Alignments for a candidate for thrB in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Mycolicibacterium vanbaalenii PYR-1

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_011781501.1 MVAN_RS21815 homoserine kinase

Query= BRENDA::P07128
         (309 letters)



>NCBI__GCF_000015305.1:WP_011781501.1
          Length = 314

 Score =  291 bits (746), Expect = 1e-83
 Identities = 160/303 (52%), Positives = 198/303 (65%), Gaps = 8/303 (2%)

Query: 1   MAIELNVGRKVTVTVPGSSANLGPGFDTLGLALSVYDTVEVEIIPSGLEVEVFGEGQGEV 60
           M   L  G   T  V  SSANLGPGFD++GLA+ +YD + VE   SGL VEV GEG G+V
Sbjct: 1   MTRTLPPGLTATAVVAASSANLGPGFDSMGLAIGLYDEIVVETTESGLVVEVEGEGSGQV 60

Query: 61  PLDGSHLVVKAIRAGLKAADAEVPGLRVVCHNNIPQSRGLGSSAAAAVAGVAAANGLA-- 118
           PLDGSHLVV+AI  GL+      PGL V C N+IP SRGLGSSAAA V G+AAANGLA  
Sbjct: 61  PLDGSHLVVRAIERGLRETGVSAPGLIVRCRNDIPHSRGLGSSAAAVVGGLAAANGLAAQ 120

Query: 119 --DFPLTQEQIVQLSSAFEGHPDNAAASVLGGAVVSWTNLSIDGKSQPQYAAVPLEVQDN 176
                ++ E++VQ+SS FEGHPDNAAA+VLGGAVV+WT     G   P+YAA P+ +  +
Sbjct: 121 TDSTLMSPERLVQVSSEFEGHPDNAAAAVLGGAVVAWT---AAGAGDPRYAAAPIRLHPD 177

Query: 177 IRATALVPNFHASTEAVRRVLPTEVTHIDARFNVSRVAVMIVALQQRPDLLWEGTRDRLH 236
           I   A VP   +ST   R +LP  V H DARFN+SR A+++VAL +RPDLL E T D LH
Sbjct: 178 IAIFAAVPQVRSSTAETRVLLPEHVRHTDARFNLSRAALLVVALTERPDLLMEATEDVLH 237

Query: 237 QPYRAEVLPITSEWVNRLRNRGYAAYLSGAGPTAMVLSTE-PIPDKVLEDARESGIKVLE 295
           QP RA  +P ++E++  LR  G  A LSGAGP  + LSTE  +P + L    + G  V  
Sbjct: 238 QPQRAAAMPASAEYLAMLRRCGVPAVLSGAGPAVLALSTETELPAEALRYGADHGFAVKR 297

Query: 296 LEV 298
           + V
Sbjct: 298 MSV 300


Lambda     K      H
   0.315    0.132    0.377 

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: 239
Number of extensions: 8
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: 309
Length of database: 314
Length adjustment: 27
Effective length of query: 282
Effective length of database: 287
Effective search space:    80934
Effective search space used:    80934
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_011781501.1 MVAN_RS21815 (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.24285.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-62  197.3   0.1    1.6e-62  197.0   0.1    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011781501.1  MVAN_RS21815 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011781501.1  MVAN_RS21815 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   0.1   1.6e-62   1.6e-62       5     270 ..      15     281 ..      12     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 1.6e-62
                                 TIGR00191   5 vPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakkvlkk 73 
                                               v assANlgpGfD++Gla+ l++e++v+    +es    +e egeg  ++p++    l+ +++++ l++
  lcl|NCBI__GCF_000015305.1:WP_011781501.1  15 VAASSANLGPGFDSMGLAIGLYDEIVVET---TESGLV-VEVEGEGSGQVPLD-GSHLVVRAIERGLRE 78 
                                               789**********************9999...666666.999999999*****.899************ PP

                                 TIGR00191  74 lgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglk....lskeelldlalllEgHpDNvap 138
                                               +g + +++ ++ +++ip +rGLGSSaaa+v++++aan la +     +s e+l+++ ++ EgHpDN+a+
  lcl|NCBI__GCF_000015305.1:WP_011781501.1  79 TGVSAPGLIVRCRNDIPHSRGLGSSAAAVVGGLAAANGLAAQTdstlMSPERLVQVSSEFEGHPDNAAA 147
                                               *************************************98765423337889****************** PP

                                 TIGR00191 139 allGGlqlavkedd....llevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlav 203
                                               a+lGG ++a +          + ++  ++++ + +++P++  sTae+R +LP++++  d+ fnls++a+
  lcl|NCBI__GCF_000015305.1:WP_011781501.1 148 AVLGGAVVAWTAAGagdpRYAAAPIRLHPDIAIFAAVPQVRSSTAETRVLLPEHVRHTDARFNLSRAAL 216
                                               *******9999888786766666666779**************************************** PP

                                 TIGR00191 204 lvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.e 270
                                               lv Al+++  +dll  a +D++hqp R+  +P+ +e   + +  g+   +lSGaGp++lal++e++ +
  lcl|NCBI__GCF_000015305.1:WP_011781501.1 217 LVVALTER--PDLLMEATEDVLHQPQRAAAMPASAEYLAMLRRCGV-PAVLSGAGPAVLALSTETElP 281
                                               ******99..9***************************99999986.568*************99853 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (314 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 7.46
//
[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