Alignments for a candidate for mmsB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Pseudomonas simiae WCS417

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate GFF4636 PS417_23720 3-hydroxyisobutyrate dehydrogenase

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



>FitnessBrowser__WCS417:GFF4636
          Length = 295

 Score =  522 bits (1345), Expect = e-153
 Identities = 262/294 (89%), Positives = 277/294 (94%)

Query: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60
           MKIAFIGLGNMGAPMARNLIKAGH+LNL DLN+ VL ELA+LGGT+S + R+AA+ AELV
Sbjct: 1   MKIAFIGLGNMGAPMARNLIKAGHALNLFDLNQTVLKELAELGGTVSESPRDAAKDAELV 60

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
           ITMLPAA HVRSVWL EDGVLAGI KGVPAVDCSTIDPQT RDVAAAAAKQ VA+ADAPV
Sbjct: 61  ITMLPAAAHVRSVWLNEDGVLAGIGKGVPAVDCSTIDPQTIRDVAAAAAKQDVAVADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180
           SGGTGGA AGTLTFMVGA PELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLL IS
Sbjct: 121 SGGTGGAQAGTLTFMVGANPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180

Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSS+ YNPWPG++ETAP+SRGYTGGFGA
Sbjct: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSDTYNPWPGVIETAPSSRGYTGGFGA 240

Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP 294
           +LMLKDLGLATEAARQ  QPV+LGAVAQQLYQ+MSQRGEGGKDFSAIINSYRKP
Sbjct: 241 DLMLKDLGLATEAARQVKQPVILGAVAQQLYQSMSQRGEGGKDFSAIINSYRKP 294


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: 381
Number of extensions: 7
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: 294
Length of database: 295
Length adjustment: 26
Effective length of query: 268
Effective length of database: 269
Effective search space:    72092
Effective search space used:    72092
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 GFF4636 PS417_23720 (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.32116.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     5e-136  438.7   4.9   5.6e-136  438.5   4.9    1.0  1  lcl|FitnessBrowser__WCS417:GFF4636  PS417_23720 3-hydroxyisobutyrate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4636  PS417_23720 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.5   4.9  5.6e-136  5.6e-136       1     288 []       5     292 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 438.5 bits;  conditional E-value: 5.6e-136
                           TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagdeg 75 
                                         fiGlGnmG+pma+nl+kagha+++fdl+ ++++el e G ++++s+ +a+++a+ vitmlPa++hv+sv++ ++g
  lcl|FitnessBrowser__WCS417:GFF4636   5 FIGLGNMGAPMARNLIKAGHALNLFDLNQTVLKELAELGGTVSESPRDAAKDAELVITMLPAAAHVRSVWLNEDG 79 
                                         9************************************************************************** PP

                           TIGR01692  76 ilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamg 150
                                         +la + k+++ +d+stid+++ r va++aa++   ++daPvsGG+gga+aGtltfmvG++ e fa  +pvl++mg
  lcl|FitnessBrowser__WCS417:GFF4636  80 VLAGIGKGVPAVDCSTIDPQTIRDVAAAAAKQDVAVADAPVSGGTGGAQAGTLTFMVGANPELFATLQPVLAQMG 154
                                         *************************************************************************** PP

                           TIGR01692 151 knivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaP 225
                                         +nivh+G++G+Gq akiCnnlllgism+Gv+ea+alg +lG+d++vla i++ s+GrcWs+dtynP+PGv+e+aP
  lcl|FitnessBrowser__WCS417:GFF4636 155 RNIVHCGEVGTGQIAKICNNLLLGISMVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSDTYNPWPGVIETAP 229
                                         *************************************************************************** PP

                           TIGR01692 226 asngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavikllr 288
                                         +s+gy+gGf+++lmlkdlgla eaa++vk++v lGa+a++ly+ ++++g g+kdfsa+i+ +r
  lcl|FitnessBrowser__WCS417:GFF4636 230 SSRGYTGGFGADLMLKDLGLATEAARQVKQPVILGAVAQQLYQSMSQRGEGGKDFSAIINSYR 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.68
//
[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