Alignments for a candidate for argE in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Halorhodospira halophila SL1

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate WP_011814831.1 HHAL_RS10330 acetylornithine deacetylase

Query= SwissProt::P23908
         (383 letters)



>NCBI__GCF_000015585.1:WP_011814831.1
          Length = 389

 Score =  314 bits (804), Expect = 3e-90
 Identities = 170/383 (44%), Positives = 222/383 (57%), Gaps = 7/383 (1%)

Query: 6   PPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNML 65
           P   E+   L+A PS+S+ E   DQ N  +   LA W + LGF+  +QP+PG  +K N++
Sbjct: 6   PALREMIAELVAEPSVSSVEADHDQGNRGITERLAGWLEGLGFDCRIQPLPGRPDKTNLI 65

Query: 66  ASI----GQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFIL 121
           A++    G   GGL L GHTDTVP D  RWT DP+ L E DG+LYGLG  DMK F A  +
Sbjct: 66  ATLAPARGPARGGLALCGHTDTVPCDPERWTGDPWRLREADGRLYGLGVTDMKAFLAVAV 125

Query: 122 DALRDVDVTKLKKPLYILATADEETSMAGARYF--AETTALRPDCAIIGEPTSLQPVRAH 179
           +A R+VD  +L+ PL +L TADEE+ M G R    A    L P  A++GEPT   PV  H
Sbjct: 126 EAAREVDPARLQAPLTLLFTADEESGMDGVRALLDAHPQGLGPRHAVVGEPTRNHPVHVH 185

Query: 180 KGHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTL 239
           KG +  A+ IQG++GHSSDP  G NA++ M   +  ++  R+ L   +H   F VP PTL
Sbjct: 186 KGMMMEALHIQGRAGHSSDPRLGRNALDAMTRVLNALIAWREELAANHHDARFAVPQPTL 245

Query: 240 NLGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELH 299
           NLGHI GGD  NRIC   ELH+D+RPLPGM   EL   L+  LA         LT   L 
Sbjct: 246 NLGHIRGGDNPNRICGEAELHIDLRPLPGMDPAELQQTLDRRLAEALGDDAVHLTRRPLF 305

Query: 300 PPIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPD 358
           P  P    P + ++V   E + G     V + TEAP++  L    +VLGPG I QAHQPD
Sbjct: 306 PAHPPMATPADAEVVRYAETVTGHPAGAVAFATEAPYLARLGMDVVVLGPGEIEQAHQPD 365

Query: 359 EYLETRFIKPTRELITQVIHHFC 381
           E ++   + PT  L+ + IH FC
Sbjct: 366 ESIDVERLAPTVALLRRFIHRFC 388


Lambda     K      H
   0.320    0.139    0.430 

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: 483
Number of extensions: 14
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: 383
Length of database: 389
Length adjustment: 30
Effective length of query: 353
Effective length of database: 359
Effective search space:   126727
Effective search space used:   126727
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_011814831.1 HHAL_RS10330 (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.29217.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-118  381.8   0.0     2e-118  381.6   0.0    1.0  1  lcl|NCBI__GCF_000015585.1:WP_011814831.1  HHAL_RS10330 acetylornithine dea


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015585.1:WP_011814831.1  HHAL_RS10330 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.6   0.0    2e-118    2e-118       2     364 ..      11     383 ..      10     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 381.6 bits;  conditional E-value: 2e-118
                                 TIGR01892   2 ilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkeg..aggl 62 
                                               ++a+Lva +svs         n  + e ++++le lg+  + +p ++  +k+nl+a+  p++g  +ggl
  lcl|NCBI__GCF_000015585.1:WP_011814831.1  11 MIAELVAEPSVSSVeadhdqGNRGITERLAGWLEGLGFDCRIQPLPGRPDKTNLIATLAPARGpaRGGL 79 
                                               7899********998999999***************************************9765589** PP

                                 TIGR01892  63 vlsGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDe 131
                                               +l GhtD+vP+d ++Wt Dp+rL+e dgrLYg+G +Dmk Fla++++a+++++ a+L++Pl l+++aDe
  lcl|NCBI__GCF_000015585.1:WP_011814831.1  80 ALCGHTDTVPCDPERWTGDPWRLREADGRLYGLGVTDMKAFLAVAVEAAREVDPARLQAPLTLLFTADE 148
                                               ********************************************************************* PP

                                 TIGR01892 132 evglaGakklieala..rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaak 198
                                               e g+ G++ l++a +    p++a+vGePt+ ++v  hkG++  +++++Gr ghss+p  G +a   +++
  lcl|NCBI__GCF_000015585.1:WP_011814831.1 149 ESGMDGVRALLDAHPqgLGPRHAVVGEPTRNHPVHVHKGMMMEALHIQGRAGHSSDPRLGRNALDAMTR 217
                                               **************98889************************************************** PP

                                 TIGR01892 199 llarlvaladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallek 267
                                               +l+ l+a +++l  ++++  F +p +tln+G+++GG+  n+i+++ el+++lRp+pGmdp+el++ l  
  lcl|NCBI__GCF_000015585.1:WP_011814831.1 218 VLNALIAWREELAANHHDARFAVPQPTLNLGHIRGGDNPNRICGEAELHIDLRPLPGMDPAELQQTLDR 286
                                               ********************************************************************9 PP

                                 TIGR01892 268 iaeevkekapgfevkveelsatpaleleedaelvalleklaGaaaevvsygteagllqelGieavvlGP 336
                                                ++e+  +     ++  + +a+p +++++dae+v+ +e ++G++a +v+++tea++l +lG++ vvlGP
  lcl|NCBI__GCF_000015585.1:WP_011814831.1 287 RLAEALGDDAVHLTRRPLFPAHPPMATPADAEVVRYAETVTGHPAGAVAFATEAPYLARLGMDVVVLGP 355
                                               999999999999999****************************************************** PP

                                 TIGR01892 337 GdidqahqpdeYveieelkrcrallerl 364
                                               G+i+qahqpde +++e l ++ all+r 
  lcl|NCBI__GCF_000015585.1:WP_011814831.1 356 GEIEQAHQPDESIDVERLAPTVALLRRF 383
                                               *************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (389 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: 6.96
//
[ok]

This GapMind analysis is from Apr 10 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