Align Putative PTS IIA-like nitrogen-regulatory protein PtsN, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate BWI76_RS25275 BWI76_RS25275 PTS IIA-like nitrogen regulatory protein PtsN
Query= TCDB::D2RXA7 (156 letters) >FitnessBrowser__Koxy:BWI76_RS25275 Length = 162 Score = 79.7 bits (195), Expect = 2e-20 Identities = 52/149 (34%), Positives = 77/149 (51%), Gaps = 2/149 (1%) Query: 7 EIDAVLTPELITLEEPPAEKAAAIEFLLDRAVDAGRVTDREAALEALLAREEETTTGVGM 66 ++ VL E + K A+E + + A ++ + EA+L RE+ +TG+G Sbjct: 9 QLSNVLNQECTRSQVHCQSKKRALEIISELAAKQLGLSS-QIVFEAILTREKMGSTGIGN 67 Query: 67 GIGIPHAKTDAVAEPTI-VFARSSAGIDFDAMDDQPATLLFLLLVPAEGGEEHLELLSSL 125 GI IPH K + + VF + I FDA+D+QP LLF LLVPA+ + HL LS + Sbjct: 68 GIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLV 127 Query: 126 SRALMHDDVRERLHEADSKAAIEETITEA 154 ++ L + RL A S + E ITEA Sbjct: 128 AKRLADKTICRRLRAAQSDEELYEIITEA 156 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: 40 Number of extensions: 2 Number of successful extensions: 2 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: 162 Length adjustment: 17 Effective length of query: 139 Effective length of database: 145 Effective search space: 20155 Effective search space used: 20155 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