Alignments for a candidate for tdcB in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Shewanella sp. ANA-3

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 7023121 Shewana3_0359 threonine dehydratase (RefSeq)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__ANA3:7023121
          Length = 547

 Score =  597 bits (1540), Expect = e-175
 Identities = 304/521 (58%), Positives = 394/521 (75%), Gaps = 11/521 (2%)

Query: 2   ADSQPLSGAPEGAE----YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQP 57
           + S+P + A E ++    YL+ +L + VY+ A+VTPL  + KLS+RL   + +KRED QP
Sbjct: 17  SQSKPGTSALEKSQLAQSYLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQP 76

Query: 58  VHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIK 117
           VHSFKLRGAY  +A L++ +   GV+ ASAGNHAQGVA S+A  GV A+IVMP  T DIK
Sbjct: 77  VHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQGVAMSAASRGVDAVIVMPETTPDIK 136

Query: 118 VDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD 177
           VDAVR  GG V+LHG  FD+A   A+E+++ +G  ++ PFD   VIAGQGT+A E+LQQ 
Sbjct: 137 VDAVRRLGGNVVLHGQAFDQANGFAMEMAKLEGRVYIAPFDDEAVIAGQGTIAQEMLQQQ 196

Query: 178 AHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGL 237
             L+ VFVPVGGGGL AG+A   K +MPQ+K++ VE ED+ACLKAA++AG PV L +VGL
Sbjct: 197 RDLEVVFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLAQVGL 256

Query: 238 FAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMK 297
           FA+GVAVKRIG E FRL + ++D+++TV SD ICAA+KD+FED RA+AEP+GAL+LAG+K
Sbjct: 257 FADGVAVKRIGTEPFRLAKWFVDEVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLK 316

Query: 298 KYIALH----NIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFL 353
           KY++ +    + +GE++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE  GSFL
Sbjct: 317 KYVSTNAAGESGKGEKVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPERPGSFL 376

Query: 354 KFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDE 413
           +FC+LL  R +TEFNYRF+    A +F G+RL++G  E ++I+  L D G+ V DLS DE
Sbjct: 377 RFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGHGELEQIINTLEDNGFEVQDLSGDE 436

Query: 414 MAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYG 473
            AKLHVRYMVGG P  PL+ERL+SFEFPE PGALL+FL TL + WNISLFHYR+HG  +G
Sbjct: 437 TAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGAAFG 496

Query: 474 RVLAAFEL--GDHEPDFETRLNELGYDCHDETNNPAFRFFL 512
           RVLA FE+  GD  P F+  L ELG+   +ET +PA++ FL
Sbjct: 497 RVLAGFEVPEGDALP-FQQFLTELGFVYQEETQSPAYQLFL 536


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: 769
Number of extensions: 26
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: 547
Length adjustment: 35
Effective length of query: 479
Effective length of database: 512
Effective search space:   245248
Effective search space used:   245248
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 7023121 Shewana3_0359 (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.4783.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.4e-236  769.2   0.2   9.7e-236  769.0   0.2    1.0  1  lcl|FitnessBrowser__ANA3:7023121  Shewana3_0359 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023121  Shewana3_0359 threonine dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  769.0   0.2  9.7e-236  9.7e-236       2     499 .]      35     536 ..      34     536 .. 0.98

  Alignments for each domain:
  == domain 1  score: 769.0 bits;  conditional E-value: 9.7e-236
                         TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaq 78 
                                       yl++il ++vy++a++tpl+  +kls+rl+ +v+lkred+qpv+sfklrGayn++aqls+ +  +Gv++asaGnhaq
  lcl|FitnessBrowser__ANA3:7023121  35 YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQ 111
                                       99*************************************************************************** PP

                         TIGR01124  79 GvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtv 155
                                       Gva+sa+  Gv avivmpettp+ikvdav+  Gg+vvlhG+++d+a+ +a+e+a+ +g  +iapfdd+ viaGqGt+
  lcl|FitnessBrowser__ANA3:7023121 112 GVAMSAASRGVDAVIVMPETTPDIKVDAVRRLGGNVVLHGQAFDQANGFAMEMAKLEGRVYIAPFDDEAVIAGQGTI 188
                                       ***************************************************************************** PP

                         TIGR01124 156 alellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavk 232
                                       a e+l+q++ dl+ vfvpvGGGGliaG+aa+ k+++p++k++gve+ed+a+lk+a+eaGe+v+l qvGlfadGvavk
  lcl|FitnessBrowser__ANA3:7023121 189 AQEMLQQQR-DLEVVFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLAQVGLFADGVAVK 264
                                       *******99.9****************************************************************** PP

                         TIGR01124 233 evGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgi....edktlvailsGan 305
                                       ++G+e frl+k ++d++v+v +de+caa+kd+fedtra++epaGal+laGlkkyv ++ +    ++++++ailsGan
  lcl|FitnessBrowser__ANA3:7023121 265 RIGTEPFRLAKWFVDEVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYVSTNAAgesgKGEKVAAILSGAN 341
                                       *******************************************************987653333789********** PP

                         TIGR01124 306 lnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eerkel 381
                                       +nf++lryvser+elGeq+ea+lav +pe++Gs+l+f+e+l +r +tefnyr++ ++ a +f G++l++   e +++
  lcl|FitnessBrowser__ANA3:7023121 342 VNFHSLRYVSERCELGEQKEAVLAVKVPERPGSFLRFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGhGELEQI 418
                                       ******************************************************************99875899*** PP

                         TIGR01124 382 larleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGady 458
                                       +++le++g++v dl+ de aklhvry+vGG + +  +erl+sfefpe+pGallkfl+tlq++wnislfhyrnhGa++
  lcl|FitnessBrowser__ANA3:7023121 419 INTLEDNGFEVQDLSGDETAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGAAF 495
                                       ***************************************************************************** PP

                         TIGR01124 459 Grvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                       Grvl+g+evp+ +a  f+qfl elg+ y++et++pay+lfl
  lcl|FitnessBrowser__ANA3:7023121 496 GRVLAGFEVPEGDALPFQQFLTELGFVYQEETQSPAYQLFL 536
                                       ****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (547 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: 11.38
//
[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:

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

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