Alignments for a candidate for asd in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Thermodesulforhabdus norvegica DSM 9990

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_093393428.1 BM091_RS03255 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_900114975.1:WP_093393428.1
          Length = 341

 Score =  351 bits (901), Expect = e-101
 Identities = 178/343 (51%), Positives = 246/343 (71%), Gaps = 8/343 (2%)

Query: 4   GLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPES 63
           G  VAVVGATGAVG  M++ LE+RNF + +L LL+S RSAG  ++F+G+E+ VQE + +S
Sbjct: 5   GFRVAVVGATGAVGNMMVRVLEERNFPVKSLKLLASARSAGKTLSFRGEEVPVQELTEDS 64

Query: 64  FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNG 123
           F  V+IALFSAG SVS+  AP A  +G +V+DN+SAFRMD + PLVVPEVN   L  H  
Sbjct: 65  FRDVDIALFSAGASVSRKFAPLAASQGCVVVDNSSAFRMDPDVPLVVPEVNPQALRNHKK 124

Query: 124 IIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEI 183
           IIANPNCSTIQMV AL+P++ A G+ +++V+T+Q+VSG G +A+ EL  Q +  +  + +
Sbjct: 125 IIANPNCSTIQMVVALKPLQDAVGIKRIVVTTFQSVSGTGKKAIFELEQQVRGWVEGKAV 184

Query: 184 EPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243
            P + P       + IAFN +P I  F +NG++ EEMKM+NET+KI   PD+QV AT VR
Sbjct: 185 PPSVYP-------HPIAFNCLPHIGSFLENGFSEEEMKMVNETRKIFEDPDIQVCATTVR 237

Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303
           +P+  GHSESV +E+ +   TVE+++ LL++APGV L D+P +  YP+P +A G+++ FV
Sbjct: 238 VPVFYGHSESVNVEL-KGLLTVEEVRRLLEKAPGVVLVDNPDRAEYPLPLNAEGRDETFV 296

Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           GRIRKD    NG  +W+V+DN+ KGAA N+VQIAE L K  L+
Sbjct: 297 GRIRKDPSVENGIVMWIVADNIRKGAATNAVQIAELLVKEGLL 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: 311
Number of extensions: 11
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: 341
Length adjustment: 29
Effective length of query: 317
Effective length of database: 312
Effective search space:    98904
Effective search space used:    98904
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_093393428.1 BM091_RS03255 (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.3758709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-148  479.8   0.1   2.5e-148  479.6   0.1    1.0  1  NCBI__GCF_900114975.1:WP_093393428.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900114975.1:WP_093393428.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.6   0.1  2.5e-148  2.5e-148       1     339 []       7     336 ..       7     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 479.6 bits;  conditional E-value: 2.5e-148
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           +va+vGatGavG+ +++vLeernfp+++l+llas+rsaGk + f+g+e+ v+e+++ sf+++dialfsaG+sv
  NCBI__GCF_900114975.1:WP_093393428.1   7 RVAVVGATGAVGNMMVRVLEERNFPVKSLKLLASARSAGKTLSFRGEEVPVQELTEDSFRDVDIALFSAGASV 79 
                                           69*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s++fap aa++g++v+Dn+safr+d+dvPLvvpevn + l+++k   iianPnCstiq+vv+Lkpl+d++++k
  NCBI__GCF_900114975.1:WP_093393428.1  80 SRKFAPLAASQGCVVVDNSSAFRMDPDVPLVVPEVNPQALRNHK--KIIANPNCSTIQMVVALKPLQDAVGIK 150
                                           ****************************************9998..9************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           r+vv t+q+vsG+Gkk++ eL++q++ ++egk   p       + ++++iafn +p+i+++ e+G+ +ee+k+
  NCBI__GCF_900114975.1:WP_093393428.1 151 RIVVTTFQSVSGTGKKAIFELEQQVRGWVEGKAVPP-------SVYPHPIAFNCLPHIGSFLENGFSEEEMKM 216
                                           *****************************9987775.......99**************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           ++etrki++++d++v at+vrvPvf+ghsesv++e++  l+veev+ lL++apgvv++d+p++ +yp Pl+a+
  NCBI__GCF_900114975.1:WP_093393428.1 217 VNETRKIFEDPDIQVCATTVRVPVFYGHSESVNVELKGLLTVEEVRRLLEKAPGVVLVDNPDRAEYPLPLNAE 289
                                           ************************************************************************* PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339
                                           g+de+fvgrirkD s e+g+ +++vaDn+rkGaa+navqiaell+ke
  NCBI__GCF_900114975.1:WP_093393428.1 290 GRDETFVGRIRKDPSVENGIVMWIVADNIRKGAATNAVQIAELLVKE 336
                                           ********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (341 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: 13.21
//
[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