Alignments for a candidate for asd in Thermophagus xiamenensis HS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Thermophagus xiamenensis HS1

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_010528892.1 GQW_RS0116150 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_000220155.1:WP_010528892.1
          Length = 337

 Score =  302 bits (774), Expect = 7e-87
 Identities = 171/345 (49%), Positives = 227/345 (65%), Gaps = 12/345 (3%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDR-NFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASP-E 62
           + +A+VGA+GAVGQ+ L  LE+R +F +D L L  S RSAG K +F+G+E+ V+E    +
Sbjct: 1   MKIAIVGASGAVGQEFLNILENRKDFPIDELVLFGSSRSAGKKYSFRGKEIEVKELQHND 60

Query: 63  SFEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHE-H 121
            F+ ++IAL SAG S S+  A    K G I+IDN+SAFRMD++ PLVVPEVN  D     
Sbjct: 61  DFKDIDIALTSAGASTSKKFAETITKYGTIMIDNSSAFRMDDDVPLVVPEVNAEDCANCP 120

Query: 122 NGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKE 181
             IIANPNC+TIQMV AL+ I     + +  V+TYQA SGAG   + EL  Q + I+  E
Sbjct: 121 RKIIANPNCTTIQMVVALKAIEDVSHIRRAHVATYQAASGAGASGMAELEGQIRQIVEGE 180

Query: 182 EIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATC 241
           +  P +      K  +Q+A N IPQ+D F DNGYT EEMKM NET+KIMH  D+QV+A C
Sbjct: 181 K--PTVQ-----KFVHQLAMNIIPQVDVFTDNGYTKEEMKMFNETRKIMHS-DIQVSAMC 232

Query: 242 VRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDV 301
           VR+PI   HSE+V++E +R   +VE+ K    +A G+ + D+P    YPMP    GK++V
Sbjct: 233 VRIPILRAHSEAVWVETERP-ISVEEAKEAFAKAKGIKIIDNPENHEYPMPLYLSGKDEV 291

Query: 302 FVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           +VGRIR DL   NG   WVV+D + KGAA N+VQIAE L + NLV
Sbjct: 292 YVGRIRSDLSNPNGLTFWVVADQIRKGAAMNAVQIAEYLIQKNLV 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: 296
Number of extensions: 12
Number of successful extensions: 6
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: 337
Length adjustment: 29
Effective length of query: 317
Effective length of database: 308
Effective search space:    97636
Effective search space used:    97636
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_010528892.1 GQW_RS0116150 (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.733884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-139  451.3   2.2   1.2e-139  451.1   2.2    1.0  1  NCBI__GCF_000220155.1:WP_010528892.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010528892.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.1   2.2  1.2e-139  1.2e-139       1     338 [.       2     332 ..       2     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 451.1 bits;  conditional E-value: 1.2e-139
                             TIGR01296   1 nvaivGatGavGqellkvLeer.nfpidklvllasersaGkkvkfkgkeleveeaeke.sfegidialfsaGg 71 
                                           ++aivGa+GavGqe+l++Le+r +fpid+lvl+ s+rsaGkk  f+gke+ev+e++++ +f++idial saG+
  NCBI__GCF_000220155.1:WP_010528892.1   2 KIAIVGASGAVGQEFLNILENRkDFPIDELVLFGSSRSAGKKYSFRGKEIEVKELQHNdDFKDIDIALTSAGA 74 
                                           69******************9846*******************************99879************* PP

                             TIGR01296  72 svskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeak 144
                                           s+sk+fa  ++k g+i+iDn+safr+d+dvPLvvpevnae+ ++ + + iianPnC+tiq+vv+Lk+++d  +
  NCBI__GCF_000220155.1:WP_010528892.1  75 STSKKFAETITKYGTIMIDNSSAFRMDDDVPLVVPEVNAEDCANCP-RKIIANPNCTTIQMVVALKAIEDVSH 146
                                           *********************************************9.99************************ PP

                             TIGR01296 145 lkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeel 217
                                           ++r  v+tYqa sGaG+ g++eL+ q++ ++eg+  ++       +kf++q+a+n+ip++d ++++Gytkee+
  NCBI__GCF_000220155.1:WP_010528892.1 147 IRRAHVATYQAASGAGASGMAELEGQIRQIVEGEKPTV-------QKFVHQLAMNIIPQVDVFTDNGYTKEEM 212
                                           ******************************99977665.......9*************************** PP

                             TIGR01296 218 kllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPle 290
                                           k+ +etrki++ +d++vsa cvr+P++++hse+v +e+e+++svee+ke + +a+g+++id+p++++yp+Pl 
  NCBI__GCF_000220155.1:WP_010528892.1 213 KMFNETRKIMH-SDIQVSAMCVRIPILRAHSEAVWVETERPISVEEAKEAFAKAKGIKIIDNPENHEYPMPLY 284
                                           ***********.************************************************************* PP

                             TIGR01296 291 avgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                            +gkdev+vgrir Dls+ +gl+ +vvaD++rkGaa+navqiae li+
  NCBI__GCF_000220155.1:WP_010528892.1 285 LSGKDEVYVGRIRSDLSNPNGLTFWVVADQIRKGAAMNAVQIAEYLIQ 332
                                           *********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (337 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: 20.96
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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