Alignments for a candidate for thrB in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Pseudomonas fluorescens FW300-N2E2

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate Pf6N2E2_4164 Homoserine kinase (EC 2.7.1.39)

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164
          Length = 316

 Score =  449 bits (1155), Expect = e-131
 Identities = 225/316 (71%), Positives = 252/316 (79%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           MSVFTPL R  LE FLAPY LGRL DF+GIA GSEN+NFF+SLE GEFVLTLVERGPVQ+
Sbjct: 1   MSVFTPLARPELETFLAPYGLGRLLDFQGIAAGSENTNFFISLEQGEFVLTLVERGPVQE 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           +PFFIELLDVLH+  LPVPYALRT DG ALR L GKPALLQPRLAG+H +Q N  HC +V
Sbjct: 61  MPFFIELLDVLHDADLPVPYALRTTDGVALRELAGKPALLQPRLAGKHIKQANTQHCAQV 120

Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180
           G+LL HLH ATR  +++R +DRGL WM E+GA L   L  + R LL  AL EI+      
Sbjct: 121 GELLAHLHLATRDNMIKRKTDRGLDWMQEEGAKLLSHLDAEPRRLLEAALDEISLQKVGI 180

Query: 181 PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA 240
            ALPRAN+HADLFRDN +F+G HL GLIDFYNACSG MLYD+AI LNDWCS+ +G LD  
Sbjct: 181 LALPRANIHADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALNDWCSDDNGVLDGP 240

Query: 241 RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFEI 300
           RARALL AYA  RPFTA EA+ WP+MLRVACVRFWLSRLIAAE+FAGQDVLIHDP EF+ 
Sbjct: 241 RARALLGAYATLRPFTAAEAQLWPTMLRVACVRFWLSRLIAAESFAGQDVLIHDPMEFQQ 300

Query: 301 RLAQRQNVEIHLPFAL 316
           RLAQRQ V   LPFAL
Sbjct: 301 RLAQRQTVHALLPFAL 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: 397
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 Pf6N2E2_4164 (Homoserine kinase (EC 2.7.1.39))
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.18108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
      2e-89  285.9   0.0    2.2e-89  285.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164  Homoserine kinase (EC 2.7.1.39)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164  Homoserine kinase (EC 2.7.1.39)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.7   0.0   2.2e-89   2.2e-89       1     306 [.       1     303 [.       1     304 [. 0.96

  Alignments for each domain:
  == domain 1  score: 285.7 bits;  conditional E-value: 2.2e-89
                                      TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPf 64 
                                                    m+v+t ++  ele+fL  y lG+ll+++Gia G en+n+++  ++g +vLtl e+    +e+Pf
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164   1 MSVFTPLARPELETFLAPYGLGRLLDFQGIAAGSENTNFFISLEQGEFVLTLVERGP-VQEMPF 63 
                                                    9*****************************************************998.899*** PP

                                      TIGR00938  65 flellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlakl 128
                                                    f+ell+ L + +lpv+ ++++ dG al eLaGkPa l   L+G+ +++  +++c++vge la+l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164  64 FIELLDVLHDADLPVPYALRTTDGVALRELAGKPALLQPRLAGKHIKQANTQHCAQVGELLAHL 127
                                                    **************************************************************** PP

                                      TIGR00938 129 hlagadfkeerkndlrleaWsilaakkfkvleqleeelaalldkelda..lkkflprdLPrgvi 190
                                                    hla+ d   +rk   r  +W  +  +k  +l +l++e  +ll++ ld   l+k+    LPr+ i
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164 128 HLATRDNMIKRKT-DRGLDWMQEEGAK--LLSHLDAEPRRLLEAALDEisLQKVGILALPRANI 188
                                                    *****99999999.67889**999999..******************72245666789****** PP

                                      TIGR00938 191 hadlfkdnvlldgdklkgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeav 254
                                                    hadlf+dn +++g +l+g+idfy aC++ +lyd+aia+ndWc + ++ ld  +a+all++y + 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164 189 HADLFRDNAMFEGTHLTGLIDFYNACSGPMLYDVAIALNDWCSDDNGVLDGPRARALLGAYATL 252
                                                    **************************************************************** PP

                                      TIGR00938 255 rpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306
                                                    rp+++ e + +p++lr+a++rf+lsrl     + ag+ v + dP ef+++L+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4164 253 RPFTAAEAQLWPTMLRVACVRFWLSRLIAAE-SFAGQDVLIHDPMEFQQRLA 303
                                                    ***************************9865.57899999*********996 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.82
//
[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