Alignments for a candidate for tdcB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pseudomonas stutzeri RCH2

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF3797 Psest_3866 threonine ammonia-lyase, biosynthetic, long form

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__psRCH2:GFF3797
          Length = 504

 Score =  523 bits (1347), Expect = e-153
 Identities = 262/499 (52%), Positives = 359/499 (71%), Gaps = 2/499 (0%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           Y++ +L + VY+ A  TPLQ   +LS R+ N IL+KRED QPV SFK+RGAY  +A L+ 
Sbjct: 5   YVKKILTSRVYDVAIETPLQPARQLSERIGNQILLKREDLQPVFSFKVRGAYNKLAQLSA 64

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
           E+ A GV+TASAGNHAQGVA ++ +LG+KA IVMP  T ++KV  VR  GG+V+LHG  F
Sbjct: 65  EELARGVVTASAGNHAQGVALAAKQLGIKATIVMPRTTPELKVQGVRARGGKVVLHGDAF 124

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGGGLAA 194
            EA A +++L +++G+ ++ P+D P VIAGQGT+A+E+L+Q    +D +FVPVGGGGL A
Sbjct: 125 PEALAYSLKLVEEKGYVYIHPYDDPDVIAGQGTVAMEILRQHQGPIDAIFVPVGGGGLVA 184

Query: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254
           G+A  +K L PQ KVI VE +DS CL+AA+ AG  V L +VGLFA+GVAV +IG  TF +
Sbjct: 185 GIAAYVKYLYPQTKVIGVEPDDSNCLQAAMAAGERVVLEQVGLFADGVAVAQIGQHTFEI 244

Query: 255 CQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHIL 314
           C+ Y+D++ITV +D ICAA+KD+++D R++ EP+GAL++AG+KKY+    + G+ L  I 
Sbjct: 245 CRHYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALSVAGIKKYVEREGVSGQVLVGID 304

Query: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADA 374
           SGANVNF  LR+V+ER ELGE+REA++AVTIPE+ GSF  FC+ +G R +TEFNYR+   
Sbjct: 305 SGANVNFDRLRHVAERAELGEKREAIIAVTIPEQPGSFKAFCEAIGKRQITEFNYRYHTD 364

Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434
           + A IFVGV+     + R  ++Q L D G+ V+DL+D+E+AKLH R+MVGG       E 
Sbjct: 365 REAHIFVGVQTHPENDPRAALVQGLRDKGFPVLDLTDNELAKLHTRHMVGGHAVGVSNEM 424

Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETRLN 493
           +  FEFPE PGAL  FLN LG  WNIS+FHYR+HG   GRV+A  ++  D        L+
Sbjct: 425 VLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPADERHLVPAALD 484

Query: 494 ELGYDCHDETNNPAFRFFL 512
           ++GY   DE+ NPA++ FL
Sbjct: 485 KIGYRYWDESENPAYKLFL 503


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: 709
Number of extensions: 46
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: 504
Length adjustment: 34
Effective length of query: 480
Effective length of database: 470
Effective search space:   225600
Effective search space used:   225600
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 GFF3797 Psest_3866 (threonine ammonia-lyase, biosynthetic, long form)
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.32386.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.7e-249  813.8   0.3   3.1e-249  813.6   0.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3797  Psest_3866 threonine ammonia-lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3797  Psest_3866 threonine ammonia-lyase, biosynthetic, long form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  813.6   0.3  3.1e-249  3.1e-249       2     499 .]       5     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 813.6 bits;  conditional E-value: 3.1e-249
                           TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 
                                         y+++il++rvy++a+etpl++a++lser++n++llkredlqpvfsfk+rGaynk+aqlsae+ a+Gv++asaGnh
  lcl|FitnessBrowser__psRCH2:GFF3797   5 YVKKILTSRVYDVAIETPLQPARQLSERIGNQILLKREDLQPVFSFKVRGAYNKLAQLSAEELARGVVTASAGNH 79 
                                         899************************************************************************ PP

                           TIGR01124  77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151
                                         aqGval+ak+lG+ka+ivmp+ttpe+kv+ v+a+Gg+vvlhG+++ ea a++l+l +ekg  +i+p+ddp+viaG
  lcl|FitnessBrowser__psRCH2:GFF3797  80 AQGVALAAKQLGIKATIVMPRTTPELKVQGVRARGGKVVLHGDAFPEALAYSLKLVEEKGYVYIHPYDDPDVIAG 154
                                         *************************************************************************** PP

                           TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226
                                         qGtva+e+lrq++ ++da+fvpvGGGGl+aG+aa+vk l+p+ kvigve++ds++l++a++aGerv l+qvGlfa
  lcl|FitnessBrowser__psRCH2:GFF3797 155 QGTVAMEILRQHQGPIDAIFVPVGGGGLVAGIAAYVKYLYPQTKVIGVEPDDSNCLQAAMAAGERVVLEQVGLFA 229
                                         *************************************************************************** PP

                           TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301
                                         dGvav ++G++tf++c++y+d++++v tde+caaikd+++dtr+++epaGal++aG+kkyv+++g++++ lv i 
  lcl|FitnessBrowser__psRCH2:GFF3797 230 DGVAVAQIGQHTFEICRHYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALSVAGIKKYVEREGVSGQVLVGID 304
                                         *************************************************************************** PP

                           TIGR01124 302 sGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeee 376
                                         sGan+nfdrlr+v+eraelGe+rea++avtipe++Gs++ f+e +G+r+itefnyr+  d +ahifvGvq++ e+
  lcl|FitnessBrowser__psRCH2:GFF3797 305 SGANVNFDRLRHVAERAELGEKREAIIAVTIPEQPGSFKAFCEAIGKRQITEFNYRYHTDREAHIFVGVQTHPEN 379
                                         ***********************************************************************9875 PP

                           TIGR01124 377 e.rkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfh 450
                                         + r+ l++ l+++g+ v+dltd+elaklh r++vGG a  v+ne +++fefperpGal +fl++l ++wnis+fh
  lcl|FitnessBrowser__psRCH2:GFF3797 380 DpRAALVQGLRDKGFPVLDLTDNELAKLHTRHMVGGHAVGVSNEMVLRFEFPERPGALFNFLNKLGGRWNISMFH 454
                                         53899********************************************************************** PP

                           TIGR01124 451 yrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                         yrnhGa+ Grv++gl+vp +e +    +l+++gyry+de+enpay+lfl
  lcl|FitnessBrowser__psRCH2:GFF3797 455 YRNHGAADGRVVAGLQVPADERHLVPAALDKIGYRYWDESENPAYKLFL 503
                                         ************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (504 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: 8.20
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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