Alignments for a candidate for tdcB in Pontimonas salivibrio CL-TW6

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pontimonas salivibrio CL-TW6

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_104913117.1 C3B54_RS02615 threonine ammonia-lyase

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_002950575.1:WP_104913117.1
          Length = 419

 Score =  335 bits (860), Expect = 1e-96
 Identities = 176/375 (46%), Positives = 251/375 (66%), Gaps = 5/375 (1%)

Query: 26  SHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNHAQGVAF 85
           S +  E LG+P++ KCENLQRTG++KIRGA N M+    E  A+GV+ ASAGNHAQGVAF
Sbjct: 40  SRYLEELLGVPVFMKCENLQRTGSYKIRGAFNRMSKLSEEERARGVVAASAGNHAQGVAF 99

Query: 86  SADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERGALFVHP 145
           +A  LG+ +T+F P      K+ ATR YGAEVVLTG        AA +  ++ GA+ + P
Sbjct: 100 AAKELGIKATIFTPTGVALPKLQATRAYGAEVVLTGDTMIGPLRAASEFAKQTGAVRIPP 159

Query: 146 FDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAIRETHP----HVRIIGV 201
           FD   V+AGQGT+GLE+L ++P+V  ++VPIGGGGL+AG+A+ +++        +++IGV
Sbjct: 160 FDHHDVVAGQGTVGLEILDQMPEVETVVVPIGGGGLMAGVASVMKQRAALEGRSIKVIGV 219

Query: 202 ETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEEIAL 261
           +   A     S++ GKIV+V V  T+ADGIAV KPG   F II+  VDEVV V+++E A 
Sbjct: 220 QATNAAPYPLSIEAGKIVEVSVKPTIADGIAVSKPGELNFDIIKHTVDEVVTVDDDETAR 279

Query: 262 AIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNIDVKTISVVVERGLVA 321
           AI+ LLER K++VE AGAV +AA+++  V   +G T  +LSGGNID   +  V+ RGL +
Sbjct: 280 AILVLLERAKMVVEPAGAVAVAAVMSGLV-KATGPTAVILSGGNIDPMILERVISRGLAS 338

Query: 322 AGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDRRSKSLPIGKTEVLIELETRGF 381
           +GRY+K+++ L D PG LAR +  +A+  AN+  + H R    L I + E+ + +ETRG 
Sbjct: 339 SGRYMKMRIPLPDRPGQLARTSEIVADENANVVEVLHTRHGTGLQISQVELELHIETRGP 398

Query: 382 EHIQEVISHLQGVGY 396
           EH ++V+  L+  GY
Sbjct: 399 EHAEQVLEALRREGY 413


Lambda     K      H
   0.319    0.137    0.383 

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: 354
Number of extensions: 10
Number of successful extensions: 3
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: 402
Length of database: 419
Length adjustment: 31
Effective length of query: 371
Effective length of database: 388
Effective search space:   143948
Effective search space used:   143948
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: 50 (23.9 bits)

Align candidate WP_104913117.1 C3B54_RS02615 (threonine ammonia-lyase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.944435.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-141  457.0   2.7   2.8e-141  456.8   2.7    1.0  1  NCBI__GCF_002950575.1:WP_104913117.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002950575.1:WP_104913117.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.8   2.7  2.8e-141  2.8e-141       1     377 [.      35     414 ..      35     417 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.8 bits;  conditional E-value: 2.8e-141
                             TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 
                                           tp+e s  l ++ g  v++k enlq+tGs+kirGa+n+++klseee+ rGvvaasaGnhaqGva+aak  gik
  NCBI__GCF_002950575.1:WP_104913117.1  35 TPMEVSRYLEELLGVPVFMKCENLQRTGSYKIRGAFNRMSKLSEEERARGVVAASAGNHAQGVAFAAKELGIK 107
                                           89*********************************************************************** PP

                             TIGR01127  74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146
                                           a+i  P    l k++at++yGaev+L G+++    ++a+e+a+++g+v + +fd + v+aGqGt+gleil+++
  NCBI__GCF_002950575.1:WP_104913117.1 108 ATIFTPTGVALPKLQATRAYGAEVVLTGDTMIGPLRAASEFAKQTGAVRIPPFDHHDVVAGQGTVGLEILDQM 180
                                           ************************************************************************* PP

                             TIGR01127 147 pdvdtvivPvGGGGLisGvasavkkln....pevkviGveaeaapslveslkegkikavesvktiaDGiavkk 215
                                           p+v+tv+vP+GGGGL++Gvas++k+        +kviGv+a +a     s+++gki++v+++ tiaDGiav k
  NCBI__GCF_002950575.1:WP_104913117.1 181 PEVETVVVPIGGGGLMAGVASVMKQRAalegRSIKVIGVQATNAAPYPLSIEAGKIVEVSVKPTIADGIAVSK 253
                                           ************************976222258**************************************** PP

                             TIGR01127 216 pgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidl 288
                                           pg+l+f+i+k++vDevv+vd++e a+ail+Llerak+v+e+aGav+vaav++  v++ g  +av++sGGnid+
  NCBI__GCF_002950575.1:WP_104913117.1 254 PGELNFDIIKHTVDEVVTVDDDETARAILVLLERAKMVVEPAGAVAVAAVMSGLVKATG-PTAVILSGGNIDP 325
                                           ***********************************************************.899********** PP

                             TIGR01127 289 nllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgk 361
                                            +le++i +gL++sgr++k++  l+D+PG+L +  e++a+++an+v++ h r  + +++++ ++el++e++g+
  NCBI__GCF_002950575.1:WP_104913117.1 326 MILERVISRGLASSGRYMKMRIPLPDRPGQLARTSEIVADENANVVEVLHTRHGTGLQISQVELELHIETRGP 398
                                           ************************************************************************* PP

                             TIGR01127 362 ehleellktlrdkgye 377
                                           eh e++l+ lr +gye
  NCBI__GCF_002950575.1:WP_104913117.1 399 EHAEQVLEALRREGYE 414
                                           ***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (419 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: 00:00:00.01
# Mc/sec: 14.93
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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