Alignments for a candidate for argG in Desulfobacca acetoxidans DSM 11109

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Desulfobacca acetoxidans DSM 11109

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_013707412.1 DESAC_RS12360 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000195295.1:WP_013707412.1
          Length = 400

 Score =  567 bits (1460), Expect = e-166
 Identities = 267/390 (68%), Positives = 322/390 (82%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           KIVLAYSGGLDTS+ILKWL ETY+  V+A+ AD+GQG+E+ E   KA  TGA++   LDL
Sbjct: 6   KIVLAYSGGLDTSVILKWLMETYQCPVVAYAADLGQGDELSEVAVKAKATGAAEVHILDL 65

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           KEEF RDF+FPM RA A+YEG YLLGTSIARPLIAK  V +A++ GA+A++HGATGKGND
Sbjct: 66  KEEFARDFIFPMFRANALYEGAYLLGTSIARPLIAKAQVEVAKKTGADAVSHGATGKGND 125

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHI 181
           QVRFELT  AL P++K+IAPWREW  QGR + +AYAE HGIPVPVTQEKPYS D NLLHI
Sbjct: 126 QVRFELTYMALAPELKIIAPWREWGLQGRADCVAYAEKHGIPVPVTQEKPYSSDRNLLHI 185

Query: 182 SYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQR 241
           S+EGG+LEDPWAEPP  MF +TQ P+EAP+ P+Y+E++F  GDPVAV+ +++SP  ++  
Sbjct: 186 SFEGGILEDPWAEPPADMFVLTQSPQEAPNTPQYLEIDFASGDPVAVDDKKMSPFQIIDH 245

Query: 242 LNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDML 301
           LN++GG HG+GRVD+VENR+VG+KSRGVYETPGGTIL  A  AVESLTLDREV+H RD L
Sbjct: 246 LNKVGGEHGIGRVDLVENRYVGLKSRGVYETPGGTILRAAHHAVESLTLDREVMHLRDSL 305

Query: 302 SPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQD 361
            P+YAELVYYG+W+APER ALQA  D   + VTG ARL+LYKGNV VVGRKAPKSLYR D
Sbjct: 306 IPRYAELVYYGYWFAPERTALQALIDEAQKPVTGTARLQLYKGNVTVVGRKAPKSLYRPD 365

Query: 362 LVSFDEAGGYDQKDAEGFIKIQALRLRVRA 391
           LV+F+  G Y Q DA GFI++ ALRL++RA
Sbjct: 366 LVTFEAGGDYQQADATGFIRLNALRLKIRA 395


Lambda     K      H
   0.319    0.137    0.402 

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: 554
Number of extensions: 11
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_013707412.1 DESAC_RS12360 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.1128.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-153  496.0   0.0   5.7e-153  495.8   0.0    1.0  1  lcl|NCBI__GCF_000195295.1:WP_013707412.1  DESAC_RS12360 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195295.1:WP_013707412.1  DESAC_RS12360 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.8   0.0  5.7e-153  5.7e-153       1     389 [.       6     394 ..       6     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.8 bits;  conditional E-value: 5.7e-153
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               k+vlaysGGlDtsv+lk+l+e   + v+a+++d+Gq+ ++l +++ ka++ Ga +  ++D +eef++d+
  lcl|NCBI__GCF_000195295.1:WP_013707412.1   6 KIVLAYSGGLDTSVILKWLMETyQCPVVAYAADLGQG-DELSEVAVKAKATGAAEVHILDLKEEFARDF 73 
                                               89********************889***********9.******************************* PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                               +f+  +ana+yeg Yll+t++aRpliak++vevakk ga+av+hG+tgKGnDqvRFel+ ++l+p+lk+
  lcl|NCBI__GCF_000195295.1:WP_013707412.1  74 IFPMFRANALYEGAYLLGTSIARPLIAKAQVEVAKKTGADAVSHGATGKGNDQVRFELTYMALAPELKI 142
                                               ********************************************************************* PP

                                 TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpi 205
                                               iaP+re+ l  R++ ++ya+++Gi+vpv++ek+ys D+nll++s E+g+LEdp++epp d++ l+++p+
  lcl|NCBI__GCF_000195295.1:WP_013707412.1 143 IAPWREWGLQgRADCVAYAEKHGIPVPVTQEKPYSSDRNLLHISFEGGILEDPWAEPPADMFVLTQSPQ 211
                                               *********99********************************************************99 PP

                                 TIGR00032 206 ektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapal 274
                                               e++ ++p+++ei+F +G Pva+++++++p+++i ++n+++g+hG+Gr+D vE+R++glKsR++YE+p+ 
  lcl|NCBI__GCF_000195295.1:WP_013707412.1 212 EAP-NTPQYLEIDFASGDPVAVDDKKMSPFQIIDHLNKVGGEHGIGRVDLVENRYVGLKSRGVYETPGG 279
                                               999.9**************************************************************** PP

                                 TIGR00032 275 llLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343
                                               ++L+ Ah+++e+l+l+++v+++++    +y+el+Y+G+wf p++ al+ali++ q+ vtGt r++l+kG
  lcl|NCBI__GCF_000195295.1:WP_013707412.1 280 TILRAAHHAVESLTLDREVMHLRDSLIPRYAELVYYGYWFAPERTALQALIDEAQKPVTGTARLQLYKG 348
                                               ********************************************************************* PP

                                 TIGR00032 344 naivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvy 389
                                               n++v+grk ++slY ++lv+fe    ++q da+Gfi++++l+ k+ 
  lcl|NCBI__GCF_000195295.1:WP_013707412.1 349 NVTVVGRKAPKSLYRPDLVTFEAGGDYQQADATGFIRLNALRLKIR 394
                                               *****************************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (400 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: 9.59
//
[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