Alignments for a candidate for astA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Halomonas desiderata SP1

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate WP_086508152.1 BZY95_RS01055 arginine N-succinyltransferase

Query= SwissProt::Q8ZPV1
         (344 letters)



>NCBI__GCF_002151265.1:WP_086508152.1
          Length = 348

 Score =  320 bits (819), Expect = 4e-92
 Identities = 171/340 (50%), Positives = 221/340 (65%), Gaps = 8/340 (2%)

Query: 4   IRPVEHADIAALMQLAGKTGGGLTSLPANEATLAARIERALKTWSGELPKGEQGYVFVLE 63
           IRP+   D+  L ++A +TG G TSLP N   LAA+I  A+  +    P   + Y FVLE
Sbjct: 3   IRPIAEGDLDELQKIARETGVGFTSLPDNREFLAAKIAAAVAAFEQRTPADRRNYFFVLE 62

Query: 64  DSETGEVGGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSELC 123
           D E+GE+ G CAIE  VG   P+Y+YR+GTL H+S +L+++  + TLFLS+DHTG +E+ 
Sbjct: 63  DEESGELAGCCAIEGQVGREVPFYHYRLGTLAHSSVQLDLHRTIDTLFLSSDHTGDAEVA 122

Query: 124 TLFLDPEWR-----KEGNGYLLSKSRFMFMAAFRDKFNEKVVAEMRGVIDEHGYSPFWQS 178
           +LFL P +R      + NG LLS  R++FMA FRD+F +KV+AEMRGV DE G SPFW+ 
Sbjct: 123 SLFLRPGFRGKERAHQRNGALLSMVRWLFMAEFRDQFPDKVLAEMRGVFDERGKSPFWEC 182

Query: 179 LGKRFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSEEAQAVIGEVHPQTAPARAV 238
           LG  FF +DF  AD L G GQK+FI ELMPK PIYT FLS+EA+A IG+VH  T PA A+
Sbjct: 183 LGSHFFPLDFDEADRLTGLGQKSFIGELMPKFPIYTPFLSDEARACIGQVHHDTRPALAM 242

Query: 239 LEKEGFRYRHYIDIFDGGPTLECDIDRVRAIRKSRL--VEVAEGQPAPGDYPACLVANEN 296
           L+KEG R+  YIDIFDGGPT+E  ID VRA+RKS    VE+  G   P   P  L A+  
Sbjct: 243 LKKEGLRWEGYIDIFDGGPTVEAYIDDVRAVRKSHCCRVEIRSGSDTPPARPRWLAASTT 302

Query: 297 YHHFRAALVRADP-QTSRLVLTAAQLDALKCRAGDHVRLV 335
              FRAA V   P +   L L+  +   L   AGD +R++
Sbjct: 303 MAEFRAAWVACGPDEEGTLTLSETEAQRLGVAAGDSLRVL 342


Lambda     K      H
   0.321    0.137    0.416 

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: 336
Number of extensions: 13
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: 344
Length of database: 348
Length adjustment: 29
Effective length of query: 315
Effective length of database: 319
Effective search space:   100485
Effective search space used:   100485
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_086508152.1 BZY95_RS01055 (arginine N-succinyltransferase)
to HMM TIGR03244 (astA: arginine N-succinyltransferase (EC 2.3.1.109))

# 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.carbon/TIGR03244.hmm
# target sequence database:        /tmp/gapView.8192.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03244  [M=336]
Accession:   TIGR03244
Description: arg_catab_AstA: arginine N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-128  412.9   0.0   4.8e-128  412.7   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508152.1  BZY95_RS01055 arginine N-succiny


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508152.1  BZY95_RS01055 arginine N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.7   0.0  4.8e-128  4.8e-128       2     334 ..       3     342 ..       2     344 .. 0.96

  Alignments for each domain:
  == domain 1  score: 412.7 bits;  conditional E-value: 4.8e-128
                                 TIGR03244   2 vrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtetgkvvG 70 
                                               +rp+ + dld+l+++a+e+GvG+tslp n+e l+++i++a+ +f+++++++ ++y+fvled e+g+++G
  lcl|NCBI__GCF_002151265.1:WP_086508152.1   3 IRPIAEGDLDELQKIARETGVGFTSLPDNREFLAAKIAAAVAAFEQRTPADRRNYFFVLEDEESGELAG 71 
                                               8******************************************************************** PP

                                 TIGR03244  71 vsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyr.....keln 134
                                                +aie +vG e pfy+yr+g++ h+s +l+++++++tlfls d+tg +e+ +lfl++ +r     +++n
  lcl|NCBI__GCF_002151265.1:WP_086508152.1  72 CCAIEGQVGREVPFYHYRLGTLAHSSVQLDLHRTIDTLFLSSDHTGDAEVASLFLRPGFRgkeraHQRN 140
                                               **********************************************************9954444578* PP

                                 TIGR03244 135 GkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiae 203
                                               G lls +r lf+aef+++f +k++aemrGv+de G+sPfWe lg++ff ldf +ad l+g+G+k+fi e
  lcl|NCBI__GCF_002151265.1:WP_086508152.1 141 GALLSMVRWLFMAEFRDQFPDKVLAEMRGVFDERGKSPFWECLGSHFFPLDFDEADRLTGLGQKSFIGE 209
                                               ********************************************************************* PP

                                 TIGR03244 204 lmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGptleaevakiravreskl 272
                                               lmPkfPiy+ +ls+ea++ ig+vh++t+Pala+l++eGlr++gy+difd+Gpt+ea+++++ravr+s+ 
  lcl|NCBI__GCF_002151265.1:WP_086508152.1 210 LMPKFPIYTPFLSDEARACIGQVHHDTRPALAMLKKEGLRWEGYIDIFDGGPTVEAYIDDVRAVRKSHC 278
                                               ********************************************************************* PP

                                 TIGR03244 273 vevavaesaaed.eaepylvanekledfrvvlvess.ldaeelvlsaeeakalkveeGdkvrvv 334
                                               + v++ + +++    ++ l a +++++fr+  v     + ++l+ls++ea++l v +Gd++rv+
  lcl|NCBI__GCF_002151265.1:WP_086508152.1 279 CRVEIRSGSDTPpARPRWLAASTTMAEFRAAWVACGpDEEGTLTLSETEAQRLGVAAGDSLRVL 342
                                               ***99887776514567899999*******99998747889*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (348 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.14
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources