Alignments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2E3

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate AO353_08485 AO353_08485 threonine dehydratase

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08485
          Length = 504

 Score =  531 bits (1368), Expect = e-155
 Identities = 263/500 (52%), Positives = 363/500 (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   QYVKKILTSRVYDVAVETPLQTARQLSERLGNKIWLKREDLQPVFSFKIRGAYNKLTQLS 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    +D +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGPIDAIFVPVGGGGLI 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 AGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFD 243

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           +C++Y+D++ITV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+ L+ + G+ L  I
Sbjct: 244 ICKDYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVELYGVTGQTLVAI 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  L + G+ V+DL+D+E+AKLH+R+MVGGR +  + E
Sbjct: 364 GSEAHIFVGVQTHPENDPRSALLASLTEQGFPVLDLTDNELAKLHIRHMVGGRAAQVVDE 423

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

Query: 493 NELGYDCHDETNNPAFRFFL 512
            E+GY   DE++NPA++ FL
Sbjct: 484 AEIGYPYWDESDNPAYQLFL 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: 702
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 AO353_08485 AO353_08485 (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.30707.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     5e-250  816.2   0.0   5.7e-250  816.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485  AO353_08485 threonine dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485  AO353_08485 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  816.0   0.0  5.7e-250  5.7e-250       1     499 []       4     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 816.0 bits;  conditional E-value: 5.7e-250
                                     TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqka 65 
                                                   +y+++il++rvy++avetpl++a++lserl+n+++lkredlqpvfsfk+rGaynk++qls+e++a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485   4 QYVKKILTSRVYDVAVETPLQTARQLSERLGNKIWLKREDLQPVFSFKIRGAYNKLTQLSDEERA 68 
                                                   699************************************************************** PP

                                     TIGR01124  66 kGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakale 130
                                                   +Gv++asaGnhaqG+al+ak lGvka+ivmp+ttpeikv+ v+++Gg+vvlhG+++ ea a++l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485  69 RGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDSFPEALAYSLK 133
                                                   ***************************************************************** PP

                                     TIGR01124 131 laqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeik 195
                                                   l +ekg  +i+p+ddp  iaGqGtva+e+lrq+  ++da+fvpvGGGGliaG+aa+vk l+peik
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485 134 LVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGPIDAIFVPVGGGGLIAGIAAYVKYLRPEIK 198
                                                   ***************************************************************** PP

                                     TIGR01124 196 vigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaa 260
                                                   +igve++ds++l++a++aGerv l +vGlfadGvav ++G++tf++ck+y+d++++v tde+caa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485 199 IIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFDICKDYVDEVITVSTDEICAA 263
                                                   ***************************************************************** PP

                                     TIGR01124 261 ikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqre 325
                                                   ikd+++dtr+++epaGal++aG+kkyv+  g++++tlvai sGan+nfdrlr+v+eraelGe re
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485 264 IKDIYDDTRSITEPAGALGVAGIKKYVELYGVTGQTLVAIDSGANVNFDRLRHVAERAELGEGRE 328
                                                   ***************************************************************** PP

                                     TIGR01124 326 allavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeee.rkellarleeag 389
                                                   a++avtipe++Gs++ f+e +G+r+itefnyr+   ++ahifvGvq++ e++ r+ lla+l+e+g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485 329 AIIAVTIPEKPGSFKAFCEAIGKRQITEFNYRYNTGSEAHIFVGVQTHPENDpRSALLASLTEQG 393
                                                   ***********************************************988553899********* PP

                                     TIGR01124 390 ykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnh 454
                                                   + v+dltd+elaklh+r++vGGraa+v +e +++fefperpGal +fl++l ++wnis+fhyrnh
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485 394 FPVLDLTDNELAKLHIRHMVGGRAAQVVDEVVLRFEFPERPGALFNFLNKLGGRWNISMFHYRNH 458
                                                   ***************************************************************** PP

                                     TIGR01124 455 GadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                                   Ga+ Grv++gl+vp+ee +    +lae+gy y+de++npay+lfl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08485 459 GAADGRVVAGLQVPHEERHLVPAALAEIGYPYWDESDNPAYQLFL 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: 00:00:00.02
# Mc/sec: 12.12
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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