Align Inositol transport system ATP-binding protein (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 152 bits (384), Expect = 1e-41 Identities = 91/243 (37%), Positives = 140/243 (57%), Gaps = 7/243 (2%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGV--HKPTKGDI 64 L M+GI K FG V AL G+ + + GEC L G+NGAGKST +K +SGV H G+I Sbjct: 7 LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66 Query: 65 LFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYA 124 L++GQPL RD+ AGI +HQ L ++P +SV+ N F+G+E R G + +D YA Sbjct: 67 LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMD-YDAMYA 125 Query: 125 NR-ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183 ++E+ +N+ P G GG +Q IA+A+ AK+LILDEPTS+L + Sbjct: 126 KADALLQELGLHDVNVALPAMHYG---GGHQQLFEIAKALAKQAKLLILDEPTSSLTSSE 182 Query: 184 TANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243 T +L ++ ++++GVA ++I+H + V D V+ G+ + T ++ + L + Sbjct: 183 TEVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITL 242 Query: 244 MAG 246 M G Sbjct: 243 MVG 245 Score = 82.0 bits (201), Expect = 2e-20 Identities = 63/229 (27%), Positives = 102/229 (44%), Gaps = 26/229 (11%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF-EGQPLHFADPRDAIAAGI 84 VS + GE + G GAG++ + + G + LF EG+PL P DAI AG+ Sbjct: 285 VSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGL 344 Query: 85 ATV---HQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKM------ 135 V + ++PL+ V N L DH YA+ ++ R++ Sbjct: 345 GMVPEDRKRHGIVPLLGVGDNI-----------TLATLDH-YAHAGHIDRQRELVAIEAQ 392 Query: 136 ----GINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATI 191 + P + LSGG +Q +A+ + KVLILDEPT + V A + I Sbjct: 393 IAERRVKTASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLI 452 Query: 192 DKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 ++ QGVA+V ++ + L + DR V+ G+ G ++ E++ Sbjct: 453 FELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGRLRGDFPNQGLTQEQV 501 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: 349 Number of extensions: 22 Number of successful extensions: 5 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: 513 Length adjustment: 29 Effective length of query: 232 Effective length of database: 484 Effective search space: 112288 Effective search space used: 112288 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