Alignments for a candidate for asd in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Dehalococcoides mccartyi 195

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_010936674.1 DET_RS05055 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_000011905.1:WP_010936674.1
          Length = 338

 Score =  348 bits (892), Expect = e-100
 Identities = 177/343 (51%), Positives = 244/343 (71%), Gaps = 8/343 (2%)

Query: 4   GLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPES 63
           G  VA+VGATG VGQ+ +K LE R+F MDT++LL+S RSAG K+  KG+E+ V+E + +S
Sbjct: 2   GYRVAIVGATGMVGQEFIKVLEKRDFPMDTVSLLASDRSAGKKMMVKGEEIEVRETAYDS 61

Query: 64  FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNG 123
           F  V+IALFSAG  +S+  AP A +  AIV+DN++AFRMD   PLVVPEVN  D+  H G
Sbjct: 62  FNNVDIALFSAGADISRHFAPIAAQHKAIVVDNSAAFRMDPKVPLVVPEVNIEDITRHKG 121

Query: 124 IIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEI 183
           IIANPNCSTIQMV AL P+ K   + +++V+T+QAVSG G  AV EL +QT+ +L+ ++ 
Sbjct: 122 IIANPNCSTIQMVVALYPLHKVNPIKRIVVTTFQAVSGTGVNAVDELQTQTRQLLDGQKA 181

Query: 184 EPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243
              +         +QIAFN +P+ID F D+GYT EE KM+ ET+KIMH  ++Q++ATCVR
Sbjct: 182 VAHVY-------SHQIAFNVLPEIDVFLDSGYTKEEWKMLEETRKIMHADNIQLSATCVR 234

Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303
           +P+ TGHSE+V IE +R     E  +++L  +PG+ + D+P+ +LYP P  A G ++VFV
Sbjct: 235 VPVITGHSEAVTIEFER-PMEPEQARDILLRSPGIKVLDEPAVKLYPHPWLATGTDEVFV 293

Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           GRIRKD+   NG  +WVV+DN+ KGAA N+VQIAE L    ++
Sbjct: 294 GRIRKDISNPNGLVMWVVADNVRKGAALNAVQIAEELVNRGMI 336


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: 310
Number of extensions: 9
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: 338
Length adjustment: 29
Effective length of query: 317
Effective length of database: 309
Effective search space:    97953
Effective search space used:    97953
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_010936674.1 DET_RS05055 (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.1874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-144  465.4   1.0   6.2e-144  465.2   1.0    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010936674.1  DET_RS05055 aspartate-semialdehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936674.1  DET_RS05055 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.2   1.0  6.2e-144  6.2e-144       1     338 [.       4     332 ..       4     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.2 bits;  conditional E-value: 6.2e-144
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               +vaivGatG vGqe++kvLe+r+fp+d++ llas+rsaGkk+ +kg+e+ev+e+   sf+++dialfsa
  lcl|NCBI__GCF_000011905.1:WP_010936674.1   4 RVAIVGATGMVGQEFIKVLEKRDFPMDTVSLLASDRSAGKKMMVKGEEIEVRETAYDSFNNVDIALFSA 72 
                                               69******************************************************************* PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                               G+ +s+ fap aa++ +iv+Dn++afr+d++vPLvvpevn e+++ +k  giianPnCstiq+vv+L p
  lcl|NCBI__GCF_000011905.1:WP_010936674.1  73 GADISRHFAPIAAQHKAIVVDNSAAFRMDPKVPLVVPEVNIEDITRHK--GIIANPNCSTIQMVVALYP 139
                                               ********************************************9988..******************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               l++   +kr+vv t+qavsG+G ++v+eL+ qt+  l+g+          a+ +++qiafn++p id +
  lcl|NCBI__GCF_000011905.1:WP_010936674.1 140 LHKVNPIKRIVVTTFQAVSGTGVNAVDELQTQTRQLLDGQKAV-------AHVYSHQIAFNVLPEIDVF 201
                                               *************************************998776.......799**************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                                + Gytkee k+l etrki++ +++++satcvrvPv+tghse+v+iefe+++++e+++++L  +pg++v
  lcl|NCBI__GCF_000011905.1:WP_010936674.1 202 LDSGYTKEEWKMLEETRKIMHADNIQLSATCVRVPVITGHSEAVTIEFERPMEPEQARDILLRSPGIKV 270
                                               ********************************************************************* PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                               +d+p  +lyp P  a+g+devfvgrirkD+s+ +gl ++vvaDn+rkGaalnavqiae l++
  lcl|NCBI__GCF_000011905.1:WP_010936674.1 271 LDEPAVKLYPHPWLATGTDEVFVGRIRKDISNPNGLVMWVVADNVRKGAALNAVQIAEELVN 332
                                               ***********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (338 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: 00:00:00.00
# Mc/sec: 11.85
//
[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