Alignments for a candidate for thrB in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Crocosphaera subtropica ATCC 51142

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_009546592.1 CCE_RS02445 homoserine kinase

Query= curated2:B2J7E8
         (304 letters)



>NCBI__GCF_000017845.1:WP_009546592.1
          Length = 305

 Score =  389 bits (999), Expect = e-113
 Identities = 194/300 (64%), Positives = 230/300 (76%), Gaps = 2/300 (0%)

Query: 4   VSAITVTVPATTANLGPGFDCIGAALKLYNEFRFTRLEEGG--LIIHVSGTEAERVQTDE 61
           +S +TVTVPATTAN+GPGFDCIGAAL LYN+F FT   E    L I V+GTEA RV  D 
Sbjct: 1   MSTVTVTVPATTANIGPGFDCIGAALTLYNQFTFTEQPEADTDLRITVTGTEAHRVSGDR 60

Query: 62  SNLLYQAFVKFYQHIEQTPPTVKIEIKLGVPLARGLGSSATAIVGGLVAANQLEGATLSQ 121
           +NLLYQAF   Y H+ +TPP + I+IKLGVPLARGLGSSATAI+GGLV AN+L G  LS 
Sbjct: 61  TNLLYQAFTHLYDHLNKTPPKIAIDIKLGVPLARGLGSSATAIIGGLVGANELAGQPLST 120

Query: 122 SQVMELAIAMEGHPDNVVPALLGGCRLAATSGTAWEICDVPWHKDVVPVVAIPNFELSTS 181
           +++MELAIA+EGHPDNVVPALLG C+L+      WEIC +PWH D++PVVAIP+FELST 
Sbjct: 121 AEIMELAIAIEGHPDNVVPALLGNCQLSVGEAENWEICQIPWHSDIIPVVAIPDFELSTE 180

Query: 182 EARGVLPTEVSRADAIFNTAHLGLLLRGLETGNGQWLKTALQDKLHQPYRKALIPSYDAV 241
           EAR VLP  +S  DAIFN A +GLL+R LE+GN QWL  A+ DKLHQPYR+ LI  Y+ V
Sbjct: 181 EARAVLPKTLSYGDAIFNIARMGLLIRALESGNEQWLNKAMADKLHQPYRQGLIEGYEFV 240

Query: 242 NIAAVSAGAYGMVISGAGPTLLALADQLHSEAVEAAMLAAWQEEGITAEVRSLSLDTQGA 301
             +A+ AGAYGMVISGAGPTLLAL      ++VE AM  AW +  I A+VRSLS+DTQGA
Sbjct: 241 QASALKAGAYGMVISGAGPTLLALTHPEKIQSVEKAMKNAWTQLEIVADVRSLSIDTQGA 300


Lambda     K      H
   0.317    0.132    0.380 

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: 324
Number of extensions: 8
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: 304
Length of database: 305
Length adjustment: 27
Effective length of query: 277
Effective length of database: 278
Effective search space:    77006
Effective search space used:    77006
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate WP_009546592.1 CCE_RS02445 (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.3147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.6e-96  307.2   0.0    5.1e-96  307.0   0.0    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009546592.1  CCE_RS02445 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009546592.1  CCE_RS02445 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.0   0.0   5.1e-96   5.1e-96       1     302 [.       4     303 ..       4     305 .] 0.96

  Alignments for each domain:
  == domain 1  score: 307.0 bits;  conditional E-value: 5.1e-96
                                 TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 
                                               ++v+vPa++AN+gpGfD++G+al+l+++++ te+ + +++   ++ +g ++++++ + + Nl+yq++++
  lcl|NCBI__GCF_000017845.1:WP_009546592.1   4 VTVTVPATTANIGPGFDCIGAALTLYNQFTFTEQPEADTDL-RITVTGTEAHRVSGD-RTNLLYQAFTH 70 
                                               689******************************55555555.5************99.9********** PP

                                 TIGR00191  70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEgHpDNvap 138
                                               ++++l+k ++ +++ ++  +pl+rGLGSSa+ai+++++ anelag++ls++e+++la+++EgHpDNv p
  lcl|NCBI__GCF_000017845.1:WP_009546592.1  71 LYDHLNKTPPKIAIDIKLGVPLARGLGSSATAIIGGLVGANELAGQPLSTAEIMELAIAIEGHPDNVVP 139
                                               ********************************************************************* PP

                                 TIGR00191 139 allGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtA 207
                                               allG +ql+v e ++ e+ ++P +s++  v++iP +e+sT+eaRavLPk  s+ d++fn +++++l+ A
  lcl|NCBI__GCF_000017845.1:WP_009546592.1 140 ALLGNCQLSVGEAENWEICQIPWHSDIIPVVAIPDFELSTEEARAVLPKTLSYGDAIFNIARMGLLIRA 208
                                               ********************************************************************* PP

                                 TIGR00191 208 lvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqe 275
                                               l s+ ++++l++am D++hqpyR+ li +++ ++  a ++ga+g+++SGaGpt+lal++ ek +  ++ 
  lcl|NCBI__GCF_000017845.1:WP_009546592.1 209 LESG-NEQWLNKAMADKLHQPYRQGLIEGYEFVQASALKAGAYGMVISGAGPTLLALTHPEKiQSVEKA 276
                                               ****.********************************************************97788888 PP

                                 TIGR00191 276 lleklakegieltvkvleldtdgaeve 302
                                               +++ +++  i + v+ l++dt+ga+v 
  lcl|NCBI__GCF_000017845.1:WP_009546592.1 277 MKNAWTQLEIVADVRSLSIDTQGANVN 303
                                               88899999999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (305 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: 7.05
//
[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