GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucO in Escherichia coli BW25113

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate 16883 b2799 L-1,2-propanediol oxidoreductase (NCBI)

Query= SwissProt::P0A9S1
         (382 letters)



>lcl|FitnessBrowser__Keio:16883 b2799 L-1,2-propanediol
           oxidoreductase (NCBI)
          Length = 382

 Score =  764 bits (1973), Expect = 0.0
 Identities = 382/382 (100%), Positives = 382/382 (100%)

Query: 1   MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLA 60
           MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLA
Sbjct: 1   MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLA 60

Query: 61  WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRS 120
           WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRS
Sbjct: 61  WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRS 120

Query: 121 LEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADM 180
           LEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADM
Sbjct: 121 LEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADM 180

Query: 181 MDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGE 240
           MDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGE
Sbjct: 181 MDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGE 240

Query: 241 EMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYR 300
           EMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYR
Sbjct: 241 EMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYR 300

Query: 301 DIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDV 360
           DIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDV
Sbjct: 301 DIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDV 360

Query: 361 CTGGNPREATLEDIVELYHTAW 382
           CTGGNPREATLEDIVELYHTAW
Sbjct: 361 CTGGNPREATLEDIVELYHTAW 382


Lambda     K      H
   0.319    0.136    0.404 

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: 776
Number of extensions: 21
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 16883 b2799 (L-1,2-propanediol oxidoreductase (NCBI))
to HMM TIGR02638 (fucO: lactaldehyde reductase (EC 1.1.1.77))

# 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/TIGR02638.hmm
# target sequence database:        /tmp/gapView.17553.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02638  [M=379]
Accession:   TIGR02638
Description: lactal_redase: lactaldehyde reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-204  664.1   1.4   3.1e-204  663.9   1.4    1.0  1  lcl|FitnessBrowser__Keio:16883  b2799 L-1,2-propanediol oxidored


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16883  b2799 L-1,2-propanediol oxidoreductase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.9   1.4  3.1e-204  3.1e-204       1     379 []       2     378 ..       2     378 .. 1.00

  Alignments for each domain:
  == domain 1  score: 663.9 bits;  conditional E-value: 3.1e-204
                       TIGR02638   1 snrlilnevsyfGaGaiedivkevkrrgfkkalvvtdkdliklgvvdkvlelldeaklayelfdevvpnPtvevvkeGl 79 
                                     +nr+ilne+++fG+Ga+ ++++evkrrg++kal+vtdk+l+++gvv+kv++++d+a la++++d+vvpnPt++vvkeGl
  lcl|FitnessBrowser__Keio:16883   2 ANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITVVKEGL 80 
                                     59***************************************************************************** PP

                       TIGR02638  80 aafkesgadyliaiGGGspidtakaigiivnnPefadvvsleGvadtkkkavpiiaipttaGtaaevtinyvitdeekk 158
                                      +f++sgadyliaiGGGsp+dt+kaigii+nnPefadv+sleG+++t+k++vpi+aipttaGtaaevtinyvitdeek+
  lcl|FitnessBrowser__Keio:16883  81 GVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKR 159
                                     ******************************************************************************* PP

                       TIGR02638 159 rklvivdpkdiPavavvdaelmlslPksltaatGldalthaiegyitkgaweltdalelkaieliaralksavedgkdk 237
                                     rk+v+vdp+diP+va++da++m ++P++l+aatG+dalthaiegyit+gaw+ltdal++kaie+ia al+ +v++  dk
  lcl|FitnessBrowser__Keio:16883 160 RKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAG--DK 236
                                     ***************************************************************************..9* PP

                       TIGR02638 238 eareelalgqyvaGmafsnvGlGlvhglahplgalydlPhGvanaillPivmefnaekagekyreiakamgvkteelse 316
                                     +a ee+algqyvaGm+fsnvGlGlvhg+ahplga+y++PhGvanaillP+vm++na+++gekyr+ia++mgvk+e++s 
  lcl|FitnessBrowser__Keio:16883 237 DAGEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVEGMSL 315
                                     ******************************************************************************* PP

                       TIGR02638 317 eeareaaveavktlskrvgiPeklselgvkeediealaeaaladvCtggnPreataeeieely 379
                                     eear+aaveav +l+++vgiP +l+++gv++edi+ala+aal+dvCtggnPreat e+i ely
  lcl|FitnessBrowser__Keio:16883 316 EEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREATLEDIVELY 378
                                     **************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (379 nodes)
Target sequences:                          1  (382 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.59
//
[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