Align TreV, component of Trehalose porter (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Putida:PP_1018 Length = 384 Score = 236 bits (601), Expect = 9e-67 Identities = 124/297 (41%), Positives = 185/297 (62%), Gaps = 10/297 (3%) Query: 2 TVELIDIVKKYGKNI--VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKI 59 T+EL ++ K YG + + I I+ GEF +++GPSG GKSTL+ +AG+E++ G I Sbjct: 3 TLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAI 62 Query: 60 IADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKL 119 + D D++ P+ R++AMVFQ+YALYP MSVR+NI F LK+R + + I E V + AKL Sbjct: 63 LIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKL 122 Query: 120 LGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQ 179 L I +L +K Q+SGGQQQRVA+ RA+ R P +L DEPLSNLDA++R R E+K + Sbjct: 123 LQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMH 182 Query: 180 KELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMN 239 + LK T +YVTHDQ EA++L D++A++ G +Q P+ +Y P ++VA F+G PMN Sbjct: 183 QRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPPMN 242 Query: 240 FLPGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVEASG--ESRYLICNFKNNNITI 294 F+P L ++ + + + G C + EA+ E R +I + I + Sbjct: 243 FIPVRLARQDGRLLAL------LDSGQARCELPLGEAADALEGREIILGIRPEQIAL 293 Lambda K H 0.318 0.137 0.385 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: 281 Number of extensions: 15 Number of successful extensions: 1 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: 324 Length of database: 384 Length adjustment: 29 Effective length of query: 295 Effective length of database: 355 Effective search space: 104725 Effective search space used: 104725 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