Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 166 bits (420), Expect = 9e-46 Identities = 89/245 (36%), Positives = 142/245 (57%), Gaps = 3/245 (1%) Query: 2 SMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61 S S P+I ++ + K F V+AL ++ GE H L+G+NGAGKST +K +SGV++ Sbjct: 17 SSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS 76 Query: 62 GDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDH 121 GDIL +G+P+ +PR A A GI +HQ L ++ +S ++N F+G EP + +G D Sbjct: 77 GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMG--LFIDE 134 Query: 122 DYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGV 181 D NR +M +++ P VG L+ +Q V IA+A+ F ++VLI+DEPT+AL Sbjct: 135 DELNRQAAAIFARMRLDM-DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193 Query: 182 RQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQ 241 + A + I ++ QGV +V+I+H + + DR +V+ GK + T + S + + Sbjct: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253 Query: 242 DMMAG 246 MM G Sbjct: 254 SMMVG 258 Score = 78.2 bits (191), Expect = 3e-19 Identities = 54/225 (24%), Positives = 96/225 (42%), Gaps = 5/225 (2%) Query: 22 ALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIA 81 A+ VS + GE G GAG++ + + G G+I+ G P DA+A Sbjct: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347 Query: 82 AGIATVHQ---HLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGIN 138 GI + + H + M V N + + + + + D +R++ I Sbjct: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSS--MGRFTRVGFMDQRAIREAAQMYVRQLAIK 405 Query: 139 LRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQG 198 +Q LSGG +Q + IA+ + +L DEPT + V + + +D + +QG Sbjct: 406 TPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465 Query: 199 VAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243 A+V I+ + L + R V+ G+ G R D + E++ + Sbjct: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510 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: 315 Number of extensions: 14 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: 520 Length adjustment: 30 Effective length of query: 231 Effective length of database: 490 Effective search space: 113190 Effective search space used: 113190 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