Alignments for a candidate for thrC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pedobacter sp. GW460-11-11-14-LB5

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate CA265_RS23465 CA265_RS23465 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>FitnessBrowser__Pedo557:CA265_RS23465
          Length = 435

 Score =  344 bits (882), Expect = 3e-99
 Identities = 188/433 (43%), Positives = 260/433 (60%), Gaps = 8/433 (1%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           MKLY+  + + +VSF +AV   + +++GL+ P ++P+     I  + K      +  I S
Sbjct: 1   MKLYSTNNKDLRVSFKEAVFNSMPQDKGLYMPIEIPQLDPEFIQNIEKYALPEIAYTIAS 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
             + DEIP E L+  +  A  F AP   ++     LELFHGP+LAFKDFG RFM++++ +
Sbjct: 61  TLLKDEIPAEDLKALIDDAINFEAPAVKLDDKTYVLELFHGPSLAFKDFGARFMSRVMAY 120

Query: 121 IA--GDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIE 178
               G++ + +L ATSGDTG AVA  F G+PN +V ILYP GK+SP+QE    T G NI 
Sbjct: 121 FLKDGEQLLDVLVATSGDTGGAVALGFLGVPNTRVTILYPEGKVSPIQELQLTTNGENIR 180

Query: 179 TVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETR 238
            V + G FD CQALVKQAF D+EL     L SANSINISRL+ Q  YYF   AQL ++  
Sbjct: 181 AVEVKGTFDDCQALVKQAFADDELNAKFRLTSANSINISRLIPQTFYYFNTYAQLKKQGF 240

Query: 239 NQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLS 298
             +V SVPSGNFG++ AGLLA  LGLPVK+FIAATNVNDTVPRFL  G +  K +  T S
Sbjct: 241 KDVVFSVPSGNFGNIGAGLLAYKLGLPVKQFIAATNVNDTVPRFLESGVYETKPSTQTYS 300

Query: 299 NAMDVSQPNNWPRVEELFRRKIWQLKEL--GYAAVDDETTQQTMRELKELGYTSEPHAAV 356
           NAMDV  P+NW R+ +LF + +  +K++   Y   DDET         +L Y + PH A+
Sbjct: 301 NAMDVGAPSNWVRIMDLFHKDVEAIKKVVTAYRFTDDETLAGIKEINSKLNYVACPHTAI 360

Query: 357 AYRAL----RDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHN 412
           AY A+    R+  +     +FL TAH  KF +   A +   +++P+++      P  +  
Sbjct: 361 AYLAVEKYRRENPSDESAAVFLSTAHACKFPDIFPADIAAKIEIPEQVKALESKPKHADQ 420

Query: 413 LPADFAALRKLMM 425
           L  DF   +K ++
Sbjct: 421 LGVDFEGFKKYLL 433


Lambda     K      H
   0.319    0.135    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: 530
Number of extensions: 28
Number of successful extensions: 4
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: 428
Length of database: 435
Length adjustment: 32
Effective length of query: 396
Effective length of database: 403
Effective search space:   159588
Effective search space used:   159588
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 CA265_RS23465 CA265_RS23465 (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.21482.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.8e-93  298.7   0.1    3.8e-93  298.3   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS23465  CA265_RS23465 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS23465  CA265_RS23465 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.3   0.1   3.8e-93   3.8e-93      12     327 ..      66     393 ..      56     399 .. 0.93

  Alignments for each domain:
  == domain 1  score: 298.3 bits;  conditional E-value: 3.8e-93
                                  TIGR00260  12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvl 77 
                                                e++++dl++    +++++++a ++   + yv+elfhgP+laFKD+g +f++ +++++l++g++   vl
  lcl|FitnessBrowser__Pedo557:CA265_RS23465  66 EIPAEDLKALIDDAINFEAPAVKLDD-KTYVLELFHGPSLAFKDFGARFMSRVMAYFLKDGEQllDVL 132
                                                789999999999************99.99**********************************878** PP

                                  TIGR00260  78 cAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife 145
                                                +AtsGdtg a+a ++ g +n +v +LyP+gk+sp++e  +t+  en++ +++kG+FDd+q+lvk++f 
  lcl|FitnessBrowser__Pedo557:CA265_RS23465 133 VATSGDTGGAVALGFLGVPNTRVTILYPEGKVSPIQELQLTTNGENIRAVEVKGTFDDCQALVKQAFA 200
                                                ***********************************77777889************************* PP

                                  TIGR00260 146 dke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglp 210
                                                d+e   k  l s+Nsin++r+  q  y+f+  +ql+k+  + vv++vpsgnfg+i +G l++k + lp
  lcl|FitnessBrowser__Pedo557:CA265_RS23465 201 DDElnaKFRLTSANSINISRLIPQTFYYFNTYAQLKKQGFKDVVFSVPSGNFGNIGAGLLAYKLG-LP 267
                                                8888889***************************************************8887776.** PP

                                  TIGR00260 211 ieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlke..sv 276
                                                  k +iaa++++d+v+rfl+sg  e+k + +T+s+Amd+g psn+ r+++l+++  + ++++ +  + 
  lcl|FitnessBrowser__Pedo557:CA265_RS23465 268 -VKQFIAATNVNDTVPRFLESGVYETKPSTQTYSNAMDVGAPSNWVRIMDLFHKDVEAIKKVVTayRF 334
                                                .8999*****************88888899******************************99655699 PP

                                  TIGR00260 277 sdeeileaikklaeeegyllephtavavaalkklvekg...vs.....atadpaKFeev 327
                                                +d+e+l  ik++  + +y++ phta+a+ a++k   ++    s     +ta+  KF+++
  lcl|FitnessBrowser__Pedo557:CA265_RS23465 335 TDDETLAGIKEINSKLNYVACPHTAIAYLAVEKYRRENpsdESaavflSTAHACKFPDI 393
                                                *********************************999887662256789********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (435 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: 8.41
//
[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