Alignments for a candidate for asd in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Desulfovibrio vulgaris Hildenborough

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate 208563 DVU3048 aspartate-semialdehyde dehydrogenase

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



>MicrobesOnline__882:208563
          Length = 349

 Score =  358 bits (920), Expect = e-104
 Identities = 190/342 (55%), Positives = 243/342 (71%), Gaps = 8/342 (2%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           L VAVVGATGAVG++MLKTLE R+F    +   +S RSAG+KV F+  ELTV+E + + F
Sbjct: 6   LVVAVVGATGAVGREMLKTLEGRDFPAAEVIPFASARSAGSKVPFRDGELTVRELTEDCF 65

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
            G++IALFSAGGS S+  AP A K G +VIDN+SA+RMD   PLVVPEVN   L  HNGI
Sbjct: 66  TGIDIALFSAGGSTSEKFAPHAAKAGCVVIDNSSAWRMDARCPLVVPEVNPHHLEAHNGI 125

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMV AL+P+  A  + +VIVSTYQAVSG G +A+ EL  Q + + N  E E
Sbjct: 126 IANPNCSTIQMVVALKPLHDAARIKRVIVSTYQAVSGTGQKAIDELDRQVRQMFNMMEPE 185

Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244
            ++ P       ++IAFN +P ID F DN YT EEMKM++ET KIM  P ++V ATCVR+
Sbjct: 186 VQVYP-------HRIAFNCLPHIDVFLDNDYTKEEMKMVHETVKIMDDPSVKVTATCVRV 238

Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304
           P+  GHSESV IE ++   T  D + +L +APGV + D+P Q++YPMP DA G++  FVG
Sbjct: 239 PVFYGHSESVNIETEK-KLTARDARAILSQAPGVQVYDNPGQKMYPMPIDAAGEDATFVG 297

Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           RIR+D    NG +LW+V+DN+ KGAA N+VQIAE L   +LV
Sbjct: 298 RIREDETIENGLNLWIVADNIRKGAALNAVQIAEELIDRDLV 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: 329
Number of extensions: 6
Number of successful extensions: 4
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 208563 DVU3048 (aspartate-semialdehyde dehydrogenase)
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.19957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     4e-153  495.4   0.1   4.7e-153  495.2   0.1    1.0  1  lcl|MicrobesOnline__882:208563  DVU3048 aspartate-semialdehyde d


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208563  DVU3048 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.2   0.1  4.7e-153  4.7e-153       2     338 ..       8     335 ..       7     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.2 bits;  conditional E-value: 4.7e-153
                       TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefapk 80 
                                     va+vGatGavG+e+lk+Le r+fp+ +++++as+rsaG kv f++ el+v+e+++  f gidialfsaGgs+s++fap+
  lcl|MicrobesOnline__882:208563   8 VAVVGATGAVGREMLKTLEGRDFPAAEVIPFASARSAGSKVPFRDGELTVRELTEDCFTGIDIALFSAGGSTSEKFAPH 86 
                                     8****************************************************************************** PP

                       TIGR01296  81 aakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqavsGa 159
                                     aakag++viDn+sa+r+d   PLvvpevn ++l+ ++  giianPnCstiq+vv+Lkpl+d+a++krv+vstYqavsG+
  lcl|MicrobesOnline__882:208563  87 AAKAGCVVIDNSSAWRMDARCPLVVPEVNPHHLEAHN--GIIANPNCSTIQMVVALKPLHDAARIKRVIVSTYQAVSGT 163
                                     ************************************9..**************************************** PP

                       TIGR01296 160 GkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedlkvsatc 238
                                     G+k+++eL  q++ ++++ e e+       + ++++iafn +p+id + ++ ytkee+k+++et ki++++ +kv+atc
  lcl|MicrobesOnline__882:208563 164 GQKAIDELDRQVRQMFNMMEPEV-------QVYPHRIAFNCLPHIDVFLDNDYTKEEMKMVHETVKIMDDPSVKVTATC 235
                                     *******************9997.......99*********************************************** PP

                       TIGR01296 239 vrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvv 317
                                     vrvPvf+ghsesv+ie+ek+l++++++ +L +apgv+v d+p +++yp+P++a+g+d++fvgrir+D + e+gl+l++v
  lcl|MicrobesOnline__882:208563 236 VRVPVFYGHSESVNIETEKKLTARDARAILSQAPGVQVYDNPGQKMYPMPIDAAGEDATFVGRIREDETIENGLNLWIV 314
                                     ******************************************************************************* PP

                       TIGR01296 318 aDnlrkGaalnavqiaellik 338
                                     aDn+rkGaalnavqiae li+
  lcl|MicrobesOnline__882:208563 315 ADNIRKGAALNAVQIAEELID 335
                                     *****************9985 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.93
//
[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