Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate AO353_25420 AO353_25420 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25420 Length = 372 Score = 281 bits (718), Expect = 3e-80 Identities = 158/341 (46%), Positives = 211/341 (61%), Gaps = 12/341 (3%) Query: 17 TPLLEIRNLTKSYDGQH----AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPS 72 T + IR + K Y H A+ + L I E F LLG SGCGK+TLLRM+AGFE P+ Sbjct: 9 TLAVSIRAVRKVYGDPHSGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPT 68 Query: 73 AGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDK----LPKAEIAS 128 G+I+L G +++ PPY RP+N +FQ YALFPHMT+ +N+AFGL+ L KA+IA Sbjct: 69 QGEILLYGENIADRPPYQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLSKAQIAE 128 Query: 129 RVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRM 188 RV EML LV M+ FA R+P QLSGGQ+QRVALAR+LA PK+LLLDEP+ ALD KLR M Sbjct: 129 RVREMLALVQMERFATRRPTQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAM 188 Query: 189 QLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAE 248 + E+ I + G+T + VTHDQEEA+TM+ RIA+++ G+ Q+G PE+IYE P R+ A+ Sbjct: 189 REELKAIQAKTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVAD 248 Query: 249 FIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEP 308 FIG N EG + E GL + HPL + V V +++RPE++ L Sbjct: 249 FIGETNFIEGTV-THVEAGLAWFAGPAGHPLPAQPCSDVNVGATVALSVRPERLHLL--- 304 Query: 309 PANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNA 349 PAN + YLG Y V L G ++ + N+ Sbjct: 305 PANTDGALPCRIDAQIYLGTDLQYQVSLNDGSRLTVRTPNS 345 Lambda K H 0.321 0.137 0.400 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: 364 Number of extensions: 16 Number of successful extensions: 3 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: 377 Length of database: 372 Length adjustment: 30 Effective length of query: 347 Effective length of database: 342 Effective search space: 118674 Effective search space used: 118674 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