Alignments for a candidate for astC in Escherichia coli BW25113

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.976.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.64
//
[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:

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