Alignments for a candidate for argE in Beijerinckia indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Beijerinckia indica ATCC 9039

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012384040.1 BIND_RS05275 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000019845.1:WP_012384040.1
          Length = 392

 Score =  234 bits (597), Expect = 3e-66
 Identities = 137/372 (36%), Positives = 193/372 (51%), Gaps = 8/372 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           ++L  L+ F +     N  +V+ +  YL    +    +P  EGD++ +F +IGPK   G 
Sbjct: 16  DMLECLISFDTESSKSNLPLVAAVEDYLREQAVDYVKVPNAEGDKAALFISIGPKVDGGV 75

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVP     WTSDPF LR EADR++GRGT DMKGF A  LA +P+     L RP
Sbjct: 76  VLSGHTDVVPVEGQSWTSDPFTLRREADRVFGRGTCDMKGFDALCLAMIPEFKQARLARP 135

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           +H+ LSYDEE  C G    IAR      +P   ++GEPT M+   AHK  A  R TV G 
Sbjct: 136 IHILLSYDEEIACTGSLDTIARFGHDLPRPAAVLVGEPTLMQVADAHKSVATYRTTVHGH 195

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVG-GPFEHVFEPPYSSLQIGTVKGGQAVN 243
             HSS+P  G +A+     ++T+    A+ L   G     F+PP S++ +GT+ GG A N
Sbjct: 196 EAHSSKPYLGASAVEAGCDLVTELYRFAEVLAAEGDPSGRFDPPASTIHVGTIHGGTARN 255

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGF-------EVEWQELSAYPALS 296
           I+   C   +E R + GV     L  +   A  +             +E       P L+
Sbjct: 256 ILAKECSFLWEFRGLPGVAQDRALRHLEDYAARVVLPKMTRYAPKASIETLVEVEVPGLA 315

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
            E  +   +L  +L        V + TEAG FQ+A +  I+CGPG I +AH+PDEYI I 
Sbjct: 316 PETGSQAESLALKLARSNRTITVPFATEAGQFQKAEVPTIVCGPGSIDQAHQPDEYIAIA 375

Query: 357 ELMACRAMVEAL 368
           ++ A  A +  L
Sbjct: 376 QIEAGIAFMRRL 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: 374
Number of extensions: 14
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: 392
Length adjustment: 30
Effective length of query: 344
Effective length of database: 362
Effective search space:   124528
Effective search space used:   124528
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 WP_012384040.1 BIND_RS05275 (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.19843.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-115  371.8   0.0   2.1e-115  371.6   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012384040.1  BIND_RS05275 acetylornithine dea


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012384040.1  BIND_RS05275 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.6   0.0  2.1e-115  2.1e-115       2     364 ..      17     387 ..      16     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 371.6 bits;  conditional E-value: 2.1e-115
                                 TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDv 70 
                                               +l+ L++fd+ s +sn++l+  vedyl+e+ v   ++p+a+g +k  l+ +iGpk+ +gg+vlsGhtDv
  lcl|NCBI__GCF_000019845.1:WP_012384040.1  17 MLECLISFDTESSKSNLPLVAAVEDYLREQAVDYVKVPNAEG-DKAALFISIGPKV-DGGVVLSGHTDV 83 
                                               6889**************************************.************9.9*********** PP

                                 TIGR01892  71 vPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGak 139
                                               vPv++++WtsDpf+L+ +++r++grGt+DmkGF al La +p+ ++a+L +P+h++ls+Dee++++G  
  lcl|NCBI__GCF_000019845.1:WP_012384040.1  84 VPVEGQSWTSDPFTLRREADRVFGRGTCDMKGFDALCLAMIPEFKQARLARPIHILLSYDEEIACTGSL 152
                                               ********************************************************************* PP

                                 TIGR01892 140 klieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva 205
                                               + i++     +rpa ++vGePt ++   ahk  a+ + tv+G+e+hss+p  G+sa+e   +l+++l +
  lcl|NCBI__GCF_000019845.1:WP_012384040.1 153 DTIARFGhdlPRPAAVLVGEPTLMQVADAHKSVATYRTTVHGHEAHSSKPYLGASAVEAGCDLVTELYR 221
                                               ****988788*********************************************************** PP

                                 TIGR01892 206 ladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.. 271
                                                a+ l   +d+   F+pp +t+++Gt++GG+a ni+a++C +  e+R +pG+  ++ l +le+ a+   
  lcl|NCBI__GCF_000019845.1:WP_012384040.1 222 FAEVLAAeGDPSGRFDPPASTIHVGTIHGGTARNILAKECSFLWEFRGLPGVAQDRALRHLEDYAARvv 290
                                               *****87699*****************************************************999966 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGP 336
                                                  +++ ap+  +++ +    p+l++e  ++++ l+ kla + ++ +v+++teag++q++ ++++v+GP
  lcl|NCBI__GCF_000019845.1:WP_012384040.1 291 lpkMTRYAPKASIETLVEVEVPGLAPETGSQAESLALKLARSnRTITVPFATEAGQFQKAEVPTIVCGP 359
                                               66666788899999999999******************99876999*********************** PP

                                 TIGR01892 337 GdidqahqpdeYveieelkrcrallerl 364
                                               G+idqahqpdeY+ i +++++ a+++rl
  lcl|NCBI__GCF_000019845.1:WP_012384040.1 360 GSIDQAHQPDEYIAIAQIEAGIAFMRRL 387
                                               *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (392 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.92
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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