Alignments for a candidate for astE in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Escherichia coli BW25113

Align succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate 15862 b1744 succinylglutamate desuccinylase (NCBI)

Query= BRENDA::P76215
         (322 letters)



>FitnessBrowser__Keio:15862
          Length = 322

 Score =  660 bits (1702), Expect = 0.0
 Identities = 322/322 (100%), Positives = 322/322 (100%)

Query: 1   MDNFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPV 60
           MDNFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPV
Sbjct: 1   MDNFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPV 60

Query: 61  EMLDALLGAISHGEIPLRWRLLVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETC 120
           EMLDALLGAISHGEIPLRWRLLVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETC
Sbjct: 61  EMLDALLGAISHGEIPLRWRLLVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETC 120

Query: 121 RARELEQCLEDFYDQGKESVRWHLDLHTAIRGSLHPQFGVLPQRDIPWDEKFLTWLGAAG 180
           RARELEQCLEDFYDQGKESVRWHLDLHTAIRGSLHPQFGVLPQRDIPWDEKFLTWLGAAG
Sbjct: 121 RARELEQCLEDFYDQGKESVRWHLDLHTAIRGSLHPQFGVLPQRDIPWDEKFLTWLGAAG 180

Query: 181 LEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSGES 240
           LEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSGES
Sbjct: 181 LEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSGES 240

Query: 241 VGIVRTPPLRYRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEY 300
           VGIVRTPPLRYRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEY
Sbjct: 241 VGIVRTPPLRYRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEY 300

Query: 301 VLFPNPLVALGLRAGLMLEKIS 322
           VLFPNPLVALGLRAGLMLEKIS
Sbjct: 301 VLFPNPLVALGLRAGLMLEKIS 322


Lambda     K      H
   0.322    0.139    0.435 

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: 580
Number of extensions: 13
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: 322
Length of database: 322
Length adjustment: 28
Effective length of query: 294
Effective length of database: 294
Effective search space:    86436
Effective search space used:    86436
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: 48 (23.1 bits)

Align candidate 15862 b1744 (succinylglutamate desuccinylase (NCBI))
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

# 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/TIGR03242.hmm
# target sequence database:        /tmp/gapView.24415.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03242  [M=319]
Accession:   TIGR03242
Description: arg_catab_astE: succinylglutamate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.2e-149  481.1   0.0   9.4e-149  480.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:15862  b1744 succinylglutamate desuccin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15862  b1744 succinylglutamate desuccinylase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.9   0.0  9.4e-149  9.4e-149       1     318 [.       3     318 ..       3     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 480.9 bits;  conditional E-value: 9.4e-149
                       TIGR03242   1 dflaltlekkepevtqgeaknvklrwldeGvlelePeaeaekslvisaGihGnetaPielleqllsdiaagklqlkvrl 79 
                                     +flaltl+ k+p++t++e ++v++rwl++Gvlel+P + ++ +lvisaGihGnetaP+e+l++ll +i++g+++l++rl
  lcl|FitnessBrowser__Keio:15862   3 NFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPVEMLDALLGAISHGEIPLRWRL 81 
                                     69***************************************************************************** PP

                       TIGR03242  80 LlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasearyhyDlhtaiRasklekfa 158
                                     L+ilGnp+al++gkRy+++d+nR+fgGr+q ++es e++Ra+eLeq++e+f+++gk+s  r+h+DlhtaiR+s++++f+
  lcl|FitnessBrowser__Keio:15862  82 LVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETCRARELEQCLEDFYDQGKESV-RWHLDLHTAIRGSLHPQFG 159
                                     **********************************************************8.******************* PP

                       TIGR03242 159 llPyqekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendlsqfqaitealralisd 237
                                     +lP+++ p+d+++l+wl+aa+l+a+++h+e+ggtf+hfs+++++a actlelGka+PfG+ndl+qf+++++a++al+s+
  lcl|FitnessBrowser__Keio:15862 160 VLPQRDIPWDEKFLTWLGAAGLEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSG 238
                                     ******************************************************************************* PP

                       TIGR03242 238 eaiparkkeelklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrveeeeerilfPnakvanGlRagl 316
                                     e++++ ++ +l+ ++vv++i+++s+sfe+h+a+d+ nf++f+kGtlla+d +er++v+++ e++lfPn+ va GlRagl
  lcl|FitnessBrowser__Keio:15862 239 ESVGIVRTPPLR-YRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEYVLFPNPLVALGLRAGL 316
                                     ***********9.****************************************************************** PP

                       TIGR03242 317 ll 318
                                     +l
  lcl|FitnessBrowser__Keio:15862 317 ML 318
                                     *8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (322 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: 00:00:00.00
# Mc/sec: 11.39
//
[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