Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 424 bits (1090), Expect = e-123 Identities = 221/368 (60%), Positives = 276/368 (75%), Gaps = 2/368 (0%) Query: 9 QAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGF 68 QA + ++I ++K +D AVDDV+LTI +GEIFALLG SG GKSTLLR+LAGF Sbjct: 10 QAMAKAEPVEFVKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGF 69 Query: 69 EQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIAS 128 E PS G+++LDG +++ +PP+ RPINMMFQSYALFPHMTVEQNIAFGLKQDKL EI+ Sbjct: 70 ETPSEGRVLLDGQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISE 129 Query: 129 RVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRM 188 RV EML LVHM ++AKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLR +M Sbjct: 130 RVAEMLKLVHMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQM 189 Query: 189 QLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAE 248 QLE+V+I+ERVGVTC+MVTHDQEEAMTMA RIAIM++G VQ+G P +IYE P R+ AE Sbjct: 190 QLELVEIIERVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAE 249 Query: 249 FIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASV-VDNVPVHVALRPEKIMLCEE 307 F+GSVN+FEG + +D ++++ P L + + + ++ ALRPEK+ + E Sbjct: 250 FVGSVNIFEGEIVADMDDHVIIECPQLDRQIYLGHGVTTRAEDKSAIYALRPEKVFVTTE 309 Query: 308 PPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCW 367 P N+A GEV IAYLG SVY+++L SG+M+ A N+ R R PTW D+V + W Sbjct: 310 QPEQPYNWAHGEVHDIAYLGGHSVYYIKLDSGKMVQAFFANSER-RLPRPTWEDKVYVSW 368 Query: 368 EVDSCVVL 375 + D VVL Sbjct: 369 DDDGGVVL 376 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: 455 Number of extensions: 10 Number of successful extensions: 3 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: 378 Length adjustment: 30 Effective length of query: 347 Effective length of database: 348 Effective search space: 120756 Effective search space used: 120756 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