Alignments for a candidate for hom_kinase in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Pseudomonas stutzeri RCH2

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate GFF4148 Psest_4221 homoserine kinase, Neisseria type

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__psRCH2:GFF4148
          Length = 317

 Score =  414 bits (1064), Expect = e-120
 Identities = 216/316 (68%), Positives = 240/316 (75%), Gaps = 1/316 (0%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           MSVFTPL+R  LEAFLAPY LGRLRDF+GI  GSENSNFFVSLE GE+VLTL+ERGP QD
Sbjct: 1   MSVFTPLQRDELEAFLAPYRLGRLRDFQGIVAGSENSNFFVSLEQGEYVLTLIERGPRQD 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           LPFFIELLDVLH  GLPVPYALR+ DG+ALR L  KPALLQPRL G+H  +PN H C EV
Sbjct: 61  LPFFIELLDVLHRAGLPVPYALRSEDGDALRELAEKPALLQPRLPGKHVVEPNPHQCAEV 120

Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180
           G LL  LH ATR  ILER SDRGL WM EQG +LA  L E    LL   LAEIA L  + 
Sbjct: 121 GRLLARLHLATREHILERASDRGLDWMQEQGPSLALSLSEDQLPLLRDGLAEIAELRPKL 180

Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240
            ALPRANLHADLFRDNVLF+G HL G+IDFYNACSG MLYDLAI +NDWCS+ +G +D  
Sbjct: 181 LALPRANLHADLFRDNVLFEGSHLTGVIDFYNACSGPMLYDLAIAVNDWCSHPNGEIDGE 240

Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQ-DVLIHDPAEFE 299
           R+  LLAAY+  R FT  EAE W  MLRVACVRFWLSRLIAA+   G+ DV + DP EF 
Sbjct: 241 RSEPLLAAYSALRRFTPAEAELWQPMLRVACVRFWLSRLIAAQRHEGKTDVQVKDPDEFH 300

Query: 300 IRLAQRQNVEIHLPFA 315
             L+ RQ+ +  LPFA
Sbjct: 301 RLLSARQHPQSVLPFA 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: 371
Number of extensions: 11
Number of successful extensions: 2
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: 317
Length adjustment: 27
Effective length of query: 289
Effective length of database: 290
Effective search space:    83810
Effective search space used:    83810
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 GFF4148 Psest_4221 (homoserine kinase, Neisseria type)
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.6961.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    1.3e-85  273.4   0.0    1.4e-85  273.2   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF4148  Psest_4221 homoserine kinase, Ne


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF4148  Psest_4221 homoserine kinase, Neisseria type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.2   0.0   1.4e-85   1.4e-85       1     306 [.       1     304 [.       1     305 [. 0.98

  Alignments for each domain:
  == domain 1  score: 273.2 bits;  conditional E-value: 1.4e-85
                           TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellthLaer 75 
                                         m+v+t +  +eleafL  y lG+l +++Gi  G ensn+++  ++g yvLtl e+    ++LPff+ell+ L   
  lcl|FitnessBrowser__psRCH2:GFF4148   1 MSVFTPLQRDELEAFLAPYRLGRLRDFQGIVAGSENSNFFVSLEQGEYVLTLIERGP-RQDLPFFIELLDVLHRA 74 
                                         9*****************************************************999.89*************** PP

                           TIGR00938  76 glpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerkndlrleaWsi 150
                                         glpv+ +++s+dG al eLa kPa l   L+G+ v +P +++c+evg  la+lhla+ ++  er+   r  +W  
  lcl|FitnessBrowser__psRCH2:GFF4148  75 GLPVPYALRSEDGDALRELAEKPALLQPRLPGKHVVEPNPHQCAEVGRLLARLHLATREHILERAS-DRGLDWMQ 148
                                         *********************************************************999999998.68889*99 PP

                           TIGR00938 151 laakkfkvleqleeelaalldkeldalkkflpr..dLPrgvihadlfkdnvlldgdklkgvidfyfaCedallyd 223
                                         +      ++  l+e++  ll++ l+ + ++ p+   LPr+ +hadlf+dnvl++g +l+gvidfy aC++ +lyd
  lcl|FitnessBrowser__psRCH2:GFF4148 149 EQGPS--LALSLSEDQLPLLRDGLAEIAELRPKllALPRANLHADLFRDNVLFEGSHLTGVIDFYNACSGPMLYD 221
                                         99988..999**********************95568************************************** PP

                           TIGR00938 224 laiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdP 298
                                         laiavndWc + ++++d ++   ll +y a r +++ e + +  +lr+a++rf+lsrl   +  +    v++kdP
  lcl|FitnessBrowser__psRCH2:GFF4148 222 LAIAVNDWCSHPNGEIDGERSEPLLAAYSALRRFTPAEAELWQPMLRVACVRFWLSRLIAAQRHEGKTDVQVKDP 296
                                         *************************************************************************** PP

                           TIGR00938 299 aeferkLk 306
                                          ef+r+L 
  lcl|FitnessBrowser__psRCH2:GFF4148 297 DEFHRLLS 304
                                         *****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (317 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: 10.00
//
[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