GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argE in Klebsiella michiganensis M5al

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BWI76_RS00840 BWI76_RS00840 acetylornithine deacetylase

Query= ecocyc::ACETYLORNDEACET-MONOMER
         (383 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS00840 BWI76_RS00840
           acetylornithine deacetylase
          Length = 383

 Score =  741 bits (1913), Expect = 0.0
 Identities = 353/383 (92%), Positives = 370/383 (96%)

Query: 1   MKNKLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRN 60
           MKNKLPPFIEIYRALIATPSISATEEALDQSN  LI LLA WF+D+GFNVEVQPVP TRN
Sbjct: 1   MKNKLPPFIEIYRALIATPSISATEEALDQSNESLINLLAGWFRDIGFNVEVQPVPDTRN 60

Query: 61  KFNMLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFI 120
           KFN+LAS G GAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHD KLYGLGTADMKGFFAFI
Sbjct: 61  KFNLLASSGHGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDNKLYGLGTADMKGFFAFI 120

Query: 121 LDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHK 180
           LDALRDVDVT+LKKPLYILATADEETSMAGARYFAETT LRPDCAIIGEPTSLQP+RAHK
Sbjct: 121 LDALRDVDVTQLKKPLYILATADEETSMAGARYFAETTQLRPDCAIIGEPTSLQPIRAHK 180

Query: 181 GHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLN 240
           GH+SNA+RIQGQSGHSSDPARGVNAIELMHDAIG I+QLRD+LKERYHY AFTVP+PTLN
Sbjct: 181 GHMSNAVRIQGQSGHSSDPARGVNAIELMHDAIGRIMQLRDDLKERYHYAAFTVPWPTLN 240

Query: 241 LGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHP 300
           LG IHGGDASNRICACCELHMDIRPLPGMTLN+LNGLLN+ALAPVSERWPGRLTV ELHP
Sbjct: 241 LGAIHGGDASNRICACCELHMDIRPLPGMTLNDLNGLLNEALAPVSERWPGRLTVSELHP 300

Query: 301 PIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY 360
           PIPGYECPP+H+LVEVVEKLLGA+T+VVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY
Sbjct: 301 PIPGYECPPDHKLVEVVEKLLGAQTDVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY 360

Query: 361 LETRFIKPTRELITQVIHHFCWH 383
           LETRFIKPTRELITQV+HHFCWH
Sbjct: 361 LETRFIKPTRELITQVVHHFCWH 383


Lambda     K      H
   0.320    0.139    0.430 

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: 649
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: 383
Length of database: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS00840 BWI76_RS00840 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

# 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.aa/TIGR01892.hmm
# target sequence database:        /tmp/gapView.26110.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01892  [M=365]
Accession:   TIGR01892
Description: AcOrn-deacetyl: acetylornithine deacetylase (ArgE)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.8e-171  555.4   0.0   3.2e-171  555.3   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00840  BWI76_RS00840 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00840  BWI76_RS00840 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  555.3   0.0  3.2e-171  3.2e-171       1     365 []      10     377 ..      10     377 .. 1.00

  Alignments for each domain:
  == domain 1  score: 555.3 bits;  conditional E-value: 3.2e-171
                               TIGR01892   1 eilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvls 65 
                                             ei+++L+a++s+sa+      sn  li+++++++++ g++vev+pv+d+++k+nlla+ G  +gaggl+l+
  lcl|FitnessBrowser__Koxy:BWI76_RS00840  10 EIYRALIATPSISATeealdqSNESLINLLAGWFRDIGFNVEVQPVPDTRNKFNLLASSG--HGAGGLLLA 78 
                                             79**********************************************************..99******* PP

                               TIGR01892  66 GhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevgla 136
                                             GhtD+vP+d+++Wt+Dpf+Lte+d++LYg+GtaDmkGF+a++L+a++d+++++LkkPl+++++aDee+++a
  lcl|FitnessBrowser__Koxy:BWI76_RS00840  79 GHTDTVPFDDGRWTRDPFTLTEHDNKLYGLGTADMKGFFAFILDALRDVDVTQLKKPLYILATADEETSMA 149
                                             *********************************************************************** PP

                               TIGR01892 137 GakkliealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvala 207
                                             Ga++++e++  rp++ai+GePtsl+++RahkG++s++v+++G++ghss+p+rGv+aiel++++++r+++l+
  lcl|FitnessBrowser__Koxy:BWI76_RS00840 150 GARYFAETTQLRPDCAIIGEPTSLQPIRAHKGHMSNAVRIQGQSGHSSDPARGVNAIELMHDAIGRIMQLR 220
                                             *********************************************************************** PP

                               TIGR01892 208 dklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapg 278
                                             d lk+++++ aFt+p++tln+G ++GG+a+n+i+a+Cel++++Rp+pGm++++l++ll++++++v+e++pg
  lcl|FitnessBrowser__Koxy:BWI76_RS00840 221 DDLKERYHYAAFTVPWPTLNLGAIHGGDASNRICACCELHMDIRPLPGMTLNDLNGLLNEALAPVSERWPG 291
                                             *********************************************************************** PP

                               TIGR01892 279 fevkveelsatpaleleedaelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYv 349
                                             + ++ e+++++p++e+++d++lv+++ekl+Ga+++vv+y+tea+++q+l ++++vlGPG+i+qahqpdeY+
  lcl|FitnessBrowser__Koxy:BWI76_RS00840 292 RLTVSELHPPIPGYECPPDHKLVEVVEKLLGAQTDVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYL 361
                                             *************************************************.********************* PP

                               TIGR01892 350 eieelkrcrallerlv 365
                                             e++++k++r+l++++v
  lcl|FitnessBrowser__Koxy:BWI76_RS00840 362 ETRFIKPTRELITQVV 377
                                             *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (383 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: 00:00:00.01
# Mc/sec: 10.09
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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