Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate AO353_07425 AO353_07425 carbon-nitrogen hydrolase
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07425 Length = 264 Score = 73.9 bits (180), Expect = 3e-18 Identities = 74/269 (27%), Positives = 117/269 (43%), Gaps = 21/269 (7%) Query: 18 AENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAKTIDESPIVKLYKLL 77 A NL +L+ +A GA +++ PE+ Y ++ + + + Sbjct: 16 AGNLQRLQKLATEA--KGADLLVFPEMFLTGY---NIGAEAVGALAEAQDGTCAQYIASI 70 Query: 78 AHKYNIVLPASFFER-DGNACYNSIAMIDADGSIMGVYRKAHIPDGIGYQEKYYFSPGSA 136 A I + + ER + YN++ +ID+ G + YRK H+ G + FS G Sbjct: 71 AKASGIAIVYGYPERAEDGQIYNAVQLIDSRGQRLANYRKTHL---FGELDHSMFSVGPD 127 Query: 137 GFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSEPHLPDYDSKDHWQR 196 F + + K+G IC+D FPE AR +AL GAE++L PTA ++ YD Sbjct: 128 EFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTA-----NMIPYDFIA--DV 180 Query: 197 VMQGHAAANMLPVLASNRYATEANDDITATYYGSSFITDHTGDKIAEADRSGDDILYATF 256 ++ A N V YA + Y G S I G +IA+A + ++ T Sbjct: 181 TVRSRAFENQCYV----AYANYCGHEGEIHYCGQSSIAAPDGSRIAQAGLD-EALIVGTL 235 Query: 257 DFAELQQQRFYWGLFRDRRPELYDEIVRK 285 D + R F DRRPELY E+ ++ Sbjct: 236 DRQLMVDSRAANRYFLDRRPELYGELNKR 264 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: 178 Number of extensions: 12 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 261 Effective length of database: 239 Effective search space: 62379 Effective search space used: 62379 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: 47 (22.7 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