Alignments for a candidate for hom_kinase in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Stenotrophomonas chelatiphaga DSM 21508

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_057506742.1 ABB28_RS00500 homoserine kinase

Query= reanno::Dyella79:N515DRAFT_0576
         (330 letters)



>NCBI__GCF_001431535.1:WP_057506742.1
          Length = 304

 Score =  388 bits (997), Expect = e-113
 Identities = 205/302 (67%), Positives = 235/302 (77%)

Query: 23  AQALAPASVGNVGIGFDILGHSVAGAGDRARVRRIDEPVVRIAAIEGCVVDLPLDPAQNT 82
           A+A APASVGNVG+GFDILGH++AG GD   VRRI E  VRI AI G  V LP + A NT
Sbjct: 3   ARAFAPASVGNVGVGFDILGHAIAGVGDTVTVRRIAEREVRIEAIRGADVPLPREAALNT 62

Query: 83  AGMALMALRKALGLRHGFELVLHKGIALGSGMGGSASSCVAALVAANALLERPLPMESLY 142
           AG +L+ALR+AL L  GF + + KGI LGSGMGGSA+SCVAALVAANALL+  L   +LY
Sbjct: 63  AGASLLALRQALDLPFGFAVEIDKGIPLGSGMGGSAASCVAALVAANALLDSALDRHALY 122

Query: 143 GFALEGEAVASGGRHGDNVGPMLLGGLVLATRDRLVRVPVPDAWHCALVHPHMVLETRKA 202
            FALEGE VASGGRHGDN+GPMLLGGLVL+T DRLV +PVP  WH  LVHP  VLETR+A
Sbjct: 123 RFALEGELVASGGRHGDNLGPMLLGGLVLSTADRLVPIPVPARWHSLLVHPDAVLETRRA 182

Query: 203 RAALAGAYQLGEFVAQSANLSLMLAGCWQGDAGLVREGLNDVLVEPRRAPLIPGFARVKQ 262
           RAAL G+Y LG+FVAQSANL+L+LAGC QGDA LVR GL DVLVEPRRAPLI GF   + 
Sbjct: 183 RAALQGSYALGDFVAQSANLALVLAGCHQGDATLVRAGLRDVLVEPRRAPLIIGFDAARA 242

Query: 263 AAMDHRAMGASISGAGPSVFGWFEQRDEAKAAAAAMAAAFAEAGLDSDTLVSPIAGPSAA 322
           AA+   AMGASISGAGPSVF WFE +  A+AAAA + AAFA +G DS   VS +A P+A 
Sbjct: 243 AALAAGAMGASISGAGPSVFAWFEDQASAQAAAAPVQAAFAASGFDSQAWVSSLAAPAAV 302

Query: 323 LI 324
           L+
Sbjct: 303 LL 304


Lambda     K      H
   0.320    0.134    0.394 

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: 337
Number of extensions: 11
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 330
Length of database: 304
Length adjustment: 27
Effective length of query: 303
Effective length of database: 277
Effective search space:    83931
Effective search space used:    83931
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_057506742.1 ABB28_RS00500 (homoserine kinase)
to HMM TIGR00191 (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/TIGR00191.hmm
# target sequence database:        /tmp/gapView.30551.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00191  [M=304]
Accession:   TIGR00191
Description: thrB: 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-54  171.1   0.0    1.7e-54  170.7   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506742.1  ABB28_RS00500 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506742.1  ABB28_RS00500 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.7   0.0   1.7e-54   1.7e-54       5     275 ..       7     276 ..       4     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 1.7e-54
                                 TIGR00191   5 vPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 
                                               +Pas  N+g+GfD+lG a+  v + + +      +++ ++++e+   + +p+  ++ l +  a  ++ +
  lcl|NCBI__GCF_001431535.1:WP_057506742.1   7 APASVGNVGVGFDILGHAIAGVGDTVTVR----RIAEREVRIEAIRGADVPLPREAALNTAGASLLALR 71 
                                               8******************9998776666....455555666666666677666666666555555444 PP

                                 TIGR00191  74 lgkr.vkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDN 135
                                               +  + + +++++++k iplg+G+G Saa+ vaa++aan+l++  l+++ l  +al+ E       H DN
  lcl|NCBI__GCF_001431535.1:WP_057506742.1  72 QALDlPFGFAVEIDKGIPLGSGMGGSAASCVAALVAANALLDSALDRHALYRFALEGELvasggrHGDN 140
                                               4444469***************************************************9********** PP

                                 TIGR00191 136 vapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavl 204
                                                +p llGGl+l++ +    + ++vP  ++++ +lv P   + T+ aRa L  +y + d v+++++la++
  lcl|NCBI__GCF_001431535.1:WP_057506742.1 141 LGPMLLGGLVLSTADRL--VPIPVP--ARWHSLLVHPDAVLETRRARAALQGSYALGDFVAQSANLALV 205
                                               **********9998777..566666..9***************************************** PP

                                 TIGR00191 205 vtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eek 272
                                                + ++++  a l++  ++D++ +p R+ li ++++ + aa ++ga+g  +SGaGp+++a  e++  ++ 
  lcl|NCBI__GCF_001431535.1:WP_057506742.1 206 LAGCHQG-DATLVRAGLRDVLVEPRRAPLIIGFDAARAAALAAGAMGASISGAGPSVFAWFEDQAsAQA 273
                                               *******.899************************************************9999985555 PP

                                 TIGR00191 273 aqe 275
                                               a+ 
  lcl|NCBI__GCF_001431535.1:WP_057506742.1 274 AAA 276
                                               554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (304 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.77
//
[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