Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate H281DRAFT_03731 H281DRAFT_03731 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::acidovorax_3H11:Ac3H11_794 (270 letters) >FitnessBrowser__Burk376:H281DRAFT_03731 Length = 270 Score = 436 bits (1120), Expect = e-127 Identities = 208/270 (77%), Positives = 241/270 (89%) Query: 1 MNEKRFQKRTLFLIAYLLFALLPIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTD 60 M +K RTL L+ Y+LFAL+P+YWM+++S +TN E +STF+ PQH T++NYK IFTD Sbjct: 1 MQDKHRWMRTLVLVVYMLFALIPLYWMLSISLRTNEETMSTFATLPQHVTFENYKIIFTD 60 Query: 61 ESWYSGYINSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLL 120 SWY GYINS+IYV +N V+++ VALPAAYAFSRY FLGDKH+FFWLLTNRMTPPAVFLL Sbjct: 61 PSWYWGYINSIIYVLMNTVMSVLVALPAAYAFSRYRFLGDKHMFFWLLTNRMTPPAVFLL 120 Query: 121 PFFQLYTTVGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFF 180 PFFQLY++VGL DT+IAVALAH+LF+VPLAVWILEGFMSG+ REIDETAYIDGY+FP FF Sbjct: 121 PFFQLYSSVGLTDTYIAVALAHMLFNVPLAVWILEGFMSGVSREIDETAYIDGYTFPAFF 180 Query: 181 MTIFLPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWATLA 240 + IFLPLIK+GVGV AFFCFMFSWVELLLARTLTSVNAKPI A MTRTVSA+GMDW L+ Sbjct: 181 VKIFLPLIKSGVGVTAFFCFMFSWVELLLARTLTSVNAKPIAAVMTRTVSAAGMDWGVLS 240 Query: 241 AAGVLTIVPGAIVIWFVRHYIAKGFAMGRV 270 AAGVLTIVPGA+VI+FVR+YIAKGFAMGRV Sbjct: 241 AAGVLTIVPGALVIYFVRNYIAKGFAMGRV 270 Lambda K H 0.332 0.141 0.451 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: 365 Number of extensions: 17 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: 270 Length of database: 270 Length adjustment: 25 Effective length of query: 245 Effective length of database: 245 Effective search space: 60025 Effective search space used: 60025 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 (22.0 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