Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate HSERO_RS11445 HSERO_RS11445 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__HerbieS:HSERO_RS11445 Length = 221 Score = 131 bits (329), Expect = 1e-35 Identities = 69/206 (33%), Positives = 130/206 (63%), Gaps = 1/206 (0%) Query: 11 LWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLV-LTYGRTWMRAPFRFYVDLIRGTP 69 +W + +L G L +V+ + ++V+G ++GL+ GL L+ R + Y+ L+RGTP Sbjct: 8 VWESWPSLVHGTLVTVEITAASLVVGCVLGLLVGLGRLSPQRRVIYGLCTIYLTLVRGTP 67 Query: 70 VFVLVLACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIG 129 + V + F+ P +G + A+ G+LGL ++ G++V+EIVRGA+Q++ RGQMEA++++G Sbjct: 68 LLVQLFLWFFGLPHVGVILPAYVCGILGLGIYSGAYVSEIVRGAIQSIERGQMEAARSLG 127 Query: 130 LTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTL 189 L + ++ V+LPQA +++P N ++K S L+S++ +A+L+ ++II+ T+ +L Sbjct: 128 LPYRMAMRRVILPQAFVRMIPPLGNEFIALIKNSALVSLLTIADLMHEGEKIISVTYRSL 187 Query: 190 EFYLFAGFLFFIINYAIELLGRHIEK 215 E YL ++ ++ L+ R +EK Sbjct: 188 ETYLAIALIYLLLTSVTTLILRRVEK 213 Lambda K H 0.330 0.142 0.443 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: 153 Number of extensions: 11 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 (21.8 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