GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Cupriavidus basilensis 4G11

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate RR42_RS02315 RR42_RS02315 threonine dehydratase

Query= SwissProt::P25306
         (595 letters)



>FitnessBrowser__Cup4G11:RR42_RS02315
          Length = 508

 Score =  425 bits (1093), Expect = e-123
 Identities = 233/503 (46%), Positives = 323/503 (64%), Gaps = 6/503 (1%)

Query: 97  YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156
           YL  IL + VYDVA E+ L  A  LS R G   + KRED Q VFSFKLRGAYN M++LS 
Sbjct: 7   YLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLSP 66

Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVLYG 213
           EEL +GVI ASAGNHAQGVAL+  RL C A I MP TTPQ+KIDAVR  GG+   +VL+G
Sbjct: 67  EELKRGVIAASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEWVEIVLHG 126

Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGG 272
            ++ +A  HA  L +K  L +I PFDDP VI GQGTI  EI RQ    +HAVF+ +GGGG
Sbjct: 127 DSYSDAYNHAAVLEKKHKLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGGG 186

Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332
           LI+G+A++ K + P  K+IGV+   + +M  S+  G RV+L  V  F+DG AV LVG+ T
Sbjct: 187 LISGIASYIKAVRPEIKVIGVQTVDSDAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKET 246

Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392
           F   +EL+D ++LV  D I A +KDV+ + R+ILE +GA+A+AG   Y E  K+K +++V
Sbjct: 247 FRITRELVDEIILVDTDAICAGLKDVFQDTRSILEPAGAMAVAGLKLYAEREKLKGQHLV 306

Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452
           AIA GANM+F +L  V E A +G  +EA+ A  + E++GSFK F   +G+ N TE  YR 
Sbjct: 307 AIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRFCEQLGTRNVTEFNYRI 366

Query: 453 TSERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANIS- 511
            +++  A I   V +   ++ EK+    +     TL+LS++EL   H++++VGG + ++ 
Sbjct: 367 -ADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGGHSPLAH 425

Query: 512 DEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKN 571
           DE+   F  PE+   L  FL + SP WNI+L  YRNQG   +++L+G QVP+ E   F++
Sbjct: 426 DELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFRD 485

Query: 572 QADKLGYPYELDNYNEAFNLVVS 594
               LGY +  +  N  + L +S
Sbjct: 486 FLATLGYVHWEETENPVYKLFLS 508


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: 696
Number of extensions: 37
Number of successful extensions: 5
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: 508
Length adjustment: 36
Effective length of query: 559
Effective length of database: 472
Effective search space:   263848
Effective search space used:   263848
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:

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