GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsB in Pseudomonas fluorescens FW300-N2E3

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate AO353_05985 AO353_05985 3-hydroxyisobutyrate dehydrogenase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985 AO353_05985
           3-hydroxyisobutyrate dehydrogenase
          Length = 294

 Score =  574 bits (1479), Expect = e-169
 Identities = 294/294 (100%), Positives = 294/294 (100%)

Query: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60
           MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV
Sbjct: 1   MKIAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELV 60

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
           ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV
Sbjct: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180
           SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS
Sbjct: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180

Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA
Sbjct: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240

Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP 294
           ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP
Sbjct: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIINSYRKP 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: 429
Number of extensions: 4
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: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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 AO353_05985 AO353_05985 (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.19167.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.4e-133  429.0  10.0   4.9e-133  428.9  10.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985  AO353_05985 3-hydroxyisobutyrate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985  AO353_05985 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.9  10.0  4.9e-133  4.9e-133       1     288 []       5     292 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 428.9 bits;  conditional E-value: 4.9e-133
                                     TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkh 65 
                                                   fiGlGnmG+pma+nl+kagh++++ dl+ +++ el + G +++a+a ea+++a+ vitmlPa+ h
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985   5 FIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELVITMLPAAVH 69 
                                                   9**************************************************************** PP

                                     TIGR01692  66 vesvyagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltf 130
                                                   v+sv++g++g+la ++k+++ +d+stid+++ar va++aa++G  ++daPvsGG+gga+aGtltf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985  70 VRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVSGGTGGAAAGTLTF 134
                                                   ***************************************************************** PP

                                     TIGR01692 131 mvGgeaeefaraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpk 195
                                                   mvG++ e fa  +pvl++mg+nivh+G++G+Gq akiCnnlll+ism+Gv+ea+alg +lG+d++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985 135 MVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAISMVGVSEAMALGDALGIDTQ 199
                                                   ***************************************************************** PP

                                     TIGR01692 196 vlaeilskssGrcWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllG 260
                                                   vla i++ s+GrcWs+++ynP+PG+ve+aPas+gy+gGf+++lmlkdlgla eaa++++++v+lG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985 200 VLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGAELMLKDLGLATEAARQAHQPVMLG 264
                                                   ***************************************************************** PP

                                     TIGR01692 261 alarelyslfaskgagkkdfsavikllr 288
                                                   a+a++ly++++++g g+kdfsa+i+ +r
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05985 265 AVAQQLYQAMSQRGEGGKDFSAIINSYR 292
                                                   *************************998 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.49
//
[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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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