GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astA in Amantichitinum ursilacus IGB-41

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate WP_053935843.1 WG78_RS00585 arginine N-succinyltransferase

Query= SwissProt::P0AE37
         (344 letters)



>NCBI__GCF_001294205.1:WP_053935843.1
          Length = 338

 Score =  346 bits (888), Expect = e-100
 Identities = 181/339 (53%), Positives = 234/339 (69%), Gaps = 2/339 (0%)

Query: 2   MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61
           M IR ++ SD+  L+ LA   G G+T+L A+   L+ARI  + ++ +G    ++  Y FV
Sbjct: 1   MRIRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDLADASYFFV 60

Query: 62  LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121
           LED  TGT+ G   IE A+G++D WYNYRVG  VHAS+EL +Y  L TLFL++D TG+SE
Sbjct: 61  LEDETTGTLVGTSGIEAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASE 120

Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181
           LC+LFL PDWRK+GNG LLS+ RF+FMA F ++F+++V+AEMRGV DE+G SPFW+SLG+
Sbjct: 121 LCSLFLLPDWRKDGNGSLLSRCRFLFMAEFPERFSERVIAEMRGVSDENGRSPFWESLGR 180

Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241
            FF MDF+RADFL   G K+FIAELMP +PIYT  LS+EAQ  IG+VHP T PAR +LE 
Sbjct: 181 HFFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQAAIGEVHPGTRPARKLLEG 240

Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVE-VAEGQPAQGDFPACLVANENYHHF 300
           EGFRY  Y+DIFD GP+LE  +  +RAIR SRL + +A     +G  P  LV+N     F
Sbjct: 241 EGFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKGGVP-WLVSNRKLGSF 299

Query: 301 RVVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCA 339
           +  L +T P  + L LTAA L  L    GD VR V L A
Sbjct: 300 KCALAQTRPLEDSLPLTAAVLARLDIEDGDVVRAVPLSA 338


Lambda     K      H
   0.321    0.136    0.411 

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: 340
Number of extensions: 11
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: 344
Length of database: 338
Length adjustment: 29
Effective length of query: 315
Effective length of database: 309
Effective search space:    97335
Effective search space used:    97335
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_053935843.1 WG78_RS00585 (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.3543768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-142  459.6   0.0   2.9e-142  459.4   0.0    1.0  1  NCBI__GCF_001294205.1:WP_053935843.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053935843.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.4   0.0  2.9e-142  2.9e-142       2     336 .]       3     336 ..       2     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 459.4 bits;  conditional E-value: 2.9e-142
                             TIGR03244   2 vrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtetgkvvGvsai 74 
                                           +r ++ sdld+ll+la+ aGvG+t+l a+ ++l++ri+++++s +g  + a+++y+fvled  tg++vG+s+i
  NCBI__GCF_001294205.1:WP_053935843.1   3 IRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDLADASYFFVLEDETTGTLVGTSGI 75 
                                           7999********************************************************************* PP

                             TIGR03244  75 eaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflfla 147
                                           eaa+G+++++ynyrvg  vhas+el+iyk+l tlfl  dltgaselC+lfl +++rk+ nG+lls++rflf+a
  NCBI__GCF_001294205.1:WP_053935843.1  76 EAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASELCSLFLLPDWRKDGNGSLLSRCRFLFMA 148
                                           ************************************************************************* PP

                             TIGR03244 148 efkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaq 220
                                           ef+erfs+++iaemrGvsde+GrsPfWe+lg++ff++df++ad+ls +G+k+fiaelmP +Piy++lls+eaq
  NCBI__GCF_001294205.1:WP_053935843.1 149 EFPERFSERVIAEMRGVSDENGRSPFWESLGRHFFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQ 221
                                           ************************************************************************* PP

                             TIGR03244 221 dvigkvhektkPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvan 293
                                           + ig+vh+ t+Pa++lle eG+ry gyvdifdaGp le+ +++ira+r+s+l +    +++ +  ++p lv+n
  NCBI__GCF_001294205.1:WP_053935843.1 222 AAIGEVHPGTRPARKLLEGEGFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKG-GVPWLVSN 293
                                           *****************************************************99999998888.9******* PP

                             TIGR03244 294 ekledfrvvlvessldaeelvlsaeeakalkveeGdkvrvval 336
                                           +kl  f+  l++++   ++l l+a+ +++l +e+Gd vr v+l
  NCBI__GCF_001294205.1:WP_053935843.1 294 RKLGSFKCALAQTRPLEDSLPLTAAVLARLDIEDGDVVRAVPL 336
                                           ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (338 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: 24.27
//
[ok]

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

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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:

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:

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:

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:

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