Align Sucrose permease; Sucrose transport protein (characterized)
to candidate BWI76_RS09125 BWI76_RS09125 MFS transporter
Query= SwissProt::P30000 (415 letters) >FitnessBrowser__Koxy:BWI76_RS09125 Length = 414 Score = 290 bits (741), Expect = 7e-83 Identities = 145/392 (36%), Positives = 233/392 (59%), Gaps = 2/392 (0%) Query: 12 YRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQD 71 Y S + FL+ +WS + + IW HLG++ T+ G LYSVN F ++L F+G + D Sbjct: 9 YILLSLFDFLYLFAWSSTMAFFVIWTTQHLGISATKTGLLYSVNAFIALLMQPFFGFISD 68 Query: 72 KLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDSF 131 K GLKK LIW + +L+ GPF IY+Y PLL +F +G +LG ++ G+ + +GCG++DS+ Sbjct: 69 KFGLKKRLIWILVAMLLPVGPFFIYLYAPLLVHSFWLGALLGGVYLGIIFNSGCGVIDSY 128 Query: 132 TEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMINMRFK 191 +K++R + FEYG R WGS G+A A+ G + +P++ FWL S+ + + M K Sbjct: 129 IDKISRRYQFEYGRVRMWGSLGWAAAAWIVGKYIDSNPNLAFWLASVAIVIAAICFMLTK 188 Query: 192 DKDHQCIAADAGGVKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAGLFES 251 + + + +K + + K+ FW+ ++F + Y+ +DQQ F +++ F + Sbjct: 189 IELTEAEMQKSSALKVSHALELAKNGQFWMLLVFTLFVTQIYDTYDQQ-FAQYFSLQFST 247 Query: 252 HDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILSCALFVNPW 311 + G R YG L S QV E L + ++P+FVNR G K AL+I +IM++RI+ A+ + P Sbjct: 248 PEEGNRWYGILASIQVCGETLFLCLMPWFVNRTGAKWALIIAGLIMSVRIVGSAIPLGPV 307 Query: 312 IISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLLSTPTGILF 371 I VK++HA+E PL ++SVFK+ ANFD +LSST++L+ +A S+ + S G L+ Sbjct: 308 WIGAVKMMHALEKPLILVSVFKFIAANFDNKLSSTVYLLVLFVA-SIATAIYSPLAGYLY 366 Query: 372 DHAGYQTVFFAISGIVCLMLLFGIFFLSKKRE 403 D G+ ++ + GI L L +F L RE Sbjct: 367 DTIGFAHTYYILGGIAGLFTLISVFTLRDNRE 398 Lambda K H 0.333 0.147 0.471 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: 514 Number of extensions: 28 Number of successful extensions: 4 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: 415 Length of database: 414 Length adjustment: 31 Effective length of query: 384 Effective length of database: 383 Effective search space: 147072 Effective search space used: 147072 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: 39 (21.5 bits) S2: 50 (23.9 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