Alignments for a candidate for argH in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Stenotrophomonas chelatiphaga DSM 21508

Align arginosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_057687279.1 ABB28_RS15360 argininosuccinate lyase

Query= reanno::Dyella79:N515DRAFT_3770
         (433 letters)



>NCBI__GCF_001431535.1:WP_057687279.1
          Length = 431

 Score =  627 bits (1617), Expect = 0.0
 Identities = 317/430 (73%), Positives = 361/430 (83%), Gaps = 1/430 (0%)

Query: 1   MTQPLWQKSGIQIDARIMRFLAGDDVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAA 60
           M   LWQK G+ +DA+I  FLAGDDV+LDREFFLHDI AS AH EGLA IG++SADE A 
Sbjct: 1   MADLLWQKPGVAVDAKIQTFLAGDDVILDREFFLHDIAASAAHAEGLAHIGILSADELAG 60

Query: 61  LKRELDALAADFSAGDFVLDESYEDGHSAIEARLTERLGDAGRRVHTGRSRNDQILVATR 120
           L+REL+ LA DF AG FVLDE YEDGHSAIEARLT+RLGDAGRR+HTGRSRNDQ+LVATR
Sbjct: 61  LQRELEVLADDFRAGRFVLDEQYEDGHSAIEARLTDRLGDAGRRIHTGRSRNDQVLVATR 120

Query: 121 LWLKDQLAVLETHCRAIAEVCLERA-AQPALPLPGYTHIQRAVVSSTAMWFAGFAEGFID 179
           LWLK++L  +      IA+V L+RA A+  LP+PGYTHIQRAVVSS  MW+AG+AE FID
Sbjct: 121 LWLKEKLQRVAQLSAEIAKVALDRADAEKDLPIPGYTHIQRAVVSSAGMWWAGWAEAFID 180

Query: 180 NTLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFARMQVSPVYAQLSRGKFEMA 239
           N +RAR T AL+D NPLGTAAGYGVNLPLDREHTT ALGFARMQVSP+YAQLSRGKFEMA
Sbjct: 181 NAIRARDTHALVDANPLGTAAGYGVNLPLDREHTTAALGFARMQVSPIYAQLSRGKFEMA 240

Query: 240 VLEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKRNPDVVELLRASYA 299
            LEA+  A LD+RR+AWDLSLFT+AEFGFV LP++YTTGSSIMPNKRNPDV+EL+RA++A
Sbjct: 241 ALEALGGATLDLRRIAWDLSLFTSAEFGFVALPAQYTTGSSIMPNKRNPDVIELMRATHA 300

Query: 300 SVAAARTEIEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARMEWHEPAMRA 359
           SVAAARTEIEQLLSLPSGY RDLQ SKG++FHG   GLAALEL+P LLA +EW    + A
Sbjct: 301 SVAAARTEIEQLLSLPSGYHRDLQGSKGAIFHGFGRGLAALELLPALLANLEWRNDKLLA 360

Query: 360 AIEPAMYATDVAIEQAAAGVPFRDAYRAAADAAASAGAGRTPEGSLAARVSPGAGHDLRL 419
            I+  MYATDVA+E A AGVPFR+AY+AAA  A +AG GRTPEGSLAARVSPGA  DLRL
Sbjct: 361 GIDSGMYATDVAVEAAVAGVPFREAYKAAAAGADTAGQGRTPEGSLAARVSPGAAADLRL 420

Query: 420 DELKARLAAL 429
           D L+AR  AL
Sbjct: 421 DVLRARWQAL 430


Lambda     K      H
   0.320    0.133    0.388 

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: 639
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: 433
Length of database: 431
Length adjustment: 32
Effective length of query: 401
Effective length of database: 399
Effective search space:   159999
Effective search space used:   159999
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_057687279.1 ABB28_RS15360 (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.9395.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.5e-88  282.2   0.0    5.9e-88  281.8   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057687279.1  ABB28_RS15360 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687279.1  ABB28_RS15360 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.0   5.9e-88   5.9e-88      19     388 ..      24     391 ..      11     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 5.9e-88
                                 TIGR00838  19 aslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiHlavEr 87 
                                               + +  D e++ +Di +s ah++ La+ gil+++e + l+++Le l+++ ++g++ l++++eD H+a+E+
  lcl|NCBI__GCF_001431535.1:WP_057687279.1  24 DDVILDREFFLHDIAASAAHAEGLAHIGILSADELAGLQRELEVLADDFRAGRFVLDEQYEDGHSAIEA 92 
                                               457789*************************************************************** PP

                                 TIGR00838  88 elidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLq 156
                                               +l+d++g d+g+++htgrsRnDqv +  rl+l++k++++a+   ++ k+ +++A++e++  +pgytH+q
  lcl|NCBI__GCF_001431535.1:WP_057687279.1  93 RLTDRLG-DAGRRIHTGRSRNDQVLVATRLWLKEKLQRVAQLSAEIAKVALDRADAEKDLPIPGYTHIQ 160
                                               *******.************************************************************* PP

                                 TIGR00838 157 rAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensld 225
                                               rA   + + +   +ae++  +  R  d+   v+ +PlG++A  g+++++dre +++ LgF+++    ++
  lcl|NCBI__GCF_001431535.1:WP_057687279.1 161 RAVVSSAGMWWAGWAEAFIDNAIRARDTHALVDANPLGTAAGYGVNLPLDREHTTAALGFARMQVSPIY 229
                                               ***************************************************************999999 PP

                                 TIGR00838 226 avsdR.DfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgk 293
                                               a  +R  f + +l a+  ++++l r+a +l lf+s+Efgfv l+ ++++gssimP K+npDv+El+R+ 
  lcl|NCBI__GCF_001431535.1:WP_057687279.1 230 AQLSRgKFEMAALEALGGATLDLRRIAWDLSLFTSAEFGFVALPAQYTTGSSIMPNKRNPDVIELMRAT 298
                                               976663799999999999*************************************************** PP

                                 TIGR00838 294 tgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknf 362
                                                + v+   t  +  l +lP+ Y +Dlq  k a+f    +   +le++  ll++l+ ++++l     ++ 
  lcl|NCBI__GCF_001431535.1:WP_057687279.1 299 HASVAAARTE-IEQLLSLPSGYHRDLQGSKGAIFHGFGRGLAALELLPALLANLEWRNDKLLA-GIDSG 365
                                               ****988665.677889*******************************************655.55566 PP

                                 TIGR00838 363 alatdlAdylvrkGvPFReaheivGe 388
                                               + atd+A   +  GvPFRea++ + +
  lcl|NCBI__GCF_001431535.1:WP_057687279.1 366 MYATDVAVEAAVAGVPFREAYKAAAA 391
                                               89*******************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (431 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.61
//
[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