Alignments for a candidate for argH in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Thiohalomonas denitrificans HLD2

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_092998813.1 BLP65_RS14905 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_900102855.1:WP_092998813.1
          Length = 463

 Score =  474 bits (1219), Expect = e-138
 Identities = 237/457 (51%), Positives = 319/457 (69%), Gaps = 2/457 (0%)

Query: 2   TKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQL 61
           T E+ W+ RF       +  F AS+GFD  + + D+ GS AHA+MLAH G+++  E + +
Sbjct: 6   TVEKPWTGRFTEPTDAFVEAFGASVGFDQRMYKQDIRGSIAHARMLAHVGVLTEAERDDI 65

Query: 62  VAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRL 121
           + GL +I  E   G F   +  EDVH  +EKRLT+++GD GKKLHT RSRNDQV TD RL
Sbjct: 66  IRGLTKIEAEIEAGDFQWSIALEDVHMNIEKRLTDLIGDAGKKLHTGRSRNDQVATDIRL 125

Query: 122 YLRDQIQQ-IKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQR 180
           YLRD+I   I  EL+  QG L+D+AE+  +T++PG+THLQ AQP++  HH+LA+ +M QR
Sbjct: 126 YLRDEIDSAIAPELKRLQGNLIDLAEREADTIMPGFTHLQTAQPITFGHHMLAWNEMLQR 185

Query: 181 DWERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEF 240
           D ERL D  +R+N+ PLG  ALAGTT+PIDR + A+ L F+    NSLDGVSDRDFAIEF
Sbjct: 186 DAERLQDCRKRINVMPLGSAALAGTTYPIDRDFAAEELGFERPTRNSLDGVSDRDFAIEF 245

Query: 241 LCAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGR 300
           L  ASL+++H+SR +EE+ILWSS +F +V L D+  TGSSIMPQKKNPDVPELVRGK+GR
Sbjct: 246 LSWASLLLMHMSRFSEELILWSSSQFDWVDLGDAFCTGSSIMPQKKNPDVPELVRGKSGR 305

Query: 301 VFGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLA 360
           V+GHL ++L +MKG PLAYNKD QEDKE LFD+++TVK  L     ++   ++ +   + 
Sbjct: 306 VYGHLTSLLTLMKGQPLAYNKDNQEDKEPLFDTIDTVKGCLRVYADMMAR-IQVKPDNMR 364

Query: 361 QAVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAF 420
           +A    FS ATD+ADYL  +GVPFR+A+ +VGK VK  +  G+ L +++LEE QQ   A 
Sbjct: 365 EAARRGFSTATDLADYLVRKGVPFRDAHEIVGKAVKLGVDTGRDLSEMKLEELQQFSGAI 424

Query: 421 AADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARA 457
             +++E ++    VAAR+  GGT   QV   + AARA
Sbjct: 425 GEEVFEVLTLEGSVAARDHVGGTAPEQVKTGVQAARA 461


Lambda     K      H
   0.320    0.135    0.384 

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: 557
Number of extensions: 21
Number of successful extensions: 3
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: 461
Length of database: 463
Length adjustment: 33
Effective length of query: 428
Effective length of database: 430
Effective search space:   184040
Effective search space used:   184040
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_092998813.1 BLP65_RS14905 (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.2689056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-201  655.2   0.0   3.3e-201  655.1   0.0    1.0  1  NCBI__GCF_900102855.1:WP_092998813.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900102855.1:WP_092998813.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.1   0.0  3.3e-201  3.3e-201       2     452 ..      11     461 ..      10     463 .] 0.99

  Alignments for each domain:
  == domain 1  score: 655.1 bits;  conditional E-value: 3.3e-201
                             TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklel 74 
                                           w+gR+++ +d  v++f as+ fD++++++Di+gsiah+++La++g+lte e++++i++L++++ e+++g++++
  NCBI__GCF_900102855.1:WP_092998813.1  11 WTGRFTEPTDAFVEAFGASVGFDQRMYKQDIRGSIAHARMLAHVGVLTEAERDDIIRGLTKIEAEIEAGDFQW 83 
                                           9************************************************************************ PP

                             TIGR00838  75 evdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvke.laealkdllkalvekAekeve 146
                                           +   eD+H+++E++l+d +g d+gkklhtgrsRnDqvatd+rlylrd++++ +a +lk l+ +l+++Ae+e +
  NCBI__GCF_900102855.1:WP_092998813.1  84 SIALEDVHMNIEKRLTDLIG-DAGKKLHTGRSRNDQVATDIRLYLRDEIDSaIAPELKRLQGNLIDLAEREAD 155
                                           ********************.****************************987********************* PP

                             TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219
                                           t+mpg+tHLq AqPit++Hh+la+ eml+rD eRl+d  kR+n+ PlGs+Alagt+++idr+++ae LgF++ 
  NCBI__GCF_900102855.1:WP_092998813.1 156 TIMPGFTHLQTAQPITFGHHMLAWNEMLQRDAERLQDCRKRINVMPLGSAALAGTTYPIDRDFAAEELGFERP 228
                                           ************************************************************************* PP

                             TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292
                                           ++nsld+vsdRDf+iE+ls+a+ll +h+sr++Eelil+ss+ f++v+l d++++gssimPqKKnpDv El+Rg
  NCBI__GCF_900102855.1:WP_092998813.1 229 TRNSLDGVSDRDFAIEFLSWASLLLMHMSRFSEELILWSSSQFDWVDLGDAFCTGSSIMPQKKNPDVPELVRG 301
                                           ************************************************************************* PP

                             TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365
                                           k+grv+G+lt+llt++K++PlaYnkD qEdke+lfd+++tv+ +l+v + +++ ++v+ ++++eaa+++f++a
  NCBI__GCF_900102855.1:WP_092998813.1 302 KSGRVYGHLTSLLTLMKGQPLAYNKDNQEDKEPLFDTIDTVKGCLRVYADMMARIQVKPDNMREAARRGFSTA 374
                                           ************************************************************************* PP

                             TIGR00838 366 tdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGt 438
                                           tdlAdylvrkGvPFR+aheivG++v+  +++G +l+e+ leelq++s ++ e+v+evl+le +v++rd  GGt
  NCBI__GCF_900102855.1:WP_092998813.1 375 TDLADYLVRKGVPFRDAHEIVGKAVKLGVDTGRDLSEMKLEELQQFSGAIGEEVFEVLTLEGSVAARDHVGGT 447
                                           ************************************************************************* PP

                             TIGR00838 439 akeevekaieeaka 452
                                           a+e+v++ +++a+a
  NCBI__GCF_900102855.1:WP_092998813.1 448 APEQVKTGVQAARA 461
                                           ********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (463 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.72
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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