GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Paraburkholderia bryophila 376MFSha3.1

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate H281DRAFT_05383 H281DRAFT_05383 D-3-phosphoglycerate dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_05383
          Length = 310

 Score =  141 bits (355), Expect = 2e-38
 Identities = 102/282 (36%), Positives = 141/282 (50%), Gaps = 19/282 (6%)

Query: 20  QHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVA 79
           QHA V+   AT      A L +   GI +      A ++   +L+ +S +  G++   V 
Sbjct: 33  QHAAVI---ATHGAMIRAVLTNGTRGISA------AEIDRMPKLEFVSALGAGYENVAVD 83

Query: 80  DLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDV 139
               RGIVL N         AD  F+L+L+  R V  L E  + G W+ ++       DV
Sbjct: 84  HARSRGIVLVNGAGTNDHCVADHAFALLLSIVRDVPRLDEATREGVWRDALP---MRPDV 140

Query: 140 QGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLAT-AD 198
            GK LGIVGLG IG  +ARR A GF+M++ Y NR        +Y     +  E LA   D
Sbjct: 141 SGKRLGIVGLGNIGEKIARRGA-GFDMEIGYHNRKPREGTSLSY----FDGVEALARWCD 195

Query: 199 FVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDV 258
           F+ +  P    T HLIGA   +++     ++N SRG+ +D  AL +AL  GTI GA LDV
Sbjct: 196 FLVIATPGGAGTHHLIGARVFEALGPDGFVVNVSRGSVLDTAALAQALVAGTIAGAALDV 255

Query: 259 FETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300
           +E EP P  + LLKL NVV  PH+G  + +   A   N   N
Sbjct: 256 YEGEPQP-PAALLKLRNVVLTPHVGGRSPDAIAAAVNNFLRN 296


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: 232
Number of extensions: 15
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: 310
Length adjustment: 27
Effective length of query: 294
Effective length of database: 283
Effective search space:    83202
Effective search space used:    83202
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