Align D-mannose and D-mannitol transporter (characterized)
to candidate BPHYT_RS34435 BPHYT_RS34435 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__BFirm:BPHYT_RS34435 Length = 427 Score = 206 bits (524), Expect = 1e-57 Identities = 118/400 (29%), Positives = 201/400 (50%), Gaps = 8/400 (2%) Query: 7 SLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWA 66 S++++ML + I YLDR +S AA K++ LS E+G++FS+F Y F IGGW Sbjct: 11 SIVLVMLCIMYFITYLDRVNVSTAAAGFGKEFHLSHTEVGLVFSAFAYPYLIFQIIGGWV 70 Query: 67 ADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYT 126 +DR+GAK TL+ +W + + LT G SL+ R+L G GEG + + W Sbjct: 71 SDRFGAKRTLIFCGAIWGVATLLTGFAGGLISLLAARVLLGFGEGATFPAATSAMARWVA 130 Query: 127 PKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKER 186 ++R A G + + + +G A++ ++ + T+GW+ SF I + L+W VW E Sbjct: 131 KEKRGFAQGITHAASRIGNAVAPGLIVLVMATWGWRESFYICGVFSLLWVGVWAITFTEH 190 Query: 187 PEGEGA---EDILRAEGQGELAAQPVFPLRFYLKQPTVLFTSLAFFSYNYTLFFFLTWFP 243 P+ +++ AA + F P ++ +F Y +TL+ FL+W P Sbjct: 191 PKDHPRITNDELSVLPAPKPKAAGVPWSKLFRRMWP----VTIVYFCYGWTLWLFLSWIP 246 Query: 244 SYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVTCLLA 303 Y ++ L ++ +I + + G +G LGG ++D++F +TG + +R ++ C+ Sbjct: 247 QYFLHSYHLQLQKSAIFASVVFFAGVIGDTLGGIVTDWIFTRTGSLKRARSWMVSVCMFF 306 Query: 304 CAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMHFLAN 363 C + + +LY ++ +A FF +T WAI D P G SG M+ + Sbjct: 307 CLLSLIPLMFTHSLYLSMACLASGFFFAEMTIGPMWAIPMDIAPEYS-GTASGMMNTGSA 365 Query: 364 TSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVAR 403 + I+ P + GFL+ + GS+ F+ + LL IG V R Sbjct: 366 LAAIISPVVGGFLIDYFGSWELPFVGSMLLMAIGVVLAFR 405 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: 553 Number of extensions: 31 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: 427 Length adjustment: 32 Effective length of query: 398 Effective length of database: 395 Effective search space: 157210 Effective search space used: 157210 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