Alignments for a candidate for argE in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Thermithiobacillus tepidarius DSM 3134

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate WP_038020139.1 G579_RS0114040 acetylornithine deacetylase

Query= SwissProt::P23908
         (383 letters)



>NCBI__GCF_000423825.1:WP_038020139.1
          Length = 395

 Score =  350 bits (899), Expect = e-101
 Identities = 182/373 (48%), Positives = 240/373 (64%), Gaps = 1/373 (0%)

Query: 10  EIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIG 69
           E+  AL+A+PS+S+ E   DQSNA +I LLA WF+DLGF VE  P  G  +K N++A++G
Sbjct: 12  EMLAALVASPSVSSPEPHWDQSNAGVIELLAAWFEDLGFAVEQVPCTGQPDKLNLIATLG 71

Query: 70  QGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDV 129
            G GGL+LAGHTDTVPFD  RW  DP  LTE DG+ YG+G ADMKGFF  +++A+RD+  
Sbjct: 72  SGPGGLVLAGHTDTVPFDVDRWRTDPLRLTEADGRWYGMGVADMKGFFPLVIEAVRDLRA 131

Query: 130 TKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHISNAIRI 189
             L++PL +LATADEE+SMAGAR        R   A+IGEPT L+PVR HKG +  ++R+
Sbjct: 132 ADLRQPLIVLATADEESSMAGARTLQALGRPRARHAVIGEPTGLRPVRLHKGIMMESLRL 191

Query: 190 QGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHIHGGDA 249
            G+SGHSS+PA G NA++ M   +G ++  R  L +R+    F V +PTLNLGHIHGGD+
Sbjct: 192 IGRSGHSSNPALGNNALDGMQRLMGALMAWRAELAQRHRNPLFEVAHPTLNLGHIHGGDS 251

Query: 250 SNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPGYECPP 309
            NRIC  CELH+D+RPLPGM ++ L   L              L    L    P  + P 
Sbjct: 252 PNRICGECELHIDLRPLPGMDMDALREELYATARQAVADSGLTLLCQPLFAGNPPLDTPA 311

Query: 310 NHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLETRFIKP 368
              +V+  E+L G   E V + TE P++Q L   T++LGPG I  AHQPDEYLE   ++P
Sbjct: 312 AAPIVQAAERLTGHAAEAVAFGTEGPYLQRLGMDTVILGPGDIACAHQPDEYLELARVRP 371

Query: 369 TRELITQVIHHFC 381
           T  L+  +I  FC
Sbjct: 372 TVALLQALIRRFC 384


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: 437
Number of extensions: 16
Number of successful extensions: 3
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: 395
Length adjustment: 30
Effective length of query: 353
Effective length of database: 365
Effective search space:   128845
Effective search space used:   128845
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 WP_038020139.1 G579_RS0114040 (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.2739877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-125  404.3   0.0   2.7e-125  404.2   0.0    1.0  1  NCBI__GCF_000423825.1:WP_038020139.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000423825.1:WP_038020139.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.2   0.0  2.7e-125  2.7e-125       1     365 []      12     380 ..      12     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 404.2 bits;  conditional E-value: 2.7e-125
                             TIGR01892   1 eilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGh 67 
                                           e+la+Lva +svs        sn+ +ie++++++e+lg+ave++p +++ +k nl+a+ G  +g gglvl+Gh
  NCBI__GCF_000423825.1:WP_038020139.1  12 EMLAALVASPSVSSPephwdqSNAGVIELLAAWFEDLGFAVEQVPCTGQPDKLNLIATLG--SGPGGLVLAGH 82 
                                           6899*********98899999***************************************..999******** PP

                             TIGR01892  68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakk 140
                                           tD+vP+d  +W +Dp+rLte dgr Yg G aDmkGF+ lv++av+dl aa+L++Pl ++++aDee ++aGa++
  NCBI__GCF_000423825.1:WP_038020139.1  83 TDTVPFDVDRWRTDPLRLTEADGRWYGMGVADMKGFFPLVIEAVRDLRAADLRQPLIVLATADEESSMAGART 155
                                           ************************************************************************* PP

                             TIGR01892 141 liealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkre 213
                                           l + + +r+++a++GePt+l++vR hkG++   +++ Gr+ghss+p+ G +a   +++l++ l+a + +l ++
  NCBI__GCF_000423825.1:WP_038020139.1 156 LQALGRPRARHAVIGEPTGLRPVRLHKGIMMESLRLIGRSGHSSNPALGNNALDGMQRLMGALMAWRAELAQR 228
                                           ************************************************************************* PP

                             TIGR01892 214 dleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveel 286
                                           + +  F++ ++tln+G+++GG+  n+i+++Cel+++lRp+pGmd+++l ++l ++a +++++   +     + 
  NCBI__GCF_000423825.1:WP_038020139.1 229 HRNPLFEVAHPTLNLGHIHGGDSPNRICGECELHIDLRPLPGMDMDALREELYATARQAVADSGLTLLCQPLF 301
                                           *****************************************************99999989998888889999 PP

                             TIGR01892 287 satpaleleedaelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcra 359
                                             +p l++++ a++v+ +e+l+G+aae+v++gte ++lq+lG+++v+lGPGdi  ahqpdeY+e+  ++++ a
  NCBI__GCF_000423825.1:WP_038020139.1 302 AGNPPLDTPAAAPIVQAAERLTGHAAEAVAFGTEGPYLQRLGMDTVILGPGDIACAHQPDEYLELARVRPTVA 374
                                           9************************************************************************ PP

                             TIGR01892 360 llerlv 365
                                           ll++l+
  NCBI__GCF_000423825.1:WP_038020139.1 375 LLQALI 380
                                           **9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (395 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.30
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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

GapMind for Amino acid biosynthesis