Align sugar transport protein 6 (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= CharProtDB::CH_091493 (507 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 233 bits (595), Expect = 8e-66 Identities = 155/477 (32%), Positives = 242/477 (50%), Gaps = 38/477 (7%) Query: 11 PAFEAKMTVYVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENN 70 P K TV ++ CV+ AA+ GL+FG DIG+ G S +F A + H Sbjct: 9 PTAHVKGTV-IYTCVL-AALAGLMFGLDIGVISGAS-------QFIKAEFAISDHT---- 55 Query: 71 YCKYDNQFLQLFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNL 130 ++ SS+ A V + A S LGR+ ++ +I F+IG L A + Sbjct: 56 --------IEWIVSSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSP 107 Query: 131 VMLIIGRLFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTA 190 LI R+ LG +G PL+L+E+AP +RG + +QLM+TIGIL+A + + TA Sbjct: 108 ETLIAARVILGLAIGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFLSD--TA 165 Query: 191 TVHPYGWRIALGGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKIRGVDDINDE 250 + WR LG IP + L G L + ++P L+ R + +E + LR++RG DE Sbjct: 166 LSYHGAWRWMLGVIAIPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRG-----DE 220 Query: 251 YESIVHACDIASQVKDPYRKLLKPASRPPF----IIGMLLQLFQQFTGINAIMFYAPVLF 306 A DI Q+K P R A P F +G LLQ+ QQFTG+N +M+YAP +F Sbjct: 221 VVVAREAADIEEQLKTPQRGWDLFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIF 280 Query: 307 QTVGFGSDAALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLIIGIILA 366 Q +G+ + A + + G NVLATF+ I L+DR GR+ +L M + ++G ++ Sbjct: 281 QEMGYDTAAQMWFTALVGLTNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMN 340 Query: 367 KDLGVTGTLGRPQALVVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAVAVSCN 426 G G+ + V + +++GFA S GPL W + SE PL+ R G V+ N Sbjct: 341 -----GGINGQTEQYTCVAMLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTN 395 Query: 427 MFFTFVIAQAFLSMLCGM-RSGIFFFFSGWIIVMGLFAFFFIPETKGIAIDDMRESV 482 V+ FLS+L + + F+ ++ V + F+ +PETKG+ ++ + ++ Sbjct: 396 WITNMVVGFTFLSLLNTIGNASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIERNL 452 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: 658 Number of extensions: 30 Number of successful extensions: 7 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: 463 Length adjustment: 34 Effective length of query: 473 Effective length of database: 429 Effective search space: 202917 Effective search space used: 202917 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 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