Alignments for a candidate for thrC in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Bacteroides thetaiotaomicron VPI-5482

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 351929 BT2401 threonine synthase (NCBI ptt file)

Query= BRENDA::P00934
         (428 letters)



>FitnessBrowser__Btheta:351929
          Length = 433

 Score =  353 bits (907), Expect = e-102
 Identities = 192/432 (44%), Positives = 271/432 (62%), Gaps = 6/432 (1%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           MK Y+        S  +AV +GL  ++GLF P  +        D +  L F   + ++  
Sbjct: 1   MKYYSTNKQAPMASLQEAVVKGLAADRGLFMPMTIKPLPQEFYDTIDTLSFQEIAYRVAD 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
           AF G++IP + L++ V    +F  P+  V  ++  LELFHGPTLAFKD GGRFMA++L +
Sbjct: 61  AFFGEDIPTDTLKQIVYDTLSFDVPLVKVADNIYSLELFHGPTLAFKDVGGRFMARLLGY 120

Query: 121 IA---GDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNI 177
                G K V +L ATSGDTG+AVA+ F G+  + V +LYP+GK+S +QEK F TLG NI
Sbjct: 121 FIKKEGQKDVNVLVATSGDTGSAVANGFLGVEGIHVYVLYPKGKVSEIQEKQFTTLGQNI 180

Query: 178 ETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQET 237
             + +DG FD CQALVK AF D+EL   L L SANSIN++R L Q  YYF A AQL +  
Sbjct: 181 TALEVDGTFDDCQALVKAAFMDKELNEHLSLTSANSINVARFLPQAFYYFYAYAQLKRAG 240

Query: 238 R-NQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQAT 296
           + +  V+ VPSGNFG++TAGL  K +GLPVKRFIAA N ND   ++L  G+++P+ + AT
Sbjct: 241 KADNAVICVPSGNFGNITAGLFGKKMGLPVKRFIAANNRNDIFYQYLQTGKYNPRPSVAT 300

Query: 297 LSNAMDVSQPNNWPRVEELFRRKIWQLK-ELGYAAVDDETTQQTMREL-KELGYTSEPHA 354
           ++NAMDV  P+N+ RV +L+      +  E+      DE  ++T++E  KE  Y  +PH 
Sbjct: 301 IANAMDVGDPSNFARVLDLYGGSHADISAEISGTTYTDEQIRETVKETWKEHHYLLDPHG 360

Query: 355 AVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLP 414
           A  YRAL++ L  GE G+FL TAHPAKF E+VE+I+GE +++P +L E       S  + 
Sbjct: 361 ACGYRALQEGLKQGETGVFLETAHPAKFLETVESIIGEAVEIPAKLQEFMKGEKKSLQMT 420

Query: 415 ADFAALRKLMMN 426
            +FA  +K +++
Sbjct: 421 KEFADFKKYLLS 432


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: 476
Number of extensions: 25
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: 433
Length adjustment: 32
Effective length of query: 396
Effective length of database: 401
Effective search space:   158796
Effective search space used:   158796
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 351929 BT2401 (threonine synthase (NCBI ptt file))
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.3411114.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
    2.3e-96  308.8   0.0    3.2e-96  308.4   0.0    1.0  1  FitnessBrowser__Btheta:351929  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Btheta:351929  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.4   0.0   3.2e-96   3.2e-96      12     335 ..      66     399 ..      56     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: 308.4 bits;  conditional E-value: 3.2e-96
                      TIGR00260  12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne...tvlcAtsGdtgaaa 88 
                                    +++  +l++ ++ ++ ++ +  +v   n+y +elfhgPtlaFKD+g++f+a ll ++ ++  +    vl+AtsGdtg+a+
  FitnessBrowser__Btheta:351929  66 DIPTDTLKQIVYDTLSFDVPLVKVAD-NIYSLELFHGPTLAFKDVGGRFMARLLGYFIKKEGQkdvNVLVATSGDTGSAV 144
                                    578889999***************99.****************************985543333779************* PP

                      TIGR00260  89 aealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinpariea 165
                                    a+++ g ++++v+vLyPkgk+s ++ek +t+l +n++ l+++G+FDd+q+lvk++f dke   +l l s+Nsin+ar + 
  FitnessBrowser__Btheta:351929 145 ANGFLGVEGIHVYVLYPKGKVSEIQEKQFTTLGQNITALEVDGTFDDCQALVKAAFMDKElneHLSLTSANSINVARFLP 224
                                    ********************************************************988778799*************** PP

                      TIGR00260 166 qktyafeiveqlgk.espdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTls 244
                                    q  y+f + +ql++  + d+ v+ vpsgnfg+i++G + kk++ lp  k++iaa++ +di  ++l++g+  p+ +++T++
  FitnessBrowser__Btheta:351929 225 QAFYYFYAYAQLKRaGKADNAVICVPSGNFGNITAGLFGKKMG-LP-VKRFIAANNRNDIFYQYLQTGKYNPRPSVATIA 302
                                    **77777888887758899******************999999.**.9******************************** PP

                      TIGR00260 245 tAmdignpsnveralelarrslgnled..lkesvsdeeileaikklaeeegyllephtavavaalkklvekg.vs...at 318
                                    +Amd+g psn+ r+l+l   s +++ +   +++ +de+i e++k+  +e++yll+ph+a +++al++ +++g ++    t
  FitnessBrowser__Btheta:351929 303 NAMDVGDPSNFARVLDLYGGSHADISAeiSGTTYTDEQIRETVKETWKEHHYLLDPHGACGYRALQEGLKQGeTGvflET 382
                                    ****************887777766551156699************************************997446789* PP

                      TIGR00260 319 adpaKFeevvealtgnk 335
                                    a+paKF e+ve + g+ 
  FitnessBrowser__Btheta:351929 383 AHPAKFLETVESIIGEA 399
                                    ***********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (433 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.45
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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