GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Synechococcus elongatus PCC 7942

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Synpcc7942_1347 Synpcc7942_1347 2-hydroxyacid dehydrogenase-like

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__SynE:Synpcc7942_1347
          Length = 331

 Score =  107 bits (267), Expect = 4e-28
 Identities = 87/274 (31%), Positives = 122/274 (44%), Gaps = 26/274 (9%)

Query: 60  ATRLKALSTISV--------GFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASA 111
           A  L+AL+ + V        GF+Q D++   R G+ +   P     + A+   +LIL   
Sbjct: 58  AITLEALAELGVEHVALRCAGFNQVDLSAAERLGLRVVRVPAYSPHAVAEHAIALILTLN 117

Query: 112 RRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYT 171
           R++       + G++       L G D+ G T+GI+G GRIG AV  +   GF   VL  
Sbjct: 118 RKIHRAYARTREGNFALD---GLVGFDLNGCTVGIIGTGRIG-AVLTQILRGFGCHVLAH 173

Query: 172 NRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINA 231
           +   NP    A GA   +L +L   A  + L  PLTP+T HL+    +  M+   +LIN 
Sbjct: 174 DLVENPDCLAA-GAVYTDLDQLWQEAQIISLHCPLTPQTYHLVNREAIAKMQPGTMLINT 232

Query: 232 SRGATVDEKALIEALQNGTIHGAGLDVFE-----------TEPLPSD--SPLLKLANVVA 278
           SRG  VD +A+IE L+   I   GLDV+E           TE +  D    LL   NVV 
Sbjct: 233 SRGGLVDTQAVIEGLKLKRIGALGLDVYEQEEPLFFQDHSTEIIHDDVFQRLLTFPNVVI 292

Query: 279 LPHIGSATHETRHAMARNAAENLVAALDGTLTSN 312
             H    T    H +A     NL     G    N
Sbjct: 293 TGHQAFLTDTALHNIAETTLSNLTDLEQGRACPN 326


Lambda     K      H
   0.317    0.131    0.366 

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: 227
Number of extensions: 10
Number of successful extensions: 2
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: 321
Length of database: 331
Length adjustment: 28
Effective length of query: 293
Effective length of database: 303
Effective search space:    88779
Effective search space used:    88779
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