Alignments for a candidate for astB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Escherichia coli BW25113

Align N-succinylarginine dihydrolase; EC 3.5.3.23 (characterized)
to candidate 15863 b1745 succinylarginine dihydrolase (NCBI)

Query= CharProtDB::CH_002938
         (447 letters)



>FitnessBrowser__Keio:15863
          Length = 447

 Score =  893 bits (2307), Expect = 0.0
 Identities = 447/447 (100%), Positives = 447/447 (100%)

Query: 1   MNAWEVNFDGLVGLTHHYAGLSFGNEASTRHRFQVSNPRLAAKQGLLKMKALADAGFPQA 60
           MNAWEVNFDGLVGLTHHYAGLSFGNEASTRHRFQVSNPRLAAKQGLLKMKALADAGFPQA
Sbjct: 1   MNAWEVNFDGLVGLTHHYAGLSFGNEASTRHRFQVSNPRLAAKQGLLKMKALADAGFPQA 60

Query: 61  VIPPHERPFIPVLRQLGFSGSDEQVLEKVARQAPHWLSSVSSASPMWVANAATIAPSADT 120
           VIPPHERPFIPVLRQLGFSGSDEQVLEKVARQAPHWLSSVSSASPMWVANAATIAPSADT
Sbjct: 61  VIPPHERPFIPVLRQLGFSGSDEQVLEKVARQAPHWLSSVSSASPMWVANAATIAPSADT 120

Query: 121 LDGKVHLTVANLNNKFHRSLEAPVTESLLKAIFNDEEKFSVHSALPQVALLGDEGAANHN 180
           LDGKVHLTVANLNNKFHRSLEAPVTESLLKAIFNDEEKFSVHSALPQVALLGDEGAANHN
Sbjct: 121 LDGKVHLTVANLNNKFHRSLEAPVTESLLKAIFNDEEKFSVHSALPQVALLGDEGAANHN 180

Query: 181 RLGGHYGEPGMQLFVYGREEGNDTRPSRYPARQTREASEAVARLNQVNPQQVIFAQQNPD 240
           RLGGHYGEPGMQLFVYGREEGNDTRPSRYPARQTREASEAVARLNQVNPQQVIFAQQNPD
Sbjct: 181 RLGGHYGEPGMQLFVYGREEGNDTRPSRYPARQTREASEAVARLNQVNPQQVIFAQQNPD 240

Query: 241 VIDQGVFHNDVIAVSNRQVLFCHQQAFARQSQLLANLRARVNGFMAIEVPATQVSVSDTV 300
           VIDQGVFHNDVIAVSNRQVLFCHQQAFARQSQLLANLRARVNGFMAIEVPATQVSVSDTV
Sbjct: 241 VIDQGVFHNDVIAVSNRQVLFCHQQAFARQSQLLANLRARVNGFMAIEVPATQVSVSDTV 300

Query: 301 STYLFNSQLLSRDDGSMMLVLPQECREHAGVWGYLNELLAADNPISELKVFDLRESMANG 360
           STYLFNSQLLSRDDGSMMLVLPQECREHAGVWGYLNELLAADNPISELKVFDLRESMANG
Sbjct: 301 STYLFNSQLLSRDDGSMMLVLPQECREHAGVWGYLNELLAADNPISELKVFDLRESMANG 360

Query: 361 GGPACLRLRVVLTEEERRAVNPAVMMNDTLFNALNDWVDRYYRDRLTAADLADPQLLREG 420
           GGPACLRLRVVLTEEERRAVNPAVMMNDTLFNALNDWVDRYYRDRLTAADLADPQLLREG
Sbjct: 361 GGPACLRLRVVLTEEERRAVNPAVMMNDTLFNALNDWVDRYYRDRLTAADLADPQLLREG 420

Query: 421 REALDVLSQLLNLGSVYPFQREGGGNG 447
           REALDVLSQLLNLGSVYPFQREGGGNG
Sbjct: 421 REALDVLSQLLNLGSVYPFQREGGGNG 447


