Alignments for a candidate for argE in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Shewanella loihica PV-4

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate 5207679 Shew_0201 acetylornithine deacetylase (RefSeq)

Query= SwissProt::P23908
         (383 letters)



>FitnessBrowser__PV4:5207679
          Length = 386

 Score =  461 bits (1185), Expect = e-134
 Identities = 219/382 (57%), Positives = 284/382 (74%), Gaps = 1/382 (0%)

Query: 1   MKNKLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRN 60
           M    P   + +R LIATPSISA E  LD SN  ++TLL+ W  DLGF+ ++Q VP TR 
Sbjct: 1   MMKTFPDIKQSFRELIATPSISALEAELDMSNQGVVTLLSQWLTDLGFDCQMQAVPDTRG 60

Query: 61  KFNMLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFI 120
           K N+LA IGQG GGLLLAGHTDTVPFD+GRW++DPFTLTE D + YGLG+ DMKGFFA +
Sbjct: 61  KHNLLAKIGQGRGGLLLAGHTDTVPFDEGRWSQDPFTLTEKDNRWYGLGSCDMKGFFALV 120

Query: 121 LDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHK 180
           ++A+R +      +PLYILA+ADEET+M GA+ FA++ A+ P+ A+IGEPT L+PV  HK
Sbjct: 121 IEAVRQMPTQDFVRPLYILASADEETTMNGAKAFAQSKAIAPEYALIGEPTGLKPVYMHK 180

Query: 181 GHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLN 240
           GH++  IRI G+SGHSSDPA+G+NAIE+MH  IG +L+L+ +L E Y  EAF+VPYPT+N
Sbjct: 181 GHLAQGIRITGRSGHSSDPAKGLNAIEIMHQVIGQLLKLKQHLAEHYREEAFSVPYPTMN 240

Query: 241 LGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHP 300
            GHIHGGDA+NRIC CC+LH+DIRPLPG+ L  L  LL   LA +S+R+PG +++ +L+P
Sbjct: 241 FGHIHGGDAANRICGCCDLHLDIRPLPGLPLEVLEQLLTQYLAELSQRYPGSISISQLYP 300

Query: 301 PIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDE 359
               +    + Q  ++V +L     EVVNY TEAP+IQ L C TLV GPGSI QAHQPDE
Sbjct: 301 GSQPFAGQADAQWSQLVAQLSNQAPEVVNYATEAPYIQQLGCQTLVWGPGSIEQAHQPDE 360

Query: 360 YLETRFIKPTRELITQVIHHFC 381
           YL+T +I  T +L+ Q+I+H C
Sbjct: 361 YLDTAYINKTVDLLKQLIYHAC 382


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: 470
Number of extensions: 8
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: 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 5207679 Shew_0201 (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.3712594.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                    -----------
     8e-137  442.1   0.0   9.2e-137  441.9   0.0    1.0  1  FitnessBrowser__PV4:5207679  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__PV4:5207679  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.9   0.0  9.2e-137  9.2e-137       3     365 .]      12     378 ..      10     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 441.9 bits;  conditional E-value: 9.2e-137
                    TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaaW 78 
                                  +++L+a++s+sa+      sn+ +++++ ++l +lg+  + + v+d++ k nlla iG  +g+ggl+l+GhtD+vP+de++W
  FitnessBrowser__PV4:5207679  12 FRELIATPSISALeaeldmSNQGVVTLLSQWLTDLGFDCQMQAVPDTRGKHNLLAKIG--QGRGGLLLAGHTDTVPFDEGRW 91 
                                  789*********999*******************************************..9********************* PP

                    TIGR01892  79 tsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkliealarrpalaivGePtsl 160
                                  ++Dpf+Ltekd+r Yg+G++DmkGF+alv++av+++ +++  +Pl++++saDee+++ Gak +++  a  p+ a++GePt+l
  FitnessBrowser__PV4:5207679  92 SQDPFTLTEKDNRWYGLGSCDMKGFFALVIEAVRQMPTQDFVRPLYILASADEETTMNGAKAFAQSKAIAPEYALIGEPTGL 173
                                  ********************************************************************************** PP

                    TIGR01892 161 vavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaFtppyatlniGtvkGGkavniiaa 242
                                  ++v  hkG+ ++ ++++Gr+ghss+p++G++aie +++++++l++l+++l +++ eeaF +py+t+n G+++GG+a n+i++
  FitnessBrowser__PV4:5207679 174 KPVYMHKGHLAQGIRITGRSGHSSDPAKGLNAIEIMHQVIGQLLKLKQHLAEHYREEAFSVPYPTMNFGHIHGGDAANRICG 255
                                  ********************************************************************************** PP

                    TIGR01892 243 aCelvlelRpipGmdpeellallekiaeevkekapgfevkveelsatpaleleedaelvalleklaGaaaevvsygteagll 324
                                  +C l+l++Rp+pG+++e l +ll++ ++e++++ pg     ++ +  + ++ ++da+  +l+++l+ +a+evv+y+tea+++
  FitnessBrowser__PV4:5207679 256 CCDLHLDIRPLPGLPLEVLEQLLTQYLAELSQRYPGSISISQLYPGSQPFAGQADAQWSQLVAQLSNQAPEVVNYATEAPYI 337
                                  ********************************************************************************** PP

                    TIGR01892 325 qelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                  q+lG++++v GPG+i+qahqpdeY+++  ++++ +ll++l+
  FitnessBrowser__PV4:5207679 338 QQLGCQTLVWGPGSIEQAHQPDEYLDTAYINKTVDLLKQLI 378
                                  *************************************9986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.69
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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