Alignments for a candidate for thrB in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Sphingomonas wittichii RW1

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_012048899.1 SWIT_RS13620 homoserine kinase

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



>NCBI__GCF_000016765.1:WP_012048899.1
          Length = 320

 Score =  387 bits (995), Expect = e-112
 Identities = 192/311 (61%), Positives = 231/311 (74%), Gaps = 1/311 (0%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60
           MAVYTQVS E +  FL RYDVG L+SAKGIAEGVENSNYL+ETT  RFILTLYEKRV   
Sbjct: 1   MAVYTQVSTEEMTAFLHRYDVGTLLSAKGIAEGVENSNYLIETTAGRFILTLYEKRVNVD 60

Query: 61  DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120
           DLP+F  L DHLAAKGL +P  ++DR G ++Q L GRPACLI+FLSG+S++HPTPAQARA
Sbjct: 61  DLPFFCALTDHLAAKGLNIPRMLRDRRGEQLQTLAGRPACLIEFLSGVSVTHPTPAQARA 120

Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180
           AG A+  MH+A+ DF L RPNS+ +  W  L  +CG  LD I PGL   +   +  +   
Sbjct: 121 AGGALGDMHKALGDFRLGRPNSLDLAGWGALAARCGADLDHIQPGLRGRVMAEVEWLEAN 180

Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGRN 240
           W R+      IHADLFPDNVLM GD+V+G+IDFYFACTDIR +D+AV H+AW F+  G  
Sbjct: 181 WPRH-LRTAVIHADLFPDNVLMLGDEVSGVIDFYFACTDIRAWDVAVTHAAWCFENDGTG 239

Query: 241 YDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKDP 300
           Y   +G AL+AGY+  F L+  ER AFP LA GAC+RF L+RAWDWLNTPADALV RKDP
Sbjct: 240 YHADLGRALVAGYDRQFGLSTDERLAFPILARGACLRFLLTRAWDWLNTPADALVTRKDP 299

Query: 301 LAYVRRLKHYA 311
           +A++RRL  YA
Sbjct: 300 IAFLRRLDFYA 310


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: 341
Number of extensions: 11
Number of successful extensions: 2
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: 320
Length adjustment: 28
Effective length of query: 291
Effective length of database: 292
Effective search space:    84972
Effective search space used:    84972
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_012048899.1 SWIT_RS13620 (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.5705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-123  395.9   0.0   7.2e-123  395.7   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012048899.1  SWIT_RS13620 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012048899.1  SWIT_RS13620 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.7   0.0  7.2e-123  7.2e-123       1     306 [.       1     307 [.       1     308 [. 0.99

  Alignments for each domain:
  == domain 1  score: 395.7 bits;  conditional E-value: 7.2e-123
                                 TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 
                                               mavyt+vs ee+ afL+ yd+G lls kGiaeGvensnyl++t+ gr++Ltlyekrv+ ++LPff +l+
  lcl|NCBI__GCF_000016765.1:WP_012048899.1   1 MAVYTQVSTEEMTAFLHRYDVGTLLSAKGIAEGVENSNYLIETTAGRFILTLYEKRVNVDDLPFFCALT 69 
                                               9******************************************************************** PP

                                 TIGR00938  70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138
                                               +hLa++gl +++ ++ r G++l++LaG+Pa+l+efL+G sv++Pt++++r++g  l  +h a  df+ +
  lcl|NCBI__GCF_000016765.1:WP_012048899.1  70 DHLAAKGLNIPRMLRDRRGEQLQTLAGRPACLIEFLSGVSVTHPTPAQARAAGGALGDMHKALGDFRLG 138
                                               ********************************************************************* PP

                                 TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207
                                               r n+l+l+ W  laa++   l++++++l   + +e++ l+ ++pr+L ++vihadlf+dnvl+ gd+++
  lcl|NCBI__GCF_000016765.1:WP_012048899.1 139 RPNSLDLAGWGALAARCGADLDHIQPGLRGRVMAEVEWLEANWPRHLRTAVIHADLFPDNVLMLGDEVS 207
                                               *****************999************************************************* PP

                                 TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddk.ldaaaakallkgyeavrpLseeekaafpvllrgaalr 275
                                               gvidfyfaC+d +++d+a++  +Wcfe+d++ ++a+  +al+ gy++++ Ls+ e+ afp+l+rga+lr
  lcl|NCBI__GCF_000016765.1:WP_012048899.1 208 GVIDFYFACTDIRAWDVAVTHAAWCFENDGTgYHADLGRALVAGYDRQFGLSTDERLAFPILARGACLR 276
                                               *****************************875999********************************** PP

                                 TIGR00938 276 fllsrlldlvftqagelvvakdPaeferkLk 306
                                               fll+r++d+ +t+a++lv+ kdP +f r+L 
  lcl|NCBI__GCF_000016765.1:WP_012048899.1 277 FLLTRAWDWLNTPADALVTRKDPIAFLRRLD 307
                                               ****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (320 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: 9.44
//
[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