Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 116 bits (290), Expect = 1e-30 Identities = 77/245 (31%), Positives = 124/245 (50%), Gaps = 18/245 (7%) Query: 11 GLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPI 70 G+ K+Y A DR D + PGEI A++G+NGAGKS+++K I G PD GEI +G+ + Sbjct: 13 GITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERV 72 Query: 71 QFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQA 130 R P +AR+ GI V+Q+ +L LS+A+N+ L +G +A KQ Sbjct: 73 TMRDPAQARERGIGMVFQHFSLFETLSVAENIALA--------LGA------KAGTPKQL 118 Query: 131 RAKLSELGL---MTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKES 187 K+ E+ M ++ + V +LS G+RQ V + R +++I+DEPT+ L +E+ Sbjct: 119 EPKIREVSQRYGMPLEP-QRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEA 177 Query: 188 RRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFM 247 + + + G I+ ISH + V + + R GR P + + + M Sbjct: 178 DELFVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLM 237 Query: 248 TGAKE 252 G E Sbjct: 238 VGDAE 242 Score = 53.5 bits (127), Expect = 9e-12 Identities = 47/207 (22%), Positives = 92/207 (44%), Gaps = 10/207 (4%) Query: 21 ALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE---IRLEGKPIQFRSPME 77 +L D ++ GEI+ + G G G+ ++ +SG + IR G + P Sbjct: 274 SLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGA 333 Query: 78 ARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKL 134 R+ G+ V P++S+ADN L ++ G++ + + R + A + Sbjct: 334 RRRHGMAFVPAERLGHGAVPSMSLADNGLL-TAYQQTGMVEQGL--IRRGRVRAFAEQVI 390 Query: 135 SELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELI 194 + T + +LSGG Q + R K++I PT + V + + + Sbjct: 391 QRFAVKT-PDAQTPAASLSGGNLQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRAL 449 Query: 195 LDVRRRGLPIVLISHNMPHVFEVADRI 221 +++R G I++IS ++ +F+++DRI Sbjct: 450 IELRDAGAAILVISEDLEELFQISDRI 476 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: 304 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 518 Length adjustment: 30 Effective length of query: 230 Effective length of database: 488 Effective search space: 112240 Effective search space used: 112240 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: 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