Alignments for a candidate for thrC in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Ferroglobus placidus DSM 10642

Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_012965250.1 FERP_RS03675 threonine synthase

Query= CharProtDB::CH_107419
         (405 letters)



>NCBI__GCF_000025505.1:WP_012965250.1
          Length = 388

 Score =  468 bits (1203), Expect = e-136
 Identities = 242/400 (60%), Positives = 306/400 (76%), Gaps = 12/400 (3%)

Query: 1   MYHLKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLP 60
           MY L+CIECG+E+  D  IY CSKC+GLLDV+YDYS IK++ +       SVWKY   LP
Sbjct: 1   MYLLRCIECGSEFDSD-FIYQCSKCNGLLDVVYDYSEIKLNFDGNNL---SVWKYKDALP 56

Query: 61  VEREPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGM 120
           V+ +PV+++EGGTPLYK +++    G+K L+VKHEG+NP+GSFKDRGMTVGVTKA+EL M
Sbjct: 57  VKIKPVSLREGGTPLYKIEKIES--GVKNLFVKHEGLNPSGSFKDRGMTVGVTKAVELKM 114

Query: 121 NTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDA 180
            TV CASTGNTSA++A+Y AKAG+  VV+LP+GKVALGK+AQALMHGAKV++++ NFD A
Sbjct: 115 RTVICASTGNTSASMAMYAAKAGLRAVVILPSGKVALGKLAQALMHGAKVIAVKDNFDKA 174

Query: 181 LALVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITAIY 240
           L +V++L  ++ +YLLNSINP+RLEGQKTI +EI D+L F VPD I +PVGNAGNI+AIY
Sbjct: 175 LEIVKSLAMRKSLYLLNSINPFRLEGQKTIAYEIYDELGF-VPDAIFVPVGNAGNISAIY 233

Query: 241 KGFREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGNPVN 300
           KGF+E   +G TD +P+M G+QA+G+ PI KA   G+  I P +NPET+ATAIRIG PVN
Sbjct: 234 KGFKELVEMGYTDEVPRMIGVQAKGANPIYKAFVKGSREIEPVKNPETIATAIRIGAPVN 293

Query: 301 ATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGVIGR 360
           A KAL AI ES G    V DEEI+ AQK LA  EGIGVEPASAAS+AG  K  +      
Sbjct: 294 AKKALRAIYESKGAVIEVGDEEIVEAQKMLAAKEGIGVEPASAASLAGALKFEE-----E 348

Query: 361 DETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAI 400
            E+ VCI TG+LLKDP  VI VC +P  V+A++D I + +
Sbjct: 349 LESAVCIATGNLLKDPDEVIRVCGKPIEVEADVDVIEKLL 388


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: 551
Number of extensions: 27
Number of successful extensions: 7
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: 388
Length adjustment: 31
Effective length of query: 374
Effective length of database: 357
Effective search space:   133518
Effective search space used:   133518
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_012965250.1 FERP_RS03675 (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.12239.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-104  333.9   0.4   6.6e-104  333.7   0.4    1.0  1  lcl|NCBI__GCF_000025505.1:WP_012965250.1  FERP_RS03675 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025505.1:WP_012965250.1  FERP_RS03675 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.7   0.4  6.6e-104  6.6e-104       1     340 []      48     365 ..      48     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 333.7 bits;  conditional E-value: 6.6e-104
                                 TIGR00260   1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkal 69 
                                               v++y+ +l+v+ +++v+l eg t+l++ +k+++ v+  nl+vk+++++P+++FKDrg   ++v++tka 
  lcl|NCBI__GCF_000025505.1:WP_012965250.1  48 VWKYKDALPVK-IKPVSLREGGTPLYKIEKIESGVK--NLFVKHEGLNPSGSFKDRG---MTVGVTKAV 110
                                               8*********8.*******************99886..5******************...********* PP

                                 TIGR00260  70 elgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqd 138
                                               el++ tv+cA++G+t+a++a ++a+ka++++vv++P+gk++   +kl++al+++akv+a+k +FD+a++
  lcl|NCBI__GCF_000025505.1:WP_012965250.1 111 ELKMRTVICASTGNTSASMA-MYAAKAGLRAVVILPSGKVA--LGKLAQALMHGAKVIAVKDNFDKALE 176
                                               ********************.********************..************************** PP

                                 TIGR00260 139 lvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekke 206
                                               +vk+++ +k  ++lns+N   p+r+e+qkt+a+ei ++lg   pd + vpv+ +gn++ai+kGf+e+ e
  lcl|NCBI__GCF_000025505.1:WP_012965250.1 177 IVKSLAMRKSLYLLNSIN---PFRLEGQKTIAYEIYDELG-FVPDAIFVPVGnAGNISAIYKGFKELVE 241
                                               ****************99...*******************.9*************************** PP

                                 TIGR00260 207 lg....lpieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnle 270
                                               +g    +p ++++++a+ga++i+++f k+  ++ep +++eT++tA++ig p+n+++al+++++s+g + 
  lcl|NCBI__GCF_000025505.1:WP_012965250.1 242 MGytdeVP-RMIGVQAKGANPIYKAFVKGSrEIEPVKNPETIATAIRIGAPVNAKKALRAIYESKGAVI 309
                                               *****99*.*******************988************************************** PP

                                 TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339
                                               ++     deei+ea+k la++eg+ +ep++a+++a+ +k  e+           e +v++ tgn lkdp
  lcl|NCBI__GCF_000025505.1:WP_012965250.1 310 EV----GDEEIVEAQKMLAAKEGIGVEPASAASLAGALKFEEEL----------ESAVCIATGNLLKDP 364
                                               **....*********************************98855..........577999999999988 PP

                                 TIGR00260 340 e 340
                                               +
  lcl|NCBI__GCF_000025505.1:WP_012965250.1 365 D 365
                                               6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (388 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.80
//
[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