Alignments for a candidate for thrC in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Steroidobacter denitrificans DSM 18526

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_066920364.1 ACG33_RS08520 threonine synthase

Query= reanno::Dyella79:N515DRAFT_0575
         (441 letters)



>NCBI__GCF_001579945.1:WP_066920364.1
          Length = 433

 Score =  432 bits (1112), Expect = e-126
 Identities = 231/425 (54%), Positives = 283/425 (66%), Gaps = 4/425 (0%)

Query: 7   YHSTRGAAHGAGIGEAIAAGLAPDGGLYVPEALPSRRPDDFDPDGTLADTAARLLRPFFA 66
           Y STR       + EAIA G+APDGGLYVPE  P     +F+ +  +A     LL PF  
Sbjct: 3   YISTRDETQKLTLSEAIARGIAPDGGLYVPERFPRFLNSNFEGESEIAGIGPLLLAPFAE 62

Query: 67  GHALAAELPAICAEAFCFDAPLRPLPQHPG-AAMLELFHGPSAAFKDFGARFLASCFRRL 125
             +LA EL  IC EAF F  PL PL   P  A++LELFHGP+ AFKD GARFLA+C +R+
Sbjct: 63  DDSLADELSVICREAFDFPVPLLPLEGAPAPASVLELFHGPTCAFKDIGARFLAACLQRI 122

Query: 126 RKAGEAPLTILVATSGDTGAAVAAAFHRQPGVEVVILYPDGLVSPRQAHQLGCFGDNVRA 185
           RK     LTILVATSGDTG AVAAAFH +P V+VV+LYP GLVS RQA QL C+G NVR 
Sbjct: 123 RKEAPRKLTILVATSGDTGGAVAAAFHDRPWVDVVVLYPKGLVSERQAQQLACWGGNVRT 182

Query: 186 LRVAGRFDDCQRMVKAALNDTALQAQRPLSSANSISLGRLLPQMAYYAHASLRWWREHRR 245
             V G FDDCQRMVK A  D +L     LSSANSI++GRLLPQM YYA A L  WR+  +
Sbjct: 183 FAVHGTFDDCQRMVKEAFQDPSLAQTHQLSSANSINIGRLLPQMTYYAKAGLEVWRQTGQ 242

Query: 246 PLNFIVPTGNLGNALAAVWVREMGLPVGAIELACNANETLPDYFAGTPYAPRAAVATLAN 305
             NFI+PTGNLGNALA +W R +GLP+G I LA NAN+T+ +Y     + PRA+V TLA+
Sbjct: 243 RANFIIPTGNLGNALACLWARHVGLPIGEIVLATNANQTITEYLHSGEWQPRASVPTLAS 302

Query: 306 AMDVGAPSNFERLRWTFPYDDDLRGQLSSHSVDDDTIRATVRRHALEHGEVFCPHTATA- 364
           AMDVG PSN ERLR      + L+GQ+S+ SVDD  IR+T+RR A E  +++CPH+ATA 
Sbjct: 303 AMDVGNPSNMERLRHLHADFETLQGQVSAFSVDDTEIRSTIRRDAHELNQLWCPHSATAA 362

Query: 365 --MHRLDLRQEKADWAVVSTAHAAKFESVVEPLIGRGVAVPPALQAMLARPAQAEAIEAS 422
               RL  R  +  W +V+TAH AKF  +VEP  GR V VP +L  +LA P Q   ++ +
Sbjct: 363 EVFRRLISRGARGHWVIVATAHPAKFNDIVEPHAGREVPVPSSLARLLALPRQEMELQPT 422

Query: 423 DDALK 427
             AL+
Sbjct: 423 LQALR 427


Lambda     K      H
   0.322    0.136    0.420 

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: 574
Number of extensions: 25
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: 441
Length of database: 433
Length adjustment: 32
Effective length of query: 409
Effective length of database: 401
Effective search space:   164009
Effective search space used:   164009
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_066920364.1 ACG33_RS08520 (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.11659.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-75  240.7   0.0    1.6e-75  240.4   0.0    1.1  1  lcl|NCBI__GCF_001579945.1:WP_066920364.1  ACG33_RS08520 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066920364.1  ACG33_RS08520 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.4   0.0   1.6e-75   1.6e-75      38     330 ..      92     394 ..      62     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: 240.4 bits;  conditional E-value: 1.6e-75
                                 TIGR00260  38 enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                                   v+elfhgPt aFKD+g +f+a  l++++++     t+l+AtsGdtg a+a a+  ++ v+vvvLy
  lcl|NCBI__GCF_001579945.1:WP_066920364.1  92 APASVLELFHGPTCAFKDIGARFLAACLQRIRKEAPRklTILVATSGDTGGAVAAAFHDRPWVDVVVLY 160
                                               55569***************************9998889****************************** PP

                                 TIGR00260 105 PkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife...dkeklklnsvNsinparieaqktya 170
                                               Pkg +s  + + +    +n++++a++G+FDd+q++vke+f+     + ++l+s+Nsin++r++ q+ty+
  lcl|NCBI__GCF_001579945.1:WP_066920364.1 161 PKGLVSERQAQQLACWGGNVRTFAVHGTFDDCQRMVKEAFQdpsLAQTHQLSSANSINIGRLLPQMTYY 229
                                               ******775555566799**********************9544455*******************888 PP

                                 TIGR00260 171 feiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepked 239
                                                 +  ++ +++ ++  + +p gn+g++l+  l ++++glpi  +  a++ +  +++++l+sg+++p+++
  lcl|NCBI__GCF_001579945.1:WP_066920364.1 230 AKAGLEVWRQTGQRANFIIPTGNLGNALAC-LWARHVGLPIGEIVLATNAN-QTITEYLHSGEWQPRAS 296
                                               888777777999******************.7777778**99998888887.9**************** PP

                                 TIGR00260 240 keTlstAmdignpsnverale...larrslgnledlkesvsdeeileaikklaeeegyllephtavava 305
                                               + Tl+ Amd+gnpsn+er+ +    ++  +g++ +   sv d ei ++i++ a+e + l  ph+a+a +
  lcl|NCBI__GCF_001579945.1:WP_066920364.1 297 VPTLASAMDVGNPSNMERLRHlhaDFETLQGQVSAF--SVDDTEIRSTIRRDAHELNQLWCPHSATAAE 363
                                               *******************99654566777777777..9****************************** PP

                                 TIGR00260 306 alkklvekg.vs.....atadpaKFeevvea 330
                                               + ++l+  g  +     ata+paKF+++ve 
  lcl|NCBI__GCF_001579945.1:WP_066920364.1 364 VFRRLISRGaRGhwvivATAHPAKFNDIVEP 394
                                               *********83345678************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (433 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.25
//
[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