Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178); 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase
Query= BRENDA::D4GSE6 (320 letters) >NCBI__GCF_000336675.1:WP_049904537.1 Length = 318 Score = 166 bits (419), Expect = 9e-46 Identities = 112/320 (35%), Positives = 161/320 (50%), Gaps = 9/320 (2%) Query: 4 LVTFGETMLRLSPPRGERLETARELEVQAGGAESNVAVAAARLGRDAAWFSKLPDSPLGR 63 +VT GETM+ + P ++ A E E GAE+NVA+ ARLG D W+SKL P G Sbjct: 5 VVTLGETMVLVYPSTTGPMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTDPHGE 64 Query: 64 RIVSELRSHSVDTDGVVWTDDADARQGVYYLEHGASPRPTNVVYDRADAAVTTLETGEFD 123 + +R VDT V +TD+A G+ + E P V Y R +A + + + Sbjct: 65 YLEFFVRGEGVDTTTVEFTDEAPT--GIMFKERREFGEPA-VHYYRHGSAASLMSPDDLP 121 Query: 124 LDAVRDAEVCFTSGITPALSETLSETTADVLDEAQNAGTTTAFDLNYRTKLWSPDE-AAE 182 +D + +AE +GITPALSE+ + T + A AG T +FD N R KLW DE E Sbjct: 122 VDYLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMRE 181 Query: 183 VYRDLLDSVDLLFAAERDAATVLGRDGDAESVARGLADDYDIETVVVTRGEEGSLAVSDG 242 DL+ D++ + A + G D D E++A D+ T VV G G++ V+DG Sbjct: 182 TMLDLVSLSDIVLPGIEEGAALFGTD-DPEAIAAACL-DHGAGTAVVKLGAAGAV-VADG 238 Query: 243 AVSEQ-GVYETE-TYDAIGTGDAFVGGFLAKHLDGGSVTESLEWASATASFKRTVEGDIA 300 + +E+ Y+ E D +G GD F GFLA ++G E+ E A+A +F TV GD Sbjct: 239 STTERVSGYDVERVVDPVGAGDGFAAGFLASRIEGQGPVEATETANAVGAFATTVAGDTE 298 Query: 301 VVTPEDVERVVAEEGDGISR 320 + V E D + R Sbjct: 299 GLPTRKELDVFVGERDAVRR 318 Lambda K H 0.312 0.130 0.365 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: 277 Number of extensions: 18 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: 320 Length of database: 318 Length adjustment: 28 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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