Align D-mannose and D-mannitol transporter (characterized)
to candidate Pf1N1B4_3380 D-glucarate permease
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3380 Length = 423 Score = 195 bits (496), Expect = 2e-54 Identities = 128/402 (31%), Positives = 196/402 (48%), Gaps = 15/402 (3%) Query: 9 IIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAAD 68 I ++F ++N +DR +LS+A P I ++ LS G+I SSFF YA GGW D Sbjct: 14 IFAIIFALTMVNLIDRVSLSIAMPTIAHEFSLSPSMQGLILSSFFWAYALLQIPGGWMID 73 Query: 69 RYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPK 128 R+G + + LW +F L G SL+ R+ G E PL + K+++ W P Sbjct: 74 RFGPHRVISWSTGLWGMFQVLAAFATGGLSLLFARVALGAAEAPLFPSGGKLISLWLAPS 133 Query: 129 RRARAIGASMSGTPLGGAISGPVVGF-IAVTYGWKISFIIIMLIGLVWAAVWFKFVKE-- 185 R+R SG+PLG A+ G ++ + IA W+++F+I + LV A + ++++++ Sbjct: 134 ERSRGAVLMDSGSPLGVALGGLIIAYLIASLDSWRLAFVIAGIATLVLAWLAWRYLRDDP 193 Query: 186 --RPEGEGAE----DILRAEGQGELAAQPVFPLRFYLKQPTVLFTSLAFFSYNYTLFFFL 239 P+ AE + RA E A PV L + + L A ++ Y F L Sbjct: 194 ASHPQVNAAELEKINAGRATPAAEAARIPVKGLGIAARSLSGLLIGRACWAMVY--FGLL 251 Query: 240 TWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVT 299 TW PSYL A G ++K + AT + +V G LG GGF+ D + +K + K +L Sbjct: 252 TWGPSYLAQARGFDIKGIGAATFVIFVCGALGSLTGGFLCDGLIRKGVSRGVAVKSLLAF 311 Query: 300 CLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMH 359 L ++ + AV L+A+ FFL + G++YW+ ARVG + G M+ Sbjct: 312 SGLVALGAFLLLPTLSNPFAAVALLAMTAFFL-MWGSLYWSFPALLAAPARVGLIGGVMN 370 Query: 360 FLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCV 401 +T GI P L G +VQ TG F + G V AV V Sbjct: 371 MAGSTGGIAVPILVGIIVQMTGGFAP---VLGFFAVCSAVFV 409 Score = 25.0 bits (53), Expect = 0.005 Identities = 11/39 (28%), Positives = 23/39 (58%) Query: 368 VGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARYVK 406 +G + +L+ S+ AF++AG+ T++ A RY++ Sbjct: 152 LGGLIIAYLIASLDSWRLAFVIAGIATLVLAWLAWRYLR 190 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: 550 Number of extensions: 37 Number of successful extensions: 5 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: 423 Length adjustment: 32 Effective length of query: 398 Effective length of database: 391 Effective search space: 155618 Effective search space used: 155618 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