Alignments for a candidate for sdaB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Dechlorosoma suillum PS

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate Dsui_0728 Dsui_0728 threonine ammonia-lyase, biosynthetic, long form

Query= SwissProt::P25306
         (595 letters)



>FitnessBrowser__PS:Dsui_0728
          Length = 503

 Score =  469 bits (1206), Expect = e-136
 Identities = 249/497 (50%), Positives = 336/497 (67%), Gaps = 3/497 (0%)

Query: 97  YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156
           YL  IL + VY+ A+E+PLELA  LS RLG  FY KRED Q VFSFKLRGAYN +++L+ 
Sbjct: 5   YLTKILNARVYEAAVETPLELAPNLSHRLGNRFYFKREDMQPVFSFKLRGAYNKIAHLTP 64

Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTF 216
            +L +GVI ASAGNHAQGVAL+  ++ C A IVMPTTTPQIK+ AV + GG+VVL G+++
Sbjct: 65  AQLQRGVICASAGNHAQGVALSAAKIGCRAVIVMPTTTPQIKVQAVASRGGEVVLAGESY 124

Query: 217 DEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQL-KDIHAVFIPVGGGGLIA 275
           DEA  HA+EL + + L ++ PFDDP VI GQGTIG EI RQ  K IHAVF+ +GGGGL A
Sbjct: 125 DEAYAHAVELEKAEKLTFVHPFDDPYVIAGQGTIGMEILRQHGKPIHAVFVAIGGGGLAA 184

Query: 276 GVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAK 335
           GVA + K + P  K+IGVE + A +M  S+  G RV+L NV  FADG AV  VGE TF  
Sbjct: 185 GVAAYIKAVRPEIKVIGVETFDADAMKQSIAAGKRVRLDNVGLFADGTAVKFVGEETFRV 244

Query: 336 CQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIA 395
           C+E +D ++LV  D I AAIKDV+++ R+ILE SGA+AIAGA  Y + +K+K++++VA+A
Sbjct: 245 CREYLDDIILVDTDAICAAIKDVFEDTRSILEPSGALAIAGAKEYAKQHKLKDKSLVAVA 304

Query: 396 SGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRFTSE 455
           SGAN +F +L  V E A +G  +EA+LA  + E+ G++K FV L+GS N TE  YRF  E
Sbjct: 305 SGANTNFDRLRFVAERAEVGEQREAVLAVTLPEKPGAYKRFVSLIGSRNITEFNYRF-HE 363

Query: 456 RKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSA-NISDEI 514
            + A +   V V   ++  K++E +K     TL+L+ +E+   H++H+VGG A  + +E+
Sbjct: 364 AREAHVFVGVQVANRAESTKLVESLKKHGYATLDLTDDEMGKLHVRHMVGGHAPQVENEL 423

Query: 515 FGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQAD 574
              F  PE+   L  FL+  S  WNI+L  YRN G     +L+G QVP AEM EF+    
Sbjct: 424 LYRFEFPERPGALMNFLNRMSSGWNISLFHYRNHGADYGRVLVGMQVPPAEMGEFQTFLQ 483

Query: 575 KLGYPYELDNYNEAFNL 591
           +LGY +  +  N A+ L
Sbjct: 484 ELGYHHWDETANPAYKL 500


Lambda     K      H
   0.317    0.135    0.382 

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: 706
Number of extensions: 35
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: 595
Length of database: 503
Length adjustment: 36
Effective length of query: 559
Effective length of database: 467
Effective search space:   261053
Effective search space used:   261053
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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SQLite3 databases

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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