Align sugar transport protein 6 (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= CharProtDB::CH_091493 (507 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 209 bits (533), Expect = 1e-58 Identities = 148/473 (31%), Positives = 241/473 (50%), Gaps = 46/473 (9%) Query: 22 FICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCKYDNQFLQL 81 F+C +AA+ GL+FG DIG+ G A+ EF + H E Sbjct: 17 FVC-FLAALAGLLFGLDIGVIAG--ALPFIADEF-----QITSHTQE------------W 56 Query: 82 FTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNLVMLIIGRLFLG 141 SS+ A V + + KLGR+ ++ +I F+ G +A A N+ +LI+ R+ LG Sbjct: 57 VVSSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLG 116 Query: 142 FGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTATVHPYGWRIAL 201 VG + PL+LSEIAP ++RG + ++QLM+TIGIL A + + TA + WR L Sbjct: 117 LAVGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSD--TAFSYTGAWRWML 174 Query: 202 GGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKIRGVDDINDEYESIVHACDIA 261 G IPA++LL G + ++P + + + + L ++R D + E + + + Sbjct: 175 GVIIIPAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLR---DTSAEAKRELDEIRES 231 Query: 262 SQVKDPYRKLLKPAS--RPPFIIGMLLQLFQQFTGINAIMFYAPVLFQTVGF-GSDAALL 318 QVK L K S R +G+LLQ+ QQFTG+N IM+YAP +F+ G+ + + Sbjct: 232 LQVKQSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMW 291 Query: 319 SAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLIIGIILAKDLGVTGT---- 374 VI G NVLATF+ I LVDR GR+ L +++A +GV GT Sbjct: 292 GTVIVGLTNVLATFIAIGLVDRWGRKPTLTLGF-----------LVMAAGMGVLGTMMHI 340 Query: 375 -LGRPQA-LVVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAVAVSCNMFFTFV 432 + P A + + ++++GFA S GPL W++ SE PL+ R G + + N + Sbjct: 341 GIHSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMI 400 Query: 433 IAQAFLSMLCGM-RSGIFFFFSGWIIVMGLFAFFFIPETKGIAIDDMRESVWK 484 + FL+ML + + F+ ++ ++ L + +PETK ++++ + ++ K Sbjct: 401 VGATFLTMLNTLGNANTFWVYAALNVLFILLTLWLVPETKHVSLEHIERNLMK 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: 594 Number of extensions: 34 Number of successful extensions: 7 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: 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 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