Alignments for a candidate for hom_kinase in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Pseudomonas putida KT2440

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate PP_0121 PP_0121 homoserine kinase

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__Putida:PP_0121
          Length = 316

 Score =  457 bits (1175), Expect = e-133
 Identities = 223/316 (70%), Positives = 257/316 (81%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           MSVFTP+ R  LE FLAPY+LGRL DF+GIA G+ENSNFFVSLE GEFVLTL+ERGP +D
Sbjct: 1   MSVFTPVTRPELETFLAPYELGRLLDFQGIAAGTENSNFFVSLEQGEFVLTLIERGPSED 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           +PFFIELLD LH   +PVPYA+R RDG  LR L GKPALLQPRL+G+H + PN  HC +V
Sbjct: 61  MPFFIELLDTLHGADMPVPYAIRDRDGNGLRELCGKPALLQPRLSGKHIKAPNNQHCAQV 120

Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180
           G+LL H+H ATR  I+ER +DRGL WML  GA L PRL  +  ALL PAL EI+A  A+ 
Sbjct: 121 GELLAHIHLATREHIIERRTDRGLDWMLASGAELLPRLTAEQAALLQPALDEISAHKAQI 180

Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240
            ALPRANLHADLFRDNV+F+G HL G+IDFYNACSG MLYD+AIT+NDWC +  G++D  
Sbjct: 181 LALPRANLHADLFRDNVMFEGTHLTGVIDFYNACSGPMLYDIAITVNDWCLDEQGAVDVP 240

Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFEI 300
           RA+ALLAAYA  RPFTA EAE WP MLRV CVRFWLSRLIAAE+FAG DV+IHDP+EFE+
Sbjct: 241 RAQALLAAYAALRPFTAAEAELWPEMLRVGCVRFWLSRLIAAESFAGMDVMIHDPSEFEV 300

Query: 301 RLAQRQNVEIHLPFAL 316
           RLAQRQ V +HLPFAL
Sbjct: 301 RLAQRQQVALHLPFAL 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: 382
Number of extensions: 7
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 PP_0121 PP_0121 (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.18909.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-93  297.0   0.0    9.5e-93  296.8   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0121  PP_0121 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0121  PP_0121 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.8   0.0   9.5e-93   9.5e-93       1     306 [.       1     303 [.       1     304 [. 0.96

  Alignments for each domain:
  == domain 1  score: 296.8 bits;  conditional E-value: 9.5e-93
                           TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellthLaer 75 
                                         m+v+t v+  ele+fL  y+lG+ll+++Gia G ensn+++  ++g +vLtl e+   +e++Pff+ell+ L   
  lcl|FitnessBrowser__Putida:PP_0121   1 MSVFTPVTRPELETFLAPYELGRLLDFQGIAAGTENSNFFVSLEQGEFVLTLIERGP-SEDMPFFIELLDTLHGA 74 
                                         9*****************************************************999.9**************** PP

                           TIGR00938  76 glpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerkndlrleaWsi 150
                                         ++pv+ +++ rdG+ l eL GkPa l   L+G+ ++ P  ++c++vge la++hla+ ++  er+   r  +W  
  lcl|FitnessBrowser__Putida:PP_0121  75 DMPVPYAIRDRDGNGLRELCGKPALLQPRLSGKHIKAPNNQHCAQVGELLAHIHLATREHIIERRT-DRGLDWML 148
                                         *********************************************************887777777.48889*99 PP

                           TIGR00938 151 laakkfkvleqleeelaalldkeldalkkflpr..dLPrgvihadlfkdnvlldgdklkgvidfyfaCedallyd 223
                                         +  ++  +l+ l +e+aall+  ld ++   ++   LPr+ +hadlf+dnv+++g +l+gvidfy aC++ +lyd
  lcl|FitnessBrowser__Putida:PP_0121 149 ASGAE--LLPRLTAEQAALLQPALDEISAHKAQilALPRANLHADLFRDNVMFEGTHLTGVIDFYNACSGPMLYD 221
                                         88888..******************999887763379************************************** PP

                           TIGR00938 224 laiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdP 298
                                         +ai+vndWc+++++ +d+ +a+all +y a rp+++ e + +p +lr++++rf+lsrl     + ag  v++ dP
  lcl|FitnessBrowser__Putida:PP_0121 222 IAITVNDWCLDEQGAVDVPRAQALLAAYAALRPFTAAEAELWPEMLRVGCVRFWLSRLIAAE-SFAGMDVMIHDP 295
                                         **********************************************************9765.57899999**** PP

                           TIGR00938 299 aeferkLk 306
                                          efe +L+
  lcl|FitnessBrowser__Putida:PP_0121 296 SEFEVRLA 303
                                         ****9986 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.46
//
[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