Alignments for a candidate for argE in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate WP_026186172.1 THITHI_RS0108030 acetylornithine deacetylase

Query= SwissProt::P23908
         (383 letters)



>NCBI__GCF_000378965.1:WP_026186172.1
          Length = 386

 Score =  341 bits (875), Expect = 2e-98
 Identities = 184/379 (48%), Positives = 233/379 (61%), Gaps = 1/379 (0%)

Query: 4   KLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFN 63
           +LP   ++   LIA PS+S+     D SN  +I  LA W +  GF+V + P+ G   K N
Sbjct: 3   RLPSLNQMLARLIALPSVSSVSPEFDMSNRAVIDELAGWCEAAGFDVAITPIDGKPGKAN 62

Query: 64  MLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDA 123
           ++A++G+G GGL+LAGHTDTVP +   W +DPF LTE DG+LYGLGT+DMK F A  L+A
Sbjct: 63  LVATMGRGPGGLVLAGHTDTVPCNPELWRQDPFRLTERDGRLYGLGTSDMKSFLALALEA 122

Query: 124 LRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHI 183
            RD+   +  +PL ILATADEE+SMAGA+            A+IGEPT L+PVR HKG +
Sbjct: 123 ARDLTPEQFHQPLVILATADEESSMAGAKAIRAAGRPLGRHAVIGEPTGLRPVRMHKGIL 182

Query: 184 SNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGH 243
              IR+ G+SGHSSDP  G NA+E MH AI  I+  R  L+ RY+   F V  PTLNLGH
Sbjct: 183 MEGIRLTGRSGHSSDPRLGNNALEGMHRAITEIIAWRAELQARYNNPLFRVSGPTLNLGH 242

Query: 244 IHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIP 303
           IHGGD  NRIC  CELH+D+RPLPGM L+EL   L   L          L V  L    P
Sbjct: 243 IHGGDNPNRICGRCELHIDLRPLPGMDLDELRQALASRLERSLADTGLELEVFRLFDGTP 302

Query: 304 GYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLE 362
             E P +  +V   E L G   E V + TE P+++ L    +VLGPG I+QAHQPDEYL 
Sbjct: 303 AMETPADAPVVRAAESLTGHAAEAVAFGTEGPYLRDLDMDVVVLGPGDIDQAHQPDEYLS 362

Query: 363 TRFIKPTRELITQVIHHFC 381
              I+PT  L+  +I  FC
Sbjct: 363 MDRIEPTLNLLRSLIRGFC 381


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: 407
Number of extensions: 17
Number of successful extensions: 4
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: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
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_026186172.1 THITHI_RS0108030 (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.940106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-122  393.3   0.0   6.2e-122  393.1   0.0    1.0  1  NCBI__GCF_000378965.1:WP_026186172.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_026186172.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.1   0.0  6.2e-122  6.2e-122       2     364 ..      10     376 ..       9     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: 393.1 bits;  conditional E-value: 6.2e-122
                             TIGR01892   2 ilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGht 68 
                                           +la+L+a++svs        sn ++i+ ++++ e++g+ v   p  ++  k nl+a++G  +g gglvl+Ght
  NCBI__GCF_000378965.1:WP_026186172.1  10 MLARLIALPSVSSVspefdmSNRAVIDELAGWCEAAGFDVAITPIDGKPGKANLVATMG--RGPGGLVLAGHT 80 
                                           6899********99999999*************************9999**********..999********* PP

                             TIGR01892  69 DvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkl 141
                                           D+vP++ + W +DpfrLte+dgrLYg+Gt+Dmk Flal+L+a++dl  ++ ++Pl ++++aDee ++aGak +
  NCBI__GCF_000378965.1:WP_026186172.1  81 DTVPCNPELWRQDPFRLTERDGRLYGLGTSDMKSFLALALEAARDLTPEQFHQPLVILATADEESSMAGAKAI 153
                                           ************************************************************************* PP

                             TIGR01892 142 iealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkred 214
                                            +a+ +  ++a++GePt+l++vR hkG+    ++++Gr+ghss+p  G +a e +++++++++a + +l+ ++
  NCBI__GCF_000378965.1:WP_026186172.1 154 RAAGRPLGRHAVIGEPTGLRPVRMHKGILMEGIRLTGRSGHSSDPRLGNNALEGMHRAITEIIAWRAELQARY 226
                                           ****9******************************************************************** PP

                             TIGR01892 215 leeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveels 287
                                            +  F++ ++tln+G+++GG+  n+i++ Cel+++lRp+pGmd++el + l + +e   +++     + ++  
  NCBI__GCF_000378965.1:WP_026186172.1 227 NNPLFRVSGPTLNLGHIHGGDNPNRICGRCELHIDLRPLPGMDLDELRQALASRLERSLADTGLELEVFRLFD 299
                                           ***************************************************9999976555555555679999 PP

                             TIGR01892 288 atpaleleedaelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcral 360
                                            tpa+e+++da++v+ +e l+G+aae+v++gte ++l++l ++ vvlGPGdidqahqpdeY+ ++ ++++ +l
  NCBI__GCF_000378965.1:WP_026186172.1 300 GTPAMETPADAPVVRAAESLTGHAAEAVAFGTEGPYLRDLDMDVVVLGPGDIDQAHQPDEYLSMDRIEPTLNL 372
                                           **********************************************************************999 PP

                             TIGR01892 361 lerl 364
                                           l+ l
  NCBI__GCF_000378965.1:WP_026186172.1 373 LRSL 376
                                           9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (386 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.51
//
[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 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 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