Alignments for a candidate for argE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Paraburkholderia bryophila 376MFSha3.1

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate H281DRAFT_04940 H281DRAFT_04940 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Burk376:H281DRAFT_04940
          Length = 387

 Score =  307 bits (787), Expect = 3e-88
 Identities = 158/371 (42%), Positives = 225/371 (60%), Gaps = 8/371 (2%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           +L  L+GF +V    N D++ +IR YL+  G+  ++    E  ++N+FATIGP E  G +
Sbjct: 9   LLSTLIGFATVSRESNLDMIGFIRDYLDELGVKSELFYNAERTKANLFATIGPHERGGIV 68

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     W+ D FRL     RLYGRGT DMKGF+A+VLAAVP      L+ P+
Sbjct: 69  LSGHTDVVPVEGQAWSVDAFRLTERDGRLYGRGTADMKGFIASVLAAVPGFVERDLKLPV 128

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           HLA SYDEE GC GV  M+A L     +P+  +IGEPT ++ +  HKGK A R  V+G  
Sbjct: 129 HLAFSYDEEVGCLGVRPMLAELERRPHKPVLCLIGEPTELKPVLGHKGKLAMRCQVKGAP 188

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPF-EHVFEPPYSSLQIGTVKGGQAVNI 244
            HS+    G+NAI   A ++++     D L    + +  F+PP+S++Q G +KGG+A+NI
Sbjct: 189 CHSAYAPYGVNAIQYAARMISRLEEIGDHLAQPEYRDERFDPPFSTVQTGVIKGGRALNI 248

Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTAEA-------LTTLGFEVEWQELSAYPALSL 297
           +P  CE +FE RA+ G D  ++   ++  AEA             ++ +Q LSAYPAL+ 
Sbjct: 249 VPAECEFDFEVRALPGFDAGQVADELQTYAEAELLPRMRAVKSDADIRFQSLSAYPALAT 308

Query: 298 EPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDE 357
            PD+  A LL  LTG      V++GTE GLF++AGI  ++CGPG + + HKPDEY+  ++
Sbjct: 309 SPDSEAARLLSLLTGSNEFGTVAFGTEGGLFEQAGIPTVVCGPGSMDQGHKPDEYLTSEQ 368

Query: 358 LMACRAMVEAL 368
           L  C AM+  L
Sbjct: 369 LSDCDAMLARL 379


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: 406
Number of extensions: 15
Number of successful extensions: 3
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: 387
Length adjustment: 30
Effective length of query: 344
Effective length of database: 357
Effective search space:   122808
Effective search space used:   122808
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 H281DRAFT_04940 H281DRAFT_04940 (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.26063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-129  418.7   0.0   1.2e-129  418.5   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04940  H281DRAFT_04940 acetylornithine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04940  H281DRAFT_04940 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.5   0.0  1.2e-129  1.2e-129       2     364 ..       9     379 ..       8     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 418.5 bits;  conditional E-value: 1.2e-129
                                    TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGh 67 
                                                  +l+ L++f +vs+ sn+d+i +++dyl+elgv+ e   +a+  +k nl+a+iGp+e +gg+vlsGh
  lcl|FitnessBrowser__Burk376:H281DRAFT_04940   9 LLSTLIGFATVSRESNLDMIGFIRDYLDELGVKSELFYNAER-TKANLFATIGPHE-RGGIVLSGH 72 
                                                  6889************************************99.*************.********* PP

                                    TIGR01892  68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeev 133
                                                  tDvvPv+++aW+ D+frLte+dgrLYgrGtaDmkGF+a vLaavp     +Lk P+hl++s+Deev
  lcl|FitnessBrowser__Burk376:H281DRAFT_04940  73 TDVVPVEGQAWSVDAFRLTERDGRLYGRGTADMKGFIASVLAAVPGFVERDLKLPVHLAFSYDEEV 138
                                                  ****************************************************************** PP

                                    TIGR01892 134 glaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaiela 196
                                                  g++G++ +++ l    ++p l ++GePt+l++v  hkGk +++ +v+G   hs+++  Gv+ai+ a
  lcl|FitnessBrowser__Burk376:H281DRAFT_04940 139 GCLGVRPMLAELErrpHKPVLCLIGEPTELKPVLGHKGKLAMRCQVKGAPCHSAYAPYGVNAIQYA 204
                                                  ********998884445667889******************************************* PP

                                    TIGR01892 197 akllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeel 261
                                                  a++++rl++  d+l + e+ +e F+pp++t++ G++kGG+a ni++a+Ce+ +e+R++pG d  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04940 205 ARMISRLEEIGDHLAQpEYRDERFDPPFSTVQTGVIKGGRALNIVPAECEFDFEVRALPGFDAGQV 270
                                                  ***************999************************************************ PP

                                    TIGR01892 262 lallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygtea 321
                                                    +l++ ae+     +++ + + +++ + lsa+pal++ +d+e+++ll  l+G+ +  +v++gte 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04940 271 ADELQTYAEAellprMRAVKSDADIRFQSLSAYPALATSPDSEAARLLSLLTGSnEFGTVAFGTEG 336
                                                  *******999888777777888899999*************************9899********* PP

                                    TIGR01892 322 gllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                  gl++++Gi++vv+GPG++dq h+pdeY+  e+l  c+a+l+rl
  lcl|FitnessBrowser__Burk376:H281DRAFT_04940 337 GLFEQAGIPTVVCGPGSMDQGHKPDEYLTSEQLSDCDAMLARL 379
                                                  ****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (387 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: 9.36
//
[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