Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate GFF1303 PGA1_c13190 ABC transporter permease protein
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Phaeo:GFF1303 Length = 276 Score = 140 bits (353), Expect = 3e-38 Identities = 91/270 (33%), Positives = 148/270 (54%), Gaps = 11/270 (4%) Query: 14 ASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAF 73 A A + ++I P+ W ++ S A + P + D L Y S V+ + + Sbjct: 15 ALAWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENY----SVVQERSD--Y 68 Query: 74 IASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYMLPPVALAVPLY 131 + L NS+ +AG +T+ +++AVPAAW+++ P+ L +++T MLP V + P+Y Sbjct: 69 MRFLWNSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPAVGVLYPIY 128 Query: 132 MGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARL-DQILRI 190 + GLL++ FGL +V + I P W+L + F IP EI AA +DGA L ++IL + Sbjct: 129 ILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKEEILYV 188 Query: 191 LTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIAT 250 LT P+A P +A++ L +LAW+E F+ L T+ +A LT IA + Y ++ Sbjct: 189 LT-PMAIPGIASTLLLNIILAWNEAFWTLNLTA-AKAAPLTAFIASYSSPEGLFYAKLSA 246 Query: 251 AGVLAALPPVLIGLIMQRALISGLTSGGVK 280 A +A P +++G Q+ L+SGLT G VK Sbjct: 247 ASTMAIAPILILGWFSQKQLVSGLTFGAVK 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: 222 Number of extensions: 13 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