Alignments for a candidate for thrB in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Xenophilus azovorans DSM 13620

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_038205143.1 Q392_RS09140 homoserine kinase

Query= SwissProt::P29364
         (316 letters)



>NCBI__GCF_000745855.1:WP_038205143.1
          Length = 353

 Score =  202 bits (513), Expect = 1e-56
 Identities = 134/333 (40%), Positives = 171/333 (51%), Gaps = 28/333 (8%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           M+VFT +      A +    LG L+  RGI  G EN+N+F S + GE+VLTL ER     
Sbjct: 1   MAVFTEVGAEEAGALMRRLGLGELQSLRGIEGGIENTNYFASTDQGEWVLTLFERLHADQ 60

Query: 61  LPFFIELLDVLHEDGLPVP-------YALRTRDGE-----------ALRRLEGKPALLQP 102
           LP+++ L+  L E GLPVP        A    D              L  + GKPA +  
Sbjct: 61  LPYYLCLMKHLAERGLPVPEPAADPTQAAPAADAHPLEVTANAPCALLHTVAGKPAAVVR 120

Query: 103 RLAGRHERQPNAHHCQEVGDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQA 162
           RLAG  E  P  HHC+E+G LL  +H A R     +P+ RGL W  E    + P L E  
Sbjct: 121 RLAGHSELAPGEHHCRELGALLARMHLAARDFPRIQPNLRGLAWWNETAPVVMPHLDEHQ 180

Query: 163 RALLAPALA--EIAALDAERPALPRANLHADLFRDNVLF------DGPHLAGLIDFYNAC 214
            ALLA  LA     A  +   ALPR  +HADLFRDN +F      + P L G+ DFY A 
Sbjct: 181 AALLAGELAYQNHVAASSAYAALPRGPVHADLFRDNAMFSEGAPGEPPRLTGVFDFYFAG 240

Query: 215 SGWMLYDLAITLNDWCSN-TDGSLDPARARALLAAYANRRPFTALEAEHWPSMLRVACVR 273
           +   L+D+A+ LNDW  +   G+ D AR  ALL AY + RP TA E    P+MLR   +R
Sbjct: 241 TDTWLFDIAVCLNDWAIDLPTGTPDAARGAALLDAYQSVRPLTAAERTLLPAMLRAGALR 300

Query: 274 FWLSRLIAAEAFAGQDVL-IHDPAEFEIRLAQR 305
           FW+SRL          +L  HDPA FE  L +R
Sbjct: 301 FWISRLWDFHLPREASMLKAHDPAHFERVLRRR 333


Lambda     K      H
   0.324    0.140    0.434 

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: 303
Number of extensions: 15
Number of successful extensions: 6
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: 316
Length of database: 353
Length adjustment: 28
Effective length of query: 288
Effective length of database: 325
Effective search space:    93600
Effective search space used:    93600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_038205143.1 Q392_RS09140 (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.10888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.5e-88  280.9   0.0    2.1e-86  276.0   0.0    2.0  1  lcl|NCBI__GCF_000745855.1:WP_038205143.1  Q392_RS09140 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_038205143.1  Q392_RS09140 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.0   0.0   2.1e-86   2.1e-86       1     306 [.       1     331 [.       1     332 [. 0.88

  Alignments for each domain:
  == domain 1  score: 276.0 bits;  conditional E-value: 2.1e-86
                                 TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 
                                               mav+t+v  ee  a +    lGel sl+Gi  G+en+ny+  td+g +vLtl+e+   a++LP++l l+
  lcl|NCBI__GCF_000745855.1:WP_038205143.1   1 MAVFTEVGAEEAGALMRRLGLGELQSLRGIEGGIENTNYFASTDQGEWVLTLFERLH-ADQLPYYLCLM 68 
                                               9******************************************************99.*********** PP

                                 TIGR00938  70 thLaerglpvakpvk..................srdGralseLaGkPaalvefLkGssvakPtaercre 120
                                               +hLaerglpv++p +                  +   ++l ++aGkPaa+v  L+G+s   P  ++cre
  lcl|NCBI__GCF_000745855.1:WP_038205143.1  69 KHLAERGLPVPEPAAdptqaapaadahplevtaNAPCALLHTVAGKPAAVVRRLAGHSELAPGEHHCRE 137
                                               **********987642211111111111111112234678899************************** PP

                                 TIGR00938 121 vgevlaklhlagadfkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflpr....dL 185
                                                g+ la++hla+ df+  + n lr  aW+ ++a    v+++l+e++aall  el++ +++ +      L
  lcl|NCBI__GCF_000745855.1:WP_038205143.1 138 LGALLARMHLAARDFPRIQPN-LRGLAWWNETAPV--VMPHLDEHQAALLAGELAYQNHVAASsayaAL 203
                                               *********************.***********99..*******************998876422227* PP

                                 TIGR00938 186 Prgvihadlfkdnvlldgd......klkgvidfyfaCedallydlaiavndWcfea.ddkldaaaakal 247
                                               Prg +hadlf+dn ++  +      +l+gv dfyfa +d++l+d+a+++ndW+++   ++ daa+  al
  lcl|NCBI__GCF_000745855.1:WP_038205143.1 204 PRGPVHADLFRDNAMFSEGapgeppRLTGVFDFYFAGTDTWLFDIAVCLNDWAIDLpTGTPDAARGAAL 272
                                               ***************964323333359****************************72568899****** PP

                                 TIGR00938 248 lkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306
                                               l++y++vrpL++ e+  +p +lr++alrf++srl+d++ ++   + +a dPa+fer L+
  lcl|NCBI__GCF_000745855.1:WP_038205143.1 273 LDAYQSVRPLTAAERTLLPAMLRAGALRFWISRLWDFHLPREASMLKAHDPAHFERVLR 331
                                               ********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (353 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 2.28
//
[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