Alignments for a candidate for argH in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Desulfatiglans anilini DSM 4660

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_028320085.1 H567_RS0101820 argininosuccinate lyase

Query= ecocyc::ARGSUCCINLYA-MONOMER
         (457 letters)



>NCBI__GCF_000422285.1:WP_028320085.1
          Length = 459

 Score =  459 bits (1180), Expect = e-133
 Identities = 236/450 (52%), Positives = 314/450 (69%), Gaps = 1/450 (0%)

Query: 4   WGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEEALN 63
           WGGRF +  D    +FN S+ FD RL  QDI+GSVA ++ L   G++  EE A++ EAL 
Sbjct: 6   WGGRFKEETDTLVNRFNASIGFDRRLYAQDILGSVAHARMLARQGIIQEEEAARMIEALG 65

Query: 64  VLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLWCKD 123
            +   +  R +     D EDIH+ VE  LI+++G LG+KLHTGRSRNDQVA D++L+ +D
Sbjct: 66  EIKRGIE-RGEIPFSEDFEDIHTLVEKNLIERIGALGEKLHTGRSRNDQVALDIRLYVRD 124

Query: 124 TVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDESRL 183
            + E +    ++Q +L+E  + N D +MPGYTHLQRAQPV  AH  LAYVEML RD +RL
Sbjct: 125 VIHETIALIGRVQESLIELGEKNVDLIMPGYTHLQRAQPVLVAHHLLAYVEMLGRDRARL 184

Query: 184 QDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLSAAA 243
            + L+R++V PLG  ALAG+ + +DRE +A  LGF   +RNS+D+VSDRD +LE L AAA
Sbjct: 185 TEGLRRVNVLPLGSAALAGSTFPLDREGVARELGFEGVSRNSMDAVSDRDFILEFLFAAA 244

Query: 244 IGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQGAL 303
             M+HLSR +E+LI +++ E GF+ +SD   +GSS+MPQKKNPD  ELIRGK GRV G L
Sbjct: 245 AVMMHLSRMSEELIIWSSQEFGFITISDGFCTGSSIMPQKKNPDVPELIRGKTGRVYGHL 304

Query: 304 TGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAAQQG 363
            G++ T+KGLPLAYNKDMQEDKEGLFDA DT   CL + A +L  +     R + AA +G
Sbjct: 305 MGLLTTMKGLPLAYNKDMQEDKEGLFDAADTLTLCLEIMARLLREVTFNAERLKAAAAEG 364

Query: 364 YANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDEDVYP 423
           Y  AT+LADYLV KGV FREAH +VG  V+ A+ +G  L DLPL E++ FS+VIDE VY 
Sbjct: 365 YLVATDLADYLVGKGVTFREAHGVVGRMVLHAMERGLELHDLPLDEMKGFSRVIDEQVYG 424

Query: 424 ILSLQSCLDKRAAKGGVSPQQVAQAIAFAQ 453
            LS ++C+ +R   GG  P++V +A+A A+
Sbjct: 425 WLSAEACVARRKLTGGTGPERVREALAAAR 454


Lambda     K      H
   0.318    0.133    0.386 

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: 525
Number of extensions: 19
Number of successful extensions: 2
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: 457
Length of database: 459
Length adjustment: 33
Effective length of query: 424
Effective length of database: 426
Effective search space:   180624
Effective search space used:   180624
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: 51 (24.3 bits)

Align candidate WP_028320085.1 H567_RS0101820 (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.14496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-199  647.0   0.0     1e-198  646.8   0.0    1.0  1  lcl|NCBI__GCF_000422285.1:WP_028320085.1  H567_RS0101820 argininosuccinate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000422285.1:WP_028320085.1  H567_RS0101820 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.8   0.0    1e-198    1e-198       1     453 [.       5     456 ..       5     458 .. 0.99

  Alignments for each domain:
  == domain 1  score: 646.8 bits;  conditional E-value: 1e-198
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               +wggR+k+e+d  v++fnas+ fD +l+++Di gs+ah+++La++gi++eeea+++ieaL e+k+ +++
  lcl|NCBI__GCF_000422285.1:WP_028320085.1   5 TWGGRFKEETDTLVNRFNASIGFDRRLYAQDILGSVAHARMLARQGIIQEEEAARMIEALGEIKRGIER 73 
                                               5******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g++ +++d eDiH+ vE++li+++g  +g+klhtgrsRnDqva d+rly+rd ++e +  +  ++++l+
  lcl|NCBI__GCF_000422285.1:WP_028320085.1  74 GEIPFSEDFEDIHTLVEKNLIERIG-ALGEKLHTGRSRNDQVALDIRLYVRDVIHETIALIGRVQESLI 141
                                               *************************.******************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               e+ ek+v+ +mpgytHLqrAqP+ +aHhllay+eml rD  Rl++ l+Rvn+ PlGs+Alag++f++dr
  lcl|NCBI__GCF_000422285.1:WP_028320085.1 142 ELGEKNVDLIMPGYTHLQRAQPVLVAHHLLAYVEMLGRDRARLTEGLRRVNVLPLGSAALAGSTFPLDR 210
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               e +a+ LgF+ v +ns+davsdRDfi+E+l+aaa +m+hlsr++Eeli++ss+Efgf+++sd +++gss
  lcl|NCBI__GCF_000422285.1:WP_028320085.1 211 EGVARELGFEGVSRNSMDAVSDRDFILEFLFAAAAVMMHLSRMSEELIIWSSQEFGFITISDGFCTGSS 279
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDv EliRgktgrv+G+l+gllt++K+lPlaYnkD+qEdke+lfda +t++ +le+++ ll+
  lcl|NCBI__GCF_000422285.1:WP_028320085.1 280 IMPQKKNPDVPELIRGKTGRVYGHLMGLLTTMKGLPLAYNKDMQEDKEGLFDAADTLTLCLEIMARLLR 348
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                               e+++n erl+ aa++++  atdlAdylv kGv FReah +vG++v +a+e+G++l++l+l+e++ +s  
  lcl|NCBI__GCF_000422285.1:WP_028320085.1 349 EVTFNAERLKAAAAEGYLVATDLADYLVGKGVTFREAHGVVGRMVLHAMERGLELHDLPLDEMKGFSRV 417
                                               ********************************************************************* PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakae 453
                                               ++e+v+  l+ e +v++r+ +GGt++e+v++a+++a++e
  lcl|NCBI__GCF_000422285.1:WP_028320085.1 418 IDEQVYGWLSAEACVARRKLTGGTGPERVREALAAARKE 456
                                               *********************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (459 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: 12.44
//
[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