Align Fructose import permease protein FruF (characterized)
to candidate HSERO_RS05180 HSERO_RS05180 sugar ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__HerbieS:HSERO_RS05180 Length = 359 Score = 220 bits (561), Expect = 4e-62 Identities = 131/349 (37%), Positives = 199/349 (57%), Gaps = 21/349 (6%) Query: 3 EKAKAEGNNFVKKLLSSNLTWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITML 62 + A + G+ + LL L + A +L++I + F L G L G LI ++ Sbjct: 12 DTAASAGSPMLAGLLRHPLVRPLGALAVLLLIDFLLVPGFFKLEIKD--GHLYGALIDII 69 Query: 63 QESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAM--------------QTLSNGMN 108 +A ++ A GMTLVI+T G+D+SVG+V+A++GA A Q +SN Sbjct: 70 NRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVDGVSQYVSNVPM 129 Query: 109 VWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVA 168 VW ++ A+ L G NG LV+ LGLQP I TLI+M+AGRG+A+++T G+ Sbjct: 130 VW-ALCAAMGAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLLTDGQ----IVTV 184 Query: 169 GNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKP 228 +P + G++ G+P + IA + +L+ LL +KTA+G+ IE+VGIN ASR+ GI+ Sbjct: 185 YYKPFFFLGGGYLFGLPFSLYIAAAMFVLLALLMKKTALGLFIESVGINPVASRLAGIRT 244 Query: 229 KKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSL 288 ++F VY A +AGL +++ D G LE+ AILAV +GGTSL GGKFSL Sbjct: 245 AALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSL 304 Query: 289 AGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIVICVMQAPKIHNL 337 GS +GA+II + TI +LGV E ++VV ++C+ Q+P+ + Sbjct: 305 VGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSPQFRRM 353 Lambda K H 0.325 0.136 0.384 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: 333 Number of extensions: 17 Number of successful extensions: 4 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: 356 Length of database: 359 Length adjustment: 29 Effective length of query: 327 Effective length of database: 330 Effective search space: 107910 Effective search space used: 107910 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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