Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate AZOBR_RS29610 AZOBR_RS29610 hypothetical protein
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >FitnessBrowser__azobra:AZOBR_RS29610 Length = 221 Score = 130 bits (326), Expect = 3e-35 Identities = 67/200 (33%), Positives = 121/200 (60%), Gaps = 1/200 (0%) Query: 21 GFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLACFYM 80 G +T++Q ++L+ +G IG++ G+ +++R+ YV++IR TP V ++ +Y Sbjct: 20 GAITTLQITLLSSAIGLFIGLLVGVSRESSGVFLRSVTSVYVEMIRATPALVQIVWLYYC 79 Query: 81 APAL-GWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALAYV 139 P + G+Q+ A + ++ L + G++V+EIVR + A+ GQ A+K+IG+ + AL + Sbjct: 80 FPIIFGYQLSAMTSIIIALGIHSGAYVSEIVRAGINAVDTGQFLAAKSIGMNHFTALRRI 139 Query: 140 LLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLF 199 +LPQA ++++P +N ++K +TL S+I V ELL + +IA T+ LE Y F F Sbjct: 140 ILPQAGQKMIPPLINEFANLMKLTTLGSMIAVYELLQESNNLIATTYRPLEVYTFLAIFF 199 Query: 200 FIINYAIELLGRHIEKRVAL 219 FII Y L + +E+R+ + Sbjct: 200 FIITYPWIWLSQRLERRLKM 219 Lambda K H 0.330 0.142 0.440 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: 139 Number of extensions: 7 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: 220 Length of database: 221 Length adjustment: 22 Effective length of query: 198 Effective length of database: 199 Effective search space: 39402 Effective search space used: 39402 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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