Align Inositol transport system ATP-binding protein (characterized)
to candidate H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Burk376:H281DRAFT_00426 Length = 503 Score = 175 bits (444), Expect = 1e-48 Identities = 96/241 (39%), Positives = 143/241 (59%), Gaps = 3/241 (1%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 PLI ++ + K F V AL V D+ GE H L+G+NGAGKST +K ++GV+ G+IL Sbjct: 3 PLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEIL 62 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 GQP+ PRDA AAGI +HQ L ++ ++V++N F+G EP ++G D D N Sbjct: 63 LGGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLG--LFLDEDKLN 120 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 E + +M +N+ P VG L+ +Q V IA+A+ F ++VLI+DEPTSAL + A Sbjct: 121 AKAREILSRMHVNI-DPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIA 179 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245 + I +++++GV VV+I+H + + DR TVL G+ + T D S E + MM Sbjct: 180 ELFRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMV 239 Query: 246 G 246 G Sbjct: 240 G 240 Score = 72.8 bits (177), Expect = 1e-17 Identities = 68/255 (26%), Positives = 102/255 (40%), Gaps = 16/255 (6%) Query: 4 SQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGD 63 SQ I ++ H G ++ VS + GE G GAG++ + + G G+ Sbjct: 254 SQGEIALEVRNLHAGPLVR--DVSFTLRKGEILGFAGLMGAGRTEVARAVFGADPVESGE 311 Query: 64 ILFEGQPLHFADPRDAIAAGIATVHQHLAMIPL---MSVSRNFFMGNEPIRKIGPLKLFD 120 I +G P DA+A GI + + L M V N M N +R L F Sbjct: 312 IFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSN--LRNFLSLNFF- 368 Query: 121 HDYANRITMEEMRKMGINL---RGPD--QAVGTLSGGERQTVAIARAVHFGAKVLILDEP 175 R M INL R P Q V LSGG +Q + IA+ + VL DEP Sbjct: 369 ---LRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLERDCDVLFFDEP 425 Query: 176 TSALGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDI 235 T + V + + + + +G A+V I+ + L + DR V+ G+ G Sbjct: 426 TRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITGELPAEQA 485 Query: 236 SAEELQDMMAGGQEL 250 + E + + Q L Sbjct: 486 TQERIMHLATQRQTL 500 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: 307 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: 503 Length adjustment: 29 Effective length of query: 232 Effective length of database: 474 Effective search space: 109968 Effective search space used: 109968 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