Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate BWI76_RS11245 BWI76_RS11245 spermidine/putrescine ABC transporter permease PotC
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__Koxy:BWI76_RS11245 Length = 261 Score = 94.7 bits (234), Expect = 2e-24 Identities = 66/222 (29%), Positives = 113/222 (50%), Gaps = 3/222 (1%) Query: 51 TLSNYREALFEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFIT 110 T + Y + D +L+ +SL +A+ + A ++G A AL R+ FRGK + Sbjct: 43 TTNWYSLLMNNDSLLQAAQHSLTMAVLSATFATLIGSLTAVALYRYRFRGKPFVSGMLFV 102 Query: 111 NRMISPIVLALPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAA 170 M IV+A+ ++ +G+ +L+ ++TF LP V+ V + +G + EAA Sbjct: 103 VMMSPDIVMAISLLVLFMLIGIQLGFWSLLFSHITFCLPFVVVTVFSRLKGFDVRMLEAA 162 Query: 171 RLEGASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFM 230 + GAS+ TI+RKI LPLA+P VA + SF S ++++ +T + P S + Sbjct: 163 KDLGASELTILRKIILPLALPAVAAGWLLSFTLSMDDVVVSSFVTGPGYEILPLKIYSMV 222 Query: 231 EGYNLPYGKIMATSTLIVIPVLIFALIASKQLVRGLTMGAVK 272 + P +AT L++ V++ IAS+ + R T G +K Sbjct: 223 KVGVSPEVNALATILLVLSLVMV---IASQLIARDKTQGTLK 261 Lambda K H 0.331 0.143 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: 195 Number of extensions: 12 Number of successful extensions: 1 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: 272 Length of database: 261 Length adjustment: 25 Effective length of query: 247 Effective length of database: 236 Effective search space: 58292 Effective search space used: 58292 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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