Alignments for a candidate for aspA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Escherichia coli BW25113

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 18166 b4139 aspartate ammonia-lyase (aspartase) (VIMSS)

Query= BRENDA::P0AC38
         (478 letters)



>FitnessBrowser__Keio:18166
          Length = 478

 Score =  947 bits (2448), Expect = 0.0
 Identities = 478/478 (100%), Positives = 478/478 (100%)

Query: 1   MSNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAM 60
           MSNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAM
Sbjct: 1   MSNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAM 60

Query: 61  ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLE 120
           ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLE
Sbjct: 61  ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLE 120

Query: 121 LMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVE 180
           LMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVE
Sbjct: 121 LMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVE 180

Query: 181 FQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLN 240
           FQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLN
Sbjct: 181 FQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLN 240

Query: 241 TPKEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRL 300
           TPKEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRL
Sbjct: 241 TPKEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRL 300

Query: 301 LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQ 360
           LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQ
Sbjct: 301 LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQ 360

Query: 361 LNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIG 420
           LNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIG
Sbjct: 361 LNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIG 420

Query: 421 HHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ 478
           HHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ
Sbjct: 421 HHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ 478


Lambda     K      H
   0.317    0.134    0.381 

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: 843
Number of extensions: 9
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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 18166 b4139 (aspartate ammonia-lyase (aspartase) (VIMSS))
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

# 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/TIGR00839.hmm
# target sequence database:        /tmp/gapView.10782.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00839  [M=468]
Accession:   TIGR00839
Description: aspA: aspartate ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.9e-280  915.4   4.9   4.4e-280  915.2   4.9    1.0  1  lcl|FitnessBrowser__Keio:18166  b4139 aspartate ammonia-lyase (a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18166  b4139 aspartate ammonia-lyase (aspartase) (VIMSS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  915.2   4.9  4.4e-280  4.4e-280       1     468 []       6     474 ..       6     474 .. 1.00

  Alignments for each domain:
  == domain 1  score: 915.2 bits;  conditional E-value: 4.4e-280
                       TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaivaacdeil 79 
                                     rie+dllG++ev+a++yyG++tlra+enf+isn+kisd+pefv+++v+vkkaaa+an+el++i++++a+ai+aacde+l
  lcl|FitnessBrowser__Keio:18166   6 RIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAMANKELQTIPKSVANAIIAACDEVL 84 
                                     89***************************************************************************** PP

                       TIGR00839  80 e.GkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndayptalkiavyeslekl 157
                                     + Gk++dqf+vdv+qGGaGtsvnmntnev+an++lel+Gh+kGeyq+lnpndhvnk+qstndaypt+++iavy+sl+kl
  lcl|FitnessBrowser__Keio:18166  85 NnGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLELMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKL 163
                                     99***************************************************************************** PP

                       TIGR00839 158 vdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikrtrelllevnlGataiGtGlnad 236
                                     vd+i++lr++fe+ka+ef+d+lkmGrtqlqdavp+tlGqef+a+++ll+++vk+i+rt+elllevnlGataiGtGln++
  lcl|FitnessBrowser__Keio:18166 164 VDAINQLREGFERKAVEFQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLNTP 242
                                     ******************************************************************************* PP

                       TIGR00839 237 keysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcndlrllssGpraGlneinlpelqaGs 315
                                     keys+l+vkklaevtG+p+vpae+lieatsd+gayv+v+galkr+avk+sk+cndlrllssGpraGlneinlpelqaGs
  lcl|FitnessBrowser__Keio:18166 243 KEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRLLSSGPRAGLNEINLPELQAGS 321
                                     ******************************************************************************* PP

                       TIGR00839 316 simpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafallesisiltnaiesltdkcveGitaneki 394
                                     simpakvnpvvpevvnqvcfkviGndttvt+aaeaGqlqlnv+epvi++a++es++iltna+++l++kc++Gitan+++
  lcl|FitnessBrowser__Keio:18166 322 SIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQLNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEV 400
                                     ******************************************************************************* PP

                       TIGR00839 395 cedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvlekdllteeelddilsvenllkpaykakklkd 468
                                     ce+yv+nsiGivt+lnpfiG++++++v+k++++tgksvr+vvle++llte+elddi+sv+nl++paykak+++d
  lcl|FitnessBrowser__Keio:18166 401 CEGYVYNSIGIVTYLNPFIGHHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTD 474
                                     ***********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (478 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: 12.40
//
[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