GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Klebsiella michiganensis M5al

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate BWI76_RS00840 BWI76_RS00840 acetylornithine deacetylase

Query= SwissProt::P23908
         (383 letters)



>FitnessBrowser__Koxy:BWI76_RS00840
          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.21123.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: 9.65
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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