Alignments for a candidate for mmsB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Phaeobacter inhibens BS107

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate GFF1712 PGA1_c17360 3-hydroxyisobutyrate dehydrogenase MmsB

Query= reanno::pseudo3_N2E3:AO353_05985
         (294 letters)



>FitnessBrowser__Phaeo:GFF1712
          Length = 291

 Score =  258 bits (658), Expect = 1e-73
 Identities = 140/289 (48%), Positives = 181/289 (62%), Gaps = 9/289 (3%)

Query: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60
           M I FIGLGNMG PMA NL KAGH +   D+     A+++  G T++A+A EAA  AE+V
Sbjct: 1   MNIGFIGLGNMGGPMAANLAKAGHDVTGFDM-----ADVSIEGVTMAASAAEAATDAEVV 55

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
           ITMLP    +R+V    D V+  ++ G   VDCST+D  +AR VA  A    +   DAPV
Sbjct: 56  ITMLPNGQILRAV---ADDVIPAMSAGATLVDCSTVDVDSARAVADQAGSANLMFVDAPV 112

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180
           SGG GGA+ GTLTFM G +   FA  +P+   MG+  VHCGE G GQ AKICNN++L I+
Sbjct: 113 SGGIGGASGGTLTFMAGGSAAAFAAAEPLFDIMGQKAVHCGEAGAGQAAKICNNMILGIT 172

Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           M+G  EA AL D LG+D Q +  ++++S+G  WS   Y P PG+   +PA   Y  GF A
Sbjct: 173 MIGTCEAFALADKLGLDRQKMFDVVSTSSGYSWSMNAYCPAPGVGPQSPADNDYQPGFAA 232

Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQA-MSQRGEGGKDFSAII 288
           ELMLKDL LA +AA  A     +GA+AQ LY   +   G  GKDFSA++
Sbjct: 233 ELMLKDLRLAQQAAHSADADTPMGALAQALYSMFVEDEGGAGKDFSAML 281


Lambda     K      H
   0.317    0.132    0.382 

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: 217
Number of extensions: 11
Number of successful extensions: 3
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: 294
Length of database: 291
Length adjustment: 26
Effective length of query: 268
Effective length of database: 265
Effective search space:    71020
Effective search space used:    71020
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 GFF1712 PGA1_c17360 (3-hydroxyisobutyrate dehydrogenase MmsB)
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.10028.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.8e-120  386.0  15.1     7e-120  385.7  15.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1712  PGA1_c17360 3-hydroxyisobutyrate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1712  PGA1_c17360 3-hydroxyisobutyrate dehydrogenase MmsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.7  15.1    7e-120    7e-120       1     284 [.       5     281 ..       5     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 385.7 bits;  conditional E-value: 7e-120
                          TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagdegi 76 
                                        fiGlGnmGgpmaanl+kagh v+ fd+    +     +G+++aasaaea+++a+vvitmlP g+  ++v    +++
  lcl|FitnessBrowser__Phaeo:GFF1712   5 FIGLGNMGGPMAANLAKAGHDVTGFDMADVSI-----EGVTMAASAAEAATDAEVVITMLPNGQILRAVA---DDV 72 
                                        9*************************986655.....6999************************99997...9** PP

                          TIGR01692  77 lakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamgkn 152
                                        ++ ++ ++ l+d+st+dvdsar+va++a ++ ++f+daPvsGG+gga  Gtltfm+Gg+a++fa+aep+++ mg++
  lcl|FitnessBrowser__Phaeo:GFF1712  73 IPAMSAGATLVDCSTVDVDSARAVADQAGSANLMFVDAPVSGGIGGASGGTLTFMAGGSAAAFAAAEPLFDIMGQK 148
                                        **************************************************************************** PP

                          TIGR01692 153 ivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaPasn 228
                                         vh+G+aGaGqaakiCnn++lgi+miG++ea+al+ klGld + +++++s+ssG +Ws+++y+P PGv +q+Pa+n
  lcl|FitnessBrowser__Phaeo:GFF1712 149 AVHCGEAGAGQAAKICNNMILGITMIGTCEAFALADKLGLDRQKMFDVVSTSSGYSWSMNAYCPAPGVGPQSPADN 224
                                        **************************************************************************** PP

                          TIGR01692 229 gykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfa.skgagkkdfsavi 284
                                        +y++Gfa++lmlkdl+laq+aa+s+ a++++Gala++lys+f  ++g  +kdfsa++
  lcl|FitnessBrowser__Phaeo:GFF1712 225 DYQPGFAAELMLKDLRLAQQAAHSADADTPMGALAQALYSMFVeDEGGAGKDFSAML 281
                                        *****************************************98689999*****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (291 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: 00:00:00.01
# Mc/sec: 7.50
//
[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