Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate GFF850 Psest_0864 ABC-type sugar transport systems, permease components
Query= SwissProt::O51924 (295 letters) >FitnessBrowser__psRCH2:GFF850 Length = 521 Score = 117 bits (292), Expect = 7e-31 Identities = 86/255 (33%), Positives = 135/255 (52%), Gaps = 18/255 (7%) Query: 56 FVGLRNYLRVL---SAREFWYSTFV-TVSFSFVSVSLETILGLSFALILN-ERLKGRGVL 110 F G N+ RVL S RE + F T +F+ ++V +GL A +L E ++G+ Sbjct: 267 FTGFANFSRVLTEPSIREPFMQIFAWTFAFAGLTVVFTLAVGLVLASLLQWELVRGKAFY 326 Query: 111 RAIVLIPWAVPTIISARTWELMYNYSYGLFNWILS-ILGVSPVNWLGTPISAFFAIVIAD 169 R ++++P+AVP IS + ++N ++G N +L + G+ P +W P A I+I + Sbjct: 327 RLMLILPYAVPGFISILVFRGLFNQNFGEINLLLEGLFGIRP-DWFSDPSLARTMILIVN 385 Query: 170 VWKTTPFMTLLLLAGLQAIPQDLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTID 229 W P+M LL + LQAIP+D YEA+ IDGAS + ITLP L L+ LI Sbjct: 386 TWLGYPYMLLLCMGLLQAIPRDQYEASAIDGASPLDNLLRITLPQLIKPLMPLLIACFAF 445 Query: 230 ALRVFDIIYVLTGGGPG--GATT---SISLLAFNYYNLG------DYGIGSAISILTFVL 278 F +I +LT GGP GATT + LL Y + D+ + +AI+ + F+L Sbjct: 446 NFNNFVLITLLTRGGPDIIGATTPAGTTDLLVSYTYRIAFQDSGQDFALAAAIATMIFIL 505 Query: 279 VLSFTIVYLKVGRFR 293 V + ++ LK+ + + Sbjct: 506 VGAMALLNLKLSKVK 520 Lambda K H 0.329 0.145 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: 380 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 295 Length of database: 521 Length adjustment: 31 Effective length of query: 264 Effective length of database: 490 Effective search space: 129360 Effective search space used: 129360 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: 50 (23.9 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