Alignments for a candidate for asd in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Desulfovibrio vulgaris Miyazaki F

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate 8501664 DvMF_2382 aspartate-semialdehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__Miya:8501664
          Length = 349

 Score =  366 bits (939), Expect = e-106
 Identities = 191/342 (55%), Positives = 248/342 (72%), Gaps = 8/342 (2%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           L VAV GATGAVG++ML TLE R F    +   +S RSAG KV F G ELTV+E + ESF
Sbjct: 6   LVVAVCGATGAVGREMLNTLEQREFPAAEVIPFASARSAGNKVPFMGGELTVRELTEESF 65

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
            GV+IALFSAGGS S+  AP AV+ G +V+DN+SA+RMDE  PLVVPEVN   L  HNGI
Sbjct: 66  RGVDIALFSAGGSTSEKFAPHAVQAGCVVVDNSSAWRMDERCPLVVPEVNAHALAAHNGI 125

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMV AL+P+  A  + +V+VSTYQAVSG G +A+ EL  Q + + N +E +
Sbjct: 126 IANPNCSTIQMVVALKPLHDAARITRVVVSTYQAVSGTGQKAIDELEKQVRQMFNMQEPD 185

Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244
             + P       ++IAFN +PQID F DN YT EEMKM+ ET KIM  P ++V ATCVR+
Sbjct: 186 VAVYP-------HRIAFNCLPQIDVFMDNDYTKEEMKMVLETVKIMEDPSVKVTATCVRV 238

Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304
           P+  GHSESV IE +R   + ++ + +L +APGV + D+P+Q++YPMP DA G++D FVG
Sbjct: 239 PVFYGHSESVNIETER-KLSAKEARAILAQAPGVRVYDNPAQKMYPMPIDAAGEDDTFVG 297

Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           RIR+D   ANG ++W+VSDN+ KGAA N+VQIAE+L + +L+
Sbjct: 298 RIREDETIANGLNMWIVSDNIRKGAALNAVQIAEALVERDLL 339


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: 308
Number of extensions: 10
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: 349
Length adjustment: 29
Effective length of query: 317
Effective length of database: 320
Effective search space:   101440
Effective search space used:   101440
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 8501664 DvMF_2382 (aspartate-semialdehyde dehydrogenase (RefSeq))
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.19845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.9e-152  491.0   0.8     1e-151  490.8   0.8    1.0  1  lcl|FitnessBrowser__Miya:8501664  DvMF_2382 aspartate-semialdehyde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501664  DvMF_2382 aspartate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.8   0.8    1e-151    1e-151       2     338 ..       8     335 ..       7     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 490.8 bits;  conditional E-value: 1e-151
                         TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefa 78 
                                       va+ GatGavG+e+l++Le+r+fp+ +++++as+rsaG+kv f g el+v+e+++esf+g+dialfsaGgs+s++fa
  lcl|FitnessBrowser__Miya:8501664   8 VAVCGATGAVGREMLNTLEQREFPAAEVIPFASARSAGNKVPFMGGELTVRELTEESFRGVDIALFSAGGSTSEKFA 84 
                                       8**************************************************************************** PP

                         TIGR01296  79 pkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqa 155
                                       p+a++ag++v+Dn+sa+r+de  PLvvpevna+ l+ ++  giianPnCstiq+vv+Lkpl+d+a++ rvvvstYqa
  lcl|FitnessBrowser__Miya:8501664  85 PHAVQAGCVVVDNSSAWRMDERCPLVVPEVNAHALAAHN--GIIANPNCSTIQMVVALKPLHDAARITRVVVSTYQA 159
                                       ***************************************..************************************ PP

                         TIGR01296 156 vsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedl 232
                                       vsG+G+k+++eL++q++ +++++e ++         ++++iafn +p+id ++++ ytkee+k++ et ki++++ +
  lcl|FitnessBrowser__Miya:8501664 160 VSGTGQKAIDELEKQVRQMFNMQEPDV-------AVYPHRIAFNCLPQIDVFMDNDYTKEEMKMVLETVKIMEDPSV 229
                                       ************************997.......78***************************************** PP

                         TIGR01296 233 kvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkDlske 309
                                       kv+atcvrvPvf+ghsesv+ie+e++ls++e++ +L +apgv v d+p +++yp+P++a+g+d++fvgrir+D + +
  lcl|FitnessBrowser__Miya:8501664 230 KVTATCVRVPVFYGHSESVNIETERKLSAKEARAILAQAPGVRVYDNPAQKMYPMPIDAAGEDDTFVGRIREDETIA 306
                                       ***************************************************************************** PP

                         TIGR01296 310 kglalfvvaDnlrkGaalnavqiaellik 338
                                       +gl++++v+Dn+rkGaalnavqiae+l++
  lcl|FitnessBrowser__Miya:8501664 307 NGLNMWIVSDNIRKGAALNAVQIAEALVE 335
                                       **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (349 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: 12.48
//
[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:

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