Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 145 bits (367), Expect = 7e-40 Identities = 93/271 (34%), Positives = 144/271 (53%), Gaps = 14/271 (5%) Query: 17 LLLAVVILA--PVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFI 74 L+L +V A P AW ++ S+ + L + WPS L+ Y + F Sbjct: 15 LVLGIVAWAVFPFAWAIVTSLKAGSALFT--VEAWPSQPSLANYAAIFKE------QPFG 66 Query: 75 ASLLNSIKVAGMATLAAVVVAVPAAWAVSRTP--AVAWSLYAVIATYMLPPVALAVPLYM 132 ++LNS+ A ++ +AV AA+A+ R L+ V+ M P VA+ L+ Sbjct: 67 RNILNSLLAASAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGLFE 126 Query: 133 GLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILT 192 + + GL N + L L YL PFT W+L + +P+E+E AAM+DGA I+ + Sbjct: 127 LVRWLGLYNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVF 186 Query: 193 LPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSD--YGLIAT 250 LPL P +A + L AF+ AW+EF +AL FT A+T+ VAIA ++G + +G I Sbjct: 187 LPLMGPALAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMA 246 Query: 251 AGVLAALPPVLIGLIMQRALISGLTSGGVKG 281 A V+ +P + + L+ QR ++SGLT+G VKG Sbjct: 247 ASVVVTVPLIGLVLLFQRRIVSGLTAGAVKG 277 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: 234 Number of extensions: 12 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: 277 Length adjustment: 26 Effective length of query: 255 Effective length of database: 251 Effective search space: 64005 Effective search space used: 64005 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