Align Inositol transport system ATP-binding protein (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 168 bits (426), Expect = 2e-46 Identities = 90/240 (37%), Positives = 144/240 (60%), Gaps = 5/240 (2%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 +++++G+ K F V+AL G+ +D+ GE H + G+NGAGKST +K +SG + G I + Sbjct: 22 ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 EG+P+ FA DA AAGIA +HQ L ++P +SV+ N ++ EP K GP D+ N Sbjct: 82 EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREP--KRGP--FVDYRTLNA 137 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 ++++G+N+ P VG LS ++Q V IA+A+ A+VLI+DEPTS+L +T Sbjct: 138 NAQRCLQRIGLNV-SPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQ 196 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + I ++R GVA+++I+H + + DR TVL G+ + T+ + E+ M G Sbjct: 197 LFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVG 256 Score = 80.1 bits (196), Expect = 9e-20 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 5/224 (2%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 +S D+ GE G GAG++ + + G + G I P+ PR+AI GIA Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349 Query: 86 TVHQHLAMIPL---MSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLRGP 142 + + L M V+ N + N +R I I +R++ I Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSN--VRAISSRGFLRFSEETAIAERYVRELAIRTPTV 407 Query: 143 DQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAVV 202 Q LSGG +Q + I++ ++ G+++L DEPT + V + +D++ GV VV Sbjct: 408 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVV 467 Query: 203 FITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 I+ + L + DR V + G + S EE+ +G Sbjct: 468 LISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASG 511 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: 298 Number of extensions: 13 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: 515 Length adjustment: 30 Effective length of query: 231 Effective length of database: 485 Effective search space: 112035 Effective search space used: 112035 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