Align Inositol transport system ATP-binding protein (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 123 bits (309), Expect = 7e-33 Identities = 77/248 (31%), Positives = 124/248 (50%), Gaps = 7/248 (2%) Query: 1 MSMSQP--LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHK 58 MS+ P ++ + GI K + + L G+ + + GE L G+NGAGKST K + G+ Sbjct: 1 MSVCAPNAVLSVSGIGKTYAQPV-LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVT 59 Query: 59 PTKGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKL 118 PT G + F+G+ A GI V Q L ++P +SV+ N F+ N P Sbjct: 60 PTTGQMQFQGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNG----GW 115 Query: 119 FDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSA 178 + + M ++G++ PD VG L G +Q V IAR + VLILDEPT+ Sbjct: 116 ISRKQLRKAAIAAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAM 175 Query: 179 LGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE 238 L R+ + I +++ +GVA+++I+H + V R VL G + + ++E Sbjct: 176 LTAREVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSE 235 Query: 239 ELQDMMAG 246 +L ++M G Sbjct: 236 QLVNLMVG 243 Score = 90.5 bits (223), Expect = 6e-23 Identities = 60/220 (27%), Positives = 106/220 (48%), Gaps = 7/220 (3%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF--EGQPLHFADPRDAIAAG 83 VS +V GE + G GAG++ ++ + G G + Q + P DA+ G Sbjct: 276 VSFEVRSGEIFGISGLIGAGRTELLRLIFGADAADSGTVALGSPAQVVSIRSPADAVGHG 335 Query: 84 IATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLR 140 IA + + ++ S+S N +GN P+ G + + A + ++ M I Sbjct: 336 IALITEDRKGEGLLLTQSISANIALGNMPVISSGGIVNSGDEMA--LAQRQIDAMRIRSS 393 Query: 141 GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVA 200 P Q V LSGG +Q V I R + VL+ DEPT + V ++ A + ++ +QG A Sbjct: 394 SPAQLVSELSGGNQQKVVIGRWLERECSVLLFDEPTRGIDVGAKFDIYALLGELTRQGKA 453 Query: 201 VVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 +V ++ ++R + + DR VL+ G+ + T +R + ++L Sbjct: 454 LVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDL 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: 319 Number of extensions: 23 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: 517 Length adjustment: 30 Effective length of query: 231 Effective length of database: 487 Effective search space: 112497 Effective search space used: 112497 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 Apr 09 2024. 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