Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate 3607560 Dshi_0972 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Dino:3607560 Length = 276 Score = 137 bits (345), Expect = 3e-37 Identities = 90/265 (33%), Positives = 144/265 (54%), Gaps = 11/265 (4%) Query: 19 LAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLL 78 + ++I P+ W ++ S A A P + D L Y +L E S A F L Sbjct: 20 IGLLIFFPILWTILTSFKTEATAIADPPVFLAFDWTLENYTAVL---ERSNYAKF---LW 73 Query: 79 NSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYMLPPVALAVPLYMGLAY 136 NSI +AG +T+ +++AVPAAW+++ P+ L +++T MLP V + P+Y+ Sbjct: 74 NSIIIAGGSTILGIMIAVPAAWSMAFVPSRRTKDILLWMLSTKMLPAVGVLYPIYLICIE 133 Query: 137 FGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARL-DQILRILTLPL 195 G+L+S L ++ + + P W+L + F IP EI AA +DGA L ++IL +LT P+ Sbjct: 134 LGILDSRVALVVILMLMNLPIIVWMLYTYFKEIPGEILEAARMDGASLKEEILYVLT-PM 192 Query: 196 AAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIATAGVLA 255 A P +A++ L F+LAW+E F+ L T+ A LT IA + + ++ A +A Sbjct: 193 AIPGIASTLLLNFILAWNEAFWTLNLTA-ANAAPLTAFIASYSSPEGLFFAKLSAASTMA 251 Query: 256 ALPPVLIGLIMQRALISGLTSGGVK 280 P +++G Q+ L+SGLT G VK Sbjct: 252 IAPILILGWFSQKQLVSGLTFGAVK 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: 213 Number of extensions: 10 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