Alignments for a candidate for thrC in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pyrolobus fumarii 1A

Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_048192698.1 PYRFU_RS07835 threonine synthase

Query= CharProtDB::CH_107419
         (405 letters)



>NCBI__GCF_000223395.1:WP_048192698.1
          Length = 413

 Score =  358 bits (918), Expect = e-103
 Identities = 187/386 (48%), Positives = 259/386 (67%), Gaps = 15/386 (3%)

Query: 4   LKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLPVER 63
           L+C+ CG  Y  D  ++ C KC  LL+V+     +     + +     VW+Y  LLPV  
Sbjct: 8   LRCVNCGEIYEPDPFLFKCRKCGSLLEVLVPVEGVSWSSFRGR----GVWRYRPLLPVSD 63

Query: 64  E--PVTIQEGGTPLYKCDR----LAEKIGIK-KLYVKHEGMNPTGSFKDRGMTVGVTKAL 116
           +  PVT+ EGGTPL +C+     L ++ G+  ++YVK EG NPTGSFKDRGMTV  + A 
Sbjct: 64  DVKPVTMGEGGTPLIRCENIEAWLRDRYGVAPRVYVKFEGANPTGSFKDRGMTVIASIAR 123

Query: 117 ELGMNTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGN 176
            L +  VA ASTGNT+++ A Y A+AG+ +V++LP GKVA GK+ Q++++GA ++ + G+
Sbjct: 124 SLRVKLVAAASTGNTASSAAAYTARAGLKMVLVLPKGKVAKGKLGQSILYGATIIEVDGS 183

Query: 177 FDDALALVRTLCSQEK--IYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAG 234
           FDDA+  V+      K  IY  NS NP+RLEGQKTI FEIA+++   VPD +++PVGN G
Sbjct: 184 FDDAMKAVQDAVEASKGGIYPFNSFNPWRLEGQKTIAFEIAEEIG--VPDFVIVPVGNGG 241

Query: 235 NITAIYKGFREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIR 294
           NI+AI+KGF E    G+ D LP+M G+QAEG+ P+  A + G       + PETVATAIR
Sbjct: 242 NISAIWKGFNELHKAGLIDKLPRMVGVQAEGAAPLATAFEKGLDKPLFVDKPETVATAIR 301

Query: 295 IGNPVNATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVD 354
           IG PVN  KAL A++ESGG    V+D+EIL+A + LA +EG+G EPA A+S+AGL KLV+
Sbjct: 302 IGRPVNWMKALRAVKESGGLFTKVSDDEILSAMRMLASMEGVGAEPAGASSLAGLLKLVE 361

Query: 355 MGVIGRDETVVCITTGHLLKDPQTVI 380
            G IG ++TVV + TGH LKDP  ++
Sbjct: 362 DGTIGNNDTVVLVATGHALKDPDAML 387


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: 496
Number of extensions: 29
Number of successful extensions: 6
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: 413
Length adjustment: 31
Effective length of query: 374
Effective length of database: 382
Effective search space:   142868
Effective search space used:   142868
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_048192698.1 PYRFU_RS07835 (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.13624.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.1e-95  304.7   0.0    4.8e-95  304.5   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_048192698.1  PYRFU_RS07835 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_048192698.1  PYRFU_RS07835 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.5   0.0   4.8e-95   4.8e-95       1     340 []      52     384 ..      52     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 4.8e-95
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.....enlyvkelfhgPtlaFKDrglqfvav 63 
                                               v+ryr +l+v+ + ++v++ eg t+l+r++++++ +        ++yvk ++++Pt++FKDrg   ++v
  lcl|NCBI__GCF_000223395.1:WP_048192698.1  52 VWRYRPLLPVSdDVKPVTMGEGGTPLIRCENIEAWLRDrygvaPRVYVKFEGANPTGSFKDRG---MTV 117
                                               8********************************66655444578*******************...*** PP

                                 TIGR00260  64 lltkalelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGd 132
                                               + + a+ l +++v+ A++G+t+++aa a+ ++a++k v ++Pkgk++  k+kl + + ++a++++++G 
  lcl|NCBI__GCF_000223395.1:WP_048192698.1 118 IASIARSLRVKLVAAASTGNTASSAA-AYTARAGLKMVLVLPKGKVA--KGKLGQSILYGATIIEVDGS 183
                                               **************************.********************..******************** PP

                                 TIGR00260 133 FDdaqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkG 200
                                               FDda ++v++++e + k ++   Ns np r+e+qkt+afei+e++g   pd v+vpv+ +gn++ai+kG
  lcl|NCBI__GCF_000223395.1:WP_048192698.1 184 FDDAMKAVQDAVEAS-KGGIYPFNSFNPWRLEGQKTIAFEIAEEIG--VPDFVIVPVGnGGNISAIWKG 249
                                               ************754.44555555555*******************..********************* PP

                                 TIGR00260 201 flekkelg....lpieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarr 264
                                               f e++++g    lp ++ +++aegaa+ +++f k+  + +   ++eT++tA++ig+p+n+ +al+++++
  lcl|NCBI__GCF_000223395.1:WP_048192698.1 250 FNELHKAGlidkLP-RMVGVQAEGAAPLATAFEKGLdKPLFVDKPETVATAIRIGRPVNWMKALRAVKE 317
                                               **************.*****************8888666677888************************ PP

                                 TIGR00260 265 slgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtg 333
                                               s+g ++++    sd+eil+a++ la  eg+ +ep++a ++a+l+klve+g   t+ ++   +vv++ tg
  lcl|NCBI__GCF_000223395.1:WP_048192698.1 318 SGGLFTKV----SDDEILSAMRMLASMEGVGAEPAGASSLAGLLKLVEDG---TIGNN--DTVVLVATG 377
                                               ********....**************************************...*****..9******** PP

                                 TIGR00260 334 nklkdpe 340
                                               + lkdp+
  lcl|NCBI__GCF_000223395.1:WP_048192698.1 378 HALKDPD 384
                                               *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (413 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: 11.21
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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