GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argE in Azospirillum brasilense Sp245

Align Acetylornithine deacetylase; AO; Acetylornithinase; EC 3.5.1.16; N-acetylornithinase; NAO (uncharacterized)
to candidate AZOBR_RS30425 AZOBR_RS30425 acetylornithine deacetylase

Query= curated2:O68873
         (380 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS30425 AZOBR_RS30425
           acetylornithine deacetylase
          Length = 385

 Score =  195 bits (495), Expect = 2e-54
 Identities = 142/375 (37%), Positives = 191/375 (50%), Gaps = 25/375 (6%)

Query: 12  LTELVAMDTTSFRPNVPLIDYAQARLEAAGFSAERQKFLDDAGVEKVNLVAVKGGSGSGR 71
           L  LVA  T S   N+ LI +A+ RLEAAG +    + +      K NL A  G +   R
Sbjct: 11  LERLVAFPTVSRDSNLDLILWAKERLEAAGATT---RLVPSEDGRKANLFASVGPAD--R 65

Query: 72  AALALVGHSDCVPYDA-AWT-DALRLTEKDGRLYARGACDTKGFIACALHAALNAE--QL 127
             + L GH+D VP D  AWT D  RLT + G LY RG  D KGF+A A+  A  A    L
Sbjct: 66  PGVLLSGHTDVVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTL 125

Query: 128 KAPLMVVLTADEEVGLTGAKKLVEAGLG---RARHAIVGEPTRLIPVRANKGYCLAEVEV 184
             PL + L+ DEEVG  G ++L++       R R  IVGEPT +  V A+KG     ++ 
Sbjct: 126 SQPLHLALSYDEEVGCLGVRRLIDMMAALPVRPRFCIVGEPTLMQVVTAHKGKTALRIDC 185

Query: 185 RGKEGHSAYPDSGASAIFRAGRFLQRLEHLALTVLRE-DLDEGFQPPFTTVNVGVIQGGK 243
           RG E HS+    G +AI  A   L  L  L   V  E   D  +  P+TT++ GVIQGG 
Sbjct: 186 RGVECHSSLAPQGMNAIHMACDMLTGLRRLQERVQTEGSRDADYDVPWTTIHAGVIQGGS 245

Query: 244 AKNVIPGACRFVVEWRPIPGQPPERVSQLLETIRQELVRDE-------PAFEAQIRVVRT 296
           A N++P  CR  +E R +P  P   V  LL+ +R E    E       PA   +I  + +
Sbjct: 246 ALNIVPNHCRLDMEIRHLPQDP---VEPLLDAVRAEAAAIETRARSAFPAAAVEIAELSS 302

Query: 297 DRGVNTRADAEVVRFL-AEASGNAPETVSFGTEAPQMTE-LGAEAVVFGPGDIRVAHQTG 354
              ++T  D+EVV F+ A   GN+   +SFGTE     + L    VV GPG I  AH+  
Sbjct: 303 YPSLDTDGDSEVVSFVKALTGGNSLGKISFGTEGGLFQQRLSLPTVVCGPGSIGEAHKPD 362

Query: 355 EYVPVEDLVRCEAVL 369
           E++  E L  C+ +L
Sbjct: 363 EFIAEEQLAACDRML 377


Lambda     K      H
   0.319    0.136    0.396 

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: 346
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: 380
Length of database: 385
Length adjustment: 30
Effective length of query: 350
Effective length of database: 355
Effective search space:   124250
Effective search space used:   124250
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 AZOBR_RS30425 AZOBR_RS30425 (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.18778.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-122  394.6   0.0   2.5e-122  394.4   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS30425  AZOBR_RS30425 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS30425  AZOBR_RS30425 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.4   0.0  2.5e-122  2.5e-122       1     362 [.       9     378 ..       9     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 394.4 bits;  conditional E-value: 2.5e-122
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               +il++Lvaf++vs+ sn+dli +++++le++g +++ +p  dg  k nl+a++Gp++ + g++lsGhtD
  lcl|FitnessBrowser__azobra:AZOBR_RS30425   9 DILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDG-RKANLFASVGPAD-RPGVLLSGHTD 75 
                                               79*****************************************.9***********9.*********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138
                                               vvPvd++aWtsDpfrLt ++g LYgrGtaDmkGF+a+++a ++      L +Plhl+ls+Deevg++G+
  lcl|FitnessBrowser__azobra:AZOBR_RS30425  76 VVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTLSQPLHLALSYDEEVGCLGV 144
                                               ********************************************************************* PP

                                 TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204
                                               ++li+++a    rp+  ivGePt ++ v ahkGk + ++  rG e hss + +G++ai++a ++l+ l 
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 145 RRLIDMMAalpVRPRFCIVGEPTLMQVVTAHKGKTALRIDCRGVECHSSLAPQGMNAIHMACDMLTGLR 213
                                               *****9998889********************************************************* PP

                                 TIGR01892 205 aladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271
                                               +l+++++  +  +  +++p++t++ G+++GG+a ni+++ C+l +e+R +p  + e ll  +++ a++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 214 RLQERVQTeGSRDADYDVPWTTIHAGVIQGGSALNIVPNHCRLDMEIRHLPQDPVEPLLDAVRAEAAAi 282
                                               ******985788999************************************999999*****9999983 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllq.elGieavvlG 335
                                                  ++   p+  v++ els +p+l+++ d+e+v +++ l+G  ++  +s+gte gl+q +l +++vv+G
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 283 etrARSAFPAAAVEIAELSSYPSLDTDGDSEVVSFVKALTGGnSLGKISFGTEGGLFQqRLSLPTVVCG 351
                                               33344557999*****************************87699***********963699******* PP

                                 TIGR01892 336 PGdidqahqpdeYveieelkrcralle 362
                                               PG+i++ah+pde++  e+l +c+ +l 
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 352 PGSIGEAHKPDEFIAEEQLAACDRMLD 378
                                               ***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (385 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: 12.29
//
[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:

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:

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:

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