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

GapMind for Amino acid biosynthesis

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

Align Meso-diaminopimelate D-dehydrogenase; DAPDH; Meso-DAP dehydrogenase; EC 1.4.1.16 (characterized)
to candidate 351507 BT1979 Meso-diaminopimelate D-dehydrogenase (NCBI ptt file)

Query= SwissProt::Q5L9Q6
         (299 letters)



>FitnessBrowser__Btheta:351507
          Length = 299

 Score =  562 bits (1449), Expect = e-165
 Identities = 285/299 (95%), Positives = 289/299 (96%)

Query: 1   MKKVRAAIVGYGNIGRYVLEALQAAPDFEIAGVVRRAGAENKPAELNDYAVVKDIKELQG 60
           MKKVRAAIVGYGNIG YVLEALQAAPDFEIAGVVRRAGAENKP EL +YAVVKDIKEL+G
Sbjct: 1   MKKVRAAIVGYGNIGHYVLEALQAAPDFEIAGVVRRAGAENKPEELANYAVVKDIKELEG 60

Query: 61  VDVAILCTPTRSVEKYAKEILAMGINTVDSFDIHTGIVDLRRELGACAKEHGAVSIISAG 120
           V+VAILCTPTRSVEKYAKE LAMGINTVDSFDIHTGIVDLRR L A AKEH AVSIISAG
Sbjct: 61  VEVAILCTPTRSVEKYAKEYLAMGINTVDSFDIHTGIVDLRRTLDATAKEHKAVSIISAG 120

Query: 121 WDPGSDSIVRTMLEAIAPKGITYTNFGPGMSMGHTVAVKAIDGVKAALSMTIPTGTGIHR 180
           WDPGSDSIVRTMLEAIAPKGITYTNFGPGMSMGHTVAVKAIDGVKAALSMTIPTGTGIHR
Sbjct: 121 WDPGSDSIVRTMLEAIAPKGITYTNFGPGMSMGHTVAVKAIDGVKAALSMTIPTGTGIHR 180

Query: 181 RMVYIELKDGYKFEEVAAAIKSDAYFVNDETHVKQVPSVDALLDMGHGVNLTRKGVSGKT 240
           RMVYIELKDGYKFEEVAAAIK+D YFVNDETHVK VPSVDALLDMGHGVNLTRKGVSGKT
Sbjct: 181 RMVYIELKDGYKFEEVAAAIKADPYFVNDETHVKLVPSVDALLDMGHGVNLTRKGVSGKT 240

Query: 241 QNQLFEFNMRINNPALTAQVLVCVARASMKQQPGCYTMVEVPVIDLLPGDREEWIGHLV 299
           QNQLFEFNMRINNPALTAQVLVCVARASMKQQPGCYTMVEVPVIDLLPGDREEWIGHLV
Sbjct: 241 QNQLFEFNMRINNPALTAQVLVCVARASMKQQPGCYTMVEVPVIDLLPGDREEWIGHLV 299


Lambda     K      H
   0.319    0.136    0.393 

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: 438
Number of extensions: 4
Number of successful extensions: 1
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: 299
Length of database: 299
Length adjustment: 27
Effective length of query: 272
Effective length of database: 272
Effective search space:    73984
Effective search space used:    73984
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: 48 (23.1 bits)

Align candidate 351507 BT1979 (Meso-diaminopimelate D-dehydrogenase (NCBI ptt file))
to HMM TIGR01921 (diaminopimelate dehydrogenase (EC 1.4.1.16))

# 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/TIGR01921.hmm
# target sequence database:        /tmp/gapView.759.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01921  [M=324]
Accession:   TIGR01921
Description: DAP-DH: diaminopimelate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-150  486.6   0.5   2.3e-150  486.2   0.5    1.1  1  lcl|FitnessBrowser__Btheta:351507  BT1979 Meso-diaminopimelate D-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351507  BT1979 Meso-diaminopimelate D-dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.2   0.5  2.3e-150  2.3e-150       1     324 []       1     299 []       1     299 [] 1.00

  Alignments for each domain:
  == domain 1  score: 486.2 bits;  conditional E-value: 2.3e-150
                          TIGR01921   1 mskiraaivGyGnlGksvekaisqaPdlelvgvfsrrdaetldeelavyavaeaekeledvdvlilctgsatdlke 76 
                                        m+k+raaivGyGn+G++v++a+++aPd+e++gv++r++ae+++eela+yav++++kele+v+v+ilct++++++k+
  lcl|FitnessBrowser__Btheta:351507   1 MKKVRAAIVGYGNIGHYVLEALQAAPDFEIAGVVRRAGAENKPEELANYAVVKDIKELEGVEVAILCTPTRSVEKY 76 
                                        9*************************************************************************** PP

                          TIGR01921  77 qkeylaafintvdsfdihadipelrrvldaaakeagkvsvisaGWdPGlfsinrvlgeavlpkgitytffGpGlsq 152
                                        +keyla++intvdsfdih++i++lrr+lda+ake+++vs+isaGWdPG++si+r+++ea++pkgityt+fGpG+s+
  lcl|FitnessBrowser__Btheta:351507  77 AKEYLAMGINTVDSFDIHTGIVDLRRTLDATAKEHKAVSIISAGWDPGSDSIVRTMLEAIAPKGITYTNFGPGMSM 152
                                        **************************************************************************** PP

                          TIGR01921 153 GhsdavrridGvkkavqytlPikdalekvrrgeaeeltgkekhkrevyvvlkegaeaekveaeiktmadyfveyet 228
                                        Gh++av++idGvk+a+++t+P                tg+++h+r+vy++lk+g+++e+v+a+ik++ +yfv++et
  lcl|FitnessBrowser__Btheta:351507 153 GHTVAVKAIDGVKAALSMTIP----------------TGTGIHRRMVYIELKDGYKFEEVAAAIKAD-PYFVNDET 211
                                        *********************................******************************.9******* PP

                          TIGR01921 229 evnlideaefdaehtgmphGgfvirkGesGktqkqllefslklernPdltasvlvavaraayrlkeagqkGaytvl 304
                                        +v+l++++++ ++++   hG++++rkG+sGktq+ql+ef+++++ nP+lta+vlv+vara++++    q+G+yt++
  lcl|FitnessBrowser__Btheta:351507 212 HVKLVPSVDALLDMG---HGVNLTRKGVSGKTQNQLFEFNMRIN-NPALTAQVLVCVARASMKQ----QPGCYTMV 279
                                        ***************...**************************.*******************....******** PP

                          TIGR01921 305 evpvillsPkdaeelikelv 324
                                        evpvi+l+P+d+ee+i++lv
  lcl|FitnessBrowser__Btheta:351507 280 EVPVIDLLPGDREEWIGHLV 299
                                        ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (324 nodes)
Target sequences:                          1  (299 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: 00:00:00.01
# Mc/sec: 9.07
//
[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