Alignments for a candidate for thrC in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Methanococcus maripaludis C5

Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_011869285.1 MMARC5_RS07825 threonine synthase

Query= CharProtDB::CH_107419
         (405 letters)



>NCBI__GCF_000016125.1:WP_011869285.1
          Length = 403

 Score =  509 bits (1311), Expect = e-149
 Identities = 255/400 (63%), Positives = 318/400 (79%), Gaps = 5/400 (1%)

Query: 5   KCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIK--IDMEKLKTECPSVWKYAKLLPVE 62
           KC  CG EY  D +IY C +C GLL++ YD+ SIK  +  E L+     VW+Y   LPV+
Sbjct: 4   KCRVCGKEYEVDAIIYNC-ECGGLLEIKYDFESIKEKVSKESLRERELGVWRYLDYLPVK 62

Query: 63  --REPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGM 120
              + V++ EGGTPLYKC+ LA+K+G+K+LYVK+EG NPTGSFKDRGMTVGVT+A ELG+
Sbjct: 63  DPAKIVSLHEGGTPLYKCENLAKKLGMKELYVKNEGANPTGSFKDRGMTVGVTRANELGV 122

Query: 121 NTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDA 180
             V CASTGNTSA+LA Y A+AG   +VLLP GKVALGK+AQA+ +GAKV+ I GNFD+A
Sbjct: 123 EVVGCASTGNTSASLAAYSARAGKKCIVLLPGGKVALGKLAQAMFYGAKVIQINGNFDEA 182

Query: 181 LALVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITAIY 240
           L +V+ L  + K+YLLNS+NP+RLEGQKTIGFEI DQLDF+VPD ++LPVGNAGNI+AI+
Sbjct: 183 LVMVKNLALENKLYLLNSVNPFRLEGQKTIGFEICDQLDFEVPDMVILPVGNAGNISAIW 242

Query: 241 KGFREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGNPVN 300
           KGF+EFK  G+ D+LPKMTGIQAEG+ PIVKAIK+G   I P+ENPET+ATAIRIGNPVN
Sbjct: 243 KGFKEFKETGMIDTLPKMTGIQAEGAQPIVKAIKAGLDKIIPDENPETIATAIRIGNPVN 302

Query: 301 ATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGVIGR 360
           A KAL AI+ SGG AESVTDEEI AAQK LA+ EGI VEPASA+S+AGL KL+DMG+I +
Sbjct: 303 AAKALDAIKSSGGLAESVTDEEITAAQKLLAQTEGIFVEPASASSIAGLIKLIDMGLIDK 362

Query: 361 DETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAI 400
           D+ +VCITTG+ LKDP   I     PT ++ +++ +R+AI
Sbjct: 363 DQKIVCITTGNGLKDPDAAIKASTMPTEIECDMEVLRKAI 402


Lambda     K      H
   0.317    0.135    0.389 

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: 618
Number of extensions: 27
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: 405
Length of database: 403
Length adjustment: 31
Effective length of query: 374
Effective length of database: 372
Effective search space:   139128
Effective search space used:   139128
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: 50 (23.9 bits)

Align candidate WP_011869285.1 MMARC5_RS07825 (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.902.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-120  387.4   0.0   3.5e-120  387.2   0.0    1.0  1  lcl|NCBI__GCF_000016125.1:WP_011869285.1  MMARC5_RS07825 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011869285.1  MMARC5_RS07825 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.2   0.0  3.5e-120  3.5e-120       1     340 []      52     379 ..      52     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 387.2 bits;  conditional E-value: 3.5e-120
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltka 68 
                                               v+ry  +l+v+  +++v+l+eg t+l+++++la+++g+++lyvk+++++Pt++FKDrg   ++v++t+a
  lcl|NCBI__GCF_000016125.1:WP_011869285.1  52 VWRYLDYLPVKdPAKIVSLHEGGTPLYKCENLAKKLGMKELYVKNEGANPTGSFKDRG---MTVGVTRA 117
                                               8**********99*********************************************...******** PP

                                 TIGR00260  69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137
                                               +elg+e+v+cA++G+t+a++a a++++a+ k++vL+P gk++   +kl++a++++akv++i+G+FD+a+
  lcl|NCBI__GCF_000016125.1:WP_011869285.1 118 NELGVEVVGCASTGNTSASLA-AYSARAGKKCIVLLPGGKVA--LGKLAQAMFYGAKVIQINGNFDEAL 183
                                               *********************.********************..************************* PP

                                 TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205
                                                +vk+++ +++ ++lnsvN   p+r+e+qkt+ fei++ql+ e pd v++pv+ +gn++ai+kGf+e+k
  lcl|NCBI__GCF_000016125.1:WP_011869285.1 184 VMVKNLALENKLYLLNSVN---PFRLEGQKTIGFEICDQLDFEVPDMVILPVGnAGNISAIWKGFKEFK 249
                                               *******************...*********************************************** PP

                                 TIGR00260 206 elg....lpieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnl 269
                                               e+g    lp ++++i+aega++iv++ + +  ++ p e++eT++tA++ignp+n+ +al+++++s+g +
  lcl|NCBI__GCF_000016125.1:WP_011869285.1 250 ETGmidtLP-KMTGIQAEGAQPIVKAIKAGLdKIIPDENPETIATAIRIGNPVNAAKALDAIKSSGGLA 317
                                               *********.*****************888899************************************ PP

                                 TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338
                                               e++    +deei+ a+k+la++eg+++ep++a ++a+l+kl++ g    +d++  +++v++ tgn+lkd
  lcl|NCBI__GCF_000016125.1:WP_011869285.1 318 ESV----TDEEITAAQKLLAQTEGIFVEPASASSIAGLIKLIDMG---LIDKD--QKIVCITTGNGLKD 377
                                               ***....**************************************...*****..************** PP

                                 TIGR00260 339 pe 340
                                               p+
  lcl|NCBI__GCF_000016125.1:WP_011869285.1 378 PD 379
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (403 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: 9.01
//
[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