Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__BFirm:BPHYT_RS11300 Length = 327 Score = 373 bits (957), Expect = e-108 Identities = 187/305 (61%), Positives = 230/305 (75%), Gaps = 1/305 (0%) Query: 4 IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63 +D++++GE MAMFVA G LA V F KR+AGAD NVAIGL+RLGFKV W+SRVGNDS Sbjct: 8 LDVITYGEAMAMFVAAETGPLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSRVGNDSF 67 Query: 64 GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123 G++V DTL EG+D V D +PTGFQLKS+ D G DP +EYFR+GSAASHL+++D Sbjct: 68 GQYVRDTLTKEGIDQGCVTTDERYPTGFQLKSKNDDGSDPAIEYFRKGSAASHLSLADYA 127 Query: 124 PA-LLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIR 182 +L+ARHLH TG+ PA+S S+REL+ HL R+AG ++SFDPNLRP LWPS A M+ Sbjct: 128 ADYVLQARHLHLTGVAPAISASSRELAFHLAREMRAAGKTISFDPNLRPTLWPSRAAMVE 187 Query: 183 EINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQLDA 242 +N LAALA WVLPG+ EG +LTG P DIA FYL+QGA V+IKLGA GAY+RT DA Sbjct: 188 GLNALAALADWVLPGIGEGEILTGYTQPDDIAKFYLEQGARGVIIKLGAQGAYFRTADDA 247 Query: 243 GFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGLP 302 + G PVA+VVDTVGAGDGFAVG++SALLE + + +AV R N IG+ A+Q GD EGLP Sbjct: 248 AMIAGQPVAKVVDTVGAGDGFAVGVVSALLEGKSLPQAVARGNRIGALAIQVIGDSEGLP 307 Query: 303 LRHEL 307 R EL Sbjct: 308 SRAEL 312 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: 385 Number of extensions: 18 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: 320 Length of database: 327 Length adjustment: 28 Effective length of query: 292 Effective length of database: 299 Effective search space: 87308 Effective search space used: 87308 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.
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