Alignments for a candidate for argG in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Acidimicrobium ferrooxidans DSM 10331

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_015799054.1 AFER_RS08595 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000023265.1:WP_015799054.1
          Length = 398

 Score =  335 bits (860), Expect = 1e-96
 Identities = 175/395 (44%), Positives = 251/395 (63%), Gaps = 5/395 (1%)

Query: 3   IVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDLK 62
           +VLAYSGGLDTS+ LKWL+     +V+A + D+GQ E++E  R +AL TGA  A  +D +
Sbjct: 5   VVLAYSGGLDTSVALKWLQVERGFDVVALSVDVGQQEDLEAVRTRALATGAIAAEVVDAR 64

Query: 63  EEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGNDQ 122
           + F  D++   ++A A YE  Y L +S++RPLI++ LV +A   GA A+AHG TGKGNDQ
Sbjct: 65  DAFADDYIARAIKADARYENRYPLVSSLSRPLISERLVEVARRYGASAVAHGCTGKGNDQ 124

Query: 123 VRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHIS 182
           VRFE+   AL PD+ V+AP R+W    R++ I Y  AHG+ +  ++E PYS+D NL   +
Sbjct: 125 VRFEVALAALAPDLTVLAPVRDWGMN-REDTIEYGRAHGVTLTQSKENPYSIDQNLWGRA 183

Query: 183 YEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQRL 242
            E G +EDPWA PP  ++  T         P+ V + F +G PV+++GERL  AAL+ RL
Sbjct: 184 VECGEMEDPWAAPPSDVWAYTAGG--LASLPDQVVIGFEQGVPVSLDGERLPLAALVDRL 241

Query: 243 NEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDMLS 302
           N I G   VGR+D+VENR VG+KSR VYE P   +L  A R +E +TL+REV H +  L 
Sbjct: 242 NRIAGSWQVGRIDMVENRRVGIKSREVYEAPAAVVLLEAHRQLEDITLEREVAHAKIELG 301

Query: 303 PKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQDL 362
            ++A LVY G W++P + A+ A+ D  ++ VTG  R++      +V GR++P SLY  +L
Sbjct: 302 LRWATLVYDGLWFSPLKHAIDAFIDEASKPVTGEVRVRFAPNAFWVDGRRSPSSLYDYEL 361

Query: 363 VSFDEAGGYDQKDAEGFIKIQALRLRVRALVEREG 397
            ++     +   DAEGF++I  L +R  A  ER+G
Sbjct: 362 ATYASEDRFRHGDAEGFVRIFGLGIRTWA--ERQG 394


Lambda     K      H
   0.319    0.137    0.402 

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: 432
Number of extensions: 18
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: 400
Length of database: 398
Length adjustment: 31
Effective length of query: 369
Effective length of database: 367
Effective search space:   135423
Effective search space used:   135423
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: 50 (23.9 bits)

Align candidate WP_015799054.1 AFER_RS08595 (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.2018884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-147  476.8   0.0   3.8e-147  476.6   0.0    1.0  1  NCBI__GCF_000023265.1:WP_015799054.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023265.1:WP_015799054.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.6   0.0  3.8e-147  3.8e-147       2     392 ..       5     392 ..       4     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 476.6 bits;  conditional E-value: 3.8e-147
                             TIGR00032   2 vvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaai 73 
                                           vvlaysGGlDtsvalk+l+ + g++v+a+ vdvGq +edl+a++ +al+ Ga  a v+Dar+ f++dy+ +ai
  NCBI__GCF_000023265.1:WP_015799054.1   5 VVLAYSGGLDTSVALKWLQVErGFDVVALSVDVGQ-QEDLEAVRTRALATGAIAAEVVDARDAFADDYIARAI 76 
                                           8******************888*************.6************************************ PP

                             TIGR00032  74 qanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrelel 146
                                           +a+a ye++Y+l+++L+Rpli+++lveva+++ga+avahGctgKGnDqvRFe+ + +l+pdl v+aPvr++ +
  NCBI__GCF_000023265.1:WP_015799054.1  77 KADARYENRYPLVSSLSRPLISERLVEVARRYGASAVAHGCTGKGNDQVRFEVALAALAPDLTVLAPVRDWGM 149
                                           ************************************************************************* PP

                             TIGR00032 147 iReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieF 219
                                            Re++iey +++G+ + ++ke++ysiD+nl+gr++E+ge+Edp+++pp d++++++   ++    p++v i+F
  NCBI__GCF_000023265.1:WP_015799054.1 150 NREDTIEYGRAHGVTLTQSKENPYSIDQNLWGRAVECGEMEDPWAAPPSDVWAYTAGGLASL---PDQVVIGF 219
                                           ********************************************************888888...888***** PP

                             TIGR00032 220 ekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkd 292
                                           e+GvPv+l+ge+l    l+ ++n+iag   vGriD+vE+R +g+KsRe+YEapa+++L++Ah++Le+ +l+++
  NCBI__GCF_000023265.1:WP_015799054.1 220 EQGVPVSLDGERLPLAALVDRLNRIAGSWQVGRIDMVENRRVGIKSREVYEAPAAVVLLEAHRQLEDITLERE 292
                                           ************************************************************************* PP

                             TIGR00032 293 vlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfe 365
                                           v++ k   + +++ l+Y Glwf+pl++a+da+i++  + vtG+vrv++      v gr+s+ slYd el+++ 
  NCBI__GCF_000023265.1:WP_015799054.1 293 VAHAKIELGLRWATLVYDGLWFSPLKHAIDAFIDEASKPVTGEVRVRFAPNAFWVDGRRSPSSLYDYELATYA 365
                                           ************************************************************************* PP

                             TIGR00032 366 kdkefdqkdaiGfikirglqikvyrek 392
                                            +++f + da+Gf++i gl i++++e+
  NCBI__GCF_000023265.1:WP_015799054.1 366 SEDRFRHGDAEGFVRIFGLGIRTWAER 392
                                           *********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (398 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: 26.69
//
[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