Aligments for a candidate for argE in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for argE in Caulobacter crescentus NA1000

Align Acetylornithine deacetylase; AO; Acetylornithinase; EC 3.5.1.16; N-acetylornithinase; NAO (uncharacterized)
to candidate CCNA_03746 CCNA_03746 acetylornithine deacetylase

Query= curated2:Q9K4Z2
         (382 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03746 CCNA_03746 acetylornithine
           deacetylase
          Length = 391

 Score =  190 bits (482), Expect = 7e-53
 Identities = 131/365 (35%), Positives = 192/365 (52%), Gaps = 20/365 (5%)

Query: 29  SNKPVIDLLSGWFSELGFSINITSVPETNG-KFNLVATYGQG-DGGLLLAGHTDTVPFDD 86
           SN  +I+ +  + +EL  ++    VP  +G K NL+A  G   +GG++L+GHTD VP D 
Sbjct: 29  SNLALIEWVEQYLAEL--NVPTRRVPNADGTKSNLMAMIGPAVEGGVVLSGHTDVVPVDG 86

Query: 87  DLWTKDPFKLTEKDDKWYGLGTIDMKGFFAFVLEACKNIDLTKLDKPLRILATADEETTM 146
             W+ DP+ LTE+D + YG GT DMKGF A  L A  ++    L KP+ +  + DEE   
Sbjct: 87  QPWSTDPWTLTERDGRLYGRGTCDMKGFLALALAAAPDLAQANLRKPVHLAFSYDEEVGC 146

Query: 147 AGAR---AIAAAQSFRPDYAVIGEPTGMVPVFMHKGHMSEAIRITGRSGHSSDPANGINA 203
            GA     + A +  RP   V+GEPT MV V  HKG  S  + +TGR  HSS    G++A
Sbjct: 147 LGAPDMIDVIAREVPRPALVVVGEPTDMVAVRAHKGIASFKVTVTGREAHSSLTHLGVSA 206

Query: 204 IEIMHQVTGQLLQLQRKLKEQYACDHFVIPQ-PTLNFGHVHGGDSPNRICGSCELHIDMR 262
             +  ++   L+ L  KL+ +   +    P+  TL  G V+GG + N +   C    D+R
Sbjct: 207 NMVAIKLMAMLVGLSEKLEREADPNSPFTPKGATLTIGQVNGGTAVNILARECVFIFDLR 266

Query: 263 PIPGVNPDEL---FMLLNQALLPIIKQW--PGAVDVYHLHEPIPAYACNTDSALIKLAEK 317
              G++P  L   F  +  AL   IK     G V V       PA+A   D      A K
Sbjct: 267 TPAGMDPVALLSDFFAMASALDAQIKAKAPEGGVKV-ERRSLTPAFAPEEDGVAEAFARK 325

Query: 318 LTGE----AVIPVNYCTEAPFIQQLGCDTIVMGPGSINQAHQPDEYLDLSAIKPTQAIIQ 373
           L G+     V+P  Y  EA   Q  G  T++ GPGSI+QAHQP+EY+++S ++   A ++
Sbjct: 326 LAGDNGPARVVP--YAAEAGQFQGAGFSTVICGPGSIDQAHQPNEYVEISQMQRGGAFMR 383

Query: 374 KLIEE 378
           +L+E+
Sbjct: 384 RLVED 388


Lambda     K      H
   0.319    0.138    0.419 

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: 344
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: 382
Length of database: 391
Length adjustment: 30
Effective length of query: 352
Effective length of database: 361
Effective search space:   127072
Effective search space used:   127072
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 CCNA_03746 CCNA_03746 (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.6993.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-176  573.3   0.2   1.2e-176  573.1   0.2    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03746  CCNA_03746 acetylornithine deace


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03746  CCNA_03746 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.1   0.2  1.2e-176  1.2e-176       1     365 []      14     386 ..      14     386 .. 0.99

  Alignments for each domain:
  == domain 1  score: 573.1 bits;  conditional E-value: 1.2e-176
                             TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 
                                           +ilakLvafd++s+rsn++lie+ve+yl+el+v+++++p+adg +ksnl+a+iGp++ +gg+vlsGhtDvvPv
  lcl|FitnessBrowser__Caulo:CCNA_03746  14 DILAKLVAFDTTSRRSNLALIEWVEQYLAELNVPTRRVPNADG-TKSNLMAMIGPAV-EGGVVLSGHTDVVPV 84 
                                           79*****************************************.************9.*************** PP

                             TIGR01892  74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146
                                           d+++W++Dp++Lte+dgrLYgrGt+DmkGFlal+Laa+pdla+a+L+kP+hl++s+Deevg++Ga+++i+++a
  lcl|FitnessBrowser__Caulo:CCNA_03746  85 DGQPWSTDPWTLTERDGRLYGRGTCDMKGFLALALAAAPDLAQANLRKPVHLAFSYDEEVGCLGAPDMIDVIA 157
                                           ************************************************************************* PP

                             TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edl 215
                                              +rpal++vGePt++vavRahkG+as+kvtv+Gre+hss ++ Gvsa+++a+kl+a+lv+l++kl+r +d+
  lcl|FitnessBrowser__Caulo:CCNA_03746 158 revPRPALVVVGEPTDMVAVRAHKGIASFKVTVTGREAHSSLTHLGVSANMVAIKLMAMLVGLSEKLEReADP 230
                                           9999****************************************************************989** PP

                             TIGR01892 216 eeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevkve 284
                                           +++Ftp++atl+iG+v+GG+avni+a++C+++++lR+++Gmdp++ll++++++a++    +k+kap+++vkve
  lcl|FitnessBrowser__Caulo:CCNA_03746 231 NSPFTPKGATLTIGQVNGGTAVNILARECVFIFDLRTPAGMDPVALLSDFFAMASAldaqIKAKAPEGGVKVE 303
                                           ******************************************************9988889************ PP

                             TIGR01892 285 elsatpaleleedaelvalleklaGa..aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355
                                           ++s+tpa+++eed++++a+++klaG+  +a+vv+y++eag++q++G+++v++GPG+idqahqp+eYvei++++
  lcl|FitnessBrowser__Caulo:CCNA_03746 304 RRSLTPAFAPEEDGVAEAFARKLAGDngPARVVPYAAEAGQFQGAGFSTVICGPGSIDQAHQPNEYVEISQMQ 376
                                           **************************999******************************************** PP

                             TIGR01892 356 rcrallerlv 365
                                           r++a+++rlv
  lcl|FitnessBrowser__Caulo:CCNA_03746 377 RGGAFMRRLV 386
                                           *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (391 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.73
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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