Alignments for a candidate for thrC in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pseudomonas fluorescens GW456-L13

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate PfGW456L13_1724 Threonine synthase (EC 4.2.3.1)

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724
          Length = 469

 Score =  511 bits (1316), Expect = e-149
 Identities = 264/462 (57%), Positives = 322/462 (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   MRYISTRGQAPALNFEDVLLAGLATDGGLYVPENLPRFTQEEIASWAGLPYHELAFRVMR 60

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

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R++DYVL +RGER  IVGATSGDTG AAIE     +N DIFIL P+ RVS VQ+RQMT+ 
Sbjct: 121 RLLDYVLEKRGERVVIVGATSGDTGSAAIEGCKHCENVDIFILHPHNRVSEVQRRQMTTI 180

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

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LG P R+VSF+VPTGNFGDIFAGY+A+ MGLPI QLI+ATN NDIL R +    Y    +
Sbjct: 241 LGGPARSVSFSVPTGNFGDIFAGYLARNMGLPINQLIVATNRNDILHRFMSGNQYVKDTL 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             T SPSMDI +SSNFERLLF+ HGR+ AA+ GLM   KQ GGF++ ++  +  R  F +
Sbjct: 301 HATLSPSMDIMVSSNFERLLFDLHGRNGAAIAGLMDSFKQGGGFSVEQERWTEARKLFDS 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE-KASGTAPMVVLATAHPAKFPDAV 419
                 +T  TI  V  + G +LDPH+AIGVK ARE + S   PMV+L TAHP KFPDAV
Sbjct: 361 LAVDDAQTCETIAEVYEQTGEVLDPHTAIGVKAARECRRSLDIPMVILGTAHPVKFPDAV 420

Query: 420 -KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460
            KA  G   +LP  L DL +R E  TVL N+LK V+ +V  H
Sbjct: 421 EKAGVGKALELPVHLSDLFERDERCTVLPNDLKAVQAFVSQH 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: 567
Number of extensions: 20
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 PfGW456L13_1724 (Threonine synthase (EC 4.2.3.1))
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.32485.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    5.1e-85  271.5   0.0    6.7e-85  271.2   0.0    1.1  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724  Threonine synthase (EC 4.2.3.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724  Threonine synthase (EC 4.2.3.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.2   0.0   6.7e-85   6.7e-85      10     336 ..      67     429 ..      58     432 .. 0.92

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 6.7e-85
                                               TIGR00260  10 vtekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfva 62 
                                                             ++++d +++ e  + +f+  ++a  +++ + n +v+elfhgPtlaFKD++lq ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724  67 IPDADFKKILEETYGVFAHSAVAplRQLNG-NEWVLELFHGPTLAFKDFALQLLG 120
                                                             458899999999999999999888899999.99********************** PP

                                               TIGR00260  63 vlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.ke 114
                                                              ll ++le+  e  ++++AtsGdtg+aa+e+ +  +nv++++L P+ ++s v   
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724 121 RLLDYVLEKRGErvVIVGATSGDTGSAAIEGCKHCENVDIFILHPHNRVSEVqRR 175
                                                             *******998777899************************************99* PP

                                               TIGR00260 115 klvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaq 166
                                                             +++t   en++ +ai+G+FDd+q++vk+ f d+     + l++vNsin+ari aq
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724 176 QMTTIFGENIHNIAIEGNFDDCQEMVKASFADQSflkGTRLVAVNSINWARIMAQ 230
                                                             ******************************977779899**************** PP

                                               TIGR00260 167 ktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaega 221
                                                             ++y+f +  qlg+ +   v ++vp gnfg+i++G+l+ +++ lpi+ l +a++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724 231 IVYYFHASLQLGGPA-RSVSFSVPTGNFGDIFAGYLARNMG-LPINQLIVATNRN 283
                                                             ************655.57****************9999999.******9999998 PP

                                               TIGR00260 222 adivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke. 274
                                                              di++rf+ + + ++ +  +Tls++mdi  +sn+er+l+ l  r+++ +  l   
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724 284 -DILHRFMSGNQYVKDTLHATLSPSMDIMVSSNFERLLFdLHGRNGAAIAGLMDs 337
                                                             .******888888888888*******************99999999888888668 PP

                                               TIGR00260 275 ........................svsdeeileaikklaeeegyllephtavava 305
                                                                                     +v d+++ e+i +++e+ g +l+phta++v+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724 338 fkqgggfsveqerwtearklfdslAVDDAQTCETIAEVYEQTGEVLDPHTAIGVK 392
                                                             899**************************************************** PP

                                               TIGR00260 306 alkklvekg...vs..atadpaKFeevve.altgnkl 336
                                                             a ++   +    +   +ta+p KF+++ve a  g+ l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1724 393 AARECRRSLdipMVilGTAHPVKFPDAVEkAGVGKAL 429
                                                             *998887666652257************977666665 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.79
//
[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