Alignments for a candidate for argG in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Thermomonospora curvata DSM 43183

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_012852507.1 TCUR_RS10670 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000024385.1:WP_012852507.1
          Length = 400

 Score =  327 bits (837), Expect = 5e-94
 Identities = 169/399 (42%), Positives = 254/399 (63%), Gaps = 3/399 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQG-EEVEEAREKALRTGASKAIALD 60
           ++VLAYSGGLDTS+ + +L E    EVIA   D+GQG E++E  R++AL  GA +A+ +D
Sbjct: 4   RVVLAYSGGLDTSVAIPYLAEQTGGEVIAVAVDVGQGGEDLEVIRKRALACGAVEAVVVD 63

Query: 61  LKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGN 120
            +EEF  DF  P ++A A+Y   Y L ++++RPLI KHL   A+E G  A+AHG TGKGN
Sbjct: 64  AREEFASDFCVPALQANALYMDRYPLVSALSRPLIVKHLAAAAKEFGGTAVAHGCTGKGN 123

Query: 121 DQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLH 180
           DQVRFE    AL PD+KVIAP R++++  R + I YAE+ G+P+ V+ + PYS+D NL  
Sbjct: 124 DQVRFEAGLAALNPDLKVIAPARDFAWT-RDKAIEYAESKGLPIDVSAKSPYSIDQNLWG 182

Query: 181 ISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQ 240
            + E G LED W  P + ++  T DP    D P+ V + F  G PVA++G  L+P  +++
Sbjct: 183 RAVETGFLEDIWNAPIEDLYDYTSDPSAQRD-PDEVVITFRAGVPVALDGRELTPLQIIE 241

Query: 241 RLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDM 300
            LN+  G  GVGR+D+VE+R VG+KSR VYE P    L  A   +E++T++R++   +  
Sbjct: 242 ELNQRAGAQGVGRIDMVEDRLVGIKSREVYEAPAAIALITAHMELENVTVERDLARFKRS 301

Query: 301 LSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQ 360
           +  ++ ELVY G WY+P + +L A+     + V+G  R+ L+ G   V GR++  SLY  
Sbjct: 302 VDQRWGELVYDGLWYSPLKRSLDAFIAESQKHVSGEIRMTLHGGRAVVTGRRSDASLYDH 361

Query: 361 DLVSFDEAGGYDQKDAEGFIKIQALRLRVRALVEREGHG 399
           DL ++D    +DQ  A+GF+++ +L  ++ A+ +R   G
Sbjct: 362 DLATYDTGDTFDQSLAKGFVELWSLPSKIAAVRDRRVQG 400


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: 418
Number of extensions: 18
Number of successful extensions: 4
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_012852507.1 TCUR_RS10670 (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.26565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-155  504.0   0.0   2.2e-155  503.8   0.0    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012852507.1  TCUR_RS10670 argininosuccinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012852507.1  TCUR_RS10670 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.8   0.0  2.2e-155  2.2e-155       1     389 [.       4     391 ..       4     396 .. 0.99

  Alignments for each domain:
  == domain 1  score: 503.8 bits;  conditional E-value: 2.2e-155
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               +vvlaysGGlDtsva+++l e+ g eviav+vdvGq+ edl+ i+++al++Ga++a+v+Dareef++d+
  lcl|NCBI__GCF_000024385.1:WP_012852507.1   4 RVVLAYSGGLDTSVAIPYLAEQtGGEVIAVAVDVGQGGEDLEVIRKRALACGAVEAVVVDAREEFASDF 72 
                                               69********************999******************************************** PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                                ++a+qana+y ++Y+l++aL+Rpli k l ++ak+ g +avahGctgKGnDqvRFe+ + +lnpdlkv
  lcl|NCBI__GCF_000024385.1:WP_012852507.1  73 CVPALQANALYMDRYPLVSALSRPLIVKHLAAAAKEFGGTAVAHGCTGKGNDQVRFEAGLAALNPDLKV 141
                                               ********************************************************************* PP

                                 TIGR00032 138 iaPvreleliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpie 206
                                               iaP+r+  ++R + ieya++kG+++ v+ +++ysiD+nl+gr++E+g LEd + +p+ed y+++ dp +
  lcl|NCBI__GCF_000024385.1:WP_012852507.1 142 IAPARDFAWTRDKAIEYAESKGLPIDVSAKSPYSIDQNLWGRAVETGFLEDIWNAPIEDLYDYTSDPSA 210
                                               *****************************************************************9988 PP

                                 TIGR00032 207 ktedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapall 275
                                               +   +p++v i+F+ GvPval+g++l+p+++i+++n+ ag++GvGriD+vEdR++g+KsRe+YEapa++
  lcl|NCBI__GCF_000024385.1:WP_012852507.1 211 QR--DPDEVVITFRAGVPVALDGRELTPLQIIEELNQRAGAQGVGRIDMVEDRLVGIKSREVYEAPAAI 277
                                               87..99*************************************************************** PP

                                 TIGR00032 276 lLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGn 344
                                                Li+Ah +Le+ + ++d ++fk+ v+++++el+Y Glw++pl+  lda+i ++q++v+G++r+ l+ G 
  lcl|NCBI__GCF_000024385.1:WP_012852507.1 278 ALITAHMELENVTVERDLARFKRSVDQRWGELVYDGLWYSPLKRSLDAFIAESQKHVSGEIRMTLHGGR 346
                                               ********************************************************************* PP

                                 TIGR00032 345 aivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvy 389
                                               a+v gr+s+ slYd++l++++  ++fdq+ a+Gf+++++l+ k+ 
  lcl|NCBI__GCF_000024385.1:WP_012852507.1 347 AVVTGRRSDASLYDHDLATYDTGDTFDQSLAKGFVELWSLPSKIA 391
                                               ****************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (400 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.10
//
[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