Alignments for a candidate for argH in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Pseudarthrobacter sulfonivorans Ar51

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_058929437.1 AU252_RS02870 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>NCBI__GCF_001484605.1:WP_058929437.1
          Length = 479

 Score =  608 bits (1569), Expect = e-179
 Identities = 309/461 (67%), Positives = 370/461 (80%), Gaps = 1/461 (0%)

Query: 2   STNEGSLWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRD 61
           +TN G+LWGGRFAGGP+DALAALSKSTHFDW LA YD+  S+AH  VL +AGLL + +  
Sbjct: 12  ATNTGALWGGRFAGGPADALAALSKSTHFDWRLARYDIAGSKAHARVLHKAGLLDDAELG 71

Query: 62  GLLAGLDSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAAL 121
           G+L  L  L  DVA G++ P  +DEDVH +LERGLI+R G  LGG+LRAGRSRNDQVA L
Sbjct: 72  GMLDALGRLDDDVASGAYLPAESDEDVHGSLERGLIERAGTQLGGKLRAGRSRNDQVATL 131

Query: 122 FRMWLRDAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHPL 181
            RM+LRD  R +A GVL  + AL  QA AH    MPG+THLQ AQPILL+HHLLAHA  L
Sbjct: 132 GRMFLRDHARIIARGVLATIEALVGQAKAHQGVAMPGRTHLQHAQPILLSHHLLAHAWAL 191

Query: 182 LRDLDRIVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFSAAADNSVDATAARDFAA 241
           LRD+ R+ D+DKRA VSPYGSGALAGSSLGLDP+A+AADLGF +A  NS+D TA+RD  A
Sbjct: 192 LRDVQRLQDWDKRAGVSPYGSGALAGSSLGLDPEAVAADLGFFSATHNSIDGTASRDVFA 251

Query: 242 EAAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGKS 301
           E A+V AMI VDLSR++E++I+W++ EF +VTLHDS+STGSSIMPQKKNPD+AELARGK+
Sbjct: 252 EFAWVTAMIGVDLSRVSEEVILWATKEFSFVTLHDSYSTGSSIMPQKKNPDVAELARGKA 311

Query: 302 GRLIGNLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQRM 361
           GRLIGNL GLLATLK  PLAYNRDLQEDKEPVFD+   LELLLPA++G++A+L FN +RM
Sbjct: 312 GRLIGNLTGLLATLKGLPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIATLKFNTERM 371

Query: 362 AELAPAGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISPE 421
             LAP G+ LATD+AEWLVRQGVPFR AHE +GAAV+ AE R V L +LTD+E AAIS  
Sbjct: 372 ESLAPQGFALATDIAEWLVRQGVPFREAHELSGAAVKQAESRDVELWDLTDEEYAAISEH 431

Query: 422 LTPQVREVLTIEGSVSARDCRGGTAPGRVAEQLNAI-GEAA 461
           LTP+VR VL+ EGS+++R+ +GGTAP  V  QL A+ GE A
Sbjct: 432 LTPEVRTVLSTEGSLNSRNSQGGTAPAAVERQLLALEGELA 472


Lambda     K      H
   0.318    0.133    0.382 

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: 667
Number of extensions: 22
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: 470
Length of database: 479
Length adjustment: 33
Effective length of query: 437
Effective length of database: 446
Effective search space:   194902
Effective search space used:   194902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_058929437.1 AU252_RS02870 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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/TIGR00838.hmm
# target sequence database:        /tmp/gapView.32213.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-178  577.9   0.0     1e-177  577.7   0.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058929437.1  AU252_RS02870 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058929437.1  AU252_RS02870 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.7   0.0    1e-177    1e-177       1     450 [.      18     467 ..      18     472 .. 0.99

  Alignments for each domain:
  == domain 1  score: 577.7 bits;  conditional E-value: 1e-177
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               lwggR+++++ +a+a++++s++fD++la++Di gs+ah+++L+kag+l + e   + +aL +l ++v++
  lcl|NCBI__GCF_001484605.1:WP_058929437.1  18 LWGGRFAGGPADALAALSKSTHFDWRLARYDIAGSKAHARVLHKAGLLDDAELGGMLDALGRLDDDVAS 86 
                                               7******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g++ + +++eD+H  +Er li++ g+++g+kl++grsRnDqvat  r++lrd+ + +a+ +++ ++alv
  lcl|NCBI__GCF_001484605.1:WP_058929437.1  87 GAYLPAESDEDVHGSLERGLIERAGTQLGGKLRAGRSRNDQVATLGRMFLRDHARIIARGVLATIEALV 155
                                               ********************************************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                                +A++++ + mpg tHLq+AqPi l+Hhlla+a++l rD++Rl+d  kR+ +sP+GsgAlag+s+++d+
  lcl|NCBI__GCF_001484605.1:WP_058929437.1 156 GQAKAHQGVAMPGRTHLQHAQPILLSHHLLAHAWALLRDVQRLQDWDKRAGVSPYGSGALAGSSLGLDP 224
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               e++a++LgF ++++ns+d++++RD  +E+  ++a++ v+lsr++Ee+il++++Ef+fv+l+d++s+gss
  lcl|NCBI__GCF_001484605.1:WP_058929437.1 225 EAVAADLGFFSATHNSIDGTASRDVFAEFAWVTAMIGVDLSRVSEEVILWATKEFSFVTLHDSYSTGSS 293
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDvaEl+Rgk+gr+iGnltgll++lK+lPlaYn+DlqEdke++fda +t+e ll +v g+++
  lcl|NCBI__GCF_001484605.1:WP_058929437.1 294 IMPQKKNPDVAELARGKAGRLIGNLTGLLATLKGLPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA 362
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                               +lk+n+er+e +a ++falatd+A++lvr+GvPFReahe++G++v++a+ + ++l +lt ee++++se+
  lcl|NCBI__GCF_001484605.1:WP_058929437.1 363 TLKFNTERMESLAPQGFALATDIAEWLVRQGVPFREAHELSGAAVKQAESRDVELWDLTDEEYAAISEH 431
                                               ********************************************************************* PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieea 450
                                               l+++v++vl+ e +++ r+++GGta+++ve+++ ++
  lcl|NCBI__GCF_001484605.1:WP_058929437.1 432 LTPEVRTVLSTEGSLNSRNSQGGTAPAAVERQLLAL 467
                                               ******************************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (479 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: 7.99
//
[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