GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Herbaspirillum seropedicae SmR1

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate HSERO_RS01420 HSERO_RS01420 serine/threonine dehydratase

Query= BRENDA::O59791
         (323 letters)



>FitnessBrowser__HerbieS:HSERO_RS01420
          Length = 326

 Score =  446 bits (1148), Expect = e-130
 Identities = 212/316 (67%), Positives = 263/316 (83%)

Query: 7   LPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALS 66
           LP++ DV  A+ERIK +A++TPVL S T + E  A++FFKCENFQ+MGAFKFRGA+NAL+
Sbjct: 10  LPSFADVLLAAERIKPWAHRTPVLRSRTADTELGAQLFFKCENFQRMGAFKFRGAMNALT 69

Query: 67  QLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMY 126
           Q +  QRK GV+TFSSGNHAQ  AL+A++LGIPA I+MP DAP AKVAAT+GYG +V+ Y
Sbjct: 70  QFDATQRKHGVITFSSGNHAQGTALAAQLLGIPAVIVMPQDAPAAKVAATRGYGAEVVTY 129

Query: 127 DRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGG 186
           DRY +DRE +   ++    +T+IPPYDHPHV+AGQGTA  EL +E GPLDALFVCLGGGG
Sbjct: 130 DRYTEDREAIGARLAAERKMTLIPPYDHPHVMAGQGTATLELLQETGPLDALFVCLGGGG 189

Query: 187 LLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYT 246
           LLSG+ALAAR  +P C++YGVEP+AGNDGQQS R G +VHIDTPKTIADGAQTQHLG YT
Sbjct: 190 LLSGAALAARALSPACKIYGVEPQAGNDGQQSLRAGQVVHIDTPKTIADGAQTQHLGKYT 249

Query: 247 FSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGII 306
           F +I+E VDDI TVSDEEL+  ++F+A RMK+VVEPTGCL FAAAR +K++L+ KR+G+I
Sbjct: 250 FGVIRELVDDIHTVSDEELVAGMRFFAERMKMVVEPTGCLGFAAARKLKDQLQGKRVGVI 309

Query: 307 ISGGNVDIERYAHFLS 322
           ISGGNVD+ + A FL+
Sbjct: 310 ISGGNVDLGKLATFLA 325


Lambda     K      H
   0.318    0.135    0.384 

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: 320
Number of extensions: 4
Number of successful extensions: 1
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: 323
Length of database: 326
Length adjustment: 28
Effective length of query: 295
Effective length of database: 298
Effective search space:    87910
Effective search space used:    87910
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: 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