Align D-mannose and D-mannitol transporter (characterized)
to candidate 17750 b3691 D-galactonate transport (VIMSS)
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Keio:17750 Length = 430 Score = 202 bits (514), Expect = 2e-56 Identities = 129/413 (31%), Positives = 211/413 (51%), Gaps = 22/413 (5%) Query: 3 GQGRSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFI 62 G+ R L ++M+F+ VI Y+DR+ L+VA+ IQ+++G++ EMG +FS+F Y Sbjct: 11 GRRRYLTLVMIFITVVICYVDRANLAVASAHIQEEFGITKAEMGYVFSAFAWLYTLCQIP 70 Query: 63 GGWAADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVN 122 GGW DR G++ T +A+ WS+ + G SL+ +R + G+ E P T ++MV Sbjct: 71 GGWFLDRVGSRVTYFIAIFGWSVATLFQGFATGLMSLIGLRAITGIFEAPAFPTNNRMVT 130 Query: 123 NWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKF 182 +W+ RA A+G SG +G A P++ +I W FI+ IG++W+ +WFK Sbjct: 131 SWFPEHERASAVGFYTSGQFVGLAFLTPLLIWIQEMLSWHWVFIVTGGIGIIWSLIWFKV 190 Query: 183 VKERPEGEGAE----DILRAEG---QGEL-----AAQPV----FPLRFYLKQPTVLFTSL 226 + +G D +R G G+ A QP+ + L F+ K ++ L Sbjct: 191 YQPPRLTKGISKAELDYIRDGGGLVDGDAPVKKEARQPLTAKDWKLVFHRK---LIGVYL 247 Query: 227 AFFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKT 286 F+ TL+FFLTWFP+YLT G+ T +P++ F+G+ L G+++D + +K Sbjct: 248 GQFAVASTLWFFLTWFPNYLTQEKGITALKAGFMTTVPFLAAFVGVLLSGWVADLLVRKG 307 Query: 287 GRMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTV 346 + F+RK ++ C L + CI A + L+ALA FF +I W+++ Sbjct: 308 FSLGFARKTPII-CGLLISTCIMGANYTNDPMMIMCLMALA-FFGNGFASITWSLVSSLA 365 Query: 347 PAARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAV 399 P +G G +F GI P + G+L Q G F A + + +IGA+ Sbjct: 366 PMRLIGLTGGVFNFAGGLGGITVPLVVGYLAQGYG-FAPALVYISAVALIGAL 417 Score = 33.9 bits (76), Expect = 1e-05 Identities = 33/161 (20%), Positives = 66/161 (40%), Gaps = 13/161 (8%) Query: 33 FIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAADR---------YGAKTTLLLAMVLW 83 ++ ++ G++ + G + + F+ + GW AD + KT ++ +++ Sbjct: 266 YLTQEKGITALKAGFMTTVPFLAAFVGVLLSGWVADLLVRKGFSLGFARKTPIICGLLIS 325 Query: 84 SLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPKRRARAIGASMS-GTP 142 + G + L+ + F G G S+T S + + P R G + Sbjct: 326 TCIMGANYTNDPMMIMCLMALAF-FGNGFASITWSLVSS--LAPMRLIGLTGGVFNFAGG 382 Query: 143 LGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFV 183 LGG VVG++A YG+ + + I + L+ A + V Sbjct: 383 LGGITVPLVVGYLAQGYGFAPALVYISAVALIGALSYILLV 423 Lambda K H 0.329 0.142 0.439 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: 604 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 430 Length of database: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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: 51 (24.3 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