Alignments for a candidate for asd in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Bacteroides thetaiotaomicron VPI-5482

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate 353162 BT3636 aspartate-semialdehyde dehydrogenase (NCBI ptt file)

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



>FitnessBrowser__Btheta:353162
          Length = 335

 Score =  327 bits (838), Expect = 3e-94
 Identities = 178/344 (51%), Positives = 233/344 (67%), Gaps = 11/344 (3%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASP-ES 63
           + VA+VG +GAVGQ+ L+ L++RNF MD L L  SKRSAGT  TF+G+++ V+     + 
Sbjct: 1   MKVAIVGVSGAVGQEFLRVLDERNFPMDELVLFGSKRSAGTTYTFRGKQIEVKLLQHNDD 60

Query: 64  FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEAD-LHEHN 122
           F+GV+IA  SAG   S+       K GA++IDN+SAFRMD + PLVVPEVN AD L    
Sbjct: 61  FKGVDIAFTSAGAGTSKEFEKTITKYGAVMIDNSSAFRMDADVPLVVPEVNAADALERPR 120

Query: 123 GIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEE 182
           G+IANPNC+TIQMV AL+ I +   +  V VSTYQA SGAG  A+ ELY Q + +L  E 
Sbjct: 121 GVIANPNCTTIQMVVALKAIEQLSHIKTVHVSTYQAASGAGAAAMDELYEQYRQVLANE- 179

Query: 183 IEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCV 242
                 PV  +K  YQ+AFN IPQID F +NGYT EEMKM NET+KIMH  D++V+ATCV
Sbjct: 180 ------PVTVEKFAYQLAFNLIPQIDVFTENGYTKEEMKMYNETRKIMHS-DVKVSATCV 232

Query: 243 RLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVF 302
           R+P    HSES+++E +R   +VE+ +    +  G+ LQD+P+++ YPMP    GK+ V+
Sbjct: 233 RVPALRAHSESIWVETERP-ISVEEAREAFAKGEGLVLQDNPAEKEYPMPLFLAGKDPVY 291

Query: 303 VGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           VGRIRKDL   NG   W+V D + KGAA N+VQIAE L K+  V
Sbjct: 292 VGRIRKDLTNENGLTFWIVGDQIKKGAALNAVQIAEYLIKVKNV 335


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: 315
Number of extensions: 13
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: 335
Length adjustment: 28
Effective length of query: 318
Effective length of database: 307
Effective search space:    97626
Effective search space used:    97626
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 353162 BT3636 (aspartate-semialdehyde dehydrogenase (NCBI ptt file))
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.12732.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     5e-140  452.3   0.3   5.8e-140  452.1   0.3    1.0  1  lcl|FitnessBrowser__Btheta:353162  BT3636 aspartate-semialdehyde de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353162  BT3636 aspartate-semialdehyde dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.1   0.3  5.8e-140  5.8e-140       1     338 [.       2     331 ..       2     332 .. 0.98

  Alignments for each domain:
  == domain 1  score: 452.1 bits;  conditional E-value: 5.8e-140
                          TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaeke.sfegidialfsaGgsvsk 75 
                                        +vaivG +GavGqe+l+vL+ernfp+d+lvl+ s+rsaG+  +f+gk++ev+ ++++ +f+g+dia+ saG+ +sk
  lcl|FitnessBrowser__Btheta:353162   2 KVAIVGVSGAVGQEFLRVLDERNFPMDELVLFGSKRSAGTTYTFRGKQIEVKLLQHNdDFKGVDIAFTSAGAGTSK 77 
                                        69****************************************************99879***************** PP

                          TIGR01296  76 efapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvs 151
                                        ef   ++k g+++iDn+safr+d dvPLvvpevna++  e++ +g+ianPnC+tiq+vv+Lk++++  ++k v vs
  lcl|FitnessBrowser__Btheta:353162  78 EFEKTITKYGAVMIDNSSAFRMDADVPLVVPEVNAADALERP-RGVIANPNCTTIQMVVALKAIEQLSHIKTVHVS 152
                                        ***************************************998.********************************* PP

                          TIGR01296 152 tYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkil 227
                                        tYqa sGaG+++++eL++q + vl  +  +        +kfa+q+afn+ip+id ++e+Gytkee+k+ +etrki+
  lcl|FitnessBrowser__Btheta:353162 153 TYQAASGAGAAAMDELYEQYRQVLANEPVT-------VEKFAYQLAFNLIPQIDVFTENGYTKEEMKMYNETRKIM 221
                                        *********************999865555.......69************************************* PP

                          TIGR01296 228 giedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrir 303
                                        + +d+kvsatcvrvP +++hses+ +e+e+++svee++e + + +g+v++d+p e++yp+Pl  +gkd v+vgrir
  lcl|FitnessBrowser__Btheta:353162 222 H-SDVKVSATCVRVPALRAHSESIWVETERPISVEEAREAFAKGEGLVLQDNPAEKEYPMPLFLAGKDPVYVGRIR 296
                                        *.************************************************************************** PP

                          TIGR01296 304 kDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                        kDl++e+gl+ ++v+D+++kGaalnavqiae lik
  lcl|FitnessBrowser__Btheta:353162 297 KDLTNENGLTFWIVGDQIKKGAALNAVQIAEYLIK 331
                                        ********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (335 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: 11.42
//
[ok]

This GapMind analysis is from Apr 09 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