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 BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 260 bits (665), Expect = 2e-74 Identities = 135/279 (48%), Positives = 188/279 (67%), Gaps = 11/279 (3%) Query: 1 MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARIT----LETVWQWPHPPYWESFRTAW 56 + RA++Y L L A +FL P+Y+++ T+ K+ ++ L W P+ +++ A Sbjct: 7 ISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPWIKAWSGAC 66 Query: 57 EAFR-----PKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPY 111 R P F NSV + + A L+S+++G+ NGYVL W FRG+ +F +IL G FIP+ Sbjct: 67 TGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVGCFIPF 126 Query: 112 QSILIPLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAG 171 Q+IL+P+ +F +GL + GLV+VHVIYGI T+ FRN+Y IP ELV+AARIDGAG Sbjct: 127 QAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAARIDGAG 186 Query: 172 FFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAGGE--A 229 FF IF ++LP+S+P F+V IWQFTQIWN+FLF + + +S PITVAL L Sbjct: 187 FFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMPITVALNNLVNTSTGV 246 Query: 230 VKWNLPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268 ++N+ MAGAI+AALPTLLVYI+ GRYF+RGL AG+VKG Sbjct: 247 KEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTAGAVKG 285 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: 283 Number of extensions: 11 Number of successful extensions: 2 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: 285 Length adjustment: 25 Effective length of query: 243 Effective length of database: 260 Effective search space: 63180 Effective search space used: 63180 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