Align Sucrose permease; Sucrose transport protein (characterized)
to candidate BWI76_RS23415 BWI76_RS23415 MFS transporter
Query= SwissProt::P30000 (415 letters) >FitnessBrowser__Koxy:BWI76_RS23415 Length = 413 Score = 309 bits (792), Expect = 9e-89 Identities = 162/408 (39%), Positives = 248/408 (60%), Gaps = 8/408 (1%) Query: 12 YRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQD 71 Y S+ F FF++WS SL +IWL +GL + G ++SV +++ + YG +QD Sbjct: 10 YPLLSALLFFFFVTWSSSGSLLSIWLHQEVGLKPGDTGIIFSVLSVSALFAQVCYGFIQD 69 Query: 72 KLGLKKPLIWCMSFILVLTGP-FMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDS 130 KLGL+K L+W ++ +L+L+GP +M++ Y LL+ N +G I G ++ GL + G G+L+S Sbjct: 70 KLGLRKNLLWYITVLLILSGPAYMLFGY--LLKINVLLGSIFGGIYIGLTFNGGIGVLES 127 Query: 131 FTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMI--NM 188 +TE++AR FE+G AR WGS G+A+ FFAG+ F+I+PH+NF + S G VF ++ + Sbjct: 128 YTERVARQSQFEFGKARMWGSLGWAVATFFAGLLFNINPHLNFAVASCSGLVFFILLARL 187 Query: 189 RFKDKDHQCIAADAGG-VKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAG 247 R H A +GG V ED + + FW V F++GT Y ++DQQ FPV+++ Sbjct: 188 RVSSAPHAMQEAVSGGKVTLEDALRLLTLPRFWALVFFVIGT-CIYGVYDQQ-FPVYFSS 245 Query: 248 LFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILSCALF 307 F + G +YGYLNSFQV LEA M P+ VNR+G KN L+ ++MA+R+++ L Sbjct: 246 QFPTLQEGNEMYGYLNSFQVFLEAAGMFCAPWLVNRIGAKNGLIFAGMVMAMRMVASGLV 305 Query: 308 VNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLLSTPT 367 P +IS+ KLLHA+E+P+ ++S+FKY+ NFDKRLSST++L+GF SS+ +LS Sbjct: 306 EGPLLISITKLLHAVELPVLLVSIFKYNSLNFDKRLSSTLYLVGFACTSSVIATVLSPLA 365 Query: 368 GILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPVPSAI 415 G ++ G+ + + +V IF L + P SAI Sbjct: 366 GYSYEKYGFAQSYLIMGLLVFCTTFISIFLLRSSKSSSDPLMPQTSAI 413 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: 518 Number of extensions: 25 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: 413 Length adjustment: 31 Effective length of query: 384 Effective length of database: 382 Effective search space: 146688 Effective search space used: 146688 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