Align Glucose facilitated diffusion protein (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)
Query= SwissProt::P21906 (473 letters) >FitnessBrowser__Keio:18059 Length = 491 Score = 400 bits (1029), Expect = e-116 Identities = 202/482 (41%), Positives = 300/482 (62%), Gaps = 11/482 (2%) Query: 1 MSSESSQGLVTRLALIAAIGGLLFGYDSAVIAAIGTPVDIHFIAPRHLSATAAASLSGMV 60 M+++ + + + L+A +GGLLFGYD+AVI+ ++ F+AP++LS +AA SL G Sbjct: 1 MNTQYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFC 60 Query: 61 VVAVLVGCVTGSLLSGWIGIRFGRRGGLLMSSICFVAAGFGAALTEKLFGTGGSALQI-- 118 V + L+GC+ G L G+ RFGRR L ++++ F +G G+A E F + + Sbjct: 61 VASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPV 120 Query: 119 --------FCFFRFLAGLGIGVVSTLTPTYIAEIAPPDKRGQMVSGQQMAIVTGALTGYI 170 F +R + G+G+G+ S L+P YIAE+AP RG++VS Q AI+ G L Y Sbjct: 121 YLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYC 180 Query: 171 FTWLLAHFGSIDWVNASGWCWSPASEGLIGIAFLLLLLTAPDTPHWLVMKGRHSEASKIL 230 + +A G W+N GW + ASE + + FL+LL T P++P WL+ +G+ +A IL Sbjct: 181 VNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGIL 240 Query: 231 ARLEPQADPNLTIQKIKAGFDKAMDKSSAGLFAFGITVVFAGVSVAAFQQLVGINAVLYY 290 ++ +Q+IK D K+ L FG+ V+ GV ++ FQQ VGIN VLYY Sbjct: 241 RKIMGNTLATQAVQEIKHSLDHGR-KTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYY 299 Query: 291 APQMFQNLGFGADTALLQTISIGVVNFIFTMIASRVVDRFGRKPLLIWGALGMAAMMAVL 350 AP++F+ LG D ALLQTI +GV+N FT++A VD+FGRKPL I GALGMA M L Sbjct: 300 APEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSL 359 Query: 351 GCCFWFKVGGVLPLASVLLYIAVFGMSWGPVCWVVLSEMFPSSIKGAAMPIAVTGQWLAN 410 G F+ + G++ L S+L Y+A F MSWGPVCWV+LSE+FP++I+G A+ IAV QWLAN Sbjct: 360 GTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419 Query: 411 ILVNFLFKVADGSPALNQTFNHGFSYLVFAALSILGGLIVARFVPETKGRSLDEIEEMWR 470 V++ F + D + L F++GFSY ++ + +L L + +FVPETKG++L+E+E +W Sbjct: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479 Query: 471 SQ 472 + Sbjct: 480 PE 481 Lambda K H 0.327 0.140 0.434 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: 613 Number of extensions: 25 Number of successful extensions: 3 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: 473 Length of database: 491 Length adjustment: 34 Effective length of query: 439 Effective length of database: 457 Effective search space: 200623 Effective search space used: 200623 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 (21.7 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