Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 160 bits (406), Expect = 4e-44 Identities = 97/261 (37%), Positives = 151/261 (57%), Gaps = 13/261 (4%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 A IL +G+ KR+ V ALD D DL GE+ AV G+NGAGKS+++K ISG D+G Sbjct: 18 APREILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDG 77 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121 I EGKP+QF S +A+ AGI ++Q L L P LS+A+N++L RE ++ + Sbjct: 78 VICYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPF-------V 130 Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 D + A+ L +GL + V LS Q+Q V +A+A + ++V+IMDEPT++ Sbjct: 131 DYRTLNANAQRCLQRIGLNV--SPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSS 188 Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 L E+ ++ +I ++R G+ I+ ISH + + E+ DR+ + R GR + + T++ Sbjct: 189 LTESETVQLFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTIN 248 Query: 242 DAVAFMTGA----KEPPREAI 258 + VA M G PPRE++ Sbjct: 249 EIVARMVGRALDDAYPPRESV 269 Score = 94.7 bits (234), Expect = 3e-24 Identities = 71/241 (29%), Positives = 117/241 (48%), Gaps = 15/241 (6%) Query: 18 RVTALDRAD------FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ 71 RV L R D FDL GEIL G GAG++ + +AI GA D G I+L P+ Sbjct: 277 RVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVT 336 Query: 72 FRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEK 128 RSP EA + GI + ++ L+ ++ +A N+ L +R G S + A E+ Sbjct: 337 IRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSN-VRAISSRGFLRFSEETAIAER 395 Query: 129 QARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESR 188 R EL + T + Q LSGG +Q + +++ GS+++ DEPT + V Sbjct: 396 YVR----ELAIRT-PTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKY 450 Query: 189 RVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMT 248 + +L+ + G+ +VLIS +P + + DRI + G V+ + + + + + + Sbjct: 451 AIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYAS 510 Query: 249 G 249 G Sbjct: 511 G 511 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: 309 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 515 Length adjustment: 29 Effective length of query: 231 Effective length of database: 486 Effective search space: 112266 Effective search space used: 112266 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