Alignments for a candidate for mmsB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Pseudomonas fluorescens FW300-N1B4

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate Pf1N1B4_1228 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_5145
         (295 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228
          Length = 295

 Score =  562 bits (1448), Expect = e-165
 Identities = 287/295 (97%), Positives = 290/295 (98%)

Query: 1   MKIAFIGLGNMGAPMARNLIKAGHALRLVDLNKAVLAELEQLGGSISASAREAAEGAELV 60
           MKIAFIGLGNMGAPMARNLIKAGH+LRLVDLNKAVLAELEQLGGSISASAREAA+GAELV
Sbjct: 1   MKIAFIGLGNMGAPMARNLIKAGHSLRLVDLNKAVLAELEQLGGSISASAREAAQGAELV 60

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIGKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
           ITMLPAAVHVRSVWLGEDGVLAGI KGVPAVDCSTIDPQTARDVAAAAAKQGV MADAPV
Sbjct: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVVMADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180
           SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS
Sbjct: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180

Query: 181 MVGVSEAMALGDALGIDTKVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           MVGVSEAMALGDALGIDT VLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA
Sbjct: 181 MVGVSEAMALGDALGIDTTVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240

Query: 241 ELMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSLRGEGGQDFSAIINGYRKPQ 295
           ELMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMS RGEGG+DFSAIIN YRKPQ
Sbjct: 241 ELMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKPQ 295


Lambda     K      H
   0.317    0.133    0.386 

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: 386
Number of extensions: 9
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: 295
Length of database: 295
Length adjustment: 26
Effective length of query: 269
Effective length of database: 269
Effective search space:    72361
Effective search space used:    72361
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 Pf1N1B4_1228 (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.6681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.7e-134  433.7   8.5   1.9e-134  433.5   8.5    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228  3-hydroxyisobutyrate dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228  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 !  433.5   8.5  1.9e-134  1.9e-134       1     288 []       5     292 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 433.5 bits;  conditional E-value: 1.9e-134
                                      TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagk 64 
                                                    fiGlGnmG+pma+nl+kagh++r+ dl+ +++ el + G +++asa ea+++a+ vitmlPa+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228   5 FIGLGNMGAPMARNLIKAGHSLRLVDLNKAVLAELEQLGGSISASAREAAQGAELVITMLPAAV 68 
                                                    9*************************************************************** PP

                                      TIGR01692  65 hvesvyagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtl 128
                                                    hv+sv++g++g+la ++k+++ +d+stid+++ar va++aa++G v++daPvsGG+gga+aGtl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228  69 HVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVVMADAPVSGGTGGAAAGTL 132
                                                    **************************************************************** PP

                                      TIGR01692 129 tfmvGgeaeefaraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGl 192
                                                    tfmvG++ e fa  +pvl++mg+nivh+G++G+Gq akiCnnlllgism+Gv+ea+alg +lG+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228 133 TFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGISMVGVSEAMALGDALGI 196
                                                    **************************************************************** PP

                                      TIGR01692 193 dpkvlaeilskssGrcWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkas 256
                                                    d+ vla i++ s+GrcWs+++ynP+PG+ve+aPas+gy+gGf+++lmlkdlgla eaa++++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228 197 DTTVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGAELMLKDLGLATEAARQAHQP 260
                                                    **************************************************************** PP

                                      TIGR01692 257 vllGalarelyslfaskgagkkdfsavikllr 288
                                                    v+lGa+a++ly++++++g g+kdfsa+i+ +r
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1228 261 VVLGAVAQQLYQAMSQRGEGGKDFSAIINSYR 292
                                                    *****************************998 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.62
//
[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