Align Inositol transport system ATP-binding protein (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 168 bits (425), Expect = 2e-46 Identities = 88/244 (36%), Positives = 147/244 (60%), Gaps = 5/244 (2%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 +S+ +++++G+ K F V+AL G+ +D+ GE H + G+NGAGKST +K +SG ++ +G Sbjct: 19 VSREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEG 78 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHD 122 + + G P+ F+ DA AAGIA +HQ L ++P +SV+ N ++ EP K GP D+ Sbjct: 79 VVRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREP--KRGP--FVDYR 134 Query: 123 YANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVR 182 N ++++G+N+ P VG LS ++Q V IA+A+ A+VLI+DEPTS+L Sbjct: 135 TLNSNAQRCLQRIGLNV-SPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTES 193 Query: 183 QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242 +T + I ++R GVA+++I+H + + DR TVL G+ + T+ + E+ Sbjct: 194 ETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVA 253 Query: 243 MMAG 246 M G Sbjct: 254 RMVG 257 Score = 89.0 bits (219), Expect = 2e-22 Identities = 60/224 (26%), Positives = 100/224 (44%), Gaps = 5/224 (2%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 +S ++ GE G GAG++ + + G +P G I +P+ PR+AI GIA Sbjct: 291 LSFELRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIA 350 Query: 86 TVHQHLAMIPL---MSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLRGP 142 + + L M VS N + N +R I I +R++GI Sbjct: 351 YLSEDRKKDGLALSMPVSANITLAN--VRAISSRGFLRFSEETAIAERYVRELGIRTPTV 408 Query: 143 DQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAVV 202 Q LSGG +Q + I++ ++ G+++L DEPT + V + +D++ GV VV Sbjct: 409 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVV 468 Query: 203 FITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 I+ + L + DR V + G+ + S EE+ +G Sbjct: 469 LISSELPELLGMTDRIAVFHEGRITAVLETRQTSQEEILHHASG 512 Lambda K H 0.321 0.137 0.395 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: 316 Number of extensions: 14 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: 261 Length of database: 516 Length adjustment: 30 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 (21.9 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