Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate BPHYT_RS11445 BPHYT_RS11445 putrescine/spermidine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__BFirm:BPHYT_RS11445 Length = 388 Score = 408 bits (1048), Expect = e-118 Identities = 205/371 (55%), Positives = 273/371 (73%) Query: 6 PRPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRML 65 P A T A +++ ++ K + AV V+L++ KGE+FALLG+SGCGKSTLLRM+ Sbjct: 17 PSLNAVTGDATDNFVQVVDVVKKFGETVAVKGVNLSVKKGELFALLGSSGCGKSTLLRMM 76 Query: 66 AGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAE 125 AG E S+G+I++DG DL+Q+PPY RP+NMMFQSYALFPHMTVE N+AFGLKQ+ +PKAE Sbjct: 77 AGLESVSSGKILIDGEDLAQLPPYRRPVNMMFQSYALFPHMTVEGNVAFGLKQEGVPKAE 136 Query: 126 IASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLR 185 + RV L LV M FAKRKP+QLSGGQ+QRVALARSL KRPKLLLLDEPM ALDK++R Sbjct: 137 LKDRVQTALELVQMGRFAKRKPNQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKQIR 196 Query: 186 DRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRY 245 R Q+E+V+IL++VGVTC+MVTHDQEEAMTMAGR+A+M+ G+ VQ+G P E+YE+P +R+ Sbjct: 197 QRTQIELVNILDKVGVTCMMVTHDQEEAMTMAGRLAVMSEGEIVQLGTPHEVYEYPNSRF 256 Query: 246 SAEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLC 305 SAEFIGS N+FEG E + D + +++P L L V + +PV +++RPE+I L Sbjct: 257 SAEFIGSTNLFEGHTVEDEPDYVFIETPDLPCRLYVSHGITGPLGMPVTISVRPERIALT 316 Query: 306 EEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRL 365 +PP N+ G V +IAY+G S+YHV+L++G+ + A + + PTWGDEV + Sbjct: 317 RKPPEGAYNWGKGVVTNIAYMGGYSLYHVKLEAGKTVIANVTSLALTEIDPPTWGDEVYV 376 Query: 366 CWEVDSCVVLT 376 W + VVLT Sbjct: 377 RWSASAGVVLT 387 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: 424 Number of extensions: 8 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: 388 Length adjustment: 30 Effective length of query: 347 Effective length of database: 358 Effective search space: 124226 Effective search space used: 124226 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