Alignments for a candidate for garR in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Sinorhizobium meliloti 1021

Align tartronate semialdehyde reductase 2 (characterized)
to candidate SM_b20679 SM_b20679 tartronate semialdehyde reductase

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



>FitnessBrowser__Smeli:SM_b20679
          Length = 294

 Score =  380 bits (977), Expect = e-110
 Identities = 195/291 (67%), Positives = 233/291 (80%), Gaps = 1/291 (0%)

Query: 3   LGFIGLGIMGTPMAINLARAGHQLHVTT-IGPVADELLSLGAVSVETARQVTEASDIIFI 61
           +GFIGLGIMGTPMA +L  AGH++  +  + P   EL+  G   VET + + E  D I +
Sbjct: 4   IGFIGLGIMGTPMARHLQDAGHEIITSKFVIPPRQELVENGLEIVETPKALAETVDTIIL 63

Query: 62  MVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSG 121
           M+PDTP+V++VLFGENG      +GK ++DMSSISPIETK FA++V E G +Y+DAPVSG
Sbjct: 64  MLPDTPEVKDVLFGENGVYYGLGEGKLVIDMSSISPIETKEFAKKVRETGAEYIDAPVSG 123

Query: 122 GEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIE 181
           GE+GA+  +LSIM GG  + FER  PLF+L+GKNITLVG  GDGQ  KVANQIIVAL IE
Sbjct: 124 GEVGAKNASLSIMAGGKPSSFERALPLFKLMGKNITLVGDCGDGQVTKVANQIIVALTIE 183

Query: 182 AVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNL 241
           AVSEAL+FASKAGADP RVR+ALMGGFASSRILEVHG+RMIKRTF PGF+I+LHQKDLNL
Sbjct: 184 AVSEALVFASKAGADPARVREALMGGFASSRILEVHGDRMIKRTFEPGFRISLHQKDLNL 243

Query: 242 ALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           ALQ AK+L ++LPNTA  QELFN CAANG S LDHS LV+ALE MANH++A
Sbjct: 244 ALQGAKSLGISLPNTAATQELFNNCAANGDSGLDHSGLVRALERMANHEVA 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: 307
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: 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 SM_b20679 SM_b20679 (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.5329.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   3.7e-128  412.8   1.0   4.1e-128  412.6   1.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20679  SM_b20679 tartronate semialdehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20679  SM_b20679 tartronate semialdehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.6   1.0  4.1e-128  4.1e-128       2     291 .]       4     293 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.6 bits;  conditional E-value: 4.1e-128
                            TIGR01505   2 vgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalG 75 
                                          +gfiGlGimG+Pm++ l  aG+++ + +   +  +el+  G e +et k+++e  d i+ m+Pd+P+v++v++G
  lcl|FitnessBrowser__Smeli:SM_b20679   4 IGFIGLGIMGTPMARHLQDAGHEIITSKFVIPPRQELVENGLEIVETPKALAETVDTIILMLPDTPEVKDVLFG 77 
                                          79****************************9******************************************* PP

                            TIGR01505  76 enGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkpll 149
                                          enG+  +  +Gk+++dmssi+P+e+ke+ak+v+e G +++daPvsGGe+ga+++ lsim GG+ + f+++ pl+
  lcl|FitnessBrowser__Smeli:SM_b20679  78 ENGVYYGLGEGKLVIDMSSISPIETKEFAKKVRETGAEYIDAPVSGGEVGAKNASLSIMAGGKPSSFERALPLF 151
                                          ************************************************************************** PP

                            TIGR01505 150 ealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlld 223
                                          +++gk+i+lvG+ G+Gq++kvanq+ival ieavsealv+a+kaG+dp +v++al+GG+a+s++le++++r+++
  lcl|FitnessBrowser__Smeli:SM_b20679 152 KLMGKNITLVGDCGDGQVTKVANQIIVALTIEAVSEALVFASKAGADPARVREALMGGFASSRILEVHGDRMIK 225
                                          ************************************************************************** PP

                            TIGR01505 224 rdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakdkv 291
                                          r+f+PGfri lhqkdl+lal+ ak++g++lP+ta+ +el++ ++a+Gd++ldhs lvrale++a+++v
  lcl|FitnessBrowser__Smeli:SM_b20679 226 RTFEPGFRISLHQKDLNLALQGAKSLGISLPNTAATQELFNNCAANGDSGLDHSGLVRALERMANHEV 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.71
//
[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