Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 131 bits (330), Expect = 2e-35 Identities = 81/245 (33%), Positives = 127/245 (51%), Gaps = 16/245 (6%) Query: 144 TTPPRFTLDNYAEVLSAA-------GIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMP 196 T P +T+D + + S A G+ F+NS+ + +P+ +I +I AF Y L Sbjct: 48 TPPTHWTIDPWIKAWSGACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWR 107 Query: 197 FPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAI 256 F G + +++ +P Q L+P+ + F G+S T G+ + H +G+ Sbjct: 108 FRGADPIFTMILVGCFIPFQAILLPMARFEG----FLGLS-NTTTGLVVVHVIYGIAFTT 162 Query: 257 YLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAI 316 RN+ +P E++++AR+DGA F IF KI+LP+S P I+QF WND L I Sbjct: 163 MFFRNFYVSIPAELVKAARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGI 222 Query: 317 VFLGAGDDKLVLTGRLVNLLGSRGG--NWEILTASAFITIVVPLIVFFALQRYLVRGLLA 374 VF +G D + +T L NL+ + G + + A A I + L+V+ RY VRGL A Sbjct: 223 VF--SGVDSMPITVALNNLVNTSTGVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTA 280 Query: 375 GSVKG 379 G+VKG Sbjct: 281 GAVKG 285 Lambda K H 0.324 0.139 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: 245 Number of extensions: 16 Number of successful extensions: 3 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: 380 Length of database: 285 Length adjustment: 28 Effective length of query: 352 Effective length of database: 257 Effective search space: 90464 Effective search space used: 90464 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 49 (23.5 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