Align D-mannose and D-mannitol transporter (characterized)
to candidate H281DRAFT_00667 H281DRAFT_00667 Sugar phosphate permease
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Burk376:H281DRAFT_00667 Length = 428 Score = 235 bits (600), Expect = 2e-66 Identities = 141/424 (33%), Positives = 216/424 (50%), Gaps = 15/424 (3%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R ++I++ FLA INY+DR+ ++VAAP IQK + +MG+I S FF YA GW Sbjct: 5 RWIVILLCFLAIAINYIDRANMAVAAPAIQKALDIGPAQMGLILSGFFWTYALMQMPFGW 64 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWY 125 DR GA+ L LA+ WSLF+ LT ++ R+L G+GE + +K+V+ W+ Sbjct: 65 FVDRIGARIALPLAVGWWSLFTALTAAATSVGAMFGCRLLLGIGEAGAYPSCAKLVSQWF 124 Query: 126 TPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKE 185 +RA A SG+ +G A+S PVV I GW+ SF+I ++G VW WF + Sbjct: 125 KRAQRALATSIFDSGSRVGSALSIPVVALIISGLGWEASFVITGVVGFVWVLGWFLVYRN 184 Query: 186 RPEGEGAEDILRAEGQGELAAQPV----FPLRFYLKQPTVLFTSLAFFSYNYTLFFFLTW 241 G+ L E G++ V P + T+ L FF N+ ++FF+TW Sbjct: 185 PSRGD-----LTGESDGDVPQTAVPGRKVPWLSLFRHRTLWGMMLGFFCLNFVIYFFITW 239 Query: 242 FPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVTCL 301 FPSYL G ++K + +IP ++ LGGF+SD ++++ + +RK +V + Sbjct: 240 FPSYLVQTRGFSLKSLGTLGMIPALMAIPSGWLGGFVSDALYRRGWSLTKARKTCMVAGM 299 Query: 302 LACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAA-RVGGVSGFMHF 360 L +V CA T +Y + +A L A W++ D P V + G +F Sbjct: 300 LLSSVITLCA-FTTNIYLMLAFFGIAYGSLAFAAASIWSLPADVAPTPDHVASIGGIQNF 358 Query: 361 LANTSGIVGPTLTGFLVQFT-GSFTSAFLLAGLLTVIGA---VCVARYVKPLSVADTGNA 416 +N +GIV T TG +V T GSFT +AG V+GA + + + ++PL V Sbjct: 359 ASNCAGIVITTFTGLMVSLTHGSFTIPLCVAGGFCVLGAFSYLVIVQKIEPLPVEGDAYD 418 Query: 417 AAQS 420 A +S Sbjct: 419 AERS 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: 562 Number of extensions: 25 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: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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