Alignments for a candidate for thrC in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Burkholderia phytofirmans PsJN

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate BPHYT_RS08960 BPHYT_RS08960 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>FitnessBrowser__BFirm:BPHYT_RS08960
          Length = 483

 Score =  839 bits (2168), Expect = 0.0
 Identities = 418/483 (86%), Positives = 446/483 (92%)

Query: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60
           MNY+STRGAG GERHTFSDILLGGLAKDGGLYLP+EYP+V+ADEL RWRTLPYADLAFEI
Sbjct: 1   MNYLSTRGAGAGERHTFSDILLGGLAKDGGLYLPAEYPRVTADELTRWRTLPYADLAFEI 60

Query: 61  LSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSNG 120
           LSKF DDI A DLRA+TR+TYTA  Y + R   +AA ITPL TLG ENGAP+SLLELSNG
Sbjct: 61  LSKFSDDIPADDLRALTRKTYTAATYCNVRDDESAAQITPLKTLGVENGAPLSLLELSNG 120

Query: 121 PTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSPH 180
           PTLAFKDMAMQL+GNLFEY LA+HGETLNILGATSGDTGSAAEYAMRGK G+ VFMLSPH
Sbjct: 121 PTLAFKDMAMQLIGNLFEYALARHGETLNILGATSGDTGSAAEYAMRGKHGISVFMLSPH 180

Query: 181 KKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWAR 240
           KKMSAFQTAQMYSLQDPNIFN+AV GVFDD QDIVKAVSNDHAFKA+ KIGTVNSINWAR
Sbjct: 181 KKMSAFQTAQMYSLQDPNIFNIAVEGVFDDAQDIVKAVSNDHAFKAKYKIGTVNSINWAR 240

Query: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300
           VVAQVVYYFKGYFAAT+SNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV
Sbjct: 241 VVAQVVYYFKGYFAATKSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300

Query: 301 LDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVEQKG 360
           LDEFFRTG YRVR A +TYHTSSPSMDISKASNFERFVFDLLGRDPARV+QLFRDVE+KG
Sbjct: 301 LDEFFRTGIYRVRKAAETYHTSSPSMDISKASNFERFVFDLLGRDPARVLQLFRDVEEKG 360

Query: 361 GFDLAASGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAREHLRP 420
           GFDLAASGDFARV EFGFVSG STH  R+ TIRDVFERY TMIDTHTADGLKVAREHL+P
Sbjct: 361 GFDLAASGDFARVKEFGFVSGSSTHDSRVDTIRDVFERYDTMIDTHTADGLKVAREHLQP 420

Query: 421 GVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKDFIAAH 480
           G+PM+VLETAQPIKFGE+IREAL +EP RPAAF GLEALPQRFEV+ A+ Q+VKDFI A+
Sbjct: 421 GIPMIVLETAQPIKFGETIREALLREPERPAAFSGLEALPQRFEVLPADVQRVKDFIVAN 480

Query: 481 TGA 483
            GA
Sbjct: 481 AGA 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: 814
Number of extensions: 15
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 BPHYT_RS08960 BPHYT_RS08960 (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.5709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    7.1e-71  225.1   0.0    9.5e-71  224.6   0.0    1.1  1  lcl|FitnessBrowser__BFirm:BPHYT_RS08960  BPHYT_RS08960 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS08960  BPHYT_RS08960 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.6   0.0   9.5e-71   9.5e-71      38     331 ..     110     443 ..      76     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 224.6 bits;  conditional E-value: 9.5e-71
                                TIGR00260  38 enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLyP 105
                                                l ++el+ gPtlaFKD+++q +++l+++al +  e   +l+AtsGdtg+aa +a++gk++++v++L P
  lcl|FitnessBrowser__BFirm:BPHYT_RS08960 110 APLSLLELSNGPTLAFKDMAMQLIGNLFEYALARHGEtlNILGATSGDTGSAAEYAMRGKHGISVFMLSP 179
                                              458889*************************9998885679***************************** PP

                                TIGR00260 106 kgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqktyaf 171
                                              + k+s     ++    + n+  +a++G FDdaqd+vk++ +d+    k+k++ vNsin+ar+ aq++y+f
  lcl|FitnessBrowser__BFirm:BPHYT_RS08960 180 HKKMSAFqTAQMYSLQDPNIFNIAVEGVFDDAQDIVKAVSNDHAfkaKYKIGTVNSINWARVVAQVVYYF 249
                                              *******99*******************************9666677*******************8888 PP

                                TIGR00260 172 eiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksg.dlepkedk 240
                                                  +  k + ++v + vpsgnfg++ +G   ++++glpiekl +a++++ d++++f ++g + + k+  
  lcl|FitnessBrowser__BFirm:BPHYT_RS08960 250 KGYFAATKSNDERVSFTVPSGNFGNVCAG-HIARMMGLPIEKLVVATNEN-DVLDEFFRTGiYRVRKAAE 317
                                              76666666999******************.6667777************9.**********644433333 PP

                                TIGR00260 241 ..eTlstAmdignpsnverale.....larrslgnledlke.......................svsdee 280
                                                +T s++mdi++ sn+er ++        r l+ + d++e                       s + ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS08960 318 tyHTSSPSMDISKASNFERFVFdllgrDPARVLQLFRDVEEkggfdlaasgdfarvkefgfvsgSSTHDS 387
                                              47899**************9998532223456667777777***********************999*** PP

                                TIGR00260 281 ileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevve.al 331
                                               +++i+ + e+   ++++hta ++++ ++ ++ g    v  ta+p KF e++  al
  lcl|FitnessBrowser__BFirm:BPHYT_RS08960 388 RVDTIRDVFERYDTMIDTHTADGLKVAREHLQPGipmiVLETAQPIKFGETIReAL 443
                                              **********************************8764449*******98876555 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: 8.67
//
[ok]

This GapMind analysis is from Apr 09 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