Alignments for a candidate for mmsB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Marinobacter adhaerens HP15

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate GFF931 HP15_910 3-hydroxyisobutyrate dehydrogenase

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__Marino:GFF931
          Length = 295

 Score =  405 bits (1040), Expect = e-118
 Identities = 205/295 (69%), Positives = 235/295 (79%), Gaps = 2/295 (0%)

Query: 1   MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60
           M  I F+GLGNMGGPMA NL+KAGH V VFDL   AV  LV +GA+ A +A +   GAE 
Sbjct: 1   MAKITFIGLGNMGGPMAGNLVKAGHEVTVFDLSKDAVAALVSEGAKTAGTAHEAASGAEC 60

Query: 61  VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120
           VI+MLPAGQHVE++YLGDDGLLA++    L+ID STIAPETAR VAE A AK +  LDAP
Sbjct: 61  VITMLPAGQHVEAVYLGDDGLLAKLPAGTLVIDSSTIAPETARGVAEVARAKDIPFLDAP 120

Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180
           VSGGVGGA+AGTL+FI GG  E F +A+P+L+ MG+NIFHAGDHG+GQVAKICNNMLL I
Sbjct: 121 VSGGVGGAKAGTLTFICGGSEEAFNKAKPILDTMGKNIFHAGDHGSGQVAKICNNMLLAI 180

Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQ 240
           LM+GT+EALALGVKNGLDPAVLSE+MKQSSGGNWALN+YNPWPGVM   PAS  Y GGF 
Sbjct: 181 LMSGTSEALALGVKNGLDPAVLSEIMKQSSGGNWALNVYNPWPGVMEGVPASRNYEGGFL 240

Query: 241 VRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKLYR 295
           V LM KDLGLA  NA   QAS P+G+LARNLF LH  A   +  LDFSSIQ+LY+
Sbjct: 241 VNLMTKDLGLAFDNAVKNQASIPMGSLARNLFQLH--AGQGNGSLDFSSIQRLYK 293


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: 381
Number of extensions: 9
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: 295
Length adjustment: 26
Effective length of query: 272
Effective length of database: 269
Effective search space:    73168
Effective search space used:    73168
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 GFF931 HP15_910 (3-hydroxyisobutyrate dehydrogenase)
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.3459717.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   1.8e-136  440.1   6.5   2.1e-136  439.9   6.5    1.0  1  FitnessBrowser__Marino:GFF931  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF931  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.9   6.5  2.1e-136  2.1e-136       1     288 []       6     293 ..       6     293 .. 1.00

  Alignments for each domain:
  == domain 1  score: 439.9 bits;  conditional E-value: 2.1e-136
                      TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagdegilakv 80 
                                    fiGlGnmGgpma nl+kagh+v+vfdls +av  lv +Ga++a +a ea+++a++vitmlPag+hve+vy+gd+g+lak+
  FitnessBrowser__Marino:GFF931   6 FIGLGNMGGPMAGNLVKAGHEVTVFDLSKDAVAALVSEGAKTAGTAHEAASGAECVITMLPAGQHVEAVYLGDDGLLAKL 85 
                                    9******************************************************************************* PP

                      TIGR01692  81 kkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamgknivhaGdaG 160
                                      ++l+idssti++++ar vae a ak   fldaPvsGGvgga+aGtltf+ Gg++e+f++a+p+l++mgkni+haGd+G
  FitnessBrowser__Marino:GFF931  86 PAGTLVIDSSTIAPETARGVAEVARAKDIPFLDAPVSGGVGGAKAGTLTFICGGSEEAFNKAKPILDTMGKNIFHAGDHG 165
                                    ******************************************************************************** PP

                      TIGR01692 161 aGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaPasngykgGfatalml 240
                                    +Gq+akiCnn+ll+i m G++ealalg+k+Gldp+vl+ei+++ssG +W+l+ ynP+PGv+e++Pas++y+gGf ++lm+
  FitnessBrowser__Marino:GFF931 166 SGQVAKICNNMLLAILMSGTSEALALGVKNGLDPAVLSEIMKQSSGGNWALNVYNPWPGVMEGVPASRNYEGGFLVNLMT 245
                                    ******************************************************************************** PP

                      TIGR01692 241 kdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavikllr 288
                                    kdlgla ++a + +as+++G+lar+l++l+a +g g +dfs++++l++
  FitnessBrowser__Marino:GFF931 246 KDLGLAFDNAVKNQASIPMGSLARNLFQLHAGQGNGSLDFSSIQRLYK 293
                                    *********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (295 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: 14.93
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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