GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Pseudomonas fluorescens GW456-L13

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PfGW456L13_949 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949
          Length = 504

 Score =  529 bits (1362), Expect = e-154
 Identities = 261/500 (52%), Positives = 361/500 (72%), Gaps = 2/500 (0%)

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

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

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLA 193
           F EA A +++L  ++G+ ++ P+D P  IAGQGT+A+E+L+Q    LD +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPQPLDAIFVPVGGGGLI 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+    + G+    I
Sbjct: 244 ICKDHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVEQRGVSGQTFVAI 303

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

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

Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDF-ETRL 492
            +  FEFPE PGAL  FLN LG  WNIS+FHYR+HG   GRV+A  ++   E       L
Sbjct: 424 VILRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPHDERHLVPAAL 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: 721
Number of extensions: 37
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 PfGW456L13_949 (Threonine dehydratase biosynthetic (EC 4.3.1.19))
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.28916.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   4.3e-249  813.1   0.0   4.8e-249  812.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949  Threonine dehydratase biosynthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949  Threonine dehydratase biosynthetic (EC 4.3.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.9   0.0  4.8e-249  4.8e-249       1     499 []       4     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 812.9 bits;  conditional E-value: 4.8e-249
                                              TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkm 56 
                                                            +y+++il++rvy++avetpl+ a++lserl+n ++lkredlqpvfsfk+rGaynk+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949   4 QYVKKILTSRVYDVAVETPLQSARQLSERLGNSIWLKREDLQPVFSFKIRGAYNKL 59 
                                                            699***************************************************** PP

                                              TIGR01124  57 aqlsaeqkakGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg 112
                                                            +qls+e++a+Gv++asaGnhaqG+al+ak lGvka+ivmp+ttpeikv+ v+++Gg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949  60 TQLSDEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGG 115
                                                            ******************************************************** PP

                                              TIGR01124 113 evvlhGenydeakakalelaqekgltfiapfddplviaGqGtvalellrqveedld 168
                                                            +vvlhG+++ ea a++l+l +ekg  +i+p+ddp  iaGqGtva+e+lrq+ ++ld
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 116 KVVLHGDSFPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPQPLD 171
                                                            ******************************************************** PP

                                              TIGR01124 169 avfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGl 224
                                                            a+fvpvGGGGliaG+aa+vk l+p+ik+igve++ds++l++a++aGerv l +vGl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 172 AIFVPVGGGGLIAGIAAYVKYLRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGL 227
                                                            ******************************************************** PP

                                              TIGR01124 225 fadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalal 280
                                                            fadGvav ++G++tf++ck+++d++++v tde+caaikd+++dtr+++epaGal++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 228 FADGVAVAQIGQHTFDICKDHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGV 283
                                                            ******************************************************** PP

                                              TIGR01124 281 aGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeek 336
                                                            aG+kkyv+++g++++t+vai sGan+nfdrlr+v+eraelGe rea++avtipe++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 284 AGIKKYVEQRGVSGQTFVAIDSGANVNFDRLRHVAERAELGEGREAIIAVTIPEKP 339
                                                            ******************************************************** PP

                                              TIGR01124 337 GsllkfvevlGeraitefnyrladdekahifvGvqlaeeee.rkellarleeagyk 391
                                                            Gs++ f+e +G+r+itefnyr+   ++ahifvGvq++ e++ r+ l+a+l+e+g+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 340 GSFKAFCEAIGKRQITEFNYRYNTGSEAHIFVGVQTHPENDpRSALIASLSEQGFP 395
                                                            ************************************988553899*********** PP

                                              TIGR01124 392 vvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnis 447
                                                            v+dltd+elaklh+r++vGGraa+v +e +++fefperpGal +fl++l ++wnis
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 396 VLDLTDNELAKLHIRHMVGGRAAHVVDEVILRFEFPERPGALFNFLNKLGGRWNIS 451
                                                            ******************************************************** PP

                                              TIGR01124 448 lfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                                            +fhyrnhGa+ Grv++gl+vp++e +    +l+e+gy y+de++npay+lfl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 452 MFHYRNHGAADGRVVAGLQVPHDERHLVPAALEEIGYPYWDESDNPAYQLFL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.27
//
[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:

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