Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911 Length = 517 Score = 130 bits (327), Expect = 6e-35 Identities = 87/248 (35%), Positives = 128/248 (51%), Gaps = 9/248 (3%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 A +L+ G+ K Y + L D L GE+LA+ G+NGAGKS++ K I G VTP G Sbjct: 5 APNAVLSVSGIGKTYAQ-PVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTG 63 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121 +++ +G+ + S +A GI V Q L L P LS+A+N+FL K G + + + L Sbjct: 64 QMQYQGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISR--KQL 121 Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 +AA+E A L + T+ V L G +Q V +AR V+I+DEPTA Sbjct: 122 RKAAIEAMAHVGLDAIDPDTL------VGELGIGHQQMVEIARNLIGDCHVLILDEPTAM 175 Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 L +E + E I ++ RG+ I+ ISH + + VA RI + R G +CV +Y Sbjct: 176 LTAREVEMLFEQITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSE 235 Query: 242 DAVAFMTG 249 V M G Sbjct: 236 QLVTLMVG 243 Score = 83.6 bits (205), Expect = 8e-21 Identities = 71/249 (28%), Positives = 115/249 (46%), Gaps = 21/249 (8%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+LT GL R + F++ GEI + G GAG++ +++ I GA D G I Sbjct: 260 PVLTVNGL----SRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIA 315 Query: 65 LEGKPIQF---RSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWF 118 L G P Q RSP++A GI + ++ L SI N+ LG PGI G F Sbjct: 316 L-GAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGN---MPGISGAGF 371 Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNIN--QAVETLSGGQRQGVAVARAAAFGSKVVIMD 176 D K+ ++ M I++ Q V LSGG +Q V + R V++ D Sbjct: 372 VDND-----KERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFD 426 Query: 177 EPTAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPK 236 EPT + V + L+ ++ R+G +V++S ++ + + DRI + G + + Sbjct: 427 EPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRD 486 Query: 237 DYTMSDAVA 245 +T + +A Sbjct: 487 SWTQDELLA 495 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: 281 Number of extensions: 12 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: 517 Length adjustment: 30 Effective length of query: 230 Effective length of database: 487 Effective search space: 112010 Effective search space used: 112010 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