Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate AZOBR_RS08170 AZOBR_RS08170 carbon-nitrogen family hydrolase
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__azobra:AZOBR_RS08170 Length = 298 Score = 314 bits (805), Expect = 1e-90 Identities = 150/280 (53%), Positives = 194/280 (69%) Query: 4 IKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAK 63 + VA Q++ + N+ +E + AA GA+IIL EL YFCK Q F LA Sbjct: 9 VTVAATQMACGWDRDANVNGVERLVRDAAARGAQIILPQELFETPYFCKDQKQDLFALAH 68 Query: 64 TIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMIDADGSIMGVYRKAHIPDGI 123 +++ P++ LA + ++V+P SFFER NA YNS+AMIDADG+++GVYRK+HIPDG Sbjct: 69 PVEDHPVIARMSALARELSVVIPTSFFERARNAYYNSLAMIDADGTVLGVYRKSHIPDGP 128 Query: 124 GYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSEP 183 GYQEKYYF+PG GF+V+ T+YA +G ICWDQWFPE+AR MALKGAEIL YPTAIGSEP Sbjct: 129 GYQEKYYFNPGDTGFQVYKTRYAAIGCAICWDQWFPESARAMALKGAEILFYPTAIGSEP 188 Query: 184 HLPDYDSKDHWQRVMQGHAAANMLPVLASNRYATEANDDITATYYGSSFITDHTGDKIAE 243 DS+ HW RVMQGHA AN++P++ASNR E D T+YGSSFI TG+ +A+ Sbjct: 189 QDGALDSQAHWTRVMQGHAGANLMPLVASNRIGREEGDTCGITFYGSSFIAGPTGELVAQ 248 Query: 244 ADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIV 283 ADR + +L A+FD + QR WG+FRDRRPELY ++ Sbjct: 249 ADRDSETVLTASFDLDRIAAQRASWGIFRDRRPELYGPLL 288 Lambda K H 0.320 0.136 0.413 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: 310 Number of extensions: 12 Number of successful extensions: 1 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: 286 Length of database: 298 Length adjustment: 26 Effective length of query: 260 Effective length of database: 272 Effective search space: 70720 Effective search space used: 70720 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 (21.8 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