Align Inositol transport system ATP-binding protein (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 167 bits (423), Expect = 4e-46 Identities = 87/247 (35%), Positives = 148/247 (59%), Gaps = 5/247 (2%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 L+ + + K F V+AL+ V + V PG L+G+NGAGKST +K ++G+++P G++ Sbjct: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 G+P+ F P A+ AGIA +HQ L ++P MS++ N ++G E ++ + DH +R Sbjct: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE---QLNGFHMIDHREMHR 143 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 T + + ++ INL P++ VG LS ERQ V IA+AV + + +LI+DEPTSA+ ++ A+ Sbjct: 144 CTAQLLERLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAH 202 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + + I ++ QG +++ITH + ++ D V G +G + + + L MM Sbjct: 203 LFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMV- 261 Query: 247 GQELATL 253 G+EL+ L Sbjct: 262 GRELSQL 268 Score = 103 bits (257), Expect = 7e-27 Identities = 71/248 (28%), Positives = 118/248 (47%), Gaps = 16/248 (6%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 MS +R+ G+ K GVS D+ GE + G G+G++ + + G+ G Sbjct: 281 MSVRDLRLDGVFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGG 331 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLF 119 +I +GQP+ +DP AI G A + + + P +SV N M P F Sbjct: 332 EICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNG---F 388 Query: 120 DHDYANRITMEEM-RKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSA 178 A R E+M +K+ + +Q + TLSGG +Q +AR + ++LILDEPT Sbjct: 389 IQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRG 448 Query: 179 LGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE 238 + V A + I + +G+AV+ I+ + L + DR V++ G +GT R + + E Sbjct: 449 IDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQE 508 Query: 239 ELQDMMAG 246 + + +G Sbjct: 509 RVMQLASG 516 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: 22 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: 521 Length adjustment: 30 Effective length of query: 231 Effective length of database: 491 Effective search space: 113421 Effective search space used: 113421 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