Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 245 bits (625), Expect = 1e-69 Identities = 135/321 (42%), Positives = 195/321 (60%), Gaps = 13/321 (4%) Query: 35 QKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVG 94 QK A SL+++I+ FS S F V NL+++ L +A T VIIT GIDLSVG Sbjct: 25 QKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLGVAATCVIITGGIDLSVG 84 Query: 95 TMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMML 154 +++ V A +L G+P+P+ + + GA GW++G+ + ++ +PPFIATLGMM++ Sbjct: 85 SVLALAGV-AAALLVKAGVPIPVAMLGGMLVGAACGWVNGICVTRMGLPPFIATLGMMLV 143 Query: 155 LKGLSLVISGTRPIY-FNDTEG---------FSAIAQDSLIGDLIPSLPIPNAVLILFLV 204 +GL+L I+G RP+ D G S I D + P +P P ++++ Sbjct: 144 ARGLALQITGARPVSGLGDAFGELGNGALFRISHIGADGFPDTVFPGIPYPVVIMVVLFA 203 Query: 205 AIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRL 264 A+ SI+L++T GR+ +A+GSN EA RLSGV V K+ Y SG + G G ++ SRL Sbjct: 204 AV--SILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRL 261 Query: 265 NSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQ 324 +AQP G YELDAIA+ VIGGTSL GG GTI GT IGAF++ VL NGL + V+ Q Sbjct: 262 VTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQ 321 Query: 325 TVVTGVIIILAVYLDILRRRR 345 ++ GV+I+ V++D LR R+ Sbjct: 322 QIIIGVVILGTVWIDQLRNRK 342 Lambda K H 0.326 0.139 0.398 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: 277 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 347 Length of database: 343 Length adjustment: 29 Effective length of query: 318 Effective length of database: 314 Effective search space: 99852 Effective search space used: 99852 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 (21.7 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