Align sugar transport protein 6 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= CharProtDB::CH_091493 (507 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 218 bits (556), Expect = 3e-61 Identities = 150/471 (31%), Positives = 247/471 (52%), Gaps = 34/471 (7%) Query: 18 TVYVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCKYDNQ 77 T+ F+C +AA+ GL+FG DIG+ G A+ EF + H E Sbjct: 13 TMTFFVC-FLAALAGLLFGLDIGVIAG--ALPFIANEF-----QISAHTQE--------- 55 Query: 78 FLQLFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNLVMLIIGR 137 SS+ A V + + KLGR+ ++ +I F+ G +A A N+ +L+I R Sbjct: 56 ---WVVSSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISR 112 Query: 138 LFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTATVHPYGW 197 + LG VG + PL+LSEIAP ++RG + ++QLM+TIGIL A + + TA + W Sbjct: 113 VLLGLAVGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSD--TAFSYSGAW 170 Query: 198 RIALGGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKIRGVDDINDEYESIVHA 257 R LG IPAV+LL G + + ++P + + + + L ++R D + E + + Sbjct: 171 RWMLGVIIIPAVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLR---DTSAEAKRELDE 227 Query: 258 CDIASQVKDPYRKLLKPAS--RPPFIIGMLLQLFQQFTGINAIMFYAPVLFQTVGFGSDA 315 + +VK L K S R +G+LLQ+ QQFTG+N IM+YAP +F+ G+ + Sbjct: 228 IRESLKVKQSGWSLFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTT 287 Query: 316 -ALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLIIGIILAKDLGVTGT 374 + VI G NVLATF+ I LVDR GR+ L+ + M + I+G ++ +G+ Sbjct: 288 EQMWGTVIVGLTNVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMM--HIGIHSA 345 Query: 375 LGRPQALVVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAVAVSCNMFFTFVIA 434 + V+ + ++++GFA S GPL W++ SE PL+ R G + + N ++ Sbjct: 346 TAQ---YFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVG 402 Query: 435 QAFLSMLCGMRSGIFFFFSGWIIVMGLF-AFFFIPETKGIAIDDMRESVWK 484 FL+ML + S F+ G + ++ +F + IPETK ++++ + ++ K Sbjct: 403 ATFLTMLNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIERNLMK 453 Lambda K H 0.329 0.144 0.446 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: 611 Number of extensions: 33 Number of successful extensions: 8 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: 507 Length of database: 464 Length adjustment: 34 Effective length of query: 473 Effective length of database: 430 Effective search space: 203390 Effective search space used: 203390 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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