Alignments for a candidate for dapD in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Acidovorax sp. GW101-3H11

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate Ac3H11_2296 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117)

Query= CharProtDB::CH_024869
         (274 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2296
          Length = 277

 Score =  360 bits (923), Expect = e-104
 Identities = 181/274 (66%), Positives = 216/274 (78%), Gaps = 4/274 (1%)

Query: 2   QQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKID-GQWVTHQWLK 60
           QQLQ II+ A++ RA ++PA A    ++AV  VIA L++G LRVA +   GQW  HQW+K
Sbjct: 3   QQLQTIIDNAWDNRASLSPAAAPKEIQDAVEHVIAELNNGTLRVATREGVGQWTVHQWIK 62

Query: 61  KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120
           KAVLLSFR+ DN+V++  +  ++DKV  KFA   E   +  G RVVPPA  R+G+FIA+ 
Sbjct: 63  KAVLLSFRLKDNEVVKAGDLGFYDKVQTKFAHLSEEEMKATGVRVVPPAVARRGSFIAKG 122

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
            +LMPSYVNIGAYV EGTMVDTWATVGSCAQIG NVHLSGGVGIGGVLEPLQA PTIIED
Sbjct: 123 AILMPSYVNIGAYVGEGTMVDTWATVGSCAQIGSNVHLSGGVGIGGVLEPLQAGPTIIED 182

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP- 239
           NCFIGARSEVVEGV+VEE SV+ MGVY+GQST I++R TGEI YGRVP+GSVVVSGNLP 
Sbjct: 183 NCFIGARSEVVEGVVVEENSVLGMGVYLGQSTPIFNRATGEISYGRVPSGSVVVSGNLPK 242

Query: 240 --SKDGKYSLYCAVIVKKVDAKTRGKVGINELLR 271
             +    YS+Y A+IVK+VDA+TR K  IN+LLR
Sbjct: 243 TAANGAPYSMYAAIIVKQVDAQTRSKTSINDLLR 276


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: 263
Number of extensions: 8
Number of successful extensions: 4
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: 277
Length adjustment: 25
Effective length of query: 249
Effective length of database: 252
Effective search space:    62748
Effective search space used:    62748
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 Ac3H11_2296 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))
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.31911.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   5.1e-134  431.9   0.9   5.8e-134  431.7   0.9    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296  2,3,4,5-tetrahydropyridine-2,6-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296  2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.7   0.9  5.8e-134  5.8e-134       1     269 [.       4     276 ..       4     277 .] 0.98

  Alignments for each domain:
  == domain 1  score: 431.7 bits;  conditional E-value: 5.8e-134
                                        TIGR00965   1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkav 61 
                                                      +lq ii++a+++ra + pa++  ++++av+++ia+l++g+lrva +  +gqw v++w+kkav
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296   4 QLQTIIDNAWDNRASLSPAAAPKEIQDAVEHVIAELNNGTLRVATREgVGQWTVHQWIKKAV 65 
                                                      6899******************************************989************* PP

                                        TIGR00965  62 llsfritdnqvlndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmp 123
                                                      llsfr++dn+v++ +   ++dkv tkfa  +e+e+k +g+r+vp+av+rrg+fiak  +lmp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296  66 LLSFRLKDNEVVKAGDLGFYDKVQTKFAHLSEEEMKATGVRVVPPAVARRGSFIAKGAILMP 127
                                                      ************************************************************** PP

                                        TIGR00965 124 syvnigayvdegtmvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigar 185
                                                      syvnigayv egtmvdtwatvgscaqig nvhlsggvgiggvleplqa p+iiedncfigar
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296 128 SYVNIGAYVGEGTMVDTWATVGSCAQIGSNVHLSGGVGIGGVLEPLQAGPTIIEDNCFIGAR 189
                                                      ************************************************************** PP

                                        TIGR00965 186 seivegviveegsvismgvfigqstkivdretgeiiygrvpagsvvvsgslps..kdgk.ks 244
                                                      se+vegv+vee sv+ mgv++gqst i++r tgei ygrvp+gsvvvsg+lp    +g  +s
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296 190 SEVVEGVVVEENSVLGMGVYLGQSTPIFNRATGEISYGRVPSGSVVVSGNLPKtaANGApYS 251
                                                      ****************************************************855444338* PP

                                        TIGR00965 245 lycavivkkvdaktrgkvsinellr 269
                                                      +y a+ivk+vda+tr+k+sin+llr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2296 252 MYAAIIVKQVDAQTRSKTSINDLLR 276
                                                      ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (277 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: 00:00:00.00
# Mc/sec: 9.01
//
[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