GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Alkalihalobacterium alkalinitrilicum DSM 22532

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_078430830.1 BK574_RS10245 phosphoglycerate dehydrogenase

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



>NCBI__GCF_002019605.1:WP_078430830.1
          Length = 524

 Score =  183 bits (464), Expect = 9e-51
 Identities = 110/304 (36%), Positives = 164/304 (53%), Gaps = 14/304 (4%)

Query: 18  LQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFD 77
           +Q++   VQ +    DA +         + S+  +T  ++E    LK ++   VG D  D
Sbjct: 27  IQKNVTEVQQELHTFDAIL---------VRSATTVTAELIEKMPNLKIIARAGVGVDNID 77

Query: 78  VADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGV 137
           +   T+ GIV+ N PD  T STA+  FS+I A AR++ +  + +K G W      A  G 
Sbjct: 78  IEAATKAGIVVVNAPDGNTISTAEHTFSMICALARKIPQANQSIKLGEWNRK---AFQGT 134

Query: 138 DVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATA 197
           +++GKTLGIVG GRIG  +A+RA   F M+ L  +        E  G     L E+L  A
Sbjct: 135 ELRGKTLGIVGFGRIGSQLAKRAK-AFEMQPLVFDPFLTKARAEKLGVVPATLEEVLEKA 193

Query: 198 DFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLD 257
           D + +  PLT +TK ++G   +   K+   LIN +RG  +DE AL   L+NG + GA LD
Sbjct: 194 DIITVHTPLTKDTKGILGMENIGKTKRGVYLINCARGGIIDEVALKHYLENGHVAGAALD 253

Query: 258 VFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVNRE 317
           VFE EP   D+ L++L NV+A PHI ++T E +  +A   +E ++  L+G   SN +N  
Sbjct: 254 VFEEEP-AIDNALIELDNVIATPHIAASTKEAQLNVAAQVSEEVLLFLEGNPVSNSINLP 312

Query: 318 VLSK 321
            LSK
Sbjct: 313 TLSK 316


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: 310
Number of extensions: 12
Number of successful extensions: 3
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: 524
Length adjustment: 31
Effective length of query: 290
Effective length of database: 493
Effective search space:   142970
Effective search space used:   142970
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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