Alignments for a candidate for argE in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Phaeobacter inhibens BS107

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF769 PGA1_c07830 acetylornithine deacetylase ArgE

Query= ecocyc::ACETYLORNDEACET-MONOMER
         (383 letters)



>FitnessBrowser__Phaeo:GFF769
          Length = 384

 Score =  202 bits (514), Expect = 1e-56
 Identities = 131/359 (36%), Positives = 194/359 (54%), Gaps = 19/359 (5%)

Query: 15  LIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGA-G 73
           LIA P++SA       SN ++I  LA+  +D G  V+V    G + K N+ A++G    G
Sbjct: 12  LIAYPTVSA------DSNLEMIAYLANRLEDCGARVDVMFDAGGQ-KANLFATLGPDTDG 64

Query: 74  GLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTKLK 133
           G++L+GH+D VP  D  WT DPFT+ E DG+LYG GT DMKGF A  L           +
Sbjct: 65  GIVLSGHSDVVPVTDQDWTSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKFAEQISR 124

Query: 134 KPLYILATADEETSMAGARYFAET---TALRPDCAIIGEPTSLQPVRAHKGHISNAIRIQ 190
           +P++   T DEE    GA +  +      L+P  A+IGEPTS++ V  HKG    + R Q
Sbjct: 125 RPIHFAFTYDEEVGCIGAGHLVQALRERGLKPRLALIGEPTSMRVVEGHKGCHEYSTRFQ 184

Query: 191 GQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEA-FTVPYPTLNLGHIHGGDA 249
           G  GH S+P RGVNA+E     +  +L LR +L++R   ++ F  P+ TLN+G ++GG A
Sbjct: 185 GLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQRTPPDSRFDPPWTTLNIGALNGGSA 244

Query: 250 SNRICACCELHMDIRPLPGMTLNELNGLL----NDALAPVSER-WPGRLTVDELHPPIPG 304
            N I +  ++  ++RP+     + +   +     D L P  +  +P      E+   + G
Sbjct: 245 HNVIASKAQVDWEMRPVQPSDADHVKDTMARYCRDTLLPAMQAIYPEASIETEVVGEVAG 304

Query: 305 YECPPNHQLVEVVEKLLGAK-TEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYL 361
                 ++  E++  LLG+   E+V + TEA   Q L    +V GPGSI QAH+ DEYL
Sbjct: 305 LTPTTQNEARELMADLLGSNAAELVPFGTEAGLFQELGMDVVVCGPGSIAQAHKADEYL 363


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: 376
Number of extensions: 19
Number of successful extensions: 6
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: 384
Length adjustment: 30
Effective length of query: 353
Effective length of database: 354
Effective search space:   124962
Effective search space used:   124962
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 GFF769 PGA1_c07830 (acetylornithine deacetylase ArgE)
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.15611.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.3e-119  383.7   0.0   4.9e-119  383.5   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF769  PGA1_c07830 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF769  PGA1_c07830 acetylornithine deacetylase ArgE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.5   0.0  4.9e-119  4.9e-119       2     364 ..       8     378 ..       7     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 383.5 bits;  conditional E-value: 4.9e-119
                         TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaaW 78 
                                       il++L+a ++vsa sn+++i y++++le+ g  v+v+  a+g +k nl+a+ Gp + +gg+vlsGh+DvvPv ++ W
  lcl|FitnessBrowser__Phaeo:GFF769   8 ILSDLIAYPTVSADSNLEMIAYLANRLEDCGARVDVMFDAGG-QKANLFATLGPDT-DGGIVLSGHSDVVPVTDQDW 82 
                                       899***************************************.***********99.9******************* PP

                         TIGR01892  79 tsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrpala 152
                                       tsDpf++ e dgrLYgrGt+DmkGF+a+ La +p+ a +  ++P+h ++++Deevg+ Ga +l++al     +p+la
  lcl|FitnessBrowser__Phaeo:GFF769  83 TSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKFAEQISRRPIHFAFTYDEEVGCIGAGHLVQALRergLKPRLA 159
                                       ******************************************************************9988889**** PP

                         TIGR01892 153 ivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edleeaFtppyatlni 228
                                       ++GePts++ v  hkG      + +G egh s+p rGv+a+e aa+ ++rl++l+  l++ +++++ F+pp++tlni
  lcl|FitnessBrowser__Phaeo:GFF769 160 LIGEPTSMRVVEGHKGCHEYSTRFQGLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQrTPPDSRFDPPWTTLNI 236
                                       **********************************************************986899************* PP

                         TIGR01892 229 GtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedael 300
                                       G ++GG+a n+ia++ ++  e+Rp+   d ++++  +     +     +++  p+  +++e++    +l +  ++e+
  lcl|FitnessBrowser__Phaeo:GFF769 237 GALNGGSAHNVIASKAQVDWEMRPVQPSDADHVKDTMARYCRDtllpaMQAIYPEASIETEVVGEVAGLTPTTQNEA 313
                                       *********************************99998776665666688899************************ PP

                         TIGR01892 301 valleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                        +l+++l+G+ aae v++gteagl+qelG++ vv+GPG+i qah++deY+ +++l +c  +l+rl
  lcl|FitnessBrowser__Phaeo:GFF769 314 RELMADLLGSnAAELVPFGTEAGLFQELGMDVVVCGPGSIAQAHKADEYLSLDQLSQCLTVLNRL 378
                                       *********99*************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (384 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: 00:00:00.01
# Mc/sec: 12.10
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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