Alignments for a candidate for thrC in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pseudarthrobacter sulfonivorans Ar51

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_056349448.1 AU252_RS18655 threonine synthase

Query= BRENDA::P9WG59
         (360 letters)



>NCBI__GCF_001484605.1:WP_056349448.1
          Length = 368

 Score =  415 bits (1067), Expect = e-121
 Identities = 220/365 (60%), Positives = 267/365 (73%), Gaps = 16/365 (4%)

Query: 9   HQPWPGVIAAYRDRLPVGDDWTPVTLLEGGTPLIAATNLSKQTGCTIHLKVEGLNPTGSF 68
           HQ W GVI  Y DRLPV +    +TL EGGTPL+ A  LS+ TG T++LKVEG+NPTGSF
Sbjct: 3   HQ-WRGVIREYADRLPVTESTRVITLGEGGTPLVHAQKLSELTGSTVYLKVEGMNPTGSF 61

Query: 69  KDRGMTMAVTDALAHGQRAVLCASTGNTSASAAAYAARAGITCAVLIPQGKIAMGKLAQA 128
           KDRGMTMA+T A+A G +AV+CASTGNTSASAAAYA  AG+ CAVL+P+GKI+MGKL+QA
Sbjct: 62  KDRGMTMAMTAAVASGAKAVVCASTGNTSASAAAYATAAGLKCAVLVPEGKISMGKLSQA 121

Query: 129 VMHGAKIIQIDGNFDDCLELARKMAADFPTISLVNSVNPVRIEGQKTAAFEIVDVLGTAP 188
           + HGA ++Q+DGNFD+CL++ARK+   +P + LVNSVNP RI+GQKT AFEIVD LG AP
Sbjct: 122 IAHGATLLQVDGNFDNCLDIARKLGESYP-VFLVNSVNPARIQGQKTGAFEIVDSLGDAP 180

Query: 189 DVHALPVGNAGNITAYWKGYTEYHQ----------LGLIDKLPRMLGTQAAGAAPLVLGE 238
           D+H LPVGNAGNITAYWKGY EY              +  K P+M G QAAGAAP V G 
Sbjct: 181 DIHVLPVGNAGNITAYWKGYKEYSAPFESETAGTLPAVSTKTPQMWGFQAAGAAPFVAGH 240

Query: 239 PVSHPETIATAIRIGSPASWTSAVEAQQQSKGRFLAASDEEILAAYHLVARVEGVFVEPA 298
           P++ P+TIATAIRIG+PASW  A+ A+ +S G   A +DE+IL A+  ++  EGVFVEP 
Sbjct: 241 PITEPDTIATAIRIGNPASWDGAIAARDESGGFIDAVTDEQILDAHRWLSAREGVFVEPG 300

Query: 299 SAASIAGLLKAIDDGWVARGSTVVCTVTGNGLKDPDTALK--DMPSVSPVPV--DPVAVV 354
           SAA +AGLLK    G V  G T+V TVTG+GLKDP  AL+  D   V PV V  D V V 
Sbjct: 301 SAAGVAGLLKKHAAGEVPTGKTIVITVTGHGLKDPQWALRTEDGSEVQPVKVSNDVVTVA 360

Query: 355 EKLGL 359
            +LGL
Sbjct: 361 AELGL 365


Lambda     K      H
   0.317    0.132    0.392 

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: 12
Number of successful extensions: 3
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: 360
Length of database: 368
Length adjustment: 29
Effective length of query: 331
Effective length of database: 339
Effective search space:   112209
Effective search space used:   112209
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_056349448.1 AU252_RS18655 (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.6505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.5e-91  290.6   0.0    1.1e-90  290.2   0.0    1.1  1  lcl|NCBI__GCF_001484605.1:WP_056349448.1  AU252_RS18655 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_056349448.1  AU252_RS18655 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.2   0.0   1.1e-90   1.1e-90       3     339 ..      11     335 ..       9     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 290.2 bits;  conditional E-value: 1.1e-90
                                 TIGR00260   3 ryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkale 70 
                                                y+  l+vt  +++++l eg t+l++++kl+e  g+  +y+k ++++Pt++FKDrg   +++++t+a  
  lcl|NCBI__GCF_001484605.1:WP_056349448.1  11 EYADRLPVTeSTRVITLGEGGTPLVHAQKLSELTGS-TVYLKVEGMNPTGSFKDRG---MTMAMTAAVA 75 
                                               678899***999*****************9987777.*******************...********** PP

                                 TIGR00260  71 lgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdl 139
                                                g+++v+cA++G+t+a+aa a+a  a++k+ vL+P+gkis   +kl +a+a++a++l+++G+FD+++d+
  lcl|NCBI__GCF_001484605.1:WP_056349448.1  76 SGAKAVVCASTGNTSASAA-AYATAAGLKCAVLVPEGKIS--MGKLSQAIAHGATLLQVDGNFDNCLDI 141
                                               *******************.********************..*************************** PP

                                 TIGR00260 140 vkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkel 207
                                                +++ e  +  ++nsvN   pari++qkt afeiv+ lg ++pd  v+pv+ +gn++a++kG++e+   
  lcl|NCBI__GCF_001484605.1:WP_056349448.1 142 ARKLGESYPVFLVNSVN---PARIQGQKTGAFEIVDSLG-DAPDIHVLPVGnAGNITAYWKGYKEYSAP 206
                                               *****999999999999...*******************.9**********************998654 PP

                                 TIGR00260 208 g..............lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralela 262
                                                               p ++ +++a gaa++v          p+++++T++tA++ignp++++ a ++ 
  lcl|NCBI__GCF_001484605.1:WP_056349448.1 207 FesetagtlpavstkTP-QMWGFQAAGAAPFVAGH-------PITEPDTIATAIRIGNPASWDGAIAAR 267
                                               4455566******9999.**********9999988.......*************************** PP

                                 TIGR00260 263 rrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevveal 331
                                                +s+g ++++    +de+il+a + l ++eg+++ep +a++va+l+k +++g   +++ +  +++v  +
  lcl|NCBI__GCF_001484605.1:WP_056349448.1 268 DESGGFIDAV----TDEQILDAHRWLSAREGVFVEPGSAAGVAGLLKKHAAG---EVPTG--KTIVITV 327
                                               **********....**************************************...*****..******* PP

                                 TIGR00260 332 tgnklkdp 339
                                               tg++lkdp
  lcl|NCBI__GCF_001484605.1:WP_056349448.1 328 TGHGLKDP 335
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (368 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: 10.04
//
[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