Align Spermidine/putrescine ABC transporter, spermidine/putrescine-binding protein, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate CCNA_03239 CCNA_03239 spermidine/putrescine-binding protein
Query= TCDB::Q97Q45 (356 letters) >FitnessBrowser__Caulo:CCNA_03239 Length = 368 Score = 198 bits (504), Expect = 2e-55 Identities = 102/300 (34%), Positives = 164/300 (54%), Gaps = 1/300 (0%) Query: 33 DSQKLVIYNWGDYIDPELLTQFTEETGIQVQYETFDSNEAMYTKIKQGGTTYDIAIPSEY 92 + KL YNW YI L F + TGI V F +N+ ++ K+K G +D+ +PS Sbjct: 46 EEAKLNFYNWDTYIGETTLGDFKKATGIDVNMSLFATNDELFAKLKAGNPGFDVVVPSNE 105 Query: 93 MINKMKDEDLLVPLDYSKIEGIENIGPEFLNQSFDPGNKFSIPYFWGTLGIVYNETMVDE 152 + +M LL PLD++KI ++NI P FLN FDPG KFS+PY W LGI Y ++ V Sbjct: 106 FVTRMSQGGLLEPLDHAKIPNMKNIDPSFLNPEFDPGRKFSMPYTWLLLGIGYRKSKVKG 165 Query: 153 APEHWDDLW-KPEYKNSIMLFDGAREVLGLGLNSLGYSLNSKDLQQLEETVDKLYKLTPN 211 P+ W L+ +YK I L + +++ L LG+S+N+ L + L K P Sbjct: 166 VPDSWKWLFDSDQYKGRIALLSESADLVRLSAKYLGHSVNNIPQDMLPKIEQMLIKQKPF 225 Query: 212 IKAIVADEMKGYMIQNNVAIGVTFSGEASQMLEKNENLRYVVPTEASNLWFDNMVIPKTV 271 +KA D + ++ V + + ++G+ +Q ++++ +L +VVP E S + D + IPK Sbjct: 226 VKAFHDDNGQDMLMSGEVDLVLEYNGDIAQAMKEDPDLDFVVPKEGSLINSDTLCIPKGA 285 Query: 272 KNQNSAYAFINFMLKPENALQNAEYVGYSTPNLPAKELLPEETKEDKAFYPDVETMKHLE 331 N+A+AFIN++L + + ++ + Y TPN AK L+PE+ K + +P + M E Sbjct: 286 PRPNNAHAFINYLLDAQAGAEISKTILYPTPNAAAKALMPEDYKNNPVIFPPADVMAKCE 345 Lambda K H 0.316 0.135 0.397 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: 320 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: 356 Length of database: 368 Length adjustment: 29 Effective length of query: 327 Effective length of database: 339 Effective search space: 110853 Effective search space used: 110853 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 (21.6 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