Align Putative PTS IIA-like nitrogen-regulatory protein PtsN, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate GFF3543 PGA1_c35960 nitrogen regulatory protein PtsN
Query= TCDB::D2RXA7 (156 letters) >FitnessBrowser__Phaeo:GFF3543 Length = 154 Score = 72.0 bits (175), Expect = 4e-18 Identities = 45/147 (30%), Positives = 71/147 (48%), Gaps = 1/147 (0%) Query: 7 EIDAVLTPELITLEEPPAEKAAAIEFLLDRAVDAGRVTDREAALEALLAREEETTTGVGM 66 +I +L PE + + + K + + D A A + + +EALL RE TGVG Sbjct: 2 QISNILKPEAVRVFGAASSKKRLFQEIADVAQLAYGLP-AQPTVEALLDRESLGPTGVGH 60 Query: 67 GIGIPHAKTDAVAEPTIVFARSSAGIDFDAMDDQPATLLFLLLVPAEGGEEHLELLSSLS 126 G+ +PHA+ D + + VF ++F A+D QP + F L P + G EHL+ L+ +S Sbjct: 61 GVALPHARLDGLDKVVGVFLVLDTPLEFGAVDRQPIDIAFALFAPEDAGVEHLKALALVS 120 Query: 127 RALMHDDVRERLHEADSKAAIEETITE 153 R L +L A + +TE Sbjct: 121 RTLREQSFCTKLRANPDPATLHTILTE 147 Lambda K H 0.313 0.130 0.347 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: 50 Number of extensions: 3 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: 156 Length of database: 154 Length adjustment: 17 Effective length of query: 139 Effective length of database: 137 Effective search space: 19043 Effective search space used: 19043 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 43 (21.2 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