Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate N515DRAFT_3233 N515DRAFT_3233 xylose ABC transporter membrane protein
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Dyella79:N515DRAFT_3233 Length = 380 Score = 141 bits (356), Expect = 2e-38 Identities = 111/373 (29%), Positives = 175/373 (46%), Gaps = 72/373 (19%) Query: 19 YVVLLVLLAI----IIFQDPT---FLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLS 71 Y +L +LLA+ + F T F++ N+SN+ Q ++ ++A G+ +I+ DLS Sbjct: 13 YKILALLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAGEIDLS 72 Query: 72 AGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLN 131 G +GL V A L + + P+A+V ++ +G +IGL NG + L Sbjct: 73 VGSLLGLLGGVVAVLTVNQGWST---------PVAIVAVL--GLGVLIGLFNGFWVTRLR 121 Query: 132 VTPFI---------------TTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFV 176 V FI TT I + +Y SP+ G + FA Sbjct: 122 VPSFIVGLGGMLAFRGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVVA 181 Query: 177 -------------------------------ALGSFRLSY-----ITFYALIAVAFVWV- 199 ALG F + I LI VA + V Sbjct: 182 LAVLRRRRRAQLQIRQLPWWADLLKVVAIGAALGVFVATLNSYGGIPLPVLILVALLAVF 241 Query: 200 --LWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSAT 257 L ++T G++I+A+GGN EA ++SGVNV L+++ + G+ AF G++ R+ + + Sbjct: 242 SYLASQTVLGRHIYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAGS 301 Query: 258 NNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYIIK 317 + G ELDAIAAC +GG S GG GTV G + G ++ ++ G++ + V+ YWQYI+K Sbjct: 302 PSAGTNGELDAIAACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIVK 361 Query: 318 GAIIIFAVALDSL 330 GAI++ AV +D L Sbjct: 362 GAILVLAVWVDVL 374 Score = 26.2 bits (56), Expect = 0.001 Identities = 42/181 (23%), Positives = 72/181 (39%), Gaps = 45/181 (24%) Query: 191 LIAVAFVWVLWNKTRFGKNIFAIGGNPEAAK-VSGVNVGLNLLMIYALSGVFYAFGGMLE 249 L+AVA +WV ++ A GG+ A+ VS + + + + A VF G ++ Sbjct: 19 LLAVAAIWVFFH--------VATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAGEID 70 Query: 250 ----------AGRIGSATNNLGFMYELDAIAACVVGGV---------------SFSGGVG 284 G + T N G+ + +A +G + SF G+G Sbjct: 71 LSVGSLLGLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRLRVPSFIVGLG 130 Query: 285 TVIGVVTGVIIFTV-------INYGLTYIG---VNPYWQYIIKGAIIIFAVALDSLKYAR 334 ++ GV++ T + L Y+G V+P W ++ AI VAL L+ R Sbjct: 131 GMLAF-RGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVVALAVLRRRR 189 Query: 335 K 335 + Sbjct: 190 R 190 Lambda K H 0.327 0.143 0.415 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: 321 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 336 Length of database: 380 Length adjustment: 29 Effective length of query: 307 Effective length of database: 351 Effective search space: 107757 Effective search space used: 107757 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: 49 (23.5 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