GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB 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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.20261.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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.16
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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