Align ABC transporter (characterized, see rationale)
to candidate AO353_07265 AO353_07265 spermidine/putrescine ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07265 Length = 374 Score = 244 bits (623), Expect = 3e-69 Identities = 137/342 (40%), Positives = 209/342 (61%), Gaps = 11/342 (3%) Query: 18 ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPRERGV 77 I++D++LEI GEF+ +GPSG GK+T L ++AG ++ G++L+ GR +N++ P +R + Sbjct: 30 IVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLAGRAINNVPPHKRDI 89 Query: 78 GMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKELSGG 137 GMVFQ+YAL+PHM+V +N++F L + +K+ + +RV + ++QLD QR P +LSGG Sbjct: 90 GMVFQNYALFPHMTVAENLAFPLTVRGLNKSDVSDRVKRVLSMVQLDAFAQRYPAQLSGG 149 Query: 138 QRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHDQVEA 197 Q+QRVA+ RA+ EP ++L DEPL LD LR M+ EI LH RLG T++YVTHDQ EA Sbjct: 150 QQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVTVVYVTHDQGEA 209 Query: 198 MTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETSLVDT 257 +T++D++ V + G ++Q+ PRELYE+P + FVA F+G N L+ RL + V Sbjct: 210 LTMSDRVAVFHQGEIQQIAPPRELYEKPKNTFVANFIG--ENNRLNGRLHSHTGDRCVVE 267 Query: 258 LVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGT-----AGVVVTAVEYLGSETYV 312 L G + G P++L IRPE VSL + + +G V + YLG V Sbjct: 268 LGRGEKVEALAVNVGKTGEPVTLSIRPERVSLNGSSESCVNRFSGRVAEFI-YLGDHVRV 326 Query: 313 HLET-GQDEPLICR--CEVSAGWQAGDRVELLLDLDNLHLFD 351 LE G+ + + + E+ GD V L ++++ D Sbjct: 327 RLEVCGKTDFFVKQPIAELDPALAVGDVVPLGWQVEHVRALD 368 Lambda K H 0.320 0.137 0.394 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: 338 Number of extensions: 17 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: 381 Length of database: 374 Length adjustment: 30 Effective length of query: 351 Effective length of database: 344 Effective search space: 120744 Effective search space used: 120744 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