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.5371.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.60
//
[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:

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:

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:

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:

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