GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Escherichia coli BW25113

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 17422 b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI)

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__Keio:17422
          Length = 406

 Score =  555 bits (1431), Expect = e-163
 Identities = 270/404 (66%), Positives = 322/404 (79%)

Query: 1   MSAPHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAH 60
           M+     + RA FD  ++P YAPA FIPV+G+GSR+WDQ G+E +DFAGGIAVT+LGH H
Sbjct: 1   MAIEQTAITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCH 60

Query: 61  PALVKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLAR 120
           PALV AL  Q + +WH+SNVFTNEPALRL RKL++ATFAERV   NSG EANE AFKLAR
Sbjct: 61  PALVNALKTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLAR 120

Query: 121 RYANDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK 180
            YA   + P K +IIA  N+FHGR+LFTV+VGGQPKYSDGFGPK   I HVP+NDL A+K
Sbjct: 121 HYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVK 180

Query: 181 AAISDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240
           A + D TCAVV+EPIQGEGGV  A   +L+G R+LCD+H ALLVFDEVQ GMGR G+LFA
Sbjct: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFA 240

Query: 241 YMHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALD 300
           YMHYGV PDIL+SAK+LGGGFPI AMLTT EIA     G+HG+TYGGNPLA AVA AA D
Sbjct: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFD 300

Query: 301 VINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360
           +INTPEVL+G++AK +RF   LQKI Q+Y +F +IRGMGLLIGA L  ++KG+ARD L A
Sbjct: 301 IINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYA 360

Query: 361 AEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404
             +  VMVL A PDV+RFAPSLV++DA+IDEG++RF  AVAK+V
Sbjct: 361 GAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVV 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: 551
Number of extensions: 14
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: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 17422 b3359 (bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI))
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.372570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.7e-209  680.5   0.3   4.2e-209  680.3   0.3    1.0  1  lcl|FitnessBrowser__Keio:17422  b3359 bifunctional acetylornithi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17422  b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotra
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  680.3   0.3  4.2e-209  4.2e-209       1     397 []       8     404 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 680.3 bits;  conditional E-value: 4.2e-209
                       TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepv 79 
                                     ++r++fdev++p+yapa+fipv+g+Gsr+wdq+gkey+dfaGGiav+alGh+hp+lv+alk q+e+lwh++n++tnep+
  lcl|FitnessBrowser__Keio:17422   8 ITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTNEPA 86 
                                     79***************************************************************************** PP

                       TIGR03246  80 lrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplp 158
                                     lrl +kl++atfa++v f nsG+eane+a+klar++a  ++++ k++i+af+n+fhGr+lftvsvGGq+kys++f+p+p
  lcl|FitnessBrowser__Keio:17422  87 LRLGRKLIEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKP 165
                                     ******************************************************************************* PP

                       TIGR03246 159 egikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymey 237
                                     ++i h+++ndl+a+ka+++d+tcav+vepiqGegGv++a+++fl+glrelcd+h+all+fdevq G+GrtG+l+aym+y
  lcl|FitnessBrowser__Keio:17422 166 ADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHY 244
                                     ******************************************************************************* PP

                       TIGR03246 238 GvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdele 316
                                     GvtpdiltsakalGgGfpi a+ltt e+a++++ G+hG+tyGGnplacava++ +d++nt+e+leG++++ ++fvd+l+
  lcl|FitnessBrowser__Keio:17422 245 GVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAKRQRFVDHLQ 323
                                     ******************************************************************************* PP

                       TIGR03246 317 kinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekavek 395
                                     ki+++y+vfs+irG+GlliGa+l+ +y+G+a+d++ a ae+Gv+vl aGpdv+rfapslv+e+++i+eG++r+++av+k
  lcl|FitnessBrowser__Keio:17422 324 KIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAK 402
                                     *****************************************************************************99 PP

                       TIGR03246 396 lv 397
                                     +v
  lcl|FitnessBrowser__Keio:17422 403 VV 404
                                     86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (406 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: 28.79
//
[ok]

This GapMind analysis is from Sep 17 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