Alignments for a candidate for argE in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Sinorhizobium meliloti 1021

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate SMa1836 SMa1836 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Smeli:SMa1836
          Length = 374

 Score =  745 bits (1923), Expect = 0.0
 Identities = 374/374 (100%), Positives = 374/374 (100%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE
Sbjct: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
           ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP
Sbjct: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180
           LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT
Sbjct: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180

Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ 240
           VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ
Sbjct: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ 240

Query: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQELSAYPALSLEPD 300
           AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQELSAYPALSLEPD
Sbjct: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQELSAYPALSLEPD 300

Query: 301 APLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMA 360
           APLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMA
Sbjct: 301 APLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMA 360

Query: 361 CRAMVEALGARCTA 374
           CRAMVEALGARCTA
Sbjct: 361 CRAMVEALGARCTA 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: 633
Number of extensions: 15
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 SMa1836 SMa1836 (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.29902.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   9.7e-174  563.5   0.0   1.1e-173  563.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMa1836  SMa1836 acetylornithine deacetyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa1836  SMa1836 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.4   0.0  1.1e-173  1.1e-173       1     364 [.       5     368 ..       5     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 563.4 bits;  conditional E-value: 1.1e-173
                          TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdea 76 
                                        eil+kLv+f+sv++++n+d+++++++yle++g+av+vlp ++g ++sn++a+iGpke a+g+++sGh+DvvP++e+
  lcl|FitnessBrowser__Smeli:SMa1836   5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEG-DRSNIFATIGPKE-ARGYIISGHMDVVPAAET 78 
                                        79*****************************************.*************.****************** PP

                          TIGR01892  77 aWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrp 149
                                        +WtsDpfrL+++++rLYgrGt+DmkGFla+vLaavp+laa++L++Plhl+ls+Dee+g++G++++i++l+   r+p
  lcl|FitnessBrowser__Smeli:SMa1836  79 GWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPLHLALSYDEEAGCRGVPHMIARLPelcRQP 154
                                        *********************************************************************9999*** PP

                          TIGR01892 150 alaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaFtppyat 225
                                          ai+GePt+++a+RahkGka+a++tvrGr+ghssrpd+G++ai+ +a++l+++va+ad+l+++++e++F+ppy++
  lcl|FitnessBrowser__Smeli:SMa1836 155 LGAIIGEPTGMRAIRAHKGKAAARLTVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSS 230
                                        **************************************************************************** PP

                          TIGR01892 226 lniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveelsatpaleleedaelv 301
                                        l+iGtvkGG+avnii+++Ce+++e+R+i+G+dp+ella+++k+ae++  +++gfev+++elsa+pal+le+da+l+
  lcl|FitnessBrowser__Smeli:SMa1836 231 LQIGTVKGGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEAL--TTLGFEVEWQELSAYPALSLEPDAPLA 304
                                        *********************************************76..9************************** PP

                          TIGR01892 302 alleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                        alle+l+G+ a+++vsygteagl+q++Gi+a+++GPGdi++ah+pdeY+ i+el++cra++e+l
  lcl|FitnessBrowser__Smeli:SMa1836 305 ALLEELTGReALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMACRAMVEAL 368
                                        *********99**************************************************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: 9.15
//
[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