Alignments for a candidate for hom_kinase in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Magnetospirillum magneticum AMB-1

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_011383206.1 AMB_RS03910 homoserine kinase

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



>NCBI__GCF_000009985.1:WP_011383206.1
          Length = 326

 Score =  265 bits (678), Expect = 9e-76
 Identities = 142/316 (44%), Positives = 192/316 (60%), Gaps = 8/316 (2%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60
           MAVYT+VS + L  F A YD+G++VS KGIAEGVEN+NYL++T +  +ILTLYEKRV   
Sbjct: 1   MAVYTEVSDDELEDFAAEYDIGQVVSCKGIAEGVENTNYLLQTDQGNYILTLYEKRVNPE 60

Query: 61  DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120
           +LP+F+GL++HLAA GL  P  I  R G  ++ L GRPA ++ FL G+     T      
Sbjct: 61  ELPFFLGLMEHLAAHGLACPTPIHGRDGKALRTLCGRPAAIVSFLKGMWSRRITLGHCAE 120

Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180
            G AMA MH A ADFPL R N++ V  W+PLFE       +I   L   +   +  +   
Sbjct: 121 LGPAMATMHLAGADFPLTRANNLSVAGWRPLFESIRPRAAEIKSDLAQSIEDELDYLEAH 180

Query: 181 WTRNDFDRCAIHADLFPDNVLMRG------DQVTGLIDFYFACTDIRVYDLAVMHSAWSF 234
           W R       IHADLFPDNV          D+++G IDFYFACTD+  YD+A+  +AW F
Sbjct: 181 WPRT-LPVGLIHADLFPDNVFFLADKAAGVDRMSGFIDFYFACTDVLAYDIAICLNAWCF 239

Query: 235 DAHGRNYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADAL 294
           +  G  ++      ++ GY    PL+  E  A P LA GA +RF L+R++DWL+TP  A+
Sbjct: 240 EEDGA-FNATKARLMLNGYRRVRPLSADELDALPLLARGAAMRFLLTRSYDWLHTPPGAM 298

Query: 295 VMRKDPLAYVRRLKHY 310
           V RKDP+ Y R+L+ +
Sbjct: 299 VKRKDPMEYYRKLRFH 314


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: 310
Number of extensions: 8
Number of successful extensions: 4
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_011383206.1 AMB_RS03910 (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.30719.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-128  412.0   0.0   9.4e-128  411.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383206.1  AMB_RS03910 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383206.1  AMB_RS03910 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.8   0.0  9.4e-128  9.4e-128       1     307 []       1     313 [.       1     313 [. 0.97

  Alignments for each domain:
  == domain 1  score: 411.8 bits;  conditional E-value: 9.4e-128
                                 TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 
                                               mavyt+vsd+ele f   yd+G+++s kGiaeGven+nyll+td+g+y+Ltlyekrv++eeLPffl l+
  lcl|NCBI__GCF_000009985.1:WP_011383206.1   1 MAVYTEVSDDELEDFAAEYDIGQVVSCKGIAEGVENTNYLLQTDQGNYILTLYEKRVNPEELPFFLGLM 69 
                                               9******************************************************************** PP

                                 TIGR00938  70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138
                                               +hLa++gl+++ p++ rdG+al +L G+Paa+v+fLkG+  ++ t+ +c+e g+ +a +hlagadf+  
  lcl|NCBI__GCF_000009985.1:WP_011383206.1  70 EHLAAHGLACPTPIHGRDGKALRTLCGRPAAIVSFLKGMWSRRITLGHCAELGPAMATMHLAGADFPLT 138
                                               ********************************************************************* PP

                                 TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdk.. 205
                                               r+n+l+ + W++l++  +  + +++++la+ +++eld+l+  +pr LP g+ihadlf+dnv++ +dk  
  lcl|NCBI__GCF_000009985.1:WP_011383206.1 139 RANNLSVAGWRPLFESIRPRAAEIKSDLAQSIEDELDYLEAHWPRTLPVGLIHADLFPDNVFFLADKaa 207
                                               **************************************************************9776422 PP

                                 TIGR00938 206 ....lkgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllr 270
                                                   ++g+idfyfaC+d+l+yd+ai++n+Wcfe+d+ ++a++a+ +l+gy++vrpLs+ e +a+p l+r
  lcl|NCBI__GCF_000009985.1:WP_011383206.1 208 gvdrMSGFIDFYFACTDVLAYDIAICLNAWCFEEDGAFNATKARLMLNGYRRVRPLSADELDALPLLAR 276
                                               22237899************************************************************* PP

                                 TIGR00938 271 gaalrfllsrlldlvftqagelvvakdPaeferkLkv 307
                                               gaa+rfll+r  d+  t++g++v+ kdP e+ rkL++
  lcl|NCBI__GCF_000009985.1:WP_011383206.1 277 GAAMRFLLTRSYDWLHTPPGAMVKRKDPMEYYRKLRF 313
                                               **********************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.54
//
[ok]

This GapMind analysis is from Apr 09 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