Alignments for a candidate for dapD in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Burkholderia phytofirmans PsJN

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate BPHYT_RS12190 BPHYT_RS12190 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= CharProtDB::CH_024869
         (274 letters)



>FitnessBrowser__BFirm:BPHYT_RS12190
          Length = 275

 Score =  410 bits (1054), Expect = e-119
 Identities = 207/271 (76%), Positives = 229/271 (84%), Gaps = 1/271 (0%)

Query: 2   QQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKK 61
           QQLQ II+TA+E RAE++P  A    REAV   I  LD G LRVAEK DG WV +QWLKK
Sbjct: 3   QQLQQIIDTAWENRAELSPKAAPADVREAVAHAIEQLDKGLLRVAEKKDGDWVVNQWLKK 62

Query: 62  AVLLSFRINDNQVIE-GAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120
           AVLLSFR+ DN  +  G  S+++DKVP KFA+Y    F   GFRVVPPA  R+G+FIA+N
Sbjct: 63  AVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKN 122

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
            VLMPSY NIGAYVDEG+MVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANP IIED
Sbjct: 123 VVLMPSYTNIGAYVDEGSMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIED 182

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240
           NCFIGARSEVVEGVIVEE SVISMGVY+GQST+IYDRETGE+ YGR+PAGSVVV+GNLPS
Sbjct: 183 NCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPS 242

Query: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLR 271
           KDG +SLYCAVIVKKVDAKTR KVG+NELLR
Sbjct: 243 KDGTHSLYCAVIVKKVDAKTRAKVGLNELLR 273


Lambda     K      H
   0.318    0.136    0.391 

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: 5
Number of successful extensions: 2
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: 274
Length of database: 275
Length adjustment: 25
Effective length of query: 249
Effective length of database: 250
Effective search space:    62250
Effective search space used:    62250
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: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate BPHYT_RS12190 BPHYT_RS12190 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

# 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/TIGR00965.hmm
# target sequence database:        /tmp/gapView.25873.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00965  [M=271]
Accession:   TIGR00965
Description: dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.6e-149  482.7   0.2   1.8e-149  482.6   0.2    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12190  BPHYT_RS12190 2,3,4,5-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12190  BPHYT_RS12190 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransfe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.6   0.2  1.8e-149  1.8e-149       1     270 [.       4     274 ..       4     275 .] 0.98

  Alignments for each domain:
  == domain 1  score: 482.6 bits;  conditional E-value: 1.8e-149
                                TIGR00965   1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdn 70 
                                              +lq+ii+ta+e+rae+ p ++ ++v+eav ++i +ld+g lrvaek dg+w+vn+w+kkavllsfr++dn
  lcl|FitnessBrowser__BFirm:BPHYT_RS12190   4 QLQQIIDTAWENRAELSPKAAPADVREAVAHAIEQLDKGLLRVAEKKDGDWVVNQWLKKAVLLSFRLEDN 73 
                                              699******************************************************************9 PP

                                TIGR00965  71 qvl.ndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvd 139
                                                +  +++++++dkv++kfa+y  + f   g+r+vp+a++rrg+fiaknvvlmpsy nigayvdeg+mvd
  lcl|FitnessBrowser__BFirm:BPHYT_RS12190  74 APMpAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGSMVD 143
                                              8552789*************************************************************** PP

                                TIGR00965 140 twatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqs 209
                                              twatvgscaqigknvhlsggvgiggvleplqa+pviiedncfigarse+vegvivee svismgv++gqs
  lcl|FitnessBrowser__BFirm:BPHYT_RS12190 144 TWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQS 213
                                              ********************************************************************** PP

                                TIGR00965 210 tkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellrt 270
                                              tki+dretge+ ygr+pagsvvv+g+lpskdg +slycavivkkvdaktr+kv++nellr+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12190 214 TKIYDRETGEVTYGRIPAGSVVVAGNLPSKDGTHSLYCAVIVKKVDAKTRAKVGLNELLRG 274
                                              ***********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (275 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.24
//
[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