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.6610.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.18
//
[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