Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate AZOBR_RS27985 AZOBR_RS27985 ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__azobra:AZOBR_RS27985 Length = 280 Score = 135 bits (341), Expect = 7e-37 Identities = 88/263 (33%), Positives = 130/263 (49%), Gaps = 4/263 (1%) Query: 6 LYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRPK-FQ 64 L+ L + L P +V AL+ PA L+ + P E+F W+ PK F Sbjct: 20 LHAAALALLLLVLFPFAWMVQMALR-PADAVLDDAVLFL--PTLENFVALWQGHFPKSFL 76 Query: 65 NSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKS 124 NSV+++ +T S +G YVL +W FR + IL P ++ IP F + Sbjct: 77 NSVLVSSLSTAASLALGVPAAYVLTRWRFRARRRVALWILATRMAPPIALTIPFFLAYRW 136 Query: 125 IGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLS 184 +GL S+ GL L+++ + I IV + +++ IP L EAA IDG G + FR V LPL+ Sbjct: 137 VGLQDSVVGLALIYMTFNISIVVWFMQTFFAAIPRSLEEAAWIDGCGVWQAFRRVTLPLA 196 Query: 185 VPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAGGEAVKWNLPMAGAILAAL 244 P A++ F WN+F FA+ LTR + VA+ E +W A L L Sbjct: 197 APGLAATAVFCFIFSWNDFFFALILTRTNAVTAPVAITNFLQYEGWEWGKIAAAGTLVML 256 Query: 245 PTLLVYILLGRYFLRGLLAGSVK 267 P L +L+ +Y +RGL AG +K Sbjct: 257 PVLAFTLLVRKYLVRGLTAGGLK 279 Lambda K H 0.330 0.146 0.461 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: 247 Number of extensions: 16 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: 268 Length of database: 280 Length adjustment: 25 Effective length of query: 243 Effective length of database: 255 Effective search space: 61965 Effective search space used: 61965 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