Alignments for a candidate for argH in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Allochromatium vinosum DSM 180

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_012969728.1 ALVIN_RS02470 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_000025485.1:WP_012969728.1
          Length = 468

 Score =  468 bits (1204), Expect = e-136
 Identities = 236/454 (51%), Positives = 309/454 (68%), Gaps = 1/454 (0%)

Query: 7   WSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAGLE 66
           W+ RF +     +  F AS+ FD  L  YD+ GS AHA MLA  GI++  E + +V GLE
Sbjct: 11  WAGRFNAPTDAFVEAFTASVDFDRRLYRYDIQGSIAHATMLARQGILTEAERDAIVTGLE 70

Query: 67  QIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLRDQ 126
           ++R     G+F   +  EDVH  VE  LT  +GD GKKLHT RSRNDQV TD RL+LRD+
Sbjct: 71  RVRARIDAGEFAWSIPLEDVHMNVESALTADIGDAGKKLHTGRSRNDQVATDVRLWLRDE 130

Query: 127 IQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWERLG 186
           I  I++E+   Q  LLD+AE+  +T++PG+THLQ AQP++  HH+LA+F+M +RD ERL 
Sbjct: 131 IDTIRTEIVRLQTALLDLAEREADTILPGFTHLQVAQPITFGHHMLAWFEMLERDRERLA 190

Query: 187 DVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAASL 246
           D  RR+N+ PLG  ALAGTT+PIDRHYTA+LL FD    NSLD VSDRDFAIEF   A++
Sbjct: 191 DCRRRMNVLPLGAAALAGTTYPIDRHYTAELLGFDRPAENSLDAVSDRDFAIEFTADAAI 250

Query: 247 IMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGHLQ 306
           +M+HLSR +EE+ILWSS +F FV L DS  TGSSIMPQKKNPDVPELVRGK+GR+FGHL 
Sbjct: 251 LMMHLSRFSEELILWSSAQFGFVELSDSFCTGSSIMPQKKNPDVPELVRGKSGRIFGHLM 310

Query: 307 AMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVTED 366
            +L +MK  PLAYNKD QEDKE LFD+V+ +K SL+    ++   +     R+  A  + 
Sbjct: 311 GLLTLMKSQPLAYNKDNQEDKEPLFDTVDNLKGSLKVYADMMAH-VTCNRDRMRAAAKQG 369

Query: 367 FSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADIYE 426
           FS ATD+ADYL  RG+PFR+A+ +VGK V   +  G+ L +L L E +Q   A   D++ 
Sbjct: 370 FSTATDLADYLVRRGIPFRDAHEIVGKAVALGVREGRDLAELTLAELRQFSDAIGEDVFA 429

Query: 427 AISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460
            ++    VAAR+  GGT   QV  A+   R +++
Sbjct: 430 VLTLEGSVAARDHIGGTAPAQVRAAIARGRRRLN 463


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: 521
Number of extensions: 18
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: 461
Length of database: 468
Length adjustment: 33
Effective length of query: 428
Effective length of database: 435
Effective search space:   186180
Effective search space used:   186180
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_012969728.1 ALVIN_RS02470 (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.880605.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-201  653.5   0.0   1.1e-200  653.4   0.0    1.0  1  NCBI__GCF_000025485.1:WP_012969728.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025485.1:WP_012969728.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.4   0.0  1.1e-200  1.1e-200       2     454 ..      11     462 ..      10     463 .. 0.99

  Alignments for each domain:
  == domain 1  score: 653.4 bits;  conditional E-value: 1.1e-200
                             TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklel 74 
                                           w+gR++  +d  v++f+as++fD +l+++Di+gsiah+++La++gilte e++ ++ +Le+++  +++g++ +
  NCBI__GCF_000025485.1:WP_012969728.1  11 WAGRFNAPTDAFVEAFTASVDFDRRLYRYDIQGSIAHATMLARQGILTEAERDAIVTGLERVRARIDAGEFAW 83 
                                           9************************************************************************ PP

                             TIGR00838  75 evdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevet 147
                                           +   eD+H++vE+ l++ +g d+gkklhtgrsRnDqvatd+rl+lrd+++++++++  l++al+++Ae+e +t
  NCBI__GCF_000025485.1:WP_012969728.1  84 SIPLEDVHMNVESALTADIG-DAGKKLHTGRSRNDQVATDVRLWLRDEIDTIRTEIVRLQTALLDLAEREADT 155
                                           ********************.**************************************************** PP

                             TIGR00838 148 lmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavv 220
                                           ++pg+tHLq AqPit++Hh+la++emlerD eRl d  +R+n+ PlG++Alagt+++idr+++aelLgFd+ +
  NCBI__GCF_000025485.1:WP_012969728.1 156 ILPGFTHLQVAQPITFGHHMLAWFEMLERDRERLADCRRRMNVLPLGAAALAGTTYPIDRHYTAELLGFDRPA 228
                                           ************************************************************************* PP

                             TIGR00838 221 ensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgk 293
                                           ensldavsdRDf+iE+ ++aa+lm+hlsr++Eelil+ss+ fgfvelsd++++gssimPqKKnpDv El+Rgk
  NCBI__GCF_000025485.1:WP_012969728.1 229 ENSLDAVSDRDFAIEFTADAAILMMHLSRFSEELILWSSAQFGFVELSDSFCTGSSIMPQKKNPDVPELVRGK 301
                                           ************************************************************************* PP

                             TIGR00838 294 tgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalat 366
                                           +gr++G+l+gllt++K++PlaYnkD qEdke+lfd++++++ +l+v + ++++++ n++r++ aak++f++at
  NCBI__GCF_000025485.1:WP_012969728.1 302 SGRIFGHLMGLLTLMKSQPLAYNKDNQEDKEPLFDTVDNLKGSLKVYADMMAHVTCNRDRMRAAAKQGFSTAT 374
                                           ************************************************************************* PP

                             TIGR00838 367 dlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGta 439
                                           dlAdylvr+G+PFR+aheivG++va  +++G +l eltl+el+++s ++ edv+ vl+le +v++rd +GGta
  NCBI__GCF_000025485.1:WP_012969728.1 375 DLADYLVRRGIPFRDAHEIVGKAVALGVREGRDLAELTLAELRQFSDAIGEDVFAVLTLEGSVAARDHIGGTA 447
                                           ************************************************************************* PP

                             TIGR00838 440 keevekaieeakael 454
                                           +++v+ ai+  + +l
  NCBI__GCF_000025485.1:WP_012969728.1 448 PAQVRAAIARGRRRL 462
                                           ********9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (468 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 31.54
//
[ok]

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