Alignments for a candidate for thrB in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Steroidobacter denitrificans DSM 18526

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_066920366.1 ACG33_RS08525 homoserine kinase

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



>NCBI__GCF_001579945.1:WP_066920366.1
          Length = 311

 Score =  281 bits (720), Expect = 1e-80
 Identities = 157/307 (51%), Positives = 194/307 (63%), Gaps = 4/307 (1%)

Query: 22  SAQALAPASVGNVGIGFDILGHSVAGAGDRARVRRIDEPVVRIAAIEGCVVDLPLDPAQN 81
           SA   APASVGNV +GFD+LGHS    GDR   RR  EP VRI AI G   +LP  P  N
Sbjct: 4   SATVFAPASVGNVAVGFDVLGHSFQAIGDRVTARRTQEPGVRITAIHGVATELPTAPENN 63

Query: 82  TAGMALMALRKALGLRHGFELVLHKGIALGSGMGGSASSCVAALVAANALLERPLPMESL 141
           TAGM ++++ + L +  G EL + KGI LGSG+GGSA+S VAA+VA +ALL RPL    L
Sbjct: 64  TAGMGVLSMVRELEVDFGIELSIEKGIPLGSGLGGSAASAVAAVVAMDALLPRPLSKIEL 123

Query: 142 YGFALEGEAVASGGRHGDNVGPMLLGGLVL--ATRDRLVR-VPVPDAWHCALVHPHMVLE 198
             FA++GE VASG  H DN+ P L GGLVL     D  V+ +PVP +  C LVHPHM+L 
Sbjct: 124 LKFAMKGEQVASGTVHVDNIAPSLFGGLVLTVGVDDPYVKQIPVPPSVRCVLVHPHMMLA 183

Query: 199 TRKARAALAGAYQLGEFVAQSANLSLMLAGCWQGDAGLVREGLNDVLVEPRRAPLIPGFA 258
           TR+AR  L  +  L + + QSANL+  L GC+  D  L+R  L DV+VEP+R  LIPGF 
Sbjct: 184 TREARQLLKRSIDLSDVIWQSANLAGFLTGCFTDDLQLIRASLEDVIVEPQRKALIPGFQ 243

Query: 259 RVKQAAMDHRAMGASISGAGPSVFGWFEQRDEAKAAAAAMAAAFAEAGLDSDTLVSPIAG 318
            VK  AM   A+G SISGAGP+VF W E+  +A     AM A FA  GL+ D  VS +  
Sbjct: 244 AVKDGAMAQGALGCSISGAGPTVFAWCEE-PQAHGVRDAMVAGFAAHGLECDAWVSTLEP 302

Query: 319 PSAALID 325
             A +ID
Sbjct: 303 IGARVID 309


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: 267
Number of extensions: 11
Number of successful extensions: 3
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: 330
Length of database: 311
Length adjustment: 28
Effective length of query: 302
Effective length of database: 283
Effective search space:    85466
Effective search space used:    85466
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_066920366.1 ACG33_RS08525 (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.5762.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.9e-69  219.8   0.0    2.2e-69  219.6   0.0    1.0  1  lcl|NCBI__GCF_001579945.1:WP_066920366.1  ACG33_RS08525 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066920366.1  ACG33_RS08525 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.6   0.0   2.2e-69   2.2e-69       2     301 ..       6     307 ..       5     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 219.6 bits;  conditional E-value: 2.2e-69
                                 TIGR00191   2 kvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkv 70 
                                               +v +Pas  N+++GfDvlG + + + + +     +qe     ++a    + ++p+ +++N +   ++ +
  lcl|NCBI__GCF_001579945.1:WP_066920366.1   6 TVFAPASVGNVAVGFDVLGHSFQAIGDRVTAR-RTQEPGVR-ITAIHGVATELPTAPENNTAGMGVLSM 72 
                                               588********************998766555.46666666.7777777799***************** PP

                                 TIGR00191  71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......Hp 133
                                               +++l+ +  +++l +ek iplg+GLG Saa+ vaav+a+++l+  +lsk ell++a+  E+      H 
  lcl|NCBI__GCF_001579945.1:WP_066920366.1  73 VRELEVD-FGIELSIEKGIPLGSGLGGSAASAVAAVVAMDALLPRPLSKIELLKFAMKGEQvasgtvHV 140
                                               *******.************************************************************* PP

                                 TIGR00191 134 DNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshla 202
                                               DN+ap+l+GGl+l+v  dd   v ++P  +++ +vlv P++ + T+eaR++L ++ +++d++ ++++la
  lcl|NCBI__GCF_001579945.1:WP_066920366.1 141 DNIAPSLFGGLVLTVGVDD-PYVKQIPVPPSVRCVLVHPHMMLATREARQLLKRSIDLSDVIWQSANLA 208
                                               ******************9.888889988**************************************** PP

                                 TIGR00191 203 vlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.e 270
                                               ++ t + ++   +l++  ++D++ +p R+ liP+++++k  a ++galg  +SGaGpt++a +ee + +
  lcl|NCBI__GCF_001579945.1:WP_066920366.1 209 GFLTGCFTD-DLQLIRASLEDVIVEPQRKALIPGFQAVKDGAMAQGALGCSISGAGPTVFAWCEEPQaH 276
                                               ********9.899******************************************************55 PP

                                 TIGR00191 271 ekaqelleklakegieltvkvleldtdgaev 301
                                                    ++  +a +g e+   v +l+  ga+v
  lcl|NCBI__GCF_001579945.1:WP_066920366.1 277 GVRDAMVAGFAAHGLECDAWVSTLEPIGARV 307
                                               5666778888888888887777777677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (311 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: 8.24
//
[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