Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate BPHYT_RS23145 BPHYT_RS23145 putrescine/spermidine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__BFirm:BPHYT_RS23145 Length = 387 Score = 404 bits (1038), Expect = e-117 Identities = 203/370 (54%), Positives = 269/370 (72%) Query: 7 RPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLA 66 RP T+ + I N+ K + AVD+V+L+I K E+FALLG+SGCGKSTLLRMLA Sbjct: 17 RPAVTTKSKSDEFVRIENVVKKFGDSTAVDNVNLSIAKNELFALLGSSGCGKSTLLRMLA 76 Query: 67 GFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEI 126 G E ++G+I +DG DL+ +PPY RP+NMMFQSYALFPHM+VE NIAFGLKQ+ PK EI Sbjct: 77 GLETVTSGRIFVDGEDLAAMPPYKRPVNMMFQSYALFPHMSVEANIAFGLKQEGTPKNEI 136 Query: 127 ASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRD 186 RV + L LV M ++A+RKPHQLSGGQ+QRVALARSL KRPKLLLLDEPM ALDKK+R Sbjct: 137 KERVADALNLVQMSKYAQRKPHQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKKIRQ 196 Query: 187 RMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYS 246 + QLE+V+I+E+V VTCVMVTHDQEEAMTMAGR+A+M+ G+ VQIG P ++YE P +R+S Sbjct: 197 KTQLELVNIIEKVDVTCVMVTHDQEEAMTMAGRLAVMSEGRIVQIGSPSQVYEFPNSRFS 256 Query: 247 AEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCE 306 AEFIGS N+FEG + + D + ++S L + V + +PV +++RPE+I + Sbjct: 257 AEFIGSTNLFEGTVVADEPDHIFVESEELESRIYVSHGITGPLGMPVGISVRPERIKVSL 316 Query: 307 EPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLC 366 + P N+A G V +AY+G S+YHVRL SG+ + + L ++H +G P++ D+V + Sbjct: 317 DKPTTPHNWARGVVADVAYMGSYSLYHVRLPSGKTVVSNLSSSHLMAEGAPSYNDDVFVY 376 Query: 367 WEVDSCVVLT 376 W S VVLT Sbjct: 377 WSPASGVVLT 386 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: 396 Number of extensions: 6 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: 377 Length of database: 387 Length adjustment: 30 Effective length of query: 347 Effective length of database: 357 Effective search space: 123879 Effective search space used: 123879 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