Align Inositol transport system ATP-binding protein (characterized)
to candidate 3609577 Dshi_2961 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Dino:3609577 Length = 511 Score = 157 bits (398), Expect = 3e-43 Identities = 93/240 (38%), Positives = 139/240 (57%), Gaps = 9/240 (3%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 L+R+ G+ K + V+A VS ++ GE H LLG+NGAGKST +K + G+ +P G + F Sbjct: 4 LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 G P +PR A +AG+A V QH ++ ++V+ N +G E K+ D A R Sbjct: 64 GGVPFAPPEPRAARSAGVAMVFQHFSLFEALTVAENIALGMEDPPKM-------RDLAAR 116 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 IT + + G+ L P + VGTLS GERQ V I R + K+LI+DEPTS L ++ Sbjct: 117 IT-QVSQAYGLPL-DPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDI 174 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + AT+ K+R +G A+++I+H + A+ D T+L GK + T + SA EL +MM G Sbjct: 175 LFATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVG 234 Score = 69.3 bits (168), Expect = 2e-16 Identities = 57/252 (22%), Positives = 105/252 (41%), Gaps = 10/252 (3%) Query: 6 PLIRMQGIEKH----FGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61 P++ ++G+ + FG+ L +S++V GE + G G G+ + +SG + + Sbjct: 250 PVLELRGLSQPATTPFGT--PLRDISLEVRAGEVLGIGGVAGNGQDELLSAISGERR-AE 306 Query: 62 GDILFEGQPLHFADPRDAIAAGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKL 118 I G P+ P G+ + + A P MS++ N + K+ Sbjct: 307 DAIFLHGTPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTENALLTGSVREKLTRNGF 366 Query: 119 FDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSA 178 D + + GP+ A LSGG Q I R V +VLI+++PT Sbjct: 367 LDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIGREVLQRPEVLIVNQPTWG 426 Query: 179 LGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE 238 + A + + + G AVV I+ ++ + + D F LN G+ G ++ E Sbjct: 427 VDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAALNGGRLSGKVPAAGLTVE 486 Query: 239 ELQDMMAGGQEL 250 ++ M+ G ++ Sbjct: 487 QIGLMLGGAHDM 498 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: 343 Number of extensions: 18 Number of successful extensions: 3 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: 511 Length adjustment: 29 Effective length of query: 232 Effective length of database: 482 Effective search space: 111824 Effective search space used: 111824 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