GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Pseudomonas putida KT2440

Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate PP_4666 PP_4666 3-hydroxyisobutyrate dehydrogenase

Query= metacyc::MONOMER-11664
         (295 letters)



>FitnessBrowser__Putida:PP_4666
          Length = 295

 Score =  575 bits (1483), Expect = e-169
 Identities = 292/295 (98%), Positives = 293/295 (99%)

Query: 1   MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELV 60
           MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNK VLAELAELGGQISPSPKDAAANSELV
Sbjct: 1   MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKAVLAELAELGGQISPSPKDAAANSELV 60

Query: 61  ITMLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120
           ITMLPAAAHVRSVYLN+DGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV
Sbjct: 61  ITMLPAAAHVRSVYLNEDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120

Query: 121 SGGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180
           SGGTGGAAAGTLTFMVGAS ELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS
Sbjct: 121 SGGTGGAAAGTLTFMVGASTELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180

Query: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240
           MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA
Sbjct: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240

Query: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD 295
           ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD
Sbjct: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD 295


Lambda     K      H
   0.317    0.134    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: 460
Number of extensions: 10
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate PP_4666 PP_4666 (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.25620.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.6e-136  439.1   5.0   4.1e-136  439.0   5.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4666  PP_4666 3-hydroxyisobutyrate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4666  PP_4666 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.0   5.0  4.1e-136  4.1e-136       1     288 []       5     292 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 439.0 bits;  conditional E-value: 4.1e-136
                           TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagdeg 75 
                                         fiGlGnmG+pma+nl+kagh++++fdl+ +++ el e G q+++s+++a+++++ vitmlPa++hv+svy+ ++g
  lcl|FitnessBrowser__Putida:PP_4666   5 FIGLGNMGAPMARNLIKAGHQLNLFDLNKAVLAELAELGGQISPSPKDAAANSELVITMLPAAAHVRSVYLNEDG 79 
                                         9************************************************************************** PP

                           TIGR01692  76 ilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamg 150
                                         +la ++ +++ +d+stid+++ar v+++aaakG  + daPvsGG+gga+aGtltfmvG++ e fa  +pvle+mg
  lcl|FitnessBrowser__Putida:PP_4666  80 VLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPVSGGTGGAAAGTLTFMVGASTELFASLKPVLEQMG 154
                                         *************************************************************************** PP

                           TIGR01692 151 knivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaP 225
                                         +nivh+G++G+Gq akiCnnlllgismiGv+ea+alg +lG+d+kvla i++ s+GrcWs+dtynP+PG++e+aP
  lcl|FitnessBrowser__Putida:PP_4666 155 RNIVHCGEVGTGQIAKICNNLLLGISMIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAP 229
                                         *************************************************************************** PP

                           TIGR01692 226 asngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavikllr 288
                                         as+gy+gGf+++lmlkdlgla eaa++++++v lGa+a++ly++++ +g g+kdfsa+++ +r
  lcl|FitnessBrowser__Putida:PP_4666 230 ASRGYTGGFGAELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYR 292
                                         ***********************************************************9887 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: 9.57
//
[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:

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