Align ABC transporter for Lactose, permease component 2 (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21654 (272 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 105 bits (262), Expect = 1e-27 Identities = 80/277 (28%), Positives = 134/277 (48%), Gaps = 17/277 (6%) Query: 11 AATYGFLGLMAFLSVFPFIWMVLGATNSSIDIIK-GKLL---------PGAAFATNVANF 60 A Y L L A +FP ++++L + ID ++ G LL P + Sbjct: 10 AVIYAALFLFALYFLFP-LYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPWIKAWSGACTG 68 Query: 61 FTLVNVPLVFWNSAKIAIVATVLTLAVSSLAGYGFEMFRSRRRERVYRAMLLTLMIPFAA 120 + F NS ++ I A +++ + + GY +R R + ++ +L+ IPF A Sbjct: 69 VRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVGCFIPFQA 128 Query: 121 LMIPLFVMMGKAGLINTHLAVVLPSI--GSAFVIFYFRQSTKAFPSELRDAAKVDGLKEW 178 +++P+ G GL NT +V+ + G AF +FR + P+EL AA++DG + Sbjct: 129 ILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAARIDGAGFF 188 Query: 179 QIFLFIYVPVMRSTYAAAFVIVFMTAWNNYLWPLIVLQTNETKTITLVISSL--ASAYYP 236 IF I +PV + + F WN++L+ IV ++ IT+ +++L S Sbjct: 189 TIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFG-IVFSGVDSMPITVALNNLVNTSTGVK 247 Query: 237 DYGVVMVGTILATLPTLAVFFFMQRQFVQGM-LGSVK 272 +Y V M G I+A LPTL V+ R FV+G+ G+VK Sbjct: 248 EYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTAGAVK 284 Lambda K H 0.331 0.141 0.422 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: 219 Number of extensions: 12 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: 272 Length of database: 285 Length adjustment: 25 Effective length of query: 247 Effective length of database: 260 Effective search space: 64220 Effective search space used: 64220 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 (21.9 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