Alignments for a candidate for thrC in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Stenotrophomonas chelatiphaga DSM 21508

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_057506743.1 ABB28_RS00505 threonine synthase

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



>NCBI__GCF_001431535.1:WP_057506743.1
          Length = 437

 Score =  508 bits (1308), Expect = e-148
 Identities = 277/433 (63%), Positives = 316/433 (72%), Gaps = 10/433 (2%)

Query: 9   STRGAAHGAGIGEAIAAGLAPDGGLYVPEALPSRRPDDFDPDGTLADTAARLLRPFFAGH 68
           STRG +    +  AIAAGLAPDGGLYVPE LP+ R     P  +LA TAA++L PFF G 
Sbjct: 5   STRGQSPAVSLSAAIAAGLAPDGGLYVPEQLPAPRQWVATP--SLAQTAAQVLAPFFDGD 62

Query: 69  ALAAELPAICAEAFCFDAPLRPLPQHPGAAMLELFHGPSAAFKDFGARFLASCFRRLRKA 128
            LA  LPAICAEAF F  PLR LP+  G  +LELFHGP+AAFKD GARFLA+   RLR  
Sbjct: 63  PLADALPAICAEAFDFPVPLRALPRR-GDHVLELFHGPTAAFKDVGARFLAATLARLRSG 121

Query: 129 GEAPLTILVATSGDTGAAVAAAFHRQPGVEVVILYPDGLVSPRQAHQLGCFGDNVRALRV 188
              PL I+VATSGDTGAAVAAAFHRQPG+ VV+LYPDG VSPRQAHQLGCFGDN++A RV
Sbjct: 122 ASTPLAIVVATSGDTGAAVAAAFHRQPGLRVVVLYPDGRVSPRQAHQLGCFGDNIQAFRV 181

Query: 189 AGRFDDCQRMVKAALNDTALQAQRPLSSANSISLGRLLPQMAYYAHASLRWWREHRRPLN 248
           AG FDDCQ +VK AL D ALQA  PLSSANSISLGRLLPQM+YYAHA+L+  +  R  LN
Sbjct: 182 AGSFDDCQALVKQALGDAALQAAVPLSSANSISLGRLLPQMSYYAHAALQHEQGGRAALN 241

Query: 249 FIVPTGNLGNALAAVWVREMGLPVGAIELACNANETLPDYFAGTPYAPRAAVATLANAMD 308
            +VPTGNLGNA+AA+  R +GLP+G I LA NAN+ LP YFAG  Y P  +VAT ANAMD
Sbjct: 242 LVVPTGNLGNAMAAILARAIGLPIGRIALATNANDVLPRYFAGADYQPAHSVATTANAMD 301

Query: 309 VGAPSNFERLRWTFPYDD-DLRGQLSSHSVDDDTIRATVRRHALEHGEVFCPHTATA--- 364
           VGAPSNFERLRW F  DD  LR   ++ +VDD  IRAT+       G+VFCPHTATA   
Sbjct: 302 VGAPSNFERLRWLFNGDDAALRQAFTAEAVDDVAIRATIASAHAGSGDVFCPHTATAVTV 361

Query: 365 MHRLDLRQEKADWAVVSTAHAAKFESVVEPLIGRGVAVPPALQAMLARPAQAEAIEASDD 424
           ++ L  +  K DWAVV+TAH AKFESVVEPLIG  VAVP AL A+L RPA AE + A   
Sbjct: 362 LNALRAKGSKGDWAVVATAHPAKFESVVEPLIGETVAVPLALDALLRRPAHAEPLAADYA 421

Query: 425 ALKQWL---LPQP 434
           AL+  L   LP P
Sbjct: 422 ALRAVLQAGLPSP 434


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: 717
Number of extensions: 34
Number of successful extensions: 5
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: 437
Length adjustment: 32
Effective length of query: 409
Effective length of database: 405
Effective search space:   165645
Effective search space used:   165645
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_057506743.1 ABB28_RS00505 (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.18976.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.3e-76  242.2   0.0    5.4e-76  241.9   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506743.1  ABB28_RS00505 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506743.1  ABB28_RS00505 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.9   0.0   5.4e-76   5.4e-76      24     335 ..      74     396 ..      62     400 .. 0.87

  Alignments for each domain:
  == domain 1  score: 241.9 bits;  conditional E-value: 5.4e-76
                                 TIGR00260  24 elfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaae 90 
                                               e+f++p + + +  +  +v+elfhgPt aFKD+g +f+a  l++++    +  ++++AtsGdtgaa+a 
  lcl|NCBI__GCF_001431535.1:WP_057506743.1  74 EAFDFPVPLRALPRRGDHVLELFHGPTAAFKDVGARFLAATLARLRSGASTplAIVVATSGDTGAAVAA 142
                                               67778888888888788*****************************9999899**************** PP

                                 TIGR00260  91 alagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvN 156
                                               a+ ++++++vvvLyP+g++sp +   +     n++ + + G FDd+q+lvk++++d     ++ l+s+N
  lcl|NCBI__GCF_001431535.1:WP_057506743.1 143 AFHRQPGLRVVVLYPDGRVSPRQAHQLGCFGDNIQAFRVAGSFDDCQALVKQALGDAAlqaAVPLSSAN 211
                                               **********************5555566899**********************966556699****** PP

                                 TIGR00260 157 sinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadi 224
                                               si  +r++ q+ +ya+ +++  ++  +  + ++vp gn+g++++++l+    glpi  +a a++ + d+
  lcl|NCBI__GCF_001431535.1:WP_057506743.1 212 SISLGRLLPQMsYYAHAALQ-HEQGGRAALNLVVPTGNLGNAMAAILARA-IGLPIGRIALATNAN-DV 277
                                               ***********666666665.555899******************66655.55******9999998.** PP

                                 TIGR00260 225 vrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnled.lke.svsdeeileaikklaee 291
                                               ++r+  + d +p ++++T ++Amd+g psn+er+ +l++  ++ l +   + +v d +i  +i  + + 
  lcl|NCBI__GCF_001431535.1:WP_057506743.1 278 LPRYFAGADYQPAHSVATTANAMDVGAPSNFERLRWLFNGDDAALRQaFTAeAVDDVAIRATIASAHAG 346
                                               ******99****************************999887776541444255566677777788788 PP

                                 TIGR00260 292 egyllephtavavaalkklvekg.vs.....atadpaKFeevvealtgnk 335
                                                g +  phta+av +l+ l +kg ++     ata+paKFe vve l g++
  lcl|NCBI__GCF_001431535.1:WP_057506743.1 347 SGDVFCPHTATAVTVLNALRAKGsKGdwavvATAHPAKFESVVEPLIGET 396
                                               999999*****************73355667*************888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (437 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: 12.23
//
[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