Align Inositol transport system ATP-binding protein (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 151 bits (382), Expect = 2e-41 Identities = 84/230 (36%), Positives = 131/230 (56%), Gaps = 7/230 (3%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 P++R+ GI K FG V A +++D+ PG LLG+NGAGKST + ++G + G I+ Sbjct: 28 PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 +G P FA PRDA+ AGI V+QH ++ M+V+ N +G P + P ++ D A Sbjct: 88 VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRPARMRDEVAA- 146 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 + E + ++ P VG LS GERQ V I + ++ ++VLILDEPT+ L R+T Sbjct: 147 ---LAERYGLAVD---PAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETD 200 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDI 235 + + ++ QG A+VFI+H ++ L V D +L RG+ + D+ Sbjct: 201 QLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADV 250 Score = 58.9 bits (141), Expect = 2e-13 Identities = 56/230 (24%), Positives = 101/230 (43%), Gaps = 10/230 (4%) Query: 23 LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLH--FADPRDAI 80 L+ VS+ V GE + G G G+ ++ + G+ +P G++ G+P FA P Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350 Query: 81 A-AGIATVHQHLAMIPLMSVSRNFFM--GNEPIRKIGPLKLFDHDYANRITMEEMRKMGI 137 A I Q LA + + NF + N+ + + + + R+ E + G Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPG- 409 Query: 138 NLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQ 197 ++ P +A LSGG Q + I R +V++ + PT L + T V + + R Sbjct: 410 DITAPARA---LSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARST 466 Query: 198 GVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247 V+ +T ++ AL + DR V+ RG+ + + D + + +M G Sbjct: 467 S-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMMAG 515 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: 350 Number of extensions: 20 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: 537 Length adjustment: 30 Effective length of query: 231 Effective length of database: 507 Effective search space: 117117 Effective search space used: 117117 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