GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2C3

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate AO356_10330 AO356_10330 threonine dehydratase

Query= BRENDA::P04968
         (514 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 AO356_10330
           threonine dehydratase
          Length = 504

 Score =  530 bits (1365), Expect = e-155
 Identities = 263/500 (52%), Positives = 360/500 (72%), Gaps = 2/500 (0%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +Y++ +L + VY+ A  TPLQ   +LS RL N IL+KRED QPV SFK+RGAY  +  L+
Sbjct: 4   QYVKKILTSRVYDVAVETPLQTARQLSERLGNSILLKREDLQPVFSFKIRGAYNKLTQLS 63

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134
           +E++A GV+TASAGNHAQG+A ++  LGVKA IVMP  T +IKV+ VR  GG+V+LHG +
Sbjct: 64  DEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDS 123

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLA 193
           F EA A +++L  ++G+ ++ P+D P  IAGQGT+A+E+L+Q    LD +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLI 183

Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253
           AG+A  +K L P IK+I VE +DS CL+AA+ AG  V LP VGLFA+GVAV +IG  TF 
Sbjct: 184 AGIAAYVKYLRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFD 243

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           +C+ ++D++ITV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+    I G+ L  I
Sbjct: 244 ICKHHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVESRGISGQTLVAI 303

Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373
            SGANVNF  LR+V+ER ELGE REA++AVTIPE+ GSF  FC+ +G R +TEFNYR+  
Sbjct: 304 DSGANVNFDRLRHVAERAELGEGREAIIAVTIPEQPGSFKAFCEAVGKRQITEFNYRYNT 363

Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433
              A IFVGV+     + R  ++  L + G+ V+DL+D+E+AKLH+R+MVGG  +H + E
Sbjct: 364 GSEAHIFVGVQTHPENDPRSALIASLTEQGFPVLDLTDNELAKLHIRHMVGGHAAHVIDE 423

Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDF-ETRL 492
            +  FEFPE PGAL  FLN LG  WNIS+FHYR+HG   GRV+A  ++   E       L
Sbjct: 424 VVLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPHDERHLVPAAL 483

Query: 493 NELGYDCHDETNNPAFRFFL 512
            E+GY   DE++NPA++ FL
Sbjct: 484 EEIGYPYWDESDNPAYQLFL 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: 707
Number of extensions: 36
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: 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 AO356_10330 AO356_10330 (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.25660.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-247  808.3   0.0   1.3e-247  808.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330  AO356_10330 threonine dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330  AO356_10330 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.1   0.0  1.3e-247  1.3e-247       1     499 []       4     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 808.1 bits;  conditional E-value: 1.3e-247
                                       TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeq 63 
                                                     +y+++il++rvy++avetpl++a++lserl+n +llkredlqpvfsfk+rGaynk++qls+e+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330   4 QYVKKILTSRVYDVAVETPLQTARQLSERLGNSILLKREDLQPVFSFKIRGAYNKLTQLSDEE 66 
                                                     699************************************************************ PP

                                       TIGR01124  64 kakGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeaka 126
                                                     +a+Gv++asaGnhaqG+al+ak lGvka+ivmp+ttpeikv+ v+++Gg+vvlhG+++ ea a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330  67 RARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDSFPEALA 129
                                                     *************************************************************** PP

                                       TIGR01124 127 kalelaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkq 189
                                                     ++l+l +ekg  +i+p+ddp  iaGqGtva+e+lrq+   lda+fvpvGGGGliaG+aa+vk 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 130 YSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLIAGIAAYVKY 192
                                                     *************************************************************** PP

                                       TIGR01124 190 llpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlv 252
                                                     l+p+ik+igve++ds++l++a++aGerv l +vGlfadGvav ++G++tf++ck+++d++++v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 193 LRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFDICKHHVDEVITV 255
                                                     *************************************************************** PP

                                       TIGR01124 253 dtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvs 315
                                                      tde+caaikd+++dtr+++epaGal++aG+kkyv+++gi+++tlvai sGan+nfdrlr+v+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 256 STDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVESRGISGQTLVAIDSGANVNFDRLRHVA 318
                                                     *************************************************************** PP

                                       TIGR01124 316 eraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeee. 377
                                                     eraelGe rea++avtipe++Gs++ f+e +G+r+itefnyr+   ++ahifvGvq++ e++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 319 ERAELGEGREAIIAVTIPEQPGSFKAFCEAVGKRQITEFNYRYNTGSEAHIFVGVQTHPENDp 381
                                                     *********************************************************988553 PP

                                       TIGR01124 378 rkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletl 440
                                                     r+ l+a+l+e+g+ v+dltd+elaklh+r++vGG aa+v +e +++fefperpGal +fl++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 382 RSALIASLTEQGFPVLDLTDNELAKLHIRHMVGGHAAHVIDEVVLRFEFPERPGALFNFLNKL 444
                                                     899************************************************************ PP

                                       TIGR01124 441 qaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                                      ++wnis+fhyrnhGa+ Grv++gl+vp++e +    +l+e+gy y+de++npay+lfl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10330 445 GGRWNISMFHYRNHGAADGRVVAGLQVPHDERHLVPAALEEIGYPYWDESDNPAYQLFL 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: 8.07
//
[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 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