Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 16521 b2422 sulfate/thiosulfate transporter subunit (NCBI)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Keio:16521 Length = 365 Score = 221 bits (563), Expect = 2e-62 Identities = 134/362 (37%), Positives = 203/362 (56%), Gaps = 21/362 (5%) Query: 4 SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEG 63 S++IA I K FG+ +VL + + + G+ + L+GPSG GK+TLL IIAGL+ T G Sbjct: 2 SIEIANIKKSFGR----TQVLNDISLDIPSGQMVALLGPSGSGKTTLLRIIAGLEHQTSG 57 Query: 64 EIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPER------QK 117 IR G +V + RDR + VFQ YAL+ ++V DNI F L + +P+ ER + Sbjct: 58 HIRFHGTDVSRLHARDRKVGFVFQHYALFRHMTVFDNIAFGLTV--LPRRERPNAAAIKA 115 Query: 118 RIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEM 177 ++ ++ M+Q++HL DR P+QLSGGQ+QRVA+ RALA +PQ+ L DEP LDA++R E+ Sbjct: 116 KVTKLLEMVQLAHLADRYPAQLSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 Query: 178 RAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVAT 237 R +++LH+ TSV+VTHDQ EA + R+ VM G ++Q PD+++ PA +V Sbjct: 176 RRWLRQLHEELKFTSVFVTHDQEEATEVADRVVVMSQGNIEQADAPDQVWREPATRFVLE 235 Query: 238 FIGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQE----TAPWR 293 F+G +N L+G + GGQF + L P+ V L +RP + + +P Sbjct: 236 FMGE--VNRLQGTIRGGQFHVGAHRWPLGYTPAYQGPVDLFLRPWEVDISRRTSLDSPLP 293 Query: 294 GRVSVVEPTGPDTYVMVDTAA---GSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSE 350 +V P G T ++V +T+ Q GE + + L A + D + E Sbjct: 294 VQVLEASPKGHYTQLVVQPLGWYNEPLTVVMHGDDAPQRGERLFVGLQHARLYNGDERIE 353 Query: 351 ER 352 R Sbjct: 354 TR 355 Lambda K H 0.318 0.135 0.388 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: 314 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 355 Length of database: 365 Length adjustment: 29 Effective length of query: 326 Effective length of database: 336 Effective search space: 109536 Effective search space used: 109536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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