GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Klebsiella michiganensis M5al

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate BWI76_RS26750 BWI76_RS26750 PfkB domain-containing protein

Query= SwissProt::P37647
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS26750
          Length = 311

 Score =  547 bits (1409), Expect = e-160
 Identities = 272/308 (88%), Positives = 288/308 (93%)

Query: 1   MSKKIAVIGECMIELSEKGADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSFS 60
           MSKKIAVIGECMIELSEKGA V RGFGGDTLNTSVYIARQ D +AL VHYVTALGTD+FS
Sbjct: 1   MSKKIAVIGECMIELSEKGAAVNRGFGGDTLNTSVYIARQTDASALGVHYVTALGTDTFS 60

Query: 61  QQMLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSAA 120
           QQML++W  ENV T L QRM +RLPGLYYIETD TGERTFYYWRNEAAAKFWLESEQSAA
Sbjct: 61  QQMLESWQSENVQTDLIQRMADRLPGLYYIETDDTGERTFYYWRNEAAAKFWLESEQSAA 120

Query: 121 ICEELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEET 180
           ICEELA FDYLYLSGISLAIL+PTSREKLL+LLRECRANGGKVIFDNNYRPRLW+SKEET
Sbjct: 121 ICEELATFDYLYLSGISLAILNPTSREKLLTLLRECRANGGKVIFDNNYRPRLWSSKEET 180

Query: 181 QQVYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIAG 240
           QQVYQQML CTDIAFLTLDDEDALWG++PV +VIARTH AGV+EVVVKRGADSCLV+IAG
Sbjct: 181 QQVYQQMLSCTDIAFLTLDDEDALWGEKPVAEVIARTHAAGVEEVVVKRGADSCLVAIAG 240

Query: 241 EGLVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRGA 300
           +  +DVPAVKLPKEKV+DTTAAGDSFSAGYLAVRLTGG AE AAKRGHLTASTVIQYRGA
Sbjct: 241 QPQLDVPAVKLPKEKVVDTTAAGDSFSAGYLAVRLTGGDAESAAKRGHLTASTVIQYRGA 300

Query: 301 IIPREAMP 308
           IIPREAMP
Sbjct: 301 IIPREAMP 308


Lambda     K      H
   0.317    0.132    0.384 

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: 441
Number of extensions: 9
Number of successful extensions: 1
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: 309
Length of database: 311
Length adjustment: 27
Effective length of query: 282
Effective length of database: 284
Effective search space:    80088
Effective search space used:    80088
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 (21.6 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