GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Pseudomonas litoralis 2SM5

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_900105005.1:WP_090273343.1
          Length = 404

 Score =  554 bits (1427), Expect = e-162
 Identities = 268/399 (67%), Positives = 321/399 (80%)

Query: 7   QVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKA 66
           QV RADFDR MVPNYAP   IPVRG+GSR+WDQ GRE ID AGGIAV SLGHAHP LV+A
Sbjct: 6   QVNRADFDRLMVPNYAPVEMIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEA 65

Query: 67  LTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDV 126
           LTEQAQ++WHVSN+ TNEPALRLA KLV ATFA++V   NSGAEANEAAFKLARR+A+D 
Sbjct: 66  LTEQAQKLWHVSNIMTNEPALRLADKLVAATFADKVLFVNSGAEANEAAFKLARRWAHDQ 125

Query: 127 YGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK 186
            GP K+EIIA SNSFHGRTLFTV+VGGQPKYS GFGP   GI+HVPYND+ AL+A IS++
Sbjct: 126 SGPDKHEIIACSNSFHGRTLFTVSVGGQPKYSQGFGPAISGISHVPYNDIAALEAQISER 185

Query: 187 TCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGV 246
           TCAVV+EP+QGEGGV+PA   YL+  R LCD++NALL+FDEVQSGMGR G+L+AYMH GV
Sbjct: 186 TCAVVVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSGV 245

Query: 247 VPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPE 306
            PDIL+SAK +GGGFPI AMLT   +A  LSVGTHG+TYGGNPL  AVAE  LD+INTP+
Sbjct: 246 APDILTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTPQ 305

Query: 307 VLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAV 366
           VLDGV  +  +  + L+ +  E G+F EIRG GLLIGA L + W+G+A  V+  A++E +
Sbjct: 306 VLDGVGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQAGQVMRLAQEEGL 365

Query: 367 MVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVR 405
           +VLQA  DVVR APSL+I +A+I E L R   A+ +L++
Sbjct: 366 LVLQAGADVVRLAPSLIIPEADIREALGRMRAALLRLIK 404


Lambda     K      H
   0.318    0.135    0.394 

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: 544
Number of extensions: 15
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: 406
Length of database: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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_090273343.1 BLU11_RS10765 (aspartate aminotransferase family protein)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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/TIGR03246.hmm
# target sequence database:        /tmp/gapView.525849.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-205  669.1   0.1   1.2e-205  668.9   0.1    1.0  1  NCBI__GCF_900105005.1:WP_090273343.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090273343.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.9   0.1  1.2e-205  1.2e-205       1     396 [.       7     402 ..       7     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 668.9 bits;  conditional E-value: 1.2e-205
                             TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgng 73 
                                           v+r++fd +mvp+yap ++ipvrg+Gsr+wdq+g+eyid+aGGiavn+lGhahp+lveal+eqa+klwh++n 
  NCBI__GCF_900105005.1:WP_090273343.1   7 VNRADFDRLMVPNYAPVEMIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVSNI 79 
                                           79*********************************************************************** PP

                             TIGR03246  74 ytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGG 146
                                           +tnep+lrla klv atfadkv f nsGaeaneaa+klar++a+d+ g++k+ei+a+ nsfhGrtlftvsvGG
  NCBI__GCF_900105005.1:WP_090273343.1  80 MTNEPALRLADKLVAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKHEIIACSNSFHGRTLFTVSVGG 152
                                           ************************************************************************* PP

                             TIGR03246 147 qakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifd 219
                                           q+kys++f+p ++gi+h++ynd++al+a+is++tcav+vep+qGegGv+pa+ ++lk++r+lcd++nallifd
  NCBI__GCF_900105005.1:WP_090273343.1 153 QPKYSQGFGPAISGISHVPYNDIAALEAQISERTCAVVVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFD 225
                                           ************************************************************************* PP

                             TIGR03246 220 evqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvl 292
                                           evq+G+GrtG+lyaym+ Gv+pdiltsak++GgGfpi a+lt +++a +l+vGthG+tyGGnpl+cavae+vl
  NCBI__GCF_900105005.1:WP_090273343.1 226 EVQSGMGRTGKLYAYMHSGVAPDILTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVL 298
                                           ************************************************************************* PP

                             TIGR03246 293 dlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaG 365
                                           d++nt+++l+Gv +r++++++ l  + ++  vfseirG+GlliGavl e+++G+a +++++a+eeG+lvl+aG
  NCBI__GCF_900105005.1:WP_090273343.1 299 DIINTPQVLDGVGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQAGQVMRLAQEEGLLVLQAG 371
                                           ************************************************************************* PP

                             TIGR03246 366 pdvvrfapslvieeeeikeGlarlekavekl 396
                                           +dvvr+apsl+i+e++i e l r+  a+ +l
  NCBI__GCF_900105005.1:WP_090273343.1 372 ADVVRLAPSLIIPEADIREALGRMRAALLRL 402
                                           *************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (404 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: 28.49
//
[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:

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