Alignments for a candidate for tdcB in Sphingomonas indica Dd16

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Sphingomonas indica Dd16

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_085217923.1 B9N75_RS05700 threonine ammonia-lyase

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_900177405.1:WP_085217923.1
          Length = 411

 Score =  283 bits (724), Expect = 6e-81
 Identities = 164/393 (41%), Positives = 233/393 (59%), Gaps = 4/393 (1%)

Query: 7   IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66
           I+ A DR+   V RT  + S   S+  G  ++ K ENLQ T A+K RGALN +       
Sbjct: 16  IRAAADRIAGAVVRTPTLLSRTLSDLTGANVWLKFENLQFTAAYKERGALNKLLLLDEAT 75

Query: 67  LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126
             +GVI ASAGNH+Q VA+    LGVP T+ MP+ TP  KV  T  +GA VVL G  FDE
Sbjct: 76  RRRGVIAASAGNHSQAVAYHGRRLGVPVTIVMPKPTPTMKVVQTEGHGATVVLHGELFDE 135

Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIA 186
           AYA A + + E G  FVHPFDDP V+AGQGT+ LE+L + P++  ++VPIGGGGLI+G+A
Sbjct: 136 AYAKAREMEGELGLTFVHPFDDPAVIAGQGTVALEMLDDAPNIDTLVVPIGGGGLISGMA 195

Query: 187 TAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVT-VTLADGIAVKKPGVNTFPIIR 245
            A +   P + ++G +    PS  Y+  +G+  ++P +  T+A+GIAVK+PG  T  ++ 
Sbjct: 196 AAAKAVKPDIAVVGAQAELYPSM-YAHIEGR--EMPSSGDTIAEGIAVKRPGDLTRQMVA 252

Query: 246 DLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGN 305
           DLVDE++LV E  I  A+  L++  K + EGAGA  LAALL             V++GGN
Sbjct: 253 DLVDEILLVPERAIETAVSLLVQIEKTVAEGAGATGLAALLTHPERFRGRNVGLVVTGGN 312

Query: 306 IDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDRRSKSL 365
           ID + ++ V+ R L  +GR  +L+V+L D PGAL  +     + + NI  + H R   +L
Sbjct: 313 IDTRLLATVLLRDLARSGRMARLRVQLHDRPGALFSVVRLFEQQQVNIVEVYHQRVFTNL 372

Query: 366 PIGKTEVLIELETRGFEHIQEVISHLQGVGYLV 398
           P     + IE E R   H+  +++ L   G+ V
Sbjct: 373 PAKDAFIDIECEARDKAHLDTLVAALGEAGFNV 405


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: 373
Number of extensions: 13
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: 411
Length adjustment: 31
Effective length of query: 371
Effective length of database: 380
Effective search space:   140980
Effective search space used:   140980
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_085217923.1 B9N75_RS05700 (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.3470375.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-130  419.0   0.0     1e-129  418.8   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085217923.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217923.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.8   0.0    1e-129    1e-129       1     378 [.      30     405 ..      30     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 418.8 bits;  conditional E-value: 1e-129
                             TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 
                                           tp   s tlsd+tga+v+lk enlq t ++k rGalnk+  l e  ++rGv+aasaGnh+q va+  ++ g++
  NCBI__GCF_900177405.1:WP_085217923.1  30 TPTLLSRTLSDLTGANVWLKFENLQFTAAYKERGALNKLLLLDEATRRRGVIAASAGNHSQAVAYHGRRLGVP 102
                                           677889******************************************************************* PP

                             TIGR01127  74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146
                                            +ivmP+ +p  kv +t++ Ga v+LhG+ fDeay+ a+e++ e g++fvh+fdD+ viaGqGt++le+l+d 
  NCBI__GCF_900177405.1:WP_085217923.1 103 VTIVMPKPTPTMKVVQTEGHGATVVLHGELFDEAYAKAREMEGELGLTFVHPFDDPAVIAGQGTVALEMLDDA 175
                                           ************************************************************************* PP

                             TIGR01127 147 pdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdl 219
                                           p++dt++vP+GGGGLisG+a+a+k ++p++ v+G +ae  ps+++ ++       +s +tia+Giavk+pgdl
  NCBI__GCF_900177405.1:WP_085217923.1 176 PNIDTLVVPIGGGGLISGMAAAAKAVKPDIAVVGAQAELYPSMYAHIEGRE--MPSSGDTIAEGIAVKRPGDL 246
                                           *********************************************987544..45789*************** PP

                             TIGR01127 220 tfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnlle 292
                                           t ++v +lvDe++ v e  i +a+ lL++ +k+vaegaGa+g+aa+l +     g++v++vv+GGnid++ll 
  NCBI__GCF_900177405.1:WP_085217923.1 247 TRQMVADLVDEILLVPERAIETAVSLLVQIEKTVAEGAGATGLAALLTHPERFRGRNVGLVVTGGNIDTRLLA 319
                                           ************************************************9999********************* PP

                             TIGR01127 293 kiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehle 365
                                           +++ ++L++sgr++++++ l+D+PGaL +++    +++ niv++ h+r+ ++++  +a + +e e ++k hl+
  NCBI__GCF_900177405.1:WP_085217923.1 320 TVLLRDLARSGRMARLRVQLHDRPGALFSVVRLFEQQQVNIVEVYHQRVFTNLPAKDAFIDIECEARDKAHLD 392
                                           ************************************************************************* PP

                             TIGR01127 366 ellktlrdkgyev 378
                                            l   l + g++v
  NCBI__GCF_900177405.1:WP_085217923.1 393 TLVAALGEAGFNV 405
                                           ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (411 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: 00:00:00.00
# Mc/sec: 26.49
//
[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 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