Alignments for a candidate for mmsB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Acidovorax sp. GW101-3H11

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate Ac3H11_2362 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2362
          Length = 294

 Score =  365 bits (936), Expect = e-106
 Identities = 194/290 (66%), Positives = 218/290 (75%), Gaps = 2/290 (0%)

Query: 4   IAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVIS 63
           IAF+GLGNMGGPMA NL KAGH V  FDL   A   L   G   A  A     GAEVVIS
Sbjct: 3   IAFIGLGNMGGPMAHNLHKAGHEVRAFDLSQPARDKLAADGVPIATDAKAAVAGAEVVIS 62

Query: 64  MLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVSG 123
           MLPA QHVE L+LG   LLA++    L+IDCSTIA  T+RKVA+AA AKG+  +DAPVSG
Sbjct: 63  MLPASQHVEGLFLGAGELLAQLPAGTLIIDCSTIAAATSRKVADAAKAKGVAFIDAPVSG 122

Query: 124 GVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILMA 183
           G GGA AGTL+F+VGG A    RARPVLE MG NIFHAG  GAGQ AKICNNMLLGILMA
Sbjct: 123 GTGGAIAGTLTFMVGGDAADLERARPVLEKMGANIFHAGSVGAGQTAKICNNMLLGILMA 182

Query: 184 GTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQVRL 243
           GT+EA+ALGV NGLDP VLSE+M++SSGGNWAL  YNP+PGVM  APAS GYAGGF   L
Sbjct: 183 GTSEAIALGVANGLDPKVLSEIMRRSSGGNWALEKYNPFPGVMEXAPASKGYAGGFGTDL 242

Query: 244 MNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKL 293
           M KDLGLA  NA AV+A+TPLG +ARNL++ H+ A   H GLDFSSI K+
Sbjct: 243 MLKDLGLAQENAMAVKAATPLGGMARNLYAAHSLAG--HGGLDFSSIIKM 290


Lambda     K      H
   0.317    0.135    0.395 

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: 371
Number of extensions: 17
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: 298
Length of database: 294
Length adjustment: 26
Effective length of query: 272
Effective length of database: 268
Effective search space:    72896
Effective search space used:    72896
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 Ac3H11_2362 (3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

# 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/TIGR01692.hmm
# target sequence database:        /tmp/gapView.27217.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01692  [M=288]
Accession:   TIGR01692
Description: HIBADH: 3-hydroxyisobutyrate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.9e-130  419.8  11.5   3.3e-130  419.6  11.5    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362  3-hydroxyisobutyrate dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362  3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.6  11.5  3.3e-130  3.3e-130       1     287 [.       5     291 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 419.6 bits;  conditional E-value: 3.3e-130
                                        TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPa 62 
                                                      fiGlGnmGgpma+nl kagh+vr+fdls  a ++l ++G+ +a+ a++av++a+vvi+mlPa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362   5 FIGLGNMGGPMAHNLHKAGHEVRAFDLSQPARDKLAADGVPIATDAKAAVAGAEVVISMLPA 66 
                                                      9************************************************************* PP

                                        TIGR01692  63 gkhvesvyagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggar 124
                                                      ++hve +++g+ ++la++  ++l+id+sti++ ++rkva++a+akG  f+daPvsGG+gga 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362  67 SQHVEGLFLGAGELLAQLPAGTLIIDCSTIAAATSRKVADAAKAKGVAFIDAPVSGGTGGAI 128
                                                      ************************************************************** PP

                                        TIGR01692 125 aGtltfmvGgeaeefaraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealal 186
                                                      aGtltfmvGg a++++ra+pvle mg ni+haG +GaGq+akiCnn+llgi m+G++ea+al
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362 129 AGTLTFMVGGDAADLERARPVLEKMGANIFHAGSVGAGQTAKICNNMLLGILMAGTSEAIAL 190
                                                      ************************************************************** PP

                                        TIGR01692 187 geklGldpkvlaeilskssGrcWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqe 248
                                                      g+++Gldpkvl+ei+++ssG +W+l+ ynP+PGv+e aPas+gy+gGf+t+lmlkdlglaqe
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362 191 GVANGLDPKVLSEIMRRSSGGNWALEKYNPFPGVMEXAPASKGYAGGFGTDLMLKDLGLAQE 252
                                                      ************************************************************** PP

                                        TIGR01692 249 aaksvkasvllGalarelyslfaskgagkkdfsavikll 287
                                                      +a +vka ++lG +ar+ly++++ +g+g++dfs++ik++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2362 253 NAMAVKAATPLGGMARNLYAAHSLAGHGGLDFSSIIKMV 291
                                                      ************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.76
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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