Alignments for a candidate for argE in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Cupriavidus basilensis 4G11

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate RR42_RS07840 RR42_RS07840 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Cup4G11:RR42_RS07840
          Length = 401

 Score =  280 bits (715), Expect = 6e-80
 Identities = 149/368 (40%), Positives = 214/368 (58%), Gaps = 11/368 (2%)

Query: 9   KLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEAR---GYI 65
           +LV + +     N  ++  +R +  + G+   +   P+GD++N+F T+         G +
Sbjct: 24  RLVSYDTTSRHSNLGLIEAVRDHFLAKGLRPHLSYNPQGDKANLFVTVPAASGSTDGGIV 83

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     WT+DPF+  +   RLYGRGT DMKGF+   LA +P L    LR P+
Sbjct: 84  LSGHTDVVPVDGQNWTTDPFKPVIRDGRLYGRGTCDMKGFIGTSLALLPTLLEARLREPV 143

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           H ALS+DEE GC G P+++A L E    P G I+GEPT MR I AHKG  A R  V+G++
Sbjct: 144 HYALSFDEEIGCMGAPYLLAELRERGVTPGGCIVGEPTSMRVIVAHKGINAYRCCVKGQA 203

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244
            HSS   +G+NAI   A ++      AD     GP++  F+ P+++ Q GT+ GG A+N 
Sbjct: 204 AHSSLTPKGVNAIEYAARLICHIRDIADEFKANGPYDRDFDVPFTTAQTGTIHGGIALNT 263

Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEW-------QELSAYPALSL 297
           IP  CE  FE R + GVDP  + A ++  A  +       E         +++A P+L +
Sbjct: 264 IPALCEFVFEFRNLPGVDPEAIFARIQGYANDVLLPKMRAEHADAGLTINKIAAAPSLDV 323

Query: 298 EPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDE 357
              A +  L+  LT    +  V+YGTEAGLFQRAGI A++CGPGDI +AHKPDE++ +D+
Sbjct: 324 AEQAAITQLVRALTADRDVNKVAYGTEAGLFQRAGIPAVVCGPGDIEQAHKPDEFVALDQ 383

Query: 358 LMACRAMV 365
           L AC A +
Sbjct: 384 LAACEAFL 391


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: 428
Number of extensions: 13
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: 401
Length adjustment: 30
Effective length of query: 344
Effective length of database: 371
Effective search space:   127624
Effective search space used:   127624
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 RR42_RS07840 RR42_RS07840 (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.4917.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-118  380.7   0.0     4e-118  380.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS07840  RR42_RS07840 acetylornithine dea


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS07840  RR42_RS07840 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.5   0.0    4e-118    4e-118       4     365 .]      23     395 ..      20     395 .. 0.96

  Alignments for each domain:
  == domain 1  score: 380.5 bits;  conditional E-value: 4e-118
                                 TIGR01892   4 akLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkeg..agglvlsGhtDv 70 
                                               ++Lv+ d++s++sn+ lie v+d++ ++g+  +   +++g +k nl+ ++ +++g  +gg+vlsGhtDv
  lcl|FitnessBrowser__Cup4G11:RR42_RS07840  23 QRLVSYDTTSRHSNLGLIEAVRDHFLAKGLRPHLSYNPQG-DKANLFVTVPAASGstDGGIVLSGHTDV 90 
                                               68**************************************.******999888552279********** PP

                                 TIGR01892  71 vPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGak 139
                                               vPvd+++Wt+Dpf+   +dgrLYgrGt+DmkGF+ + La +p l  a+L++P+h +ls+Dee+g++Ga+
  lcl|FitnessBrowser__Cup4G11:RR42_RS07840  91 VPVDGQNWTTDPFKPVIRDGRLYGRGTCDMKGFIGTSLALLPTLLEARLREPVHYALSFDEEIGCMGAP 159
                                               ********************************************************************* PP

                                 TIGR01892 140 klieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva 205
                                               +l++ l      p   ivGePts++ + ahkG+ + +  v+G+ +hss + +Gv+aie aa+l+ ++ +
  lcl|FitnessBrowser__Cup4G11:RR42_RS07840 160 YLLAELRergVTPGGCIVGEPTSMRVIVAHKGINAYRCCVKGQAAHSSLTPKGVNAIEYAARLICHIRD 228
                                               ***999956666999****************************************************** PP

                                 TIGR01892 206 ladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.. 271
                                                ad+ k  ++++  F++p++t + Gt++GG a n i+a Ce+v+e+R +pG+dpe++ a ++  a++  
  lcl|FitnessBrowser__Cup4G11:RR42_RS07840 229 IADEFKAnGPYDRDFDVPFTTAQTGTIHGGIALNTIPALCEFVFEFRNLPGVDPEAIFARIQGYANDvl 297
                                               *****99789999*************************************************9999966 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGP 336
                                                  +++++ + +  +++  a p+l++ e+a + +l++ l+ +   + v+ygteagl+q++Gi+avv+GP
  lcl|FitnessBrowser__Cup4G11:RR42_RS07840 298 lpkMRAEHADAGLTINKIAAAPSLDVAEQAAITQLVRALTADrDVNKVAYGTEAGLFQRAGIPAVVCGP 366
                                               66667788888999**************************99899************************ PP

                                 TIGR01892 337 GdidqahqpdeYveieelkrcrallerlv 365
                                               Gdi+qah+pde+v +++l +c+a+l+++v
  lcl|FitnessBrowser__Cup4G11:RR42_RS07840 367 GDIEQAHKPDEFVALDQLAACEAFLHKVV 395
                                               *************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (401 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.81
//
[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