Lambda     K      H
   0.318    0.133    0.391 

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: 860
Number of extensions: 23
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: 447
Length of database: 447
Length adjustment: 33
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
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: 51 (24.3 bits)

Align candidate 15863 b1745 (succinylarginine dihydrolase (NCBI))
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

# 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/TIGR03241.hmm
# target sequence database:        /tmp/gapView.16571.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03241  [M=443]
Accession:   TIGR03241
Description: arg_catab_astB: succinylarginine dihydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.8e-247  807.5   0.3     2e-247  807.3   0.3    1.0  1  lcl|FitnessBrowser__Keio:15863  b1745 succinylarginine dihydrola


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15863  b1745 succinylarginine dihydrolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  807.3   0.3    2e-247    2e-247       1     443 []       3     440 ..       3     440 .. 1.00

  Alignments for each domain:
  == domain 1  score: 807.3 bits;  conditional E-value: 2e-247
                       TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklGfsGs 79 
                                     a+evnfdGlvGlth+yaGlsfGn+ast+++ +vsnp+laakqGllkmkalad+Gf q+v++p+erp i++lr+lGfsGs
  lcl|FitnessBrowser__Keio:15863   3 AWEVNFDGLVGLTHHYAGLSFGNEASTRHRFQVSNPRLAAKQGLLKMKALADAGFPQAVIPPHERPFIPVLRQLGFSGS 81 
                                     79***************************************************************************** PP

                       TIGR03241  80 deevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkaifadekkfa 158
                                     de+vlek+ar+ap++ls+vssas+mw+anaat++psadt dg+vh+t+anlnnkfhrs+ea++te++lkaif+de+kf+
  lcl|FitnessBrowser__Keio:15863  82 DEQVLEKVARQAPHWLSSVSSASPMWVANAATIAPSADTLDGKVHLTVANLNNKFHRSLEAPVTESLLKAIFNDEEKFS 160
                                     ******************************************************************************* PP

                       TIGR03241 159 vhealpavallGdeGaanhtrlgaeydepgvelfvyGraalerepkpkryparqtleasqavarlhqleeekvvyaqqn 237
                                     vh+alp+vallGdeGaanh+rlg++y+epg++lfvyGr++  ++++p+ryparqt+eas+avarl+q+++++v++aqqn
  lcl|FitnessBrowser__Keio:15863 161 VHSALPQVALLGDEGAANHNRLGGHYGEPGMQLFVYGREE-GNDTRPSRYPARQTREASEAVARLNQVNPQQVIFAQQN 238
                                     ***************************************9.99************************************ PP

                       TIGR03241 238 pdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsqllske 316
                                     pdvidqGvfhndviavsnr+vlf+h++af +qsq+l++lra+++++    +aievp+++vsv+d+vs+ylfnsqlls++
  lcl|FitnessBrowser__Keio:15863 239 PDVIDQGVFHNDVIAVSNRQVLFCHQQAFARQSQLLANLRARVNGF----MAIEVPATQVSVSDTVSTYLFNSQLLSRD 313
                                     *******************************************997....9**************************** PP

                       TIGR03241 317 dgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnpkvllsdalfa 395
                                     dg+m+lv+p+ecre++ vw yl+el+aad+pi+e+kvfdlresm nGGGpaclrlrvvl+++e++avnp+v+++d+lf+
  lcl|FitnessBrowser__Keio:15863 314 DGSMMLVLPQECREHAGVWGYLNELLAADNPISELKVFDLRESMANGGGPACLRLRVVLTEEERRAVNPAVMMNDTLFN 392
                                     ******************************************************************************* PP

                       TIGR03241 396 tlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                     +ln+wvdr+yrdrl+a+dladpqll+e+r+ald+l+q+lnlGsvy+fq
  lcl|FitnessBrowser__Keio:15863 393 ALNDWVDRYYRDRLTAADLADPQLLREGREALDVLSQLLNLGSVYPFQ 440
                                     ***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (447 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: 00:00:00.02
# Mc/sec: 7.64
//
[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