Alignments for a candidate for dapA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapA in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate H281DRAFT_01480 H281DRAFT_01480 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::Q9X1K9
         (294 letters)



>FitnessBrowser__Burk376:H281DRAFT_01480
          Length = 299

 Score =  168 bits (426), Expect = 1e-46
 Identities = 97/297 (32%), Positives = 160/297 (53%), Gaps = 19/297 (6%)

Query: 1   MFRGVGTAIVTPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVS 60
           +F G+   ++TPF +  +D  +   LVR   + G+  ++ LGTTGE   ++  E++ +++
Sbjct: 3   IFSGIWVPLITPFADAAVDHAAVRALVRRYADAGIAGIVALGTTGEPAALSAAEQDAVLA 62

Query: 61  RTLEIV-----------DGK--IPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYN 107
             L+             D K  +PV+VG   N+T+   + + Q   L   GVL+  PYY 
Sbjct: 63  TILDAAQAGGARADASTDSKPALPVVVGVSGNNTQSMRERIAQLNSLPVAGVLMAAPYYI 122

Query: 108 KPTQEGLYQHYKYISERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDI 167
           +P+Q G+  H+  +++ ++  +V+Y++P RTGV +  +T   +AA  +    I+      
Sbjct: 123 RPSQAGIVGHFMALADASEKPVVLYDIPYRTGVRLELDTLMTLAAHPR----IQAVKDCA 178

Query: 168 DQIDRTVSLTKQARSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSG 227
             +D T++L +  R    V +G D + F  +C GG G I+  ++V P++ V L     +G
Sbjct: 179 GSLDTTLALIRDGR--LQVLAGEDMQMFNTMCLGGSGAIAASAHVQPERFVALYRALAAG 236

Query: 228 NLEKSREVHRKLRPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELL 284
            LE++R +   L PL+  LF E NP PVKA L   G I +ELRLP+  ASEK VE L
Sbjct: 237 ALEEARRIFHALAPLIDTLFAEPNPAPVKAMLASQGLIRDELRLPMTRASEKLVERL 293


Lambda     K      H
   0.316    0.135    0.378 

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: 181
Number of extensions: 4
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: 294
Length of database: 299
Length adjustment: 26
Effective length of query: 268
Effective length of database: 273
Effective search space:    73164
Effective search space used:    73164
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 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate H281DRAFT_01480 H281DRAFT_01480 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.7597.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    8.4e-77  243.8   0.0    9.4e-77  243.6   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01480  H281DRAFT_01480 4-hydroxy-tetrah


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01480  H281DRAFT_01480 4-hydroxy-tetrahydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.6   0.0   9.4e-77   9.4e-77       4     281 ..       9     295 ..       6     299 .] 0.97

  Alignments for each domain:
  == domain 1  score: 243.6 bits;  conditional E-value: 9.4e-77
                                    TIGR00674   4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn... 66 
                                                  + liTPf +   vd aa+  l+++  ++g+ +iv++GtTGE a+Ls  E+ +v+ + ++ ++    
  lcl|FitnessBrowser__Burk376:H281DRAFT_01480   9 VPLITPFADAA-VDHAAVRALVRRYADAGIAGIVALGTTGEPAALSAAEQDAVLATILDAAQAgga 73 
                                                  679****9988.***********************************************999899* PP

                                    TIGR00674  67 ..........rvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaee 122
                                                             +pv++G+++n+t+   e +++++ l+v+gvl+ +PyY +P+q G++ hf a+a++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01480  74 radastdskpALPVVVGVSGNNTQSMRERIAQLNSLPVAGVLMAAPYYIRPSQAGIVGHFMALADA 139
                                                  ********999******************************************************* PP

                                    TIGR00674 123 velPiilYnvPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDalt 188
                                                  +e+P++lY++P Rtgv le +t++ La++++i a+K+++g+l+    +++  +  ++vl+G+D  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_01480 140 SEKPVVLYDIPYRTGVRLELDTLMTLAAHPRIQAVKDCAGSLDTTLALIR--DGRLQVLAGEDMQM 203
                                                  *******************************************9999998..557*********** PP

                                    TIGR00674 189 leilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtala 254
                                                   + ++lG++G i   ++v p+++  +++a ++g+ eear i + l +l+++lf e+NP pvK++la
  lcl|FitnessBrowser__Burk376:H281DRAFT_01480 204 FNTMCLGGSGAIAASAHVQPERFVALYRALAAGALEEARRIFHALAPLIDTLFAEPNPAPVKAMLA 269
                                                  ****************************************************************** PP

                                    TIGR00674 255 llgliekdelRlPLtelseekkeklke 281
                                                   +gli   elRlP+t +se+  e+l++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01480 270 SQGLIRD-ELRLPMTRASEKLVERLAA 295
                                                  ******9.**********998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.92
//
[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