Align Inositol transport system ATP-binding protein (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 166 bits (421), Expect = 7e-46 Identities = 88/241 (36%), Positives = 143/241 (59%), Gaps = 3/241 (1%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 PLI ++ + K F V AL V ++ GE H L+G+NGAGKST +K ++GV+ G+IL Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 +EGQP+ F PR+A A G+ +HQ L ++ +++++N F+G EP ++G D D N Sbjct: 63 YEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLG--LFLDEDKLN 120 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 + + +M + L P V +L+ +Q V IA+A+ F ++VLI+DEPTSAL + A Sbjct: 121 AQAHDILARMHVTL-DPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIA 179 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245 + I ++K+GV +++I+H + + DR TVL G+ + T D + + + MM Sbjct: 180 ELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMV 239 Query: 246 G 246 G Sbjct: 240 G 240 Score = 75.9 bits (185), Expect = 2e-18 Identities = 60/222 (27%), Positives = 93/222 (41%), Gaps = 6/222 (2%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 VS + GE G GAG++ + + G G+I+ +G +P DA+A GI Sbjct: 274 VSFALRKGEILGFAGLMGAGRTEVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIG 333 Query: 86 TVHQHLAMIPL---MSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEE-MRKMGINLRG 141 + + L MSV N M N +RK L F R T + + I Sbjct: 334 YLSEDRKRFGLATGMSVESNIVMSN--LRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPS 391 Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201 Q V LSGG +Q + IA+ + VL DEPT + V + + + + QG A+ Sbjct: 392 ATQEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAI 451 Query: 202 VFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243 V I+ + L + DR V+ G+ G + E + + Sbjct: 452 VMISSELPEILRMSDRIVVMCEGRITGELAAAGATQERIMQL 493 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: 323 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: 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