Alignments for a candidate for tdcB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pseudomonas putida KT2440

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PP_3446 PP_3446 threonine deaminase

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Putida:PP_3446
          Length = 530

 Score =  545 bits (1405), Expect = e-159
 Identities = 276/501 (55%), Positives = 361/501 (72%), Gaps = 2/501 (0%)

Query: 14  AEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGL 73
           +E +R +L APVY+ A  TPLQ    LS+ L N +L+KRED QP  SFK+RGAY  ++ L
Sbjct: 29  SEQVRRILAAPVYDLAIETPLQAAPALSAALGNQVLLKREDLQPTFSFKIRGAYTRLSRL 88

Query: 74  TEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGA 133
           T+ Q+  GVITASAGNHAQGVA +++ LG+KA IVMPT T  +KV+ VR  GG V+LHG 
Sbjct: 89  TDVQRERGVITASAGNHAQGVALAASHLGMKATIVMPTTTPSLKVEGVRSRGGHVVLHGE 148

Query: 134 NFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGGGL 192
           +F  A   A++L+  +G T+VPPFD P VIAGQGT+A+E+L+Q    LD +FVPVGGGGL
Sbjct: 149 SFPHALTHALKLADSEGATFVPPFDDPDVIAGQGTVAMEILRQRPGALDAIFVPVGGGGL 208

Query: 193 AAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETF 252
            AG+A  +K L P +KVI VE  DS CL+AA+  G  V LP+VG FA+GVAV +IG   F
Sbjct: 209 IAGIAAYVKYLRPDVKVIGVEPADSNCLQAAMAVGERVILPQVGTFADGVAVAQIGAHCF 268

Query: 253 RLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAH 312
            LC+ ++D+++TV SD +CAA+KD+++D R++ EPSGALA+AG+KKY+A   ++G+ L  
Sbjct: 269 ELCRHFVDEVVTVSSDELCAAIKDIYDDTRSITEPSGALAVAGIKKYVAREGVQGQTLVA 328

Query: 313 ILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFA 372
           I SGANVNF  LR+V+ER ELGEQREA++AVTIPE+ GSF  FC  LG R +TEFNYRF 
Sbjct: 329 IDSGANVNFDRLRHVAERAELGEQREAIIAVTIPEQPGSFRAFCHALGKRQITEFNYRFY 388

Query: 373 DAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQ 432
             K A +FVGV+     + R+++L  L + GYSV+DL+D+E+AKLHVR+ VGG  +    
Sbjct: 389 PGKEARLFVGVQTHPVHDPREQLLASLREQGYSVLDLTDNELAKLHVRHTVGGHAASGAD 448

Query: 433 ERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETR 491
           ER+  FEFPE PGALL FL  LG  WNISLFHYR+HG    RV AA E+  D      + 
Sbjct: 449 ERVLRFEFPERPGALLGFLERLGKRWNISLFHYRNHGAAEARVFAALEVPADELAGLPST 508

Query: 492 LNELGYDCHDETNNPAFRFFL 512
           L+E+GY   DET+NPA++ FL
Sbjct: 509 LDEMGYRYWDETDNPAYKLFL 529


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: 736
Number of extensions: 38
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: 530
Length adjustment: 35
Effective length of query: 479
Effective length of database: 495
Effective search space:   237105
Effective search space used:   237105
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 PP_3446 PP_3446 (threonine deaminase)
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.12623.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.4e-239  779.5   0.0   7.4e-239  779.3   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3446  PP_3446 threonine deaminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3446  PP_3446 threonine deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  779.3   0.0  7.4e-239  7.4e-239       2     499 .]      31     529 ..      30     529 .. 0.99

  Alignments for each domain:
  == domain 1  score: 779.3 bits;  conditional E-value: 7.4e-239
                           TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 
                                          +r+il a vy+ a+etpl+ a  ls+ l+n+vllkredlqp fsfk+rGay+++++l++ q+ +Gvi+asaGnh
  lcl|FitnessBrowser__Putida:PP_3446  31 QVRRILAAPVYDLAIETPLQAAPALSAALGNQVLLKREDLQPTFSFKIRGAYTRLSRLTDVQRERGVITASAGNH 105
                                         5799*********************************************************************** PP

                           TIGR01124  77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151
                                         aqGval+a++lG+ka+ivmp+ttp++kv+ v+++Gg+vvlhGe++ +a ++al+la+ +g tf++pfddp+viaG
  lcl|FitnessBrowser__Putida:PP_3446 106 AQGVALAASHLGMKATIVMPTTTPSLKVEGVRSRGGHVVLHGESFPHALTHALKLADSEGATFVPPFDDPDVIAG 180
                                         *************************************************************************** PP

                           TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226
                                         qGtva+e+lrq    lda+fvpvGGGGliaG+aa+vk l+p++kvigve+ ds++l++a++ Gerv l qvG fa
  lcl|FitnessBrowser__Putida:PP_3446 181 QGTVAMEILRQRPGALDAIFVPVGGGGLIAGIAAYVKYLRPDVKVIGVEPADSNCLQAAMAVGERVILPQVGTFA 255
                                         *************************************************************************** PP

                           TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301
                                         dGvav ++G++ f+lc++++d++v+v +de+caaikd+++dtr+++ep+Gala+aG+kkyva++g++++tlvai 
  lcl|FitnessBrowser__Putida:PP_3446 256 DGVAVAQIGAHCFELCRHFVDEVVTVSSDELCAAIKDIYDDTRSITEPSGALAVAGIKKYVAREGVQGQTLVAID 330
                                         *************************************************************************** PP

                           TIGR01124 302 sGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee. 375
                                         sGan+nfdrlr+v+eraelGeqrea++avtipe++Gs++ f++ lG+r+itefnyr+ + ++a++fvGvq++   
  lcl|FitnessBrowser__Putida:PP_3446 331 SGANVNFDRLRHVAERAELGEQREAIIAVTIPEQPGSFRAFCHALGKRQITEFNYRFYPGKEARLFVGVQTHPVh 405
                                         ***********************************************************************9873 PP

                           TIGR01124 376 eerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfh 450
                                         + r++lla+l+e+gy+v+dltd+elaklhvr+ vGG aa+  +er+++fefperpGall fle l ++wnislfh
  lcl|FitnessBrowser__Putida:PP_3446 406 DPREQLLASLREQGYSVLDLTDNELAKLHVRHTVGGHAASGADERVLRFEFPERPGALLGFLERLGKRWNISLFH 480
                                         56999********************************************************************** PP

                           TIGR01124 451 yrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                         yrnhGa+  rv+++levp +e + + ++l+e+gyry+det+npay+lfl
  lcl|FitnessBrowser__Putida:PP_3446 481 YRNHGAAEARVFAALEVPADELAGLPSTLDEMGYRYWDETDNPAYKLFL 529
                                         ************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (530 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: 12.88
//
[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, 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

GapMind for catabolism of small carbon sources