Align Uncharacterized protein (characterized, see rationale)
to candidate BWI76_RS08665 BWI76_RS08665 6-phosphogluconolactonase
Query= uniprot:Q881W7 (359 letters) >FitnessBrowser__Koxy:BWI76_RS08665 Length = 331 Score = 163 bits (413), Expect = 5e-45 Identities = 107/345 (31%), Positives = 170/345 (49%), Gaps = 25/345 (7%) Query: 8 YISSPADGLISQYRLDEQSGALSLVEQTKAGDQVNPMAISPDGKALFAALRSKPYQVLSF 67 Y +SP I + LD +G L+LV+ A QV PM +SP+ + L+ +R + ++VL++ Sbjct: 6 YTASPESQQIHVWDLD-LAGKLTLVQVVDAPGQVQPMVVSPNKEYLYVGVRPE-FRVLAY 63 Query: 68 SIEPATGHLKPLSQAPLAESLAYLSTDRSGRFLFGASYGADLLSVQPIDAQHRPSDSIET 127 I P G L +APL S ++STD GRF+F ASY A +SV P+ P +++ Sbjct: 64 RIAPDNGALTFAGEAPLPGSPTHISTDHQGRFVFSASYNAGCVSVTPL-VDGLPREAVAV 122 Query: 128 YKTGMHAHSVRTDPSNRFVYAGNLGVDRVLQYRLEPKDGKLVPIGEGFVAVPDNTGPRHL 187 + HS P NR ++ L DR+ + L DG L V + GPRH+ Sbjct: 123 VEGLEGCHSANISPDNRTLWVPALKQDRICLFTLS-DDGFLAEQEPAEVTTVEGAGPRHM 181 Query: 188 AFSSDGRFLYVVGEMSGTVTAFLINEKTGALKQVSQADGIPARLKLAPGQARDARNNDLK 247 F + ++ Y V E++ +V + + + G ++ V D +P Sbjct: 182 VFHPNQQYGYCVNELNSSVDVWELKDPHGKIECVQTLDMMP------------------- 222 Query: 248 DDPTPRIWAADIRLAPDGKWLFISERTTSSVSVFKVDPAKGNVTFVENYPVEEKQPRNIA 307 D WAADI L PDG+ L+ +RT S +++F V G+V +E Y E QPR Sbjct: 223 PDFAGVRWAADIHLTPDGRHLYACDRTASIITIFSVS-EDGSVLSIEGYQNTETQPRGFN 281 Query: 308 VSPNGRWLLVSGEKSDKVGSYAI-GASGALKRVSEAPSGKGALWI 351 + +G++L+ +G+KS + Y I G G L+ G+G +W+ Sbjct: 282 LDHSGKYLIAAGQKSHHIAVYEIEGEQGLLEEKGRYAVGQGPMWV 326 Lambda K H 0.314 0.132 0.383 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: 36 Number of successful extensions: 9 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: 359 Length of database: 331 Length adjustment: 29 Effective length of query: 330 Effective length of database: 302 Effective search space: 99660 Effective search space used: 99660 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: 42 (22.0 bits) S2: 49 (23.5 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