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.3913227.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.47
//
[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