Alignments for a candidate for argG in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Desulfobacter vibrioformis DSM 8776

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_035236042.1 Q366_RS02655 argininosuccinate synthase

Query= SwissProt::Q9X2A1
         (409 letters)



>NCBI__GCF_000745975.1:WP_035236042.1
          Length = 408

 Score =  553 bits (1426), Expect = e-162
 Identities = 262/400 (65%), Positives = 334/400 (83%)

Query: 2   KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVED 61
           KEKVVLAYSGGLDTSVILKWL E+G++V AY+A++GQ +DF A ++KALK GASKV++ED
Sbjct: 3   KEKVVLAYSGGLDTSVILKWLLEQGYEVFAYMADIGQDEDFQAAEQKALKIGASKVFIED 62

Query: 62  LRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGN 121
           +++EFVTDYIF     N +YEGRYLLGTAIARP+IAK+Q++IA++ GA+YV+HGATGKGN
Sbjct: 63  MKKEFVTDYIFPVFKSNTVYEGRYLLGTAIARPIIAKKQIDIAKQVGARYVSHGATGKGN 122

Query: 122 DQVRFELTYAALNPNLKVISPWKDPEFLAKFKGRTDLINYAMEKGIPIKVSKKRPYSEDE 181
           DQVRFEL+Y ALNP +KVI+PWK+P+FL  F+GR+DL+ YA + GIP K +  +PYSED+
Sbjct: 123 DQVRFELSYYALNPAIKVIAPWKNPDFLNAFQGRSDLLAYAEKHGIPTKQTAAKPYSEDD 182

Query: 182 NLMHISHEAGKLEDPAHIPDEDVFTWTVSPKDAPDEETLLEIHFENGIPVKVVNLKDGTE 241
           NL+HISHEAG LEDP  + DE +++ TVSP+ APD  T + I F+NGIPVKV NL+DGTE
Sbjct: 183 NLLHISHEAGILEDPGAVCDESIYSRTVSPEKAPDIPTRITIAFKNGIPVKVKNLEDGTE 242

Query: 242 KTDPLELFEYLNEVGAKNGVGRLDMVENRFIGIKSRGVYETPGATILWIAHRDLEGITMD 301
           KTD LELF YLN++GA+NG+GRLDMVENRF+GIKSRGVYETPG  IL  AH+D+EGI MD
Sbjct: 243 KTDALELFLYLNQLGAQNGIGRLDMVENRFVGIKSRGVYETPGGAILHEAHKDIEGIAMD 302

Query: 302 KEVMHLRDMLAPKFAELIYNGFWFSPEMEFLLAAFRKAQENVTGKVTVSIYKGNVMPVAR 361
           +EVM LRDMLAP+  EL+Y GFWFSPEMEFL+AA  K+QE + G+VT+ ++KG   P+AR
Sbjct: 303 REVMRLRDMLAPRLGELVYYGFWFSPEMEFLMAAMDKSQELIDGEVTLKLFKGVAYPIAR 362

Query: 362 YSPYSLYNPELSSMDVEGGFDATDSKGFINIHALRLKVHQ 401
            SP SLYN  LSSMD+ GG++  +++GFI ++A+RL  H+
Sbjct: 363 TSPSSLYNQNLSSMDITGGYNQENAEGFIRVNAIRLMAHR 402


Lambda     K      H
   0.318    0.137    0.400 

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: 577
Number of extensions: 14
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: 409
Length of database: 408
Length adjustment: 31
Effective length of query: 378
Effective length of database: 377
Effective search space:   142506
Effective search space used:   142506
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: 50 (23.9 bits)

Align candidate WP_035236042.1 Q366_RS02655 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.27500.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-147  476.2   0.0   6.2e-147  475.9   0.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035236042.1  Q366_RS02655 argininosuccinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035236042.1  Q366_RS02655 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.9   0.0  6.2e-147  6.2e-147       1     389 [.       5     401 ..       5     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 475.9 bits;  conditional E-value: 6.2e-147
                                 TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdyl 69 
                                               kvvlaysGGlDtsv+lk+l e+g+ev+a+++d+Gq +ed++a+e+kalk+Ga k  + D ++efv+dy+
  lcl|NCBI__GCF_000745975.1:WP_035236042.1   5 KVVLAYSGGLDTSVILKWLLEQGYEVFAYMADIGQ-DEDFQAAEQKALKIGASKVFIEDMKKEFVTDYI 72 
                                               8**********************************.6******************************** PP

                                 TIGR00032  70 faaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkvi 138
                                               f+  + n+vyeg+Yll+ta+aRp+iakk++++ak+ ga+ v+hG+tgKGnDqvRFels ++lnp +kvi
  lcl|NCBI__GCF_000745975.1:WP_035236042.1  73 FPVFKSNTVYEGRYLLGTAIARPIIAKKQIDIAKQVGARYVSHGATGKGNDQVRFELSYYALNPAIKVI 141
                                               ********************************************************************* PP

                                 TIGR00032 139 aPvreleli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvk 202
                                               aP+++ ++      R+++++ya+++Gi+++++ +k+ys D+nll++s+Eag+LEdp ++  e iy+ ++
  lcl|NCBI__GCF_000745975.1:WP_035236042.1 142 APWKNPDFLnafqgRSDLLAYAEKHGIPTKQTAAKPYSEDDNLLHISHEAGILEDPGAVCDESIYSRTV 210
                                               ********************************************************************* PP

                                 TIGR00032 203 dpiektedepevveieFekGvPvaln.....geslepvelilkaneiagkhGvGriDivEdRiiglKsR 266
                                               +p++++ d p  ++i+F++G+Pv+++      e+ +++el+l +n+++ ++G+Gr+D+vE+R +g+KsR
  lcl|NCBI__GCF_000745975.1:WP_035236042.1 211 SPEKAP-DIPTRITIAFKNGIPVKVKnledgTEKTDALELFLYLNQLGAQNGIGRLDMVENRFVGIKSR 278
                                               998888.99****************98888667888********************************* PP

                                 TIGR00032 267 eiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGt 335
                                               ++YE+p+ ++L++Ahkd+e   ++++v++++++   +++el+Y+G+wf+p++e l a+++k+qe + G+
  lcl|NCBI__GCF_000745975.1:WP_035236042.1 279 GVYETPGGAILHEAHKDIEGIAMDREVMRLRDMLAPRLGELVYYGFWFSPEMEFLMAAMDKSQELIDGE 347
                                               ********************************************************************* PP

                                 TIGR00032 336 vrvklfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvy 389
                                               v++klfkG a+ i+r+s+ slY+++l+s++ +  ++q++a+Gfi++++++ +  
  lcl|NCBI__GCF_000745975.1:WP_035236042.1 348 VTLKLFKGVAYPIARTSPSSLYNQNLSSMDITGGYNQENAEGFIRVNAIRLMAH 401
                                               ************************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (408 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.66
//
[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