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_RS31030 AZOBR_RS31030 acetylornithine deacetylase

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



>FitnessBrowser__azobra:AZOBR_RS31030
          Length = 398

 Score =  173 bits (438), Expect = 9e-48
 Identities = 125/375 (33%), Positives = 177/375 (47%), Gaps = 31/375 (8%)

Query: 6   PPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLG------FNVEVQPVPGTR 59
           P  +E+ R LIA  + S        SN DLI  + D   +LG      FN E       R
Sbjct: 15  PRTLELLRDLIAFDTTSRN------SNLDLIHYIRDHLAELGVSSTLVFNEE-------R 61

Query: 60  NKFNMLASIG-QGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFA 118
            K N+ A+IG    GG+ L+GHTD VP DD  W+ DPFTLTE DGKL+G GTADMKGF A
Sbjct: 62  TKANLYATIGPMDRGGVCLSGHTDVVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIA 121

Query: 119 FILDALRDVDVTKLKKPLYILATADEETSMAGARYFAET---TALRPDCAIIGEPTSLQP 175
             L    D     L  P++   + DEE    G           A++P   I+GEPT ++ 
Sbjct: 122 AALAMAPDFLAANLTTPVHYAFSYDEELGCLGVPGLLTQLAGMAVKPRLCIVGEPTRMRV 181

Query: 176 VRAHKGHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYE-AFTV 234
           +  HKG ++   R+ G + HSS   +GVNA+E   + +  +  +     E+  ++  + +
Sbjct: 182 IVGHKGKVALRCRVHGHACHSSLAPQGVNAVEYAAELVSFLRGMGRRFAEQGPFDHDYDI 241

Query: 235 PYPTLNLGHIHGGDASNRICACCELHMDIRPLP----GMTLNELNGLLNDALAPVSERWP 290
           PY T++ G + GG A N + +      +IR L        L EL          +    P
Sbjct: 242 PYTTVHTGVMEGGTARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLEPEMRAVRP 301

Query: 291 GRLTVDELHPPIPGYECPPNHQLVEVVEKLLGAKTE-VVNYCTEAPFIQTLC--PTLVLG 347
                 E     P  + PP  + V +V+ L        V + TE     ++   P +V G
Sbjct: 302 DAGFSWETLSDSPALDTPPESEEVTLVKNLAEQNGHGKVAFGTEGALFTSIANIPAVVCG 361

Query: 348 PGSINQAHQPDEYLE 362
           PG I QAH+PDEY+E
Sbjct: 362 PGDIEQAHKPDEYVE 376


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: 382
Number of extensions: 17
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: 383
Length of database: 398
Length adjustment: 31
Effective length of query: 352
Effective length of database: 367
Effective search space:   129184
Effective search space used:   129184
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_RS31030 AZOBR_RS31030 (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.21832.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.3e-118  379.7   0.0   8.3e-118  379.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS31030  AZOBR_RS31030 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS31030  AZOBR_RS31030 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.5   0.0  8.3e-118  8.3e-118       1     364 [.      19     390 ..      19     391 .. 0.96

  Alignments for each domain:
  == domain 1  score: 379.5 bits;  conditional E-value: 8.3e-118
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               e+l++L+afd++s+ sn+dli+y++d+l+elgv+   + + + ++k nl a+iGp + +gg+ lsGhtD
  lcl|FitnessBrowser__azobra:AZOBR_RS31030  19 ELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEE-RTKANLYATIGPMD-RGGVCLSGHTD 85 
                                               6799******************************98776655.5************9.*********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138
                                               vvPvd++ W+sDpf+Lte+dg+L+grGtaDmkGF+a++La +pd  aa+L  P+h ++s+Dee g++G+
  lcl|FitnessBrowser__azobra:AZOBR_RS31030  86 VVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAANLTTPVHYAFSYDEELGCLGV 154
                                               ********************************************************************* PP

                                 TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204
                                               + l+ +la    +p+l ivGePt+++ +  hkGk++ + +v+G+  hss + +Gv+a+e aa+l++ l 
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 155 PGLLTQLAgmaVKPRLCIVGEPTRMRVIVGHKGKVALRCRVHGHACHSSLAPQGVNAVEYAAELVSFLR 223
                                               ****99988889********************************************************* PP

                                 TIGR01892 205 aladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271
                                               ++  +  + +++++ ++ py+t++ G+++GG+a ni+++   +++e+R ++  + + +l++l++ a++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 224 GMGRRFAEqGPFDHDYDIPYTTVHTGVMEGGTARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTl 292
                                               *****98879*************************************************9999998875 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqe.lGieavvlG 335
                                                  +++  p+ +  +e+ls  pal++++++e v l+++la +     v++gte +l+++ + i+avv+G
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 293 epeMRAVRPDAGFSWETLSDSPALDTPPESEEVTLVKNLAEQnGHGKVAFGTEGALFTSiANIPAVVCG 361
                                               566778899*******************************9977889********99983579****** PP

                                 TIGR01892 336 PGdidqahqpdeYveieelkrcrallerl 364
                                               PGdi+qah+pdeYve++el r++ +l+rl
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 362 PGDIEQAHKPDEYVELSELARAERFLHRL 390
                                               *************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (398 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: 8.78
//
[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