Alignments for a candidate for argE in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Xanthobacter autotrophicus Py2

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012114603.1 XAUT_RS13000 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000017645.1:WP_012114603.1
          Length = 397

 Score =  301 bits (772), Expect = 2e-86
 Identities = 164/375 (43%), Positives = 228/375 (60%), Gaps = 8/375 (2%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           + + EIL KL+   S+   PN +VV+ I   + +    V  LP   G+++ +  +IGP++
Sbjct: 5   VSSEEILDKLISISSITDTPNEEVVAAIAA-IAAPFARVRRLPNAGGEKTALLISIGPED 63

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
             G ++S H DVV      WTS+PFR+     RLYGRGT+DMKGF+A VLAA+P  AA  
Sbjct: 64  RPGIVLSAHTDVVAVEGQPWTSNPFRIAARDGRLYGRGTSDMKGFIACVLAALPAFAAAD 123

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180
              P+H+ALSYDEE GC+G   ++A +  L  +PL  I+GEPT M+  RAHKGK   R T
Sbjct: 124 PLTPVHVALSYDEEIGCKGAGDLVAAVAALPARPLMCIVGEPTAMKVKRAHKGKTGWRAT 183

Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ 240
             GR+GHS+ P Q  NA+  +A +  +    AD L  G  +  F+PPY++L IG++ GG 
Sbjct: 184 ALGRTGHSALPHQAANAVTALARLAARLADLADELKTGAQDRAFDPPYATLHIGSLHGGG 243

Query: 241 AVNIIPDSCEVEFEARAISGVDPAELL----APVRKTAEALTTLGFEVE--WQELSAYPA 294
           A+N++PD   +EFE R I G D   L     A V++    L     E +   +ELSAYPA
Sbjct: 244 ALNVVPDRAVMEFELRTIPGSDTNTLFRRIEALVQEARAVLKAQAPEADLLLEELSAYPA 303

Query: 295 LSLEPDAPLAALLEELTGREALP-AVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYI 353
           L+   DAP AA +  LTG   +P  +++GTEAGL+ +AGI  ++CGPGDI RAHK DE+I
Sbjct: 304 LATASDAPEAAAVARLTGDNGVPGTIAFGTEAGLYAQAGIPTLVCGPGDIARAHKADEWI 363

Query: 354 LIDELMACRAMVEAL 368
             +EL  C AM+  L
Sbjct: 364 GREELAQCDAMLARL 378


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: 394
Number of extensions: 20
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: 397
Length adjustment: 30
Effective length of query: 344
Effective length of database: 367
Effective search space:   126248
Effective search space used:   126248
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 WP_012114603.1 XAUT_RS13000 (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.931287.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-115  371.9   1.4     2e-115  371.7   1.4    1.0  1  NCBI__GCF_000017645.1:WP_012114603.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_012114603.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.7   1.4    2e-115    2e-115       1     364 [.       9     378 ..       9     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 371.7 bits;  conditional E-value: 2e-115
                             TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 
                                           eil kL+++ s++ ++n +++  +++  ++    v++lp+a+g ek+ ll +iGp++ + g+vls htDvv v
  NCBI__GCF_000017645.1:WP_012114603.1   9 EILDKLISISSITDTPNEEVVAAIAAI-AAPFARVRRLPNAGG-EKTALLISIGPED-RPGIVLSAHTDVVAV 78 
                                           79********************99875.556679*********.***********99.*************** PP

                             TIGR01892  74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146
                                           ++++Wts+pfr+  +dgrLYgrGt+DmkGF+a+vLaa+p  aaa+   P+h++ls+Dee+g++Ga +l++a+a
  NCBI__GCF_000017645.1:WP_012114603.1  79 EGQPWTSNPFRIAARDGRLYGRGTSDMKGFIACVLAALPAFAAADPLTPVHVALSYDEEIGCKGAGDLVAAVA 151
                                           *********************************************************************9998 PP

                             TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredle 216
                                               rp + ivGePt ++  RahkGk   + t  Gr ghs+ p++ ++a++ +a+l arl +lad+lk + ++
  NCBI__GCF_000017645.1:WP_012114603.1 152 alpARPLMCIVGEPTAMKVKRAHKGKTGWRATALGRTGHSALPHQAANAVTALARLAARLADLADELKTGAQD 224
                                           8889********************************************************************* PP

                             TIGR01892 217 eaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevkvee 285
                                            aF+ppyatl+iG ++GG a n++++  ++++elR+ipG d + l   +e++ +e    +k++ap+ +   ee
  NCBI__GCF_000017645.1:WP_012114603.1 225 RAFDPPYATLHIGSLHGGGALNVVPDRAVMEFELRTIPGSDTNTLFRRIEALVQEaravLKAQAPEADLLLEE 297
                                           ******************************************99887777766666665999*********** PP

                             TIGR01892 286 lsatpaleleedaelvalleklaGa..aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkr 356
                                           lsa+pal++  da+ +a +++l+G+   + ++++gteagl  ++Gi+++v+GPGdi +ah++de++  eel +
  NCBI__GCF_000017645.1:WP_012114603.1 298 LSAYPALATASDAPEAAAVARLTGDngVPGTIAFGTEAGLYAQAGIPTLVCGPGDIARAHKADEWIGREELAQ 370
                                           *************************88899******************************************* PP

                             TIGR01892 357 crallerl 364
                                           c+a+l+rl
  NCBI__GCF_000017645.1:WP_012114603.1 371 CDAMLARL 378
                                           *****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (397 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: 19.02
//
[ok]

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