Alignments for a candidate for ilvA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Dinoroseobacter shibae DFL-12

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate 3610092 Dshi_3473 threonine dehydratase (RefSeq)

Query= reanno::Pedo557:CA265_RS15860
         (416 letters)



>FitnessBrowser__Dino:3610092
          Length = 413

 Score =  384 bits (987), Expect = e-111
 Identities = 203/405 (50%), Positives = 269/405 (66%), Gaps = 4/405 (0%)

Query: 14  ASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQDALIN 73
           A+  ++ +   TPL+ N  LS  Y A I+LKREDL  VRSYK+RGA+N IS    +    
Sbjct: 11  AASAMRPLFPATPLQMNIHLSERYGAEIWLKREDLSPVRSYKIRGAFNAISKRVAEGQTQ 70

Query: 74  GVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGDTFDD 133
              CASAGNHAQGVAY+C+  G+ GVIFMP  TP+QK+ +T +FGG  +++ LVGD FDD
Sbjct: 71  -FACASAGNHAQGVAYACQHFGVHGVIFMPVTTPRQKIDKTRIFGGTAIDIELVGDYFDD 129

Query: 134 CLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLP-DLDMIVMPVGGGGLASGV 192
            L  A  Y  E SATF+ PFDD  VIEGQ+TV VE+ E L    DM+++PVGGGGL+SG+
Sbjct: 130 TLAAAQRYCTEASATFLSPFDDADVIEGQSTVAVELLEQLEGPPDMVILPVGGGGLSSGM 189

Query: 193 SAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGHITYEYCK 252
             Y +    +V L  VEP GA S+  A+E G P TL ++D FVDGAAV RIG   +E  +
Sbjct: 190 KRYFEVCGVQVDLRLVEPCGARSLAKALETGAPQTLSKVDNFVDGAAVARIGARPFEILR 249

Query: 253 EL-LDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQITGKTVVCIVSGG 311
           ++  D +   PE +IC T+L++ N + IV+EPAGAL+V  LD L+D ITGK VVC+ SGG
Sbjct: 250 DVPPDHVLGAPEDRICHTMLEMLNVEGIVLEPAGALAVDVLDTLRDSITGKRVVCVTSGG 309

Query: 312 NNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDITRFEFIKKTNK 371
           N D ER+ E+KE+SL + GLK YFI+R PQRPGALK F+   LGP DDI RFE++KK+ +
Sbjct: 310 NFDFERLPEVKERSLRYAGLKKYFILRLPQRPGALKEFLG-FLGPDDDIARFEYLKKSAR 368

Query: 372 ENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416
             G  L+GIE  +   +  L  R+    F   ++ +D  L E+L+
Sbjct: 369 NFGSVLIGIETKDAGAFEQLFARLDAAGFPFRDITEDALLAEFLI 413


Lambda     K      H
   0.318    0.138    0.392 

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: 465
Number of extensions: 20
Number of successful extensions: 5
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: 416
Length of database: 413
Length adjustment: 31
Effective length of query: 385
Effective length of database: 382
Effective search space:   147070
Effective search space used:   147070
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 3610092 Dshi_3473 (threonine dehydratase (RefSeq))
to HMM TIGR02079 (ilvA: threonine dehydratase (EC 4.3.1.19))

# 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/TIGR02079.hmm
# target sequence database:        /tmp/gapView.16068.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02079  [M=410]
Accession:   TIGR02079
Description: THD1: threonine dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.7e-166  538.0   0.0   7.6e-166  537.9   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610092  Dshi_3473 threonine dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610092  Dshi_3473 threonine dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.9   0.0  7.6e-166  7.6e-166       4     410 .]       9     413 .]       6     413 .] 0.97

  Alignments for each domain:
  == domain 1  score: 537.9 bits;  conditional E-value: 7.6e-166
                         TIGR02079   4 ekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynkl.kqlsdeelekgvvcasaGnhaqGv 79 
                                       ++a+  +++++  tPlq+n +lse+y+aei+lkredl+ vrsyk+rGa+n++ k++++   +  + casaGnhaqGv
  lcl|FitnessBrowser__Dino:3610092   9 HRAASAMRPLFPATPLQMNIHLSERYGAEIWLKREDLSPVRSYKIRGAFNAIsKRVAEG--QTQFACASAGNHAQGV 83 
                                       689999**********************************************4455544..45699*********** PP

                         TIGR02079  80 ayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfddkdiieGqgt 156
                                       ayac+++gv+g++fmPvttP+qk+dk+++fGg  i++ lvGd fd++ aaa++ + +  +t++ Pfdd d+ieGq+t
  lcl|FitnessBrowser__Dino:3610092  84 AYACQHFGVHGVIFMPVTTPRQKIDKTRIFGGTAIDIELVGDYFDDTLAAAQRYCTEASATFLSPFDDADVIEGQST 160
                                       ***************************************************************************** PP

                         TIGR02079 157 vaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkagevvtldkidkfvdGaa 233
                                       vave+leqle + +d+v++pvGGGGl+sG+  y++    + ++  veP Ga sl ++l++g + tl k+d+fvdGaa
  lcl|FitnessBrowser__Dino:3610092 161 VAVELLEQLEGP-PDMVILPVGGGGLSSGMKRYFEVCGVQVDLRLVEPCGARSLAKALETGAPQTLSKVDNFVDGAA 236
                                       **********98.**************************************************************** PP

                         TIGR02079 234 vkrvGdlnfkalkkvvd.evtlveegavcstildlynkegivaePaGalsiaaleelseeikgktvvcvvsGgnndi 309
                                       v+r+G   f++l++v   +v   +e+++c t+l+++n egiv+ePaGal++  l++l++ i+gk vvcv sGgn+d+
  lcl|FitnessBrowser__Dino:3610092 237 VARIGARPFEILRDVPPdHVLGAPEDRICHTMLEMLNVEGIVLEPAGALAVDVLDTLRDSITGKRVVCVTSGGNFDF 313
                                       ***************865999******************************************************** PP

                         TIGR02079 310 erleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksnretGevliGielsdkedfeGll 386
                                       erl+e+kersl+y Glk+yf++++pqr+Gal+efl   lGP+ddi++fey+kks+r++G+vliGie++d+  fe l+
  lcl|FitnessBrowser__Dino:3610092 314 ERLPEVKERSLRYAGLKKYFILRLPQRPGALKEFLG-FLGPDDDIARFEYLKKSARNFGSVLIGIETKDAGAFEQLF 389
                                       ***********************************9.**************************************** PP

                         TIGR02079 387 erlkaadieyeainenetlyellv 410
                                       +rl+aa+  +++i+e+  l e+l+
  lcl|FitnessBrowser__Dino:3610092 390 ARLDAAGFPFRDITEDALLAEFLI 413
                                       *****************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (410 nodes)
Target sequences:                          1  (413 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.05
//
[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