Alignments for a candidate for ilvA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Shewanella loihica PV-4

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 5207772 Shew_0293 threonine dehydratase (RefSeq)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__PV4:5207772
          Length = 516

 Score =  589 bits (1518), Expect = e-173
 Identities = 300/498 (60%), Positives = 376/498 (75%), Gaps = 2/498 (0%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           YL+ +L + VY+ A+VTPL  + KLS+RL   + +KRED QPVHSFKLRGAY  +A L++
Sbjct: 16  YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAELSQ 75

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
           E+   GV+ ASAGNHAQGVA S++  GV A+IVMP  T DIKVDAVR  GG V+L+G +F
Sbjct: 76  EECQRGVVCASAGNHAQGVAMSASARGVSAVIVMPQTTPDIKVDAVRRLGGTVVLYGQSF 135

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAG 195
           D A   A +L++ +G  +V PFD   VIAGQGT+A E+LQQ   L+ VFVPVGGGGL AG
Sbjct: 136 DMANEHAQQLARDEGRIYVAPFDDEAVIAGQGTVAQEMLQQQRDLEVVFVPVGGGGLIAG 195

Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255
           +A   K +MPQ+K+I VE EDSACLKAAL+A   V L +VGLFA+GVAVK+IG E FRL 
Sbjct: 196 IAAYYKAVMPQVKIIGVEPEDSACLKAALEADERVVLSQVGLFADGVAVKQIGAEPFRLA 255

Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILS 315
           +EY+D ++TV SD ICAA+KD+FED RA+AEP+GAL+LAG+KKYI     +G+++A ILS
Sbjct: 256 REYVDQVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYIGDEG-KGQKVAAILS 314

Query: 316 GANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAK 375
           GANVNFH LRYVSERCELGEQ+EA+LAV +PE  G FL+FC+LL  R++TEFNYRF+  +
Sbjct: 315 GANVNFHSLRYVSERCELGEQKEAILAVKVPEHPGIFLRFCELLEKRAMTEFNYRFSSRE 374

Query: 376 NACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQERL 435
            A +F G+RLS G  E  EI+  L   G+ V DLS DE AKLHVRYMVGG P  PLQERL
Sbjct: 375 KAVVFAGIRLSHGQAELDEIVARLEGDGFEVQDLSHDETAKLHVRYMVGGLPPEPLQERL 434

Query: 436 YSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEP-DFETRLNE 494
           +SFEFPE PGAL +FL TL + WNISLFHYR+HG  YGRVLA FE+ + +   F+  L E
Sbjct: 435 FSFEFPEHPGALFKFLTTLRSKWNISLFHYRNHGAAYGRVLAGFEVPESDSVAFQQFLTE 494

Query: 495 LGYDCHDETNNPAFRFFL 512
           LG+   +ET +PA++ FL
Sbjct: 495 LGFVYQEETQSPAYKLFL 512


Lambda     K      H
   0.321    0.138    0.403 

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: 736
Number of extensions: 26
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: 514
Length of database: 516
Length adjustment: 35
Effective length of query: 479
Effective length of database: 481
Effective search space:   230399
Effective search space used:   230399
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: 52 (24.6 bits)

Align candidate 5207772 Shew_0293 (threonine dehydratase (RefSeq))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (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/TIGR01124.hmm
# target sequence database:        /tmp/gapView.20582.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01124  [M=499]
Accession:   TIGR01124
Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.2e-238  777.2   0.4   3.7e-238  777.0   0.4    1.0  1  lcl|FitnessBrowser__PV4:5207772  Shew_0293 threonine dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207772  Shew_0293 threonine dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  777.0   0.4  3.7e-238  3.7e-238       2     499 .]      16     512 ..      15     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 777.0 bits;  conditional E-value: 3.7e-238
                        TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaqG 79 
                                      yl++il ++vy++a++tpl+  +kls+rl+ +v+lkred+qpv+sfklrGayn++a+ls+e+  +Gv++asaGnhaqG
  lcl|FitnessBrowser__PV4:5207772  16 YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAELSQEECQRGVVCASAGNHAQG 93 
                                      89**************************************************************************** PP

                        TIGR01124  80 valsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtval 157
                                      va+sa+  Gv+avivmp+ttp+ikvdav+  Gg vvl+G+++d a+++a++la+++g  ++apfdd+ viaGqGtva 
  lcl|FitnessBrowser__PV4:5207772  94 VAMSASARGVSAVIVMPQTTPDIKVDAVRRLGGTVVLYGQSFDMANEHAQQLARDEGRIYVAPFDDEAVIAGQGTVAQ 171
                                      ****************************************************************************** PP

                        TIGR01124 158 ellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevG 235
                                      e+l+q++ dl+ vfvpvGGGGliaG+aa+ k+++p++k+igve+edsa+lk+alea erv l+qvGlfadGvavk++G
  lcl|FitnessBrowser__PV4:5207772 172 EMLQQQR-DLEVVFVPVGGGGLIAGIAAYYKAVMPQVKIIGVEPEDSACLKAALEADERVVLSQVGLFADGVAVKQIG 248
                                      *****99.9********************************************************************* PP

                        TIGR01124 236 detfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlry 313
                                      +e frl++ey+d++v+v +de+caa+kd+fedtra++epaGal+laGlkky+  +g ++++++ailsGan+nf++lry
  lcl|FitnessBrowser__PV4:5207772 249 AEPFRLAREYVDQVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYIGDEG-KGQKVAAILSGANVNFHSLRY 325
                                      ****************************************************9887.899****************** PP

                        TIGR01124 314 vseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eerkellarleeagy 390
                                      vser+elGeq+ea+lav +pe++G +l+f+e+l +ra+tefnyr++ +eka +f G++l++  +e +e++arle  g+
  lcl|FitnessBrowser__PV4:5207772 326 VSERCELGEQKEAILAVKVPEHPGIFLRFCELLEKRAMTEFNYRFSSREKAVVFAGIRLSHGqAELDEIVARLEGDGF 403
                                      ***********************************************************9874799************ PP

                        TIGR01124 391 kvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevp 468
                                      +v dl++de aklhvry+vGG + +  +erl+sfefpe+pGal kfl+tl ++wnislfhyrnhGa+yGrvl+g+evp
  lcl|FitnessBrowser__PV4:5207772 404 EVQDLSHDETAKLHVRYMVGGLPPEPLQERLFSFEFPEHPGALFKFLTTLRSKWNISLFHYRNHGAAYGRVLAGFEVP 481
                                      ****************************************************************************** PP

                        TIGR01124 469 deeaeefeqflaelgyryedetenpayrlfl 499
                                      ++++ +f+qfl elg+ y++et++pay+lfl
  lcl|FitnessBrowser__PV4:5207772 482 ESDSVAFQQFLTELGFVYQEETQSPAYKLFL 512
                                      ******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (516 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.30
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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