Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS25335 AZOBR_RS25335 putative ABC transporter (ATP-binding protein)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__azobra:AZOBR_RS25335 Length = 365 Score = 248 bits (634), Expect = 2e-70 Identities = 152/358 (42%), Positives = 201/358 (56%), Gaps = 28/358 (7%) Query: 9 LAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVV 68 LAK Y PP L L L + GE + L+GPSGCGK+T LR+IAGL SGG + +GG + Sbjct: 15 LAKRYGTAPPALAALSLEVAGGELLGLVGPSGCGKTTALRLIAGLTPASGGRVLVGGRDI 74 Query: 69 NDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALL 128 LPA R + +VFQNYAL+PHM+ DN+AFGLR PAAE R E A++ L L Sbjct: 75 TALPAHARGIGLVFQNYALFPHMTAADNVAFGLRMRGLPAAERHARTAEALAMVRLSHLG 134 Query: 129 ERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTT 188 RKPRA+SGGQQQR A+ARA+ P++ L DEPLSNLDA LRA+L +I+ L +RL T Sbjct: 135 GRKPRALSGGQQQRVALARALAIRPNLLLLDEPLSNLDAGLRAELLAEIRTLQRRLGITA 194 Query: 189 VYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG----TPAMNFLS 244 ++VTHDQ EA+ + DR+ +++DGR+ Q G+P E++ P + F AGF+G PA L+ Sbjct: 195 LFVTHDQGEALAVCDRIAVLRDGRLEQVGTPREVHDRPASGFVAGFVGRTNRIPAER-LA 253 Query: 245 GTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPV 304 G R G L A A V L VRP +R+ G A L P Sbjct: 254 GGALRVGGTLLPALAD-------------GPAGPVDLFVRPHRIRV-GAAGGAGGL--PA 297 Query: 305 SVELVEILGADALLTTRCGDQTLTALVPADRLP-------QPGATLTLALDQHELHVF 355 + LG L+ G +T P + P PG T+ L+ D ++ VF Sbjct: 298 VLRGTAFLGDRIALSLEAGGAPVTVDWPVEAAPPAPGPALTPGETVALSWDPADMAVF 355 Lambda K H 0.321 0.137 0.403 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: 496 Number of extensions: 19 Number of successful extensions: 2 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: 406 Length of database: 365 Length adjustment: 30 Effective length of query: 376 Effective length of database: 335 Effective search space: 125960 Effective search space used: 125960 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 (21.8 bits) S2: 50 (23.9 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