GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdaB in Pseudomonas fluorescens GW456-L13

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate PfGW456L13_949 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= SwissProt::P25306
         (595 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 Threonine
           dehydratase biosynthetic (EC 4.3.1.19)
          Length = 504

 Score =  422 bits (1085), Expect = e-122
 Identities = 227/501 (45%), Positives = 321/501 (64%), Gaps = 4/501 (0%)

Query: 94  LFQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSN 153
           L QY+  IL S VYDVA+E+PL+ A +LS+RLG + ++KRED Q VFSFK+RGAYN ++ 
Sbjct: 2   LEQYVKKILTSRVYDVAVETPLQSARQLSERLGNSIWLKREDLQPVFSFKIRGAYNKLTQ 61

Query: 154 LSREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYG 213
           LS EE  +GV+TASAGNHAQG+ALA + L   A IVMP TTP+IK++ VR+ GG VVL+G
Sbjct: 62  LSDEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHG 121

Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQ-LKDIHAVFIPVGGGG 272
            +F EA  ++L+L ++ G  YI P+DDP  I GQGT+  EI RQ  + + A+F+PVGGGG
Sbjct: 122 DSFPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPQPLDAIFVPVGGGG 181

Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332
           LIAG+A + K + P+ KIIGVEP  +  +  ++  G RV L  V  FADGVAVA +G++T
Sbjct: 182 LIAGIAAYVKYLRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHT 241

Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392
           F  C++ +D ++ V+ D I AAIKD+YD+ R+I E +GA+ +AG   Y E   +  +  V
Sbjct: 242 FDICKDHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVEQRGVSGQTFV 301

Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452
           AI SGAN++F +L  V E A LG G+EA++A  + E+ GSFK F   +G    TE  YR+
Sbjct: 302 AIDSGANVNFDRLRHVAERAELGEGREAIIAVTIPEKPGSFKAFCEAIGKRQITEFNYRY 361

Query: 453 TSERKNALILYRVNVDKESD-LEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG-SANI 510
            +    A I   V    E+D    +I  +       L+L+ NEL   H++H+VGG +A++
Sbjct: 362 NT-GSEAHIFVGVQTHPENDPRSALIASLSEQGFPVLDLTDNELAKLHIRHMVGGRAAHV 420

Query: 511 SDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFK 570
            DE+   F  PE+   L  FL+    RWNI++  YRN G  +  ++ G QVP  E     
Sbjct: 421 VDEVILRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPHDERHLVP 480

Query: 571 NQADKLGYPYELDNYNEAFNL 591
              +++GYPY  ++ N A+ L
Sbjct: 481 AALEEIGYPYWDESDNPAYQL 501


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: 730
Number of extensions: 36
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: 504
Length adjustment: 36
Effective length of query: 559
Effective length of database: 468
Effective search space:   261612
Effective search space used:   261612
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: 53 (25.0 bits)

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:

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:

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:

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, or view the source code.

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