GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Sinorhizobium meliloti 1021

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate SMc01943 SMc01943 2-hydroxyacid dehydrogenase

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



>FitnessBrowser__Smeli:SMc01943
          Length = 325

 Score =  207 bits (527), Expect = 3e-58
 Identities = 132/307 (42%), Positives = 167/307 (54%), Gaps = 9/307 (2%)

Query: 7   WKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPA--MLEGATRLK 64
           W    E VLA         +       A   AL++ D  + +     PA     G  R +
Sbjct: 14  WPQAVERVLAERFDTVLNEEDRPLDRSALADALRNFDAVLPTVSDRLPADVFTGGGLRTR 73

Query: 65  ALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAG 124
            L    VG++  D       GIV+ NTP VLT+ TAD   SL+LA+ARR  E    V+AG
Sbjct: 74  ILGNFGVGYNHIDAGAAKEAGIVVTNTPGVLTDCTADLAVSLLLAAARRTGEGERQVRAG 133

Query: 125 HWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS-ANPQAEEAY 183
            W       + G  V GKTLGI+G GRIG A+A+R   GF+M +++ NRS   P+    +
Sbjct: 134 AWDGWRPTHMIGTKVTGKTLGIIGFGRIGKAMAKRCHFGFDMDIVFYNRSRVAPEEAARF 193

Query: 184 GARRVELAE-LLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKAL 242
           GAR+++  E +L  ADFV L  P   E +HLI AA L +MK +A LIN SRG  VDE AL
Sbjct: 194 GARQLDTVEDVLRAADFVSLHCPGGGENRHLINAARLAAMKPAAYLINTSRGDVVDEAAL 253

Query: 243 IEALQNGTIHGAGLDVFETEPLPSDSP--LLKLANVVALPHIGSATHETRHAMARNAAEN 300
           I AL+ G I GAGLDV+E EP   D P  L  L NVV LPH+GSAT ETR AM     +N
Sbjct: 254 IAALEKGVIRGAGLDVYEAEP---DVPTRLRALENVVLLPHLGSATEETRTAMGMKVVDN 310

Query: 301 LVAALDG 307
           + A   G
Sbjct: 311 ITAFFAG 317


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: 217
Number of extensions: 7
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: 325
Length adjustment: 28
Effective length of query: 293
Effective length of database: 297
Effective search space:    87021
Effective search space used:    87021
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