Align ABC transporter for D-glucosamine, periplasmic substrate-binding component (characterized)
to candidate Synpcc7942_1276 Synpcc7942_1276 extracellular solute-binding protein, family 3
Query= reanno::pseudo3_N2E3:AO353_21710 (282 letters) >FitnessBrowser__SynE:Synpcc7942_1276 Length = 260 Score = 91.3 bits (225), Expect = 2e-23 Identities = 73/236 (30%), Positives = 114/236 (48%), Gaps = 15/236 (6%) Query: 1 MQRRLSLFTACVFLFAATASAVGIAQAADSRLDNVLKRGHLIVGTGSTNAPWHFQGADGK 60 ++R L L T+ + F A+ G AAD L+ + +RG+LIVG + AP +Q A G+ Sbjct: 10 LRRWLLLGTSVLASFFYGANTSGTI-AAD--LETIKRRGYLIVGVQANVAPLSWQDAQGQ 66 Query: 61 LQGFDIDIGRMVAKGLFNDPSKVEFVVQSSDARIPNLLTDKVDMSCQFITVTASRAQQVA 120 QGF++D+ R +A L + + V F S R+P LL D+VD+ +TVT +R + Sbjct: 67 WQGFEVDLARSLAAELLGNSAAVRFEGLQSRDRLPALLADRVDLLIAQMTVTDARQRVAQ 126 Query: 121 FTLPYYREGVGLLLPANSKYKEIEDLKAAGDSVTVAVLQNVYAEELVHQALPKAKVDQYD 180 F+ PYYR+ +GLL + VAVLQ A L+ P+ + Sbjct: 127 FSRPYYRDRIGLL-----------TRRGITQPQRVAVLQGSSAIPLLRWQAPELALVGVK 175 Query: 181 SVDLMYQAVNSGRADTAATDQSSVKYLMVQNPGRYRSPTYAWSPQTYACAVKRGDQ 236 S A++ G+ D A D+ ++ Q+ RY+ W A A+ +G Q Sbjct: 176 SYAAAQTALDRGQVDGIAADRLVLQQWQRQS-DRYQLLPQQWGDFPLAIALPQGLQ 230 Lambda K H 0.319 0.133 0.394 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: 174 Number of extensions: 7 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: 282 Length of database: 260 Length adjustment: 25 Effective length of query: 257 Effective length of database: 235 Effective search space: 60395 Effective search space used: 60395 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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