GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Desulfarculus baarsii DSM 2075

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_013257581.1 DEBA_RS03780 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_000143965.1:WP_013257581.1
          Length = 341

 Score =  350 bits (897), Expect = e-101
 Identities = 183/339 (53%), Positives = 237/339 (69%), Gaps = 9/339 (2%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           MS+Q+ VA+ GATGAVG  M++ L+ER+FP+ EL LLASERS GK  ++ G+ + VQ + 
Sbjct: 1   MSKQYRVAVAGATGAVGNQMIQCLEERDFPIGELRLLASERSRGKRLKYKGEDIEVQVLG 60

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
           E  +  V IALFSAGG  S +W+P AA+AG VVIDN++ +R D ++PLVVPEVNP A+A 
Sbjct: 61  EGSFQGVDIALFSAGGGTSLEWSPKAAQAGAVVIDNSAAWRMDPEVPLVVPEVNPHAVAG 120

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQ-TAKL 179
           F+ + IIANPNCSTIQM+V LKPI+D  GIER+ V+TYQ+VSG G+  I EL GQ  A  
Sbjct: 121 FKKKGIIANPNCSTIQMVVVLKPIHDLAGIERVVVSTYQAVSGTGQKAIVELQGQLKAIY 180

Query: 180 LNGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRV 239
                 +   +   IA N +P ID F+DNGYTKEEMKMV ET KI  DP+I V+ TCVRV
Sbjct: 181 CQDAQPQAKVYPHVIAQNVLPHIDIFLDNGYTKEEMKMVHETVKIMEDPTIKVSATCVRV 240

Query: 240 PVFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPT-----QVRDAGGKDHVL 294
           PV YGH+EA ++ T   I A+Q  + L +  G+++    D P         DA G+D  L
Sbjct: 241 PVIYGHSEACNITTARKISAQQAREALAKAPGVKV---VDDPANKLYPMPLDAAGQDLTL 297

Query: 295 VGRVRNDISHHSGINLWVVADNVRKGAATNAVQIAELLV 333
           VGR+R D+S   G++LW+VADN+RKGAA NAVQIAELL+
Sbjct: 298 VGRIREDVSQEKGLDLWLVADNIRKGAAANAVQIAELLI 336


Lambda     K      H
   0.319    0.135    0.395 

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: 319
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: 337
Length of database: 341
Length adjustment: 28
Effective length of query: 309
Effective length of database: 313
Effective search space:    96717
Effective search space used:    96717
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_013257581.1 DEBA_RS03780 (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.1339426.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-149  481.1   0.1   9.8e-149  481.0   0.1    1.0  1  NCBI__GCF_000143965.1:WP_013257581.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013257581.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.0   0.1  9.8e-149  9.8e-149       1     338 [.       6     337 ..       6     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 481.0 bits;  conditional E-value: 9.8e-149
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           +va+ GatGavG+++++ Leer+fpi +l+llasers+Gk++k+kg+++ev+ + + sf+g+dialfsaGg +
  NCBI__GCF_000143965.1:WP_013257581.1   6 RVAVAGATGAVGNQMIQCLEERDFPIGELRLLASERSRGKRLKYKGEDIEVQVLGEGSFQGVDIALFSAGGGT 78 
                                           69*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s e+ pkaa+ag++viDn++a+r+d++vPLvvpevn + ++ +kkkgiianPnCstiq+vvvLkp++d a+++
  NCBI__GCF_000143965.1:WP_013257581.1  79 SLEWSPKAAQAGAVVIDNSAAWRMDPEVPLVVPEVNPHAVAGFKKKGIIANPNCSTIQMVVVLKPIHDLAGIE 151
                                           ************************************************************************* PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           rvvvstYqavsG+G+k++ eL+ q+ka++  ++ +p     +ak +++ ia n++p+id + ++Gytkee+k+
  NCBI__GCF_000143965.1:WP_013257581.1 152 RVVVSTYQAVSGTGQKAIVELQGQLKAIYC-QDAQP-----QAKVYPHVIAQNVLPHIDIFLDNGYTKEEMKM 218
                                           ***************************985.55555.....9******************************* PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           ++et ki++++ +kvsatcvrvPv++ghse+ +i +++++s+++++e L +apgv+v+ddp ++lyp+Pl+a+
  NCBI__GCF_000143965.1:WP_013257581.1 219 VHETVKIMEDPTIKVSATCVRVPVIYGHSEACNITTARKISAQQAREALAKAPGVKVVDDPANKLYPMPLDAA 291
                                           ************************************************************************* PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                           g+d ++vgrir+D+s+ekgl+l++vaDn+rkGaa navqiaelli+
  NCBI__GCF_000143965.1:WP_013257581.1 292 GQDLTLVGRIREDVSQEKGLDLWLVADNIRKGAAANAVQIAELLIA 337
                                           *******************************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.61
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

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:

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:

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:

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