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.15749.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  lcl|FitnessBrowser__Cola:Echvi_0713  Echvi_0713 aspartate-semialdehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0713  Echvi_0713 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms)
   #    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 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvsk 75 
                                          +a+vGatG vG e+l+vL+e+nfp d+l l+asersaGkk++fk+ke++v  + +++ e+ dia+fsaGg +sk
  lcl|FitnessBrowser__Cola:Echvi_0713   3 LAVVGATGLVGSEILEVLAEHNFPFDELLLVASERSAGKKIAFKDKEYTVIGLAQAVSEKPDIAIFSAGGDTSK 76 
                                          79************************************************************************ PP

                            TIGR01296  76 efapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvv 149
                                          e+apk+a+ag+iv+Dn+sa+r+d+   Lvvpe+na++lk      iianPnCstiq+v +L  l+d++++krvv
  lcl|FitnessBrowser__Cola:Echvi_0713  77 EWAPKFAEAGTIVVDNSSAWRMDPTKKLVVPEINAKSLKIDD--RIIANPNCSTIQMVLALTKLRDRYGIKRVV 148
                                          **************************************9887..8***************************** PP

                            TIGR01296 150 vstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfet 223
                                          vstYq+v G+G k+v++L+++      gke e        k+++++i  n++p+id ++++Gytkee+k+++et
  lcl|FitnessBrowser__Cola:Echvi_0713 149 VSTYQSVTGSGLKAVNQLQDER----AGKEGE--------KAYPHKIDLNVLPHIDVFQDNGYTKEEMKMINET 210
                                          ***************9998875....456666........689******************************* PP

                            TIGR01296 224 rkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdev 297
                                          +ki++++ ++v+at+vr+Pv+ ghsesv++ef++++++eevkelL   pgvvv dd  +n+yp+P++a +kdev
  lcl|FitnessBrowser__Cola:Echvi_0713 211 KKIFEDPSIQVTATTVRIPVMGGHSESVNVEFKEDFDLEEVKELLAATPGVVVEDDVANNVYPMPMNAHKKDEV 284
                                          ************************************************************************** PP

                            TIGR01296 298 fvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                          fvgr+r+D s+ ++l++++vaDnlrkGaa+navqiae l++
  lcl|FitnessBrowser__Cola:Echvi_0713 285 FVGRLRRDESQPNTLNMWIVADNLRKGAATNAVQIAEYLVE 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.16
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

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