Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 171 bits (434), Expect = 2e-47 Identities = 93/247 (37%), Positives = 150/247 (60%), Gaps = 5/247 (2%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 L+ + I K F V+ALA V + V PG L+G+NGAGKST +K ++G+++P G+I Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 G+P+ F P A AGIA +HQ L ++P MS++ N ++G E ++ L + +H +R Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGRE---QLNSLHMVNHREMHR 139 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 T E + ++ INL P++ VG LS ERQ V IA+AV + + +LI+DEPTSA+ ++ A+ Sbjct: 140 CTAELLARLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + + I ++ QG +V+ITH + A+ D V G +G + ++++ L MM Sbjct: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV- 257 Query: 247 GQELATL 253 G+EL+ L Sbjct: 258 GRELSQL 264 Score = 98.2 bits (243), Expect = 3e-25 Identities = 64/225 (28%), Positives = 111/225 (49%), Gaps = 7/225 (3%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 VS D+ GE + G G+G++ +T+ G+ + G I +G+ + +DP AI G A Sbjct: 291 VSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFA 350 Query: 86 TVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEM-RKMGINLRG 141 + + + P +SV N M P F A R E+M +K+ + Sbjct: 351 LLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNG---FIQQKALRALCEDMCKKLRVKTPS 407 Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201 +Q + TLSGG +Q +AR + ++LILDEPT + V A + I + +G+AV Sbjct: 408 LEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAV 467 Query: 202 VFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + I+ + L + DR V++ G+ +GT R + + E++ + +G Sbjct: 468 IMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 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: 291 Number of extensions: 19 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 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