Alignments for a candidate for argE in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Sphingomonas koreensis DSMZ 15582

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Ga0059261_1675 Ga0059261_1675 acetylornithine deacetylase (ArgE)

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Korea:Ga0059261_1675
          Length = 395

 Score =  275 bits (704), Expect = 1e-78
 Identities = 151/373 (40%), Positives = 211/373 (56%), Gaps = 10/373 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           EIL  LVGF +V    N D++ W+R YL SHG+A  +  G +  ++N+FATIG  E  G 
Sbjct: 16  EILRTLVGFPTVSRDSNLDLIHWVRDYLASHGVASVLTSGKDPGKANLFATIGSGEG-GI 74

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVP     W S+PF L      L+GRGT DMKGF+AA LA VP LA+  L  P
Sbjct: 75  VLSGHSDVVPVDGQDWHSNPFVLEERDGLLFGRGTCDMKGFIAACLAKVPMLASANLNEP 134

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           +HLA+S+DEE GC+G  HMI  L     +P G ++GEPT M  +  HK  +A    V G 
Sbjct: 135 VHLAISFDEEIGCKGAGHMIEELVARGLRPRGCVVGEPTSMEPVIGHKTGSAYGCAVHGL 194

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHV-FEPPYSSLQIGTVKGGQAVN 243
             HSS    G+NAI   A ++ +  A A RL      H  +  P+S+L  G ++GGQA N
Sbjct: 195 EAHSSLAPYGVNAIFYAARLIARIEAIAARLRAEERRHPGYSVPFSTLSAGVIEGGQASN 254

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAE-------ALTTLGFEVEWQELSAYPALS 296
           I+P  C   F+ R +   DP  ++A ++   +            G  +E       P  +
Sbjct: 255 IVPALCRFRFDIRTLPWTDPDAIIAELQTYIDHELLPEMRAVHAGARIEITMNGRVPGFA 314

Query: 297 LEPDAPLAALLEELTGREALPA-VSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILI 355
           ++ DAPL   ++ L G  A P  V++G+EAGLFQ  G+  I+CGPG I +AHKPDE++ +
Sbjct: 315 IDADAPLTRHVQRLAGSNAEPGFVAFGSEAGLFQARGVPTILCGPGSIEQAHKPDEFVAL 374

Query: 356 DELMACRAMVEAL 368
           D+L  C   ++ L
Sbjct: 375 DQLARCEDFLDRL 387


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: 432
Number of extensions: 21
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: 395
Length adjustment: 30
Effective length of query: 344
Effective length of database: 365
Effective search space:   125560
Effective search space used:   125560
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 Ga0059261_1675 Ga0059261_1675 (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.29053.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-122  395.6   0.0   1.2e-122  395.4   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1675  Ga0059261_1675 acetylornithine d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1675  Ga0059261_1675 acetylornithine deacetylase (ArgE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.4   0.0  1.2e-122  1.2e-122       1     364 [.      16     387 ..      16     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 395.4 bits;  conditional E-value: 1.2e-122
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               eil+ Lv+f++vs+ sn+dli++v+dyl+++gva       d   k nl+a+iG  +g+gg+vlsGh+D
  lcl|FitnessBrowser__Korea:Ga0059261_1675  16 EILRTLVGFPTVSRDSNLDLIHWVRDYLASHGVASVLTSGKDP-GKANLFATIG--SGEGGIVLSGHSD 81 
                                               79*******************************9988888887.9*********..999********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138
                                               vvPvd++ W s+pf L e+dg L+grGt+DmkGF+a+ La vp la a+L +P+hl++s+Dee+g++Ga
  lcl|FitnessBrowser__Korea:Ga0059261_1675  82 VVPVDGQDWHSNPFVLEERDGLLFGRGTCDMKGFIAACLAKVPMLASANLNEPVHLAISFDEEIGCKGA 150
                                               ********************************************************************* PP

                                 TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204
                                                ++ie l     rp+  +vGePts+ +v  hk   +    v+G e+hss +  Gv+ai+ aa+l+ar++
  lcl|FitnessBrowser__Korea:Ga0059261_1675 151 GHMIEELVargLRPRGCVVGEPTSMEPVIGHKTGSAYGCAVHGLEAHSSLAPYGVNAIFYAARLIARIE 219
                                               *****9988999********************************************************* PP

                                 TIGR01892 205 aladklkredlee.aFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271
                                               a a +l+ e+  + ++ +p++tl  G+++GG+a+ni++a C++ +++R++p  dp+++ a+l++  ++ 
  lcl|FitnessBrowser__Korea:Ga0059261_1675 220 AIAARLRAEERRHpGYSVPFSTLSAGVIEGGQASNIVPALCRFRFDIRTLPWTDPDAIIAELQTYIDHe 288
                                               ******996555427***********************************************9988766 PP

                                 TIGR01892 272 ....vkekapgfevkveelsatpaleleedaelvalleklaGa..aaevvsygteagllqelGieavvl 334
                                                   +++ + g  +++ +    p++++++da+l + +++laG+  ++  v++g+eagl+q  G++++++
  lcl|FitnessBrowser__Korea:Ga0059261_1675 289 llpeMRAVHAGARIEITMNGRVPGFAIDADAPLTRHVQRLAGSnaEPGFVAFGSEAGLFQARGVPTILC 357
                                               77667778888999999999**********************9656669******************** PP

                                 TIGR01892 335 GPGdidqahqpdeYveieelkrcrallerl 364
                                               GPG+i+qah+pde+v +++l rc+++l rl
  lcl|FitnessBrowser__Korea:Ga0059261_1675 358 GPGSIEQAHKPDEFVALDQLARCEDFLDRL 387
                                               ***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (395 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: 9.00
//
[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