Alignments for a candidate for thrB in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Bradyrhizobium sp. BTAi1

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_012041253.1 BBTA_RS04475 homoserine kinase

Query= reanno::Korea:Ga0059261_3253
         (319 letters)



>NCBI__GCF_000015165.1:WP_012041253.1
          Length = 326

 Score =  283 bits (723), Expect = 5e-81
 Identities = 154/311 (49%), Positives = 191/311 (61%), Gaps = 4/311 (1%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60
           MAVYT V+A+ LA FL  YD+GEL+S KGIAEGVENSN+L+ TT+  FILTLYEKRV   
Sbjct: 1   MAVYTDVAADELADFLKTYDIGELLSYKGIAEGVENSNFLLHTTKGYFILTLYEKRVAVD 60

Query: 61  DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120
           DLPYF+GL+ HLA +G+  P   ++R G     L+GRPA +I FL G+    P  A    
Sbjct: 61  DLPYFLGLMAHLAERGVSCPQPARNRDGAVYSTLSGRPAAIINFLEGLWPRKPNVAHCAG 120

Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180
            G A+A+MH A  DFPL R N + V  W  LF +     D +  GL   L   +  +  +
Sbjct: 121 VGTALARMHLAGRDFPLVRKNPLSVSGWMSLFAQAADRADTVQAGLSALLSAELDVLARS 180

Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDA-HGR 239
           W   D     IHADLFPDNV   GDQ++GLIDF F+C DI  YD+A+  +AW F+A H  
Sbjct: 181 WP-TDLPEGVIHADLFPDNVFFLGDQLSGLIDFPFSCNDILAYDVAICLNAWCFEADHSL 239

Query: 240 NYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKD 299
           N   A   A    Y    PL++ E AA P LA GA IRF L+R  DWLN PA ALV  KD
Sbjct: 240 NVTKA--RAFFHAYGRERPLSQAELAALPLLARGAAIRFLLTRLVDWLNVPAGALVKPKD 297

Query: 300 PLAYVRRLKHY 310
           PL YVR+L+ +
Sbjct: 298 PLEYVRKLRFH 308


Lambda     K      H
   0.323    0.138    0.429 

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: 329
Number of extensions: 12
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: 319
Length of database: 326
Length adjustment: 28
Effective length of query: 291
Effective length of database: 298
Effective search space:    86718
Effective search space used:    86718
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_012041253.1 BBTA_RS04475 (homoserine kinase)
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.23734.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-127  409.0   0.0   7.3e-127  408.8   0.0    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012041253.1  BBTA_RS04475 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012041253.1  BBTA_RS04475 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.8   0.0  7.3e-127  7.3e-127       1     307 []       1     307 [.       1     307 [. 1.00

  Alignments for each domain:
  == domain 1  score: 408.8 bits;  conditional E-value: 7.3e-127
                                 TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 
                                               mavyt+v+ +el  fL+ yd+Gells kGiaeGvensn+ll t+kg ++Ltlyekrv  ++LP+fl l+
  lcl|NCBI__GCF_000015165.1:WP_012041253.1   1 MAVYTDVAADELADFLKTYDIGELLSYKGIAEGVENSNFLLHTTKGYFILTLYEKRVAVDDLPYFLGLM 69 
                                               9******************************************************************** PP

                                 TIGR00938  70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138
                                                hLaerg+++++p ++rdG+  s+L+G+Paa+++fL+G+  +kP +++c+ vg  la++hlag df+  
  lcl|NCBI__GCF_000015165.1:WP_012041253.1  70 AHLAERGVSCPQPARNRDGAVYSTLSGRPAAIINFLEGLWPRKPNVAHCAGVGTALARMHLAGRDFPLV 138
                                               ********************************************************************* PP

                                 TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207
                                               rkn l+   W  l+a+  + +++++++l+all++eld+l + +p dLP+gvihadlf+dnv++ gd+l+
  lcl|NCBI__GCF_000015165.1:WP_012041253.1 139 RKNPLSVSGWMSLFAQAADRADTVQAGLSALLSAELDVLARSWPTDLPEGVIHADLFPDNVFFLGDQLS 207
                                               ********************************************************************* PP

                                 TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276
                                               g+idf f+C+d l+yd+ai++n+Wcfead++l++++a+a+ ++y + rpLs+ e aa+p l+rgaa+rf
  lcl|NCBI__GCF_000015165.1:WP_012041253.1 208 GLIDFPFSCNDILAYDVAICLNAWCFEADHSLNVTKARAFFHAYGRERPLSQAELAALPLLARGAAIRF 276
                                               ********************************************************************* PP

                                 TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLkv 307
                                               ll+rl+d+ + +ag+lv++kdP e+ rkL++
  lcl|NCBI__GCF_000015165.1:WP_012041253.1 277 LLTRLVDWLNVPAGALVKPKDPLEYVRKLRF 307
                                               ****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (326 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: 8.45
//
[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