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_142248010.1 BK574_RS21120 D-glycerate dehydrogenase

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



>NCBI__GCF_002019605.1:WP_142248010.1
          Length = 326

 Score =  235 bits (600), Expect = 1e-66
 Identities = 128/286 (44%), Positives = 178/286 (62%), Gaps = 10/286 (3%)

Query: 22  AQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADL 81
           ++V+Q +  + DA  + + D          +    L    +LK ++ ++VG+D  DV   
Sbjct: 37  SEVLQKELERADALFSLVSDP---------LRSQQLAKCPKLKVIANMAVGYDNIDVEHA 87

Query: 82  TRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQG 141
           T +GIV+ +TPDVLT++TAD  F+L+LA+AR++ E  +++K   WQ      L G DV  
Sbjct: 88  TNKGIVVCHTPDVLTDTTADLTFALLLATARKIPEATDYIKNDQWQQWSPYLLAGTDVHH 147

Query: 142 KTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVC 201
           KT+GIVG+GRIG AVA+RA  GF+M++LY NRS   + E+  GA+     ELL  +D+V 
Sbjct: 148 KTIGIVGMGRIGEAVAKRAK-GFDMEILYHNRSRKMETEQQLGAKYCSFEELLQQSDYVV 206

Query: 202 LQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFET 261
              P TP TK L      + MK SAI INASRG  V+E AL EAL+ G I  AGLDVF  
Sbjct: 207 CLAPFTPVTKELFDQQAFQQMKNSAIFINASRGGLVNEAALQEALEKGVIQAAGLDVFAE 266

Query: 262 EPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
           EP+ ++ PL++L NVVA+PHIGSAT ETR AM +   EN+   L+G
Sbjct: 267 EPVRANHPLVQLPNVVAIPHIGSATVETRDAMVKMTVENIKKVLEG 312


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: 228
Number of extensions: 8
Number of successful extensions: 2
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: 326
Length adjustment: 28
Effective length of query: 293
Effective length of database: 298
Effective search space:    87314
Effective search space used:    87314
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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