Align D-mannose and D-mannitol transporter (characterized)
to candidate PfGW456L13_2130 Hexuronate transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2130 Length = 436 Score = 217 bits (552), Expect = 6e-61 Identities = 134/408 (32%), Positives = 209/408 (51%), Gaps = 18/408 (4%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R I+++LF+ VINYLDRS LS+AAP + D G+ +G+IFS+F YAA GGW Sbjct: 19 RFFIMVLLFITVVINYLDRSNLSIAAPALTSDLGIDPIHVGLIFSAFGWTYAAMQIPGGW 78 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWY 125 DR + +A++LWS+ + + F +L ++R+ G E P S++V W+ Sbjct: 79 LVDRVPPRILYSVALLLWSVATVMLGFAGSFIALFVLRMAVGALEAPAYPINSRVVTTWF 138 Query: 126 TPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKE 185 + RA AIG SG +G A PV+ ++ +GW + F+ +G+VWA +W+ +E Sbjct: 139 PERERATAIGFYTSGQFVGLAFLTPVLAWLQHEFGWHMVFVTTGAVGIVWAVIWYAVYRE 198 Query: 186 RPEGEGAEDI---LRAEGQGEL---AAQPVFPLRFYLKQPTVLFTS-------LAFFSYN 232 + +GA D L EG G + A Q +F ++ T L F N Sbjct: 199 PRDFKGANDAEIDLIREGGGLVDIQAEQARVKAKFSWTDLGIVLTKRKLWGIYLGQFCLN 258 Query: 233 YTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFS 292 TL+FFLTWFP+YL G++ + +P++ F+G+ GF SDF+ ++ + F+ Sbjct: 259 STLWFFLTWFPTYLVKYRGMDFIKSGLLASLPFLAAFIGVLCSGFFSDFLIRRGYTVGFA 318 Query: 293 RKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVG 352 RK+ +++ LL I + +T P VI FF +I W+++ PA +G Sbjct: 319 RKLPIISGLLISTSIIGANFVEST--PLVIAFLALAFFGNGLASITWSLVSTLAPARLLG 376 Query: 353 GVSGFMHFLANTSGIVGPTLTGFLVQFTG-SFTSAFLLAGLLTVIGAV 399 G +F+ N S I P + GFL TG SF A +L +IGA+ Sbjct: 377 LTGGVFNFIGNLSAIATPIVIGFLA--TGDSFAPAITYISVLALIGAL 422 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: 603 Number of extensions: 34 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: 430 Length of database: 436 Length adjustment: 32 Effective length of query: 398 Effective length of database: 404 Effective search space: 160792 Effective search space used: 160792 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