Alignments for a candidate for argE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Azospirillum brasilense Sp245

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AZOBR_RS30425 AZOBR_RS30425 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__azobra:AZOBR_RS30425
          Length = 385

 Score =  292 bits (747), Expect = 1e-83
 Identities = 159/376 (42%), Positives = 228/376 (60%), Gaps = 10/376 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           +IL +LV F +V    N D++ W +  LE+ G    ++P  +G ++N+FA++GP +  G 
Sbjct: 9   DILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDGRKANLFASVGPADRPGV 68

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVP     WTSDPFRL   A  LYGRGT DMKGF+AA +A   + +   L +P
Sbjct: 69  LLSGHTDVVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTLSQP 128

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           LHLALSYDEE GC GV  +I  +  L  +P   I+GEPT M+ + AHKGK A R+  RG 
Sbjct: 129 LHLALSYDEEVGCLGVRRLIDMMAALPVRPRFCIVGEPTLMQVVTAHKGKTALRIDCRGV 188

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVN 243
             HSS   QG+NAIH    +LT      +R+   G  +  ++ P++++  G ++GG A+N
Sbjct: 189 ECHSSLAPQGMNAIHMACDMLTGLRRLQERVQTEGSRDADYDVPWTTIHAGVIQGGSALN 248

Query: 244 IIPDSCEVEFEARAISGVDPAE-LLAPVRKTAEALTTL------GFEVEWQELSAYPALS 296
           I+P+ C ++ E R +   DP E LL  VR  A A+ T          VE  ELS+YP+L 
Sbjct: 249 IVPNHCRLDMEIRHLP-QDPVEPLLDAVRAEAAAIETRARSAFPAAAVEIAELSSYPSLD 307

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355
            + D+ + + ++ LTG  +L  +S+GTE GLF QR  +  ++CGPG IG AHKPDE+I  
Sbjct: 308 TDGDSEVVSFVKALTGGNSLGKISFGTEGGLFQQRLSLPTVVCGPGSIGEAHKPDEFIAE 367

Query: 356 DELMACRAMVEALGAR 371
           ++L AC  M++ L  R
Sbjct: 368 EQLAACDRMLDLLLTR 383


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: 367
Number of extensions: 15
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: 385
Length adjustment: 30
Effective length of query: 344
Effective length of database: 355
Effective search space:   122120
Effective search space used:   122120
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 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.23200.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: 7.10
//
[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