Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate SMa0711 SMa0711 ABC transporter permease
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Smeli:SMa0711 Length = 276 Score = 155 bits (392), Expect = 9e-43 Identities = 92/281 (32%), Positives = 156/281 (55%), Gaps = 9/281 (3%) Query: 3 RQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLL 62 +++ L ++ ++A ++ V+L P+ WL + ++S A++ P ++WP++ S + + Sbjct: 2 QRTTLQTLSLYAGLAVVCGVLLFPIYWLFVTALSTLAEIRQLPPSFWPAEPQWSTFAKV- 60 Query: 63 SAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWSLYA--VIATYM 120 L NS A + ++VV+V A +++SR ++ M Sbjct: 61 -----GTERPIFLWLWNSTLAALGSVALSMVVSVFAGYSLSRFSVKGGRSLGLFILTAKM 115 Query: 121 LPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMID 180 LP L +PL+ GL+ S++ L L + T++ PFTTW+LK FD+IPRE+E AAM+D Sbjct: 116 LPATLLVIPLFGIFRSMGLIGSLWSLVLAHATLIIPFTTWMLKGYFDTIPRELEQAAMVD 175 Query: 181 GARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLF-TSDQRAKTLTVAIADLAG 239 G L + LP+A P +A +AL+AF+L+W ++ YA F T+ Q + T + I + G Sbjct: 176 GCSPLGALFRVVLPVATPGLAATALYAFVLSWADYAYARTFLTNAQGSWTANLGITTMKG 235 Query: 240 GRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280 V+D+ I+ A V ALP +LI L ++R L+ GLT+G K Sbjct: 236 EYVTDWNEISAAAVFIALPIILIYLFLERYLVGGLTAGAEK 276 Lambda K H 0.325 0.136 0.402 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: 215 Number of extensions: 9 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: 281 Length of database: 276 Length adjustment: 25 Effective length of query: 256 Effective length of database: 251 Effective search space: 64256 Effective search space used: 64256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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