GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Nocardiopsis baichengensis YIM 90130

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_040685231.1 C892_RS0101795 D-2-hydroxyacid dehydrogenase family protein

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



>NCBI__GCF_000341205.1:WP_040685231.1
          Length = 315

 Score =  157 bits (396), Expect = 4e-43
 Identities = 98/255 (38%), Positives = 139/255 (54%), Gaps = 9/255 (3%)

Query: 55  AMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRV 114
           A+L    RL+ L T        D+      G+ +  T   ++  TA+  ++LIL  AR +
Sbjct: 59  ALLGRLPRLRLLVTTGRRNASIDLEAAEAAGVTVCGTSSTISP-TAELTWALILGLARHL 117

Query: 115 -VELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNR 173
             E   + + G WQ ++G      D+ G+TLG++GLGRIGG VAR  A  F M VL  + 
Sbjct: 118 PAENRAFRQGGPWQSTVG-----ADLHGRTLGVLGLGRIGGRVAR-VATAFGMPVLAWSE 171

Query: 174 SANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINAS 232
           +   +     GAR      ELLA +D V + + L+  T+ L+G AEL++M+  A L+N S
Sbjct: 172 NLTEERAAEAGARLARGKEELLAGSDVVSVHLQLSERTRGLLGEAELRAMRPHAYLVNTS 231

Query: 233 RGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHA 292
           R   VD  AL+ AL+ G I GAGLDVF+TEP+P D P+  L NV+A PH+G  T      
Sbjct: 232 RSGIVDRSALLRALRGGWIAGAGLDVFDTEPVPEDDPMRTLPNVLATPHLGYVTERNYRT 291

Query: 293 MARNAAENLVAALDG 307
               A E++ A LDG
Sbjct: 292 FYTEAVEDIAAFLDG 306


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: 220
Number of extensions: 10
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: 321
Length of database: 315
Length adjustment: 27
Effective length of query: 294
Effective length of database: 288
Effective search space:    84672
Effective search space used:    84672
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 24 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