Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Dino:3609759 Length = 275 Score = 142 bits (359), Expect = 6e-39 Identities = 86/281 (30%), Positives = 151/281 (53%), Gaps = 12/281 (4%) Query: 3 RQSPLFSVFIHASALLLAV-VILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTL 61 +Q F +HA ++ A+ V+L P+ W+ + + D+ L + P+ L + T+ Sbjct: 4 KQRKQFWSAVHAVLIIAAMFVMLVPILWIFLAAFKSHVDVYQLKLFFTPT---LENFGTV 60 Query: 62 LSAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATY 119 L NS VA + + A+ +A AA++ SR V + L ++AT Sbjct: 61 FDDPYRLG-----EKLFNSTVVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQ 115 Query: 120 MLPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMI 179 LP V + +P ++ GLL++ GL LV L I+ PF W++K D IP + E AAM+ Sbjct: 116 FLPAVVIILPFFIMFRDIGLLDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMV 175 Query: 180 DGARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAG 239 DG+ Q++ + LP+AAP + TS +F F++AW+EF +AL+ T ++ A TL + +A G Sbjct: 176 DGSSRLQVIWNIVLPMAAPGLLTSGIFCFIIAWNEFLFALILT-NKDAVTLPIGLALFKG 234 Query: 240 GRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280 + L++ AG++ P ++ L++++ + G+T G V+ Sbjct: 235 EEGDLWNLLSAAGIIIMAPMFVLALMIRKYFVQGMTMGAVR 275 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: 194 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: 281 Length of database: 275 Length adjustment: 25 Effective length of query: 256 Effective length of database: 250 Effective search space: 64000 Effective search space used: 64000 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