Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate PP_5137 PP_5137 ferric iron ABC transporter, ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Putida:PP_5137 Length = 352 Score = 218 bits (556), Expect = 2e-61 Identities = 114/255 (44%), Positives = 170/255 (66%), Gaps = 6/255 (2%) Query: 2 ATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61 A +++RN++K +GA L ++ L I GE + L+GPSGCGK+TL+ CIAGLE G Sbjct: 8 AQIKVRNIHKRFGAFT--ALNDVSLDIAAGELVCLLGPSGCGKTTLLRCIAGLERQDRGT 65 Query: 62 IMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAK 121 + IG++D+S +SP+ RD ++FQSYAL+P ++V NI +GL QA VA + + Sbjct: 66 LYIGERDISDLSPQARDYGILFQSYALFPNLTVEANIAYGLTGSGREQAR--QRVAEMLE 123 Query: 122 LLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 L+ + + PGQLSGGQQQRVA+ RALA P + L DEP+S LDA++R + TE++ + Sbjct: 124 LVGLSGSEKKYPGQLSGGQQQRVALARALAPSPSLLLLDEPMSALDARVREHLCTELRQL 183 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPM 241 ++L TT+ VTH+Q EAM + D++AVM +G ++Q+ TP+EIY++PA FVA F+G Sbjct: 184 QRQLGITTLMVTHNQDEAMLMADRIAVMNNGQVEQYATPQEIYDHPATPFVAEFVGQG-- 241 Query: 242 NFVPLRLQRKDGRLV 256 N++P + LV Sbjct: 242 NWLPFQRSSDSHALV 256 Lambda K H 0.318 0.135 0.382 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: 364 Number of extensions: 9 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: 386 Length of database: 352 Length adjustment: 30 Effective length of query: 356 Effective length of database: 322 Effective search space: 114632 Effective search space used: 114632 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