Alignments for a candidate for tdcB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Herbaspirillum seropedicae SmR1

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate HSERO_RS19510 HSERO_RS19510 threonine dehydratase

Query= SwissProt::A0FKE6
         (606 letters)



>FitnessBrowser__HerbieS:HSERO_RS19510
          Length = 508

 Score =  531 bits (1368), Expect = e-155
 Identities = 276/505 (54%), Positives = 358/505 (70%), Gaps = 7/505 (1%)

Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166
           +YL  IL+++VYDVA ETPL+ A  LS+R+   ++ KRED+Q VFSFK+RGAYN MA L 
Sbjct: 4   DYLKKILTARVYDVAQETPLELANTLSQRIDNRIYFKREDMQSVFSFKLRGAYNKMAHLT 63

Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGATVVLVGDS 226
             QL++GVIC+SAGNHAQGVALSA RLGC AVIVMP TTP +K  +VK  G  VVL GDS
Sbjct: 64  PAQLKRGVICASAGNHAQGVALSAARLGCRAVIVMPTTTPQVKIDAVKARGGEVVLFGDS 123

Query: 227 YDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGGGLI 286
           + +A  +A    + +  TF+ PFD P VI GQGTVGMEI RQ  D IHAIFV +GGGGLI
Sbjct: 124 FTDAYEHALTLEKKQKLTFVHPFDDPYVIAGQGTVGMEILRQHPDPIHAIFVAIGGGGLI 183

Query: 287 AGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETYR 346
           AG+A+Y+K V PDIKIIGV+  D++A+A SL  G+RV L  VG F+DG AVK+VGEET+R
Sbjct: 184 AGVASYVKAVRPDIKIIGVQTTDSDAMARSLKAGRRVALPDVGLFSDGTAVKLVGEETFR 243

Query: 347 LCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAY-----CKYYGLKGE 401
           + +EL+D V++V  DA+C +IKD+F++ RSI+EPAGALA+AGA+AY          +KGE
Sbjct: 244 IAKELVDEVIIVDTDAVCTAIKDIFQDTRSIVEPAGALAVAGAKAYVERAKASKKPIKGE 303

Query: 402 NVVAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFK 461
           +++ I  GANMNFDRLR V E+AD G  REAV A  +PE+ GSF++F E VGP N+TEF 
Sbjct: 304 SLITIACGANMNFDRLRFVAEMADAGEAREAVFAVTIPEERGSFRRFCETVGPRNVTEFN 363

Query: 462 YRYNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTN 521
           YR  SD + A V   + +    E   +    E A    ++LT ++L K H+RHL+GG+++
Sbjct: 364 YRI-SDAKAAHVFVGIQVSAADEAGKIARNFEKAGFGVLDLTHDELAKVHIRHLVGGKSD 422

Query: 522 V-HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVE 580
           +  +ELL RF FPE+PGALMKFL + +P WNISLFHYR QG     +L+G+QVP  E+ E
Sbjct: 423 LTGDELLYRFEFPERPGALMKFLSSMNPGWNISLFHYRNQGGDVGRILIGLQVPKKEMKE 482

Query: 581 FEGRADSLGYEYAMESLNEAYQLIM 605
           F      LGY +  ES N  Y+L +
Sbjct: 483 FRAFLAQLGYRHWDESKNPLYKLFL 507


Lambda     K      H
   0.318    0.136    0.393 

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: 703
Number of extensions: 32
Number of successful extensions: 6
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: 606
Length of database: 508
Length adjustment: 36
Effective length of query: 570
Effective length of database: 472
Effective search space:   269040
Effective search space used:   269040
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate HSERO_RS19510 HSERO_RS19510 (threonine dehydratase)
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.17683.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     2e-249  814.2   0.3   2.3e-249  814.0   0.3    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19510  HSERO_RS19510 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19510  HSERO_RS19510 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.0   0.3  2.3e-249  2.3e-249       1     499 []       4     507 ..       4     507 .. 0.99

  Alignments for each domain:
  == domain 1  score: 814.0 bits;  conditional E-value: 2.3e-249
                                  TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGv 68 
                                                dyl++il+arvy++a+etple a++ls+r++nr+++kred+q vfsfklrGaynkma+l++ q  +Gv
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510   4 DYLKKILTARVYDVAQETPLELANTLSQRIDNRIYFKREDMQSVFSFKLRGAYNKMAHLTPAQLKRGV 71 
                                                89****************************************************************** PP

                                  TIGR01124  69 iaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekg 136
                                                i+asaGnhaqGvalsa++lG++avivmp+ttp++k+davka+Ggevvl G+++ +a+++al l++++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510  72 ICASAGNHAQGVALSAARLGCRAVIVMPTTTPQVKIDAVKARGGEVVLFGDSFTDAYEHALTLEKKQK 139
                                                ******************************************************************** PP

                                  TIGR01124 137 ltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaeds 204
                                                ltf++pfddp viaGqGtv++e+lrq+ ++++a+fv++GGGGliaGva++vk+++p+ik+igv+++ds
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 140 LTFVHPFDDPYVIAGQGTVGMEILRQHPDPIHAIFVAIGGGGLIAGVASYVKAVRPDIKIIGVQTTDS 207
                                                ******************************************************************** PP

                                  TIGR01124 205 aalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravl 272
                                                +a++++l+aG+rv l +vGlf+dG+avk vG+etfr++ke++d+++ vdtd+vc+aikd+f+dtr+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 208 DAMARSLKAGRRVALPDVGLFSDGTAVKLVGEETFRIAKELVDEVIIVDTDAVCTAIKDIFQDTRSIV 275
                                                ******************************************************************** PP

                                  TIGR01124 273 epaGalalaGlkkyvak.....kgiedktlvailsGanlnfdrlryvseraelGeqreallavtipee 335
                                                epaGala+aG k+yv++     k i++++l++i++Gan+nfdrlr+v+e a+ Ge rea++avtipee
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 276 EPAGALAVAGAKAYVERakaskKPIKGESLITIACGANMNFDRLRFVAEMADAGEAREAVFAVTIPEE 343
                                                **************97522222568999**************************************** PP

                                  TIGR01124 336 kGsllkfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelakl 403
                                                +Gs+++f+e +G r++tefnyr++d+++ah+fvG+q++  +e+ ++++++e+ag+ v+dlt+delak+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 344 RGSFRRFCETVGPRNVTEFNYRISDAKAAHVFVGIQVSAADEAGKIARNFEKAGFGVLDLTHDELAKV 411
                                                ******************************************************************** PP

                                  TIGR01124 404 hvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdee 471
                                                h+r+lvGG+++ + +e ly+fefperpGal+kfl+++++ wnislfhyrn G+d Gr+l+gl+vp++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 412 HIRHLVGGKSDLTGDELLYRFEFPERPGALMKFLSSMNPGWNISLFHYRNQGGDVGRILIGLQVPKKE 479
                                                ******************************************************************** PP

                                  TIGR01124 472 aeefeqflaelgyryedetenpayrlfl 499
                                                ++ef  fla+lgyr +de++np y+lfl
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 480 MKEFRAFLAQLGYRHWDESKNPLYKLFL 507
                                                ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (508 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.55
//
[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