Alignments for a candidate for asd in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Echinicola vietnamensis KMM 6221, DSM 17526

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate Echvi_0713 Echvi_0713 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms)

Query= metacyc::MONOMER-6564
         (346 letters)



>FitnessBrowser__Cola:Echvi_0713
          Length = 329

 Score =  315 bits (807), Expect = 1e-90
 Identities = 169/343 (49%), Positives = 233/343 (67%), Gaps = 15/343 (4%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           + +AVVGATG VG ++L+ L + NF  D L L++S+RSAG K+ FK +E TV   +    
Sbjct: 1   MKLAVVGATGLVGSEILEVLAEHNFPFDELLLVASERSAGKKIAFKDKEYTVIGLAQAVS 60

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
           E  +IA+FSAGG  S+  AP+  + G IV+DN+SA+RMD    LVVPE+N   L   + I
Sbjct: 61  EKPDIAIFSAGGDTSKEWAPKFAEAGTIVVDNSSAWRMDPTKKLVVPEINAKSLKIDDRI 120

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMV AL  +R  YG+ +V+VSTYQ+V+G+G +AV +L             +
Sbjct: 121 IANPNCSTIQMVLALTKLRDRYGIKRVVVSTYQSVTGSGLKAVNQL-------------Q 167

Query: 185 PEIMPVKGDKKH-YQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243
            E    +G+K + ++I  N +P ID FQDNGYT EEMKMINETKKI   P +QV AT VR
Sbjct: 168 DERAGKEGEKAYPHKIDLNVLPHIDVFQDNGYTKEEMKMINETKKIFEDPSIQVTATTVR 227

Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303
           +P+  GHSESV +E  ++D  +E++K LL   PGV ++DD +  +YPMP +A  K++VFV
Sbjct: 228 IPVMGGHSESVNVEF-KEDFDLEEVKELLAATPGVVVEDDVANNVYPMPMNAHKKDEVFV 286

Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           GR+R+D  + N  ++W+V+DNL KGAA N+VQIAE L + +LV
Sbjct: 287 GRLRRDESQPNTLNMWIVADNLRKGAATNAVQIAEYLVEHSLV 329


Lambda     K      H
   0.314    0.131    0.366 

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: 287
Number of extensions: 8
Number of successful extensions: 3
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: 346
Length of database: 329
Length adjustment: 28
Effective length of query: 318
Effective length of database: 301
Effective search space:    95718
Effective search space used:    95718
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_0713 Echvi_0713 (aspartate-semialdehyde dehydrogenase (peptidoglycan organisms))
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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.aa/TIGR01296.hmm
# target sequence database:        /tmp/gapView.175122.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: aspartate-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.3e-135  436.1   0.9   5.8e-135  435.7   0.9    1.2  1  FitnessBrowser__Cola:Echvi_0713  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Cola:Echvi_0713  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.7   0.9  5.8e-135  5.8e-135       2     338 ..       3     325 ..       2     326 .. 0.97

  Alignments for each domain:
  == domain 1  score: 435.7 bits;  conditional E-value: 5.8e-135
                        TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefap 79 
                                      +a+vGatG vG e+l+vL+e+nfp d+l l+asersaGkk++fk+ke++v  + +++ e+ dia+fsaGg +ske+ap
  FitnessBrowser__Cola:Echvi_0713   3 LAVVGATGLVGSEILEVLAEHNFPFDELLLVASERSAGKKIAFKDKEYTVIGLAQAVSEKPDIAIFSAGGDTSKEWAP 80 
                                      79**************************************************************************** PP

                        TIGR01296  80 kaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqavs 157
                                      k+a+ag+iv+Dn+sa+r+d+   Lvvpe+na++lk      iianPnCstiq+v +L  l+d++++krvvvstYq+v 
  FitnessBrowser__Cola:Echvi_0713  81 KFAEAGTIVVDNSSAWRMDPTKKLVVPEINAKSLKIDD--RIIANPNCSTIQMVLALTKLRDRYGIKRVVVSTYQSVT 156
                                      **********************************9887..8************************************* PP

                        TIGR01296 158 GaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedlkvs 235
                                      G+G k+v++L+++      gke e        k+++++i  n++p+id ++++Gytkee+k+++et+ki++++ ++v+
  FitnessBrowser__Cola:Echvi_0713 157 GSGLKAVNQLQDER----AGKEGE--------KAYPHKIDLNVLPHIDVFQDNGYTKEEMKMINETKKIFEDPSIQVT 222
                                      *******9998875....456666........689******************************************* PP

                        TIGR01296 236 atcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkDlskekgla 313
                                      at+vr+Pv+ ghsesv++ef++++++eevkelL   pgvvv dd  +n+yp+P++a +kdevfvgr+r+D s+ ++l+
  FitnessBrowser__Cola:Echvi_0713 223 ATTVRIPVMGGHSESVNVEFKEDFDLEEVKELLAATPGVVVEDDVANNVYPMPMNAHKKDEVFVGRLRRDESQPNTLN 300
                                      ****************************************************************************** PP

                        TIGR01296 314 lfvvaDnlrkGaalnavqiaellik 338
                                      +++vaDnlrkGaa+navqiae l++
  FitnessBrowser__Cola:Echvi_0713 301 MWIVADNLRKGAATNAVQIAEYLVE 325
                                      *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (329 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: 00:00:00.00
# Mc/sec: 18.72
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis