Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate H281DRAFT_05181 H281DRAFT_05181 putrescine transport system ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Burk376:H281DRAFT_05181 Length = 388 Score = 409 bits (1051), Expect = e-119 Identities = 208/378 (55%), Positives = 272/378 (71%), Gaps = 4/378 (1%) Query: 3 DAIPRPQAKTRKALTPLLE----IRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGK 58 D + P A A+ E I ++ K + AV V+L++ KGE+FALLG+SGCGK Sbjct: 10 DRVAAPSAGGNAAMNDAAENFVQIVDVVKKFGETVAVKQVNLSVKKGELFALLGSSGCGK 69 Query: 59 STLLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQ 118 STLLRMLAG E ++G+I++DG DL+Q+PPY RP+NMMFQSYALFPHMTVE N+AFGLKQ Sbjct: 70 STLLRMLAGLETVTSGKILIDGEDLAQLPPYRRPVNMMFQSYALFPHMTVESNVAFGLKQ 129 Query: 119 DKLPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMG 178 + +PKAE+ RV L LV M FA RKPHQLSGGQ+QRVALARSL KRPKLLLLDEPM Sbjct: 130 EGVPKAELKDRVQTALELVQMGRFANRKPHQLSGGQQQRVALARSLVKRPKLLLLDEPMS 189 Query: 179 ALDKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIY 238 ALDK++R R Q+E+V+IL+ VGVTC+MVTHDQEEAMTMAGR+A+M+ G+ VQ+G P E+Y Sbjct: 190 ALDKQIRQRTQIELVNILDTVGVTCIMVTHDQEEAMTMAGRLAVMSEGEIVQLGTPHEVY 249 Query: 239 EHPTTRYSAEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALR 298 E+P +R+SAEFIGS N+FEG E + D + +++P L L V+ + +PV +++R Sbjct: 250 EYPNSRFSAEFIGSTNLFEGHTVEDEPDHVFIETPDLTCRLYVNHGITGPLGMPVTISVR 309 Query: 299 PEKIMLCEEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPT 358 PE+I L +PP N+ G V +IAY+G S+YHV+L SG+ + A + + PT Sbjct: 310 PERIALTRKPPEGAYNWGKGVVTNIAYMGGYSLYHVKLDSGKTVIANVTSLALTEIDPPT 369 Query: 359 WGDEVRLCWEVDSCVVLT 376 WGDEV + W + VVLT Sbjct: 370 WGDEVYVRWSASAGVVLT 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: 10 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