Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_000009985.1:WP_011385946.1 Length = 265 Score = 121 bits (304), Expect = 1e-32 Identities = 73/249 (29%), Positives = 129/249 (51%), Gaps = 5/249 (2%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 + P+L R + +G V AL F + GE+ ++IG NGAGK+SM+ +SG P Sbjct: 3 VTDNPVLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPTS 62 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGRE--IRKPGIMGKWF 118 G + ++G+ + SP G+ +QNLAL +S+ DN+ +GR + G + Sbjct: 63 GRVFMDGRDVTGLSPNVRATLGLGRTFQNLALFGHMSVLDNIMVGRHHLLGNNAATGALY 122 Query: 119 RSLDRAAMEKQARAKLSE-LGLMTIQNINQAVE-TLSGGQRQGVAVARAAAFGSKVVIMD 176 E R K+ + + + I +I +AV TL G R+ V +ARA A KV+++D Sbjct: 123 WLSGARKEELAHRRKVEDIIDFLEIAHIRKAVAGTLPYGLRKRVELARAMAVEPKVILLD 182 Query: 177 EPTAALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINP 235 EP A + ++E + I+D+ G+ +++I H+M V +++ R+ + GR++ P Sbjct: 183 EPMAGMNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEFGRKIAEGLP 242 Query: 236 KDYTMSDAV 244 + ++ V Sbjct: 243 DEVMNNERV 251 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: 154 Number of extensions: 8 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: 260 Length of database: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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