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_16855 AO356_16855 threonine synthase

Query= curated2:Q58860
         (405 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16855
          Length = 417

 Score =  221 bits (563), Expect = 3e-62
 Identities = 139/381 (36%), Positives = 206/381 (54%), Gaps = 10/381 (2%)

Query: 4   RCIKCGKTYDVDEIIYTC---ECGGLLEIIYDYEEIKDKVSEEKLRKREI-GVWRYLEYL 59
           +C+ C ++Y   E+ Y C      G L+ +YDY  +K + S + L      G+WRY   +
Sbjct: 11  QCLVCDRSYQPHEVSYYCPHCNIDGALDALYDYPTLKREWSRDSLAHDHARGMWRYDRLM 70

Query: 60  PVKDESKIVSLCEGGTPLY-RCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRAN 118
           P+     I  L  G TPLY R   L K   IK ++VK+E   PTGS KDR   + V  A 
Sbjct: 71  PLSSTQFIPPLLVGNTPLYSRPELLGKGARIK-VFVKDESRQPTGSLKDRASALAVAHAM 129

Query: 119 ELGVEVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGN 178
           + G   V  ASTGN +++LA  SA  G   ++ LP+      KLAQ   YGA+++ V G 
Sbjct: 130 QSGARTVAVASTGNAASALAGMSASLGLHNVIYLPKS-APREKLAQMQGYGAEIVLVDGQ 188

Query: 179 FDDALDMVKQLAKEKLIY-LLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGN 237
           +D+A +      ++   Y     IN +  EG+KT+AFE+C+QLNWQVPD V VPVGN   
Sbjct: 189 YDEAFEQCLNACEKHGWYNRTTGINSYMSEGKKTVAFEMCEQLNWQVPDLVFVPVGNGCI 248

Query: 238 ISAIWKGFKEFEITGIIDELPKMTGIQADGAKPIVEAFR-KRAKDIIPYKNPETIATAIR 296
           + +++KGF +    G I+ +P++ G+QA+ +  +  A+R  R+        P ++A++I 
Sbjct: 249 LGSVYKGFFDLLQLGWIERIPRLIGVQAEHSNFMYRAWRHDRSMQQTERLPPTSLASSIN 308

Query: 297 IGNPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLE 356
           +  P +  KA+ A+ +S G    V+D  IV A   LA   G+F E  +AS+ AGL K  E
Sbjct: 309 VALPRDRLKAMRAVTASDGEFICVSDPSIVAAASRLAASTGVFPEAGAASAFAGLLKYAE 368

Query: 357 EGIIDRDERIVCITTGHGLKD 377
               D  +  V + TG GLKD
Sbjct: 369 TH-PDTPQTAVILITGSGLKD 388


Lambda     K      H
   0.317    0.137    0.395 

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: 412
Number of extensions: 27
Number of successful extensions: 6
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: 405
Length of database: 417
Length adjustment: 31
Effective length of query: 374
Effective length of database: 386
Effective search space:   144364
Effective search space used:   144364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate AO356_16855 AO356_16855 (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.12901.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-55  174.2   0.0    2.3e-55  174.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855  AO356_16855 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855  AO356_16855 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.0   0.0   2.3e-55   2.3e-55       1     339 [.      63     389 ..      63     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 2.3e-55
                                       TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfva 62 
                                                     ++ry  +++ +  + +  l  g+t+l+  p+l  +    +++vk+++  Pt++ KDr+    a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855  63 MWRYDRLMPLSsTQFIPPLLVGNTPLYSRPELLGKGARIKVFVKDESRQPTGSLKDRA---SA 122
                                                     699999999996666678999**********9955555599*****************...99 PP

                                       TIGR00260  63 vlltkalelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenak 125
                                                      ++++a + g+ tv++A++G+ ++a+a ++++  +++ v+ +Pk       ekl++   ++a+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855 123 LAVAHAMQSGARTVAVASTGNAASALA-GMSASLGLHNVIYLPKS-AP--REKLAQMQGYGAE 181
                                                     ***************************.****************9.33..7************ PP

                                       TIGR00260 126 vlaikGdFDdaqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvp 188
                                                     ++ ++G++D+a + + +++e++  ++      in +  e++kt+afe++eql+++ pd v vp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855 182 IVLVDGQYDEAFEQCLNACEKHGWYN--RTTGINSYMSEGKKTVAFEMCEQLNWQVPDLVFVP 242
                                                     *******************7655443..33345599*************************** PP

                                       TIGR00260 189 vp.sgnfgailkGflekkelg....lpieklaiaaegaadivrrflksgdlepkedk..eTls 244
                                                     v+ +  +g+++kGf+ + +lg     p + ++++ae ++ ++r+ ++++ +++ e++    l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855 243 VGnGCILGSVYKGFFDLLQLGwierIP-RLIGVQAEHSNFMYRAWRHDRSMQQTERLppTSLA 304
                                                     **99999*****************999.*********************777777766699** PP

                                       TIGR00260 245 tAmdignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaal 307
                                                      ++++  p +  +a++++  s+g++  +    sd +i+ a  +la++ g++ e  +a a a+l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855 305 SSINVALPRDRLKAMRAVTASDGEFICV----SDPSIVAAASRLAASTGVFPEAGAASAFAGL 363
                                                     *************************999....******************************* PP

                                       TIGR00260 308 kklvekgvsatadpaKFeevvealtgnklkdp 339
                                                     +k +e       +p+  +++v  +tg +lkd 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16855 364 LKYAET------HPDTPQTAVILITGSGLKDT 389
                                                     **9883......6887799**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (417 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: 12.97
//
[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