Align Trehalose transport system permease protein SugB (characterized)
to candidate AZOBR_RS27985 AZOBR_RS27985 ABC transporter permease
Query= SwissProt::P9WG01 (274 letters) >FitnessBrowser__azobra:AZOBR_RS27985 Length = 280 Score = 171 bits (432), Expect = 2e-47 Identities = 96/253 (37%), Positives = 146/253 (57%), Gaps = 5/253 (1%) Query: 21 LLPVLWIFSLSLKPTSTVKDGKLIPSTVTFDNYRGIFRGDLFSSALINSIGIGLITTVIA 80 L P W+ ++L+P V D ++ T +N+ +++G F + +NS+ + ++T + Sbjct: 32 LFPFAWMVQMALRPADAVLDDAVL-FLPTLENFVALWQGH-FPKSFLNSVLVSSLSTAAS 89 Query: 81 VVLGAMAAYAVARLEFPGKRLLIGAALLITMFPSISLVTPLFNIERAIGLFDTWPGLILP 140 + LG AAY + R F +R + L M P I+L P F R +GL D+ GL L Sbjct: 90 LALGVPAAYVLTRWRFRARRRVALWILATRMAPPIALTIPFFLAYRWVGLQDSVVGLALI 149 Query: 141 YITFALPLAIYTLSAFFREIPWDLEKAAKMDGATPGQAFRKVIVPLAAPGLVTAAILVFI 200 Y+TF + + ++ + FF IP LE+AA +DG QAFR+V +PLAAPGL A+ FI Sbjct: 150 YMTFNISIVVWFMQTFFAAIPRSLEEAAWIDGCGVWQAFRRVTLPLAAPGLAATAVFCFI 209 Query: 201 FAWNDLLLALSLTATKAAITAPVAIANFTGSSQFEEPTGSIAAGAIVITIPIIVFVLIFQ 260 F+WND AL LT T A+TAPVAI NF +E G IAA ++ +P++ F L+ + Sbjct: 210 FSWNDFFFALILTRTN-AVTAPVAITNFLQYEGWE--WGKIAAAGTLVMLPVLAFTLLVR 266 Query: 261 RRIVAGLTSGAVK 273 + +V GLT+G +K Sbjct: 267 KYLVRGLTAGGLK 279 Lambda K H 0.327 0.141 0.418 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: 217 Number of extensions: 9 Number of successful extensions: 4 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: 274 Length of database: 280 Length adjustment: 25 Effective length of query: 249 Effective length of database: 255 Effective search space: 63495 Effective search space used: 63495 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 (21.7 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