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; TS; EC 4.2.3.1 (characterized)
to candidate BPHYT_RS08960 BPHYT_RS08960 threonine synthase

Query= SwissProt::P23669
         (481 letters)



>FitnessBrowser__BFirm:BPHYT_RS08960
          Length = 483

 Score =  521 bits (1342), Expect = e-152
 Identities = 276/484 (57%), Positives = 342/484 (70%), Gaps = 18/484 (3%)

Query: 1   MDYISTRDASRTPAR-FSDILLGGLAPDGGLYLPATYPQLDDAQLSKWREVLANEGYAAL 59
           M+Y+STR A       FSDILLGGLA DGGLYLPA YP++   +L++WR +     YA L
Sbjct: 1   MNYLSTRGAGAGERHTFSDILLGGLAKDGGLYLPAEYPRVTADELTRWRTL----PYADL 56

Query: 60  AAEVISLFVDDIPVEDIKAITARAYTYPKF----NSEDIVPVTELED-------NIYLGH 108
           A E++S F DDIP +D++A+T + YT   +    + E    +T L+         + L  
Sbjct: 57  AFEILSKFSDDIPADDLRALTRKTYTAATYCNVRDDESAAQITPLKTLGVENGAPLSLLE 116

Query: 109 LSEGPTAAFKDMAMQLLGELFEYELRRRNETINILGATSGDTGSSAEYAMRGREGIRVFM 168
           LS GPT AFKDMAMQL+G LFEY L R  ET+NILGATSGDTGS+AEYAMRG+ GI VFM
Sbjct: 117 LSNGPTLAFKDMAMQLIGNLFEYALARHGETLNILGATSGDTGSAAEYAMRGKHGISVFM 176

Query: 169 LTPAGRMTPFQQAQMFGLDDPNIFNIALDGVFDDCQDVVKAVSADAEFKKDNRIGAVNSI 228
           L+P  +M+ FQ AQM+ L DPNIFNIA++GVFDD QD+VKAVS D  FK   +IG VNSI
Sbjct: 177 LSPHKKMSAFQTAQMYSLQDPNIFNIAVEGVFDDAQDIVKAVSNDHAFKAKYKIGTVNSI 236

Query: 229 NWARLMAQVVYYVSSWIRTTTSNDQKVSFSVPTGNFGDICAGHIARQMGLPIDRLIVATN 288
           NWAR++AQVVYY   +   T SND++VSF+VP+GNFG++CAGHIAR MGLPI++L+VATN
Sbjct: 237 NWARVVAQVVYYFKGYFAATKSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATN 296

Query: 289 ENDVLDEFFRTGDYRVRSSADTHETSSPSMDISRASNFERFIFDLLGRDATRVNDLFGTQ 348
           ENDVLDEFFRTG YRVR +A+T+ TSSPSMDIS+ASNFERF+FDLLGRD  RV  LF   
Sbjct: 297 ENDVLDEFFRTGIYRVRKAAETYHTSSPSMDISKASNFERFVFDLLGRDPARVLQLFRDV 356

Query: 349 VRQGGFSLADDANFEKAAAEYGFASGRSTHADRVATIADVHSRLDVLIDPHTADGVHVAR 408
             +GGF LA   +F +   E+GF SG STH  RV TI DV  R D +ID HTADG+ VAR
Sbjct: 357 EEKGGFDLAASGDFAR-VKEFGFVSGSSTHDSRVDTIRDVFERYDTMIDTHTADGLKVAR 415

Query: 409 QWRDEVNTPIIVLETALPVKFADTIVEAIGEAPQTPERFAAIMDAPFKVSDLPNDTDAVK 468
           +   +   P+IVLETA P+KF +TI EA+   P+ P  F+ +   P +   LP D   VK
Sbjct: 416 E-HLQPGIPMIVLETAQPIKFGETIREALLREPERPAAFSGLEALPQRFEVLPADVQRVK 474

Query: 469 QYIV 472
            +IV
Sbjct: 475 DFIV 478


Lambda     K      H
   0.319    0.135    0.390 

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: 646
Number of extensions: 16
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: 481
Length of database: 483
Length adjustment: 34
Effective length of query: 447
Effective length of database: 449
Effective search space:   200703
Effective search space used:   200703
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.25877.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.55
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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