Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate HSERO_RS12120 HSERO_RS12120 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS12120 Length = 266 Score = 182 bits (461), Expect = 8e-51 Identities = 101/252 (40%), Positives = 156/252 (61%), Gaps = 6/252 (2%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 + E IL + K +G V AL L GE+ ++GDNGAGKS++IK ++G G Sbjct: 7 SDEIILELDQVSKFFGPVIALQNVSLRLRRGEVHCLLGDNGAGKSTLIKLLAGVHQASSG 66 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGRE-IRKPGIMGKWFRS 120 + ++GKP++F SP EA G+ TVYQ+LAL P LS+A N FLGRE +RK + G Sbjct: 67 QYLVDGKPVRFESPKEALDVGVATVYQDLALVPLLSVARNFFLGREPVRK--LFGVTVMD 124 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 ++ AA + A+ KL+E+G+M +++ + + T+SGG++Q +A+ARA FG++V+I+DEPTA Sbjct: 125 MELAA--RTAKEKLAEMGIM-VRDAHHPIGTMSGGEKQCLAIARAIHFGARVLILDEPTA 181 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTM 240 ALGVK+S VL+LI R RG+ ++ I+HN+ H + + D + G+ L + Sbjct: 182 ALGVKQSFNVLKLIHRARERGISVIFITHNVHHAYPIGDTFTLLNRGKSLGSFAKDRISK 241 Query: 241 SDAVAFMTGAKE 252 + + M G E Sbjct: 242 EEVLDMMAGGAE 253 Lambda K H 0.321 0.136 0.383 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: 172 Number of extensions: 6 Number of successful extensions: 2 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: 260 Length of database: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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