Alignments for a candidate for tdcB in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Rhodospirillum centenum SW SW; ATCC 51521

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_012568310.1 RC1_RS15150 threonine ammonia-lyase

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_000016185.1:WP_012568310.1
          Length = 427

 Score =  285 bits (730), Expect = 1e-81
 Identities = 169/402 (42%), Positives = 235/402 (58%), Gaps = 4/402 (0%)

Query: 2   LPYTL--IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFM 59
           LP +L  I+ A + LR +V  T  I S   S+  G  I+ K ENLQ T +FK RGA N +
Sbjct: 24  LPVSLDDIRAAAEALRGQVVETPCIPSRTLSQITGAEIWVKFENLQFTASFKERGAFNKL 83

Query: 60  TSQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVL 119
            +   E   +GV+  SAGNHAQGVA+ A  LGVP+T+ MPE TP  KV  T ++GA VVL
Sbjct: 84  RTLTEEERRRGVVAMSAGNHAQGVAYHAGRLGVPATIVMPEGTPFVKVEHTENFGARVVL 143

Query: 120 TGRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGG 179
            G N  E+   A +   E G + VHP+DD  V+AGQGT+ LE+L   PD+  ++VP+GGG
Sbjct: 144 KGANLGESQIEAERLVREEGLVLVHPYDDAEVIAGQGTVALEMLAAAPDLEVLVVPVGGG 203

Query: 180 GLIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVN 239
           GLI+GIATA +   P + ++GVE  A  +   +L +G+   V    T+A+GIAVK  G  
Sbjct: 204 GLISGIATAAKAVKPDIEVVGVEVEAYAAVAQAL-RGEPPHVGGD-TIAEGIAVKNVGRL 261

Query: 240 TFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVC 299
           T  IIR LVDEV+LV + E+  A+   L   K + EGAGA  LAA+LN        K   
Sbjct: 262 TLQIIRALVDEVMLVPDAEVERAVALFLNIEKTVAEGAGAAGLAAVLNHPERFQGRKVGL 321

Query: 300 VLSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHD 359
           VL GGNID + ++ V+ R LV  GR + L++ + D PG L R+ + + EA  NI    H 
Sbjct: 322 VLCGGNIDSRLLAQVIMRQLVREGRLIALRIAIPDRPGGLGRITSVVGEAGGNIIEAMHQ 381

Query: 360 RRSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLVDVL 401
           R   +  +  T++ + +E R   H  +V+  L+  G+ V +L
Sbjct: 382 RLFTTATVKSTDIDLTIECRSARHAAKVVQALRDAGFGVKIL 423


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: 368
Number of extensions: 11
Number of successful extensions: 2
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: 427
Length adjustment: 31
Effective length of query: 371
Effective length of database: 396
Effective search space:   146916
Effective search space used:   146916
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_012568310.1 RC1_RS15150 (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.439574.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-133  430.9   4.7   2.4e-133  430.7   4.7    1.0  1  NCBI__GCF_000016185.1:WP_012568310.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016185.1:WP_012568310.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.7   4.7  2.4e-133  2.4e-133       1     380 []      45     422 ..      45     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 430.7 bits;  conditional E-value: 2.4e-133
                             TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 
                                           tp + s tls+itgae+++k enlq t sfk rGa+nk+++l+eee++rGvva saGnhaqGva+ a + g++
  NCBI__GCF_000016185.1:WP_012568310.1  45 TPCIPSRTLSQITGAEIWVKFENLQFTASFKERGAFNKLRTLTEEERRRGVVAMSAGNHAQGVAYHAGRLGVP 117
                                           78999******************************************************************** PP

                             TIGR01127  74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146
                                           a+ivmPe +p  kv+ t+++Ga v+L+Ga++ e++  ae+l +eeg+v+vh++dD +viaGqGt++le+l+  
  NCBI__GCF_000016185.1:WP_012568310.1 118 ATIVMPEGTPFVKVEHTENFGARVVLKGANLGESQIEAERLVREEGLVLVHPYDDAEVIAGQGTVALEMLAAA 190
                                           ************************************************************************* PP

                             TIGR01127 147 pdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdl 219
                                           pd+++++vPvGGGGLisG+a+a+k ++p++ v+Gve ea  +++++l+ + +  +   +tia+Giavk++g+l
  NCBI__GCF_000016185.1:WP_012568310.1 191 PDLEVLVVPVGGGGLISGIATAAKAVKPDIEVVGVEVEAYAAVAQALRGEPP--HVGGDTIAEGIAVKNVGRL 261
                                           ***********************************************86554..45789************** PP

                             TIGR01127 220 tfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnlle 292
                                           t +i++ lvDev+ v + e+ +a+ l+l+ +k+vaegaGa+g+aavl++    +g+kv++v++GGnid +ll 
  NCBI__GCF_000016185.1:WP_012568310.1 262 TLQIIRALVDEVMLVPDAEVERAVALFLNIEKTVAEGAGAAGLAAVLNHPERFQGRKVGLVLCGGNIDSRLLA 334
                                           ************************************************9999********************* PP

                             TIGR01127 293 kiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehle 365
                                           ++i+++Lv++gr++ ++  ++D+PG L +++ v+ e+++ni+++ h+rl +  ++  + + l++e +  +h  
  NCBI__GCF_000016185.1:WP_012568310.1 335 QVIMRQLVREGRLIALRIAIPDRPGGLGRITSVVGEAGGNIIEAMHQRLFTTATVKSTDIDLTIECRSARHAA 407
                                           ************************************************************************* PP

                             TIGR01127 366 ellktlrdkgyevkv 380
                                           ++ + lrd g+ vk+
  NCBI__GCF_000016185.1:WP_012568310.1 408 KVVQALRDAGFGVKI 422
                                           ***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (427 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.28
//
[ok]

This GapMind analysis is from Apr 09 2024. 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