GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Marivita geojedonensis DPG-138

Align Acetylornithine deacetylase; AO; Acetylornithinase; EC 3.5.1.16; N-acetylornithinase; NAO (uncharacterized)
to candidate WP_085635729.1 MGEO_RS05565 acetylornithine deacetylase

Query= curated2:O68873
         (380 letters)



>NCBI__GCF_002115805.1:WP_085635729.1
          Length = 388

 Score =  181 bits (458), Expect = 4e-50
 Identities = 133/389 (34%), Positives = 184/389 (47%), Gaps = 33/389 (8%)

Query: 9   RATLTELVAMDTTSFRPNVPLIDYAQARLEAAGFSAERQKFLDDAGVEKVNLVAVKGGSG 68
           R  L +LV   T S   N+PLID+ +  L   G  + R    DD    K  L A  G   
Sbjct: 8   RQILDQLVKFPTVSRDTNLPLIDWVEEYLSEHGVQSHRHVKSDDP--TKAALFAHVGPEV 65

Query: 69  SGRAALALVGHSDCVPYDAA-W-TDALRLTEKDGRLYARGACDTKGFIACALHAALNAEQ 126
            G   L+  GH+D VP D   W TD   + EKDG+L+ RG  D KGF A A+ A + A+ 
Sbjct: 66  GGGVVLS--GHTDVVPTDGQPWSTDPFTVIEKDGKLFGRGTTDMKGFDALAIWALVEAQH 123

Query: 127 --LKAPLMVVLTADEEVGLTGAKKLVEAGLG---RARHAIVGEPTRLIPVRANKGYCLAE 181
             +  P+ V L+ DEE+G TGA  L+EA  G   +A   IVGEPT L  V  +KG     
Sbjct: 124 RGVSRPVQVALSYDEEIGCTGAPPLIEAMQGVVPKAETVIVGEPTMLKAVTGHKGGNTFW 183

Query: 182 VEVRGKEGHSAYPDSGASAIFRAGRFLQ---RLEHLALTVLREDLDEGFQPPFTTVNVGV 238
           V + G E HS+   +G SAI    + ++   R+   +       +   F PP+T V+VG 
Sbjct: 184 VHMHGFEVHSSIMHTGVSAIMYGAKLIEWANRMNAESAAAEPGPIAAQFNPPYTNVHVGQ 243

Query: 239 IQGGKAKNVIPGACRFVVEWRPIPGQPPERVSQLLETIRQELVRDEPAFEAQIRVVRTDR 298
           I+GG A N+    C F + +R +PG+  E+    L     E+       EA+++ VR + 
Sbjct: 244 IKGGTAHNITAKDCEFGLGFRVVPGETLEQWESKLREAAAEI-------EAEMKAVRPEA 296

Query: 299 GVNTRADAEVVRFLAEASG------------NAPETVSFGTEAPQMTELGAEAVVFGPGD 346
            +       +  F  E  G            N  + VS+GTEA      G   VV GPGD
Sbjct: 297 WIEITPVFSLPPFKPEDGGAAETLVRQLTGDNGTQYVSYGTEASHFQSAGYSVVVCGPGD 356

Query: 347 IRVAHQTGEYVPVEDLVRCEAVLARAVAH 375
           I VAHQ  EY+ V      +A + R + H
Sbjct: 357 IAVAHQPDEYITVAQFNEGQAFMERLLEH 385


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: 374
Number of extensions: 20
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: 388
Length adjustment: 30
Effective length of query: 350
Effective length of database: 358
Effective search space:   125300
Effective search space used:   125300
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 WP_085635729.1 MGEO_RS05565 (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.948007.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.2e-117  376.1   0.0     1e-116  375.9   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085635729.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085635729.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.9   0.0    1e-116    1e-116       2     364 ..      10     382 ..       9     383 .. 0.95

  Alignments for each domain:
  == domain 1  score: 375.9 bits;  conditional E-value: 1e-116
                             TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvd 74 
                                           il +Lv f++vs+ +n++li++ve+yl e+gv+ ++    d+ +k  l+a +Gp++  gg+vlsGhtDvvP+d
  NCBI__GCF_002115805.1:WP_085635729.1  10 ILDQLVKFPTVSRDTNLPLIDWVEEYLSEHGVQSHRHVKSDDPTKAALFAHVGPEV-GGGVVLSGHTDVVPTD 81 
                                           999****************************************************9.79************** PP

                             TIGR01892  75 eaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala. 146
                                           +++W++Dpf++ ekdg+L+grGt+DmkGF al++ a+ + +   + +P+ ++ls+Dee+g++Ga+ liea+  
  NCBI__GCF_002115805.1:WP_085635729.1  82 GQPWSTDPFTVIEKDGKLFGRGTTDMKGFDALAIWALVEAQHRGVSRPVQVALSYDEEIGCTGAPPLIEAMQg 154
                                           **********************************************************************999 PP

                             TIGR01892 147 ..rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaaklla...rlvaladklkred 214
                                             ++++++ivGePt l+av  hkG  ++ v+++G e hss  ++Gvsai+  akl++   r+ a++   + ++
  NCBI__GCF_002115805.1:WP_085635729.1 155 vvPKAETVIVGEPTMLKAVTGHKGGNTFWVHMHGFEVHSSIMHTGVSAIMYGAKLIEwanRMNAESAAAEPGP 227
                                           999************************************************9999972225556666677799 PP

                             TIGR01892 215 leeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevkv 283
                                               F+ppy+ +++G++kGG+a ni a+ Ce+ l +R +pG ++e+  ++l+++a+e    +k+  p+  +++
  NCBI__GCF_002115805.1:WP_085635729.1 228 IAAQFNPPYTNVHVGQIKGGTAHNITAKDCEFGLGFRVVPGETLEQWESKLREAAAEieaeMKAVRPEAWIEI 300
                                           9****************************************************99994444556678888888 PP

                             TIGR01892 284 eelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355
                                             +   p +++e+ + ++ l+++l+G+  ++ vsygtea  +q++G + vv+GPGdi +ahqpdeY+ + +++
  NCBI__GCF_002115805.1:WP_085635729.1 301 TPVFSLPPFKPEDGGAAETLVRQLTGDnGTQYVSYGTEASHFQSAGYSVVVCGPGDIAVAHQPDEYITVAQFN 373
                                           889999*********************89******************************************** PP

                             TIGR01892 356 rcrallerl 364
                                           +++a++erl
  NCBI__GCF_002115805.1:WP_085635729.1 374 EGQAFMERL 382
                                           *******97 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 19.11
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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:

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