.......eaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtls 132
                                               +v++ e+G+        ++a +Gk++vdmssi+P+++k++a  v+++G  +ldaPvsGGe+ga+ + l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS19860  75 AVLFAEKGVAaalkgagKQAAHGKIVVDMSSISPIATKDFAARVNKLGAAYLDAPVSGGEVGAKAASLT 143
                                               *******986333333345778*********************************************** PP

                                 TIGR01505 133 imvGGdkavfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavl 201
                                               imvGG +  fd+vkpl+++lgk+++lvG+nG+Gqt+kvanq+ivalni+avseal++a+kaG+dp +v+
  lcl|FitnessBrowser__Cup4G11:RR42_RS19860 144 IMVGGPQESFDEVKPLFDLLGKNVTLVGGNGDGQTTKVANQIIVALNIQAVSEALLFASKAGADPARVR 212
                                               ********************************************************************* PP

                                 TIGR01505 202 qalrGGlagstvleakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradG 270
                                               qal+GG+a+s++le+++er+++r+f+PGfri+lhqkdl+lal+ aka+g+alP+ta+ +el+++++a+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS19860 213 QALMGGFAASRILEVHGERMVKRTFDPGFRIELHQKDLNLALQGAKALGVALPNTATAQELFNTCAANG 281
                                               ********************************************************************* PP

                                 TIGR01505 271 dgtldhsalvraleklakdkv 291
                                                g+ dhsal ra+e ++++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS19860 282 LGKQDHSALCRAIEIMSNHEI 302
                                               ******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (308 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: 9.35
//
[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
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