Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate Synpcc7942_2145 Synpcc7942_2145 hypothetical protein
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__SynE:Synpcc7942_2145 Length = 295 Score = 223 bits (567), Expect = 5e-63 Identities = 120/292 (41%), Positives = 178/292 (60%), Gaps = 8/292 (2%) Query: 2 ANIKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDL 61 + ++VA+ QL+F+D + ++ + I +AA GA++I+ PE+ YFC+ ++ FD Sbjct: 3 STLRVALAQLAFSDQPVIDRDRVTAAIREAAAAGAELIVLPEIHGGYYFCQTEDPAQFDR 62 Query: 62 AKTIDESPIVKLYKLLAHKYNIVLPASFFERDGNACY-NSIAMIDADGSIMGVYRKAHIP 120 A++I P Y +A + ++VL S FER Y N+ +I+ DG+I G YRK HIP Sbjct: 63 AESIP-GPSTDYYSAIARELSVVLILSLFERRAAGLYHNTAVVIERDGTIAGRYRKMHIP 121 Query: 121 DGIGYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIG 180 D Y EK+YF+PG GF+ T K+GV +CWDQW+PEAAR+MAL GAE+L+YPTAIG Sbjct: 122 DDPAYYEKFYFTPGDLGFEPIQTSVGKLGVLVCWDQWYPEAARLMALAGAELLIYPTAIG 181 Query: 181 SEPH-LPDYDSK--DHWQRVMQGHAAANMLPVLASNRYATEANDDITAT---YYGSSFIT 234 +P +P+ + + WQ V +GHA AN +PVL+ NR E + D A ++GSSFI Sbjct: 182 WDPQDVPEEQQRQLEAWQTVQRGHAIANGIPVLSVNRVGFEPSPDPAAAGSQFWGSSFIA 241 Query: 235 DHTGDKIAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIVRKY 286 G+ +A+A ++L A D +Q R W RDRR + Y ++VR+Y Sbjct: 242 GPQGEWLAKAGDREPELLIADLDRDRSEQVRRIWPFLRDRRIDAYGDLVRRY 293 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: 278 Number of extensions: 19 Number of successful extensions: 5 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: 295 Length adjustment: 26 Effective length of query: 260 Effective length of database: 269 Effective search space: 69940 Effective search space used: 69940 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