Alignments for a candidate for thrC in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Methanobacterium lacus AL-21

Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_013644215.1 METBO_RS03125 threonine synthase

Query= CharProtDB::CH_107419
         (405 letters)



>NCBI__GCF_000191585.1:WP_013644215.1
          Length = 399

 Score =  486 bits (1251), Expect = e-142
 Identities = 247/398 (62%), Positives = 305/398 (76%), Gaps = 4/398 (1%)

Query: 4   LKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLPV-E 62
           +KCI CG EY  DE+IYTC KCD  L+V+  +  I  D+   +    ++WKY + LPV E
Sbjct: 2   MKCISCGEEYEIDEIIYTCKKCDSTLEVVSSHPDISKDIFSCRKS--TMWKYKEFLPVDE 59

Query: 63  REPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGMNT 122
            + V+++EGGTP  KCD+L  ++GI  LYVK EG NPTGSFKDRGM+VG+TKA+ELG+NT
Sbjct: 60  TKIVSLEEGGTPFCKCDKLGSELGID-LYVKVEGSNPTGSFKDRGMSVGMTKAVELGVNT 118

Query: 123 VACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDALA 182
           V CASTGNTSA+LA Y A+AG   +VLLPAGKVALGK+AQA+ HGA+V+SIRGNFD+AL 
Sbjct: 119 VGCASTGNTSASLAAYAARAGKRCIVLLPAGKVALGKLAQAMFHGAEVISIRGNFDEALE 178

Query: 183 LVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITAIYKG 242
            V +L  + ++YLLNS+NPYRLEGQKTIGFEI D L +K PDRIVLPVGNAGNI+AI+KG
Sbjct: 179 TVTSLALEGQLYLLNSVNPYRLEGQKTIGFEIVDDLGWKSPDRIVLPVGNAGNISAIWKG 238

Query: 243 FREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGNPVNAT 302
            +EF   G  D LP MTGIQAE S PI  A++ G   I P ++PET+ATAIRIG PV+A 
Sbjct: 239 IKEFHEAGFMDDLPMMTGIQAEMSAPITNAVRQGKNTIEPVKDPETIATAIRIGAPVSAQ 298

Query: 303 KALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGVIGRDE 362
           KAL AI ES G A++VTD+EIL+AQK LAR EGIGVEPASAAS+AGL K+V+ G + + E
Sbjct: 299 KALRAIYESNGYADTVTDDEILSAQKLLARKEGIGVEPASAASIAGLLKMVESGEVDKGE 358

Query: 363 TVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAI 400
            VVCI TGHLLKDP T ID C EP  +DA++  + + I
Sbjct: 359 QVVCIVTGHLLKDPNTAIDACVEPLEIDADVKTLSKII 396


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: 573
Number of extensions: 28
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: 399
Length adjustment: 31
Effective length of query: 374
Effective length of database: 368
Effective search space:   137632
Effective search space used:   137632
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_013644215.1 METBO_RS03125 (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.1295874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-118  380.5   0.0   4.2e-118  380.3   0.0    1.0  1  NCBI__GCF_000191585.1:WP_013644215.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000191585.1:WP_013644215.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.3   0.0  4.2e-118  4.2e-118       1     340 []      48     373 ..      48     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 380.3 bits;  conditional E-value: 4.2e-118
                             TIGR00260   1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 
                                           +++y+e+l+v e+++v+l+eg t++ +++kl +e+g+ +lyvk ++++Pt++FKDrg   ++v++tka elg+
  NCBI__GCF_000191585.1:WP_013644215.1  48 MWKYKEFLPVDETKIVSLEEGGTPFCKCDKLGSELGI-DLYVKVEGSNPTGSFKDRG---MSVGMTKAVELGV 116
                                           69***********************************.*******************...************* PP

                             TIGR00260  74 etvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifed 146
                                           +tv+cA++G+t+a++a a+a++a+ +++vL+P+gk++   +kl++a++++a+v++i+G+FD+a+++v++++ +
  NCBI__GCF_000191585.1:WP_013644215.1 117 NTVGCASTGNTSASLA-AYAARAGKRCIVLLPAGKVA--LGKLAQAMFHGAEVISIRGNFDEALETVTSLALE 186
                                           ****************.********************..********************************** PP

                             TIGR00260 147 keklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg....lpiekl 214
                                            + ++lnsvN   p+r+e+qkt+ feiv++lg++spd++v+pv+ +gn++ai+kG++e++e+g    lp +++
  NCBI__GCF_000191585.1:WP_013644215.1 187 GQLYLLNSVN---PYRLEGQKTIGFEIVDDLGWKSPDRIVLPVGnAGNISAIWKGIKEFHEAGfmddLP-MMT 255
                                           **********...********************************************************.*** PP

                             TIGR00260 215 aiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeileaik 286
                                           +i+ae +a+i +++++++  +ep +d+eT++tA++ig p+++++al+++++s+g+++ +    +d+eil+a+k
  NCBI__GCF_000191585.1:WP_013644215.1 256 GIQAEMSAPITNAVRQGKnTIEPVKDPETIATAIRIGAPVSAQKALRAIYESNGYADTV----TDDEILSAQK 324
                                           ******************999**************************************....********** PP

                             TIGR00260 287 klaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340
                                           +la++eg+ +ep++a+++a+l+k+ve+g   ++d++  e+vv+++tg+ lkdp+
  NCBI__GCF_000191585.1:WP_013644215.1 325 LLARKEGIGVEPASAASIAGLLKMVESG---EVDKG--EQVVCIVTGHLLKDPN 373
                                           ****************************...***99..*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (399 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.05
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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