Alignments for a candidate for garR in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Burkholderia phytofirmans PsJN

Align tartronate semialdehyde reductase 2 (characterized)
to candidate BPHYT_RS24130 BPHYT_RS24130 tartronate semialdehyde reductase

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



>FitnessBrowser__BFirm:BPHYT_RS24130
          Length = 297

 Score =  377 bits (968), Expect = e-109
 Identities = 187/290 (64%), Positives = 227/290 (78%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIFI 61
           K GFIGLGIMG PMA NL + G  L   T   V D+L+  GAV+ ++   V   +D+IFI
Sbjct: 3   KAGFIGLGIMGKPMAANLLKNGVALAAFTRSGVPDDLVQAGAVACDSPAAVGAQADVIFI 62

Query: 62  MVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSG 121
           MVPDTP VE VLFGE G       G+T+VDMSSISP+ T+ FA +V E G DYLDAPVSG
Sbjct: 63  MVPDTPDVERVLFGEQGLASVLRAGQTVVDMSSISPMATREFAARVRESGADYLDAPVSG 122

Query: 122 GEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIE 181
           GE+GA+ G+L+IMVGG+ A F+ VKPLF+++GKN+TL+GG G GQ CKVANQ+IVA  IE
Sbjct: 123 GEVGAKAGSLTIMVGGETATFDAVKPLFDMMGKNVTLIGGVGAGQVCKVANQVIVAATIE 182

Query: 182 AVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNL 241
           AV EALL ASKAG DP RVR+ALMGGFASSRILEVHGERM KRTF+PGF+I LHQKDLNL
Sbjct: 183 AVGEALLLASKAGVDPARVREALMGGFASSRILEVHGERMTKRTFDPGFRIELHQKDLNL 242

Query: 242 ALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291
           AL +A++L ++LPNTATCQ LFN C A+GG   DHSA+V+ALE +A+H++
Sbjct: 243 ALSTAQSLGVSLPNTATCQALFNACVAHGGKAWDHSAMVRALEFLADHEI 292


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: 330
Number of extensions: 8
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: 297
Length adjustment: 26
Effective length of query: 266
Effective length of database: 271
Effective search space:    72086
Effective search space used:    72086
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 BPHYT_RS24130 BPHYT_RS24130 (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.1432.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   7.2e-126  405.3   7.3   8.1e-126  405.1   7.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS24130  BPHYT_RS24130 tartronate semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS24130  BPHYT_RS24130 tartronate semialdehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.1   7.3  8.1e-126  8.1e-126       1     291 []       3     292 ..       3     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.1 bits;  conditional E-value: 8.1e-126
                                TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqve 70 
                                              k gfiGlGimGkPm+ nllk G  l ++t+   + d+l+ aGa++ ++ ++v  +advi++mvPd+P+ve
  lcl|FitnessBrowser__BFirm:BPHYT_RS24130   3 KAGFIGLGIMGKPMAANLLKNGVALAAFTRS-GVPDDLVQAGAVACDSPAAVGAQADVIFIMVPDTPDVE 71 
                                              789***************************9.99************************************ PP

                                TIGR01505  71 evalGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdka 140
                                               v++Ge+G+    + G+++vdmssi+P++++e+a  v+e G d+ldaPvsGGe+ga+ g l+imvGG+ a
  lcl|FitnessBrowser__BFirm:BPHYT_RS24130  72 RVLFGEQGLASVLRAGQTVVDMSSISPMATREFAARVRESGADYLDAPVSGGEVGAKAGSLTIMVGGETA 141
                                              ********************************************************************** PP

                                TIGR01505 141 vfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlag 210
                                               fd vkpl++++gk+++l+G+ GaGq++kvanqviva  ieav eal+la+kaGvdp +v++al+GG+a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS24130 142 TFDAVKPLFDMMGKNVTLIGGVGAGQVCKVANQVIVAATIEAVGEALLLASKAGVDPARVREALMGGFAS 211
                                              ********************************************************************** PP

                                TIGR01505 211 stvleakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalv 280
                                              s++le+++er+ +r+f+PGfri+lhqkdl+lal +a+++g++lP+ta+++ l++a+ a+G+   dhsa+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS24130 212 SRILEVHGERMTKRTFDPGFRIELHQKDLNLALSTAQSLGVSLPNTATCQALFNACVAHGGKAWDHSAMV 281
                                              ********************************************************************** PP

                                TIGR01505 281 raleklakdkv 291
                                              rale la++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS24130 282 RALEFLADHEI 292
                                              *******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (297 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: 00:00:00.01
# Mc/sec: 6.79
//
[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