Align Inositol transport system ATP-binding protein (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 168 bits (426), Expect = 2e-46 Identities = 90/254 (35%), Positives = 151/254 (59%), Gaps = 6/254 (2%) Query: 1 MSMSQP-LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKP 59 +S+ +P L+ + + K F V+AL+ V + V PG L+G+NGAGKST +K ++G+++P Sbjct: 19 VSLDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQP 78 Query: 60 TKGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLF 119 G++ G+P+ F P A+ AGIA +HQ L ++P MS++ N ++G E ++ L + Sbjct: 79 DAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE---QLNGLHMV 135 Query: 120 DHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSAL 179 DH +R T + ++ I L P++ VG LS ERQ V IA+AV + + +LI+DEPTSA+ Sbjct: 136 DHGEMHRCTARLLERLRIKL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAI 194 Query: 180 GVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEE 239 + A++ + I ++ QG +++ITH + A+ D V G +G + + + Sbjct: 195 TETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDS 254 Query: 240 LQDMMAGGQELATL 253 L MM G+EL+ L Sbjct: 255 LISMMV-GRELSQL 267 Score = 107 bits (266), Expect = 7e-28 Identities = 69/226 (30%), Positives = 113/226 (50%), Gaps = 7/226 (3%) Query: 25 GVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGI 84 GVS D+ GE + G G+G++ + + GV T G+I +GQP+ +DP AI G Sbjct: 293 GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGF 352 Query: 85 ATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEM-RKMGINLR 140 A + + + P +SV N M P +G F A R E+M +K+ + Sbjct: 353 ALLTEDRKLSGLFPCLSVLENMEMAVLP-HYVG--NGFIQQKALRALCEDMCKKLRVKTP 409 Query: 141 GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVA 200 +Q + TLSGG +Q +AR + ++LILDEPT + V A + I + +G+A Sbjct: 410 SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMA 469 Query: 201 VVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 V+ I+ + L + DR V++ G +GT R + + E + + +G Sbjct: 470 VIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 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: 300 Number of extensions: 20 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: 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 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