GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Herbaspirillum seropedicae SmR1

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate HSERO_RS07550 HSERO_RS07550 bifunctional glyoxylate/hydroxypyruvate reductase B

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



>FitnessBrowser__HerbieS:HSERO_RS07550
          Length = 319

 Score =  351 bits (901), Expect = e-101
 Identities = 190/307 (61%), Positives = 226/307 (73%), Gaps = 3/307 (0%)

Query: 4   IVAWKSLPEDVLAYLQQHAQVVQVDATQHDA---FVAALKDADGGIGSSVKITPAMLEGA 60
           +V +K LPE ++  LQ    +   D    D    F+AAL  A G IG+S+ IT AMLE A
Sbjct: 5   VVVYKKLPEHLVQRLQAEFDLTLFDRITDDNRADFIAALATAHGMIGASLPITNAMLEAA 64

Query: 61  TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120
            +LK +STISVG D FD+    +RG++LA+TP VLTE+TADT+F+LILASARRVVELAE+
Sbjct: 65  PQLKIVSTISVGVDNFDLDYFRQRGLMLAHTPGVLTEATADTIFALILASARRVVELAEY 124

Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180
           VKAG W+ SIG A FGV+V GKTLG++G+GRIG AVARRA  GF M +LY NR  +P+AE
Sbjct: 125 VKAGRWKGSIGEAQFGVNVHGKTLGLIGMGRIGSAVARRAHHGFGMPILYHNRRPDPEAE 184

Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240
              GAR V   +LLA ADFVC+ +PLTP+T+ + GA E   MK+SAI INASRG  VDE 
Sbjct: 185 RELGARYVSKEDLLAQADFVCVMLPLTPQTERMFGAPEFALMKRSAIFINASRGRIVDEA 244

Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300
           ALI ALQ+ TIHGAGLDVFE EPLP  SPLLKL NVVALPHIGSATHETR AMA  A  N
Sbjct: 245 ALIAALQDKTIHGAGLDVFEVEPLPLQSPLLKLPNVVALPHIGSATHETRLAMAELAVTN 304

Query: 301 LVAALDG 307
           L+A L G
Sbjct: 305 LIAGLRG 311


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: 292
Number of extensions: 6
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: 319
Length adjustment: 28
Effective length of query: 293
Effective length of database: 291
Effective search space:    85263
Effective search space used:    85263
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