Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 168 bits (425), Expect = 2e-46 Identities = 96/243 (39%), Positives = 142/243 (58%), Gaps = 6/243 (2%) Query: 5 QPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG-D 63 +PL+ MQGI K F + L V + V+PGE H L+G+NGAGKST +K +SG ++ G + Sbjct: 4 EPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGE 63 Query: 64 ILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDY 123 I GQ + DP A A GIA ++Q L++ P +SV+ N ++G E R D Sbjct: 64 IRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGW----TIDRKG 119 Query: 124 ANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183 +E ++++G P V +LS ERQ V IARA+H AK+L++DEPT+ L R+ Sbjct: 120 MEAGCIEVLQRLGAEFT-PATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRE 178 Query: 184 TANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243 T + A I ++R QG+A+++I+H + A+ DR +VL G +G R +SAE L M Sbjct: 179 TDRLFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKM 238 Query: 244 MAG 246 M G Sbjct: 239 MVG 241 Score = 75.1 bits (183), Expect = 3e-18 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 10/232 (4%) Query: 27 SVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLH-FADPRDAIAAGIA 85 S D+ GE + G GAG++ + + T G + G+ + P DAI AG+ Sbjct: 277 SFDLHAGEVLGIAGLVGAGRTELARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVV 336 Query: 86 TVHQHLAMIPL---MSVSRNFFM-GNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLRG 141 + + L MSV+ N + P G + D D+A + + + ++ + I + Sbjct: 337 YLTEDRKAQGLFLDMSVADNINVCACVPDAHAGGV--LDRDHALQRSNDAIKSLSIRVAS 394 Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201 G LSGG +Q V +AR + VLILDEPT + + + + I+++ + G+ + Sbjct: 395 GKVNAGALSGGNQQKVLLARLLEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGI 454 Query: 202 VFITHNVRHALAVGDRFTVLNRGK---TLGTAQRGDISAEELQDMMAGGQEL 250 V I+ + + DR ++ G+ +G A IS E + D+ GG ++ Sbjct: 455 VVISSELPEIIGTCDRVLIMREGQLVAEVGGASGQAISQERIIDLATGGDQV 506 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: 303 Number of extensions: 15 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: 510 Length adjustment: 29 Effective length of query: 232 Effective length of database: 481 Effective search space: 111592 Effective search space used: 111592 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