Align Phospho-furanose lactonase; EC 3.1.1.25 (characterized)
to candidate BWI76_RS14780 BWI76_RS14780 phosphotriesterase
Query= SwissProt::Q4A724 (353 letters) >FitnessBrowser__Koxy:BWI76_RS14780 Length = 323 Score = 152 bits (385), Expect = 9e-42 Identities = 104/336 (30%), Positives = 164/336 (48%), Gaps = 32/336 (9%) Query: 7 RTVLGDIPVEKLGITDCHDHFIKNGGPEVEEHIDFLMLN-VDASIKEFKEFIDRGGSTIV 65 RT+ GDI +LG+T HDH E D L+L+ AS +E +F + GG I Sbjct: 5 RTLNGDISAHQLGVTYSHDHIYCIPPYWAERQDDDLLLDDPQASERELSDFREAGGRAIY 64 Query: 66 TMDPPNVGRDVLKTLEIANAVKNLGGNVIMSTGFHKAKFYDK--------YSSWLAVVPT 117 P+ GR +A + ++I + GF+K + ++ W+ Sbjct: 65 DATAPDYGRQAAAVAAMAQRQQL---HIIATAGFNKGFLWSSKRPGSAQTFAEWIEHSEI 121 Query: 118 EEIVKMCVAEIEEGMDEYNYNGPVVKRSKAKAGIIKAGTGYGAIDRLELKALEVAARTSI 177 +E+V+ E+ EG ++ + +AG++K GTGY I LE K +EV R Sbjct: 122 DELVEHVCREVTEG----------IEGTAHRAGVVKCGTGYNTISPLEEKTMEVIVRAQQ 171 Query: 178 LTGCPILVHTQLGTMALEVAKHLIGFGANPDKIQISHLNKNPDKYYYEKVIKETGVTLCF 237 TG P+ HT++GTM LE A+ +G + ++ +H+++NPD + + + I TG L F Sbjct: 172 RTGAPMHSHTEMGTMGLEQARIFKKWGLDLSRLCFAHMDRNPDPWLHRQ-IANTGAFLSF 230 Query: 238 DGPDRVKYYPDSLLAENIKYLVDKGLQKHITLSLDAGRILYQRNYGLTKGKQTFGLAYLF 297 DG R+KY+P+ + + I L +G QK I + D R +Y GK GL ++ Sbjct: 231 DGISRIKYHPEHIRTQAILALCQRGYQKQILIGGDFARKSMSAHY----GKGGLGLKFIL 286 Query: 298 D----RFLPLLKQVGVSKEAIF-DILVNNPKRVLAF 328 + RFL ++ G EA+ D V+NP R LAF Sbjct: 287 NDWRPRFLEEAREAGFDGEALLHDFFVDNPARYLAF 322 Lambda K H 0.319 0.139 0.402 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: 293 Number of extensions: 22 Number of successful extensions: 6 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: 353 Length of database: 323 Length adjustment: 28 Effective length of query: 325 Effective length of database: 295 Effective search space: 95875 Effective search space used: 95875 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 (21.7 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