Align Glutamine--fructose-6-phosphate aminotransferase [isomerizing]; EC 2.6.1.16 (characterized, see rationale)
to candidate WP_011653250.1 RL_RS19655 SIS domain-containing protein
Query= uniprot:Q92VI1 (339 letters) >NCBI__GCF_000009265.1:WP_011653250.1 Length = 340 Score = 491 bits (1263), Expect = e-143 Identities = 259/339 (76%), Positives = 286/339 (84%), Gaps = 1/339 (0%) Query: 1 MSISKDRPAGLIAIDREMARQHADAIASYEGATATAQRIAASLKSTGRLLLLGMGGSHAV 60 M+ + RPAGL AIDREMARQHADAIASYE A A + AASLK TGRLLL+GMGGSHAV Sbjct: 3 MTSKRPRPAGLAAIDREMARQHADAIASYEAAQPMAAKAAASLKKTGRLLLIGMGGSHAV 62 Query: 61 GRAVEPLYRALGIEAVAVPLSEQLGEPLSIEGKTILVTSQSGESAEVLRWFRETDGGTSE 120 RAVEPLYR LGI+AVA+PLSEQLG+PL I G+TI VTSQSGESAEV+RWF ET GGT E Sbjct: 63 NRAVEPLYRTLGIDAVALPLSEQLGQPLPIAGRTIFVTSQSGESAEVVRWFNET-GGTKE 121 Query: 121 TFGLTLEEDAFLAKAVPSLVGSGGTERAFAATRSLTVTFALHLAVLAALGADPADALRAL 180 TFGLTLE ++FLA+ PSLVGSGGTE AFAATRSLTVTFALHLA+L+ALG DP AL AL Sbjct: 122 TFGLTLEGNSFLARTAPSLVGSGGTELAFAATRSLTVTFALHLAILSALGEDPDTALAAL 181 Query: 181 RDPEAPVIDGALAALADVGAIVTSGRKLQGLAEAIALGLTELSRLPCFSLEGGQLRHGPM 240 + PE I AL+AL +V +VTSGR+LQG+AEA+ALGLTELSR PCFSLEGGQLRHGPM Sbjct: 182 KAPEDHDIAAALSALENVATVVTSGRRLQGIAEALALGLTELSRRPCFSLEGGQLRHGPM 241 Query: 241 EMLGASVGVVLFRAADPTAKLVGAMATSAAEAGSPVIVFDASDESPAAGATTIRFKPAAG 300 EMLG +GVVLFR D TA LV AMATSA E G+PVI+FDAS ++P AGA TIRF PA G Sbjct: 242 EMLGPEIGVVLFRGMDETADLVTAMATSAVETGAPVILFDASGQAPVAGAVTIRFAPATG 301 Query: 301 LAAILAMLPVAQSLMIAFADARVENAGTPVRSTKVTRSE 339 LAAI AMLPVAQ LMIAFADARVENAGTPVRSTK+TRSE Sbjct: 302 LAAIFAMLPVAQRLMIAFADARVENAGTPVRSTKITRSE 340 Lambda K H 0.316 0.131 0.356 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: 375 Number of extensions: 8 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: 339 Length of database: 340 Length adjustment: 28 Effective length of query: 311 Effective length of database: 312 Effective search space: 97032 Effective search space used: 97032 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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