Alignments for a candidate for thrC in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pseudomonas fluorescens FW300-N2C3

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate AO356_27150 AO356_27150 threonine synthase

Query= curated2:P29363
         (469 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27150
          Length = 467

 Score =  400 bits (1027), Expect = e-116
 Identities = 201/465 (43%), Positives = 292/465 (62%), Gaps = 16/465 (3%)

Query: 1   MRYISTRGQAPALNFEDVLLAGLASDGGLYVPENLPRFTLEEIASWVGLPYHELAFRVMR 60
           M+Y+STR       F +VL+   A DGGLYVP  +PRF  EE++    LP+HELA  V+ 
Sbjct: 1   MKYVSTRTPGRTFEFSEVLMGSYAPDGGLYVPRKVPRFKKEELSKLEWLPFHELARHVIE 60

Query: 61  PFVAGSIADADFKKILEETYGVFAHDAVAPLRQLNGNEWVLELFHGPTLAFKDFALQLLG 120
           PF+ G +      ++LE+T+  F ++AVAPL Q   NEW+LELFHGP+ A++DF LQL+ 
Sbjct: 61  PFLGGWVEQDQLSRMLEDTFDCFTNNAVAPLYQTASNEWLLELFHGPSGAYQDFGLQLMS 120

Query: 121 RLLDHVLAKRGERVVIMGATSGDTGSAAIEGCRRCDNVDIFIMHPHNRVSEVQRRQMTTI 180
           R ++H L K G++ +I+G T GDTG+AAI+       V + ++HP   ++   RR++ ++
Sbjct: 121 RFINHDLLKSGKKALIVGCTGGDTGAAAIKAFSGMTGVTLLVLHPSKELTAEDRRRLLSV 180

Query: 181 LGDNIHNIAIEGNFDDCQEMVKASFADQGFLKGTRLVAVNSINWARIMAQIVYYFHAALQ 240
              N+ NI I G++ DC  + +  F  Q       LV+ NS++W R++A + +YF++ALQ
Sbjct: 181 EEGNVINIEIAGDYSDCHRLCE-QFLKQNNDAQQHLVSFNSVHWVRVLAHLSFYFYSALQ 239

Query: 241 LGAPHRSVAFSVPTGNFGDIFAGYLARNMGLPVSQLIVATNRNDILHRFMSGNRYDKDTL 300
           LGAP R VAFSVPTGNFG ++AGY+A+ MGLP+ QLIVATN N  LH F+  N Y ++ +
Sbjct: 240 LGAPKRQVAFSVPTGNFGALYAGYIAKQMGLPIRQLIVATNANAGLHHFLQSNLYSRNEI 299

Query: 301 HPSLSPSMDIMVSSNFERLLFDLHGRNGKAVAELLDAFKASGKLSVEDQRWTEARKLFDS 360
             + +P+M++ ++SNFERL + +  R G+ VA  +   +  G + +E   W EARKLFDS
Sbjct: 300 RTTKTPTMNVSLASNFERLQWSILNRCGEKVARNMQLLEGEGTIHLEQDEWLEARKLFDS 359

Query: 361 LAVSDEQTCETIAEVYRSSGELLDPHTAIGVRAARECRRSLSVPMVTLGTAHPVKFPEAV 420
           LAV D      I EV+  SG L+ P+TAIG+RAAR  RRSL +PM++L T HP K   A 
Sbjct: 360 LAVDDADAFSCIHEVFAQSGYLVSPNTAIGLRAARVSRRSLLIPMISLATTHPSKIGAAT 419

Query: 421 EKAGI------GQAPALPAHLADLFEREERCTVLPNELAKVQAFV 459
           +K+ I      G APA           E+ CT +PN++  + + V
Sbjct: 420 DKSEIFGHLNTGGAPA---------STEQDCTSIPNDIGALTSLV 455


Lambda     K      H
   0.322    0.137    0.407 

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: 541
Number of extensions: 17
Number of successful extensions: 2
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: 469
Length of database: 467
Length adjustment: 33
Effective length of query: 436
Effective length of database: 434
Effective search space:   189224
Effective search space used:   189224
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 AO356_27150 AO356_27150 (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.14428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    8.8e-56  175.4   0.0    1.1e-55  175.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150  AO356_27150 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150  AO356_27150 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   0.0   1.1e-55   1.1e-55      26     309 ..      83     395 ..      62     426 .. 0.84

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 1.1e-55
                                       TIGR00260  26 frspklaeevga..enlyvkelfhgPtlaFKDrglqfvavlltk..alelgnetvlcAtsGdt 84 
                                                     f+++++ +++ +   n +++elfhgP++a+ D+glq ++  +++  ++  +++++++ t Gdt
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150  83 FTNNAV-APLYQtaSNEWLLELFHGPSGAYQDFGLQLMSRFINHdlLKSGKKALIVGCTGGDT 144
                                                     333333.344333578899***********************975456667779********* PP

                                       TIGR00260  85 gaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife. 145
                                                     gaaa++a++g+ +v  +vL P+ ++      +l+ +  +n+  ++i Gd+ d+ +l+++ ++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150 145 GAAAIKAFSGMTGVTLLVLHPSKELTAEdRRRLLSVEEGNVINIEIAGDYSDCHRLCEQFLKq 207
                                                     ***********************99977899*******************************5 PP

                                       TIGR00260 146 .dkeklklnsvNsinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekke 206
                                                      ++ +  l+s Ns+ + r++a    y+++++ qlg   + +v+++vp gnfga+++G+ +k++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150 208 nNDAQQHLVSFNSVHWVRVLAHLsFYFYSAL-QLG-APKRQVAFSVPTGNFGALYAGYIAKQM 268
                                                     5555999****************55555555.667.68899****************999999 PP

                                       TIGR00260 207 lglpieklaiaaegaadivrrflksgdlepkedk.eTlstAmdignpsnverale.larrslg 267
                                                     + lpi+ l +a++ +   +++fl+s  l+ +++   T  + m+++  sn+er+ + + +r ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150 269 G-LPIRQLIVATNAN-AGLHHFLQSN-LYSRNEIrTTKTPTMNVSLASNFERLQWsILNRCGE 328
                                                     9.**99999888887.99*****999.666666659999****************86666665 PP

                                       TIGR00260 268 nledlke.........................svsdeeileaikklaeeegyllephtavava 305
                                                     ++    +                         +v d++  + i+++ ++ gyl+ p ta++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150 329 KVARNMQllegegtihleqdewlearklfdslAVDDADAFSCIHEVFAQSGYLVSPNTAIGLR 391
                                                     55444345667***************************************************9 PP

                                       TIGR00260 306 alkk 309
                                                     a + 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27150 392 AARV 395
                                                     9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (467 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: 12.33
//
[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