Align TreV, component of Trehalose porter (characterized)
to candidate 15562 b1441 predicted spermidine/putrescine transporter subunit (NCBI)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Keio:15562 Length = 337 Score = 212 bits (540), Expect = 9e-60 Identities = 118/302 (39%), Positives = 186/302 (61%), Gaps = 10/302 (3%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 VE ++ + YG ++G++ I+ GEFF +LGPSG GK+T L+++AG E+L G I Sbjct: 5 VEFDNVSRLYGDVRAVDGVSIAIKDGEFFSMLGPSGSGKTTCLRLIAGFEQLSGGAISIF 64 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G ++ PP +R+V VFQ+YAL+P+MS+ DN+A+ L ++G+ K++ ++A + + + Sbjct: 65 GKPASNLPPWERDVNTVFQDYALFPHMSILDNVAYGLMVKGVNKKQRHAMAQEALEKVAL 124 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 + +K +Q+SGGQ+QRVA+ARA+V P LLDEPL LD ++R + ELK++Q+ L Sbjct: 125 GFVHQRKPSQLSGGQRQRVAIARALVNEPRVLLLDEPLGALDLKLREQMQLELKKLQQSL 184 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 TFI+VTHDQ EALS++DR+A+ + G+ EQV P+ LY P+T +VA FVG N Sbjct: 185 GITFIFVTHDQGEALSMSDRVAVFNNGRIEQVDSPRDLYMRPRTPFVAGFVG--TSNVFD 242 Query: 243 GELMKEK----AQEIGFRPEWVEV---GKGNLSCMVESVEASGESRYLICNFKNNNITIL 295 G LM EK RPE + + G+ + +++V+ G + ++ Sbjct: 243 G-LMAEKLCGMTGSFALRPEHIRLNTPGELQANGTIQAVQYQGAATRFELKLNGGEKLLV 301 Query: 296 SQ 297 SQ Sbjct: 302 SQ 303 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: 271 Number of extensions: 9 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: 337 Length adjustment: 28 Effective length of query: 296 Effective length of database: 309 Effective search space: 91464 Effective search space used: 91464 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