GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Klebsiella michiganensis M5al

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate BWI76_RS27485 BWI76_RS27485 aminoimidazole riboside kinase

Query= metacyc::MONOMER-12748
         (320 letters)



>FitnessBrowser__Koxy:BWI76_RS27485
          Length = 319

 Score =  102 bits (253), Expect = 2e-26
 Identities = 89/291 (30%), Positives = 130/291 (44%), Gaps = 11/291 (3%)

Query: 36  GADSNVAIGLARLGFKVAWLSRVGNDSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKS 95
           GA +NV + +ARLG    ++  +G+D  GRF+    +  G+D   +R D    +   + +
Sbjct: 31  GASANVGVCVARLGGTCGFIGCLGDDDAGRFLRQVFQDNGVDVSSLRLDASLTSAVLIVN 90

Query: 96  REDGGDDPRVEYFRRGSAASHLAISDLDPALLRARHLHATGIPPALSDS-ARELSGHLMH 154
               G +    Y     A ++++  DL P   +    + + I   L+DS ARE       
Sbjct: 91  LTADG-ERSFTYLVHPGADTYVSPQDL-PTFRKYEWFYFSSI--GLTDSPAREACLEGAR 146

Query: 155 TQRSAGHSVSFDPNLRPALWPSEALMIREINRLAALAHWVLPGLAEGRLLTGRDDPADIA 214
             R AG  V FD NLR  +W + A +   I R AALA        E   L+G     D  
Sbjct: 147 RMREAGGYVLFDVNLRSKMWRNTAEIPDLIARSAALASICKVSADELCQLSGASHWQDAR 206

Query: 215 AFYLDQGAEAVVIKLGAHGAYYRTQLDAGFVEGVPVAQVVDTVGAGDGFAVGLISALLES 274
            +  D G +  +I LGA GA   T  +  F+   P  +VVDT GAGD F  GL+  L   
Sbjct: 207 YYMRDLGCDTTIISLGAEGALLIT-AEGEFLFPAPRVEVVDTTGAGDAFVGGLLFTLSRE 265

Query: 275 RG-----ILEAVQRANWIGSRAVQSRGDMEGLPLRHELPEHTPSLKTASAL 320
                  + EA+  AN  G+ AV ++G M  LP   +L     S   A A+
Sbjct: 266 NYWNHALLAEAISNANACGAMAVTAKGAMTALPYPDQLNTFLSSRSLAQAM 316


Lambda     K      H
   0.321    0.138    0.414 

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: 214
Number of extensions: 18
Number of successful extensions: 5
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: 320
Length of database: 319
Length adjustment: 28
Effective length of query: 292
Effective length of database: 291
Effective search space:    84972
Effective search space used:    84972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. 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