Alignments for a candidate for dapA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapA in Herbaspirillum seropedicae SmR1

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate HSERO_RS16395 HSERO_RS16395 dihydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__HerbieS:HSERO_RS16395
          Length = 292

 Score =  352 bits (902), Expect = e-102
 Identities = 172/291 (59%), Positives = 219/291 (75%)

Query: 1   MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60
           MI GS+VA+VTP    G LD+D L KL+D+H+ EGT++IV VGTTGES T+ +EEH ++I
Sbjct: 1   MIKGSIVAIVTPMHQDGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELI 60

Query: 61  RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120
           +  V+    RIP+IAGTG NST EA+ LTE AK  GADA L V PYYN+PTQEGMY HF+
Sbjct: 61  KVAVEHTAKRIPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFK 120

Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180
            IAE+V +P ILYNVPGRT  DM  ET+ RL++V  I+G+K+ATG++ R  ++I    K 
Sbjct: 121 KIAESVDLPVILYNVPGRTVADMSNETILRLAQVKGIVGVKDATGNIARGTDLIRLAPKS 180

Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240
           F VYSGDDATA+ LML GG GNISVTANVAPR M +LC AAM G+ A A  +N++L+PLH
Sbjct: 181 FAVYSGDDATAIALMLYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPLH 240

Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
             LF+E NP+P+KWA+ EMGLIP G+RLPL  L    H+ +R A+R++GVL
Sbjct: 241 NKLFVEPNPVPLKWAMQEMGLIPSGMRLPLAPLGAAYHDTVRAALRESGVL 291


Lambda     K      H
   0.319    0.134    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: 292
Number of extensions: 13
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: 292
Length of database: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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 HSERO_RS16395 HSERO_RS16395 (dihydrodipicolinate 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.11346.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.1e-115  369.9   0.0   3.4e-115  369.8   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS16395  HSERO_RS16395 dihydrodipicolinat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS16395  HSERO_RS16395 dihydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.8   0.0  3.4e-115  3.4e-115       1     284 [.       4     286 ..       4     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.8 bits;  conditional E-value: 3.4e-115
                                  TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrv 68 
                                                g+++A++TP+++dgs+d++ l kli+ +i++g+d+iv+vGtTGEs+t s+eE+ ++i+vave +++r+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16395   4 GSIVAIVTPMHQDGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELIKVAVEHTAKRI 71 
                                                589***************************************************************** PP

                                  TIGR00674  69 pviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRt 136
                                                p+iaGtg+n+t+eaielt++a+k+g+d+ l+v+PyYn+PtqeG+y hfk+iae+v+lP+ilYnvP+Rt
  lcl|FitnessBrowser__HerbieS:HSERO_RS16395  72 PIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFKKIAESVDLPVILYNVPGRT 139
                                                ******************************************************************** PP

                                  TIGR00674 137 gvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVas 204
                                                +++++ et++rLa+ + iv++K+a+g+++r + +++ a+++f+v+sGdDa++ ++++ G++G iSV++
  lcl|FitnessBrowser__HerbieS:HSERO_RS16395 140 VADMSNETILRLAQVKGIVGVKDATGNIARGTDLIRLAPKSFAVYSGDDATAIALMLYGGAGNISVTA 207
                                                ***************9**************************************************** PP

                                  TIGR00674 205 nvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtels 272
                                                nvap++++e++ aa+ g++++a e+++kll+l+++lf+e+NP+p+K+a++ +gli +  +RlPL++l 
  lcl|FitnessBrowser__HerbieS:HSERO_RS16395 208 NVAPRDMHELCVAAMSGNIARAVELNNKLLPLHNKLFVEPNPVPLKWAMQEMGLIPS-GMRLPLAPLG 274
                                                *********************************************************.*********9 PP

                                  TIGR00674 273 eekkeklkevlk 284
                                                   +++++++l+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16395 275 AAYHDTVRAALR 286
                                                999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (292 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: 7.42
//
[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