Alignments for a candidate for thrC in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Acidithiobacillus ferrooxidans ATCC 23270

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012536159.1 AFE_RS02240 threonine synthase

Query= BRENDA::P9WG59
         (360 letters)



>NCBI__GCF_000021485.1:WP_012536159.1
          Length = 376

 Score =  355 bits (910), Expect = e-102
 Identities = 197/367 (53%), Positives = 244/367 (66%), Gaps = 26/367 (7%)

Query: 12  WPGVIAAYRDRLPVGDDWTPVTLLEGGTPLIAATNLSKQTGCTIHL--KVEGLNPTGSFK 69
           + G+I  YR  LP+  +   V+L EG TPLI   NL +Q G  + L  K EGLNPTGSFK
Sbjct: 4   YTGIIDHYRAFLPLAPETPAVSLGEGNTPLIECINLPRQLGLDLRLFLKFEGLNPTGSFK 63

Query: 70  DRGMTMAVTDALAHGQRAVLCASTGNTSASAAAYAARAGITCAVLIPQGKIAMGKLAQAV 129
           DRGM MAVT A   G   V+CASTGNTSA+AAAYAARAG+   V+IP+GKIA+GKL+QA+
Sbjct: 64  DRGMAMAVTKAKEDGSEMVICASTGNTSAAAAAYAARAGMRAFVVIPEGKIALGKLSQAM 123

Query: 130 MHGAKIIQIDGNFDDCLELARKMAADFPTISLVNSVNPVRIEGQKTAAFEIVDVLGTAPD 189
           MHGA ++QI GNFD  +++ +++AA+ P I+LVNSVNP R++GQKTAAFEI++ LG APD
Sbjct: 124 MHGAMVLQIRGNFDAGMQIVQEVAANAP-ITLVNSVNPYRLQGQKTAAFEIIEALGEAPD 182

Query: 190 VHALPVGNAGNITAYWKGYTE-----------------------YHQLGLIDKLPRMLGT 226
            HALPVGNAGNITA+W GY E                        +  G   K P+MLG 
Sbjct: 183 YHALPVGNAGNITAHWMGYCEATDGRTDKSQPLTASCKFCNGTCSYGHGKAGKRPKMLGF 242

Query: 227 QAAGAAPLVLGEPVSHPETIATAIRIGSPASWTSAVEAQQQSKGRFLAASDEEILAAYHL 286
           QAAG+AP ++G  V  PETIATAIRIG P SW  A   Q +S G F + SD EIL A   
Sbjct: 243 QAAGSAPFIVGHYVKDPETIATAIRIGHPMSWDQAHRVQAESGGWFGSHSDAEILEAQRW 302

Query: 287 VARVEGVFVEPASAASIAGLLKAIDDGWVARGSTVVCTVTGNGLKDPDTALKDMPSVSPV 346
           +A+ EGVF EPASA S+AG++     G +  G+TVVCT+TG+GLKDPDTA+     V  V
Sbjct: 303 LAQYEGVFCEPASATSVAGVVAEARAGKIEAGATVVCTLTGHGLKDPDTAIAQGGEVLTV 362

Query: 347 PVDPVAV 353
                AV
Sbjct: 363 DASLEAV 369


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: 377
Number of extensions: 15
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: 360
Length of database: 376
Length adjustment: 30
Effective length of query: 330
Effective length of database: 346
Effective search space:   114180
Effective search space used:   114180
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_012536159.1 AFE_RS02240 (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.8256.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-92  296.8   0.0    7.1e-92  294.1   0.0    1.9  1  lcl|NCBI__GCF_000021485.1:WP_012536159.1  AFE_RS02240 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021485.1:WP_012536159.1  AFE_RS02240 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.1   0.0   7.1e-92   7.1e-92       2     340 .]       9     350 ..       8     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.1 bits;  conditional E-value: 7.1e-92
                                 TIGR00260   2 vryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltka 68 
                                                 yr++l+   e+++v+l eg+t+l+++ +l++++g+  +l++k ++++Pt++FKDrg   +a+++tka
  lcl|NCBI__GCF_000021485.1:WP_012536159.1   9 DHYRAFLPLApETPAVSLGEGNTPLIECINLPRQLGLdLRLFLKFEGLNPTGSFKDRG---MAMAVTKA 74 
                                               579******99**************************99*******************...******** PP

                                 TIGR00260  69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137
                                               +e+g e+v+cA++G+t+aaaa a+a++a+++++v++P+gki+   +kl +a++++a vl+i+G+FD+  
  lcl|NCBI__GCF_000021485.1:WP_012536159.1  75 KEDGSEMVICASTGNTSAAAA-AYAARAGMRAFVVIPEGKIA--LGKLSQAMMHGAMVLQIRGNFDAGM 140
                                               *********************.********************..************************* PP

                                 TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205
                                               ++v+e++ + +++++nsvN   p+r+++qkt+afei+e+lg e+pd  ++pv+ +gn++a ++G++e+ 
  lcl|NCBI__GCF_000021485.1:WP_012536159.1 141 QIVQEVAANAPITLVNSVN---PYRLQGQKTAAFEIIEALG-EAPDYHALPVGnAGNITAHWMGYCEAT 205
                                               ************9999999...*******************.**************************9 PP

                                 TIGR00260 206 elg...........................lpieklaiaaegaadivrrflksgdlepkedkeTlstAm 247
                                                +                            +p ++l+++a g+a+++            +d+eT++tA+
  lcl|NCBI__GCF_000021485.1:WP_012536159.1 206 DGRtdksqpltasckfcngtcsyghgkagkRP-KMLGFQAAGSAPFIVGH-------YVKDPETIATAI 266
                                               99899************************999.**********9987766.......6789******** PP

                                 TIGR00260 248 dignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvs 316
                                               +ig+p ++++a ++  +s+g + +     sd+eilea++ la+ eg+++ep++a++va++   + +g  
  lcl|NCBI__GCF_000021485.1:WP_012536159.1 267 RIGHPMSWDQAHRVQAESGGWFGSH----SDAEILEAQRWLAQYEGVFCEPASATSVAGVVAEARAG-- 329
                                               ************************9....************************************99.. PP

                                 TIGR00260 317 atadpaKFeevvealtgnklkdpe 340
                                                +++ +  ++vv+ ltg++lkdp+
  lcl|NCBI__GCF_000021485.1:WP_012536159.1 330 -KIEAG--ATVVCTLTGHGLKDPD 350
                                               .*****..**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (376 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 3.15
//
[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