Alignments for a candidate for dapA in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapA in Sphingomonas koreensis DSMZ 15582

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Ga0059261_0213 Ga0059261_0213 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::Q8UGL3
         (294 letters)



>FitnessBrowser__Korea:Ga0059261_0213
          Length = 293

 Score =  293 bits (749), Expect = 4e-84
 Identities = 159/295 (53%), Positives = 205/295 (69%), Gaps = 4/295 (1%)

Query: 1   MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60
           MF GSIPALITPF  NG   E  F   VEWQIAEGS+ LVPVGTTGE+ TL+ DEH  VV
Sbjct: 1   MFTGSIPALITPFR-NGDFAEDVFRDFVEWQIAEGSSALVPVGTTGEAATLAKDEHFEVV 59

Query: 61  ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120
            +C++    R+PVIAG GSN+T  AI     A++AGADA+L+V PYYN+P+Q+G+F HF 
Sbjct: 60  RVCVDQVRGRIPVIAGTGSNDTRVAIGNVKAAKDAGADAVLMVPPYYNRPSQEGIFRHFE 119

Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHK-NIIGVKDATGKLDRVSEQRISCG 179
           AVA   +LPIV+YN+P R+V D+ PET+  +V+A     + +KDATG L RVS  R +  
Sbjct: 120 AVAAECELPIVLYNVPGRTVTDIQPETVIRIVQAFPGKFVAIKDATGDLARVSMHRAALR 179

Query: 180 KDFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMP 239
             F QLSG D TAL FNA GGVGCISVTANVAP+LC++FQAA   G+ A AL   DRL  
Sbjct: 180 AGFAQLSGNDDTALAFNAMGGVGCISVTANVAPKLCAQFQAAWAEGNTALALALHDRLFA 239

Query: 240 LHRAIFMEPGVCGTKYALSKTRGG-NRRVRSPLMSTLEPATEAAIDAALKHAGLM 293
           LH A+F +      KYA++K R   +  +R P++   E A++AA+DAA++ AG++
Sbjct: 240 LHNAMFTDASPGPVKYAVNKLRPEISAELRLPMVEPGE-ASKAAVDAAMQAAGII 293


Lambda     K      H
   0.317    0.133    0.384 

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: 288
Number of extensions: 10
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: 294
Length of database: 293
Length adjustment: 26
Effective length of query: 268
Effective length of database: 267
Effective search space:    71556
Effective search space used:    71556
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: 48 (23.1 bits)

Align candidate Ga0059261_0213 Ga0059261_0213 (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.21119.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.8e-95  303.6   0.0    5.4e-95  303.5   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0213  Ga0059261_0213 4-hydroxy-tetrahy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0213  Ga0059261_0213 4-hydroxy-tetrahydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.5   0.0   5.4e-95   5.4e-95       1     284 [.       4     288 ..       4     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.5 bits;  conditional E-value: 5.4e-95
                                 TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvp 69 
                                               g+++AliTPf++      +++   +e qi++g++a+v+vGtTGE+atL+++E+ +v++v v+ v++r+p
  lcl|FitnessBrowser__Korea:Ga0059261_0213   4 GSIPALITPFRNGD-FAEDVFRDFVEWQIAEGSSALVPVGTTGEAATLAKDEHFEVVRVCVDQVRGRIP 71 
                                               589*******9877.99**************************************************** PP

                                 TIGR00674  70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138
                                               viaGtgsn t+ ai  +k a+++g+d+vl+v PyYn+P+qeG+++hf+a+a+e+elPi+lYnvP+Rt++
  lcl|FitnessBrowser__Korea:Ga0059261_0213  72 VIAGTGSNDTRVAIGNVKAAKDAGADAVLMVPPYYNRPSQEGIFRHFEAVAAECELPIVLYNVPGRTVT 140
                                               ********************************************************************* PP

                                 TIGR00674 139 slepetvkrLaeeve..ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasn 205
                                               +++petv+r+++  +  +vaiK+a+gdl+rvs  +a   + f+ lsG+D ++l++ a+G+ G iSV++n
  lcl|FitnessBrowser__Korea:Ga0059261_0213 141 DIQPETVIRIVQAFPgkFVAIKDATGDLARVSMHRAALRAGFAQLSGNDDTALAFNAMGGVGCISVTAN 209
                                               ***********998778**************************************************** PP

                                 TIGR00674 206 vapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelsee 274
                                               vapk+++++ +a++eg+t+ a+ +h +l+ l++a+f+++ P pvK+a++ l    ++elRlP++e  e 
  lcl|FitnessBrowser__Korea:Ga0059261_0213 210 VAPKLCAQFQAAWAEGNTALALALHDRLFALHNAMFTDASPGPVKYAVNKLRPEISAELRLPMVEPGEA 278
                                               ***************************************************999999**********99 PP

                                 TIGR00674 275 kkeklkevlk 284
                                               +k  ++++++
  lcl|FitnessBrowser__Korea:Ga0059261_0213 279 SKAAVDAAMQ 288
                                               9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (293 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: 00:00:00.01
# Mc/sec: 6.81
//
[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