Alignments for a candidate for thrB in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Pseudomonas benzenivorans DSM 8628

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_090445975.1 BLS63_RS14830 homoserine kinase

Query= SwissProt::P29364
         (316 letters)



>NCBI__GCF_900100495.1:WP_090445975.1
          Length = 316

 Score =  468 bits (1204), Expect = e-137
 Identities = 240/316 (75%), Positives = 255/316 (80%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           MSVFTPLER  LEAFLAPY LGRLRDF+GIA GSENSNFFVSLE GEFVLTL+ERGP  D
Sbjct: 1   MSVFTPLERHELEAFLAPYGLGRLRDFQGIAAGSENSNFFVSLEQGEFVLTLIERGPSDD 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           LPFFIELLDVLH  GLPVPYALRT  GEALR L  KPALLQPRL G+H   PN HHC EV
Sbjct: 61  LPFFIELLDVLHAAGLPVPYALRTESGEALRSLAEKPALLQPRLPGKHVAWPNPHHCAEV 120

Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180
           G LL  LH ATR R LER SDRGL WMLE+G +LA +L +    LL  ALAEI AL    
Sbjct: 121 GGLLARLHLATRERPLERKSDRGLDWMLEEGPSLALKLADAQLPLLRAALAEIHALKPRI 180

Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240
            ALPRANLHADLFRDNVLFDG HLAG+IDFYNACSG MLYDLAI LNDWCS  DG LDP 
Sbjct: 181 LALPRANLHADLFRDNVLFDGNHLAGVIDFYNACSGPMLYDLAIALNDWCSEADGRLDPH 240

Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFEI 300
           RA+ALL AYA  RPF+A EAE WP+MLR+ACVRFWLSRLIAA++FAGQ VLIHDPAEF  
Sbjct: 241 RAQALLGAYAALRPFSAAEAELWPAMLRIACVRFWLSRLIAADSFAGQQVLIHDPAEFRR 300

Query: 301 RLAQRQNVEIHLPFAL 316
           RL QRQ VE+ LPFAL
Sbjct: 301 RLEQRQQVEVALPFAL 316


Lambda     K      H
   0.324    0.140    0.434 

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: 408
Number of extensions: 11
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: 316
Length of database: 316
Length adjustment: 27
Effective length of query: 289
Effective length of database: 289
Effective search space:    83521
Effective search space used:    83521
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_090445975.1 BLS63_RS14830 (homoserine kinase)
to HMM TIGR00938 (thrB: homoserine kinase (EC 2.7.1.39))

# 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/TIGR00938.hmm
# target sequence database:        /tmp/gapView.25408.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00938  [M=307]
Accession:   TIGR00938
Description: thrB_alt: homoserine kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.3e-91  290.4   0.0    9.5e-91  290.3   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090445975.1  BLS63_RS14830 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090445975.1  BLS63_RS14830 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.3   0.0   9.5e-91   9.5e-91       1     306 [.       1     303 [.       1     304 [. 0.97

  Alignments for each domain:
  == domain 1  score: 290.3 bits;  conditional E-value: 9.5e-91
                                 TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 
                                               m+v+t +  +eleafL  y lG+l +++Gia G ensn+++  ++g +vLtl e+   +++LPff+ell
  lcl|NCBI__GCF_900100495.1:WP_090445975.1   1 MSVFTPLERHELEAFLAPYGLGRLRDFQGIAAGSENSNFFVSLEQGEFVLTLIERGP-SDDLPFFIELL 68 
                                               9*****************************************************999.9********** PP

                                 TIGR00938  70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138
                                               + L + glpv+ ++++++G+al +La kPa l   L+G+ va P +++c+evg  la+lhla+ + + e
  lcl|NCBI__GCF_900100495.1:WP_090445975.1  69 DVLHAAGLPVPYALRTESGEALRSLAEKPALLQPRLPGKHVAWPNPHHCAEVGGLLARLHLATRERPLE 137
                                               ********************************************************************* PP

                                 TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflpr..dLPrgvihadlfkdnvlldgdk 205
                                               rk   r  +W  +      ++ +l + +  ll++ l+ ++ + pr   LPr+ +hadlf+dnvl+dg++
  lcl|NCBI__GCF_900100495.1:WP_090445975.1 138 RKS-DRGLDWMLEEGPS--LALKLADAQLPLLRAALAEIHALKPRilALPRANLHADLFRDNVLFDGNH 203
                                               **9.67889*9998888..9999999999***************95568******************** PP

                                 TIGR00938 206 lkgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaal 274
                                               l+gvidfy aC++ +lydlaia+ndWc ead++ld ++a+all++y a rp+s+ e + +p +lr a++
  lcl|NCBI__GCF_900100495.1:WP_090445975.1 204 LAGVIDFYNACSGPMLYDLAIALNDWCSEADGRLDPHRAQALLGAYAALRPFSAAEAELWPAMLRIACV 272
                                               ********************************************************************* PP

                                 TIGR00938 275 rfllsrlldlvftqagelvvakdPaeferkLk 306
                                               rf+lsrl     + ag+ v + dPaef+r+L+
  lcl|NCBI__GCF_900100495.1:WP_090445975.1 273 RFWLSRLIAA-DSFAGQQVLIHDPAEFRRRLE 303
                                               *******975.567999*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (316 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: 10.11
//
[ok]

This GapMind analysis is from Apr 10 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