Alignments for a candidate for argE in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Shewanella amazonensis SB2B

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate 6936058 Sama_0255 acetylornithine deacetylase (RefSeq)

Query= SwissProt::P23908
         (383 letters)



>FitnessBrowser__SB2B:6936058
          Length = 383

 Score =  452 bits (1164), Expect = e-132
 Identities = 218/378 (57%), Positives = 278/378 (73%), Gaps = 1/378 (0%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNM 64
           +P     + +LI  PSISATE  LD SN  +I LL DWF DLGF+ +V  V GTR+K N+
Sbjct: 4   IPDLKSRFSSLIYAPSISATEPQLDMSNHSVIALLNDWFSDLGFDCQVTKVAGTRDKRNL 63

Query: 65  LASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDAL 124
           LA IG G GGLLLAGHTDTVPFD+GRW++DPF LTE D + YGLG+ DMKGFFA IL+A 
Sbjct: 64  LAKIGSGEGGLLLAGHTDTVPFDEGRWSQDPFVLTEKDDRWYGLGSCDMKGFFALILEAA 123

Query: 125 RDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHIS 184
           +D+ +  L+KPLYI A+ADEET+M GA+ FA  T +RP+ AIIGEPT L+PV  HKGH++
Sbjct: 124 KDLPLHNLQKPLYIFASADEETTMEGAKAFAANTGIRPEYAIIGEPTGLKPVYMHKGHLA 183

Query: 185 NAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHI 244
             IRI G+SGHSSDPARG+NAIE+MH  IG +L+L+ +L + Y  +AF+VPYPT+N GHI
Sbjct: 184 QGIRITGRSGHSSDPARGLNAIEIMHKVIGQLLKLKQHLADNYREDAFSVPYPTMNFGHI 243

Query: 245 HGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPG 304
           HGGDA+NRIC CC+LH+DIRPLPG+ L +L  +L + L  ++  +PG + +  L+P    
Sbjct: 244 HGGDAANRICGCCDLHLDIRPLPGLALEDLELMLVNYLQDITRDYPGSVDIRTLYPGSEA 303

Query: 305 YECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLET 363
           +    +    ++VE L G + EVVNY TEAP+I  L C TLVLGPGSINQAHQPDEY+  
Sbjct: 304 FAGVKDSAWTQLVESLSGQQAEVVNYATEAPYINKLGCQTLVLGPGSINQAHQPDEYMAM 363

Query: 364 RFIKPTRELITQVIHHFC 381
             +KPT EL+ Q+IH  C
Sbjct: 364 DQLKPTVELLKQLIHKAC 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: 454
Number of extensions: 12
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: 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 6936058 Sama_0255 (acetylornithine deacetylase (RefSeq))
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.31699.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.1e-138  446.3   0.0     5e-138  446.0   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6936058  Sama_0255 acetylornithine deacet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936058  Sama_0255 acetylornithine deacetylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.0   0.0    5e-138    5e-138       5     365 .]      13     377 ..      10     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 446.0 bits;  conditional E-value: 5e-138
                         TIGR01892   5 kLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvde 75 
                                        L+  +s+sa+      sn  +i +++d++ +lg+  +v +va++++k nlla iG  +g+ggl+l+GhtD+vP+de
  lcl|FitnessBrowser__SB2B:6936058  13 SLIYAPSISATepqldmSNHSVIALLNDWFSDLGFDCQVTKVAGTRDKRNLLAKIG--SGEGGLLLAGHTDTVPFDE 87 
                                       68888899998899999***************************************..999**************** PP

                         TIGR01892  76 aaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkliealarrpala 152
                                       ++W++Dpf Ltekd+r Yg+G++DmkGF+al+L+a++dl  ++L+kPl++ +saDee+++ Gak +++ +  rp+ a
  lcl|FitnessBrowser__SB2B:6936058  88 GRWSQDPFVLTEKDDRWYGLGSCDMKGFFALILEAAKDLPLHNLQKPLYIFASADEETTMEGAKAFAANTGIRPEYA 164
                                       ***************************************************************************** PP

                         TIGR01892 153 ivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaFtppyatlniG 229
                                       i+GePt+l++v  hkG+ ++ ++++Gr+ghss+p+rG++aie ++k++++l++l+++l +++ e+aF +py+t+n G
  lcl|FitnessBrowser__SB2B:6936058 165 IIGEPTGLKPVYMHKGHLAQGIRITGRSGHSSDPARGLNAIEIMHKVIGQLLKLKQHLADNYREDAFSVPYPTMNFG 241
                                       ***************************************************************************** PP

                         TIGR01892 230 tvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveelsatpaleleedaelvallek 306
                                       +++GG+a n+i+++C l+l++Rp+pG+ +e+l   l + +++++++ pg      + +   a++  +d+   +l+e 
  lcl|FitnessBrowser__SB2B:6936058 242 HIHGGDAANRICGCCDLHLDIRPLPGLALEDLELMLVNYLQDITRDYPGSVDIRTLYPGSEAFAGVKDSAWTQLVES 318
                                       ************************************************988888888999***************** PP

                         TIGR01892 307 laGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                       l+G++aevv+y+tea+++++lG++++vlGPG+i+qahqpdeY+ +++lk++ +ll++l+
  lcl|FitnessBrowser__SB2B:6936058 319 LSGQQAEVVNYATEAPYINKLGCQTLVLGPGSINQAHQPDEYMAMDQLKPTVELLKQLI 377
                                       ********************************************************986 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: 7.55
//
[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:

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