Alignments for a candidate for tdcB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Shewanella oneidensis MR-1

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 203422 SO4344 threonine dehydratase (NCBI ptt file)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__MR1:203422
          Length = 545

 Score =  598 bits (1542), Expect = e-175
 Identities = 303/523 (57%), Positives = 389/523 (74%), Gaps = 12/523 (2%)

Query: 2   ADSQPLSGAPEGAE-------YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKRED 54
           A+SQP   +P   E       YL+ +L + VY+ A+VTPL  + KLS+RL   + +KRED
Sbjct: 12  AESQPAQASPASVEKSQLAQHYLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKRED 71

Query: 55  RQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATA 114
            QPVHSFKLRGAY  +A L++ +   GV+ ASAGNHAQGVA S+A  GV A+IVMP  T 
Sbjct: 72  MQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQGVAMSAASRGVDAVIVMPETTP 131

Query: 115 DIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELL 174
           DIKVDAVR  GG V+LHG  FD+A   A+ ++QQ+G  ++ PFD   VIAGQGT+A E+L
Sbjct: 132 DIKVDAVRRLGGNVVLHGQAFDQANGFAMTMAQQEGRVYIAPFDDEAVIAGQGTIAQEML 191

Query: 175 QQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPR 234
           QQ   L+ +FVPVGGGGL AG+A   K +MPQ+K++ VE ED+ACLKAA++AG PV L +
Sbjct: 192 QQQRDLEVIFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLSQ 251

Query: 235 VGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALA 294
           VGLFA+GVAVKRIG E FR+ +  +D ++TV SD ICAA+KD+FED RA+AEP+GAL+LA
Sbjct: 252 VGLFADGVAVKRIGTEPFRVAKLCVDAVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLA 311

Query: 295 GMKKYIALH----NIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKG 350
           G+KKY++ +    + RGE++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE  G
Sbjct: 312 GLKKYVSTNATGESGRGEKVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPERPG 371

Query: 351 SFLKFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLS 410
           SFL+FC+LL  R +TEFNYRF+    A +F G+RL++G  E ++I+  L D G+ V DLS
Sbjct: 372 SFLRFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGHGELEQIINTLEDNGFEVQDLS 431

Query: 411 DDEMAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGT 470
            DE AKLHVRYMVGG P  PL+ERL+SFEFPE PGALL+FL TL + WNISLFHYR+HG 
Sbjct: 432 GDETAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGA 491

Query: 471 DYGRVLAAFELGDHEP-DFETRLNELGYDCHDETNNPAFRFFL 512
            +GRVLA FE+   +   F+  L ELG+   +ET +PA++ FL
Sbjct: 492 AFGRVLAGFEVPASDALPFQQFLTELGFVYQEETQSPAYQLFL 534


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: 776
Number of extensions: 25
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: 514
Length of database: 545
Length adjustment: 35
Effective length of query: 479
Effective length of database: 510
Effective search space:   244290
Effective search space used:   244290
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 203422 SO4344 (threonine dehydratase (NCBI ptt file))
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.13742.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-234  765.4   0.3   1.4e-234  765.2   0.3    1.0  1  lcl|FitnessBrowser__MR1:203422  SO4344 threonine dehydratase (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203422  SO4344 threonine dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  765.2   0.3  1.4e-234  1.4e-234       2     499 .]      33     534 ..      32     534 .. 0.98

  Alignments for each domain:
  == domain 1  score: 765.2 bits;  conditional E-value: 1.4e-234
                       TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaqGv 80 
                                     yl++il ++vy++a++tpl+  +kls+rl+ +v+lkred+qpv+sfklrGayn++aqls+ +  +Gv++asaGnhaqGv
  lcl|FitnessBrowser__MR1:203422  33 YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQGV 111
                                     99***************************************************************************** PP

                       TIGR01124  81 alsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtvalel 159
                                     a+sa+  Gv avivmpettp+ikvdav+  Gg+vvlhG+++d+a+ +a+ +aq++g  +iapfdd+ viaGqGt+a e+
  lcl|FitnessBrowser__MR1:203422 112 AMSAASRGVDAVIVMPETTPDIKVDAVRRLGGNVVLHGQAFDQANGFAMTMAQQEGRVYIAPFDDEAVIAGQGTIAQEM 190
                                     ******************************************************************************* PP

                       TIGR01124 160 lrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdet 238
                                     l+q++ dl+ +fvpvGGGGliaG+aa+ k+++p++k++gve+ed+a+lk+a+eaGe+v+l+qvGlfadGvavk++G+e 
  lcl|FitnessBrowser__MR1:203422 191 LQQQR-DLEVIFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLSQVGLFADGVAVKRIGTEP 268
                                     ***99.9************************************************************************ PP

                       TIGR01124 239 frlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgi....edktlvailsGanlnfdrlry 313
                                     fr++k  +d +v+v +de+caa+kd+fedtra++epaGal+laGlkkyv ++      ++++++ailsGan+nf++lry
  lcl|FitnessBrowser__MR1:203422 269 FRVAKLCVDAVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYVSTNATgesgRGEKVAAILSGANVNFHSLRY 347
                                     *************************************************997653333789****************** PP

                       TIGR01124 314 vseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eerkellarleeagyk 391
                                     vser+elGeq+ea+lav +pe++Gs+l+f+e+l +r +tefnyr++ ++ a +f G++l++   e ++++++le++g++
  lcl|FitnessBrowser__MR1:203422 348 VSERCELGEQKEAVLAVKVPERPGSFLRFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGhGELEQIINTLEDNGFE 426
                                     **********************************************************99875899************* PP

                       TIGR01124 392 vvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpde 470
                                     v dl+ de aklhvry+vGG + +  +erl+sfefpe+pGallkfl+tlq++wnislfhyrnhGa++Grvl+g+evp +
  lcl|FitnessBrowser__MR1:203422 427 VQDLSGDETAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGAAFGRVLAGFEVPAS 505
                                     ******************************************************************************* PP

                       TIGR01124 471 eaeefeqflaelgyryedetenpayrlfl 499
                                     +a  f+qfl elg+ y++et++pay+lfl
  lcl|FitnessBrowser__MR1:203422 506 DALPFQQFLTELGFVYQEETQSPAYQLFL 534
                                     ****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (545 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: 00:00:00.03
# Mc/sec: 8.08
//
[ok]

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

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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 catabolism of small carbon sources