Alignments for a candidate for thrC in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Methylococcus capsulatus Bath

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_010959941.1 MCA_RS02960 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_000008325.1:WP_010959941.1
          Length = 380

 Score =  402 bits (1034), Expect = e-117
 Identities = 196/371 (52%), Positives = 268/371 (72%), Gaps = 23/371 (6%)

Query: 3   RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSF 62
           R+ G+I++Y+  LPV   T I++L EG+TPLI  +N+ R +G + ++Y+KYEGLNPTGSF
Sbjct: 6   RYTGLIERYRDRLPVSAETRIISLGEGDTPLIRLENIPRLLGRRVELYVKYEGLNPTGSF 65

Query: 63  KDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQA 122
           KDRGMT+A+++AVE G RA+ICASTGNTSA+AAAYAARAG+ A+VL+P G +A+GKL+QA
Sbjct: 66  KDRGMTMAVTRAVEEGSRAIICASTGNTSAAAAAYAARAGITAFVLIPDGKIAMGKLAQA 125

Query: 123 MIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPD 182
           M+YG+ V+ I+G FDD + +V+++    PV IVNS+NPYR++GQKTAAFEI D LG APD
Sbjct: 126 MMYGSVVIQIKGNFDDGMRLVKEVAGEAPVTIVNSINPYRLQGQKTAAFEIVDELGRAPD 185

Query: 183 YHFIPVGNAGNITAYWKGFKIYYEEGK----------------------ITKLPRMMGWQ 220
           YH +PVGNAGNITA+W G+  Y   G+                       T  P+M+G+Q
Sbjct: 186 YHCLPVGNAGNITAHWIGYSEYACGGRDCVTEACAFCNGECRFVSGGPVSTSRPKMVGYQ 245

Query: 221 AEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLI 280
           A G+AP ++G+ + +P+T+ATAI+IG+P SW+ A + ++ESGG  D  SD EIL A KL+
Sbjct: 246 ASGSAPFLRGHMVDHPETVATAIRIGHPQSWEQAWQVSRESGGWFDECSDEEILAAQKLL 305

Query: 281 ASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVC-EEPITV 339
              EGVFCEPASA S+AG ++ +R G    G  V  TLTGNGLKDPDTAI  C ++P+T+
Sbjct: 306 TEREGVFCEPASATSLAGALRDIRSGKIPEGSTVVLTLTGNGLKDPDTAIAQCTQKPVTI 365

Query: 340 PPDFDEVVKVL 350
             + D V + +
Sbjct: 366 EAELDSVKRAI 376


Lambda     K      H
   0.317    0.136    0.400 

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: 427
Number of extensions: 19
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: 352
Length of database: 380
Length adjustment: 30
Effective length of query: 322
Effective length of database: 350
Effective search space:   112700
Effective search space used:   112700
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: 49 (23.5 bits)

Align candidate WP_010959941.1 MCA_RS02960 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.928.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.4e-96  307.0   0.0    1.2e-95  306.5   0.0    1.2  1  lcl|NCBI__GCF_000008325.1:WP_010959941.1  MCA_RS02960 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010959941.1  MCA_RS02960 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.5   0.0   1.2e-95   1.2e-95       1     340 []      11     352 ..      11     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 306.5 bits;  conditional E-value: 1.2e-95
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 
                                               ++ryr  l+v+ e+++++l eg t+l+r +++++ +g   +lyvk ++++Pt++FKDrg   +++++t+
  lcl|NCBI__GCF_000008325.1:WP_010959941.1  11 IERYRDRLPVSaETRIISLGEGDTPLIRLENIPRLLGRrVELYVKYEGLNPTGSFKDRG---MTMAVTR 76 
                                               78************************************99*******************...******* PP

                                 TIGR00260  68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136
                                               a e+g  +++cA++G+t+aaaa a+a++a++ ++vL+P+gki+   +kl++a++++  v++ikG+FDd 
  lcl|NCBI__GCF_000008325.1:WP_010959941.1  77 AVEEGSRAIICASTGNTSAAAA-AYAARAGITAFVLIPDGKIA--MGKLAQAMMYGSVVIQIKGNFDDG 142
                                               **********************.********************..************************ PP

                                 TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204
                                                +lvke++++ + + +ns+N   p+r+++qkt+afeiv++lg ++pd  ++pv+ +gn++a + G+ e+
  lcl|NCBI__GCF_000008325.1:WP_010959941.1 143 MRLVKEVAGEAPVTIVNSIN---PYRLQGQKTAAFEIVDELG-RAPDYHCLPVGnAGNITAHWIGYSEY 207
                                               ********998877777776...*******************.9************************* PP

                                 TIGR00260 205 kelg..........................lpieklaiaaegaadivrrflksgdlepkedkeTlstAm 247
                                                 +g                          +p ++ + +a g+a+++r            ++eT++tA+
  lcl|NCBI__GCF_000008325.1:WP_010959941.1 208 ACGGrdcvteacafcngecrfvsggpvstsRP-KMVGYQASGSAPFLRGH-------MVDHPETVATAI 268
                                               *****************************999.**********9999988.......67789******* PP

                                 TIGR00260 248 dignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvs 316
                                               +ig+p ++e+a+++ r+s+g +++     sdeeil a+k+l e+eg+++ep++a+++a+ ++ + +g  
  lcl|NCBI__GCF_000008325.1:WP_010959941.1 269 RIGHPQSWEQAWQVSRESGGWFDEC----SDEEILAAQKLLTEREGVFCEPASATSLAGALRDIRSG-- 331
                                               ************************9....**************************************.. PP

                                 TIGR00260 317 atadpaKFeevvealtgnklkdpe 340
                                                +++++  ++vv+ ltgn+lkdp+
  lcl|NCBI__GCF_000008325.1:WP_010959941.1 332 -KIPEG--STVVLTLTGNGLKDPD 352
                                               .*****..**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (380 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.91
//
[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