Alignments for a candidate for asd in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Desulfovibrio gracilis DSM 16080

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_078716451.1 B5D49_RS04345 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_900167125.1:WP_078716451.1
          Length = 342

 Score =  355 bits (910), Expect = e-102
 Identities = 187/346 (54%), Positives = 243/346 (70%), Gaps = 8/346 (2%)

Query: 1   MGRGLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEAS 60
           M +   VAV GATGAVG++MLK LE R F    +   +S RS G K+ F+G ELTVQE +
Sbjct: 1   MSKNPRVAVCGATGAVGREMLKVLEQREFPASEVVPFASARSKGKKLPFRGGELTVQELT 60

Query: 61  PESFEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHE 120
            + FEG ++ALFSAGGS S+  AP A K G  V+DN+SA+RM+   PLVVPEVN  DL  
Sbjct: 61  HDCFEGFDVALFSAGGSTSETYAPSAAKLGCTVVDNSSAWRMNPECPLVVPEVNPHDLKW 120

Query: 121 HNGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNK 180
           H GIIANPNCSTIQMV AL+PI     + +V+VSTYQAVSG+G +A+ EL +Q + + N 
Sbjct: 121 HKGIIANPNCSTIQMVVALQPIHLEARIKRVVVSTYQAVSGSGQKAINELETQVRRLFNG 180

Query: 181 EEIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAAT 240
           +E+ PE  P       +QIAFN +PQID F ++GYT EEMKM+NET KIM  P+++V AT
Sbjct: 181 QEVVPEAYP-------HQIAFNCLPQIDVFLEDGYTKEEMKMVNETIKIMGDPNIKVTAT 233

Query: 241 CVRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKND 300
            VR+P+  GHSESV IE +    T +D + LL  +PG+ + D P +Q YPM  DA G ++
Sbjct: 234 TVRVPVFYGHSESVNIETE-SKLTADDCRALLATSPGIEVVDYPEKQAYPMALDATGLDE 292

Query: 301 VFVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           VFVGRIR+D    NG +LWVVSDN+ KGAA N+VQIAE+L +++L+
Sbjct: 293 VFVGRIREDHTVENGLNLWVVSDNIRKGAALNAVQIAETLLEMDLM 338


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: 327
Number of extensions: 13
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: 342
Length adjustment: 29
Effective length of query: 317
Effective length of database: 313
Effective search space:    99221
Effective search space used:    99221
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 WP_078716451.1 B5D49_RS04345 (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.11544.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-150  486.6   0.0   2.1e-150  486.4   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078716451.1  B5D49_RS04345 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078716451.1  B5D49_RS04345 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.4   0.0  2.1e-150  2.1e-150       1     337 [.       6     333 ..       6     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.4 bits;  conditional E-value: 2.1e-150
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               +va+ GatGavG+e+lkvLe+r+fp++++v++as+rs+Gkk+ f+g el+v+e+++  feg d+alfsa
  lcl|NCBI__GCF_900167125.1:WP_078716451.1   6 RVAVCGATGAVGREMLKVLEQREFPASEVVPFASARSKGKKLPFRGGELTVQELTHDCFEGFDVALFSA 74 
                                               69******************************************************************* PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                               Ggs+s+++ap+aak g++v+Dn+sa+r++++ PLvvpevn ++lk +k  giianPnCstiq+vv+L+p
  lcl|NCBI__GCF_900167125.1:WP_078716451.1  75 GGSTSETYAPSAAKLGCTVVDNSSAWRMNPECPLVVPEVNPHDLKWHK--GIIANPNCSTIQMVVALQP 141
                                               *********************************************998..******************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               ++ ea++krvvvstYqavsG+G+k+++eL+ q++  ++g+e  p       +++++qiafn +p+id +
  lcl|NCBI__GCF_900167125.1:WP_078716451.1 142 IHLEARIKRVVVSTYQAVSGSGQKAINELETQVRRLFNGQEVVP-------EAYPHQIAFNCLPQIDVF 203
                                               *****************************************997.......99**************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                                edGytkee+k+++et ki+g++++kv+at+vrvPvf+ghsesv+ie+e +l++++ + lL  +pg+ v
  lcl|NCBI__GCF_900167125.1:WP_078716451.1 204 LEDGYTKEEMKMVNETIKIMGDPNIKVTATTVRVPVFYGHSESVNIETESKLTADDCRALLATSPGIEV 272
                                               ********************************************************************* PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337
                                               +d p++++yp+ l+a+g devfvgrir+D + e+gl+l+vv+Dn+rkGaalnavqiae+l 
  lcl|NCBI__GCF_900167125.1:WP_078716451.1 273 VDYPEKQAYPMALDATGLDEVFVGRIREDHTVENGLNLWVVSDNIRKGAALNAVQIAETLL 333
                                               **********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (342 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: 7.78
//
[ok]

This GapMind analysis is from Apr 10 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