Alignments for a candidate for argE in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Sedimenticola selenatireducens DSM 17993

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate WP_037374548.1 A3GO_RS0102105 acetylornithine deacetylase

Query= SwissProt::P23908
         (383 letters)



>NCBI__GCF_000428045.1:WP_037374548.1
          Length = 381

 Score =  369 bits (946), Expect = e-106
 Identities = 190/377 (50%), Positives = 248/377 (65%), Gaps = 1/377 (0%)

Query: 6   PPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNML 65
           P  I +   LIA PS+S+     DQSN  +I  LADW +  GF VEV P+PG  +KFN++
Sbjct: 4   PALIPMIEQLIAAPSVSSISPQWDQSNEQVIQHLADWCRSAGFQVEVLPIPGHASKFNLV 63

Query: 66  ASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALR 125
           AS G+G GGL+L+GHTDTVP+D+ RW  DPF L E D +LYGLGT+DMK FFA +L+A+R
Sbjct: 64  ASAGKGPGGLVLSGHTDTVPYDEQRWQSDPFRLVERDNRLYGLGTSDMKAFFALVLEAVR 123

Query: 126 DVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHISN 185
            +D+++LK+PL +LATADEE++M GA+   ET       A+IGEPT L+PVR HKG    
Sbjct: 124 GLDLSQLKQPLTLLATADEESNMCGAQSLLETNRRLGRYAVIGEPTGLKPVRMHKGISME 183

Query: 186 AIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHIH 245
            IR+ G+SGHSS+PA GVNA+E M+  IG IL  RD L+ R+    F V  PTLNLGHIH
Sbjct: 184 IIRLHGRSGHSSNPALGVNALEGMYRVIGDILAWRDELQARHKNPLFEVEVPTLNLGHIH 243

Query: 246 GGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPGY 305
           GGD  NRICA CEL +D+RPLPGM L +L+  L   L  +      RL +    P IP  
Sbjct: 244 GGDNPNRICASCELQIDLRPLPGMVLQDLHDELAQRLERLMSGSELRLEIITPFPGIPSM 303

Query: 306 ECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLETR 364
           E   + ++V   E+L G     V + TEAP++Q L   TL+LGPG I+QAHQP+E++   
Sbjct: 304 ETAADSEIVRTAEQLTGHTASSVAFGTEAPYLQQLGMETLILGPGDIDQAHQPNEFIGLE 363

Query: 365 FIKPTRELITQVIHHFC 381
            I+P   L+  +I  FC
Sbjct: 364 RIQPMVGLLQGLIRSFC 380


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: 448
Number of extensions: 19
Number of successful extensions: 2
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: 381
Length adjustment: 30
Effective length of query: 353
Effective length of database: 351
Effective search space:   123903
Effective search space used:   123903
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_037374548.1 A3GO_RS0102105 (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.3691727.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-126  407.1   0.0   3.9e-126  406.9   0.0    1.0  1  NCBI__GCF_000428045.1:WP_037374548.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000428045.1:WP_037374548.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.9   0.0  3.9e-126  3.9e-126       3     362 ..      10     373 ..       8     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 406.9 bits;  conditional E-value: 3.9e-126
                             TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                           +++L+a +svs        sn ++i++++d+ +++g++vevlp ++ a k+nl+a+ G  +g gglvlsGhtD
  NCBI__GCF_000428045.1:WP_037374548.1  10 IEQLIAAPSVSSIspqwdqSNEQVIQHLADWCRSAGFQVEVLPIPGHASKFNLVASAG--KGPGGLVLSGHTD 80 
                                           5789******998899999***************************************..999********** PP

                             TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkli 142
                                           +vP+de++W sDpfrL e+d+rLYg+Gt+Dmk F+alvL+av+ l+  +Lk+Pl l+++aDee  + Ga++l+
  NCBI__GCF_000428045.1:WP_037374548.1  81 TVPYDEQRWQSDPFRLVERDNRLYGLGTSDMKAFFALVLEAVRGLDLSQLKQPLTLLATADEESNMCGAQSLL 153
                                           ************************************************************************* PP

                             TIGR01892 143 ealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredl 215
                                           e+  r  + a++GePt+l++vR hkG+    ++++Gr+ghss+p+ Gv+a e + ++++ ++a +d+l+ ++ 
  NCBI__GCF_000428045.1:WP_037374548.1 154 ETNRRLGRYAVIGEPTGLKPVRMHKGISMEIIRLHGRSGHSSNPALGVNALEGMYRVIGDILAWRDELQARHK 226
                                           ************************************************************************* PP

                             TIGR01892 216 eeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveelsa 288
                                           +  F+++ +tln+G+++GG+  n+i+a+Cel+++lRp+pGm +++l  +l + +e +      +   +   + 
  NCBI__GCF_000428045.1:WP_037374548.1 227 NPLFEVEVPTLNLGHIHGGDNPNRICASCELQIDLRPLPGMVLQDLHDELAQRLERLMSGSELRLEIITPFPG 299
                                           ***************************************************9999986666666666777888 PP

                             TIGR01892 289 tpaleleedaelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrall 361
                                           +p++e+ +d+e+v+ +e+l+G++a  v++gtea++lq+lG+e+++lGPGdidqahqp+e++ +e +++   ll
  NCBI__GCF_000428045.1:WP_037374548.1 300 IPSMETAADSEIVRTAEQLTGHTASSVAFGTEAPYLQQLGMETLILGPGDIDQAHQPNEFIGLERIQPMVGLL 372
                                           9999**************************************************************9988777 PP

                             TIGR01892 362 e 362
                                           +
  NCBI__GCF_000428045.1:WP_037374548.1 373 Q 373
                                           6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (381 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: 28.46
//
[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