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.32487.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.40
//
[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:

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