Align TreV, component of Trehalose porter (characterized)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Putida:PP_1484 Length = 343 Score = 221 bits (562), Expect = 3e-62 Identities = 120/307 (39%), Positives = 187/307 (60%), Gaps = 12/307 (3%) Query: 1 MTVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60 + V+ + + +G+ ++ ++ I GEFF +LGPSG GK+T L+++AG E+ G I Sbjct: 3 LAVQFTQVSRTFGEVKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGSIR 62 Query: 61 ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120 G + PP +R+V VFQ+YAL+P+M+V +NIA+ LK++G+ K E R E+A ++ Sbjct: 63 IQGVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVKGVGKAERHSRAEEALAMV 122 Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180 ++ +K Q+SGGQ+QRVALARA+V P LLDEPL LD ++R +GELK++Q+ Sbjct: 123 ALAGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQR 182 Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNF 240 +L TFI+VTHDQ EALS++DR+A+ ++G+ EQV P+ LY P T +VA+FVG N Sbjct: 183 QLGITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVG--TSNV 240 Query: 241 LPGELMKE---KAQEIGFRPEWVEVG-------KGNLSCMVESVEASGESRYLICNFKNN 290 + GEL + RPE + +G + +S ++ V+ G + N Sbjct: 241 VRGELAMQINGSPAPFSIRPELIRLGDPVVTSHEVQVSGVLHDVQYQGSATRYELQLDNG 300 Query: 291 NITILSQ 297 + +SQ Sbjct: 301 QLLAVSQ 307 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: 266 Number of extensions: 11 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: 343 Length adjustment: 28 Effective length of query: 296 Effective length of database: 315 Effective search space: 93240 Effective search space used: 93240 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