GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Burkholderia phytofirmans PsJN

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BPHYT_RS31960 BPHYT_RS31960 hypothetical protein

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



>FitnessBrowser__BFirm:BPHYT_RS31960
          Length = 316

 Score =  160 bits (406), Expect = 3e-44
 Identities = 107/316 (33%), Positives = 157/316 (49%), Gaps = 5/316 (1%)

Query: 3   KIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATR 62
           +++A   +    L  L+   ++V       +     + DAD  I   V++   + + A R
Sbjct: 6   RVLATSPIHLSALPILEPSCELVVAPDDSEETLRKFVADADALI-VRVRLPDDIFDHAPR 64

Query: 63  LKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVK 122
           LKA     VG D   V   TR  I +AN PD  T++ A+ V   ILA AR    L    +
Sbjct: 65  LKACVRHGVGLDFIPVERATRADIAVANLPDSNTQAVAEHVVGAILAMARGFDRLPRAWR 124

Query: 123 AGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEA 182
              W   +     G++++ +T+GIVGLGRIG  VA     GF M+VL  +  A       
Sbjct: 125 NDGWL--VRQTFQGIELRDRTVGIVGLGRIGLQVAAALHHGFGMRVLGCDNGAREGLPSY 182

Query: 183 YGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKAL 242
                +E   + + +DF+ L  PL   T+HL+ A  L   K  A+L+NA+RG  +D+ AL
Sbjct: 183 VDQTSIE--NVFSGSDFITLHAPLVKSTRHLVNAELLSLAKPGALLVNAARGGLIDDDAL 240

Query: 243 IEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLV 302
           + AL++G I  A LDVFE EPLP D P   + NV+  PH+ + T E    M+  AA  +V
Sbjct: 241 VAALRSGQIGCAALDVFEPEPLPPDHPYWSIDNVLLTPHVAAFTSEGLVRMSTGAARAVV 300

Query: 303 AALDGTLTSNIVNREV 318
             L G    ++VN EV
Sbjct: 301 EILHGRRPEHLVNEEV 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: 226
Number of extensions: 11
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: 316
Length adjustment: 27
Effective length of query: 294
Effective length of database: 289
Effective search space:    84966
Effective search space used:    84966
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