Align TreU, component of Trehalose porter (characterized)
to candidate SM_b21219 SM_b21219 sugar ABC transporter permease
Query= TCDB::Q97ZC1 (267 letters) >FitnessBrowser__Smeli:SM_b21219 Length = 281 Score = 123 bits (309), Expect = 4e-33 Identities = 81/276 (29%), Positives = 146/276 (52%), Gaps = 15/276 (5%) Query: 3 LWVYLGAIVVGIYFLFPLYILVLLAFNSPKYTVLAKFPSLLPVSLTLNNLLTALQ----- 57 ++++ A+++ + L P+ L++++ SP + AK + P + L+ T L Sbjct: 10 VFIHASALLLAVVILAPVAWLLIMSI-SPAADLSAKPLAWWPSDIDLSRYRTLLSAVENS 68 Query: 58 -GTAFIDPFIKSLETATLVGIITIALAIPAGYGLSRLPRAIAYSIIILLLVTNMMPAIVI 116 G AFI + S++ A + + + +A+PA + +SR P A+A+S+ ++ T M+P + + Sbjct: 69 AGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTP-AVAWSLYAVI-ATYMLPPVAL 126 Query: 117 GIPIAVDFLKLHLFESVVGLALAQTLITLPLATFILQGTFSSIPIDLEHQARVDGANLFN 176 +P+ + L SV GLAL I P T++L+ F SIP ++E A +DGA L Sbjct: 127 AVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQ 186 Query: 177 RLFSVLLPLAAPGIAAAFLISWMFSWDEFTYAILLIPYHSTLPVTI-YQDVTRGNL---- 231 L + LPLAAP +A + L +++ +WDEF YA+L +T+ D+ G + Sbjct: 187 ILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYG 246 Query: 232 LAGIAFSLIFTLPVIILTFALQKYLRGEYLAGGIKG 267 L A ++ LP +++ +Q+ L +GG+KG Sbjct: 247 LIATA-GVLAALPPVLIGLIMQRALISGLTSGGVKG 281 Lambda K H 0.330 0.146 0.431 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: 192 Number of extensions: 10 Number of successful extensions: 3 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: 267 Length of database: 281 Length adjustment: 25 Effective length of query: 242 Effective length of database: 256 Effective search space: 61952 Effective search space used: 61952 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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