Alignments for a candidate for tdcB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Sphingomonas koreensis DSMZ 15582

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Ga0059261_3694 Ga0059261_3694 threonine ammonia-lyase, medium form

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__Korea:Ga0059261_3694
          Length = 420

 Score =  301 bits (772), Expect = 2e-86
 Identities = 176/405 (43%), Positives = 243/405 (60%), Gaps = 8/405 (1%)

Query: 2   LPYTL--IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFM 59
           LP TL  +Q A  R+   V  T  +HS   S+  G  +Y K ENLQ T A+K RGALN +
Sbjct: 18  LPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTL 77

Query: 60  TSQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVL 119
                 A AKGVI ASAGNHAQG+A+  + LG+P T+ MP+STP  KV  T  +GA ++L
Sbjct: 78  LQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKVMQTESHGATIIL 137

Query: 120 TGRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGG 179
            G  FDEAYA A Q +   G  FVHPFDDP ++AGQGT+ LE+L + P +  ++VPIGGG
Sbjct: 138 EGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAPAIDTLIVPIGGG 197

Query: 180 GLIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPV-TVTLADGIAVKKPGV 238
           GLI+G  T  +     + ++GV+    PS      +      P+   TLA+GIAVK+PG 
Sbjct: 198 GLISGALTVAKAADKPIEVVGVQAELFPS---MFNRFTGAHEPIGGDTLAEGIAVKEPGG 254

Query: 239 NTFPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTV 298
            T  I+  LVDE++LV E  +  A+  LL+  K +VEGAGA  LAAL+  +     GKTV
Sbjct: 255 LTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMT-QPERFRGKTV 313

Query: 299 -CVLSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIIT 357
             +L+GGNID + ++ V+ R L  +GR  +L++ L D PGAL ++A    E   NI  ++
Sbjct: 314 GVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVARIFQEQTVNILELS 373

Query: 358 HDRRSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLVDVLK 402
           H R   +LP     + +E ETR   H++ +IS LQ  GY V +++
Sbjct: 374 HQRIFTNLPAKGLSLDVECETRDRAHLERLISALQEAGYEVRLIE 418


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: 385
Number of extensions: 12
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: 420
Length adjustment: 31
Effective length of query: 371
Effective length of database: 389
Effective search space:   144319
Effective search space used:   144319
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 Ga0059261_3694 Ga0059261_3694 (threonine ammonia-lyase, medium form)
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.2075.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-131  423.9   0.0   3.2e-131  423.7   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3694  Ga0059261_3694 threonine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3694  Ga0059261_3694 threonine ammonia-lyase, medium form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.7   0.0  3.2e-131  3.2e-131       1     379 [.      39     415 ..      39     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 423.7 bits;  conditional E-value: 3.2e-131
                                 TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 
                                               tp  +s+tlsd+tga vylk enlq t ++k rGaln + +l +  + +Gv+aasaGnhaqG a+  ++
  lcl|FitnessBrowser__Korea:Ga0059261_3694  39 TPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTLLQLDDAARAKGVIAASAGNHAQGLAYHGNR 107
                                               78889**************************************************************** PP

                                 TIGR01127  70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138
                                                gi+ +ivmP+s+p  kv +t+s Ga +iL+G++fDeay++a++l++ +g++fvh+fdD+ +iaGqGt+
  lcl|FitnessBrowser__Korea:Ga0059261_3694 108 LGIPVTIVMPKSTPTVKVMQTESHGATIILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTV 176
                                               ********************************************************************* PP

                                 TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207
                                                le+l+d p +dt+ivP+GGGGLisG  +++k     + v+Gv+ae  ps+ + +    +++    +t+
  lcl|FitnessBrowser__Korea:Ga0059261_3694 177 FLEMLADAPAIDTLIVPIGGGGLISGALTVAKAADKPIEVVGVQAELFPSMFNRFTG--AHEPIGGDTL 243
                                               *****************************************************9975..4567789*** PP

                                 TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkk 276
                                               a+Giavk+pg lt +iv+ lvDe++ v+e ++ +a+ lLl+ +k+v+egaGa+g+aa++ +     gk+
  lcl|FitnessBrowser__Korea:Ga0059261_3694 244 AEGIAVKEPGGLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQPERFRGKT 312
                                               ************************************************************9999***** PP

                                 TIGR01127 277 vavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskei 345
                                               v+v+++GGnid++ll +++ ++L++sgr+++++  l+D+PGaL++++ + +e+  ni++++h+r+ +++
  lcl|FitnessBrowser__Korea:Ga0059261_3694 313 VGVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVARIFQEQTVNILELSHQRIFTNL 381
                                               ********************************************************************* PP

                                 TIGR01127 346 algaakvelelevkgkehleellktlrdkgyevk 379
                                               +    ++ +e e++++ hle+l + l++ gyev+
  lcl|FitnessBrowser__Korea:Ga0059261_3694 382 PAKGLSLDVECETRDRAHLERLISALQEAGYEVR 415
                                               *******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (420 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.44
//
[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
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