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 GFF997 PGA1_c10140 acetylornithine deacetylase ArgE

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Phaeo:GFF997
          Length = 388

 Score =  218 bits (554), Expect = 3e-61
 Identities = 134/374 (35%), Positives = 191/374 (51%), Gaps = 10/374 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGD-RSNIFATIGPKEARG 63
           EI+ KL+ F +V    N  +V W+ GYL SHGI       P+   ++ +FA +GP     
Sbjct: 9   EIMTKLISFPTVSSETNLPLVDWVEGYLASHGITAHRWVDPDQPHKAAVFAHVGPDVEGA 68

Query: 64  YIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRR 123
            ++SGH DVVP     W SDPF +     + +GRGT DMKGF A  + A+       + R
Sbjct: 69  VVLSGHTDVVPIEGQPWDSDPFTVVERDGKYFGRGTCDMKGFDALAIWALVAAHHRGVAR 128

Query: 124 PLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRG 183
           PL LALS+DEE GC G P MI  + ++  +    I+GEP+ MR +  HKG       + G
Sbjct: 129 PLQLALSFDEEVGCTGAPPMIVAMQDVLPKGSCVIVGEPSVMRPVTGHKGGIGYSTHLVG 188

Query: 184 RSGHSSRPDQGLNAIHGVAGVLTQAVA-EADRLVGGPFE--HVFEPPYSSLQIGTVKGGQ 240
              HSS    G++AI   A ++  A A  A+ +   P +   +F PP+++  +G + GG 
Sbjct: 189 FEVHSSLMHTGVSAIMQGARLIDWANARNAENMAKTPDDVAALFTPPFTTCHVGMINGGT 248

Query: 241 AVNIIPDSCEVEFEARAISGVDPAE----LLAPVRKTAEALTTL--GFEVEWQELSAYPA 294
           A NI    C    + R + G   AE     LA VR     +  +     ++  +    P 
Sbjct: 249 AHNITAKDCRFVMDFRVVPGESAAEWEAAYLAKVRDIEAEMQVVHPDTRIDVSKKFNVPG 308

Query: 295 LSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYIL 354
           L  E +     L+  LTG      VSYGTEAG FQ AG  A+ICGPGDI +AH+P+EYI 
Sbjct: 309 LVPEVEGEAETLVRALTGDNGTHVVSYGTEAGQFQEAGYSAVICGPGDIAQAHQPNEYID 368

Query: 355 IDELMACRAMVEAL 368
           + +  A    ++ L
Sbjct: 369 VSQFNAGHRFMQQL 382


Lambda     K      H
   0.319    0.137    0.410 

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: 426
Number of extensions: 18
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: 374
Length of database: 388
Length adjustment: 30
Effective length of query: 344
Effective length of database: 358
Effective search space:   123152
Effective search space used:   123152
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF997 PGA1_c10140 (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.9217.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-116  375.2   0.1     2e-116  375.0   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF997  PGA1_c10140 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF997  PGA1_c10140 acetylornithine deacetylase ArgE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.0   0.1    2e-116    2e-116       1     365 []       9     383 ..       9     383 .. 0.95

  Alignments for each domain:
  == domain 1  score: 375.0 bits;  conditional E-value: 2e-116
                         TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaa 77 
                                       ei++kL++f++vs  +n++l+++ve+yl+++g+++++   +d+ +k  ++a +Gp + +g++vlsGhtDvvP+++++
  lcl|FitnessBrowser__Phaeo:GFF997   9 EIMTKLISFPTVSSETNLPLVDWVEGYLASHGITAHRWVDPDQPHKAAVFAHVGPDV-EGAVVLSGHTDVVPIEGQP 84 
                                       79******************************************************9.9****************** PP

                         TIGR01892  78 WtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrpal 151
                                       W sDpf++ e+dg+ +grGt+DmkGF al++ a+   +   + +Pl l+ls+Deevg++Ga+ +i a+    ++ ++
  lcl|FitnessBrowser__Phaeo:GFF997  85 WDSDPFTVVERDGKYFGRGTCDMKGFDALAIWALVAAHHRGVARPLQLALSFDEEVGCTGAPPMIVAMQdvlPKGSC 161
                                       **********************************9999999***********************998887889**** PP

                         TIGR01892 152 aivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva.ladklkr..edleeaFtppyat 225
                                       +ivGeP  +++v  hkG +    ++ G e hss  ++Gvsai++ a+l+  + a  a+++ +  +d+   Ftpp++t
  lcl|FitnessBrowser__Phaeo:GFF997 162 VIVGEPSVMRPVTGHKGGIGYSTHLVGFEVHSSLMHTGVSAIMQGARLIDWANArNAENMAKtpDDVAALFTPPFTT 238
                                       *************************************************988652678888756678889******* PP

                         TIGR01892 226 lniGtvkGGkavniiaaaCelvlelRpipGmdpee....llallekiaeevkekapgfevkveelsatpaleleeda 298
                                        ++G ++GG+a ni a+ C++v+++R +pG   +e     la++++i +e++  +p++ ++v ++   p+l +e ++
  lcl|FitnessBrowser__Phaeo:GFF997 239 CHVGMINGGTAHNITAKDCRFVMDFRVVPGESAAEweaaYLAKVRDIEAEMQVVHPDTRIDVSKKFNVPGLVPEVEG 315
                                       ******************************99876222256789999999999************************ PP

                         TIGR01892 299 elvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                       e++ l++ l+G+  ++vvsygteag++qe+G +av++GPGdi qahqp+eY++++++++++ ++++l+
  lcl|FitnessBrowser__Phaeo:GFF997 316 EAETLVRALTGDnGTHVVSYGTEAGQFQEAGYSAVICGPGDIAQAHQPNEYIDVSQFNAGHRFMQQLI 383
                                       ************89***************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (388 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: 00:00:00.01
# Mc/sec: 9.92
//
[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