Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 393 bits (1009), Expect = e-114 Identities = 202/359 (56%), Positives = 254/359 (70%), Gaps = 1/359 (0%) Query: 18 PLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 PL+ ++K + AV+ V L I+KGE F+LLGASGCGK+TLLRMLAGFE P+ G+I+ Sbjct: 21 PLIRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRIL 80 Query: 78 LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137 +DG D+++VPPY RP+NMMFQSYALFPHM+V NIAFGLKQD L K I +V L LV Sbjct: 81 IDGQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELV 140 Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197 M F+ RKPHQLSGGQRQRVALAR LAK PK++LLDEP+ ALDKKLR+ QLE+V+I + Sbjct: 141 QMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQD 200 Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFE 257 RVG+T VMVTHDQ EAMTM+ RI +MN G Q+G P +IYE+P TR+ A+FIG+ N+F+ Sbjct: 201 RVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANMFQ 260 Query: 258 GVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAV 317 G ++ E L + P L H L V +V PV V +RPEK+M+ + PA+G N+A Sbjct: 261 GSVR-GGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDKPASGLNWAE 319 Query: 318 GEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVLT 376 G V IAYLGD+S+YHVRL SG+ I A N H + TW D V L W +VLT Sbjct: 320 GVVSDIAYLGDVSIYHVRLASGRKIQALRTNLHHGEESRLTWEDPVFLAWHPADSLVLT 378 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: 402 Number of extensions: 12 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: 377 Length of database: 379 Length adjustment: 30 Effective length of query: 347 Effective length of database: 349 Effective search space: 121103 Effective search space used: 121103 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