Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_011612342.1 TERY_RS13460 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_000014265.1:WP_011612342.1 Length = 381 Score = 298 bits (764), Expect = 1e-85 Identities = 162/362 (44%), Positives = 234/362 (64%), Gaps = 8/362 (2%) Query: 20 LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79 +E+R + K ++G AV V I +GE F++LG SGCGK+T LR++AGFE PSAG+I++ Sbjct: 19 VELRKVFKVFEGHTAVKGVDFNIRQGEFFSILGPSGCGKTTTLRLIAGFETPSAGEIIIR 78 Query: 80 GVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHM 139 G +SQ P Y RP+N +FQSYALF H++V+ NIAFGL+ +L K E +V + L LV M Sbjct: 79 GQSMSQTPAYRRPVNTVFQSYALFNHLSVKDNIAFGLRIKRLGKTETEEKVAQALQLVKM 138 Query: 140 QEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERV 199 ++FA R P+Q+SGGQ+QRVALAR+L RP +LLLDEP+GALD KLR +MQ+E+ +I + + Sbjct: 139 EKFADRYPNQISGGQQQRVALARALVNRPAVLLLDEPLGALDLKLRKQMQMELSNIHKDL 198 Query: 200 GVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEGV 259 GVT VMVTHDQ+EAM+M+ RIA+M+ G+ QIG P+EIYE P + + A+FIG N+F+G Sbjct: 199 GVTFVMVTHDQQEAMSMSDRIAVMHEGRIEQIGSPQEIYECPESPFVADFIGDTNLFQGC 258 Query: 260 LKERQEDGLVLDS-PGL---VHPLKVDA-DASVVDNVPVHVALRPEKIMLCEEPPANGCN 314 ++ LV+ + GL KV+ + + V +++RPEK+ L PP N Sbjct: 259 VEYNNNSSLVVKTDSGLNISAEYKKVNGKNGEIYGGTSVVLSVRPEKVNLSLYPPDVSEN 318 Query: 315 FAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVV 374 G + ++ Y+G Y V L SG + + N R LP + + W +C+ Sbjct: 319 CFEGRLRNVMYMGTHVHYQVNLLSGDQMMVRQPNTER---TLPNLDTPMYVYWSKQNCLA 375 Query: 375 LT 376 L+ Sbjct: 376 LS 377 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: 333 Number of extensions: 13 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: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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 24 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