Alignments for a candidate for thrC in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Burkholderia vietnamiensis G4

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011885005.1 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>NCBI__GCF_000016205.1:WP_011885005.1
          Length = 483

 Score =  872 bits (2252), Expect = 0.0
 Identities = 438/483 (90%), Positives = 456/483 (94%)

Query: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60
           MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI
Sbjct: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60

Query: 61  LSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSNG 120
           L+KFCDD+ A DLRAITRRTYTA VY + R G NA DITPL  LGTE G  +SLLELSNG
Sbjct: 61  LTKFCDDVPADDLRAITRRTYTAAVYSNTRHGENACDITPLKPLGTEQGTALSLLELSNG 120

Query: 121 PTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSPH 180
           PTLAFKDMAMQLLGNLFEYTLAKHGE LNILGATSGDTGSAAEYAMRGK GVRVFMLSPH
Sbjct: 121 PTLAFKDMAMQLLGNLFEYTLAKHGEALNILGATSGDTGSAAEYAMRGKAGVRVFMLSPH 180

Query: 181 KKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWAR 240
           +KMSAFQTAQM+SLQDPNIFNLAV GVFDDCQDIVKAVSNDHAFKA+ KIGTVNSINWAR
Sbjct: 181 RKMSAFQTAQMFSLQDPNIFNLAVEGVFDDCQDIVKAVSNDHAFKARHKIGTVNSINWAR 240

Query: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300
           VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPI KLVVATNENDV
Sbjct: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIAKLVVATNENDV 300

Query: 301 LDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVEQKG 360
           LDEFFRTG YRVRSAQ+TYHTSSPSMDISKASNFERFVFDLLGRDPARV+QLFRDV++KG
Sbjct: 301 LDEFFRTGVYRVRSAQNTYHTSSPSMDISKASNFERFVFDLLGRDPARVMQLFRDVDEKG 360

Query: 361 GFDLAASGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAREHLRP 420
           GFDLAASGDFARVA+FGFVSGRS+HADRIATIRDVF RY TMIDTHTADG+KVAREHL  
Sbjct: 361 GFDLAASGDFARVAQFGFVSGRSSHADRIATIRDVFARYDTMIDTHTADGVKVAREHLDA 420

Query: 421 GVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKDFIAAH 480
           GVPMVVLETAQPIKFGE+IREAL +E  RPAAFDGLEALPQRF+VV A+AQQVKDFIAAH
Sbjct: 421 GVPMVVLETAQPIKFGETIREALEREAERPAAFDGLEALPQRFDVVKADAQQVKDFIAAH 480

Query: 481 TGA 483
           TGA
Sbjct: 481 TGA 483


Lambda     K      H
   0.320    0.135    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: 852
Number of extensions: 14
Number of successful extensions: 1
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_011885005.1 (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.32583.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.8e-71  225.9   0.0    4.9e-71  225.6   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011885005.1  threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011885005.1  threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.6   0.0   4.9e-71   4.9e-71      38     331 ..     110     443 ..      80     450 .. 0.87

  Alignments for each domain:
  == domain 1  score: 225.6 bits;  conditional E-value: 4.9e-71
                                 TIGR00260  38 enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                                 l ++el+ gPtlaFKD+++q +++l+++ l +  e   +l+AtsGdtg+aa +a++gka+v+v++L 
  lcl|NCBI__GCF_000016205.1:WP_011885005.1 110 TALSLLELSNGPTLAFKDMAMQLLGNLFEYTLAKHGEalNILGATSGDTGSAAEYAMRGKAGVRVFMLS 178
                                               578899***********************98776666578***************************** PP

                                 TIGR00260 105 Pkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqkty 169
                                               P+ k+s     +++   + n+  la++G FDd+qd+vk++ +d+     +k++ vNsin+ar+ aq++y
  lcl|NCBI__GCF_000016205.1:WP_011885005.1 179 PHRKMSAFqTAQMFSLQDPNIFNLAVEGVFDDCQDIVKAVSNDHAfkaRHKIGTVNSINWARVVAQVVY 247
                                               ********99*******************************96666779******************88 PP

                                 TIGR00260 170 afeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksg.dlepk 237
                                               +f    +  + + ++v + vpsgnfg++ +G   ++++glpi+kl +a++++ d++++f ++g + + +
  lcl|NCBI__GCF_000016205.1:WP_011885005.1 248 YFKGYFAATRSNDERVSFTVPSGNFGNVCAG-HIARMMGLPIAKLVVATNEN-DVLDEFFRTGvYRV-R 313
                                               8876666666999******************.6667777************9.**********5333.3 PP

                                 TIGR00260 238 edk...eTlstAmdignpsnverale.larrslgnledlke...........................s 275
                                               + +   +T s++mdi++ sn+er ++ l  r  + + +l                             +
  lcl|NCBI__GCF_000016205.1:WP_011885005.1 314 SAQntyHTSSPSMDISKASNFERFVFdLLGRDPARVMQLFRdvdekggfdlaasgdfarvaqfgfvsgR 382
                                               333247899**************9998766666655555445667***********************9 PP

                                 TIGR00260 276 vsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevve.al 331
                                                s ++ + +i+ + ++   ++++hta +v++ ++ +++g    v  ta+p KF e++  al
  lcl|NCBI__GCF_000016205.1:WP_011885005.1 383 SSHADRIATIRDVFARYDTMIDTHTADGVKVAREHLDAGvpmvVLETAQPIKFGETIReAL 443
                                               ***************************************8753339*******99887455 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (483 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: 13.97
//
[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