Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate BWI76_RS09465 BWI76_RS09465 polyamine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Koxy:BWI76_RS09465 Length = 392 Score = 700 bits (1806), Expect = 0.0 Identities = 348/377 (92%), Positives = 364/377 (96%) Query: 1 MNDAIPRPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKST 60 +ND IPRPQAKT KALTPLLEIRNLTKS+DGQHAVDDV+LTIYKGEIFALLGASGCGKST Sbjct: 16 VNDVIPRPQAKTPKALTPLLEIRNLTKSFDGQHAVDDVNLTIYKGEIFALLGASGCGKST 75 Query: 61 LLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDK 120 LLRMLAGFEQP+AGQI+LDGVDL++VPPY RPINMMFQSYALFPHMTVEQNIAFGLKQDK Sbjct: 76 LLRMLAGFEQPTAGQIVLDGVDLARVPPYQRPINMMFQSYALFPHMTVEQNIAFGLKQDK 135 Query: 121 LPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 180 LPKAEI SRV EML LVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL Sbjct: 136 LPKAEITSRVQEMLALVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 195 Query: 181 DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH 240 DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH Sbjct: 196 DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH 255 Query: 241 PTTRYSAEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPE 300 PTTRYSAEFIGSVNVFEG++KERQEDGLVLDSPGL HPLKVD DASVVDNVPV VALRPE Sbjct: 256 PTTRYSAEFIGSVNVFEGLVKERQEDGLVLDSPGLTHPLKVDPDASVVDNVPVWVALRPE 315 Query: 301 KIMLCEEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWG 360 KIMLCE+PPA+G NFAVGEVI+IAYLGDLS+YHVRLKSGQM+SAQLQN HR+RKG PTWG Sbjct: 316 KIMLCEDPPADGYNFAVGEVIYIAYLGDLSIYHVRLKSGQMLSAQLQNEHRYRKGAPTWG 375 Query: 361 DEVRLCWEVDSCVVLTV 377 DEVRLCW+ DSCVVLTV Sbjct: 376 DEVRLCWDADSCVVLTV 392 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: 624 Number of extensions: 7 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: 392 Length adjustment: 30 Effective length of query: 347 Effective length of database: 362 Effective search space: 125614 Effective search space used: 125614 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