Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate Pf6N2E2_629 2-ketogluconate kinase (EC 2.7.1.13)
Query= reanno::pseudo3_N2E3:AO353_21335 (645 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_629 Length = 324 Score = 100 bits (248), Expect = 1e-25 Identities = 101/337 (29%), Positives = 140/337 (41%), Gaps = 37/337 (10%) Query: 11 QLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLKSAMLSRVGDD 70 + D++ G L A Q G L V F K + G+ +N+A G +RL K A LSRVG D Sbjct: 3 EFDVLSFGETMAMLVADQRGD-LASVDQFHKRIAGADSNVAIGLSRLDFKVAWLSRVGAD 61 Query: 71 HMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGLKDRETFPLV-FYRENCADMALRAED 129 +GRF+V++L EG D + VDP T D + P V ++R A L + Sbjct: 62 SLGRFVVQTLENEGLDCRHVAVDPTHPTGFQFKSRTDDGSDPQVEYFRRGSAASHLSIDS 121 Query: 130 ISEAFIASSKALLITGTHFSTDGVYKA-SIQALE-----YAEKHNVKRILDID--YRPVL 181 I+ + L+ H G+ A S+ A E + R L D RP L Sbjct: 122 IAPS--------LLEARHLHATGIVPALSVTAREMSFELMSRMRAAGRSLSFDPNMRPSL 173 Query: 182 WGLAGKADGETRFVADQQVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLSALRNVRRLT 241 WG T +++ +LP G E L+ G +D Sbjct: 174 WG-----SESTMITEINRLAALAHWVLP------GLGEGRLLT-GFDDPADIAAFYLDQG 221 Query: 242 AATLVVKLGPQGCTVIHGVIPVRLEDGAIYPGVRV-EVLNVLGAGDAFMSGFLSGWLEDA 300 A +V+KLG G L+ G I PGV V +V++ +GAGD F G +S LE Sbjct: 222 AELVVIKLGADG-----AYYRTALDQGVI-PGVPVAQVVDTVGAGDGFAVGLISALLEGQ 275 Query: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFN 337 + Q AN G V +PTR EL FN Sbjct: 276 AITEAVQRANWIGSRAVQSRGDMEGLPTRIELLAEFN 312 Lambda K H 0.321 0.138 0.412 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: 437 Number of extensions: 19 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: 645 Length of database: 324 Length adjustment: 33 Effective length of query: 612 Effective length of database: 291 Effective search space: 178092 Effective search space used: 178092 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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