Alignments for a candidate for thrC in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pseudomonas stutzeri RCH2

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate GFF3067 Psest_3125 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__psRCH2:GFF3067
          Length = 469

 Score =  504 bits (1298), Expect = e-147
 Identities = 261/462 (56%), Positives = 321/462 (69%), Gaps = 2/462 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+Y+STRG+AP L F D LLAGLA DGGLY+P+  P+FT E+I +  G  Y E+A  V+ 
Sbjct: 1   MRYISTRGQAPALNFEDVLLAGLASDGGLYVPENLPRFTVEEIASWAGLPYHELAFRVMR 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF  G IP ADF++++ E YG F H A+ PL Q + NE+VLELFHGPTLAFKD A+QLL 
Sbjct: 61  PFVAGSIPDADFKQILEETYGVFAHSAIAPLRQLNGNEWVLELFHGPTLAFKDFALQLLG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R++DYVLA+RGER  I+GATSGDTG AAIE     +N DIFIL P+ RVS VQ+RQMT+ 
Sbjct: 121 RLLDYVLAKRGERVVIMGATSGDTGSAAIEGCRRCENVDIFILHPHQRVSEVQRRQMTTI 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
              N+H ++IEGNFDDCQ +VK  F D  F     L  VNSINWARIM Q+VYYF AAL 
Sbjct: 181 AGDNIHNIAIEGNFDDCQEMVKASFADQAFLKGTRLVAVNSINWARIMAQIVYYFHAALQ 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LG P R+V+F+VPTGNFGDIFAGY+A+ MGLPI QLI+ATN NDIL R +    Y+   +
Sbjct: 241 LGGPARSVAFSVPTGNFGDIFAGYLARNMGLPINQLIVATNRNDILHRFMSGNRYDKDTL 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             + SPSMDI +SSNFERLLF+ HGR+  AV  L+ G + SG  ++ E   +  R  F +
Sbjct: 301 HASLSPSMDIMVSSNFERLLFDLHGRNGKAVAELLDGFRASGKLSVEEDRWTEARKLFDS 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE-KASGTAPMVVLATAHPAKFPDAV 419
                ++T ATI  V  + G +LDPH+AIGV  ARE + S + PMV L TAHP KFPDAV
Sbjct: 361 LAVDDEQTCATIAQVFKETGEVLDPHTAIGVHAARECRRSLSIPMVTLGTAHPVKFPDAV 420

Query: 420 -KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460
            KA  G    LPA L DL +R E  TVL NELK V+ +V  H
Sbjct: 421 EKAGIGQALALPAHLADLFERGERCTVLPNELKAVQAFVGQH 462


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: 551
Number of extensions: 22
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: 469
Length adjustment: 33
Effective length of query: 430
Effective length of database: 436
Effective search space:   187480
Effective search space used:   187480
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 GFF3067 Psest_3125 (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.19948.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      1e-82  264.0   0.0    1.3e-82  263.7   0.0    1.1  1  lcl|FitnessBrowser__psRCH2:GFF3067  Psest_3125 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3067  Psest_3125 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.7   0.0   1.3e-82   1.3e-82      10     336 ..      67     429 ..      58     433 .. 0.91

  Alignments for each domain:
  == domain 1  score: 263.7 bits;  conditional E-value: 1.3e-82
                           TIGR00260  10 vtekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 
                                         ++++d +++ e  + +f+  ++a  +++ + n +v+elfhgPtlaFKD++lq ++ ll ++l +  e  ++++At
  lcl|FitnessBrowser__psRCH2:GFF3067  67 IPDADFKQILEETYGVFAHSAIAplRQLNG-NEWVLELFHGPTLAFKDFALQLLGRLLDYVLAKRGErvVIMGAT 140
                                         558899999999999999999888899999.99***************************98766655799**** PP

                           TIGR00260  81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klk 151
                                         sGdtg+aa+e+ ++ +nv++++L P+ ++s v   +++t    n++ +ai+G+FDd+q++vk+ f d+     + 
  lcl|FitnessBrowser__psRCH2:GFF3067 141 SGDTGSAAIEGCRRCENVDIFILHPHQRVSEVqRRQMTTIAGDNIHNIAIEGNFDDCQEMVKASFADQAflkGTR 215
                                         ********************************99*******************************9887788999 PP

                           TIGR00260 152 lnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivr 226
                                         l++vNsin+ari aq++y+f ++ qlg+ +   v+++vp gnfg+i++G+l+ +++ lpi+ l +a++ + di++
  lcl|FitnessBrowser__psRCH2:GFF3067 216 LVAVNSINWARIMAQIVYYFHAALQLGGPA-RSVAFSVPTGNFGDIFAGYLARNMG-LPINQLIVATNRN-DILH 287
                                         ***************************655.57****************9999999.******9999998.**** PP

                           TIGR00260 227 rflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.........................s 275
                                         rf+ +   ++ +  + ls++mdi  +sn+er+l+ l  r+++ + +l                           +
  lcl|FitnessBrowser__psRCH2:GFF3067 288 RFMSGNRYDKDTLHASLSPSMDIMVSSNFERLLFdLHGRNGKAVAELLDgfrasgklsveedrwtearklfdslA 362
                                         **776655555555*******************98888888888887669************************* PP

                           TIGR00260 276 vsdeeileaikklaeeegyllephtavavaalkklvekg....vs.atadpaKFeevve.altgnkl 336
                                         v de++  +i ++ +e g +l+phta++v a ++   +     v+ +ta+p KF+++ve a  g+ l
  lcl|FitnessBrowser__psRCH2:GFF3067 363 VDDEQTCATIAQVFKETGEVLDPHTAIGVHAARECRRSLsipmVTlGTAHPVKFPDAVEkAGIGQAL 429
                                         *******************************999888766665227************977777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (469 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 14.49
//
[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