Alignments for a candidate for argE in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Sinorhizobium medicae WSM419

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate YP_001314282.1 Smed_5605 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000017145.1:YP_001314282.1
          Length = 374

 Score =  689 bits (1777), Expect = 0.0
 Identities = 345/374 (92%), Positives = 351/374 (93%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           MQAAEILGKLVGFRSVVGLPN+D VSWIRGYLE HGIAVDVLPGPEGDRSNIFATIGPKE
Sbjct: 1   MQAAEILGKLVGFRSVVGLPNDDAVSWIRGYLECHGIAVDVLPGPEGDRSNIFATIGPKE 60

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
           A GYI+SGHMDVVPA E GWTSDPF LR E  RLYGRGTTDMKGFLAA LAAVPKLAAMP
Sbjct: 61  AHGYILSGHMDVVPATEAGWTSDPFILRAEGGRLYGRGTTDMKGFLAAGLAAVPKLAAMP 120

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180
           LRRPLHLA SYDEEAGCRGVPHMIAR+PELCRQPLGAIIGEP+GMRAIRAHKGKAAARLT
Sbjct: 121 LRRPLHLAFSYDEEAGCRGVPHMIARMPELCRQPLGAIIGEPSGMRAIRAHKGKAAARLT 180

Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ 240
           VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEA RL GGPFEHVFEPPYSSLQIGTVKGGQ
Sbjct: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEAVRLAGGPFEHVFEPPYSSLQIGTVKGGQ 240

Query: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQELSAYPALSLEPD 300
           AVNIIPDSCEVE EARAISGVDPAELL PVRK AEALT LGFEVEWQELSAYPALSLEP 
Sbjct: 241 AVNIIPDSCEVELEARAISGVDPAELLTPVRKIAEALTALGFEVEWQELSAYPALSLEPH 300

Query: 301 APLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMA 360
           APLAALLE LTGRE LPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHK DEYILIDELMA
Sbjct: 301 APLAALLEALTGREPLPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKADEYILIDELMA 360

Query: 361 CRAMVEALGARCTA 374
           C+AM+EALGA C A
Sbjct: 361 CQAMIEALGAHCIA 374


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: 592
Number of extensions: 16
Number of successful extensions: 1
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: 374
Length adjustment: 30
Effective length of query: 344
Effective length of database: 344
Effective search space:   118336
Effective search space used:   118336
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 YP_001314282.1 Smed_5605 (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.27957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-163  530.6   0.0   1.2e-163  530.4   0.0    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001314282.1  Smed_5605 acetylornithine deacet


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001314282.1  Smed_5605 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.4   0.0  1.2e-163  1.2e-163       1     364 [.       5     368 ..       5     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 530.4 bits;  conditional E-value: 1.2e-163
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               eil+kLv+f+sv++++n d ++++++yle +g+av+vlp ++g ++sn++a+iGpke a g++lsGh+D
  lcl|NCBI__GCF_000017145.1:YP_001314282.1   5 EILGKLVGFRSVVGLPNDDAVSWIRGYLECHGIAVDVLPGPEG-DRSNIFATIGPKE-AHGYILSGHMD 71 
                                               79*****************************************.*************.*********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138
                                               vvP+ ea+WtsDpf L+ + grLYgrGt+DmkGFla+ Laavp+laa++L++Plhl++s+Dee+g++G+
  lcl|NCBI__GCF_000017145.1:YP_001314282.1  72 VVPATEAGWTSDPFILRAEGGRLYGRGTTDMKGFLAAGLAAVPKLAAMPLRRPLHLAFSYDEEAGCRGV 140
                                               ********************************************************************* PP

                                 TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204
                                               +++i++++   r+p  ai+GeP +++a+RahkGka+a++tvrGr+ghssrpd+G++ai+ +a++l+++v
  lcl|NCBI__GCF_000017145.1:YP_001314282.1 141 PHMIARMPelcRQPLGAIIGEPSGMRAIRAHKGKAAARLTVRGRSGHSSRPDQGLNAIHGVAGVLTQAV 209
                                               *******9999********************************************************** PP

                                 TIGR01892 205 aladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevk 273
                                               a+a +l ++++e++F+ppy++l+iGtvkGG+avnii+++Ce++le+R+i+G+dp+ell++++kiae++ 
  lcl|NCBI__GCF_000017145.1:YP_001314282.1 210 AEAVRLAGGPFEHVFEPPYSSLQIGTVKGGQAVNIIPDSCEVELEARAISGVDPAELLTPVRKIAEAL- 277
                                               ******************************************************************76. PP

                                 TIGR01892 274 ekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidq 341
                                                +a+gfev+++elsa+pal+le+ a+l+alle l+G+ ++++vsygteagl+q++Gi+a+++GPGdi++
  lcl|NCBI__GCF_000017145.1:YP_001314282.1 278 -TALGFEVEWQELSAYPALSLEPHAPLAALLEALTGRePLPAVSYGTEAGLFQRAGIDAIICGPGDIGR 345
                                               .9***********************************99****************************** PP

                                 TIGR01892 342 ahqpdeYveieelkrcrallerl 364
                                               ah++deY+ i+el++c+a++e+l
  lcl|NCBI__GCF_000017145.1:YP_001314282.1 346 AHKADEYILIDELMACQAMIEAL 368
                                               ********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (374 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.00
//
[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