Alignments for a candidate for garR in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for garR in Paraburkholderia bryophila 376MFSha3.1

Align tartronate semialdehyde reductase 2 (characterized)
to candidate H281DRAFT_00785 H281DRAFT_00785 2-hydroxy-3-oxopropionate reductase

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



>FitnessBrowser__Burk376:H281DRAFT_00785
          Length = 302

 Score =  377 bits (968), Expect = e-109
 Identities = 193/292 (66%), Positives = 233/292 (79%), Gaps = 3/292 (1%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADEL-LSLGAVSVETARQVTEASDIIF 60
           K+GFIGLGIMG  MA NL + GH L V    PV ++L  S   VS  TA  V +A+DI+ 
Sbjct: 3   KIGFIGLGIMGAHMARNLLKGGHTLFVNGAYPVPEDLGKSTNVVSDSTA--VAQAADIVI 60

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           IMVPDTP V  VLF ++G       GK ++DMSSISP++T+ FA+++N LG DYLDAPVS
Sbjct: 61  IMVPDTPDVANVLFADDGVAAGLTAGKLVIDMSSISPLDTQAFAKKINALGVDYLDAPVS 120

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GARE TL+IMVGG E  F + KPLFEL+GKNI+L+G NG GQTCKVANQIIVALNI
Sbjct: 121 GGEVGAREATLTIMVGGPEKAFAQAKPLFELMGKNISLIGDNGAGQTCKVANQIIVALNI 180

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           EAV+EALLFAS++GADP RVR+ALMGGFASSRILEVHGERM KRTFNPGF+I LHQKDLN
Sbjct: 181 EAVAEALLFASRSGADPERVRKALMGGFASSRILEVHGERMTKRTFNPGFRIELHQKDLN 240

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           LAL  A+ L + LP+TA+ Q+LF+ CAANGG   DHSA+V+ALE+MAN+++A
Sbjct: 241 LALDGARKLGIALPHTASAQQLFSVCAANGGKAWDHSAMVRALEIMANYEVA 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: 322
Number of extensions: 6
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: 302
Length adjustment: 26
Effective length of query: 266
Effective length of database: 276
Effective search space:    73416
Effective search space used:    73416
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 H281DRAFT_00785 H281DRAFT_00785 (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.28240.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     5e-123  395.9   5.7   5.6e-123  395.8   5.7    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00785  H281DRAFT_00785 2-hydroxy-3-oxop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00785  H281DRAFT_00785 2-hydroxy-3-oxopropionate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.8   5.7  5.6e-123  5.6e-123       1     291 []       3     291 ..       3     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 395.8 bits;  conditional E-value: 5.6e-123
                                    TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPds 66 
                                                  k+gfiGlGimG  m++nllk G+ l v     ++ ++ l   +++++   +v+++ad++++mvPd+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00785   3 KIGFIGLGIMGAHMARNLLKGGHTLFVNGAY-PVPED-LGKSTNVVSDSTAVAQAADIVIIMVPDT 66 
                                                  89************************99887.56555.5667788888899*************** PP

                                    TIGR01505  67 PqveevalGenGileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtls 132
                                                  P+v +v++ ++G+  +   Gk+++dmssi+Pl+++ +ak+++++G+d+ldaPvsGGe+ga+e+tl+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00785  67 PDVANVLFADDGVAAGLTAGKLVIDMSSISPLDTQAFAKKINALGVDYLDAPVSGGEVGAREATLT 132
                                                  ****************************************************************** PP

                                    TIGR01505 133 imvGGdkavfdkvkpllealgksivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpk 198
                                                  imvGG +  f ++kpl+e++gk+i l+G+nGaGqt+kvanq+ivalnieav+eal++a+++G+dp+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00785 133 IMVGGPEKAFAQAKPLFELMGKNISLIGDNGAGQTCKVANQIIVALNIEAVAEALLFASRSGADPE 198
                                                  ****************************************************************** PP

                                    TIGR01505 199 avlqalrGGlagstvleakkerlldrdfkPGfridlhqkdlalaldaakavgaalPvtavvaella 264
                                                  +v++al+GG+a+s++le+++er+ +r+f+PGfri+lhqkdl+lald a+ +g+alP ta+ ++l++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00785 199 RVRKALMGGFASSRILEVHGERMTKRTFNPGFRIELHQKDLNLALDGARKLGIALPHTASAQQLFS 264
                                                  ****************************************************************** PP

                                    TIGR01505 265 alradGdgtldhsalvraleklakdkv 291
                                                   ++a+G+   dhsa+vrale +a+ +v
  lcl|FitnessBrowser__Burk376:H281DRAFT_00785 265 VCAANGGKAWDHSAMVRALEIMANYEV 291
                                                  ***********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (302 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: 11.27
//
[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