Alignments for a candidate for argE in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Pseudomonas simiae WCS417

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF3695 PS417_18910 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__WCS417:GFF3695
          Length = 385

 Score =  274 bits (700), Expect = 3e-78
 Identities = 143/373 (38%), Positives = 217/373 (58%), Gaps = 8/373 (2%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           M + E+L +LV F +     N  ++ ++R YL+ HG+A  ++      ++N+ ATIGP E
Sbjct: 1   MNSRELLAQLVRFDTTSRESNLALIDFVRTYLQDHGVACALVYNEHKSKANLLATIGPAE 60

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
             G ++SGH DVVP     W+  PF L  +  +LYGRGT DMKG++A VLA VP L    
Sbjct: 61  VPGIVLSGHTDVVPVEGQRWSVAPFDLTEKDGKLYGRGTADMKGYIACVLACVPALVKAS 120

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180
           LR P+H+ALSYDEE GC GV  +I R  E   +PL  +IGEPT ++ +  HKGK A R  
Sbjct: 121 LRMPVHIALSYDEEVGCLGVRSLIERFHEQPVKPLLCVIGEPTELKPVLGHKGKLAMRCH 180

Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGP-FEHVFEPPYSSLQIGTVKGG 239
           V G + HS+    G+NAI   A ++++ V   + L      +  F P +S++Q G + GG
Sbjct: 181 VHGAACHSAYAPAGVNAIEYAACLISELVRLGETLKAPQHLDQRFAPAFSTVQTGLINGG 240

Query: 240 QAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAE-----ALTTLGFE--VEWQELSAY 292
           +A+NI+P  C  +FE R++   DP ++   ++  AE     A+  +  +  +   ELS+Y
Sbjct: 241 KALNIVPQDCSFDFEVRSLPAQDPWQVARQLQAYAEQTLLPAMRAVSEQSAISLSELSSY 300

Query: 293 PALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEY 352
           P L+   ++  A  + +  G      V++GTE GLF +AGI  ++CGPG + + HKPDE+
Sbjct: 301 PGLATSLESQAAEWVAQFCGSREFATVAFGTEGGLFDQAGIPTVVCGPGSMEQGHKPDEF 360

Query: 353 ILIDELMACRAMV 365
           I + +L AC  M+
Sbjct: 361 ISVAQLQACDRML 373


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: 352
Number of extensions: 20
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: 385
Length adjustment: 30
Effective length of query: 344
Effective length of database: 355
Effective search space:   122120
Effective search space used:   122120
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 GFF3695 PS417_18910 (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.2452.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.5e-124  399.6   0.0   7.4e-124  399.4   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF3695  PS417_18910 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3695  PS417_18910 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.4   0.0  7.4e-124  7.4e-124       1     364 [.       5     376 ..       5     377 .. 0.96

  Alignments for each domain:
  == domain 1  score: 399.4 bits;  conditional E-value: 7.4e-124
                           TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvde 75 
                                         e+la+Lv fd++s+ sn++li++v+ yl+++gva   + +  +  k nlla+iGp+e   g+vlsGhtDvvPv++
  lcl|FitnessBrowser__WCS417:GFF3695   5 ELLAQLVRFDTTSRESNLALIDFVRTYLQDHGVACALVYNEHK-SKANLLATIGPAE-VPGIVLSGHTDVVPVEG 77 
                                         6799*******************************99988877.************9.9**************** PP

                           TIGR01892  76 aaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...r 147
                                         ++W+  pf Ltekdg+LYgrGtaDmkG++a+vLa vp l +a L+ P+h++ls+Deevg++G+++lie+      
  lcl|FitnessBrowser__WCS417:GFF3695  78 QRWSVAPFDLTEKDGKLYGRGTADMKGYIACVLACVPALVKASLRMPVHIALSYDEEVGCLGVRSLIERFHeqpV 152
                                         *********************************************************************986668 PP

                           TIGR01892 148 rpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edleeaFtp 221
                                         +p l ++GePt+l++v  hkGk +++ +v+G   hs+++  Gv+aie aa l+++lv+l ++lk  ++l++ F p
  lcl|FitnessBrowser__WCS417:GFF3695 153 KPLLCVIGEPTELKPVLGHKGKLAMRCHVHGAACHSAYAPAGVNAIEYAACLISELVRLGETLKApQHLDQRFAP 227
                                         8999************************************************************98999****** PP

                           TIGR01892 222 pyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkveelsatpa 291
                                          ++t++ G ++GGka ni+++ C + +e+R++p +dp ++  +l++ ae+     +++   +  +   els +p+
  lcl|FitnessBrowser__WCS417:GFF3695 228 AFSTVQTGLINGGKALNIVPQDCSFDFEVRSLPAQDPWQVARQLQAYAEQtllpaMRAVSEQSAISLSELSSYPG 302
                                         **********************************************99987777555555566778999****** PP

                           TIGR01892 292 leleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                         l++  ++++++ +++  G+ +  +v++gte gl+ ++Gi++vv+GPG+++q h+pde++ + +l++c+ +l+r+
  lcl|FitnessBrowser__WCS417:GFF3695 303 LATSLESQAAEWVAQFCGSrEFATVAFGTEGGLFDQAGIPTVVCGPGSMEQGHKPDEFISVAQLQACDRMLARV 376
                                         ******************9899*************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (385 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.70
//
[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