GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Klebsiella michiganensis M5al

Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate BWI76_RS18360 BWI76_RS18360 aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase family protein

Query= BRENDA::O57809
         (325 letters)



>FitnessBrowser__Koxy:BWI76_RS18360
          Length = 328

 Score =  212 bits (540), Expect = 9e-60
 Identities = 132/321 (41%), Positives = 187/321 (58%), Gaps = 14/321 (4%)

Query: 9   LAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68
           L  FPR+ELI   TP++YLP +S  +G +++IKRDD+T L +GGNK+RKLE+L  DAL +
Sbjct: 6   LTLFPRLELIGAPTPLEYLPRLSDYLGREIFIKRDDVTPLAMGGNKLRKLEFLAADALRE 65

Query: 69  GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVL------RGKEEL-KGNYLLDKIMGIE 121
           GAD +IT GA+ SNH   T   A KLGL  + +L      R +  L  GN LL  +   +
Sbjct: 66  GADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTRAENYLTNGNRLLLDLFNTQ 125

Query: 122 TRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE-- 179
             + DA    +     EE+A  ++ +G +PY IP GG++ +G LGYV +  EIA Q E  
Sbjct: 126 VEMCDALT--DPNAQLEELATRIEAQGYRPYTIPVGGSNALGALGYVESALEIAQQCEGA 183

Query: 180 VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLG 239
           V+  S+VVA+GS GT AGL++GL  L  +   +G+ V R       K+  L +  A  L 
Sbjct: 184 VELSSVVVASGSAGTHAGLAVGLEQLMPNAELIGVTVSRKVADQLPKVAALQQAVANSLE 243

Query: 240 VKVEVRPELYDYSFGE-YGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVD-LARKG 297
           ++ +   +L+D  F   YG    E    ++ +   EGI+LDPVYTGKA  GL+D +++K 
Sbjct: 244 LEAKAGIQLWDDYFAPGYGTPNDEGMAAVKLLAQLEGILLDPVYTGKAMAGLIDGISQKR 303

Query: 298 ELGE-KILFIHTGGISGTFHY 317
              E  ILF+HTGG    F Y
Sbjct: 304 FKDEGPILFVHTGGAPALFAY 324


Lambda     K      H
   0.319    0.142    0.402 

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: 281
Number of extensions: 17
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: 325
Length of database: 328
Length adjustment: 28
Effective length of query: 297
Effective length of database: 300
Effective search space:    89100
Effective search space used:    89100
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 (21.7 bits)
S2: 48 (23.1 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