GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Klebsiella michiganensis M5al

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate BWI76_RS00980 BWI76_RS00980 PLP-dependent threonine dehydratase

Query= SwissProt::P25306
         (595 letters)



>FitnessBrowser__Koxy:BWI76_RS00980
          Length = 514

 Score =  383 bits (984), Expect = e-111
 Identities = 216/502 (43%), Positives = 306/502 (60%), Gaps = 6/502 (1%)

Query: 96  QYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLS 155
           +YL  +L +PVY+ A  +PL+  EKLS RL     +KRED+Q V SFKLRGAY MM+ L+
Sbjct: 15  EYLRAVLRAPVYEAAQITPLQKMEKLSSRLDNVVLVKREDRQPVHSFKLRGAYAMMAGLT 74

Query: 156 REELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKT 215
            E+   GVITASAGNHAQGVA +  RL   A IVMPT T  IK+DAVR  GG+V+L+G  
Sbjct: 75  EEQKSHGVITASAGNHAQGVAFSASRLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134

Query: 216 FDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAVFIPVGGGGLIA 275
           FDEA+  A+EL+++ G  ++PPFD P VI GQGT+  E+ +Q   I  VF+PVGGGGL A
Sbjct: 135 FDEAKAKAIELAQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHIDRVFVPVGGGGLAA 194

Query: 276 GVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAK 335
           GVA   KQ+ P  K+I VE   +A +  +L  GH V L  V  FA+GVAV  +G+ TF  
Sbjct: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254

Query: 336 CQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIA 395
           CQE +D +V V +D I AA+KD++++ R + E SGA+A+AG   Y   + I+ E +  + 
Sbjct: 255 CQEYLDDIVTVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIAQHNIRGERLAHVL 314

Query: 396 SGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRFTSE 455
           SGAN++F  L  V+E   LG  +EALLA  + E++GSF  F  L+G  + TE  YRF ++
Sbjct: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRF-AD 373

Query: 456 RKNALILYRVNVDKESDLEKMIED-MKSSNMTTLNLSHNELVVDHLKHLVGG--SANISD 512
            KNA I   V + +  +  K I + +     + ++LS +E+   H++++VGG  S  + +
Sbjct: 374 AKNACIFVGVRLSRGLEERKEILNLLHEGGYSVVDLSDDEMAKLHVRYMVGGRPSQPLQE 433

Query: 513 EIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQ 572
            +F  F  PE    L  FL      WNI+L  YR+ G     +L  F++   E D F+ +
Sbjct: 434 RLF-SFEFPESPGALLKFLHTLGTHWNISLFHYRSHGTDYGRVLAAFELGDHEPD-FETR 491

Query: 573 ADKLGYPYELDNYNEAFNLVVS 594
             +LGY    ++ N AF   ++
Sbjct: 492 LHELGYDCHDESNNPAFRFFLA 513


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: 675
Number of extensions: 31
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: 595
Length of database: 514
Length adjustment: 36
Effective length of query: 559
Effective length of database: 478
Effective search space:   267202
Effective search space used:   267202
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