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 (EC 4.2.3.1) (characterized)
to candidate AO356_15130 AO356_15130 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_15130
          Length = 454

 Score =  330 bits (845), Expect = 8e-95
 Identities = 176/415 (42%), Positives = 251/415 (60%), Gaps = 7/415 (1%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+YVSTR  A  + F   +L+ +A DGGL++P E PQF ++ I      +Y E+A  V+ 
Sbjct: 1   MRYVSTRNSAVQVDFEKVVLSAIAEDGGLFVPVELPQFESQDIANWSTLAYDELAYRVMR 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF G  IP ADF+R+++EA   F H ++ PL Q D NE+VLELFHGPT + KD A QL A
Sbjct: 61  PFVGEAIPEADFKRVLKEAGSQFSHRSLAPLHQVDRNEWVLELFHGPTRSSKDFAAQLQA 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R++ Y L +RG RA ++G T+GDTG AAIEAF   D TD+ +++P   V   Q + + ++
Sbjct: 121 RLVQYFLRKRGRRAVVIGVTNGDTGLAAIEAFKHCDETDVVVIYPEAGVLQDQLQDLQAT 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
               VH ++++G+FD+CQ LV  +F   E   A+S    NS NW  +M Q+V+YF A L 
Sbjct: 181 AHPRVHQVAVDGSFDECQTLVTQLFRQHE---AISF---NSSNWVSVMAQLVFYFHAVLQ 234

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LG   R + F+VP  +F +++AGY+A++MGLPI Q+I+ATN ND L +      Y     
Sbjct: 235 LGGGQRPIGFSVPAASFAEVYAGYIAQKMGLPITQMIVATNQNDALHQFFLKNHYSRLRA 294

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
           ++T SP+MD+ I SN ER L+E +G D  AV  LM   +  G  TI+ +     R    +
Sbjct: 295 SKTLSPAMDLSIFSNLERFLWELYGHDDQAVSALMHTFETRGEMTIANEFWLQARMIIDS 354

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAR-EKASGTAPMVVLATAHPAK 414
              + ++T   I S+    GY++DPH+A GV  AR  + S  APMV L    PAK
Sbjct: 355 YAVSDEQTLEEITSLYRDTGYVIDPHTATGVLAARLYRRSLVAPMVTLGEISPAK 409


Lambda     K      H
   0.320    0.135    0.389 

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: 425
Number of extensions: 13
Number of successful extensions: 3
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: 463
Length of database: 454
Length adjustment: 33
Effective length of query: 430
Effective length of database: 421
Effective search space:   181030
Effective search space used:   181030
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: 51 (24.3 bits)

Align candidate AO356_15130 AO356_15130 (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.8357.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
      2e-60  190.7   0.0    2.6e-60  190.3   0.0    1.1  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130  AO356_15130 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130  AO356_15130 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.0   2.6e-60   2.6e-60      12     308 ..      69     389 ..      58     415 .. 0.83

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 2.6e-60
                                       TIGR00260  12 ekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelg 72 
                                                     e+d + + +   + f    la  ++v   n +v+elfhgPt + KD++ q  a l++++l + 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130  69 EADFKRVLKEAGSQFSHRSLAplHQVDR-NEWVLELFHGPTRSSKDFAAQLQARLVQYFLRKR 130
                                                     5566666555556665554443377776.99***************************98654 PP

                                       TIGR00260  73 ne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkekl..vt.alaenakvlaik 130
                                                         +v++ t Gdtg aa+ea++   + +vvv+yP+ ++   +++l  ++ +    ++ +a++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130 131 GRraVVIGVTNGDTGLAAIEAFKHCDETDVVVIYPEAGVL--QDQLqdLQaTAHPRVHQVAVD 191
                                                     4335999*****************************9998..55542244044557999**** PP

                                       TIGR00260 131 GdFDdaqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgn 193
                                                     G FD++q+lv+++f ++e++ +ns N   +  + aq + +f +v qlg   +  + ++vp++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130 192 GSFDECQTLVTQLFRQHEAISFNSSN---WVSVMAQLVFYFHAVLQLG-GGQRPIGFSVPAAS 250
                                                     **************999999998888...*******************.56678********* PP

                                       TIGR00260 194 fgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnve 256
                                                     f ++++G+ + k++ lpi  + +a++++ d +++f  + + +  +  +Tls+Amd ++ sn e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130 251 FAEVYAGYIAQKMG-LPITQMIVATNQN-DALHQFFLKNHYSRLRASKTLSPAMDLSIFSNLE 311
                                                     *************9.********99999.777777666668889999**************** PP

                                       TIGR00260 257 rale.larrslgnledlke.........................svsdeeileaikklaeeeg 293
                                                     r l+ l  + ++ + +l +                         +vsde++le+i  l++  g
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130 312 RFLWeLYGHDDQAVSALMHtfetrgemtianefwlqarmiidsyAVSDEQTLEEITSLYRDTG 374
                                                     ***96666666777777559999**************************************** PP

                                       TIGR00260 294 yllephtavavaalk 308
                                                     y+++phta++v a +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15130 375 YVIDPHTATGVLAAR 389
                                                     ***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (454 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: 9.26
//
[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